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R.; Voyles, Jamie; Misra, Vikram title: Activation of Innate Immune-Response Genes in Little Brown Bats (Myotis lucifugus) Infected with the Fungus Pseudogymnoascus destructans date: 2014-11-12 journal: PLoS One DOI: 10.1371/journal.pone.0112285 sha: doc_id: 1455 cord_uid: n7quwr4s file: cache/cord-006960-9pho3hk6.json key: cord-006960-9pho3hk6 authors: Prakash, R.; Pabbaraju, K.; Wong, S.; Wong, A.; Tellier, R.; Kaler, K. V. I. 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Hindiyeh, Musa; Muhsen, Khitam; Cohen, Dani; Mendelson, Ella; Sofer, Danit title: Evaluation of Four Different Systems for Extraction of RNA from Stool Suspensions Using MS-2 Coliphage as an Exogenous Control for RT-PCR Inhibition date: 2012-07-16 journal: PLoS One DOI: 10.1371/journal.pone.0039455 sha: doc_id: 715 cord_uid: zl1s82yi file: cache/cord-001843-ceatyj3o.json key: cord-001843-ceatyj3o authors: Huang, Yong; Xing, Na; Wang, Zengguo; Zhang, Xiujuan; Zhao, Xiaomin; Du, Qian; Chang, Lingling; Tong, Dewen title: Ultrasensitive Detection of RNA and DNA Viruses Simultaneously Using Duplex UNDP-PCR Assay date: 2015-11-06 journal: PLoS One DOI: 10.1371/journal.pone.0141545 sha: doc_id: 1843 cord_uid: ceatyj3o file: cache/cord-007427-iqwojhq2.json key: cord-007427-iqwojhq2 authors: Dedkov, Vladimir G.; Magassouba, N.’Faly; Safonova, Marina V.; Naydenova, Ekaterina V.; Ayginin, Andrey A.; Soropogui, Barre; Kourouma, Fode; Camara, Amara B.; Camara, Jacob; Kritzkiy, Andrey A.; Tuchkov, Igor V.; 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Hwan Jung, Young; Bum Cho, Hong; Kim, Hee-tae; Kim, Kwang-sun title: Positive control synthesis method for COVID-19 diagnosis by one-step real-time RT-PCR date: 2020-10-12 journal: Clin Chim Acta DOI: 10.1016/j.cca.2020.10.001 sha: doc_id: 259886 cord_uid: j0bpp7iw file: cache/cord-260231-vayxg23a.json key: cord-260231-vayxg23a authors: Hsien Koh, Tse; Ling Tan, Ai; Lee Tan, Mee; Wang, Grace; Peng Song, Keang title: Epidemiology of Clostridium difficile infection in a large teaching hospital in Singapore date: 2007-08-31 journal: Pathology DOI: 10.1080/00313020701444507 sha: doc_id: 260231 cord_uid: vayxg23a file: cache/cord-260168-rb7j94dh.json key: cord-260168-rb7j94dh authors: Gu, Jiang; Xie, Zhigang; Gao, Zhancheng; Liu, Jinhua; Korteweg, Christine; Ye, Juxiang; Lau, Lok Ting; Lu, Jie; Gao, Zifen; Zhang, Bo; McNutt, Michael A; Lu, Min; Anderson, Virginia M; Gong, Encong; Yu, Albert Cheung Hoi; Lipkin, W Ian title: H5N1 infection of the respiratory tract and beyond: a molecular pathology study date: 2007-09-27 journal: Lancet DOI: 10.1016/s0140-6736(07)61515-3 sha: doc_id: 260168 cord_uid: rb7j94dh file: cache/cord-260431-eksl7pp8.json key: cord-260431-eksl7pp8 authors: Sun, Heting; 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Fraisse, Audrey; Martin-Latil, Sandra; Delannoy, Sabine; Fach, Patrick; Perelle, Sylvie title: A Novel High-Throughput Method for Molecular Detection of Human Pathogenic Viruses Using a Nanofluidic Real-Time PCR System date: 2016-01-29 journal: PLoS One DOI: 10.1371/journal.pone.0147832 sha: doc_id: 260647 cord_uid: 7bjhobg7 file: cache/cord-260690-h5pjv2dw.json key: cord-260690-h5pjv2dw authors: Druce, Julian; Tran, Thomas; Kelly, Heath; Kaye, Matthew; Chibo, Doris; Kostecki, Renata; Amiri, Abdul; Catton, Mike; Birch, Chris title: Laboratory diagnosis and surveillance of human respiratory viruses by PCR in Victoria, Australia, 2002–2003 date: 2004-11-12 journal: J Med Virol DOI: 10.1002/jmv.20246 sha: doc_id: 260690 cord_uid: h5pjv2dw file: cache/cord-260700-u12aa739.json key: cord-260700-u12aa739 authors: Kainulainen, Leena; Vuorinen, Tytti; Rantakokko-Jalava, Kaisu; Österback, Riikka; Ruuskanen, Olli title: Recurrent and persistent respiratory tract viral infections in patients with primary hypogammaglobulinemia date: 2010-06-10 journal: J Allergy Clin Immunol DOI: 10.1016/j.jaci.2010.04.016 sha: doc_id: 260700 cord_uid: u12aa739 parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. file: cache/cord-015324-y44sfr0c.json key: cord-015324-y44sfr0c authors: nan title: Scientific Programme date: 2007-09-01 journal: Pediatr Nephrol DOI: 10.1007/s00467-007-0558-3 sha: doc_id: 15324 cord_uid: y44sfr0c file: cache/cord-260791-2gmrsm8q.json key: cord-260791-2gmrsm8q authors: Iwata, Takanori title: PCR detection and new therapies for COVID-19 date: 2020-06-23 journal: J Periodontal Implant Sci DOI: 10.5051/jpis.2020.50.3.133 sha: doc_id: 260791 cord_uid: 2gmrsm8q file: cache/cord-261089-aul4ifso.json key: cord-261089-aul4ifso authors: Yuan, Wen; Wang, Jing; Xu, Fengjiao; Huang, Bihong; Lian, Yuexiao; Rao, Dan; Yin, Xueqin; Wu, Miaoli; Zhu, Yujun; Zhang, Yu; Huang, Ren; Guo, Pengju title: Development of a duplex real-time RT-PCR for the simultaneous detection and differentiation of Theiler’s murine encephalomyelitis virus and rat theilovirus date: 2016-07-07 journal: J Virol Methods DOI: 10.1016/j.jviromet.2016.07.004 sha: doc_id: 261089 cord_uid: aul4ifso file: cache/cord-261128-j55v4clu.json key: cord-261128-j55v4clu authors: Gagliardi, T.B.; Paula, F.E.; Iwamoto, M.A.; Proença‐Modena, J.L.; Santos, A.E.; Camara, A.A.; Cervi, M.C.; Cintra, O.A.L.; Arruda, E. title: Concurrent detection of other respiratory viruses in children shedding viable human respiratory syncytial virus date: 2013-07-16 journal: J Med Virol DOI: 10.1002/jmv.23648 sha: doc_id: 261128 cord_uid: j55v4clu file: cache/cord-261134-zarq507s.json key: cord-261134-zarq507s authors: Pulford, David; Meyer, Hermann; Brightwell, Gale; Damon, Inger; Kline, Richard; Ulaeto, David title: Amplification refractory mutation system PCR assays for the detection of variola and Orthopoxvirus date: 2004-02-13 journal: J Virol Methods DOI: 10.1016/j.jviromet.2004.01.001 sha: doc_id: 261134 cord_uid: zarq507s file: cache/cord-261237-0hbijukt.json key: cord-261237-0hbijukt authors: Hou, Peili; Zhao, Guimin; Wang, Hongmei; He, Chengqiang; Huan, Yanjun; He, Hongbin title: Development of a recombinase polymerase amplification combined with lateral-flow dipstick assay for detection of bovine ephemeral fever virus date: 2017-12-26 journal: Mol Cell Probes DOI: 10.1016/j.mcp.2017.12.003 sha: doc_id: 261237 cord_uid: 0hbijukt file: cache/cord-261279-6mef38eo.json key: cord-261279-6mef38eo authors: Chu, Daniel K W; Pan, Yang; Cheng, Samuel M S; Hui, Kenrie P Y; Krishnan, Pavithra; Liu, Yingzhi; Ng, Daisy Y M; Wan, Carrie K C; Yang, Peng; Wang, Quanyi; Peiris, Malik; Poon, Leo L M title: Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia date: 2020-01-31 journal: Clin Chem DOI: 10.1093/clinchem/hvaa029 sha: doc_id: 261279 cord_uid: 6mef38eo file: cache/cord-261735-03hvi4el.json key: cord-261735-03hvi4el authors: Rodrigues, R.; Telles, J.-N.; Essere, K.; Ducournau, C.; Roqueplo, C.; Levieuge, A.; Davoust, B.; Parola, P.; Paranhos-Baccalà, G.; Peyrefitte, C.N. title: Development of a one step real time RT-PCR assay to detect and quantify Dugbe virus date: 2011-06-14 journal: J Virol Methods DOI: 10.1016/j.jviromet.2011.06.003 sha: doc_id: 261735 cord_uid: 03hvi4el file: cache/cord-015394-uj7fe5y6.json key: cord-015394-uj7fe5y6 authors: nan title: Scientific Abstracts date: 2008-12-23 journal: Reprod Sci DOI: 10.1177/19337191080150020102 sha: doc_id: 15394 cord_uid: uj7fe5y6 file: cache/cord-262592-0rdiosxd.json key: cord-262592-0rdiosxd authors: Cuevas, José M.; Combe, Marine; Torres-Puente, Manoli; Garijo, Raquel; Guix, Susana; Buesa, Javier; Rodríguez-Díaz, Jesús; Sanjuán, Rafael title: Human norovirus hyper-mutation revealed by ultra-deep sequencing date: 2016-04-17 journal: Infect Genet Evol DOI: 10.1016/j.meegid.2016.04.017 sha: doc_id: 262592 cord_uid: 0rdiosxd file: cache/cord-262328-q7mt0xve.json key: cord-262328-q7mt0xve authors: Wajnberg, Ania; Mansour, Mayce; Leven, Emily; Bouvier, Nicole M; Patel, Gopi; Firpo-Betancourt, Adolfo; Mendu, Rao; Jhang, Jeffrey; Arinsburg, Suzanne; Gitman, Melissa; Houldsworth, Jane; Sordillo, Emilia; Paniz-Mondolfi, Alberto; Baine, Ian; Simon, Viviana; Aberg, Judith; Krammer, Florian; Reich, David; Cordon-Cardo, Carlos title: Humoral response and PCR positivity in patients with COVID-19 in the New York City region, USA: an observational study date: 2020-09-25 journal: Lancet Microbe DOI: 10.1016/s2666-5247(20)30120-8 sha: doc_id: 262328 cord_uid: q7mt0xve file: cache/cord-261419-8dcqnifn.json key: cord-261419-8dcqnifn authors: Ma, Qing-Hu; Tian, Bing; Li, Yun-Liang title: Overexpression of a wheat jasmonate-regulated lectin increases pathogen resistance date: 2009-12-01 journal: Biochimie DOI: 10.1016/j.biochi.2009.11.008 sha: doc_id: 261419 cord_uid: 8dcqnifn file: cache/cord-262730-1dxeg8ci.json key: cord-262730-1dxeg8ci authors: Barón-Sánchez, J.; Santiago, C.; Goizueta-San Martín, G.; Arca, R.; Fernández, R. title: Smell and taste disorders in Spanish patients with mild COVID-19 date: 2020-10-08 journal: nan DOI: 10.1016/j.nrleng.2020.07.007 sha: doc_id: 262730 cord_uid: 1dxeg8ci file: cache/cord-262826-2usqmujy.json key: cord-262826-2usqmujy authors: She, Rosemary C.; Polage, Christopher R.; Caram, Lauren B.; Taggart, Edward W.; Hymas, Weston C.; Woods, Christopher W.; Schmader, Kenneth; Petti, Cathy A. title: Performance of diagnostic tests to detect respiratory viruses in older adults date: 2010-07-31 journal: Diagnostic Microbiology and Infectious Disease DOI: 10.1016/j.diagmicrobio.2010.02.020 sha: doc_id: 262826 cord_uid: 2usqmujy file: cache/cord-263142-o8qbqxhx.json key: cord-263142-o8qbqxhx authors: Cavalcante, Liliane T. F.; Muniz, Cláudia P.; Jia, Hongwei; Augusto, Anderson M.; Troccoli, Fernando; Medeiros, Sheila de O.; Dias, Carlos G. A.; Switzer, William M.; Soares, Marcelo A.; Santos, André F. title: Clinical and Molecular Features of Feline Foamy Virus and Feline Leukemia Virus Co-Infection in Naturally-Infected Cats date: 2018-12-11 journal: Viruses DOI: 10.3390/v10120702 sha: doc_id: 263142 cord_uid: o8qbqxhx file: cache/cord-263417-jgu8kc5k.json key: cord-263417-jgu8kc5k authors: Yan, Yong; Luo, Jian-Yong; Chen, Yin; Wang, Heng-Hui; Zhu, Guo-Ying; He, Pei-Yan; Guo, Jin-Lei; Lei, Yong-Liang; Chen, Zhong-Wen title: A multiplex liquid-chip assay based on Luminex xMAP technology for simultaneous detection of six common respiratory viruses date: 2017-06-17 journal: Oncotarget DOI: 10.18632/oncotarget.18533 sha: doc_id: 263417 cord_uid: jgu8kc5k file: cache/cord-261823-pgluidj8.json key: cord-261823-pgluidj8 authors: Wang, Ji; Cai, Kun; Zhang, Ruiqing; He, Xiaozhou; Shen, Xinxin; Liu, Jun; Xu, Junqiang; Qiu, Feng; Lei, Wenwen; Wang, Jinrong; Li, Xinna; Gao, Yuan; Jiang, Yongzhong; Xu, Wenbo; Ma, Xuejun title: Novel One-Step Single-Tube Nested Quantitative Real-Time PCR Assay for Highly Sensitive Detection of SARS-CoV-2 date: 2020-05-22 journal: Anal Chem DOI: 10.1021/acs.analchem.0c01884 sha: doc_id: 261823 cord_uid: pgluidj8 file: cache/cord-262599-19aj551d.json key: cord-262599-19aj551d authors: Fongaro, Gislaine; Nascimento, Mariana A do; Rigotto, Caroline; Ritterbusch, Giseli; da Silva, Alessandra D’ A; Esteves, Paulo A; Barardi, Célia R M title: Evaluation and molecular characterization of human adenovirus in drinking water supplies: viral integrity and viability assays date: 2013-05-28 journal: Virol J DOI: 10.1186/1743-422x-10-166 sha: doc_id: 262599 cord_uid: 19aj551d file: cache/cord-263134-0p4zy5t2.json key: cord-263134-0p4zy5t2 authors: de Paz, Hector David; Brotons, Pedro; Muñoz-Almagro, Carmen title: Molecular isothermal techniques for combating infectious diseases: towards low-cost point-of-care diagnostics date: 2014-07-23 journal: Expert Rev Mol Diagn DOI: 10.1586/14737159.2014.940319 sha: doc_id: 263134 cord_uid: 0p4zy5t2 file: cache/cord-263389-m6x9gxwe.json key: cord-263389-m6x9gxwe authors: AlGhounaim, M.; Xiao, Y.; Caya, C.; Papenburg, J. title: Diagnostic yield and clinical impact of routine cell culture for respiratory viruses among children with a negative multiplex RT-PCR result date: 2017-07-29 journal: J Clin Virol DOI: 10.1016/j.jcv.2017.07.015 sha: doc_id: 263389 cord_uid: m6x9gxwe file: cache/cord-259717-e8ljkv2y.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-259717-e8ljkv2y authors: Holtz, Lori R.; Cao, Song; Zhao, Guoyan; Bauer, Irma K.; Denno, Donna M.; Klein, Eileen J.; Antonio, Martin; Stine, O. Colin; Snelling, Thomas L.; Kirkwood, Carl D.; Wang, David title: Geographic variation in the eukaryotic virome of human diarrhea date: 2014-11-01 journal: Virology DOI: 10.1016/j.virol.2014.09.012 sha: doc_id: 259717 cord_uid: e8ljkv2y file: cache/cord-263538-0wozg085.json key: cord-263538-0wozg085 authors: Cooch, P. B.; Watson, A.; Olarte, A.; Crawford, E. D.; CLIAhub Consortium,; DeRisi, J.; Greenhouse, B.; Hakim, J.; Turcios, K.; Atkinson-McEvoy, L.; Hirsch, R.; Keller, R. L.; Ruel, T.; Cohen-Ross, A.; Leon, A.; Bardach, N. title: Supervised self-collected SARS-CoV-2 testing in indoor summer camps to inform school reopening date: 2020-10-23 journal: nan DOI: 10.1101/2020.10.21.20214338 sha: doc_id: 263538 cord_uid: 0wozg085 file: cache/cord-261329-k1p7fo0e.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-261329-k1p7fo0e authors: Nidzworski, Dawid; Rabalski, Lukasz; Gromadzka, Beata title: Detection and differentiation of virulent and avirulent strains of Newcastle disease virus by real-time PCR date: 2010-12-28 journal: J Virol Methods DOI: 10.1016/j.jviromet.2010.12.015 sha: doc_id: 261329 cord_uid: k1p7fo0e file: cache/cord-263279-afdmegq0.json key: cord-263279-afdmegq0 authors: Uhteg, Katharine; Jarrett, Junko; Richards, Mahmia; Howard, Craig; Morehead, Elizabeth; Geahr, Melissa; Gluck, Linda; Hanlon, Ann; Ellis, Brandon; Kaur, Harsimar; Simner, Patricia; Carroll, Karen C.; Mostafa, Heba H. title: Comparing the analytical performance of three SARS-CoV-2 molecular diagnostic assays date: 2020-04-26 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104384 sha: doc_id: 263279 cord_uid: afdmegq0 file: cache/cord-263763-a8wgvgz2.json key: cord-263763-a8wgvgz2 authors: Çelik, Ersin; Çora, Ahmet Rıfkı title: Treatment Approach to Coronavirus Disease (COVID-19) Seen Early After Open Heart Surgery. Case Report date: 2020-07-02 journal: SN Compr Clin Med DOI: 10.1007/s42399-020-00377-y sha: doc_id: 263763 cord_uid: a8wgvgz2 file: cache/cord-031907-ilhr3iu5.json key: cord-031907-ilhr3iu5 authors: nan title: ISEV2020 Abstract Book date: 2020-07-15 journal: nan DOI: 10.1080/20013078.2020.1784511 sha: doc_id: 31907 cord_uid: ilhr3iu5 file: cache/cord-260866-bzdd4f5h.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-260866-bzdd4f5h authors: Barceló, Damià title: Wastewater-Based Epidemiology to Monitor COVID-19 Outbreak: Present and Future Diagnostic Methods to be in Your Radar date: 2020-09-14 journal: nan DOI: 10.1016/j.cscee.2020.100042 sha: doc_id: 260866 cord_uid: bzdd4f5h file: cache/cord-261160-g92zhv19.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-261160-g92zhv19 authors: Rowland, Raymond R.R; Lawson, Steven; Rossow, Kurt; Benfield, David A title: Lymphoid tissue tropism of porcine reproductive and respiratory syndrome virus replication during persistent infection of pigs originally exposed to virus in utero date: 2003-10-30 journal: Vet Microbiol DOI: 10.1016/j.vetmic.2003.07.006 sha: doc_id: 261160 cord_uid: g92zhv19 file: cache/cord-263735-sos2ovng.json key: cord-263735-sos2ovng authors: Li, K.; Wu, X.; Zhong, Y.; Qin, W.; Zhang, Z. title: Diagnostic performance of CT and its key signs for COVID-19: A systematic review and meta-analysis date: 2020-05-26 journal: nan DOI: 10.1101/2020.05.24.20111773 sha: doc_id: 263735 cord_uid: sos2ovng file: cache/cord-264071-hg0qslyx.json key: cord-264071-hg0qslyx authors: Camelo-Castillo, Anny; Henares, Desirée; Brotons, Pedro; Galiana, Antonio; Rodríguez, Juan Carlos; Mira, Alex; Muñoz-Almagro, Carmen title: Nasopharyngeal Microbiota in Children With Invasive Pneumococcal Disease: Identification of Bacteria With Potential Disease-Promoting and Protective Effects date: 2019-01-28 journal: Front Microbiol DOI: 10.3389/fmicb.2019.00011 sha: doc_id: 264071 cord_uid: hg0qslyx file: cache/cord-263567-6uacorpp.json key: cord-263567-6uacorpp authors: Collignon, C.; Zahra, A.; Guenego, L.; Gautier, R.; Madelenat, A. title: Polyarthrite associée à une leishmaniose chez un jeune chien date: 2009-03-31 journal: Pratique Médicale et Chirurgicale de l'Animal de Compagnie DOI: 10.1016/j.anicom.2009.01.002 sha: doc_id: 263567 cord_uid: 6uacorpp file: cache/cord-261867-6n0g3bz5.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-261867-6n0g3bz5 authors: Evermann, James F.; Ledbetter, Eric C.; Maes, Roger K. title: Canine Reproductive, Respiratory, and Ocular Diseases due to Canine Herpesvirus date: 2011-10-28 journal: Vet Clin North Am Small Anim Pract DOI: 10.1016/j.cvsm.2011.08.007 sha: doc_id: 261867 cord_uid: 6n0g3bz5 file: cache/cord-263426-l32gyiky.json key: cord-263426-l32gyiky authors: Najafi, Hamideh; Madadgar, Omid; Jamshidi, Shahram; Ghalyanchi Langeroudi, Arash; Darzi Lemraski, Mahdieh title: Molecular and clinical study on prevalence of feline herpesvirus type 1 and calicivirus in correlation with feline leukemia and immunodeficiency viruses date: 2014 journal: Vet Res Forum DOI: nan sha: doc_id: 263426 cord_uid: l32gyiky file: cache/cord-264261-98h1bmb2.json key: cord-264261-98h1bmb2 authors: Caruana, Giorgia; Croxatto, Antony; Coste, Alix T.; Opota, Onya; Lamoth, Frederic; Jaton, Katia; Greub, Gilbert title: Diagnostic strategies for SARS-CoV-2 infection and interpretation of microbiological results date: 2020-06-25 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.06.019 sha: doc_id: 264261 cord_uid: 98h1bmb2 file: cache/cord-264716-igl25jhg.json key: cord-264716-igl25jhg authors: Koo, B.S.; Lee, H.R.; Jeon, E.O.; Han, M.S.; Min, K.C.; Lee, S.B.; Mo, I.P. title: Molecular survey of enteric viruses in commercial chicken farms in Korea with a history of enteritis date: 2013-11-01 journal: Poult Sci DOI: 10.3382/ps.2013-03280 sha: doc_id: 264716 cord_uid: igl25jhg file: cache/cord-010092-uftc8inx.json key: cord-010092-uftc8inx authors: nan title: Abstract of 29th Regional Congress of the ISBT date: 2019-06-07 journal: Vox Sang DOI: 10.1111/vox.12792 sha: doc_id: 10092 cord_uid: uftc8inx file: cache/cord-261442-r4vgt0h3.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-261442-r4vgt0h3 authors: Huh, Hee Jae; Park, Kyung Sun; Kim, Ji-Youn; Kwon, Hyeon Jeong; Kim, Jong-Won; Ki, Chang-Seok; Lee, Nam Yong title: Comparison of the AnyplexTM II RV16 and Seeplex® RV12 ACE assays for the detection of respiratory viruses date: 2014-08-31 journal: Diagnostic Microbiology and Infectious Disease DOI: 10.1016/j.diagmicrobio.2014.01.025 sha: doc_id: 261442 cord_uid: r4vgt0h3 file: cache/cord-262467-epqqd8n8.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-262467-epqqd8n8 authors: Chen, Jun; Lu, Hongzhou; Melino, Gerry; Boccia, Stefania; Piacentini, Mauro; Ricciardi, Walter; Wang, Ying; Shi, Yufang; Zhu, Tongyu title: COVID-19 infection: the China and Italy perspectives date: 2020-06-08 journal: Cell Death Dis DOI: 10.1038/s41419-020-2603-0 sha: doc_id: 262467 cord_uid: epqqd8n8 file: cache/cord-263976-b9shffb3.json key: cord-263976-b9shffb3 authors: Shaukat, Shahzad; Angez, Mehar; Alam, Muhammad Masroor; Jebbink, Maarten F; Deijs, Martin; Canuti, Marta; Sharif, Salmaan; de Vries, Michel; Khurshid, Adnan; Mahmood, Tariq; van der Hoek, Lia; Zaidi, Syed Sohail Zahoor title: Identification and characterization of unrecognized viruses in stool samples of non-polio acute flaccid paralysis children by simplified VIDISCA date: 2014-08-12 journal: Virol J DOI: 10.1186/1743-422x-11-146 sha: doc_id: 263976 cord_uid: b9shffb3 file: cache/cord-263118-6sf41rsj.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-263118-6sf41rsj authors: Landry, Marie L.; Cohen, Sandra; Ferguson, David title: Real-time PCR compared to Binax NOW and cytospin-immunofluorescence for detection of influenza in hospitalized patients date: 2008-07-18 journal: J Clin Virol DOI: 10.1016/j.jcv.2008.06.006 sha: doc_id: 263118 cord_uid: 6sf41rsj file: cache/cord-263570-6notzm6s.json key: cord-263570-6notzm6s authors: Elia, Gabriella; Cavalli, Alessandra; Desario, Costantina; Lorusso, Eleonora; Lucente, Maria Stella; Decaro, Nicola; Martella, Vito; Buonavoglia, Canio title: Detection of infectious canine parvovirus type 2 by mRNA real-time RT-PCR date: 2007-08-10 journal: J Virol Methods DOI: 10.1016/j.jviromet.2007.06.017 sha: doc_id: 263570 cord_uid: 6notzm6s file: cache/cord-262485-sx2q5ol4.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-262485-sx2q5ol4 authors: Davda, Jayeshkumar Narsibhai; Frank, Keith; Prakash, Sivakumar; Purohit, Gunjan; Vijayashankar, Devi Prasad; Vedagiri, Dhiviya; Tallapaka, Karthik Bharadwaj; Harshan, Krishnan Harinivas; Siva, Archana Bharadwaj; Mishra, Rakesh Kumar; Dhawan, Jyotsna; Siddiqi, Imran title: An Inexpensive RT-PCR Endpoint Diagnostic Assay for SARS-CoV-2 Using Nested PCR: Direct Assessment of Detection Efficiency of RT-qPCR Tests and Suitability for Surveillance date: 2020-06-08 journal: bioRxiv DOI: 10.1101/2020.06.08.139477 sha: doc_id: 262485 cord_uid: sx2q5ol4 file: cache/cord-263302-z5uhrta5.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-263302-z5uhrta5 authors: Zhang, Xuming; Liu, Runzhong title: Identification of a Noncanonical Signal for Transcription of a Novel Subgenomic mRNA of Mouse Hepatitis Virus: Implication for the Mechanism of Coronavirus RNA Transcription date: 2000-12-05 journal: Virology DOI: 10.1006/viro.2000.0637 sha: doc_id: 263302 cord_uid: z5uhrta5 file: cache/cord-264107-6doie8pj.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-264107-6doie8pj authors: Marando, Marco; Tamburello, Adriana; Gianella, Pietro title: False-Negative Nasopharyngeal Swab RT-PCR Assays in Typical COVID-19: Role of Ultra-low-dose Chest CT and Bronchoscopy in Diagnosis date: 2020-04-24 journal: Eur J Case Rep Intern Med DOI: 10.12890/2020_001680 sha: doc_id: 264107 cord_uid: 6doie8pj file: cache/cord-264880-0tmd9knh.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-264880-0tmd9knh authors: Li, Zhao; Liu, Yong; Wei, Qingquan; Liu, Yuanjie; Liu, Wenwen; Zhang, Xuelian; Yu, Yude title: Picoliter Well Array Chip-Based Digital Recombinase Polymerase Amplification for Absolute Quantification of Nucleic Acids date: 2016-04-13 journal: PLoS One DOI: 10.1371/journal.pone.0153359 sha: doc_id: 264880 cord_uid: 0tmd9knh file: cache/cord-265221-qtkwciym.json key: cord-265221-qtkwciym authors: Bahadur, Gulam; Acharya, Santanu; Muneer, Asif; Huirne, Judith; Łukaszuk, Mariusz; Doreski, Pablo Alexis; Homburg, Roy title: SARS-CoV-2: diagnostic and design conundrums, and the male factor infertility date: 2020-06-03 journal: Reprod Biomed Online DOI: 10.1016/j.rbmo.2020.05.014 sha: doc_id: 265221 cord_uid: qtkwciym file: cache/cord-265237-sxh2nqre.json key: cord-265237-sxh2nqre authors: Weile, Jan; Knabbe, Cornelius title: Current applications and future trends of molecular diagnostics in clinical bacteriology date: 2009-04-18 journal: Anal Bioanal Chem DOI: 10.1007/s00216-009-2779-8 sha: doc_id: 265237 cord_uid: sxh2nqre file: cache/cord-265258-2rmtsyns.json key: cord-265258-2rmtsyns authors: Domanska‐Blicharz, K.; Lisowska, A.; Pikuła, A.; Sajewicz‐Krukowska, J. title: Specific detection of GII‐1 lineage of infectious bronchitis virus date: 2017-07-03 journal: Lett Appl Microbiol DOI: 10.1111/lam.12753 sha: doc_id: 265258 cord_uid: 2rmtsyns file: cache/cord-265978-i0fu8e0p.json key: cord-265978-i0fu8e0p authors: Amer, Haitham M.; Almajhdi, Fahad N. title: Development of a SYBR Green I based real-time RT-PCR assay for detection and quantification of bovine coronavirus date: 2011-06-30 journal: Molecular and Cellular Probes DOI: 10.1016/j.mcp.2011.03.001 sha: doc_id: 265978 cord_uid: i0fu8e0p file: cache/cord-266025-bkm486jd.json key: cord-266025-bkm486jd authors: Tao, Ying; Tang, Kevin; Shi, Mang; Conrardy, Christina; Li, Kenneth S.M.; Lau, Susanna K.P.; Anderson, Larry J.; Tong, Suxiang title: Genomic characterization of seven distinct bat coronaviruses in Kenya() date: 2012-04-26 journal: Virus Res DOI: 10.1016/j.virusres.2012.04.007 sha: doc_id: 266025 cord_uid: bkm486jd file: cache/cord-022940-atbjwpo5.json key: cord-022940-atbjwpo5 authors: nan title: Poster Sessions date: 2016-09-07 journal: FEBS J DOI: 10.1111/febs.13808 sha: doc_id: 22940 cord_uid: atbjwpo5 file: cache/cord-265634-7n4cvgs4.json key: cord-265634-7n4cvgs4 authors: Dhar, Arun K.; Roux, Michelle M.; Klimpel, Kurt R. title: Quantitative assay for measuring the Taura syndrome virus and yellow head virus load in shrimp by real-time RT-PCR using SYBR Green chemistry date: 2002-03-26 journal: J Virol Methods DOI: 10.1016/s0166-0934(02)00042-3 sha: doc_id: 265634 cord_uid: 7n4cvgs4 file: cache/cord-266036-qhlo99l7.json key: cord-266036-qhlo99l7 authors: Axell-House, Dierdre B.; Lavingia, Richa; Rafferty, Megan; Clark, Eva; Amirian, E. Susan; Chiao, Elizabeth Y. title: The Estimation of Diagnostic Accuracy of Tests for COVID-19: A Scoping Review date: 2020-08-31 journal: J Infect DOI: 10.1016/j.jinf.2020.08.043 sha: doc_id: 266036 cord_uid: qhlo99l7 file: cache/cord-264392-he1vekrt.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-264392-he1vekrt authors: Lambeth, L. S.; Yu, M.; Anderson, D. E.; Crameri, G.; Eaton, B. T.; Wang, L.-F. title: Complete genome sequence of Nariva virus, a rodent paramyxovirus date: 2008-12-23 journal: Arch Virol DOI: 10.1007/s00705-008-0287-3 sha: doc_id: 264392 cord_uid: he1vekrt file: cache/cord-264944-7xj27r98.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-264944-7xj27r98 authors: Koopmans, Marion; Monroe, Stephan S.; Coffield, Lisa M.; Zaki, Sherif R. title: Optimization of extraction and PCR amplification of RNA extracts from paraffin-embedded tissue in different fixatives date: 1993-07-31 journal: Journal of Virological Methods DOI: 10.1016/0166-0934(93)90076-4 sha: doc_id: 264944 cord_uid: 7xj27r98 file: cache/cord-265268-5xu9hj2n.json key: cord-265268-5xu9hj2n authors: Ahmed, W.; Gyawali, P.; Toze, S. title: Evaluation of Glass Wool Filters and Hollow-Fiber Ultrafiltration Concentration Methods for qPCR Detection of Human Adenoviruses and Polyomaviruses in River Water date: 2016-08-13 journal: Water Air Soil Pollut DOI: 10.1007/s11270-016-3026-5 sha: doc_id: 265268 cord_uid: 5xu9hj2n file: cache/cord-266156-xmf4emln.json key: cord-266156-xmf4emln authors: Miller, Tyler E.; Garcia Beltran, Wilfredo F.; Bard, Adam Z.; Gogakos, Tasos; Anahtar, Melis N.; Astudillo, Michael Gerino; Yang, Diane; Thierauf, Julia; Fisch, Adam S.; Mahowald, Grace K.; Fitzpatrick, Megan J.; Nardi, Valentina; Feldman, Jared; Hauser, Blake M.; Caradonna, Timothy M.; Marble, Hetal D.; Ritterhouse, Lauren L.; Turbett, Sara E.; Batten, Julie; Georgantas, Nicholas Zeke; Alter, Galit; Schmidt, Aaron G.; Harris, Jason B.; Gelfand, Jeffrey A.; Poznansky, Mark C.; Bernstein, Bradley E.; Louis, David N.; Dighe, Anand; Charles, Richelle C.; Ryan, Edward T.; Branda, John A.; Pierce, Virginia M.; Murali, Mandakolathur R.; Iafrate, A. John; Rosenberg, Eric S.; Lennerz, Jochen K. title: Clinical sensitivity and interpretation of PCR and serological COVID‐19 diagnostics for patients presenting to the hospital date: 2020-08-28 journal: FASEB J DOI: 10.1096/fj.202001700rr sha: doc_id: 266156 cord_uid: xmf4emln file: cache/cord-266466-5sgfx7oq.json key: cord-266466-5sgfx7oq authors: Mansour, Amani; Atoui, Rola; Kanso, Kamal; Mohsen, Rami; Fares, Youssef; Fares, Jawad title: First Case of an Infant with COVID-19 in the Middle East date: 2020-04-03 journal: Cureus DOI: 10.7759/cureus.7520 sha: doc_id: 266466 cord_uid: 5sgfx7oq file: cache/cord-266150-wox7pnkr.json key: cord-266150-wox7pnkr authors: Torres, Juan Pablo; Piñera, Cecilia; De La Maza, Verónica; Lagomarcino, Anne J; Simian, Daniela; Torres, Bárbara; Urquidi, Cinthya; Valenzuela, María Teresa; O’Ryan, Miguel title: SARS-CoV-2 antibody prevalence in blood in a large school community subject to a Covid-19 outbreak: a cross-sectional study date: 2020-07-10 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa955 sha: doc_id: 266150 cord_uid: wox7pnkr file: cache/cord-266175-4jyltfus.json key: cord-266175-4jyltfus authors: Brendish, Nathan J; Poole, Stephen; Naidu, Vasanth V; Mansbridge, Christopher T; Norton, Nicholas J; Wheeler, Helen; Presland, Laura; Kidd, Stephen; Cortes, Nicholas J; Borca, Florina; Phan, Hang; Babbage, Gavin; Visseaux, Benoit; Ewings, Sean; Clark, Tristan W title: Clinical impact of molecular point-of-care testing for suspected COVID-19 in hospital (COV-19POC): a prospective, interventional, non-randomised, controlled study date: 2020-10-08 journal: Lancet Respir Med DOI: 10.1016/s2213-2600(20)30454-9 sha: doc_id: 266175 cord_uid: 4jyltfus file: cache/cord-266499-g1lajsp8.json key: cord-266499-g1lajsp8 authors: Han, Jae-Ik; Chang, Dong-Woo; Na, Ki-Jeong title: A multiplex quantitative real-time polymerase chain reaction panel for detecting neurologic pathogens in dogs with meningoencephalitis date: 2015-09-21 journal: J Vet Sci DOI: 10.4142/jvs.2015.16.3.341 sha: doc_id: 266499 cord_uid: g1lajsp8 file: cache/cord-268251-mcg1v24t.json key: cord-268251-mcg1v24t authors: Martins, Ronaldo Bragança; Carney, Sharon; Goldemberg, Daniel; Bonine, Lucas; Spano, Liliana Cruz; Siqueira, Marilda; Checon, Rita Elizabeth title: Detection of respiratory viruses by real-time polymerase chain reaction in outpatients with acute respiratory infection date: 2014-09-17 journal: Mem Inst Oswaldo Cruz DOI: 10.1590/0074-0276140046 sha: doc_id: 268251 cord_uid: mcg1v24t file: cache/cord-266670-jxgywvwx.json key: cord-266670-jxgywvwx authors: Wong, Mark; Xagoraraki, Irene; Rose, Joan B. title: Chapter 13 Recent Advances and Future Needs in Environmental Virology date: 2007-09-06 journal: Perspect Med Virol DOI: 10.1016/s0168-7069(07)17013-0 sha: doc_id: 266670 cord_uid: jxgywvwx file: cache/cord-268094-ubz0q7e9.json key: cord-268094-ubz0q7e9 authors: Curland, N.; Gethöffer, F.; van Neer, A.; Ziegler, L.; Heffels-Redmann, U.; Lierz, M.; Baumgärtner, W.; Wohlsein, P.; Völker, I.; Lapp, S.; Bello, A.; Pfankuche, V. M.; Braune, S.; Runge, M.; Moss, A.; Rautenschlein, S.; Jung, A.; Teske, L.; Strube, C.; Schulz, J.; Bodewes, R.; Osterhaus, A. D. M. E.; Siebert, U. title: Investigation into diseases in free-ranging ring-necked pheasants (Phasianus colchicus) in northwestern Germany during population decline with special reference to infectious pathogens date: 2018-02-06 journal: Eur DOI: 10.1007/s10344-018-1173-2 sha: doc_id: 268094 cord_uid: ubz0q7e9 file: cache/cord-266523-qd5asgg8.json key: cord-266523-qd5asgg8 authors: Wilson, N.; Baker, M. G.; Eichner, M. title: Estimating the Impact of Control Measures to Prevent Outbreaks of COVID-19 Associated with Air Travel into a COVID-19-free country: A Simulation Modelling Study date: 2020-06-12 journal: nan DOI: 10.1101/2020.06.10.20127977 sha: doc_id: 266523 cord_uid: qd5asgg8 file: cache/cord-268233-ibxufjrv.json key: cord-268233-ibxufjrv authors: Nagappa, Bharathnag; Marimuthu, Yamini title: Seroconversion rate and diagnostic accuracy of serological tests for COVID-19 date: 2020-05-30 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa676 sha: doc_id: 268233 cord_uid: ibxufjrv file: cache/cord-268468-036i1082.json key: cord-268468-036i1082 authors: Asif, Muhammad; Ajmal, Muhammad; Ashraf, Ghazala; Muhammad, Nadeem; Aziz, Ayesha; Iftikhar, Tayyaba; Wang, Junlei; Liu, Hongfang title: The role of biosensors in COVID-19 outbreak date: 2020-09-18 journal: Curr Opin Electrochem DOI: 10.1016/j.coelec.2020.08.011 sha: doc_id: 268468 cord_uid: 036i1082 file: cache/cord-267928-dflkggjt.json key: cord-267928-dflkggjt authors: Kantola, Kalle; Sadeghi, Mohammadreza; Lahtinen, Anne; Koskenvuo, Minna; Aaltonen, Leena-Maija; Möttönen, Merja; Rahiala, Jaana; Saarinen-Pihkala, Ulla; Riikonen, Pekka; Jartti, Tuomas; Ruuskanen, Olli; Söderlund-Venermo, Maria; Hedman, Klaus title: Merkel cell polyomavirus DNA in tumor-free tonsillar tissues and upper respiratory tract samples: Implications for respiratory transmission and latency date: 2009-05-22 journal: J Clin Virol DOI: 10.1016/j.jcv.2009.04.008 sha: doc_id: 267928 cord_uid: dflkggjt file: cache/cord-268567-2xoubkxb.json key: cord-268567-2xoubkxb authors: Samannodi, Mohammed; Hansen, Michael; Allana, Ambreen; Hasbun, Rodrigo title: Compliance with international guidelines in adults with encephalitis date: 2020-04-14 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104369 sha: doc_id: 268567 cord_uid: 2xoubkxb file: cache/cord-268817-wx96wwpg.json key: cord-268817-wx96wwpg authors: Karp, Donna Grace; Cuda, Deanne; Tandel, Devangkumar; Danh, Kenneth; Robinson, Peter V.; Seftel, David; Tian, Honglin; Pandori, Mark; Miller, Kevin W. P.; Tsai, Cheng-T. title: Sensitive and Specific Detection of SARS-CoV-2 Antibodies Using a High-Throughput, Fully Automated Liquid-Handling Robotic System date: 2020-08-20 journal: SLAS Technol DOI: 10.1177/2472630320950663 sha: doc_id: 268817 cord_uid: wx96wwpg file: cache/cord-268977-hcg2rrhl.json key: cord-268977-hcg2rrhl authors: Feikin, Daniel R.; Njenga, M. Kariuki; Bigogo, Godfrey; Aura, Barrack; Aol, George; Audi, Allan; Jagero, Geoffrey; Muluare, Peter Ochieng; Gikunju, Stella; Nderitu, Leonard; Balish, Amanda; Winchell, Jonas; Schneider, Eileen; Erdman, Dean; Oberste, M. Steven; Katz, Mark A.; Breiman, Robert F. title: Etiology and Incidence of Viral and Bacterial Acute Respiratory Illness among Older Children and Adults in Rural Western Kenya, 2007–2010 date: 2012-08-24 journal: PLoS One DOI: 10.1371/journal.pone.0043656 sha: doc_id: 268977 cord_uid: hcg2rrhl file: cache/cord-268455-btuzihsy.json key: cord-268455-btuzihsy authors: de Santiago, Javier; Yelo, Carmen; F Chereguini, Maria; Conde, Ana; Galipienzo, Javier; Salvatierra, David; Linero, Manuel; Alonso, Sonsoles title: COVID-19: gynecologic cancer surgery at a single center in Madrid date: 2020-07-07 journal: Int J Gynecol Cancer DOI: 10.1136/ijgc-2020-001638 sha: doc_id: 268455 cord_uid: btuzihsy file: cache/cord-268721-n6dsc4ig.json key: cord-268721-n6dsc4ig authors: Pawlowski, Colin; Wagner, Tyler; Puranik, Arjun; Murugadoss, Karthik; Loscalzo, Liam; Venkatakrishnan, AJ; Pruthi, Rajiv K; Houghton, Damon E; O'Horo, John C; Morice, William G; Williams, Amy W; Gores, Gregory J; Halamka, John; Badley, Andrew D; Barnathan, Elliot S; Makimura, Hideo; Khan, Najat; Soundararajan, Venky title: Inference from longitudinal laboratory tests characterizes temporal evolution of COVID-19-associated coagulopathy (CAC) date: 2020-08-17 journal: eLife DOI: 10.7554/elife.59209 sha: doc_id: 268721 cord_uid: n6dsc4ig file: cache/cord-269627-mx1mjdqc.json key: cord-269627-mx1mjdqc authors: Thiry, Etienne; Addie, Diane; Belák, Sándor; Boucraut-Baralon, Corine; Egberink, Herman; Frymus, Tadeusz; Gruffydd-Jones, Tim; Hartmann, Katrin; Hosie, Margaret J.; Lloret, Albert; Lutz, Hans; Marsilio, Fulvio; Pennisi, Maria Grazia; Radford, Alan D.; Truyen, Uwe; Horzinek, Marian C. title: Feline herpesvirus infection. ABCD guidelines on prevention and management date: 2009-07-31 journal: Journal of Feline Medicine & Surgery DOI: 10.1016/j.jfms.2009.05.003 sha: doc_id: 269627 cord_uid: mx1mjdqc file: cache/cord-267671-ys43n672.json key: cord-267671-ys43n672 authors: Whary, Mark T.; Baumgarth, Nicole; Fox, James G.; Barthold, Stephen W. title: Biology and Diseases of Mice date: 2015-07-10 journal: Laboratory Animal Medicine DOI: 10.1016/b978-0-12-409527-4.00003-1 sha: doc_id: 267671 cord_uid: ys43n672 file: cache/cord-269194-b1wlr3t7.json key: cord-269194-b1wlr3t7 authors: Engstrom-Melnyk, Julia; Rodriguez, Pedro L.; Peraud, Olivier; Hein, Raymond C. title: Chapter 5 Clinical Applications of Quantitative Real-Time PCR in Virology date: 2015-12-31 journal: Methods in Microbiology DOI: 10.1016/bs.mim.2015.04.005 sha: doc_id: 269194 cord_uid: b1wlr3t7 file: cache/cord-269948-zfbu9646.json key: cord-269948-zfbu9646 authors: Teo, Jeanette; Pietro, Patrizia Di; Biagio, Floriana San; Capozzoli, Monica; Deng, Yi-Mo; Barr, Ian; Caldwell, Natalie; Ong, Kian-Leong; Sato, Mitsuharu; Tan, Rosemary; Lin, Raymond title: VereFlu™: an integrated multiplex RT-PCR and microarray assay for rapid detection and identification of human influenza A and B viruses using lab-on-chip technology date: 2011-04-19 journal: Arch Virol DOI: 10.1007/s00705-011-0999-7 sha: doc_id: 269948 cord_uid: zfbu9646 file: cache/cord-269407-6i66zf0e.json key: cord-269407-6i66zf0e authors: Rutvisuttinunt, Wiriya; Klungthong, Chonticha; Thaisomboonsuk, Butsaya; Chinnawirotpisan, Piyawan; Ajariyakhajorn, Chuanpis; Manasatienkij, Wudtichai; Phonpakobsin, Thipwipha; Lon, Chanthap; Saunders, David; Wangchuk, Sonam; Shrestha, Sanjaya K.; Velasco, John Mark S.; Alera, Maria Theresa P.; Simasathien, Sriluck; Buddhari, Darunee; Jarman, Richard G.; Macareo, Louis R; Yoon, In-Kyu; Fernandez, Stefan title: Retrospective use of next-generation sequencing reveals the presence of Enteroviruses in acute influenza-like illness respiratory samples collected in South/South-East Asia during 2010–2013 date: 2017-07-14 journal: J Clin Virol DOI: 10.1016/j.jcv.2017.07.004 sha: doc_id: 269407 cord_uid: 6i66zf0e file: cache/cord-269726-z0frgm7s.json key: cord-269726-z0frgm7s authors: Gidari, Anna; Nofri, Marco; Saccarelli, Luca; Bastianelli, Sabrina; Sabbatini, Samuele; Bozza, Silvia; Camilloni, Barbara; Fusco-Moffa, Igino; Monari, Claudia; De Robertis, Edoardo; Mencacci, Antonella; Francisci, Daniela title: Is recurrence possible in coronavirus disease 2019 (COVID-19)? Case series and systematic review of literature date: 2020-10-10 journal: Eur J Clin Microbiol Infect Dis DOI: 10.1007/s10096-020-04057-6 sha: doc_id: 269726 cord_uid: z0frgm7s file: cache/cord-270579-rf933a0y.json key: cord-270579-rf933a0y authors: van Kruijssen, Alida M.; Templeton, Kate E.; van der Plas, Roos N.; van Doorn, H. Rogier; Claas, Eric C. J.; Sukhai, Ram N.; Kuijper, Ed J. title: Detection of respiratory pathogens by real-time PCR in children with clinical suspicion of pertussis date: 2006-12-20 journal: Eur J Pediatr DOI: 10.1007/s00431-006-0378-7 sha: doc_id: 270579 cord_uid: rf933a0y file: cache/cord-269839-jxqs51o5.json key: cord-269839-jxqs51o5 authors: Bitome-Essono, Paul-Yannick; Ollomo, Benjamin; Arnathau, Céline; Durand, Patrick; Mokoudoum, Nancy Diamella; Yacka-Mouele, Lauriane; Okouga, Alain-Prince; Boundenga, Larson; Mve-Ondo, Bertrand; Obame-Nkoghe, Judicaël; Mbehang-Nguema, Philippe; Njiokou, Flobert; Makanga, Boris; Wattier, Rémi; Ayala, Diego; Ayala, Francisco J; Renaud, Francois; Rougeron, Virginie; Bretagnolle, Francois; Prugnolle, Franck; Paupy, Christophe title: Tracking zoonotic pathogens using blood-sucking flies as 'flying syringes' date: 2017-03-28 journal: eLife DOI: 10.7554/elife.22069 sha: doc_id: 269839 cord_uid: jxqs51o5 file: cache/cord-270526-o4hsr4pm.json key: cord-270526-o4hsr4pm authors: An, Dong-Jun; Kim, Tae-Young; Song, Dae-Sub; Kang, Bo-Kyu; Park, Bong-Kyun title: An immunochromatography assay for rapid antemortem diagnosis of dogs suspected to have canine distemper date: 2007-10-24 journal: J Virol Methods DOI: 10.1016/j.jviromet.2007.09.006 sha: doc_id: 270526 cord_uid: o4hsr4pm file: cache/cord-270929-utn21ce1.json key: cord-270929-utn21ce1 authors: Wise, Annabel G.; Kiupel, Matti; Maes, Roger K. title: Molecular characterization of a novel coronavirus associated with epizootic catarrhal enteritis (ECE) in ferrets date: 2006-05-25 journal: Virology DOI: 10.1016/j.virol.2006.01.031 sha: doc_id: 270929 cord_uid: utn21ce1 file: cache/cord-271130-6s79q1c1.json key: cord-271130-6s79q1c1 authors: Filoni, Claudia; Helfer-Hungerbuehler, A. Katrin; Catão-Dias, José Luiz; Marques, Mara Cristina; Torres, Luciana Neves; Reinacher, Manfred; Hofmann-Lehmann, Regina title: Putative progressive and abortive feline leukemia virus infection outcomes in captive jaguarundis (Puma yagouaroundi) date: 2017-11-17 journal: Virol J DOI: 10.1186/s12985-017-0889-z sha: doc_id: 271130 cord_uid: 6s79q1c1 file: cache/cord-005460-ezrn8cva.json key: cord-005460-ezrn8cva authors: nan title: Physicians – Poster Session date: 2017-07-28 journal: Bone Marrow Transplant DOI: 10.1038/bmt.2017.134 sha: doc_id: 5460 cord_uid: ezrn8cva file: cache/cord-270964-kxze0470.json key: cord-270964-kxze0470 authors: Lau, Kwok-Kwong; Yu, Wai-Cho; Chu, Chung-Ming; Lau, Suet-Ting; Sheng, Bun; Yuen, Kwok-Yung title: Possible Central Nervous System Infection by SARS Coronavirus date: 2004-02-17 journal: Emerg Infect Dis DOI: 10.3201/eid1002.030638 sha: doc_id: 270964 cord_uid: kxze0470 file: cache/cord-271339-wt5o9sgm.json key: cord-271339-wt5o9sgm authors: Chen, Chao-Ju; Hsieh, Li-Ling; Lin, Shu-Kai; Wang, Chu-Feng; Huang, Yi-Hui; Lin, Shang-Yi; Lu, Po-Liang title: Optimization of the CDC Protocol of Molecular Diagnosis of COVID-19 for Timely Diagnosis date: 2020-05-21 journal: Diagnostics (Basel) DOI: 10.3390/diagnostics10050333 sha: doc_id: 271339 cord_uid: wt5o9sgm file: cache/cord-271341-fszljnax.json key: cord-271341-fszljnax authors: Lei, Pinggui; Fan, Bing; Sun, Yipeng title: COVID-19 Carrier or Pneumonia: Positive Real-Time Reverse-Transcriptase Polymerase Chain Reaction but Negative or Positive Chest CT Results date: 2020-05-06 journal: Korean J Radiol DOI: 10.3348/kjr.2020.0360 sha: doc_id: 271341 cord_uid: fszljnax file: cache/cord-010119-t1x9gknd.json key: cord-010119-t1x9gknd authors: nan title: Abstract Presentations from the AABB Annual Meeting San Diego, CA ctober 7‐10, 2017 date: 2017-09-04 journal: Transfusion DOI: 10.1111/trf.14286 sha: doc_id: 10119 cord_uid: t1x9gknd file: cache/cord-271421-4dk7mkut.json key: cord-271421-4dk7mkut authors: Balsalobre-Arenas, Luz; Alarcón-Cavero, Teresa title: Rapid diagnosis of gastrointestinal tract infections due to parasites, viruses, and bacteria date: 2017-07-31 journal: Enfermedades infecciosas y microbiologia clinica (English ed.) 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Almodóvar, Ana Esmeralda Barrero; Amigo, Víctor Jorge; Arcos, Mercedes Ramírez; Caballero, Mónica Chávez; Martino, María del Carmen Serrano title: DETECCIÓN VIRAL Y RESPUESTA SEROLÓGICA EN PACIENTES CRÍTICOS INTUBADOS CON SARS-CoV-2. 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Coste-Burel, M.; Costa-Mattioli, M.; Besse, B.; Chomel, J.; Billaudel, S.; Ferré, V. title: Application of a Real-Time Polymerase Chain Reaction with Internal Positive Control for Detection and Quantification of Enterovirus in Cerebrospinal Fluid date: 2002-07-13 journal: Eur J Clin Microbiol Infect Dis DOI: 10.1007/s10096-002-0766-5 sha: doc_id: 274567 cord_uid: xd37wxxf file: cache/cord-274676-wtizb7hk.json key: cord-274676-wtizb7hk authors: Lee, Seung-Hun; VanBik, Dorene; Kim, Ha-Young; Lee, Yu-Ran; Kim, Jong Wan; Chae, Myeongju; Oh, Sang-Ik; Goo, Youn-Kyoung; Kwon, Oh-Deog; Kwak, Dongmi title: Multilocus typing of Cryptosporidium spp. in young calves with diarrhea in Korea date: 2016-10-15 journal: Vet Parasitol DOI: 10.1016/j.vetpar.2016.09.019 sha: doc_id: 274676 cord_uid: wtizb7hk file: cache/cord-274568-flqc3jjd.json key: cord-274568-flqc3jjd authors: Naguib, Michael; Moustafa, Fathi; Salman, Mustafa Thaer; Saeed, Nermin Kamal; Al-Qahtani, Manaf title: The use of radiological imaging alongside reverse transcriptase PCR in diagnosing novel coronavirus disease 2019: a narrative review date: 2020-07-08 journal: Future microbiology DOI: 10.2217/fmb-2020-0098 sha: doc_id: 274568 cord_uid: flqc3jjd file: cache/cord-274644-gr1eaj6k.json key: cord-274644-gr1eaj6k authors: Chen, Zhao-Chi; Chang, Tien-Li; Li, Ching-Hao; Su, Kai-Wen; Liu, Cheng-Che title: Thermally stable and uniform DNA amplification with picosecond laser ablated graphene rapid thermal cycling device date: 2019-12-15 journal: Biosens Bioelectron DOI: 10.1016/j.bios.2019.111581 sha: doc_id: 274644 cord_uid: gr1eaj6k file: cache/cord-274656-dngumjns.json key: cord-274656-dngumjns authors: Mori, Masahiro; Hosoya, Mitsuaki; Hiwasa, Takaki; Hayakawa, Sei; Uzawa, Akiyuki; Kuwabara, Satoshi title: Detection of mumps virus RNA in cerebrospinal fluid of patients with neuromyelitis optica date: 2011-04-06 journal: Neurol Sci DOI: 10.1007/s10072-011-0564-x sha: doc_id: 274656 cord_uid: dngumjns file: cache/cord-274707-mxh38hwd.json key: cord-274707-mxh38hwd authors: Laureano, Ana Flávia Santarine; Riboldi, Márcia title: The different tests for the diagnosis of COVID-19 - A review in Brazil so far date: 2020 journal: JBRA Assist Reprod DOI: 10.5935/1518-0557.20200046 sha: doc_id: 274707 cord_uid: mxh38hwd file: cache/cord-274805-b3mqkfhh.json key: cord-274805-b3mqkfhh authors: Onodera, Kenji; 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Pang, Victor Fei; Pan, Chu-Hsiang; Chen, Tsu-Han; Jong, Ming-Hwa; Huang, Tien-Shine; Jeng, Chian-Ren title: Development of a reverse transcription multiplex real-time PCR for the detection and genotyping of classical swine fever virus date: 2009-05-04 journal: J Virol Methods DOI: 10.1016/j.jviromet.2009.04.029 sha: doc_id: 274954 cord_uid: 06c3ymc3 file: cache/cord-275413-e2rhioty.json key: cord-275413-e2rhioty authors: Rowland, Raymond R.R. title: The interaction between PRRSV and the late gestation pig fetus date: 2010-09-09 journal: Virus Res DOI: 10.1016/j.virusres.2010.09.001 sha: doc_id: 275413 cord_uid: e2rhioty file: cache/cord-275232-0sg0hv9w.json key: cord-275232-0sg0hv9w authors: Yeung, Siu-Wai; Lee, Thomas Ming-Hung; Cai, Hong; Hsing, I-Ming title: A DNA biochip for on-the-spot multiplexed pathogen identification date: 2006-09-25 journal: Nucleic Acids Res DOI: 10.1093/nar/gkl702 sha: doc_id: 275232 cord_uid: 0sg0hv9w file: cache/cord-275275-wy8d6cw3.json key: cord-275275-wy8d6cw3 authors: Rovida, Francesca; 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Lu, Jiaxuan; Wang, Ningning; He, Wan-Ting; Zhang, Letian; Zhao, Wen; Su, Shuo title: Development of a TaqMan-probe-based multiplex real-time PCR for the simultaneous detection of emerging and reemerging swine coronaviruses date: 2020-06-03 journal: Virulence DOI: 10.1080/21505594.2020.1771980 sha: doc_id: 276542 cord_uid: lxwls664 file: cache/cord-276739-84vf5bts.json key: cord-276739-84vf5bts authors: Sakurai, Akira; Nomura, Namiko; Nanba, Reiko; Sinkai, Takayuki; Iwaki, Tsunehito; Obayashi, Taminori; Hashimoto, Kazuhiro; Hasegawa, Michiya; Sakoda, Yoshihiro; Naito, Akihiro; Morizane, Yoshihito; Hosaka, Mitsugu; Tsuboi, Kunio; Kida, Hiroshi; Kai, Akemi; Shibasaki, Futoshi title: Rapid typing of influenza viruses using super high-speed quantitative real-time PCR date: 2011-08-22 journal: J Virol Methods DOI: 10.1016/j.jviromet.2011.08.015 sha: doc_id: 276739 cord_uid: 84vf5bts file: cache/cord-277025-gmy51dx4.json key: cord-277025-gmy51dx4 authors: Pfefferle, Susanne; Huang, Jiabin; Nörz, Dominik; 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Lakshmana; Reddy, Gopal title: Rapid detection and differentiation of dengue virus serotypes by NS1 specific reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay in patients presenting to a tertiary care hospital in Hyderabad, India date: 2014-10-24 journal: J Virol Methods DOI: 10.1016/j.jviromet.2014.10.005 sha: doc_id: 276718 cord_uid: 3lujp0oy file: cache/cord-276978-xl4u7n6r.json key: cord-276978-xl4u7n6r authors: Jonassen, Christine Monceyron title: Detection and Sequence Characterization of the 3′-End of Coronavirus Genomes Harboring the Highly Conserved RNA Motif s2m date: 2007-11-28 journal: SARS- and Other Coronaviruses DOI: 10.1007/978-1-59745-181-9_3 sha: doc_id: 276978 cord_uid: xl4u7n6r file: cache/cord-277125-s11obc7w.json key: cord-277125-s11obc7w authors: Kim, Hyeong Rae; An, Sanggwon; Hwang, Jungho title: An integrated system of air sampling and simultaneous enrichment for rapid biosensing of airborne coronavirus and influenza virus date: 2020-09-26 journal: Biosens Bioelectron DOI: 10.1016/j.bios.2020.112656 sha: doc_id: 277125 cord_uid: s11obc7w file: cache/cord-277057-ww41t4k2.json key: cord-277057-ww41t4k2 authors: Sakthivel, Senthilkumar K.; Whitaker, Brett; Lu, Xiaoyan; Oliveira, Danielle B.L.; Stockman, Lauren J.; Kamili, Shifaq; Oberste, M. Steven; Erdman, Dean D. title: Comparison of fast-track diagnostics respiratory pathogens multiplex real-time RT-PCR assay with in-house singleplex assays for comprehensive detection of human respiratory viruses() date: 2012-07-11 journal: J Virol Methods DOI: 10.1016/j.jviromet.2012.07.010 sha: doc_id: 277057 cord_uid: ww41t4k2 file: cache/cord-277265-p8pns7r9.json key: cord-277265-p8pns7r9 authors: Malik, Yashpal Singh; Verma, Atul; Kumar, Naveen; Deol, Pallavi; Kumar, Deepak; Ghosh, Souvik; Dhama, Kuldeep title: Biotechnological innovations in farm and pet animal disease diagnosis date: 2019-09-20 journal: Genomics and Biotechnological Advances in Veterinary, Poultry, and Fisheries DOI: 10.1016/b978-0-12-816352-8.00013-8 sha: doc_id: 277265 cord_uid: p8pns7r9 file: cache/cord-277357-lpurk7pe.json key: cord-277357-lpurk7pe authors: González-González, Everardo; Trujillo-de Santiago, Grissel; Lara-Mayorga, Itzel Montserrat; Martínez-Chapa, Sergio Omar; Alvarez, Mario Moisés title: Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection date: 2020-08-13 journal: PLoS One DOI: 10.1371/journal.pone.0237418 sha: doc_id: 277357 cord_uid: lpurk7pe file: cache/cord-277276-j2qzhvzi.json key: cord-277276-j2qzhvzi authors: Al-Ayed, Mohamed S.; Asaad, Ahmed M.; Qureshi, Mohamed A.; Ameen, Mohammed S. title: Viral etiology of respiratory infections in children in southwestern Saudi Arabia using multiplex reverse-transcriptase polymerase chain reaction date: 2014 journal: Saudi Med J DOI: nan sha: doc_id: 277276 cord_uid: j2qzhvzi file: cache/cord-277359-za2hh71g.json key: cord-277359-za2hh71g authors: Chae, Kum Ju; Jin, Gong Yong; Lee, Chang-Seop; Lee, Heung Bum; Lee, Ju-Hyung; Kwon, Keun-Sang title: Positive conversion of COVID-19 after two consecutive negative RT-PCR results: A role of low-dose CT date: 2020-06-09 journal: Eur J Radiol DOI: 10.1016/j.ejrad.2020.109122 sha: doc_id: 277359 cord_uid: za2hh71g file: cache/cord-279101-c763gzq2.json key: cord-279101-c763gzq2 authors: Xu, Sen; Jing, Ming; Liu, Wen-Ying; Dong, He; Kong, De-Min; Wang, Ya-Ru; Zhang, Han-Han; Yue, Zhen; Li, You-Jie; Jiao, Fei; Xie, Shu-Yang title: Identification and characterization of a novel L-type lectin (MjLTL2) from kuruma shrimp (Marsupenaeus japonicus) date: 2020-01-13 journal: Fish Shellfish Immunol DOI: 10.1016/j.fsi.2020.01.022 sha: doc_id: 279101 cord_uid: c763gzq2 file: cache/cord-277838-931sco95.json key: cord-277838-931sco95 authors: Erles, Kerstin; Toomey, Crista; Brooks, Harriet W; Brownlie, Joe title: Detection of a group 2 coronavirus in dogs with canine infectious respiratory disease date: 2003-06-05 journal: Virology DOI: 10.1016/s0042-6822(03)00160-0 sha: doc_id: 277838 cord_uid: 931sco95 file: cache/cord-278176-o9glkhyv.json key: cord-278176-o9glkhyv authors: Houng, Huo-Shu H; Norwood, David; Ludwig, George V; Sun, Wellington; Lin, Minta; Vaughn, David W title: Development and evaluation of an efficient 3′-noncoding region based SARS coronavirus (SARS-CoV) RT-PCR assay for detection of SARS-CoV infections date: 2004-09-01 journal: J Virol Methods DOI: 10.1016/j.jviromet.2004.04.008 sha: doc_id: 278176 cord_uid: o9glkhyv file: cache/cord-278635-vwdxr1bl.json key: cord-278635-vwdxr1bl authors: Świętoń, Edyta; Tarasiuk, Karolina; Śmietanka, Krzysztof title: Low pathogenic avian influenza virus isolates with different levels of defective genome segments vary in pathogenicity and transmission efficiency date: 2020-08-28 journal: Vet Res DOI: 10.1186/s13567-020-00833-6 sha: doc_id: 278635 cord_uid: vwdxr1bl file: cache/cord-277909-rn1dow26.json key: cord-277909-rn1dow26 authors: Gunson, R.N.; Collins, T.C.; Carman, W.F. title: Practical experience of high throughput real time PCR in the routine diagnostic virology setting date: 2006-02-07 journal: J Clin Virol DOI: 10.1016/j.jcv.2005.12.006 sha: doc_id: 277909 cord_uid: rn1dow26 file: cache/cord-277988-dhzln0n3.json key: cord-277988-dhzln0n3 authors: Mcheik, Jiad N.; Dichamp, Isabelle; Levard, Guillaume; Ragot, Stéphanie; Beby‐Defaux, Agnès; Grosos, Céline; Couvrat, Véronique; Agius, Gérard title: Infantile hypertrophic pyloric stenosis: Are viruses involved? date: 2010-10-27 journal: J Med Virol DOI: 10.1002/jmv.21913 sha: doc_id: 277988 cord_uid: dhzln0n3 file: cache/cord-279223-qvih5qas.json key: cord-279223-qvih5qas authors: Hascoët, Jean-Michel; Jellimann, Jean-Marc; Hartard, Cedric; Wittwer, Apolline; Jeulin, Hélène; Franck, Patricia; Morel, Olivier title: Case Series of COVID-19 Asymptomatic Newborns With Possible Intrapartum Transmission of SARS-CoV-2 date: 2020-09-29 journal: Front Pediatr DOI: 10.3389/fped.2020.568979 sha: doc_id: 279223 cord_uid: qvih5qas file: cache/cord-279229-2226jnfl.json key: cord-279229-2226jnfl authors: Savan, R; Kono, T; Itami, T; Sakai, M title: Loop‐mediated isothermal amplification: an emerging technology for detection of fish and shellfish pathogens date: 2005-11-22 journal: J Fish Dis DOI: 10.1111/j.1365-2761.2005.00670.x sha: doc_id: 279229 cord_uid: 2226jnfl file: cache/cord-279577-iwqr2d0r.json key: cord-279577-iwqr2d0r authors: Kaur, Taranjit; Singh, Jatinder; Tong, Suxiang; Humphrey, Charles; Clevenger, Donna; Tan, Wendy; Szekely, Brian; Wang, Yuhuan; Li, Yan; Alex Muse, Epaphras; Kiyono, Mieko; Hanamura, Shunkichi; Inoue, Eiji; Nakamura, Michio; Huffman, Michael A.; Jiang, Baoming; Nishida, Toshisada title: Descriptive epidemiology of fatal respiratory outbreaks and detection of a human‐related metapneumovirus in wild chimpanzees (Pan troglodytes) at Mahale Mountains National Park, Western Tanzania date: 2008-06-11 journal: Am J Primatol DOI: 10.1002/ajp.20565 sha: doc_id: 279577 cord_uid: iwqr2d0r file: cache/cord-279644-g9cr9m96.json key: cord-279644-g9cr9m96 authors: Abedi Kiasari, Bahman; Vallely, Pamela J.; Klapper, Paul E. title: Merkel cell polyomavirus DNA in immunocompetent and immunocompromised patients with respiratory disease date: 2011-10-19 journal: J Med Virol DOI: 10.1002/jmv.22222 sha: doc_id: 279644 cord_uid: g9cr9m96 file: cache/cord-280442-jtvez46y.json key: cord-280442-jtvez46y authors: Wu, Xuan; Song, Zengxu; Zhai, Xiwen; Zuo, Lei; Mei, Xueran; Xiang, Rong; Kang, Zhuangzhuang; Zhou, Long; Wang, Hongning title: Simultaneous and visual detection of infectious bronchitis virus and Newcastle disease virus by multiple LAMP and lateral flow dipstick date: 2019-11-01 journal: Poultry Science DOI: 10.3382/ps/pez372 sha: doc_id: 280442 cord_uid: jtvez46y file: cache/cord-281653-zogtpm7a.json key: cord-281653-zogtpm7a authors: Thurman, Kathleen A.; Warner, Agnes K.; Cowart, Kelley C.; Benitez, Alvaro J.; Winchell, Jonas M. title: Detection of Mycoplasma pneumoniae, Chlamydia pneumoniae, and Legionella spp. in clinical specimens using a single-tube multiplex real-time PCR assay() date: 2011-03-11 journal: Diagn Microbiol Infect Dis DOI: 10.1016/j.diagmicrobio.2010.11.014 sha: doc_id: 281653 cord_uid: zogtpm7a file: cache/cord-281871-3j64de2i.json key: cord-281871-3j64de2i authors: Sinagra, G; Porcari, A; Gentile, P; Artico, J; Fabris, E; Bussani, R; Merlo, M title: Viral presence guided immunomodulation in lymphocytic myocarditis: An update date: 2020-07-19 journal: Eur J Heart Fail DOI: 10.1002/ejhf.1969 sha: doc_id: 281871 cord_uid: 3j64de2i file: cache/cord-277659-afysef1e.json key: cord-277659-afysef1e authors: Hamilton, F.; Muir, P.; Attwood, M.; Noel, A.; Vipond, B.; Hopes, R.; Moran, E.; Maskell, N.; Warwick, D.; Albur, M.; Turner, J.; MacGowan, A. 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Moe, Christine L; Jaykus, Lee-Ann; Cronin, Mike; Grosso, Lynell; Aarle, Pierre van title: Evaluation of the NucliSens® Basic Kit assay for detection of Norwalk virus RNA in stool specimens date: 2003-01-16 journal: J Virol Methods DOI: 10.1016/s0166-0934(02)00286-0 sha: doc_id: 281174 cord_uid: 3c1vue0y file: cache/cord-281529-2rec51xg.json key: cord-281529-2rec51xg authors: Haagmans, Bart L; Al Dhahiry, Said H S; Reusken, Chantal B E M; Raj, V Stalin; Galiano, Monica; Myers, Richard; Godeke, Gert-Jan; Jonges, Marcel; Farag, Elmoubasher; Diab, Ayman; Ghobashy, Hazem; Alhajri, Farhoud; Al-Thani, Mohamed; Al-Marri, Salih A; Al Romaihi, Hamad E; Al Khal, Abdullatif; Bermingham, Alison; Osterhaus, Albert D M E; AlHajri, Mohd M; Koopmans, Marion P G title: Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation date: 2013-12-17 journal: Lancet Infect Dis DOI: 10.1016/s1473-3099(13)70690-x sha: doc_id: 281529 cord_uid: 2rec51xg file: cache/cord-280865-shwxhak9.json key: cord-280865-shwxhak9 authors: Zhang, Dan; Mao, Haiyan; Lou, Xiuyu; Pan, Junhang; Yan, Hao; Tang, Hongfeng; Shu, Yan; Zhao, Yun; Cheng, Xiaoli; Tao, Hong; Zhang, Yanjun; Ma, Xuejun title: Clinical evaluation of a panel of multiplex quantitative real-time reverse transcription polymerase chain reaction assays for the detection of 16 respiratory viruses associated with community-acquired pneumonia date: 2018-06-30 journal: Arch Virol DOI: 10.1007/s00705-018-3921-8 sha: doc_id: 280865 cord_uid: shwxhak9 file: cache/cord-281844-c0uhcatg.json key: cord-281844-c0uhcatg authors: Costa, Lusmaia D.C.; Costa, Paulo Sucasas; Camargos, Paulo A.M. title: Exacerbation of asthma and airway infection: is the virus the villain? date: 2014-12-31 journal: Jornal de Pediatria DOI: 10.1016/j.jped.2014.07.001 sha: doc_id: 281844 cord_uid: c0uhcatg file: cache/cord-277804-ujabzic4.json key: cord-277804-ujabzic4 authors: Yuk, Seong-su; Kwon, Jung-Hoon; Noh, Jin-Yong; Hong, Woo-tack; Gwon, Gyeong-Bin; Jeong, Jei-Hyun; Jeong, Sol; Youn, Ha-Na; Heo, Yong-Hwan; Lee, Joong-Bok; Park, Seung-Yong; Choi, In-Soo; Song, Chang-Seon title: Comparison between dot-immunoblotting assay and clinical sign determination method for quantifying avian infectious bronchitis virus vaccine by titration in embryonated eggs date: 2016-01-21 journal: J Virol Methods DOI: 10.1016/j.jviromet.2016.01.008 sha: doc_id: 277804 cord_uid: ujabzic4 file: cache/cord-278833-wlhmcdcn.json key: cord-278833-wlhmcdcn authors: Rutschke, Nils; Zimmermann, Jan; Möller, Ronny; Klöck, Gerd; Winterhalter, Mathias; Leune, Annika title: Hot start reverse transcriptase: an approach for improved real-time RT-PCR performance date: 2015-06-21 journal: J Anal Sci Technol DOI: 10.1186/s40543-015-0063-4 sha: doc_id: 278833 cord_uid: wlhmcdcn file: cache/cord-279551-py2awuav.json key: cord-279551-py2awuav authors: Willi, Barbara; Spiri, Andrea M.; Meli, Marina L.; Grimm, Felix; Beatrice, Laura; Riond, Barbara; Bley, Tim; Jordi, Rolf; Dennler, Matthias; Hofmann-Lehmann, Regina title: Clinical and molecular investigation of a canine distemper outbreak and vector-borne infections in a group of rescue dogs imported from Hungary to Switzerland date: 2015-07-16 journal: BMC Vet Res DOI: 10.1186/s12917-015-0471-0 sha: doc_id: 279551 cord_uid: py2awuav file: cache/cord-281887-b511bjdy.json key: cord-281887-b511bjdy authors: Ribeiro, Reitan; Wainstein, Alberto Julius Alves; de Castro Ribeiro, Heber Salvador; Pinheiro, Rodrigo Nascimento; Oliveira, Alexandre Ferreira title: Perioperative Cancer Care in the Context of Limited Resources during the COVID-19 Pandemic: Brazilian Society of Surgical Oncology Recommendations date: 2020-09-26 journal: Ann Surg Oncol DOI: 10.1245/s10434-020-09098-x sha: doc_id: 281887 cord_uid: b511bjdy file: cache/cord-282321-svoshzz8.json key: cord-282321-svoshzz8 authors: Eboigbodin, Kevin; Filén, Sanna; Ojalehto, Tuomas; Brummer, Mirko; Elf, Sonja; Pousi, Kirsi; Hoser, Mark title: Reverse transcription strand invasion based amplification (RT-SIBA): a method for rapid detection of influenza A and B date: 2016-04-11 journal: Appl Microbiol Biotechnol DOI: 10.1007/s00253-016-7491-y sha: doc_id: 282321 cord_uid: svoshzz8 file: cache/cord-279563-4lu1n0s7.json key: cord-279563-4lu1n0s7 authors: Gorzalski, Andrew J.; Tian, Honglin; Laverdure, Chris; Morzunov, Sergey; Verma, Subhash C.; VanHooser, Stephanie; 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Scott, Justine A.; Le, Mylinh H.; Shebl, Fatma M.; Panella, Christopher; Losina, Elena; Flanagan, Clare; Gaeta, Jessie M.; Neilan, Anne; Hyle, Emily P.; Mohareb, Amir; Reddy, Krishna P.; Siedner, Mark J.; Harling, Guy; Weinstein, Milton C.; Ciaranello, Andrea; Kazemian, Pooyan; Freedberg, Kenneth A. title: Clinical Outcomes, Costs, and Cost-effectiveness of Strategies for People Experiencing Sheltered Homelessness During the COVID-19 Pandemic date: 2020-10-20 journal: medRxiv DOI: 10.1101/2020.08.07.20170498 sha: doc_id: 283409 cord_uid: ynwgdz52 file: cache/cord-282968-kjvvoveq.json key: cord-282968-kjvvoveq authors: Qu, Renjun; Miao, Yujing; Cui, Yingjing; Cao, Yiwen; Zhou, Ying; Tang, Xiaoqing; Yang, Jie; Wang, Fangquan title: Selection of reference genes for the quantitative real-time PCR normalization of gene expression in Isatis indigotica fortune date: 2019-03-25 journal: BMC Mol Biol DOI: 10.1186/s12867-019-0126-y sha: doc_id: 282968 cord_uid: kjvvoveq file: cache/cord-283641-2u16otbf.json key: cord-283641-2u16otbf authors: Vainionpää, R.; 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Guo, Xinyu; Qiang, Jun title: A retrospective study of the initial 25 COVID-19 patients in Luoyang, China date: 2020-05-26 journal: Jpn J Radiol DOI: 10.1007/s11604-020-00988-4 sha: doc_id: 284625 cord_uid: to6w5hm2 file: cache/cord-284608-ba7wq52t.json key: cord-284608-ba7wq52t authors: Sias, Catia; Salichos, Leonidas; Lapa, Daniele; Del Nonno, Franca; Baiocchini, Andrea; Capobianchi, Maria Rosaria; Garbuglia, Anna Rosa title: Alpha, Beta, gamma human PapillomaViruses (HPV) detection with a different sets of primers in oropharyngeal swabs, anal and cervical samples date: 2019-03-04 journal: Virol J DOI: 10.1186/s12985-019-1132-x sha: doc_id: 284608 cord_uid: ba7wq52t file: cache/cord-284366-snajbvr9.json key: cord-284366-snajbvr9 authors: Han, Zhiyong; Battaglia, Fortunato; Terlecky, Stanley R title: Discharged COVID‐19 Patients Testing Positive Again for SARS‐CoV‐2 RNA: A Minireview of Published Studies from China date: 2020-07-01 journal: J Med Virol DOI: 10.1002/jmv.26250 sha: doc_id: 284366 cord_uid: snajbvr9 file: cache/cord-284423-fzz8g3rq.json key: cord-284423-fzz8g3rq authors: Wang, Hui-yu; Wu, Shao-qiang; Jiang, Li; Xiao, Rong-hai; Li, Ting; Mei, Lin; Lv, Ji-zhou; Liu, Jia-jia; Lin, Xiang-mei; Han, Xue-qing title: Establishment and optimization of a liquid bead array for the simultaneous detection of ten insect-borne pathogens date: 2018-07-31 journal: Parasit Vectors DOI: 10.1186/s13071-018-2996-0 sha: doc_id: 284423 cord_uid: fzz8g3rq file: cache/cord-284367-cy61pjcb.json key: cord-284367-cy61pjcb authors: MULEYA, Walter; SASAKI, Michihito; ORBA, Yasuko; ISHII, Akihiro; THOMAS, Yuka; NAKAGAWA, Emiko; OGAWA, Hirohito; HANG’OMBE, Bernard; NAMANGALA, Boniface; MWEENE, Aaron; TAKADA, Ayato; KIMURA, Takashi; SAWA, Hirofumi title: Molecular Epidemiology of Paramyxoviruses in Frugivorous Eidolon helvum Bats in Zambia date: 2013-12-31 journal: J Vet Med Sci DOI: 10.1292/jvms.13-0518 sha: doc_id: 284367 cord_uid: cy61pjcb file: cache/cord-284372-v95fzp8n.json key: cord-284372-v95fzp8n authors: Coyle, Peter V; Ong, Grace M; O'Neill, Hugh J; McCaughey, Conall; De Ornellas, Dennis; 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Alberto; Garcia, Josefina; Chauca, Gloria; Gamero, Maria E.; Sovero, Merly; Bordones, Slave; Villalobos, Iris; Melchor, Angel; Halsey, Eric S. title: Sentinel Surveillance of Influenza-Like Illness in Two Hospitals in Maracay, Venezuela: 2006–2010 date: 2012-09-11 journal: PLoS One DOI: 10.1371/journal.pone.0044511 sha: doc_id: 289017 cord_uid: vwye3pk9 file: cache/cord-289114-ifnk41oq.json key: cord-289114-ifnk41oq authors: Singh, Angaraj; Kumar, Manoj; Dubey, Ashutosh Kumar title: Effect of pre‐existing diseases on COVID‐19 infection and role of new sensors and biomaterials for its detection and treatment date: 2020-10-28 journal: Med Devices Sens DOI: 10.1002/mds3.10140 sha: doc_id: 289114 cord_uid: ifnk41oq file: cache/cord-288701-nx9fg4yn.json key: cord-288701-nx9fg4yn authors: Mari, Viviana; Losurdo, Michele; Lucente, Maria Stella; Lorusso, Eleonora; Elia, Gabriella; Martella, Vito; Patruno, Giovanni; Buonavoglia, Domenico; Decaro, Nicola title: Multiplex real-time RT-PCR assay for bovine viral diarrhea virus type 1, type 2 and HoBi-like pestivirus date: 2015-12-17 journal: J Virol Methods DOI: 10.1016/j.jviromet.2015.12.003 sha: doc_id: 288701 cord_uid: nx9fg4yn file: cache/cord-289200-6yhz1a23.json key: cord-289200-6yhz1a23 authors: Yang, Ziyi; 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Piceci Sparascio, Francesca; Sohrabi, Hamidreza; Mousavifar, Leila; Roy, René; Scribano, Daniela; De Luca, Alessandro; Ambrosi, Cecilia; Sarshar, Meysam title: The Global Emergency of Novel Coronavirus (SARS-CoV-2): An Update of the Current Status and Forecasting date: 2020-08-05 journal: Int J Environ Res Public Health DOI: 10.3390/ijerph17165648 sha: doc_id: 291916 cord_uid: 5yqc3zcx file: cache/cord-292172-aqsc9fbl.json key: cord-292172-aqsc9fbl authors: Al Amin, Md.; Mahfujur Rahman, Md.; Razimi, Mohd Shahril Ahmad; Chowdhury, Zaira Zaman; Hussain, Muhammad Nasri Md.; Desa, Mohd Nasir Mohd title: Screening of commercial meat products from supermarket chains for feline derivatives using SP-PCR-RLFP and lab-on-a-chip date: 2020-06-09 journal: J Food Compost Anal DOI: 10.1016/j.jfca.2020.103565 sha: doc_id: 292172 cord_uid: aqsc9fbl file: cache/cord-292347-d7xq7x5g.json key: cord-292347-d7xq7x5g authors: Carter, Linda J.; Garner, Linda V.; Smoot, Jeffrey W.; Li, Yingzhu; Zhou, Qiongqiong; 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Bessi, Hlima; Ennaji, Moulay Mustapha title: Chapter 7 Scientific Advances in the Diagnosis of Emerging and Reemerging Viral Human Pathogens date: 2020-12-31 journal: Emerging and Reemerging Viral Pathogens DOI: 10.1016/b978-0-12-814966-9.00007-x sha: doc_id: 292575 cord_uid: vsswxwdi file: cache/cord-292742-mio4przi.json key: cord-292742-mio4przi authors: McAloose, Denise; Laverack, Melissa; Wang, Leyi; Killian, Mary Lea; Caserta, Leonardo C.; Yuan, Fangfeng; Mitchell, Patrick K.; Queen, Krista; Mauldin, Matthew R.; Cronk, Brittany D.; Bartlett, Susan L.; Sykes, John M.; Zec, Stephanie; Stokol, Tracy; Ingerman, Karen; Delaney, Martha A.; Fredrickson, Richard; Ivančić, Marina; Jenkins-Moore, Melinda; Mozingo, Katie; Franzen, Kerrie; Bergeson, Nichole Hines; Goodman, Laura; Wang, Haibin; Fang, Ying; Olmstead, Colleen; McCann, Colleen; Thomas, Patrick; Goodrich, Erin; Elvinger, François; Smith, David C.; Tong, Suxiang; Slavinski, Sally; Calle, Paul P.; Terio, Karen; Torchetti, Mia Kim; Diel, Diego G. title: From People to Panthera: Natural SARS-CoV-2 Infection in Tigers and Lions at the Bronx Zoo date: 2020-10-13 journal: mBio DOI: 10.1128/mbio.02220-20 sha: doc_id: 292742 cord_uid: mio4przi file: cache/cord-292928-a4bn30ul.json key: cord-292928-a4bn30ul authors: Ghosh, Bipasha; 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Hägglund, Sara; Larsen, Lars-Erik; Belák, Sándor title: Evaluation of a single-tube fluorogenic RT-PCR assay for detection of bovine respiratory syncytial virus in clinical samples date: 2004-11-17 journal: J Virol Methods DOI: 10.1016/j.jviromet.2004.09.016 sha: doc_id: 302024 cord_uid: zz7mt6be file: cache/cord-302207-ljpfgih2.json key: cord-302207-ljpfgih2 authors: Lichtmannsperger, Katharina; Hinney, Barbara; Joachim, Anja; Wittek, Thomas title: Molecular characterization of Giardia intestinalis and Cryptosporidium parvum from calves with diarrhoea in Austria and evaluation of point-of-care tests date: 2019-07-12 journal: Comp Immunol Microbiol Infect Dis DOI: 10.1016/j.cimid.2019.101333 sha: doc_id: 302207 cord_uid: ljpfgih2 file: cache/cord-302459-grs2x26l.json key: cord-302459-grs2x26l authors: Matin, Farhana; Jeet, Varinder; Moya, Leire; Selth, Luke A.; Chambers, Suzanne; Clements, Judith A.; Batra, Jyotsna title: A Plasma Biomarker Panel of Four MicroRNAs for the Diagnosis of Prostate Cancer date: 2018-04-27 journal: Sci Rep DOI: 10.1038/s41598-018-24424-w sha: doc_id: 302459 cord_uid: grs2x26l file: cache/cord-302486-z36hcvrx.json key: cord-302486-z36hcvrx authors: Cobo, Fernando; 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Zhang, Jie; Sun, De-hui; Chu, Yue-feng; Cai, Xue-peng; Liu, Xiang-tao; Luo, Xue-nong; Liu, Qing; Liu, Yong-sheng title: Rapid detection of porcine circovirus type 2 by loop-mediated isothermal amplification date: 2008-03-19 journal: J Virol Methods DOI: 10.1016/j.jviromet.2008.01.023 sha: doc_id: 302829 cord_uid: 1o1jo8uk file: cache/cord-302871-x3mjov5l.json key: cord-302871-x3mjov5l authors: Ribeiro, Juliane; Headley, Selwyn Arlington; Diniz, Jaqueline Assumpção; Pereira, Alfredo Hajime Tanaka; Lorenzetti, Elis; Alfieri, Amauri Alcindo; Alfieri, Alice Fernandes title: Extra-intestinal detection of canine kobuvirus in a puppy from Southern Brazil date: 2016-11-25 journal: Arch Virol DOI: 10.1007/s00705-016-3164-5 sha: doc_id: 302871 cord_uid: x3mjov5l file: cache/cord-303665-l57e54hu.json key: cord-303665-l57e54hu authors: Lahrich, S.; Laghrib, F.; Farahi, A.; Bakasse, M.; Saqrane, S.; El Mhammedi, M. 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Szer, Jeff; Jawdat, Dunia; Wood, William A.; Brazauskas, Ruta; Lehmann, Leslie; Pasquini, Marcelo C.; Seber, Adriana; Lu, Pei Hua; Atsuta, Yoshiko; Riches, Marcie; Perales, Miguel-Angel; Worel, Nina; Okamoto, Shinichiro; Srivastava, Alok; Chemaly, Roy F.; Cordonnier, Catherine; Dandoy, Christopher E.; Wingard, John R.; Kharfan-Dabaja, Mohamed A.; Hamadani, Mehdi; Majhail, Navneet S.; Waghmare, Alpana A.; Chao, Nelson; Kröger, Nicolaus; Shaw, Bronwen; Mohty, Mohamad; Niederwieser, Dietger; Greinix, Hildegard; Hashmi, Shahrukh K. title: Real-world issues and potential solutions in HCT during the COVID-19 pandemic: Perspectives from the WBMT and the CIBMTR's Health Services and International Studies Committee date: 2020-07-24 journal: Biol Blood Marrow Transplant DOI: 10.1016/j.bbmt.2020.07.021 sha: doc_id: 349838 cord_uid: p6vfzbla file: cache/cord-350211-vuxs5wtt.json key: cord-350211-vuxs5wtt authors: Johanna, Barón‐Sánchez; Santiago, Cristina; Martín, Gabriela Goizueta‐San; Arca, Roberta; Fernández, Ruth title: Afectación del sentido del olfato y el gusto en la enfermedad leve por coronavirus (COVID-19) en pacientes españoles date: 2020-07-28 journal: Neurologia DOI: 10.1016/j.nrl.2020.07.006 sha: doc_id: 350211 cord_uid: vuxs5wtt file: cache/cord-350172-w3yoxhsg.json key: cord-350172-w3yoxhsg authors: Mertens, Pascal; De Vos, Nathalie; Martiny, Delphine; Jassoy, Christian; Mirazimi, Ali; Cuypers, Lize; Van den Wijngaert, Sigi; Monteil, Vanessa; Melin, Pierrette; Stoffels, Karolien; Yin, Nicolas; Mileto, Davide; Delaunoy, Sabrina; Magein, Henri; Lagrou, Katrien; Bouzet, Justine; Serrano, Gabriela; Wautier, Magali; Leclipteux, Thierry; Van Ranst, Marc; Vandenberg, Olivier title: Development and Potential Usefulness of the COVID-19 Ag Respi-Strip Diagnostic Assay in a Pandemic Context date: 2020-05-08 journal: Front Med (Lausanne) DOI: 10.3389/fmed.2020.00225 sha: doc_id: 350172 cord_uid: w3yoxhsg file: cache/cord-350296-6bq0tps2.json key: cord-350296-6bq0tps2 authors: Olsvik, Pål A; Søfteland, Liv; Lie, Kai K title: Selection of reference genes for qRT-PCR examination of wild populations of Atlantic cod Gadus morhua date: 2008-07-16 journal: BMC Res Notes DOI: 10.1186/1756-0500-1-47 sha: doc_id: 350296 cord_uid: 6bq0tps2 file: cache/cord-350398-w75flrwv.json key: cord-350398-w75flrwv authors: Sampath, Rangarajan; Mulholland, Niveen; Blyn, Lawrence B.; Massire, Christian; Whitehouse, Chris A.; Waybright, Nicole; Harter, Courtney; Bogan, Joseph; Miranda, Mary Sue; Smith, David; Baldwin, Carson; Wolcott, Mark; Norwood, David; Kreft, Rachael; Frinder, Mark; Lovari, Robert; Yasuda, Irene; Matthews, Heather; Toleno, Donna; Housley, Roberta; Duncan, David; Li, Feng; Warren, Robin; Eshoo, Mark W.; Hall, Thomas A.; Hofstadler, Steven A.; Ecker, David J. title: Comprehensive Biothreat Cluster Identification by PCR/Electrospray-Ionization Mass Spectrometry date: 2012-06-29 journal: PLoS One DOI: 10.1371/journal.pone.0036528 sha: doc_id: 350398 cord_uid: w75flrwv file: cache/cord-350593-bvmg7f15.json key: cord-350593-bvmg7f15 authors: McDonald, R.S.; Sambol, A.R.; Heimbuch, B.K.; Brown, T.L.; Hinrichs, S.H.; Wander, J.D. title: Proportional mouse model for aerosol infection by influenza date: 2012-08-21 journal: J Appl Microbiol DOI: 10.1111/j.1365-2672.2012.05402.x sha: doc_id: 350593 cord_uid: bvmg7f15 file: cache/cord-350807-qdq96723.json key: cord-350807-qdq96723 authors: Reckziegel, Maria; Weber-Osel, Claudia; Egerer, Renate; Gruhn, Bernd; Kubek, Florian; Walther, Mario; Wilhelm, Stefanie; Zell, Roland; Krumbholz, Andi title: Viruses and atypical bacteria in the respiratory tract of immunocompromised and immunocompetent patients with airway infection date: 2020-05-27 journal: Eur J Clin Microbiol Infect Dis DOI: 10.1007/s10096-020-03878-9 sha: doc_id: 350807 cord_uid: qdq96723 file: cache/cord-350890-ajxvjkmq.json key: cord-350890-ajxvjkmq authors: Hsieh, Yi-Fan; Lee, Da-Sheng; Chen, Ping-Hei; Liao, Shao-Kai; Yeh, Shiou-Hwei; Chen, Pei-Jer; Yang, An-Shik title: A real-time convective PCR machine in a capillary tube instrumented with a CCD-based fluorometer date: 2013-07-05 journal: Sens Actuators B Chem DOI: 10.1016/j.snb.2013.04.003 sha: doc_id: 350890 cord_uid: ajxvjkmq file: cache/cord-351038-k2m6woow.json key: cord-351038-k2m6woow authors: Arun Krishnan, R.; Elizabeth Thomas, Rhema; Sukumaran, Ajaikumar; Paul, Jofy K.; Vasudevan, D. M. title: COVID-19: Current Trends in Invitro Diagnostics date: 2020-06-27 journal: Indian J Clin Biochem DOI: 10.1007/s12291-020-00906-5 sha: doc_id: 351038 cord_uid: k2m6woow file: cache/cord-351643-8ce807ub.json key: cord-351643-8ce807ub authors: Poon, LLM; Mak, PWY; Li, OTW; Chan, KH; Cheung, CL; Ma, ES; Yen, HL; Vijaykrishna, D; Guan, Y; Peiris, JSM title: Rapid detection of reassortment of pandemic H1N1/2009 influenza virus date: 2010-08-01 journal: Clinical Chemistry DOI: 10.1373/clinchem.2010.149179 sha: doc_id: 351643 cord_uid: 8ce807ub file: cache/cord-351100-llyl97ry.json key: cord-351100-llyl97ry authors: Cariani, Lisa; Orena, Beatrice Silvia; Ambrogi, Federico; Gambazza, Simone; Maraschini, Anna; Dodaro, Antonella; Oggioni, Massimo; Orlandi, Annarosa; Pirrone, Alessia; Uceda Renteria, Sara; Bernazzani, Mara; Cantù, Anna Paola; Ceriotti, Ferruccio; Lunghi, Giovanna title: Time Length of Negativization and Cycle Threshold Values in 182 Healthcare Workers with Covid-19 in Milan, Italy: An Observational Cohort Study date: 2020-07-23 journal: Int J Environ Res Public Health DOI: 10.3390/ijerph17155313 sha: doc_id: 351100 cord_uid: llyl97ry file: cache/cord-351125-asrezu1f.json key: cord-351125-asrezu1f authors: Lee, Sangmin; Kim, Junki; Cheon, Doo-Sung; Moon, Eun-A; Seo, Dong Joo; Jung, Soontag; Shin, Hansaem; Choi, Changsun title: Identification of Cystoisospora ohioensis in a Diarrheal Dog in Korea date: 2018-08-31 journal: Korean J Parasitol DOI: 10.3347/kjp.2018.56.4.371 sha: doc_id: 351125 cord_uid: asrezu1f file: cache/cord-351492-8jv7ip67.json key: cord-351492-8jv7ip67 authors: Urwin, S. 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Joseph-Strauss, D.; Rahat, A.; Sharkia, I.; Adam, M.; Kitsberg, D.; Fialkoff, G.; Lotem, M.; Gershon, O.; Schmidtner, A.-K.; Oiknine-Djian, E.; Klochendler, A.; Sadeh, R.; Dor, Y.; Wolf, D.; Habib, N.; Friedman, N. title: ApharSeq: An Extraction-free Early-Pooling Protocol for Massively Multiplexed SARS-CoV-2 Detection date: 2020-08-13 journal: nan DOI: 10.1101/2020.08.08.20170746 sha: doc_id: 351864 cord_uid: zozrj7w5 file: cache/cord-352562-qfb478sf.json key: cord-352562-qfb478sf authors: Yamamoto, Lidia; dos Santos, Emilly Henrique; Pinto, Lacyane Silva; Rocha, Mussya Cisotto; Kanunfre, Kelly Aparecida; Vallada, Marcelo Genofre; Okay, Thelma Suely title: SARS-CoV-2 infections with emphasis on pediatric patients: a narrative review date: 2020-09-04 journal: Revista do Instituto de Medicina Tropical de Sao Paulo DOI: 10.1590/s1678-9946202062065 sha: doc_id: 352562 cord_uid: qfb478sf file: cache/cord-352831-ydlix2o7.json key: cord-352831-ydlix2o7 authors: Hase, Ryota; Kurita, Takashi; 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P.; Chen, D.; Huang, G.; Zhang, M.; Qu, G.; Fan, W.; Lin, H.; Li, D.; Pei, B. title: Analysis of factors associated early diagnosis in coronavirus disease 2019 (COVID-19) date: 2020-04-14 journal: nan DOI: 10.1101/2020.04.09.20059352 sha: doc_id: 355014 cord_uid: los6q1k4 file: cache/cord-355988-4eldkteb.json key: cord-355988-4eldkteb authors: SAMPATH, RANGARAJAN; HALL, THOMAS A.; MASSIRE, CHRISTIAN; LI, FENG; BLYN, LAWRENCE B.; ESHOO, MARK W.; HOFSTADLER, STEVEN A.; ECKER, DAVID J. title: Rapid Identification of Emerging Infectious Agents Using PCR and Electrospray Ionization Mass Spectrometry date: 2007-04-23 journal: Ann N Y Acad Sci DOI: 10.1196/annals.1408.008 sha: doc_id: 355988 cord_uid: 4eldkteb file: cache/cord-354943-wxhbwcfr.json key: cord-354943-wxhbwcfr authors: Guo, Li; Ren, Lili; Yang, Siyuan; Xiao, Meng; Chang, De; Yang, Fan; Dela Cruz, Charles S; Wang, Yingying; Wu, Chao; Xiao, Yan; Zhang, Lulu; Han, Lianlian; Dang, Shengyuan; Xu, Yan; Yang, Qi-Wen; Xu, Sheng-Yong; Zhu, Hua-Dong; Xu, Ying-Chun; Jin, Qi; Sharma, Lokesh; Wang, Linghang; Wang, Jianwei title: Profiling Early Humoral Response to Diagnose Novel Coronavirus Disease (COVID-19) date: 2020-03-21 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa310 sha: doc_id: 354943 cord_uid: wxhbwcfr file: cache/cord-356370-jjl1hbeb.json key: cord-356370-jjl1hbeb authors: Sahajpal, Nikhil Shri; Njau, Allan; Mondal, Ashis K; Ananth, Sudha; Chaubey, Alka; Rojiani, Amyn; Kolhe, Ravindra title: Role of clinical laboratories in response to the COVID-19 pandemic date: 2020-06-19 journal: Future medicinal chemistry DOI: 10.4155/fmc-2020-0129 sha: doc_id: 356370 cord_uid: jjl1hbeb file: cache/cord-356007-6b0w36l9.json key: cord-356007-6b0w36l9 authors: Alanazi, Khalid H.; Killerby, Marie E.; Biggs, Holly M.; Abedi, Glen R.; Jokhdar, Hani; Alsharef, Ali A.; Mohammed, Mutaz; Abdalla, Osman; Almari, Aref; Bereagesh, Samar; Tawfik, Sameh; Alresheedi, Husain; Alhakeem, Raafat F.; Hakawi, Ahmed; Alfalah, Haitham; Amer, Hala; Thornburg, Natalie J.; Tamin, Azaibi; Trivedi, Suvang; Tong, Suxiang; Lu, Xiaoyan; Queen, Krista; Li, Yan; Sakthivel, Senthilkumar K.; Tao, Ying; Zhang, Jing; Paden, Clinton R.; Al-Abdely, Hail M.; Assiri, Abdullah M.; Gerber, Susan I.; Watson, John T. title: Scope and extent of healthcare-associated Middle East respiratory syndrome coronavirus transmission during two contemporaneous outbreaks in Riyadh, Saudi Arabia, 2017 date: 2018-12-31 journal: Infect Control Hosp Epidemiol DOI: 10.1017/ice.2018.290 sha: doc_id: 356007 cord_uid: 6b0w36l9 file: cache/cord-355489-tkvfneje.json key: cord-355489-tkvfneje authors: Mendez, Jairo A; Usme-Ciro, Jose A; Domingo, Cristina; Rey, Gloria J; Sanchez, Juan A; Tenorio, Antonio; Gallego-Gomez, Juan C title: Phylogenetic history demonstrates two different lineages of dengue type 1 virus in Colombia date: 2010-09-14 journal: Virol J DOI: 10.1186/1743-422x-7-226 sha: doc_id: 355489 cord_uid: tkvfneje Reading metadata file and updating bibliogrpahics === updating bibliographic database Building study carrel named keyword-pcr-cord === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 84972 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 86052 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 85050 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 84913 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 85163 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 85508 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 85503 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 85648 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 86407 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 84932 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 86015 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-005309-147erliy author: Senanayake, Savithra D. title: Precise large deletions by the PCR-based overlap extension method date: 1995 pages: extension: .txt txt: ./txt/cord-005309-147erliy.txt cache: ./cache/cord-005309-147erliy.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-005309-147erliy.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 86370 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 87613 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 86454 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 86667 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-000322-8ctsa9sd author: Ninove, Laetitia title: RNA and DNA Bacteriophages as Molecular Diagnosis Controls in Clinical Virology: A Comprehensive Study of More than 45,000 Routine PCR Tests date: 2011-02-09 pages: extension: .txt txt: ./txt/cord-000322-8ctsa9sd.txt cache: ./cache/cord-000322-8ctsa9sd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000322-8ctsa9sd.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-000483-zgapjjjw author: Faux, Cassandra E. title: Usefulness of Published PCR Primers in Detecting Human Rhinovirus Infection date: 2011-02-17 pages: extension: .txt txt: ./txt/cord-000483-zgapjjjw.txt cache: ./cache/cord-000483-zgapjjjw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-000483-zgapjjjw.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 86188 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 86427 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 88425 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 88764 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 87332 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 88176 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 86834 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 87382 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 91. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 87623 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 87949 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-000664-085v7n6k author: Cordey, Samuel title: Pilot Evaluation of RT-PCR/Electrospray Ionization Mass Spectrometry (PLEX-ID/Flu assay) on Influenza-Positive Specimens date: 2012-05-09 pages: extension: .txt txt: ./txt/cord-000664-085v7n6k.txt cache: ./cache/cord-000664-085v7n6k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000664-085v7n6k.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-003047-3ejfxj6r author: Bai, Jianfa title: Comparison data of a two-target real-time PCR assay with and without an internal control in detecting Salmonella enterica from cattle lymph nodes date: 2018-04-22 pages: extension: .txt txt: ./txt/cord-003047-3ejfxj6r.txt cache: ./cache/cord-003047-3ejfxj6r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003047-3ejfxj6r.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 88397 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 88988 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 87572 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 90553 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 89170 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-001134-8ljgxnhf author: Lin, Chao-Nan title: Comparison of viremia of type II porcine reproductive and respiratory syndrome virus in naturally infected pigs by zip nucleic acid probe-based real-time PCR date: 2013-09-12 pages: extension: .txt txt: ./txt/cord-001134-8ljgxnhf.txt cache: ./cache/cord-001134-8ljgxnhf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001134-8ljgxnhf.txt' === file2bib.sh === id: cord-007427-iqwojhq2 author: Dedkov, Vladimir G. title: Development and Evaluation of a One-Step Quantitative RT-PCR Assay for Detection of Lassa Virus date: 2019-06-03 pages: extension: .txt txt: ./txt/cord-007427-iqwojhq2.txt cache: ./cache/cord-007427-iqwojhq2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007427-iqwojhq2.txt' /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 90934 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 90559 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 91032 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 92440 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-001455-n7quwr4s author: Rapin, Noreen title: Activation of Innate Immune-Response Genes in Little Brown Bats (Myotis lucifugus) Infected with the Fungus Pseudogymnoascus destructans date: 2014-11-12 pages: extension: .txt txt: ./txt/cord-001455-n7quwr4s.txt cache: ./cache/cord-001455-n7quwr4s.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001455-n7quwr4s.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-002852-m4l2l2r1 author: Munyua, Peninah M. title: Detection of influenza A virus in live bird markets in Kenya, 2009–2011 date: 2012-04-19 pages: extension: .txt txt: ./txt/cord-002852-m4l2l2r1.txt cache: ./cache/cord-002852-m4l2l2r1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002852-m4l2l2r1.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-000235-782iew86 author: Kapoor, A title: Human bocaviruses are highly diverse, dispersed, recombination prone, and prevalent enteric infections date: 2010-06-01 pages: extension: .txt txt: ./txt/cord-000235-782iew86.txt cache: ./cache/cord-000235-782iew86.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000235-782iew86.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 93804 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 93374 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 90758 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 92627 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 93575 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-000010-prsvv6l9 author: Qin, Jian title: Studying copy number variations using a nanofluidic platform date: 2008-08-18 pages: extension: .txt txt: ./txt/cord-000010-prsvv6l9.txt cache: ./cache/cord-000010-prsvv6l9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000010-prsvv6l9.txt' === file2bib.sh === id: cord-001787-lj1nd922 author: Liu, Ying title: Enhancing production of ergosterol in Pichia pastoris GS115 by over-expression of 3-hydroxy-3-methylglutaryl CoA reductase from Glycyrrhiza uralensis date: 2014-04-02 pages: extension: .txt txt: ./txt/cord-001787-lj1nd922.txt cache: ./cache/cord-001787-lj1nd922.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001787-lj1nd922.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 93854 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-004003-rlgzgyzn author: Lee, Jeewon title: Applying a Linear Amplification Strategy to Recombinase Polymerase Amplification for Uniform DNA Library Amplification date: 2019-11-12 pages: extension: .txt txt: ./txt/cord-004003-rlgzgyzn.txt cache: ./cache/cord-004003-rlgzgyzn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004003-rlgzgyzn.txt' === file2bib.sh === id: cord-011966-7k2cxy8a author: Jang, Seong Sik title: The Epidemiological Characteristics of the Korean Bat Paramyxovirus between 2016 and 2019 date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-011966-7k2cxy8a.txt cache: ./cache/cord-011966-7k2cxy8a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-011966-7k2cxy8a.txt' === file2bib.sh === id: cord-006960-9pho3hk6 author: Prakash, R. title: Droplet Microfluidic Chip Based Nucleic Acid Amplification and Real-Time Detection of Influenza Viruses date: 2013-12-27 pages: extension: .txt txt: ./txt/cord-006960-9pho3hk6.txt cache: ./cache/cord-006960-9pho3hk6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-006960-9pho3hk6.txt' === file2bib.sh === id: cord-002376-970934vm author: Mikel, Pavel title: Preparation of MS2 Phage-Like Particles and Their Use As Potential Process Control Viruses for Detection and Quantification of Enteric RNA Viruses in Different Matrices date: 2016-12-01 pages: extension: .txt txt: ./txt/cord-002376-970934vm.txt cache: ./cache/cord-002376-970934vm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002376-970934vm.txt' === file2bib.sh === id: cord-001843-ceatyj3o author: Huang, Yong title: Ultrasensitive Detection of RNA and DNA Viruses Simultaneously Using Duplex UNDP-PCR Assay date: 2015-11-06 pages: extension: .txt txt: ./txt/cord-001843-ceatyj3o.txt cache: ./cache/cord-001843-ceatyj3o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001843-ceatyj3o.txt' === file2bib.sh === id: cord-014942-4hk0veck author: Boone, Stephanie A. title: The Prevalence of Human Parainfluenza Virus 1 on Indoor Office Fomites date: 2010-02-09 pages: extension: .txt txt: ./txt/cord-014942-4hk0veck.txt cache: ./cache/cord-014942-4hk0veck.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-014942-4hk0veck.txt' === file2bib.sh === id: cord-003505-qr6ukfti author: Tabraue-Chávez, Mavys title: A colorimetric strategy based on dynamic chemistry for direct detection of Trypanosomatid species date: 2019-03-06 pages: extension: .txt txt: ./txt/cord-003505-qr6ukfti.txt cache: ./cache/cord-003505-qr6ukfti.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003505-qr6ukfti.txt' === file2bib.sh === id: cord-004810-g0y7ied0 author: Lee, S. K. title: S1 glycoprotein gene analysis of infectious bronchitis viruses isolated in Korea date: 2003-11-13 pages: extension: .txt txt: ./txt/cord-004810-g0y7ied0.txt cache: ./cache/cord-004810-g0y7ied0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004810-g0y7ied0.txt' === file2bib.sh === id: cord-005752-tur57xd9 author: Linden, Saara title: Parechovirus infection preceding Guillain–Barré syndrome date: 2012-05-12 pages: extension: .txt txt: ./txt/cord-005752-tur57xd9.txt cache: ./cache/cord-005752-tur57xd9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-005752-tur57xd9.txt' === file2bib.sh === id: cord-000715-zl1s82yi author: Shulman, Lester M. title: Evaluation of Four Different Systems for Extraction of RNA from Stool Suspensions Using MS-2 Coliphage as an Exogenous Control for RT-PCR Inhibition date: 2012-07-16 pages: extension: .txt txt: ./txt/cord-000715-zl1s82yi.txt cache: ./cache/cord-000715-zl1s82yi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000715-zl1s82yi.txt' === file2bib.sh === id: cord-001858-nmi39n6h author: Petriccione, Milena title: Reference gene selection for normalization of RT-qPCR gene expression data from Actinidia deliciosa leaves infected with Pseudomonas syringae pv. actinidiae date: 2015-11-19 pages: extension: .txt txt: ./txt/cord-001858-nmi39n6h.txt cache: ./cache/cord-001858-nmi39n6h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001858-nmi39n6h.txt' === file2bib.sh === id: cord-000113-d0eur1hq author: Fooks, Anthony R. title: Emerging Technologies for the Detection of Rabies Virus: Challenges and Hopes in the 21st Century date: 2009-09-29 pages: extension: .txt txt: ./txt/cord-000113-d0eur1hq.txt cache: ./cache/cord-000113-d0eur1hq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000113-d0eur1hq.txt' === file2bib.sh === id: cord-007068-vcfs41eb author: Moradi, Tony title: Use of Procalcitonin and a Respiratory Polymerase Chain Reaction Panel to Reduce Antibiotic Use via an Electronic Medical Record Alert date: 2019-10-22 pages: extension: .txt txt: ./txt/cord-007068-vcfs41eb.txt cache: ./cache/cord-007068-vcfs41eb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007068-vcfs41eb.txt' === file2bib.sh === id: cord-000180-howix091 author: MacLeod, Iain J. title: Binding of Herpes Simplex Virus Type-1 Virions Leads to the Induction of Intracellular Signalling in the Absence of Virus Entry date: 2010-03-05 pages: extension: .txt txt: ./txt/cord-000180-howix091.txt cache: ./cache/cord-000180-howix091.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000180-howix091.txt' === file2bib.sh === id: cord-000750-l9ozvlae author: Betts, Corinne title: Pip6-PMO, A New Generation of Peptide-oligonucleotide Conjugates With Improved Cardiac Exon Skipping Activity for DMD Treatment date: 2012-08-14 pages: extension: .txt txt: ./txt/cord-000750-l9ozvlae.txt cache: ./cache/cord-000750-l9ozvlae.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000750-l9ozvlae.txt' === file2bib.sh === id: cord-003850-in7he5o4 author: Xiu, Leshan title: Simultaneous detection of eleven sexually transmitted agents using multiplexed PCR coupled with MALDI-TOF analysis date: 2019-08-28 pages: extension: .txt txt: ./txt/cord-003850-in7he5o4.txt cache: ./cache/cord-003850-in7he5o4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003850-in7he5o4.txt' === file2bib.sh === id: cord-006450-si5168pb author: Jouneau, S. title: Which patients should be tested for viruses on bronchoalveolar lavage fluid? date: 2012-12-14 pages: extension: .txt txt: ./txt/cord-006450-si5168pb.txt cache: ./cache/cord-006450-si5168pb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-006450-si5168pb.txt' === file2bib.sh === id: cord-007066-zn10rnrm author: Park, Noh Jin title: Characterization of RNA in Saliva date: 2006-06-01 pages: extension: .txt txt: ./txt/cord-007066-zn10rnrm.txt cache: ./cache/cord-007066-zn10rnrm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-007066-zn10rnrm.txt' === file2bib.sh === id: cord-017363-dmb42kna author: Vemulapalli, Ramesh title: Real-Time Reverse Transcription Polymerase Chain Reaction for Rapid Detection of Transmissible Gastroenteritis Virus date: 2015-09-10 pages: extension: .txt txt: ./txt/cord-017363-dmb42kna.txt cache: ./cache/cord-017363-dmb42kna.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-017363-dmb42kna.txt' === file2bib.sh === id: cord-007047-7ty9mxa9 author: Reller, L. Barth title: Implications of New Technology for Infectious Diseases Practice date: 2006-11-15 pages: extension: .txt txt: ./txt/cord-007047-7ty9mxa9.txt cache: ./cache/cord-007047-7ty9mxa9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007047-7ty9mxa9.txt' === file2bib.sh === id: cord-000736-6f8vyziv author: Pripuzova, Natalia title: Development of Real-Time PCR Array for Simultaneous Detection of Eight Human Blood-Borne Viral Pathogens date: 2012-08-17 pages: extension: .txt txt: ./txt/cord-000736-6f8vyziv.txt cache: ./cache/cord-000736-6f8vyziv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000736-6f8vyziv.txt' === file2bib.sh === id: cord-016417-3cwwmyv9 author: Sluijter, J. P. G. title: Quantitative Real-Time PCR date: 2006 pages: extension: .txt txt: ./txt/cord-016417-3cwwmyv9.txt cache: ./cache/cord-016417-3cwwmyv9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016417-3cwwmyv9.txt' === file2bib.sh === id: cord-013589-3l8kar3k author: Doummar, Diane title: Biallelic PDE2A variants: a new cause of syndromic paroxysmal dyskinesia date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-013589-3l8kar3k.txt cache: ./cache/cord-013589-3l8kar3k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-013589-3l8kar3k.txt' === file2bib.sh === id: cord-010235-hu6o1ggc author: Atmar, Robert L. title: Nonculturable agents of viral gastroenteritis date: 1997-12-01 pages: extension: .txt txt: ./txt/cord-010235-hu6o1ggc.txt cache: ./cache/cord-010235-hu6o1ggc.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-010235-hu6o1ggc.txt' === file2bib.sh === id: cord-000830-jiy4cp4n author: Cobo, Fernando title: Application of Molecular Diagnostic Techniques for Viral Testing date: 2012-11-30 pages: extension: .txt txt: ./txt/cord-000830-jiy4cp4n.txt cache: ./cache/cord-000830-jiy4cp4n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000830-jiy4cp4n.txt' === file2bib.sh === id: cord-001655-uqw74ra0 author: Stenglein, Mark D. title: Widespread Recombination, Reassortment, and Transmission of Unbalanced Compound Viral Genotypes in Natural Arenavirus Infections date: 2015-05-20 pages: extension: .txt txt: ./txt/cord-001655-uqw74ra0.txt cache: ./cache/cord-001655-uqw74ra0.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001655-uqw74ra0.txt' === file2bib.sh === id: cord-018865-melttpiq author: Yu, Tian-fei title: Express Transmissible Gastroenteritis Virus Spike Gene B and C Antigen Sites in Multiple Expression Systems date: 2012 pages: extension: .txt txt: ./txt/cord-018865-melttpiq.txt cache: ./cache/cord-018865-melttpiq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018865-melttpiq.txt' === file2bib.sh === id: cord-016020-awanrm9u author: Fox, Julie D. title: Respiratory Pathogens date: 2007 pages: extension: .txt txt: ./txt/cord-016020-awanrm9u.txt cache: ./cache/cord-016020-awanrm9u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-016020-awanrm9u.txt' === file2bib.sh === id: cord-002560-pue5q5wp author: Moreno, Paloma S. title: Characterisation of the canine faecal virome in healthy dogs and dogs with acute diarrhoea using shotgun metagenomics date: 2017-06-01 pages: extension: .txt txt: ./txt/cord-002560-pue5q5wp.txt cache: ./cache/cord-002560-pue5q5wp.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002560-pue5q5wp.txt' === file2bib.sh === id: cord-020568-c5425959 author: Blatny, Janet Martha title: Detecting and Responding to Bioterrorism date: 2007 pages: extension: .txt txt: ./txt/cord-020568-c5425959.txt cache: ./cache/cord-020568-c5425959.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-020568-c5425959.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 94787 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 94919 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 3581 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 3668 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 3817 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-002178-ggtxuulg author: Mauk, Michael G. title: Integrated Microfluidic Nucleic Acid Isolation, Isothermal Amplification, and Amplicon Quantification date: 2015-10-20 pages: extension: .txt txt: ./txt/cord-002178-ggtxuulg.txt cache: ./cache/cord-002178-ggtxuulg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-002178-ggtxuulg.txt' === file2bib.sh === id: cord-015683-a9a82of4 author: Gupta, Varsha title: Molecular Diagnostics date: 2016-10-23 pages: extension: .txt txt: ./txt/cord-015683-a9a82of4.txt cache: ./cache/cord-015683-a9a82of4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-015683-a9a82of4.txt' === file2bib.sh === id: cord-017767-zj1h5ixf author: Shieh, Wun-Ju title: Advanced Pathology Techniques for Detecting Emerging Infectious Disease Pathogens date: 2012-04-05 pages: extension: .txt txt: ./txt/cord-017767-zj1h5ixf.txt cache: ./cache/cord-017767-zj1h5ixf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-017767-zj1h5ixf.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 90. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 4787 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-015763-5lx179pa author: Thellier, D. title: Quels prélèvements aux urgences pour le diagnostic microbiologique d’une infection pulmonaire communautaire grave du sujet immunocompétent ? date: 2014-09-23 pages: extension: .txt txt: ./txt/cord-015763-5lx179pa.txt cache: ./cache/cord-015763-5lx179pa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-015763-5lx179pa.txt' === file2bib.sh === id: cord-000979-cav9n18w author: Hoppe, Sebastian title: Rapid Identification of Novel Immunodominant Proteins and Characterization of a Specific Linear Epitope of Campylobacter jejuni date: 2013-05-29 pages: extension: .txt txt: ./txt/cord-000979-cav9n18w.txt cache: ./cache/cord-000979-cav9n18w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000979-cav9n18w.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-011322-olvqgs85 author: El-Senousy, Waled M. title: Clinical and Environmental Surveillance of Rotavirus Common Genotypes Showed High Prevalence of Common P Genotypes in Egypt date: 2020-04-11 pages: extension: .txt txt: ./txt/cord-011322-olvqgs85.txt cache: ./cache/cord-011322-olvqgs85.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-011322-olvqgs85.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-021052-qydc404w author: Fernandez-Flores, Angel title: Aportaciones de la anatomía patológica en el diagnóstico de las infecciones cutáneas: una perspectiva histórica date: 2015-11-02 pages: extension: .txt txt: ./txt/cord-021052-qydc404w.txt cache: ./cache/cord-021052-qydc404w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-021052-qydc404w.txt' === file2bib.sh === id: cord-021402-wq770ik9 author: Relford, Roberta L. title: New Diagnostic Tools for Infectious Disease date: 2009-05-15 pages: extension: .txt txt: ./txt/cord-021402-wq770ik9.txt cache: ./cache/cord-021402-wq770ik9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-021402-wq770ik9.txt' === file2bib.sh === id: cord-027498-cfzfgzqi author: Hattori, Takeshi title: Older age is associated with sustained detection of SARS-CoV-2 in nasopharyngeal swab samples date: 2020-06-21 pages: extension: .txt txt: ./txt/cord-027498-cfzfgzqi.txt cache: ./cache/cord-027498-cfzfgzqi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-027498-cfzfgzqi.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 7292 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 93054 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 3199 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 3311 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 7624 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-009376-a35a92gh author: Lovatt, Archie title: Applications of quantitative PCR in the biosafety and genetic stability assessment of biotechnology products date: 2002-01-07 pages: extension: .txt txt: ./txt/cord-009376-a35a92gh.txt cache: ./cache/cord-009376-a35a92gh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-009376-a35a92gh.txt' === file2bib.sh === id: cord-015941-4fz79wzf author: Hu, Yuan title: Molecular Techniques for Blood and Blood Product Screening date: 2018-11-10 pages: extension: .txt txt: ./txt/cord-015941-4fz79wzf.txt cache: ./cache/cord-015941-4fz79wzf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-015941-4fz79wzf.txt' /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-017948-fqhl1qb4 author: Hu, Yuan title: Molecular Techniques for Blood and Blood Product Screening date: 2012-04-05 pages: extension: .txt txt: ./txt/cord-017948-fqhl1qb4.txt cache: ./cache/cord-017948-fqhl1qb4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-017948-fqhl1qb4.txt' === file2bib.sh === id: cord-029775-mntcor5d author: Oka, Tomoichiro title: Polymerase chain reaction primer sets for the detection of genetically diverse human sapoviruses date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-029775-mntcor5d.txt cache: ./cache/cord-029775-mntcor5d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-029775-mntcor5d.txt' === file2bib.sh === id: cord-017072-qwe1ne3q author: Poritz, Mark A. title: Multiplex PCR for Detection and Identification of Microbial Pathogens date: 2018-11-10 pages: extension: .txt txt: ./txt/cord-017072-qwe1ne3q.txt cache: ./cache/cord-017072-qwe1ne3q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017072-qwe1ne3q.txt' === file2bib.sh === id: cord-018944-du42ho11 author: Shin, Jeong Hwan title: Nucleic Acid Extraction and Enrichment date: 2018-11-10 pages: extension: .txt txt: ./txt/cord-018944-du42ho11.txt cache: ./cache/cord-018944-du42ho11.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-018944-du42ho11.txt' === file2bib.sh === id: cord-016000-le22pknc author: Saikumar, G. title: Porcine Circovirus date: 2019-06-06 pages: extension: .txt txt: ./txt/cord-016000-le22pknc.txt cache: ./cache/cord-016000-le22pknc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-016000-le22pknc.txt' === file2bib.sh === id: cord-029710-ythz9ax0 author: Homayounieh, Fatemeh title: CT Radiomics, Radiologists and Clinical Information in Predicting Outcome of Patients with COVID-19 Pneumonia date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-029710-ythz9ax0.txt cache: ./cache/cord-029710-ythz9ax0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-029710-ythz9ax0.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 12004 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 89529 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 10752 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-024080-eh3ztsv5 author: Dheda, Keertan title: Diagnosis of COVID-19: Considerations, Controversies and Challenges in South Africa date: 2020-04-17 pages: extension: .txt txt: ./txt/cord-024080-eh3ztsv5.txt cache: ./cache/cord-024080-eh3ztsv5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-024080-eh3ztsv5.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-025634-31n5fvex author: Zhuge, Shurui title: The prevalence of occult HBV infection in immunized children with HBsAg-positive parents: a hospital-based analysis date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-025634-31n5fvex.txt cache: ./cache/cord-025634-31n5fvex.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-025634-31n5fvex.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 89. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 10824 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 97287 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 90577 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 96101 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 96500 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 10308 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 10450 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 11703 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 12186 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-025232-5itrsfmk author: Yan, Yuqian title: Construction and Characterization of a Novel Recombinant Attenuated and Replication-Deficient Candidate Human Adenovirus Type 3 Vaccine: “Adenovirus Vaccine Within an Adenovirus Vector” date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-025232-5itrsfmk.txt cache: ./cache/cord-025232-5itrsfmk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-025232-5itrsfmk.txt' === file2bib.sh === id: cord-034689-se1hdn61 author: Smith, David L. title: A Characteristic Chest Radiographic Pattern in the Setting of COVID-19 Pandemic date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-034689-se1hdn61.txt cache: ./cache/cord-034689-se1hdn61.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-034689-se1hdn61.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-048470-33mqfj2t author: Takano, T title: Quantitative measurement of thyroglobulin mRNA in peripheral blood of patients after total thyroidectomy date: 2001-07-17 pages: extension: .txt txt: ./txt/cord-048470-33mqfj2t.txt cache: ./cache/cord-048470-33mqfj2t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-048470-33mqfj2t.txt' === file2bib.sh === id: cord-034746-uxhpufnv author: Nusshag, Christian title: Glomerular filtration barrier dysfunction in a self-limiting, RNA virus-induced glomerulopathy resembles findings in idiopathic nephrotic syndromes date: 2020-11-05 pages: extension: .txt txt: ./txt/cord-034746-uxhpufnv.txt cache: ./cache/cord-034746-uxhpufnv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-034746-uxhpufnv.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 14671 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 15463 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 14690 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 91. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 91. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 15105 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-102511-7zgd45fl author: Khodakov, Dmitriy title: Donut PCR: a rapid, portable, multiplexed, and quantitative DNA detection platform with single-nucleotide specificity date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-102511-7zgd45fl.txt cache: ./cache/cord-102511-7zgd45fl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-102511-7zgd45fl.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-023830-w218ogsk author: Perlin, David title: Rapid Detection of Bioterrorism Pathogens date: 2008-09-10 pages: extension: .txt txt: ./txt/cord-023830-w218ogsk.txt cache: ./cache/cord-023830-w218ogsk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-023830-w218ogsk.txt' === file2bib.sh === id: cord-029183-3aotgq6m author: Monard, Céline title: Multicenter evaluation of a syndromic rapid multiplex PCR test for early adaptation of antimicrobial therapy in adult patients with pneumonia date: 2020-07-14 pages: extension: .txt txt: ./txt/cord-029183-3aotgq6m.txt cache: ./cache/cord-029183-3aotgq6m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-029183-3aotgq6m.txt' === file2bib.sh === id: cord-140318-xtx8hl14 author: Martin, Alexandra title: High-sensitivity COVID-19 group testing by digital PCR date: 2020-06-03 pages: extension: .txt txt: ./txt/cord-140318-xtx8hl14.txt cache: ./cache/cord-140318-xtx8hl14.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-140318-xtx8hl14.txt' === file2bib.sh === id: cord-022034-o27mh4wz author: OLANO, JUAN P. title: Distinguishing Tropical Infectious Diseases from Bioterrorism date: 2009-05-15 pages: extension: .txt txt: ./txt/cord-022034-o27mh4wz.txt cache: ./cache/cord-022034-o27mh4wz.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-022034-o27mh4wz.txt' === file2bib.sh === id: cord-007564-ljqrxjvv author: Leroy, O. title: 04 – Apport des explorations microbiologiques au diagnostic des infections des voies respiratoires basses date: 2006-11-13 pages: extension: .txt txt: ./txt/cord-007564-ljqrxjvv.txt cache: ./cache/cord-007564-ljqrxjvv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-007564-ljqrxjvv.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 18537 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 91. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 91. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-021596-5s8lksxp author: Colegrove, Kathleen M. title: Pinnipediae date: 2018-10-26 pages: extension: .txt txt: ./txt/cord-021596-5s8lksxp.txt cache: ./cache/cord-021596-5s8lksxp.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-021596-5s8lksxp.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 16802 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 17457 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 18244 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-004133-32w6g7qk author: Walker, Faye M. title: Advances in Directly Amplifying Nucleic Acids from Complex Samples date: 2019-09-30 pages: extension: .txt txt: ./txt/cord-004133-32w6g7qk.txt cache: ./cache/cord-004133-32w6g7qk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-004133-32w6g7qk.txt' === file2bib.sh === id: cord-048359-lz37rh82 author: Li, Jin title: s-RT-MELT for rapid mutation scanning using enzymatic selection and real time DNA-melting: new potential for multiplex genetic analysis date: 2007-06-01 pages: extension: .txt txt: ./txt/cord-048359-lz37rh82.txt cache: ./cache/cord-048359-lz37rh82.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-048359-lz37rh82.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-103563-7a3wdduq author: Nunez-Bajo, Estefania title: Ultra-Low-Cost Integrated Silicon-based Transducer for On-Site, Genetic Detection of Pathogens date: 2020-03-25 pages: extension: .txt txt: ./txt/cord-103563-7a3wdduq.txt cache: ./cache/cord-103563-7a3wdduq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-103563-7a3wdduq.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-254064-qxgpehuy author: Chacko, J. title: Hydroxychloroquine in COVID-19: A systematic review and meta-analysis date: 2020-05-19 pages: extension: .txt txt: ./txt/cord-254064-qxgpehuy.txt cache: ./cache/cord-254064-qxgpehuy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254064-qxgpehuy.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 18585 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 20267 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 90. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 90. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 90. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 14217 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 89. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 19652 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 18955 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 20222 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 20231 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 88. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 90. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 88. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 89. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 89. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 87. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 89. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 88. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 88. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 87. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 87. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 20313 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 86. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: Resource temporarily unavailable parallel: Warning: No more processes: Decreasing number of running jobs to 88. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 87. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-158252-l43ztxsl author: Pawlowski, Colin title: Longitudinal laboratory testing tied to PCR diagnostics in COVID-19 patients reveals temporal evolution of distinctive coagulopathy signatures date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-158252-l43ztxsl.txt cache: ./cache/cord-158252-l43ztxsl.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-158252-l43ztxsl.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-252694-36ijqwge author: Heidinger, Benedikt H. title: Radiologische Manifestationen von Lungenerkrankungen bei COVID-19 date: 2020-09-08 pages: extension: .txt txt: ./txt/cord-252694-36ijqwge.txt cache: ./cache/cord-252694-36ijqwge.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252694-36ijqwge.txt' /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-023698-wvk200j0 author: Hammerschlag, Margaret R. title: Chlamydia pneumoniae date: 2014-10-31 pages: extension: .txt txt: ./txt/cord-023698-wvk200j0.txt cache: ./cache/cord-023698-wvk200j0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-023698-wvk200j0.txt' === file2bib.sh === id: cord-255871-dau9tz6u author: Lee, Mi-Kyung title: Survey of Clinical Laboratory Practices for 2015 Middle East Respiratory Syndrome Coronavirus Outbreak in the Republic of Korea date: 2015-12-18 pages: extension: .txt txt: ./txt/cord-255871-dau9tz6u.txt cache: ./cache/cord-255871-dau9tz6u.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255871-dau9tz6u.txt' === file2bib.sh === id: cord-252198-gs52k4lq author: Onions, David title: Validation of the safety of MDCK cells as a substrate for the production of a cell-derived influenza vaccine date: 2010-09-30 pages: extension: .txt txt: ./txt/cord-252198-gs52k4lq.txt cache: ./cache/cord-252198-gs52k4lq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252198-gs52k4lq.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-022053-idft1p6d author: Pecora, Nicole title: New Technologies for the Diagnosis of Infection date: 2017-07-21 pages: extension: .txt txt: ./txt/cord-022053-idft1p6d.txt cache: ./cache/cord-022053-idft1p6d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-022053-idft1p6d.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-252268-o63ep08b author: Carolan, Louise A. title: TaqMan real time RT-PCR assays for detecting ferret innate and adaptive immune responses date: 2014-09-01 pages: extension: .txt txt: ./txt/cord-252268-o63ep08b.txt cache: ./cache/cord-252268-o63ep08b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-252268-o63ep08b.txt' === file2bib.sh === id: cord-018721-othar2uv author: Schwab, Stefan title: Infektionen date: 2012-03-17 pages: extension: .txt txt: ./txt/cord-018721-othar2uv.txt cache: ./cache/cord-018721-othar2uv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-018721-othar2uv.txt' /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-254101-613aftc1 author: Wang, Ping title: Establishment of a transgenic mouse model with liver-specific expression of secretory immunoglobulin D date: 2012-04-14 pages: extension: .txt txt: ./txt/cord-254101-613aftc1.txt cache: ./cache/cord-254101-613aftc1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254101-613aftc1.txt' === file2bib.sh === id: cord-252347-vnn4135b author: Lee, Wai-Ming title: A Diverse Group of Previously Unrecognized Human Rhinoviruses Are Common Causes of Respiratory Illnesses in Infants date: 2007-10-03 pages: extension: .txt txt: ./txt/cord-252347-vnn4135b.txt cache: ./cache/cord-252347-vnn4135b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-252347-vnn4135b.txt' === file2bib.sh === id: cord-103163-0rreoh4o author: Smith, Sydni Caet title: Reovirus RNA recombination is sequence directed and generates internally deleted defective genome segments during passage date: 2020-10-22 pages: extension: .txt txt: ./txt/cord-103163-0rreoh4o.txt cache: ./cache/cord-103163-0rreoh4o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-103163-0rreoh4o.txt' === file2bib.sh === id: cord-255019-iie8wxb4 author: Chen, Xin title: Acute lower respiratory tract infections by human metapneumovirus in children in Southwest China: A 2‐year study date: 2010-06-25 pages: extension: .txt txt: ./txt/cord-255019-iie8wxb4.txt cache: ./cache/cord-255019-iie8wxb4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-255019-iie8wxb4.txt' === file2bib.sh === id: cord-022310-yc6xtw0s author: Lappin, Michael R. title: Microbiology and Infectious Disease date: 2011-12-15 pages: extension: .txt txt: ./txt/cord-022310-yc6xtw0s.txt cache: ./cache/cord-022310-yc6xtw0s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-022310-yc6xtw0s.txt' === file2bib.sh === id: cord-021772-5v4gor2v author: Levine, Gwendolyn J. title: Cerebrospinal Fluid and Central Nervous System Cytology date: 2019-05-31 pages: extension: .txt txt: ./txt/cord-021772-5v4gor2v.txt cache: ./cache/cord-021772-5v4gor2v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-021772-5v4gor2v.txt' === file2bib.sh === id: cord-254506-cxdklz4u author: Castellvi, J. title: Impact On Clinical Practice Of The Preoperative Screening Of Covid-19 Infection In Surgical Oncological Patients. Prospective Cohort Study date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-254506-cxdklz4u.txt cache: ./cache/cord-254506-cxdklz4u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254506-cxdklz4u.txt' === file2bib.sh === id: cord-032134-mvj7i1er author: Ballauff, Antje title: Funktions- und Laboruntersuchungen date: 2013 pages: extension: .txt txt: ./txt/cord-032134-mvj7i1er.txt cache: ./cache/cord-032134-mvj7i1er.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-032134-mvj7i1er.txt' === file2bib.sh === id: cord-103787-qhftb6d7 author: Garcia, Elizabeth P. title: Scalable Transcriptional Analysis Routine—Multiplexed Quantitative Real-Time Polymerase Chain Reaction Platform for Gene Expression Analysis and Molecular Diagnostics date: 2005-10-31 pages: extension: .txt txt: ./txt/cord-103787-qhftb6d7.txt cache: ./cache/cord-103787-qhftb6d7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-103787-qhftb6d7.txt' === file2bib.sh === id: cord-256130-zhlvvuj4 author: Nordén, Rickard title: Quantification of Torque Teno Virus and Epstein-Barr Virus Is of Limited Value for Predicting the Net State of Immunosuppression After Lung Transplantation date: 2018-03-06 pages: extension: .txt txt: ./txt/cord-256130-zhlvvuj4.txt cache: ./cache/cord-256130-zhlvvuj4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-256130-zhlvvuj4.txt' === file2bib.sh === id: cord-255026-fdp6mies author: Belák, Sándor title: Molecular diagnosis of viral diseases, present trends and future aspects: A view from the OIE Collaborating Centre for the Application of Polymerase Chain Reaction Methods for Diagnosis of Viral Diseases in Veterinary Medicine date: 2007-07-26 pages: extension: .txt txt: ./txt/cord-255026-fdp6mies.txt cache: ./cache/cord-255026-fdp6mies.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255026-fdp6mies.txt' === file2bib.sh === id: cord-255545-nycdhdsd author: Schoenike, Barry title: Quantitative sense-specific determination of murine coronavirus RNA by reverse transcription polymerase chain reaction date: 1999-03-10 pages: extension: .txt txt: ./txt/cord-255545-nycdhdsd.txt cache: ./cache/cord-255545-nycdhdsd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-255545-nycdhdsd.txt' === file2bib.sh === id: cord-256702-lwxt4587 author: Song, Lingjie title: A case of SARS-CoV-2 carrier for 32 days with several times false negative nucleic acid tests date: 2020-04-06 pages: extension: .txt txt: ./txt/cord-256702-lwxt4587.txt cache: ./cache/cord-256702-lwxt4587.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-256702-lwxt4587.txt' === file2bib.sh === id: cord-257284-dash9udv author: Decaro, Nicola title: Development and validation of a real-time PCR assay for specific and sensitive detection of canid herpesvirus 1 date: 2010-07-30 pages: extension: .txt txt: ./txt/cord-257284-dash9udv.txt cache: ./cache/cord-257284-dash9udv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-257284-dash9udv.txt' === file2bib.sh === id: cord-256244-f5zsy56p author: Funakoshi, Yu title: Enterovirus D68 respiratory infection in a children's hospital in Japan in 2015 date: 2019-08-22 pages: extension: .txt txt: ./txt/cord-256244-f5zsy56p.txt cache: ./cache/cord-256244-f5zsy56p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256244-f5zsy56p.txt' === file2bib.sh === id: cord-252604-1u14i4v1 author: Smith, Alvin W. title: Vesivirus viremia and seroprevalence in humans date: 2006-03-22 pages: extension: .txt txt: ./txt/cord-252604-1u14i4v1.txt cache: ./cache/cord-252604-1u14i4v1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-252604-1u14i4v1.txt' === file2bib.sh === id: cord-253502-v2hh3w3r author: Leung, C.W. title: Clinical picture, diagnosis, treatment and outcome of severe acute respiratory syndrome (SARS) in children date: 2004-11-05 pages: extension: .txt txt: ./txt/cord-253502-v2hh3w3r.txt cache: ./cache/cord-253502-v2hh3w3r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-253502-v2hh3w3r.txt' === file2bib.sh === id: cord-257521-1amcsgmj author: Hirsilä, Maija title: Detection by Reverse Transcription–Polymerase Chain Reaction of Influenza C in Nasopharyngeal Secretions of Adults with a Common Cold date: 2001-04-15 pages: extension: .txt txt: ./txt/cord-257521-1amcsgmj.txt cache: ./cache/cord-257521-1amcsgmj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257521-1amcsgmj.txt' === file2bib.sh === id: cord-256456-rg366bk2 author: Kulcsar, Gabor title: Testing for viral contaminants of veterinary vaccines in Hungary date: 2010-05-31 pages: extension: .txt txt: ./txt/cord-256456-rg366bk2.txt cache: ./cache/cord-256456-rg366bk2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256456-rg366bk2.txt' === file2bib.sh === id: cord-256338-ovj63ith author: bhattacharya, b. title: SARS-CoV-2 RT-PCR profile in 298 Indian COVID-19 patients : a retrospective observational study date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-256338-ovj63ith.txt cache: ./cache/cord-256338-ovj63ith.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-256338-ovj63ith.txt' === file2bib.sh === id: cord-255983-3dq99xz9 author: Do, Lien Anh Ha title: A sensitive real-time PCR for detection and subgrouping of human respiratory syncytial virus date: 2012-01-17 pages: extension: .txt txt: ./txt/cord-255983-3dq99xz9.txt cache: ./cache/cord-255983-3dq99xz9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-255983-3dq99xz9.txt' === file2bib.sh === id: cord-017543-60q9iecq author: Tian, Wei-Chang title: Microfluidic Applications in Biodefense date: 2008-08-23 pages: extension: .txt txt: ./txt/cord-017543-60q9iecq.txt cache: ./cache/cord-017543-60q9iecq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017543-60q9iecq.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 27719 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-256982-t6urqus7 author: Wellinghausen, Nele title: Evaluation of the SARS-CoV-2-IgG response in outpatients by five commercial immunoassays date: 2020-09-16 pages: extension: .txt txt: ./txt/cord-256982-t6urqus7.txt cache: ./cache/cord-256982-t6urqus7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256982-t6urqus7.txt' === file2bib.sh === id: cord-258008-t78svobg author: Bruijnesteijn van Coppenraet, L.E.S. title: Comparison of two commercial molecular assays for simultaneous detection of respiratory viruses in clinical samples using two automatic electrophoresis detection systems date: 2010-08-05 pages: extension: .txt txt: ./txt/cord-258008-t78svobg.txt cache: ./cache/cord-258008-t78svobg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-258008-t78svobg.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 86. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 86. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-258819-4boe6t1v author: Waller, Joseph V. title: The Limited Sensitivity of Chest Computed Tomography Relative to Reverse Transcription Polymerase Chain Reaction for Severe Acute Respiratory Syndrome Coronavirus-2 Infection: A Systematic Review on COVID-19 Diagnostics date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-258819-4boe6t1v.txt cache: ./cache/cord-258819-4boe6t1v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-258819-4boe6t1v.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 28783 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 85. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 87. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-257398-fmkfo5ju author: Meng, Qing-Bin title: Clinical application of combined detection of SARS-CoV-2-specific antibody and nucleic acid date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-257398-fmkfo5ju.txt cache: ./cache/cord-257398-fmkfo5ju.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-257398-fmkfo5ju.txt' === file2bib.sh === id: cord-258250-zueo1xfa author: Hirotsu, Yosuke title: Comparison of Automated SARS-CoV-2 Antigen Test for COVID-19 Infection with Quantitative RT-PCR using 313 Nasopharyngeal Swabs Including from 7 Serially Followed Patients date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-258250-zueo1xfa.txt cache: ./cache/cord-258250-zueo1xfa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-258250-zueo1xfa.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-258021-xhx74vr6 author: Waterer, Grant W. title: Diagnosing Viral and Atypical Pathogens in the Setting of Community-Acquired Pneumonia date: 2016-12-21 pages: extension: .txt txt: ./txt/cord-258021-xhx74vr6.txt cache: ./cache/cord-258021-xhx74vr6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258021-xhx74vr6.txt' === file2bib.sh === id: cord-260457-m1jbpo5l author: Allander, Tobias title: Human Bocavirus and Acute Wheezing in Children date: 2007-04-01 pages: extension: .txt txt: ./txt/cord-260457-m1jbpo5l.txt cache: ./cache/cord-260457-m1jbpo5l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-260457-m1jbpo5l.txt' === file2bib.sh === id: cord-254250-l0v602x9 author: Hooper, Chantelle title: A Novel RNA Virus, Macrobrachium rosenbergii Golda Virus (MrGV), Linked to Mass Mortalities of the Larval Giant Freshwater Prawn in Bangladesh date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-254250-l0v602x9.txt cache: ./cache/cord-254250-l0v602x9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-254250-l0v602x9.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 84. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 31188 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 32492 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 31421 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 32169 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 90545 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 31638 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-260431-eksl7pp8 author: Sun, Heting title: Isolation and Identification of Feline Herpesvirus Type 1 from a South China Tiger in China date: 2014-02-28 pages: extension: .txt txt: ./txt/cord-260431-eksl7pp8.txt cache: ./cache/cord-260431-eksl7pp8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260431-eksl7pp8.txt' === file2bib.sh === id: cord-259324-g8kv4pvq author: Ko, Suk-Min title: Expression of the protective antigen for PEDV in transgenic duckweed, Lemna minor date: 2011-10-28 pages: extension: .txt txt: ./txt/cord-259324-g8kv4pvq.txt cache: ./cache/cord-259324-g8kv4pvq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-259324-g8kv4pvq.txt' /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 85. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 86. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 32963 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 86. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-256931-wj0esjwi author: Gelfer, Gita title: The clinical impact of the detection of potential etiologic pathogens of community-acquired pneumonia date: 2015-08-05 pages: extension: .txt txt: ./txt/cord-256931-wj0esjwi.txt cache: ./cache/cord-256931-wj0esjwi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256931-wj0esjwi.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 32937 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 34071 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 83. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-259886-j0bpp7iw author: Cho, Hyejin title: Positive control synthesis method for COVID-19 diagnosis by one-step real-time RT-PCR date: 2020-10-12 pages: extension: .txt txt: ./txt/cord-259886-j0bpp7iw.txt cache: ./cache/cord-259886-j0bpp7iw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259886-j0bpp7iw.txt' /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-258724-1qhen1bj author: Young, Barnaby E title: Viral dynamics and immune correlates of COVID-19 disease severity date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-258724-1qhen1bj.txt cache: ./cache/cord-258724-1qhen1bj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258724-1qhen1bj.txt' === file2bib.sh === id: cord-260404-leifaqda author: Ishak, Anthony M. title: Prevalence of Mycoplasma haemofelis, ‘Candidatus Mycoplasma haemominutum’, Bartonella species, Ehrlichia species, and Anaplasma phagocytophilum DNA in the blood of cats with anemia date: 2006-07-17 pages: extension: .txt txt: ./txt/cord-260404-leifaqda.txt cache: ./cache/cord-260404-leifaqda.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260404-leifaqda.txt' === file2bib.sh === id: cord-259988-3s7b5ovi author: Decaro, Nicola title: Virological and molecular characterization of a mammalian orthoreovirus type 3 strain isolated from a dog in Italy date: 2005-08-10 pages: extension: .txt txt: ./txt/cord-259988-3s7b5ovi.txt cache: ./cache/cord-259988-3s7b5ovi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259988-3s7b5ovi.txt' === file2bib.sh === id: cord-259422-5ex12eun author: Graat, Judith M title: A prospective, community-based study on virologic assessment among elderly people with and without symptoms of acute respiratory infection date: 2003-12-11 pages: extension: .txt txt: ./txt/cord-259422-5ex12eun.txt cache: ./cache/cord-259422-5ex12eun.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259422-5ex12eun.txt' === file2bib.sh === id: cord-259590-ot933axv author: Fielding, Burtram C title: Human coronavirus NL63: a clinically important virus? date: 2011-03-02 pages: extension: .txt txt: ./txt/cord-259590-ot933axv.txt cache: ./cache/cord-259590-ot933axv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-259590-ot933axv.txt' === file2bib.sh === id: cord-260231-vayxg23a author: Hsien Koh, Tse title: Epidemiology of Clostridium difficile infection in a large teaching hospital in Singapore date: 2007-08-31 pages: extension: .txt txt: ./txt/cord-260231-vayxg23a.txt cache: ./cache/cord-260231-vayxg23a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260231-vayxg23a.txt' === file2bib.sh === id: cord-259458-o2yts5pq author: O’Grady, Kerry‐Ann F. title: Successful application of a simple specimen transport method for the conduct of respiratory virus surveillance in remote Indigenous communities in Australia date: 2011-03-21 pages: extension: .txt txt: ./txt/cord-259458-o2yts5pq.txt cache: ./cache/cord-259458-o2yts5pq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259458-o2yts5pq.txt' === file2bib.sh === id: cord-254115-hwy962a4 author: Reslova, Nikol title: xMAP Technology: Applications in Detection of Pathogens date: 2017-01-25 pages: extension: .txt txt: ./txt/cord-254115-hwy962a4.txt cache: ./cache/cord-254115-hwy962a4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254115-hwy962a4.txt' === file2bib.sh === id: cord-257600-0plhquk9 author: Calles, Antonio title: Outcomes of COVID-19 in Patients With Lung Cancer Treated in a Tertiary Hospital in Madrid date: 2020-09-16 pages: extension: .txt txt: ./txt/cord-257600-0plhquk9.txt cache: ./cache/cord-257600-0plhquk9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257600-0plhquk9.txt' === file2bib.sh === id: cord-259823-ia1g5dt4 author: Gowin, Ewelina title: Assessment of the Usefulness of Multiplex Real-Time PCR Tests in the Diagnostic and Therapeutic Process of Pneumonia in Hospitalized Children: A Single-Center Experience date: 2017-01-15 pages: extension: .txt txt: ./txt/cord-259823-ia1g5dt4.txt cache: ./cache/cord-259823-ia1g5dt4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259823-ia1g5dt4.txt' === file2bib.sh === id: cord-261134-zarq507s author: Pulford, David title: Amplification refractory mutation system PCR assays for the detection of variola and Orthopoxvirus date: 2004-02-13 pages: extension: .txt txt: ./txt/cord-261134-zarq507s.txt cache: ./cache/cord-261134-zarq507s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-261134-zarq507s.txt' === file2bib.sh === id: cord-260481-twk5kvd3 author: Täufer, Matthias title: Rapid, large-scale, and effective detection of COVID-19 via non-adaptive testing date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-260481-twk5kvd3.txt cache: ./cache/cord-260481-twk5kvd3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-260481-twk5kvd3.txt' === file2bib.sh === id: cord-260700-u12aa739 author: Kainulainen, Leena title: Recurrent and persistent respiratory tract viral infections in patients with primary hypogammaglobulinemia date: 2010-06-10 pages: extension: .txt txt: ./txt/cord-260700-u12aa739.txt cache: ./cache/cord-260700-u12aa739.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-260700-u12aa739.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 85. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 38577 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 84. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 85. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 85. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-260250-t48y27wg author: Decaro, Nicola title: Quantitation of canine coronavirus RNA in the faeces of dogs by TaqMan RT-PCR date: 2004-05-07 pages: extension: .txt txt: ./txt/cord-260250-t48y27wg.txt cache: ./cache/cord-260250-t48y27wg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260250-t48y27wg.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 84. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 37562 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-258768-bjjfkfgg author: McElligott, Susan title: Detection and genetic characterization of canine parvoviruses and coronaviruses in southern Ireland date: 2010-11-24 pages: extension: .txt txt: ./txt/cord-258768-bjjfkfgg.txt cache: ./cache/cord-258768-bjjfkfgg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-258768-bjjfkfgg.txt' === file2bib.sh === id: cord-260690-h5pjv2dw author: Druce, Julian title: Laboratory diagnosis and surveillance of human respiratory viruses by PCR in Victoria, Australia, 2002–2003 date: 2004-11-12 pages: extension: .txt txt: ./txt/cord-260690-h5pjv2dw.txt cache: ./cache/cord-260690-h5pjv2dw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260690-h5pjv2dw.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-261279-6mef38eo author: Chu, Daniel K W title: Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia date: 2020-01-31 pages: extension: .txt txt: ./txt/cord-261279-6mef38eo.txt cache: ./cache/cord-261279-6mef38eo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261279-6mef38eo.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-260168-rb7j94dh author: Gu, Jiang title: H5N1 infection of the respiratory tract and beyond: a molecular pathology study date: 2007-09-27 pages: extension: .txt txt: ./txt/cord-260168-rb7j94dh.txt cache: ./cache/cord-260168-rb7j94dh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-260168-rb7j94dh.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-259747-sl9q63oc author: Remmelink, Myriam title: Unspecific post-mortem findings despite multiorgan viral spread in COVID-19 patients date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-259747-sl9q63oc.txt cache: ./cache/cord-259747-sl9q63oc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259747-sl9q63oc.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 39314 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 40170 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 40720 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 40241 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 83. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 84. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-263763-a8wgvgz2 author: Çelik, Ersin title: Treatment Approach to Coronavirus Disease (COVID-19) Seen Early After Open Heart Surgery. Case Report date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-263763-a8wgvgz2.txt cache: ./cache/cord-263763-a8wgvgz2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-263763-a8wgvgz2.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-262826-2usqmujy author: She, Rosemary C. title: Performance of diagnostic tests to detect respiratory viruses in older adults date: 2010-07-31 pages: extension: .txt txt: ./txt/cord-262826-2usqmujy.txt cache: ./cache/cord-262826-2usqmujy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262826-2usqmujy.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-261089-aul4ifso author: Yuan, Wen title: Development of a duplex real-time RT-PCR for the simultaneous detection and differentiation of Theiler’s murine encephalomyelitis virus and rat theilovirus date: 2016-07-07 pages: extension: .txt txt: ./txt/cord-261089-aul4ifso.txt cache: ./cache/cord-261089-aul4ifso.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-261089-aul4ifso.txt' === file2bib.sh === id: cord-261735-03hvi4el author: Rodrigues, R. title: Development of a one step real time RT-PCR assay to detect and quantify Dugbe virus date: 2011-06-14 pages: extension: .txt txt: ./txt/cord-261735-03hvi4el.txt cache: ./cache/cord-261735-03hvi4el.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261735-03hvi4el.txt' === file2bib.sh === id: cord-263417-jgu8kc5k author: Yan, Yong title: A multiplex liquid-chip assay based on Luminex xMAP technology for simultaneous detection of six common respiratory viruses date: 2017-06-17 pages: extension: .txt txt: ./txt/cord-263417-jgu8kc5k.txt cache: ./cache/cord-263417-jgu8kc5k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-263417-jgu8kc5k.txt' /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-261823-pgluidj8 author: Wang, Ji title: Novel One-Step Single-Tube Nested Quantitative Real-Time PCR Assay for Highly Sensitive Detection of SARS-CoV-2 date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-261823-pgluidj8.txt cache: ./cache/cord-261823-pgluidj8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261823-pgluidj8.txt' === file2bib.sh === id: cord-002757-upwe0cpj author: Sullivan, Kathleen E. title: Emerging Infections and Pertinent Infections Related to Travel for Patients with Primary Immunodeficiencies date: 2017-08-07 pages: extension: .txt txt: ./txt/cord-002757-upwe0cpj.txt cache: ./cache/cord-002757-upwe0cpj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-002757-upwe0cpj.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-260647-7bjhobg7 author: Coudray-Meunier, Coralie title: A Novel High-Throughput Method for Molecular Detection of Human Pathogenic Viruses Using a Nanofluidic Real-Time PCR System date: 2016-01-29 pages: extension: .txt txt: ./txt/cord-260647-7bjhobg7.txt cache: ./cache/cord-260647-7bjhobg7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-260647-7bjhobg7.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-260728-4w23kwzu author: Timmermans, Ans title: Human Sentinel Surveillance of Influenza and Other Respiratory Viral Pathogens in Border Areas of Western Cambodia date: 2016-03-30 pages: extension: .txt txt: ./txt/cord-260728-4w23kwzu.txt cache: ./cache/cord-260728-4w23kwzu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260728-4w23kwzu.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 83. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 42962 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 82. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 43074 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 83. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 42428 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 84. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 82. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 82. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 43738 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-261237-0hbijukt author: Hou, Peili title: Development of a recombinase polymerase amplification combined with lateral-flow dipstick assay for detection of bovine ephemeral fever virus date: 2017-12-26 pages: extension: .txt txt: ./txt/cord-261237-0hbijukt.txt cache: ./cache/cord-261237-0hbijukt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-261237-0hbijukt.txt' === file2bib.sh === id: cord-263279-afdmegq0 author: Uhteg, Katharine title: Comparing the analytical performance of three SARS-CoV-2 molecular diagnostic assays date: 2020-04-26 pages: extension: .txt txt: ./txt/cord-263279-afdmegq0.txt cache: ./cache/cord-263279-afdmegq0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-263279-afdmegq0.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-261329-k1p7fo0e author: Nidzworski, Dawid title: Detection and differentiation of virulent and avirulent strains of Newcastle disease virus by real-time PCR date: 2010-12-28 pages: extension: .txt txt: ./txt/cord-261329-k1p7fo0e.txt cache: ./cache/cord-261329-k1p7fo0e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-261329-k1p7fo0e.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-255975-ymw9avlm author: Ho, Yen‐Peng title: Advances in mass spectrometry for the identification of pathogens date: 2011-05-09 pages: extension: .txt txt: ./txt/cord-255975-ymw9avlm.txt cache: ./cache/cord-255975-ymw9avlm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-255975-ymw9avlm.txt' === file2bib.sh === id: cord-264261-98h1bmb2 author: Caruana, Giorgia title: Diagnostic strategies for SARS-CoV-2 infection and interpretation of microbiological results date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-264261-98h1bmb2.txt cache: ./cache/cord-264261-98h1bmb2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-264261-98h1bmb2.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 45098 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 43998 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-263426-l32gyiky author: Najafi, Hamideh title: Molecular and clinical study on prevalence of feline herpesvirus type 1 and calicivirus in correlation with feline leukemia and immunodeficiency viruses date: 2014 pages: extension: .txt txt: ./txt/cord-263426-l32gyiky.txt cache: ./cache/cord-263426-l32gyiky.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263426-l32gyiky.txt' === file2bib.sh === id: cord-259717-e8ljkv2y author: Holtz, Lori R. title: Geographic variation in the eukaryotic virome of human diarrhea date: 2014-11-01 pages: extension: .txt txt: ./txt/cord-259717-e8ljkv2y.txt cache: ./cache/cord-259717-e8ljkv2y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259717-e8ljkv2y.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 83. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 81. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 81. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 45571 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-263118-6sf41rsj author: Landry, Marie L. title: Real-time PCR compared to Binax NOW and cytospin-immunofluorescence for detection of influenza in hospitalized patients date: 2008-07-18 pages: extension: .txt txt: ./txt/cord-263118-6sf41rsj.txt cache: ./cache/cord-263118-6sf41rsj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263118-6sf41rsj.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 82. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 80. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 82. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 81. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 80. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-263735-sos2ovng author: Li, K. title: Diagnostic performance of CT and its key signs for COVID-19: A systematic review and meta-analysis date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-263735-sos2ovng.txt cache: ./cache/cord-263735-sos2ovng.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-263735-sos2ovng.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 47025 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 47141 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-265221-qtkwciym author: Bahadur, Gulam title: SARS-CoV-2: diagnostic and design conundrums, and the male factor infertility date: 2020-06-03 pages: extension: .txt txt: ./txt/cord-265221-qtkwciym.txt cache: ./cache/cord-265221-qtkwciym.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265221-qtkwciym.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-260866-bzdd4f5h author: Barceló, Damià title: Wastewater-Based Epidemiology to Monitor COVID-19 Outbreak: Present and Future Diagnostic Methods to be in Your Radar date: 2020-09-14 pages: extension: .txt txt: ./txt/cord-260866-bzdd4f5h.txt cache: ./cache/cord-260866-bzdd4f5h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260866-bzdd4f5h.txt' /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-263567-6uacorpp author: Collignon, C. title: Polyarthrite associée à une leishmaniose chez un jeune chien date: 2009-03-31 pages: extension: .txt txt: ./txt/cord-263567-6uacorpp.txt cache: ./cache/cord-263567-6uacorpp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263567-6uacorpp.txt' /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-262485-sx2q5ol4 author: Davda, Jayeshkumar Narsibhai title: An Inexpensive RT-PCR Endpoint Diagnostic Assay for SARS-CoV-2 Using Nested PCR: Direct Assessment of Detection Efficiency of RT-qPCR Tests and Suitability for Surveillance date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-262485-sx2q5ol4.txt cache: ./cache/cord-262485-sx2q5ol4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262485-sx2q5ol4.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 81. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 80. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 46415 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 46436 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 79. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 79. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 81. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-263976-b9shffb3 author: Shaukat, Shahzad title: Identification and characterization of unrecognized viruses in stool samples of non-polio acute flaccid paralysis children by simplified VIDISCA date: 2014-08-12 pages: extension: .txt txt: ./txt/cord-263976-b9shffb3.txt cache: ./cache/cord-263976-b9shffb3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263976-b9shffb3.txt' === file2bib.sh === id: cord-263134-0p4zy5t2 author: de Paz, Hector David title: Molecular isothermal techniques for combating infectious diseases: towards low-cost point-of-care diagnostics date: 2014-07-23 pages: extension: .txt txt: ./txt/cord-263134-0p4zy5t2.txt cache: ./cache/cord-263134-0p4zy5t2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263134-0p4zy5t2.txt' === file2bib.sh === id: cord-261160-g92zhv19 author: Rowland, Raymond R.R title: Lymphoid tissue tropism of porcine reproductive and respiratory syndrome virus replication during persistent infection of pigs originally exposed to virus in utero date: 2003-10-30 pages: extension: .txt txt: ./txt/cord-261160-g92zhv19.txt cache: ./cache/cord-261160-g92zhv19.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-261160-g92zhv19.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-264880-0tmd9knh author: Li, Zhao title: Picoliter Well Array Chip-Based Digital Recombinase Polymerase Amplification for Absolute Quantification of Nucleic Acids date: 2016-04-13 pages: extension: .txt txt: ./txt/cord-264880-0tmd9knh.txt cache: ./cache/cord-264880-0tmd9knh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264880-0tmd9knh.txt' === file2bib.sh === id: cord-263570-6notzm6s author: Elia, Gabriella title: Detection of infectious canine parvovirus type 2 by mRNA real-time RT-PCR date: 2007-08-10 pages: extension: .txt txt: ./txt/cord-263570-6notzm6s.txt cache: ./cache/cord-263570-6notzm6s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263570-6notzm6s.txt' === file2bib.sh === id: cord-266466-5sgfx7oq author: Mansour, Amani title: First Case of an Infant with COVID-19 in the Middle East date: 2020-04-03 pages: extension: .txt txt: ./txt/cord-266466-5sgfx7oq.txt cache: ./cache/cord-266466-5sgfx7oq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266466-5sgfx7oq.txt' === file2bib.sh === id: cord-264071-hg0qslyx author: Camelo-Castillo, Anny title: Nasopharyngeal Microbiota in Children With Invasive Pneumococcal Disease: Identification of Bacteria With Potential Disease-Promoting and Protective Effects date: 2019-01-28 pages: extension: .txt txt: ./txt/cord-264071-hg0qslyx.txt cache: ./cache/cord-264071-hg0qslyx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264071-hg0qslyx.txt' === file2bib.sh === id: cord-017867-8cn4c6cu author: Collántes-Fernández, Esther title: Trichomonas date: 2017-11-08 pages: extension: .txt txt: ./txt/cord-017867-8cn4c6cu.txt cache: ./cache/cord-017867-8cn4c6cu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-017867-8cn4c6cu.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 79. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50831 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50417 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50804 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 80. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50477 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 51369 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 78. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-265258-2rmtsyns author: Domanska‐Blicharz, K. title: Specific detection of GII‐1 lineage of infectious bronchitis virus date: 2017-07-03 pages: extension: .txt txt: ./txt/cord-265258-2rmtsyns.txt cache: ./cache/cord-265258-2rmtsyns.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265258-2rmtsyns.txt' === file2bib.sh === id: cord-265978-i0fu8e0p author: Amer, Haitham M. title: Development of a SYBR Green I based real-time RT-PCR assay for detection and quantification of bovine coronavirus date: 2011-06-30 pages: extension: .txt txt: ./txt/cord-265978-i0fu8e0p.txt cache: ./cache/cord-265978-i0fu8e0p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-265978-i0fu8e0p.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-023134-y665agnh author: nan title: Oral Research Communications of the 22(nd) ECVIM‐CA Congress date: 2012-11-20 pages: extension: .txt txt: ./txt/cord-023134-y665agnh.txt cache: ./cache/cord-023134-y665agnh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-023134-y665agnh.txt' === file2bib.sh === id: cord-266156-xmf4emln author: Miller, Tyler E. title: Clinical sensitivity and interpretation of PCR and serological COVID‐19 diagnostics for patients presenting to the hospital date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-266156-xmf4emln.txt cache: ./cache/cord-266156-xmf4emln.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-266156-xmf4emln.txt' === file2bib.sh === id: cord-268468-036i1082 author: Asif, Muhammad title: The role of biosensors in COVID-19 outbreak date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-268468-036i1082.txt cache: ./cache/cord-268468-036i1082.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268468-036i1082.txt' === file2bib.sh === id: cord-264392-he1vekrt author: Lambeth, L. S. title: Complete genome sequence of Nariva virus, a rodent paramyxovirus date: 2008-12-23 pages: extension: .txt txt: ./txt/cord-264392-he1vekrt.txt cache: ./cache/cord-264392-he1vekrt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264392-he1vekrt.txt' === file2bib.sh === id: cord-264944-7xj27r98 author: Koopmans, Marion title: Optimization of extraction and PCR amplification of RNA extracts from paraffin-embedded tissue in different fixatives date: 1993-07-31 pages: extension: .txt txt: ./txt/cord-264944-7xj27r98.txt cache: ./cache/cord-264944-7xj27r98.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-264944-7xj27r98.txt' === file2bib.sh === id: cord-262467-epqqd8n8 author: Chen, Jun title: COVID-19 infection: the China and Italy perspectives date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-262467-epqqd8n8.txt cache: ./cache/cord-262467-epqqd8n8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262467-epqqd8n8.txt' === file2bib.sh === id: cord-265268-5xu9hj2n author: Ahmed, W. title: Evaluation of Glass Wool Filters and Hollow-Fiber Ultrafiltration Concentration Methods for qPCR Detection of Human Adenoviruses and Polyomaviruses in River Water date: 2016-08-13 pages: extension: .txt txt: ./txt/cord-265268-5xu9hj2n.txt cache: ./cache/cord-265268-5xu9hj2n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265268-5xu9hj2n.txt' === file2bib.sh === id: cord-270579-rf933a0y author: van Kruijssen, Alida M. title: Detection of respiratory pathogens by real-time PCR in children with clinical suspicion of pertussis date: 2006-12-20 pages: extension: .txt txt: ./txt/cord-270579-rf933a0y.txt cache: ./cache/cord-270579-rf933a0y.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-270579-rf933a0y.txt' === file2bib.sh === id: cord-261867-6n0g3bz5 author: Evermann, James F. title: Canine Reproductive, Respiratory, and Ocular Diseases due to Canine Herpesvirus date: 2011-10-28 pages: extension: .txt txt: ./txt/cord-261867-6n0g3bz5.txt cache: ./cache/cord-261867-6n0g3bz5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261867-6n0g3bz5.txt' === file2bib.sh === id: cord-268455-btuzihsy author: de Santiago, Javier title: COVID-19: gynecologic cancer surgery at a single center in Madrid date: 2020-07-07 pages: extension: .txt txt: ./txt/cord-268455-btuzihsy.txt cache: ./cache/cord-268455-btuzihsy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-268455-btuzihsy.txt' === file2bib.sh === id: cord-266036-qhlo99l7 author: Axell-House, Dierdre B. title: The Estimation of Diagnostic Accuracy of Tests for COVID-19: A Scoping Review date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-266036-qhlo99l7.txt cache: ./cache/cord-266036-qhlo99l7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266036-qhlo99l7.txt' === file2bib.sh === id: cord-266150-wox7pnkr author: Torres, Juan Pablo title: SARS-CoV-2 antibody prevalence in blood in a large school community subject to a Covid-19 outbreak: a cross-sectional study date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-266150-wox7pnkr.txt cache: ./cache/cord-266150-wox7pnkr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266150-wox7pnkr.txt' === file2bib.sh === id: cord-268567-2xoubkxb author: Samannodi, Mohammed title: Compliance with international guidelines in adults with encephalitis date: 2020-04-14 pages: extension: .txt txt: ./txt/cord-268567-2xoubkxb.txt cache: ./cache/cord-268567-2xoubkxb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-268567-2xoubkxb.txt' === file2bib.sh === id: cord-263302-z5uhrta5 author: Zhang, Xuming title: Identification of a Noncanonical Signal for Transcription of a Novel Subgenomic mRNA of Mouse Hepatitis Virus: Implication for the Mechanism of Coronavirus RNA Transcription date: 2000-12-05 pages: extension: .txt txt: ./txt/cord-263302-z5uhrta5.txt cache: ./cache/cord-263302-z5uhrta5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-263302-z5uhrta5.txt' === file2bib.sh === id: cord-271341-fszljnax author: Lei, Pinggui title: COVID-19 Carrier or Pneumonia: Positive Real-Time Reverse-Transcriptase Polymerase Chain Reaction but Negative or Positive Chest CT Results date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-271341-fszljnax.txt cache: ./cache/cord-271341-fszljnax.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-271341-fszljnax.txt' === file2bib.sh === id: cord-270964-kxze0470 author: Lau, Kwok-Kwong title: Possible Central Nervous System Infection by SARS Coronavirus date: 2004-02-17 pages: extension: .txt txt: ./txt/cord-270964-kxze0470.txt cache: ./cache/cord-270964-kxze0470.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-270964-kxze0470.txt' === file2bib.sh === id: cord-268817-wx96wwpg author: Karp, Donna Grace title: Sensitive and Specific Detection of SARS-CoV-2 Antibodies Using a High-Throughput, Fully Automated Liquid-Handling Robotic System date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-268817-wx96wwpg.txt cache: ./cache/cord-268817-wx96wwpg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-268817-wx96wwpg.txt' === file2bib.sh === id: cord-268094-ubz0q7e9 author: Curland, N. title: Investigation into diseases in free-ranging ring-necked pheasants (Phasianus colchicus) in northwestern Germany during population decline with special reference to infectious pathogens date: 2018-02-06 pages: extension: .txt txt: ./txt/cord-268094-ubz0q7e9.txt cache: ./cache/cord-268094-ubz0q7e9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-268094-ubz0q7e9.txt' === file2bib.sh === id: cord-266670-jxgywvwx author: Wong, Mark title: Chapter 13 Recent Advances and Future Needs in Environmental Virology date: 2007-09-06 pages: extension: .txt txt: ./txt/cord-266670-jxgywvwx.txt cache: ./cache/cord-266670-jxgywvwx.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-266670-jxgywvwx.txt' === file2bib.sh === id: cord-271339-wt5o9sgm author: Chen, Chao-Ju title: Optimization of the CDC Protocol of Molecular Diagnosis of COVID-19 for Timely Diagnosis date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-271339-wt5o9sgm.txt cache: ./cache/cord-271339-wt5o9sgm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-271339-wt5o9sgm.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 77. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 57391 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-272696-1jg46veg author: Tang, An title: Detection of Novel Coronavirus by RT-PCR in Stool Specimen from Asymptomatic Child, China date: 2020-06-17 pages: extension: .txt txt: ./txt/cord-272696-1jg46veg.txt cache: ./cache/cord-272696-1jg46veg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272696-1jg46veg.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 56418 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 57304 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 76. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 57909 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 91. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 78. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 78. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 80. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 79. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 90. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 57824 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 58550 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 77. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 75. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 78. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 89. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 76. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 77. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 79. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 77. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 88. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 74. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-273859-tr4s5i7h author: Luis García Garmendia, José title: DETECCIÓN VIRAL Y RESPUESTA SEROLÓGICA EN PACIENTES CRÍTICOS INTUBADOS CON SARS-CoV-2. IMPLICACIONES PARA RETIRADA DE AISLAMIENTO date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-273859-tr4s5i7h.txt cache: ./cache/cord-273859-tr4s5i7h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273859-tr4s5i7h.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 73. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-273829-t5cuop5c author: Görgülü, Özkan title: rRT-PCR Results of a Covid-19 Diagnosed Geriatric Patient date: 2020-10-17 pages: extension: .txt txt: ./txt/cord-273829-t5cuop5c.txt cache: ./cache/cord-273829-t5cuop5c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-273829-t5cuop5c.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 57653 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 58660 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-269726-z0frgm7s author: Gidari, Anna title: Is recurrence possible in coronavirus disease 2019 (COVID-19)? Case series and systematic review of literature date: 2020-10-10 pages: extension: .txt txt: ./txt/cord-269726-z0frgm7s.txt cache: ./cache/cord-269726-z0frgm7s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269726-z0frgm7s.txt' === file2bib.sh === id: cord-268721-n6dsc4ig author: Pawlowski, Colin title: Inference from longitudinal laboratory tests characterizes temporal evolution of COVID-19-associated coagulopathy (CAC) date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-268721-n6dsc4ig.txt cache: ./cache/cord-268721-n6dsc4ig.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-268721-n6dsc4ig.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable parallel: Warning: No more processes: Decreasing number of running jobs to 78. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 59486 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 75. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 59793 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-268977-hcg2rrhl author: Feikin, Daniel R. title: Etiology and Incidence of Viral and Bacterial Acute Respiratory Illness among Older Children and Adults in Rural Western Kenya, 2007–2010 date: 2012-08-24 pages: extension: .txt txt: ./txt/cord-268977-hcg2rrhl.txt cache: ./cache/cord-268977-hcg2rrhl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268977-hcg2rrhl.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 76. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 60365 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 60286 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 75. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 74. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-273840-jjm7y07m author: Vabret, Astrid title: Detection of the New Human Coronavirus HKU1: A Report of 6 Cases date: 2006-03-01 pages: extension: .txt txt: ./txt/cord-273840-jjm7y07m.txt cache: ./cache/cord-273840-jjm7y07m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-273840-jjm7y07m.txt' /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 61970 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-270929-utn21ce1 author: Wise, Annabel G. title: Molecular characterization of a novel coronavirus associated with epizootic catarrhal enteritis (ECE) in ferrets date: 2006-05-25 pages: extension: .txt txt: ./txt/cord-270929-utn21ce1.txt cache: ./cache/cord-270929-utn21ce1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270929-utn21ce1.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-271669-dkg6229j author: Han, Seung Beom title: Respiratory Viral Infections in Children and Adolescents with Hematological Malignancies date: 2019-01-01 pages: extension: .txt txt: ./txt/cord-271669-dkg6229j.txt cache: ./cache/cord-271669-dkg6229j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271669-dkg6229j.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-273846-l0elcfe8 author: Ganapathy, Kannan title: Effects of cold storage on detection of avian infectious bronchitis virus in chicken carcasses and local antibodies in tracheal washes date: 2005-02-24 pages: extension: .txt txt: ./txt/cord-273846-l0elcfe8.txt cache: ./cache/cord-273846-l0elcfe8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-273846-l0elcfe8.txt' === file2bib.sh === id: cord-010027-r0tl01kq author: nan title: Dublin Pathology 2015. 8th Joint Meeting of the British Division of the International Academy of Pathology and the Pathological Society of Great Britain & Ireland date: 2015-09-15 pages: extension: .txt txt: ./txt/cord-010027-r0tl01kq.txt cache: ./cache/cord-010027-r0tl01kq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-010027-r0tl01kq.txt' === file2bib.sh === id: cord-271130-6s79q1c1 author: Filoni, Claudia title: Putative progressive and abortive feline leukemia virus infection outcomes in captive jaguarundis (Puma yagouaroundi) date: 2017-11-17 pages: extension: .txt txt: ./txt/cord-271130-6s79q1c1.txt cache: ./cache/cord-271130-6s79q1c1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271130-6s79q1c1.txt' === file2bib.sh === id: cord-274567-xd37wxxf author: Monpoeho, S. title: Application of a Real-Time Polymerase Chain Reaction with Internal Positive Control for Detection and Quantification of Enterovirus in Cerebrospinal Fluid date: 2002-07-13 pages: extension: .txt txt: ./txt/cord-274567-xd37wxxf.txt cache: ./cache/cord-274567-xd37wxxf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-274567-xd37wxxf.txt' === file2bib.sh === id: cord-023308-af5nihyi author: nan title: COPD SIG: Poster Session 2 date: 2008-03-12 pages: extension: .txt txt: ./txt/cord-023308-af5nihyi.txt cache: ./cache/cord-023308-af5nihyi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-023308-af5nihyi.txt' === file2bib.sh === id: cord-272955-kkkrkgg1 author: Belsy, Acosta title: Molecular characterization of adenoviral infections in Cuba: report of an unusual association of species D adenoviruses with different clinical syndromes date: 2009-03-12 pages: extension: .txt txt: ./txt/cord-272955-kkkrkgg1.txt cache: ./cache/cord-272955-kkkrkgg1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272955-kkkrkgg1.txt' === file2bib.sh === id: cord-274656-dngumjns author: Mori, Masahiro title: Detection of mumps virus RNA in cerebrospinal fluid of patients with neuromyelitis optica date: 2011-04-06 pages: extension: .txt txt: ./txt/cord-274656-dngumjns.txt cache: ./cache/cord-274656-dngumjns.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274656-dngumjns.txt' === file2bib.sh === id: cord-274438-tgslabi2 author: Schnee, Sarah Valerie title: Performance of the Alere i RSV assay for point-of-care detection of respiratory syncytial virus in children date: 2017-12-13 pages: extension: .txt txt: ./txt/cord-274438-tgslabi2.txt cache: ./cache/cord-274438-tgslabi2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-274438-tgslabi2.txt' === file2bib.sh === id: cord-273179-bpnak9ov author: Ma, Fen-lian title: Quantitative detection of human Malawi polyomavirus in nasopharyngeal aspirates, sera, and feces in Beijing, China, using real-time TaqMan-based PCR date: 2017-08-14 pages: extension: .txt txt: ./txt/cord-273179-bpnak9ov.txt cache: ./cache/cord-273179-bpnak9ov.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273179-bpnak9ov.txt' === file2bib.sh === id: cord-274289-8g9tuyrc author: Liang, Xiao title: Evaluation of Fast Technology Analysis (FTA) Cards as an improved method for specimen collection and shipment targeting viruses associated with Bovine Respiratory Disease Complex date: 2014-06-15 pages: extension: .txt txt: ./txt/cord-274289-8g9tuyrc.txt cache: ./cache/cord-274289-8g9tuyrc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274289-8g9tuyrc.txt' === file2bib.sh === id: cord-273608-dxx3p1x5 author: Deng, Jikui title: Respiratory virus multiplex RT-PCR assay sensitivities and influence factors in hospitalized children with lower respiratory tract infections date: 2013-04-11 pages: extension: .txt txt: ./txt/cord-273608-dxx3p1x5.txt cache: ./cache/cord-273608-dxx3p1x5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-273608-dxx3p1x5.txt' === file2bib.sh === id: cord-273343-als886fe author: McClenahan, Shasta D. title: Discovery of a Bovine Enterovirus in Alpaca date: 2013-08-12 pages: extension: .txt txt: ./txt/cord-273343-als886fe.txt cache: ./cache/cord-273343-als886fe.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273343-als886fe.txt' === file2bib.sh === id: cord-274184-hm516x6p author: Elli, Luca title: Endoscopy during the Covid-19 outbreak: experience and recommendations from a single center in a high-incidence scenario date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-274184-hm516x6p.txt cache: ./cache/cord-274184-hm516x6p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-274184-hm516x6p.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 65444 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 66487 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 73. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 74. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 87. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 66245 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 72. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 92483 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-274127-12x5cc8i author: Jeong, Ji Hun title: Comparison of sputum and nasopharyngeal swabs for detection of respiratory viruses date: 2014-05-06 pages: extension: .txt txt: ./txt/cord-274127-12x5cc8i.txt cache: ./cache/cord-274127-12x5cc8i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274127-12x5cc8i.txt' === file2bib.sh === id: cord-274568-flqc3jjd author: Naguib, Michael title: The use of radiological imaging alongside reverse transcriptase PCR in diagnosing novel coronavirus disease 2019: a narrative review date: 2020-07-08 pages: extension: .txt txt: ./txt/cord-274568-flqc3jjd.txt cache: ./cache/cord-274568-flqc3jjd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274568-flqc3jjd.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-274805-b3mqkfhh author: Onodera, Kenji title: Selection for 3′ end triplets for polymerase chain reaction primers date: 2004-12-31 pages: extension: .txt txt: ./txt/cord-274805-b3mqkfhh.txt cache: ./cache/cord-274805-b3mqkfhh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274805-b3mqkfhh.txt' === file2bib.sh === id: cord-271920-1dzkgt6w author: Carpenter, Christopher R. title: Diagnosing COVID‐19 in the Emergency Department: A Scoping Review of Clinical Exam, Labs, Imaging Accuracy and Biases date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-271920-1dzkgt6w.txt cache: ./cache/cord-271920-1dzkgt6w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271920-1dzkgt6w.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-277359-za2hh71g author: Chae, Kum Ju title: Positive conversion of COVID-19 after two consecutive negative RT-PCR results: A role of low-dose CT date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-277359-za2hh71g.txt cache: ./cache/cord-277359-za2hh71g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-277359-za2hh71g.txt' === file2bib.sh === id: cord-275275-wy8d6cw3 author: Rovida, Francesca title: Molecular detection of gastrointestinal viral infections in hospitalized patients date: 2013-09-12 pages: extension: .txt txt: ./txt/cord-275275-wy8d6cw3.txt cache: ./cache/cord-275275-wy8d6cw3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275275-wy8d6cw3.txt' === file2bib.sh === id: cord-274676-wtizb7hk author: Lee, Seung-Hun title: Multilocus typing of Cryptosporidium spp. in young calves with diarrhea in Korea date: 2016-10-15 pages: extension: .txt txt: ./txt/cord-274676-wtizb7hk.txt cache: ./cache/cord-274676-wtizb7hk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274676-wtizb7hk.txt' === file2bib.sh === id: cord-274707-mxh38hwd author: Laureano, Ana Flávia Santarine title: The different tests for the diagnosis of COVID-19 - A review in Brazil so far date: 2020 pages: extension: .txt txt: ./txt/cord-274707-mxh38hwd.txt cache: ./cache/cord-274707-mxh38hwd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-274707-mxh38hwd.txt' === file2bib.sh === id: cord-269194-b1wlr3t7 author: Engstrom-Melnyk, Julia title: Chapter 5 Clinical Applications of Quantitative Real-Time PCR in Virology date: 2015-12-31 pages: extension: .txt txt: ./txt/cord-269194-b1wlr3t7.txt cache: ./cache/cord-269194-b1wlr3t7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-269194-b1wlr3t7.txt' === file2bib.sh === id: cord-276739-84vf5bts author: Sakurai, Akira title: Rapid typing of influenza viruses using super high-speed quantitative real-time PCR date: 2011-08-22 pages: extension: .txt txt: ./txt/cord-276739-84vf5bts.txt cache: ./cache/cord-276739-84vf5bts.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276739-84vf5bts.txt' === file2bib.sh === id: cord-274828-67yeag50 author: Dybkær, Karen title: Identification of acute myeloid leukemia patients with diminished expression of CD13 myeloid transcripts by competitive reverse transcription polymerase chain reaction (RT-PCR) date: 2000-04-21 pages: extension: .txt txt: ./txt/cord-274828-67yeag50.txt cache: ./cache/cord-274828-67yeag50.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-274828-67yeag50.txt' === file2bib.sh === id: cord-277125-s11obc7w author: Kim, Hyeong Rae title: An integrated system of air sampling and simultaneous enrichment for rapid biosensing of airborne coronavirus and influenza virus date: 2020-09-26 pages: extension: .txt txt: ./txt/cord-277125-s11obc7w.txt cache: ./cache/cord-277125-s11obc7w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277125-s11obc7w.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 69995 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 70211 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 71644 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 72028 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-017331-ru7mvfc0 author: Samanta, Indranil title: Infectious Diseases date: 2017-02-25 pages: extension: .txt txt: ./txt/cord-017331-ru7mvfc0.txt cache: ./cache/cord-017331-ru7mvfc0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-017331-ru7mvfc0.txt' === file2bib.sh === id: cord-275787-5s442sy2 author: Banerjee, Arinjay title: Generation and Characterization of Eptesicus fuscus (Big brown bat) kidney cell lines immortalized using the Myotis polyomavirus large T-antigen date: 2016-09-14 pages: extension: .txt txt: ./txt/cord-275787-5s442sy2.txt cache: ./cache/cord-275787-5s442sy2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-275787-5s442sy2.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 86. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 70952 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-277357-lpurk7pe author: González-González, Everardo title: Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-277357-lpurk7pe.txt cache: ./cache/cord-277357-lpurk7pe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277357-lpurk7pe.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 72729 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 71811 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-277057-ww41t4k2 author: Sakthivel, Senthilkumar K. title: Comparison of fast-track diagnostics respiratory pathogens multiplex real-time RT-PCR assay with in-house singleplex assays for comprehensive detection of human respiratory viruses() date: 2012-07-11 pages: extension: .txt txt: ./txt/cord-277057-ww41t4k2.txt cache: ./cache/cord-277057-ww41t4k2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 7 resourceName b'cord-277057-ww41t4k2.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 73145 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 72344 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-271504-t3y1w9ef author: Luo, Zichao title: Combating the Coronavirus Pandemic: Early Detection, Medical Treatment, and a Concerted Effort by the Global Community date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-271504-t3y1w9ef.txt cache: ./cache/cord-271504-t3y1w9ef.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271504-t3y1w9ef.txt' === file2bib.sh === id: cord-281653-zogtpm7a author: Thurman, Kathleen A. title: Detection of Mycoplasma pneumoniae, Chlamydia pneumoniae, and Legionella spp. in clinical specimens using a single-tube multiplex real-time PCR assay() date: 2011-03-11 pages: extension: .txt txt: ./txt/cord-281653-zogtpm7a.txt cache: ./cache/cord-281653-zogtpm7a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-281653-zogtpm7a.txt' === file2bib.sh === id: cord-279223-qvih5qas author: Hascoët, Jean-Michel title: Case Series of COVID-19 Asymptomatic Newborns With Possible Intrapartum Transmission of SARS-CoV-2 date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-279223-qvih5qas.txt cache: ./cache/cord-279223-qvih5qas.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279223-qvih5qas.txt' === file2bib.sh === id: cord-279644-g9cr9m96 author: Abedi Kiasari, Bahman title: Merkel cell polyomavirus DNA in immunocompetent and immunocompromised patients with respiratory disease date: 2011-10-19 pages: extension: .txt txt: ./txt/cord-279644-g9cr9m96.txt cache: ./cache/cord-279644-g9cr9m96.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279644-g9cr9m96.txt' === file2bib.sh === id: cord-279101-c763gzq2 author: Xu, Sen title: Identification and characterization of a novel L-type lectin (MjLTL2) from kuruma shrimp (Marsupenaeus japonicus) date: 2020-01-13 pages: extension: .txt txt: ./txt/cord-279101-c763gzq2.txt cache: ./cache/cord-279101-c763gzq2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279101-c763gzq2.txt' === file2bib.sh === id: cord-278833-wlhmcdcn author: Rutschke, Nils title: Hot start reverse transcriptase: an approach for improved real-time RT-PCR performance date: 2015-06-21 pages: extension: .txt txt: ./txt/cord-278833-wlhmcdcn.txt cache: ./cache/cord-278833-wlhmcdcn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278833-wlhmcdcn.txt' === file2bib.sh === id: cord-281871-3j64de2i author: Sinagra, G title: Viral presence guided immunomodulation in lymphocytic myocarditis: An update date: 2020-07-19 pages: extension: .txt txt: ./txt/cord-281871-3j64de2i.txt cache: ./cache/cord-281871-3j64de2i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-281871-3j64de2i.txt' === file2bib.sh === id: cord-280865-shwxhak9 author: Zhang, Dan title: Clinical evaluation of a panel of multiplex quantitative real-time reverse transcription polymerase chain reaction assays for the detection of 16 respiratory viruses associated with community-acquired pneumonia date: 2018-06-30 pages: extension: .txt txt: ./txt/cord-280865-shwxhak9.txt cache: ./cache/cord-280865-shwxhak9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280865-shwxhak9.txt' === file2bib.sh === id: cord-278176-o9glkhyv author: Houng, Huo-Shu H title: Development and evaluation of an efficient 3′-noncoding region based SARS coronavirus (SARS-CoV) RT-PCR assay for detection of SARS-CoV infections date: 2004-09-01 pages: extension: .txt txt: ./txt/cord-278176-o9glkhyv.txt cache: ./cache/cord-278176-o9glkhyv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278176-o9glkhyv.txt' === file2bib.sh === id: cord-279229-2226jnfl author: Savan, R title: Loop‐mediated isothermal amplification: an emerging technology for detection of fish and shellfish pathogens date: 2005-11-22 pages: extension: .txt txt: ./txt/cord-279229-2226jnfl.txt cache: ./cache/cord-279229-2226jnfl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279229-2226jnfl.txt' === file2bib.sh === Traceback (most recent call last): File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 2646, in get_loc return self._engine.get_loc(key) File "pandas/_libs/index.pyx", line 111, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1619, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1627, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'cord-266738-8xx1xm2d' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/data-disk/reader-compute/reader-cord/bin/file2bib.py", line 64, in if ( bibliographics.loc[ escape ,'author'] ) : author = bibliographics.loc[ escape,'author'] File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 1762, in __getitem__ return self._getitem_tuple(key) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 1272, in _getitem_tuple return self._getitem_lowerdim(tup) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 1389, in _getitem_lowerdim section = self._getitem_axis(key, axis=i) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 1965, in _getitem_axis return self._get_label(key, axis=axis) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 625, in _get_label return self.obj._xs(label, axis=axis) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/generic.py", line 3537, in xs loc = self.index.get_loc(key) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 2648, in get_loc return self._engine.get_loc(self._maybe_cast_indexer(key)) File "pandas/_libs/index.pyx", line 111, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1619, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1627, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'cord-266738-8xx1xm2d' === file2bib.sh === id: cord-277659-afysef1e author: Hamilton, F. title: Kinetics and performance of the Abbott Architect SARS-CoV-2 IgG antibody assay date: 2020-07-04 pages: extension: .txt txt: ./txt/cord-277659-afysef1e.txt cache: ./cache/cord-277659-afysef1e.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277659-afysef1e.txt' === file2bib.sh === id: cord-277838-931sco95 author: Erles, Kerstin title: Detection of a group 2 coronavirus in dogs with canine infectious respiratory disease date: 2003-06-05 pages: extension: .txt txt: ./txt/cord-277838-931sco95.txt cache: ./cache/cord-277838-931sco95.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277838-931sco95.txt' === file2bib.sh === id: cord-279577-iwqr2d0r author: Kaur, Taranjit title: Descriptive epidemiology of fatal respiratory outbreaks and detection of a human‐related metapneumovirus in wild chimpanzees (Pan troglodytes) at Mahale Mountains National Park, Western Tanzania date: 2008-06-11 pages: extension: .txt txt: ./txt/cord-279577-iwqr2d0r.txt cache: ./cache/cord-279577-iwqr2d0r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-279577-iwqr2d0r.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-278635-vwdxr1bl author: Świętoń, Edyta title: Low pathogenic avian influenza virus isolates with different levels of defective genome segments vary in pathogenicity and transmission efficiency date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-278635-vwdxr1bl.txt cache: ./cache/cord-278635-vwdxr1bl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-278635-vwdxr1bl.txt' === file2bib.sh === id: cord-282321-svoshzz8 author: Eboigbodin, Kevin title: Reverse transcription strand invasion based amplification (RT-SIBA): a method for rapid detection of influenza A and B date: 2016-04-11 pages: extension: .txt txt: ./txt/cord-282321-svoshzz8.txt cache: ./cache/cord-282321-svoshzz8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-282321-svoshzz8.txt' === file2bib.sh === id: cord-277265-p8pns7r9 author: Malik, Yashpal Singh title: Biotechnological innovations in farm and pet animal disease diagnosis date: 2019-09-20 pages: extension: .txt txt: ./txt/cord-277265-p8pns7r9.txt cache: ./cache/cord-277265-p8pns7r9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-277265-p8pns7r9.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 77224 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 78873 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 77977 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 78922 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-281887-b511bjdy author: Ribeiro, Reitan title: Perioperative Cancer Care in the Context of Limited Resources during the COVID-19 Pandemic: Brazilian Society of Surgical Oncology Recommendations date: 2020-09-26 pages: extension: .txt txt: ./txt/cord-281887-b511bjdy.txt cache: ./cache/cord-281887-b511bjdy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281887-b511bjdy.txt' === file2bib.sh === id: cord-281529-2rec51xg author: Haagmans, Bart L title: Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation date: 2013-12-17 pages: extension: .txt txt: ./txt/cord-281529-2rec51xg.txt cache: ./cache/cord-281529-2rec51xg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-281529-2rec51xg.txt' === file2bib.sh === Traceback (most recent call last): File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 2646, in get_loc return self._engine.get_loc(key) File "pandas/_libs/index.pyx", line 111, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1619, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1627, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'cord-324559-p92y5er2' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/data-disk/reader-compute/reader-cord/bin/file2bib.py", line 64, in if ( bibliographics.loc[ escape ,'author'] ) : author = bibliographics.loc[ escape,'author'] File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 1762, in __getitem__ return self._getitem_tuple(key) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 1272, in _getitem_tuple return self._getitem_lowerdim(tup) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 1389, in _getitem_lowerdim section = self._getitem_axis(key, axis=i) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 1965, in _getitem_axis return self._get_label(key, axis=axis) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexing.py", line 625, in _get_label return self.obj._xs(label, axis=axis) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/generic.py", line 3537, in xs loc = self.index.get_loc(key) File "/data-disk/python/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 2648, in get_loc return self._engine.get_loc(self._maybe_cast_indexer(key)) File "pandas/_libs/index.pyx", line 111, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1619, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1627, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'cord-324559-p92y5er2' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 78766 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-281162-2pu7x5rj author: Etemadi, Mohammad Reza title: Diversity of respiratory viruses detected among hospitalized children with acute lower respiratory tract infections at Hospital Serdang, Malaysia date: 2019-03-22 pages: extension: .txt txt: ./txt/cord-281162-2pu7x5rj.txt cache: ./cache/cord-281162-2pu7x5rj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281162-2pu7x5rj.txt' === file2bib.sh === id: cord-277804-ujabzic4 author: Yuk, Seong-su title: Comparison between dot-immunoblotting assay and clinical sign determination method for quantifying avian infectious bronchitis virus vaccine by titration in embryonated eggs date: 2016-01-21 pages: extension: .txt txt: ./txt/cord-277804-ujabzic4.txt cache: ./cache/cord-277804-ujabzic4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277804-ujabzic4.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 79496 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-281844-c0uhcatg author: Costa, Lusmaia D.C. title: Exacerbation of asthma and airway infection: is the virus the villain? date: 2014-12-31 pages: extension: .txt txt: ./txt/cord-281844-c0uhcatg.txt cache: ./cache/cord-281844-c0uhcatg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281844-c0uhcatg.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 80534 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 89716 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-283409-ynwgdz52 author: Baggett, Travis P. title: Clinical Outcomes, Costs, and Cost-effectiveness of Strategies for People Experiencing Sheltered Homelessness During the COVID-19 Pandemic date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-283409-ynwgdz52.txt cache: ./cache/cord-283409-ynwgdz52.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-283409-ynwgdz52.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 80676 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-277909-rn1dow26 author: Gunson, R.N. title: Practical experience of high throughput real time PCR in the routine diagnostic virology setting date: 2006-02-07 pages: extension: .txt txt: ./txt/cord-277909-rn1dow26.txt cache: ./cache/cord-277909-rn1dow26.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-277909-rn1dow26.txt' === file2bib.sh === id: cord-279980-49yv65gm author: WANARATANA, S. title: The potential of house flies to act as a vector of avian influenza subtype H5N1 under experimental conditions date: 2010-12-01 pages: extension: .txt txt: ./txt/cord-279980-49yv65gm.txt cache: ./cache/cord-279980-49yv65gm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-279980-49yv65gm.txt' === file2bib.sh === id: cord-284262-lddmo1sv author: Li, Linlin title: Circovirus in Tissues of Dogs with Vasculitis and Hemorrhage date: 2013-04-17 pages: extension: .txt txt: ./txt/cord-284262-lddmo1sv.txt cache: ./cache/cord-284262-lddmo1sv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-284262-lddmo1sv.txt' === file2bib.sh === id: cord-279551-py2awuav author: Willi, Barbara title: Clinical and molecular investigation of a canine distemper outbreak and vector-borne infections in a group of rescue dogs imported from Hungary to Switzerland date: 2015-07-16 pages: extension: .txt txt: ./txt/cord-279551-py2awuav.txt cache: ./cache/cord-279551-py2awuav.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279551-py2awuav.txt' === file2bib.sh === id: cord-279576-wt4crton author: Fajardo, Álvaro title: Evaluation Of SYBR Green Real Time PCR For Detecting SARS-CoV-2 From Clinical Samples date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-279576-wt4crton.txt cache: ./cache/cord-279576-wt4crton.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279576-wt4crton.txt' === file2bib.sh === id: cord-280442-jtvez46y author: Wu, Xuan title: Simultaneous and visual detection of infectious bronchitis virus and Newcastle disease virus by multiple LAMP and lateral flow dipstick date: 2019-11-01 pages: extension: .txt txt: ./txt/cord-280442-jtvez46y.txt cache: ./cache/cord-280442-jtvez46y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-280442-jtvez46y.txt' === file2bib.sh === id: cord-274128-kgtr77e7 author: Hochstetter, Axel title: Lab-on-a-Chip Technologies for the Single Cell Level: Separation, Analysis, and Diagnostics date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-274128-kgtr77e7.txt cache: ./cache/cord-274128-kgtr77e7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274128-kgtr77e7.txt' === file2bib.sh === id: cord-284313-rg3krh7d author: Wood, Lisa G. title: Persistent Airway Obstruction After Virus Infection Is Not Associated With Airway Inflammation date: 2007-02-28 pages: extension: .txt txt: ./txt/cord-284313-rg3krh7d.txt cache: ./cache/cord-284313-rg3krh7d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284313-rg3krh7d.txt' === file2bib.sh === id: cord-284625-to6w5hm2 author: Duan, Xiaopei title: A retrospective study of the initial 25 COVID-19 patients in Luoyang, China date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-284625-to6w5hm2.txt cache: ./cache/cord-284625-to6w5hm2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284625-to6w5hm2.txt' === file2bib.sh === id: cord-284367-cy61pjcb author: MULEYA, Walter title: Molecular Epidemiology of Paramyxoviruses in Frugivorous Eidolon helvum Bats in Zambia date: 2013-12-31 pages: extension: .txt txt: ./txt/cord-284367-cy61pjcb.txt cache: ./cache/cord-284367-cy61pjcb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284367-cy61pjcb.txt' === file2bib.sh === id: cord-284366-snajbvr9 author: Han, Zhiyong title: Discharged COVID‐19 Patients Testing Positive Again for SARS‐CoV‐2 RNA: A Minireview of Published Studies from China date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-284366-snajbvr9.txt cache: ./cache/cord-284366-snajbvr9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284366-snajbvr9.txt' === file2bib.sh === id: cord-283309-ovx5fzsg author: Yang, Yong-Le title: Characterization of a novel bat-HKU2-like swine enteric alphacoronavirus (SeACoV) infection in cultured cells and development of a SeACoV infectious clone date: 2019-08-09 pages: extension: .txt txt: ./txt/cord-283309-ovx5fzsg.txt cache: ./cache/cord-283309-ovx5fzsg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283309-ovx5fzsg.txt' === file2bib.sh === id: cord-284423-fzz8g3rq author: Wang, Hui-yu title: Establishment and optimization of a liquid bead array for the simultaneous detection of ten insect-borne pathogens date: 2018-07-31 pages: extension: .txt txt: ./txt/cord-284423-fzz8g3rq.txt cache: ./cache/cord-284423-fzz8g3rq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284423-fzz8g3rq.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 84395 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-284372-v95fzp8n author: Coyle, Peter V title: A touchdown nucleic acid amplification protocol as an alternative to culture backup for immunofluorescence in the routine diagnosis of acute viral respiratory tract infections date: 2004-10-25 pages: extension: .txt txt: ./txt/cord-284372-v95fzp8n.txt cache: ./cache/cord-284372-v95fzp8n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-284372-v95fzp8n.txt' === file2bib.sh === id: cord-286555-rz88g3ze author: Petrovan, Vlad title: Evaluation of Commercial qPCR Kits for Detection of SARS-CoV-2 in Pooled Samples date: 2020-07-11 pages: extension: .txt txt: ./txt/cord-286555-rz88g3ze.txt cache: ./cache/cord-286555-rz88g3ze.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286555-rz88g3ze.txt' === file2bib.sh === id: cord-280846-bbv6f5gf author: Greninger, Alexander L. title: A Metagenomic Analysis of Pandemic Influenza A (2009 H1N1) Infection in Patients from North America date: 2010-10-18 pages: extension: .txt txt: ./txt/cord-280846-bbv6f5gf.txt cache: ./cache/cord-280846-bbv6f5gf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280846-bbv6f5gf.txt' === file2bib.sh === id: cord-287104-4k8pqbc0 author: Lee, J. Y. title: Development of Rapid and Specific Detection for the Human Aichivirus A Using the Loop-Mediated Isothermal Amplification from Water Samples date: 2019-04-04 pages: extension: .txt txt: ./txt/cord-287104-4k8pqbc0.txt cache: ./cache/cord-287104-4k8pqbc0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-287104-4k8pqbc0.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 86878 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-285587-rggfg60a author: Meligy, Bassant title: Detection of viral acute lower respiratory tract infection in hospitalized infants using real-time PCR date: 2015-12-30 pages: extension: .txt txt: ./txt/cord-285587-rggfg60a.txt cache: ./cache/cord-285587-rggfg60a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285587-rggfg60a.txt' === file2bib.sh === id: cord-017199-dn413uud author: Heineman, M.J. title: 21 Infecties, ziekte en zwangerschap date: 2016 pages: extension: .txt txt: ./txt/cord-017199-dn413uud.txt cache: ./cache/cord-017199-dn413uud.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-017199-dn413uud.txt' === file2bib.sh === id: cord-284644-9k2oox64 author: Sharma, Vikrant title: Evaluation of clinical applicability of reverse transcription-loop-mediated isothermal amplification assay for detection and subtyping of Influenza A viruses date: 2017-12-15 pages: extension: .txt txt: ./txt/cord-284644-9k2oox64.txt cache: ./cache/cord-284644-9k2oox64.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284644-9k2oox64.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 92872 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-284608-ba7wq52t author: Sias, Catia title: Alpha, Beta, gamma human PapillomaViruses (HPV) detection with a different sets of primers in oropharyngeal swabs, anal and cervical samples date: 2019-03-04 pages: extension: .txt txt: ./txt/cord-284608-ba7wq52t.txt cache: ./cache/cord-284608-ba7wq52t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284608-ba7wq52t.txt' === file2bib.sh === id: cord-286360-wrrqb387 author: Pratelli, A title: Development of a nested PCR assay for the detection of canine coronavirus date: 1999-06-02 pages: extension: .txt txt: ./txt/cord-286360-wrrqb387.txt cache: ./cache/cord-286360-wrrqb387.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286360-wrrqb387.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 88417 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 88077 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-287447-5lzzobl3 author: Keyaerts, Els title: In vitro inhibition of severe acute respiratory syndrome coronavirus by chloroquine date: 2004-10-08 pages: extension: .txt txt: ./txt/cord-287447-5lzzobl3.txt cache: ./cache/cord-287447-5lzzobl3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287447-5lzzobl3.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 87497 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-284777-z7bd3a91 author: Sun, Ning title: Reverse transcription recombinase polymerase amplification with lateral flow dipsticks for detection of influenza A virus and subtyping of H1 and H3 date: 2018-10-27 pages: extension: .txt txt: ./txt/cord-284777-z7bd3a91.txt cache: ./cache/cord-284777-z7bd3a91.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-284777-z7bd3a91.txt' === file2bib.sh === id: cord-286096-h275nner author: Huijskens, Elisabeth G. W. title: Viral and bacterial aetiology of community‐acquired pneumonia in adults date: 2012-08-22 pages: extension: .txt txt: ./txt/cord-286096-h275nner.txt cache: ./cache/cord-286096-h275nner.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286096-h275nner.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 88640 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-286065-x0g67pnb author: Metzgar, David title: The IRIDICA BAC BSI Assay: Rapid, Sensitive and Culture-Independent Identification of Bacteria and Candida in Blood date: 2016-07-06 pages: extension: .txt txt: ./txt/cord-286065-x0g67pnb.txt cache: ./cache/cord-286065-x0g67pnb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286065-x0g67pnb.txt' === file2bib.sh === id: cord-289200-6yhz1a23 author: Yang, Ziyi title: Vertical Transmission of Severe Acute Respiratory Syndrome Coronavirus 2: A Systematic Review date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-289200-6yhz1a23.txt cache: ./cache/cord-289200-6yhz1a23.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289200-6yhz1a23.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 85. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 89683 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-288692-v471648u author: Yip, Shea Ping title: Use of Dual TaqMan Probes to Increase the Sensitivity of 1-Step Quantitative Reverse Transcription-PCR: Application to the Detection of SARS Coronavirus date: 2005-10-01 pages: extension: .txt txt: ./txt/cord-288692-v471648u.txt cache: ./cache/cord-288692-v471648u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-288692-v471648u.txt' === file2bib.sh === id: cord-287843-snra23sy author: Lee, Wan‐Ji title: Prevalence and molecular epidemiology of human coronavirus HKU1 in patients with acute respiratory illness date: 2012-11-14 pages: extension: .txt txt: ./txt/cord-287843-snra23sy.txt cache: ./cache/cord-287843-snra23sy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-287843-snra23sy.txt' === file2bib.sh === id: cord-289050-9w7ks01n author: Donoso, Alejandro F. title: Fatal hemorrhagic pneumonia caused by human metapneumovirus in an immunocompetent child date: 2008-08-25 pages: extension: .txt txt: ./txt/cord-289050-9w7ks01n.txt cache: ./cache/cord-289050-9w7ks01n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289050-9w7ks01n.txt' === file2bib.sh === id: cord-290513-ygqin14x author: Stevens, Barry J. title: Reporting radiographers’ interpretation and use of the British Society of Thoracic Imaging’s coding system when reporting COVID-19 chest x-rays date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-290513-ygqin14x.txt cache: ./cache/cord-290513-ygqin14x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-290513-ygqin14x.txt' === file2bib.sh === id: cord-289216-g4kqi560 author: Malecki, M. title: Analysis of external quality assessment samples revealed crucial performance differences between commercial RT-PCR assays for SARS-CoV-2 detection when taking extraction methods and real-time-PCR instruments into account date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-289216-g4kqi560.txt cache: ./cache/cord-289216-g4kqi560.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289216-g4kqi560.txt' === file2bib.sh === id: cord-288962-jgtoehcr author: Andréoletti, Laurent title: Differential detection of rhinoviruses and enteroviruses RNA sequences associated with classical immunofluorescence assay detection of respiratory virus antigens in nasopharyngeal swabs from infants with bronchiolitis date: 2000-06-06 pages: extension: .txt txt: ./txt/cord-288962-jgtoehcr.txt cache: ./cache/cord-288962-jgtoehcr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-288962-jgtoehcr.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 93059 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 92176 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 92588 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 4224 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-288253-wqrhiq08 author: Park, Jung-Eun title: Development of transgenic mouse model expressing porcine aminopeptidase N and its susceptibility to porcine epidemic diarrhea virus date: 2015-02-02 pages: extension: .txt txt: ./txt/cord-288253-wqrhiq08.txt cache: ./cache/cord-288253-wqrhiq08.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288253-wqrhiq08.txt' === file2bib.sh === id: cord-289745-qtorq2qq author: Esper, Frank title: Evidence of a Novel Human Coronavirus That Is Associated with Respiratory Tract Disease in Infants and Young Children date: 2005-02-15 pages: extension: .txt txt: ./txt/cord-289745-qtorq2qq.txt cache: ./cache/cord-289745-qtorq2qq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-289745-qtorq2qq.txt' === file2bib.sh === id: cord-288306-0chcsqe7 author: Wang, Lihua title: Recent Advances in the Diagnosis of Classical Swine Fever and Future Perspectives date: 2020-08-15 pages: extension: .txt txt: ./txt/cord-288306-0chcsqe7.txt cache: ./cache/cord-288306-0chcsqe7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288306-0chcsqe7.txt' === file2bib.sh === id: cord-290540-r0d6oaez author: Rottier, Peter J.M. title: The molecular dynamics of feline coronaviruses date: 1999-09-01 pages: extension: .txt txt: ./txt/cord-290540-r0d6oaez.txt cache: ./cache/cord-290540-r0d6oaez.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290540-r0d6oaez.txt' === file2bib.sh === id: cord-288556-o8i6j3b2 author: Li, Yanpeng title: Virome of a Feline Outbreak of Diarrhea and Vomiting Includes Bocaviruses and a Novel Chapparvovirus date: 2020-05-04 pages: extension: .txt txt: ./txt/cord-288556-o8i6j3b2.txt cache: ./cache/cord-288556-o8i6j3b2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-288556-o8i6j3b2.txt' === file2bib.sh === id: cord-288327-r20zowty author: Coiras, M.T. title: Oligonucleotide array for simultaneous detection of respiratory viruses using a reverse‐line blot hybridization assay date: 2005-04-15 pages: extension: .txt txt: ./txt/cord-288327-r20zowty.txt cache: ./cache/cord-288327-r20zowty.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-288327-r20zowty.txt' === file2bib.sh === id: cord-287931-cxqzac4a author: Huang, Weiwei title: An easy operating pathogen microarray (EOPM) platform for rapid screening of vertebrate pathogens date: 2013-09-20 pages: extension: .txt txt: ./txt/cord-287931-cxqzac4a.txt cache: ./cache/cord-287931-cxqzac4a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287931-cxqzac4a.txt' === file2bib.sh === id: cord-291026-99cit4ig author: Lung, O. title: Insulated Isothermal Reverse Transcriptase PCR (iiRT‐PCR) for Rapid and Sensitive Detection of Classical Swine Fever Virus date: 2015-01-27 pages: extension: .txt txt: ./txt/cord-291026-99cit4ig.txt cache: ./cache/cord-291026-99cit4ig.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291026-99cit4ig.txt' === file2bib.sh === id: cord-291029-oldket3n author: Sefers, Susan E. title: QIAamp MinElute Virus kit effectively extracts viral nucleic acids from cerebrospinal fluids and nasopharyngeal swabs() date: 2005-07-21 pages: extension: .txt txt: ./txt/cord-291029-oldket3n.txt cache: ./cache/cord-291029-oldket3n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-291029-oldket3n.txt' === file2bib.sh === id: cord-291281-ygrh8ces author: Durner, J. title: Critical Questions when Interpreting Coronavirus PCR Diagnostics date: 2020-06-14 pages: extension: .txt txt: ./txt/cord-291281-ygrh8ces.txt cache: ./cache/cord-291281-ygrh8ces.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-291281-ygrh8ces.txt' === file2bib.sh === id: cord-289735-iw3uq2z9 author: Tsou, P. title: Association between multiple respiratory viral infections and pediatric intensive care unit admission among infants with bronchiolitis date: 2019-11-25 pages: extension: .txt txt: ./txt/cord-289735-iw3uq2z9.txt cache: ./cache/cord-289735-iw3uq2z9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-289735-iw3uq2z9.txt' === file2bib.sh === id: cord-289744-suiqh3gv author: Lafolie, Jérémy title: Assessment of blood enterovirus PCR testing in paediatric populations with fever without source, sepsis-like disease, or suspected meningitis: a prospective, multicentre, observational cohort study date: 2018-10-30 pages: extension: .txt txt: ./txt/cord-289744-suiqh3gv.txt cache: ./cache/cord-289744-suiqh3gv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289744-suiqh3gv.txt' === file2bib.sh === id: cord-288701-nx9fg4yn author: Mari, Viviana title: Multiplex real-time RT-PCR assay for bovine viral diarrhea virus type 1, type 2 and HoBi-like pestivirus date: 2015-12-17 pages: extension: .txt txt: ./txt/cord-288701-nx9fg4yn.txt cache: ./cache/cord-288701-nx9fg4yn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-288701-nx9fg4yn.txt' === file2bib.sh === id: cord-291954-wormplcu author: Sakulkonkij, Parichart title: A family cluster of diagnosed coronavirus disease 2019 (COVID‐19) kidney transplant recipient in Thailand date: 2020-08-08 pages: extension: .txt txt: ./txt/cord-291954-wormplcu.txt cache: ./cache/cord-291954-wormplcu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291954-wormplcu.txt' === file2bib.sh === id: cord-289114-ifnk41oq author: Singh, Angaraj title: Effect of pre‐existing diseases on COVID‐19 infection and role of new sensors and biomaterials for its detection and treatment date: 2020-10-28 pages: extension: .txt txt: ./txt/cord-289114-ifnk41oq.txt cache: ./cache/cord-289114-ifnk41oq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289114-ifnk41oq.txt' === file2bib.sh === id: cord-290456-cgrn5c36 author: Soliman, Mohamed A. R. title: Endoscopic endonasal skull base surgery during the COVID-19 pandemic: A developing country perspective date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-290456-cgrn5c36.txt cache: ./cache/cord-290456-cgrn5c36.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290456-cgrn5c36.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 96387 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-291958-g4jlg9pw author: Silva, Camila S title: Human Respiratory Coronaviruses Detected In Patients with Influenza-Like Illness in Arkansas, USA date: 2014-03-26 pages: extension: .txt txt: ./txt/cord-291958-g4jlg9pw.txt cache: ./cache/cord-291958-g4jlg9pw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-291958-g4jlg9pw.txt' === file2bib.sh === id: cord-289017-vwye3pk9 author: Comach, Guillermo title: Sentinel Surveillance of Influenza-Like Illness in Two Hospitals in Maracay, Venezuela: 2006–2010 date: 2012-09-11 pages: extension: .txt txt: ./txt/cord-289017-vwye3pk9.txt cache: ./cache/cord-289017-vwye3pk9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-289017-vwye3pk9.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 98214 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 303 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 84. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 622 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 98194 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 1382 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-291360-z19ri377 author: Lan, Fan-Yun title: COVID-19 symptoms predictive of healthcare workers’ SARS-CoV-2 PCR results date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-291360-z19ri377.txt cache: ./cache/cord-291360-z19ri377.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-291360-z19ri377.txt' === file2bib.sh === id: cord-291961-usl8z6ep author: Zheng, Wen-zhi title: Human polyomavirus type six in respiratory samples from hospitalized children with respiratory tract infections in Beijing, China date: 2015-10-13 pages: extension: .txt txt: ./txt/cord-291961-usl8z6ep.txt cache: ./cache/cord-291961-usl8z6ep.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291961-usl8z6ep.txt' === file2bib.sh === id: cord-292772-xdic7rcy author: Petini, Matteo title: Nested–polymerase chain reaction detection of Pneumocystis carinii f. sp. canis in a suspected immunocompromised Cavalier King Charles spaniel with multiple infections date: 2019-04-26 pages: extension: .txt txt: ./txt/cord-292772-xdic7rcy.txt cache: ./cache/cord-292772-xdic7rcy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-292772-xdic7rcy.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-289612-4x5t4c5u author: Alsuliman, Tamim title: COVID-19 paraclinical diagnostic tools: Updates and future trends date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-289612-4x5t4c5u.txt cache: ./cache/cord-289612-4x5t4c5u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289612-4x5t4c5u.txt' === file2bib.sh === id: cord-292281-fui9all6 author: Pratelli, A. title: High‐cell‐passage canine coronavirus vaccine providing sterilising immunity date: 2007-09-14 pages: extension: .txt txt: ./txt/cord-292281-fui9all6.txt cache: ./cache/cord-292281-fui9all6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292281-fui9all6.txt' === file2bib.sh === id: cord-291860-dw1sfzqx author: van Boheemen, Sander title: Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients date: 2019-12-16 pages: extension: .txt txt: ./txt/cord-291860-dw1sfzqx.txt cache: ./cache/cord-291860-dw1sfzqx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291860-dw1sfzqx.txt' === file2bib.sh === id: cord-292347-d7xq7x5g author: Carter, Linda J. title: Assay Techniques and Test Development for COVID-19 Diagnosis date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-292347-d7xq7x5g.txt cache: ./cache/cord-292347-d7xq7x5g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-292347-d7xq7x5g.txt' === file2bib.sh === id: cord-294155-94skyx5f author: Terrosi, Chiara title: Human bocavirus detection in an atopic child affected by pneumonia associated with wheezing date: 2007-08-07 pages: extension: .txt txt: ./txt/cord-294155-94skyx5f.txt cache: ./cache/cord-294155-94skyx5f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294155-94skyx5f.txt' === file2bib.sh === id: cord-292828-29jbf9ik author: Alsaleh, Asma N title: Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control date: 2014-01-09 pages: extension: .txt txt: ./txt/cord-292828-29jbf9ik.txt cache: ./cache/cord-292828-29jbf9ik.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-292828-29jbf9ik.txt' === file2bib.sh === id: cord-292172-aqsc9fbl author: Al Amin, Md. title: Screening of commercial meat products from supermarket chains for feline derivatives using SP-PCR-RLFP and lab-on-a-chip date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-292172-aqsc9fbl.txt cache: ./cache/cord-292172-aqsc9fbl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-292172-aqsc9fbl.txt' === file2bib.sh === id: cord-293849-p3j2keyo author: Renaud, Christian title: Comparison of FilmArray Respiratory Panel and laboratory-developed real-time reverse transcription–polymerase chain reaction assays for respiratory virus detection date: 2012-12-31 pages: extension: .txt txt: ./txt/cord-293849-p3j2keyo.txt cache: ./cache/cord-293849-p3j2keyo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-293849-p3j2keyo.txt' === file2bib.sh === id: cord-295296-jtjx1vgd author: Tiwari, Shashi Kant title: `In-silico primer designing and PCR for detection of novel coronavirus-19 date: 2020-10-23 pages: extension: .txt txt: ./txt/cord-295296-jtjx1vgd.txt cache: ./cache/cord-295296-jtjx1vgd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-295296-jtjx1vgd.txt' === file2bib.sh === id: cord-292312-cwrqorn1 author: Sales, M. J. T. title: Fernando de Noronha: how an island controlled the community transmission of COVID-19 in Brazil date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-292312-cwrqorn1.txt cache: ./cache/cord-292312-cwrqorn1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292312-cwrqorn1.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 6535 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 5812 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-294138-h7sfd1wa author: McIver, David J. title: Coronavirus surveillance of wildlife in the Lao People’s Democratic Republic detects viral RNA in rodents date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-294138-h7sfd1wa.txt cache: ./cache/cord-294138-h7sfd1wa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294138-h7sfd1wa.txt' === file2bib.sh === id: cord-293590-0xn6mqh6 author: Peña, Andrea A title: An evaluation of potential reference genes for stability of expression in two salmonid cell lines after infection with either Piscirickettsia salmonis or IPNV date: 2010-04-14 pages: extension: .txt txt: ./txt/cord-293590-0xn6mqh6.txt cache: ./cache/cord-293590-0xn6mqh6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-293590-0xn6mqh6.txt' === file2bib.sh === id: cord-292031-weiwksh6 author: Ramírez-Castillo, Flor Yazmín title: Waterborne Pathogens: Detection Methods and Challenges date: 2015-05-21 pages: extension: .txt txt: ./txt/cord-292031-weiwksh6.txt cache: ./cache/cord-292031-weiwksh6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292031-weiwksh6.txt' === file2bib.sh === id: cord-294335-qnu19ru5 author: Yousaf, Anna R title: A prospective cohort study in non-hospitalized household contacts with SARS-CoV-2 infection: symptom profiles and symptom change over time date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-294335-qnu19ru5.txt cache: ./cache/cord-294335-qnu19ru5.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294335-qnu19ru5.txt' === file2bib.sh === id: cord-284376-plwyjhl8 author: Fu, Xinmiao title: Simulating and forecasting the cumulative confirmed cases of SARS-CoV-2 in China by Boltzmann function-based regression analyses date: 2020-05-31 pages: extension: .txt txt: ./txt/cord-284376-plwyjhl8.txt cache: ./cache/cord-284376-plwyjhl8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-284376-plwyjhl8.txt' === file2bib.sh === id: cord-294546-0otd1heg author: Prendki, V. title: Accuracy of comprehensive PCR analysis of nasopharyngeal and oropharyngeal swabs for CT-scan-confirmed pneumonia in elderly patients: a prospective cohort study date: 2019-01-12 pages: extension: .txt txt: ./txt/cord-294546-0otd1heg.txt cache: ./cache/cord-294546-0otd1heg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-294546-0otd1heg.txt' === file2bib.sh === id: cord-293629-1cno01un author: Vila Estapé, Jordi title: Métodos moleculares de diagnóstico de infecciones respiratorias. ¿Ha cambiado el esquema diagnóstico? date: 2016-07-31 pages: extension: .txt txt: ./txt/cord-293629-1cno01un.txt cache: ./cache/cord-293629-1cno01un.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293629-1cno01un.txt' === file2bib.sh === id: cord-292742-mio4przi author: McAloose, Denise title: From People to Panthera: Natural SARS-CoV-2 Infection in Tigers and Lions at the Bronx Zoo date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-292742-mio4przi.txt cache: ./cache/cord-292742-mio4przi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292742-mio4przi.txt' === file2bib.sh === id: cord-293966-5c466xvz author: Fehr, Anthony R. title: Bacterial Artificial Chromosome-Based Lambda Red Recombination with the I-SceI Homing Endonuclease for Genetic Alteration of MERS-CoV date: 2019-09-14 pages: extension: .txt txt: ./txt/cord-293966-5c466xvz.txt cache: ./cache/cord-293966-5c466xvz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-293966-5c466xvz.txt' === file2bib.sh === id: cord-294947-g4ntyddb author: Zhu, Yu title: Establishment of a nanoparticle-assisted RT-PCR assay to distinguish field strains and attenuated strains of porcine epidemic diarrhea virus date: 2016-06-10 pages: extension: .txt txt: ./txt/cord-294947-g4ntyddb.txt cache: ./cache/cord-294947-g4ntyddb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294947-g4ntyddb.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 7905 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-296109-kco85lqn author: Vanuytsel, Kim title: Rapid Implementation of a SARS-CoV-2 Diagnostic qRT-PCR Test with Emergency Use Authorization at a Large Academic Safety-Net Hospital date: 2020-05-19 pages: extension: .txt txt: ./txt/cord-296109-kco85lqn.txt cache: ./cache/cord-296109-kco85lqn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296109-kco85lqn.txt' === file2bib.sh === id: cord-298462-xpx3orvs author: Lin, Feng title: Quantification of human bocavirus in lower respiratory tract infections in China date: 2007-01-31 pages: extension: .txt txt: ./txt/cord-298462-xpx3orvs.txt cache: ./cache/cord-298462-xpx3orvs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-298462-xpx3orvs.txt' === file2bib.sh === id: cord-293234-ouykx6g5 author: Puig-Barberà, J. title: Effectiveness of the 2010–2011 seasonal influenza vaccine in preventing confirmed influenza hospitalizations in adults: A case–case comparison, case-control study date: 2012-08-24 pages: extension: .txt txt: ./txt/cord-293234-ouykx6g5.txt cache: ./cache/cord-293234-ouykx6g5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-293234-ouykx6g5.txt' === file2bib.sh === id: cord-295401-3p6q92x4 author: Gueudin, M title: Quantitation of respiratory syncytial virus RNA in nasal aspirates of children by real-time RT-PCR assay date: 2003-02-18 pages: extension: .txt txt: ./txt/cord-295401-3p6q92x4.txt cache: ./cache/cord-295401-3p6q92x4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-295401-3p6q92x4.txt' === file2bib.sh === id: cord-296392-2u9mz6d3 author: Sarıgül, Figen title: Investigation of compatibility of severe acute respiratory syndrome coronavirus 2 reverse transcriptase-PCR kits containing different gene targets during coronavirus disease 2019 pandemic date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-296392-2u9mz6d3.txt cache: ./cache/cord-296392-2u9mz6d3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296392-2u9mz6d3.txt' === file2bib.sh === id: cord-296593-ox6x53vj author: Sonoo, M. title: Correlation between PCR Examination Rate among the Population and the Containment of Pandemic of COVID-19 date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-296593-ox6x53vj.txt cache: ./cache/cord-296593-ox6x53vj.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296593-ox6x53vj.txt' === file2bib.sh === id: cord-297396-r1p7xn3a author: Ng, Ming-Yen title: Development and Validation of Risk Prediction Models for COVID-19 Positivity in a Hospital Setting date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-297396-r1p7xn3a.txt cache: ./cache/cord-297396-r1p7xn3a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297396-r1p7xn3a.txt' === file2bib.sh === id: cord-296736-jsm6o5pq author: Chidlow, Glenys R. title: An Economical Tandem Multiplex Real-Time PCR Technique for the Detection of a Comprehensive Range of Respiratory Pathogens date: 2009-06-08 pages: extension: .txt txt: ./txt/cord-296736-jsm6o5pq.txt cache: ./cache/cord-296736-jsm6o5pq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296736-jsm6o5pq.txt' === file2bib.sh === id: cord-299585-fkg8d6ym author: Wang, Leyi title: Development of a triplex real-time RT-PCR assay for detection and differentiation of three US genotypes of porcine hemagglutinating encephalomyelitis virus date: 2019-04-05 pages: extension: .txt txt: ./txt/cord-299585-fkg8d6ym.txt cache: ./cache/cord-299585-fkg8d6ym.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299585-fkg8d6ym.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 12673 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-292575-vsswxwdi author: Hammou, Rahma Ait title: Chapter 7 Scientific Advances in the Diagnosis of Emerging and Reemerging Viral Human Pathogens date: 2020-12-31 pages: extension: .txt txt: ./txt/cord-292575-vsswxwdi.txt cache: ./cache/cord-292575-vsswxwdi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292575-vsswxwdi.txt' === file2bib.sh === id: cord-298991-5qae0ege author: Aiello, Francesco title: Coronavirus disease 2019 (SARS-CoV-2) and colonization of ocular tissues and secretions: a systematic review date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-298991-5qae0ege.txt cache: ./cache/cord-298991-5qae0ege.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298991-5qae0ege.txt' === file2bib.sh === id: cord-298600-cnolne6k author: Majeed, Talal title: The Role of the Computed Tomography (CT) Thorax in the Diagnosis of COVID-19 for Patients Presenting with Acute Surgical Emergencies. A Single Institute Experience date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-298600-cnolne6k.txt cache: ./cache/cord-298600-cnolne6k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298600-cnolne6k.txt' === file2bib.sh === id: cord-293421-0ksn0fc7 author: Rodriguez, J. M. title: Detection of animal pathogens by using the polymerasechain reaction (PCR) date: 1997-05-31 pages: extension: .txt txt: ./txt/cord-293421-0ksn0fc7.txt cache: ./cache/cord-293421-0ksn0fc7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293421-0ksn0fc7.txt' === file2bib.sh === id: cord-299537-lbx1plqx author: Wang, Wei title: Molecular monitoring of causative viruses in child acute respiratory infection in endemo-epidemic situations in Shanghai date: 2010-09-19 pages: extension: .txt txt: ./txt/cord-299537-lbx1plqx.txt cache: ./cache/cord-299537-lbx1plqx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-299537-lbx1plqx.txt' === file2bib.sh === id: cord-287466-ag5y781z author: Cowley, J.A. title: Nidoviruses of Fish and Crustaceans date: 2016-09-09 pages: extension: .txt txt: ./txt/cord-287466-ag5y781z.txt cache: ./cache/cord-287466-ag5y781z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-287466-ag5y781z.txt' === file2bib.sh === id: cord-300285-su2fueox author: Gajurel, Kiran title: Persistently positive severe acute respiratory syndrome coronavirus 2 (SARS‐COV2) nasopharyngeal PCR in a kidney transplant recipient date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-300285-su2fueox.txt cache: ./cache/cord-300285-su2fueox.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-300285-su2fueox.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 13155 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-299737-r34d0rx7 author: Grant, Paul R title: Extraction-free COVID-19 (SARS-CoV-2) diagnosis by RT-PCR to increase capacity for national testing programmes during a pandemic date: 2020-04-08 pages: extension: .txt txt: ./txt/cord-299737-r34d0rx7.txt cache: ./cache/cord-299737-r34d0rx7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-299737-r34d0rx7.txt' === file2bib.sh === id: cord-298002-jvnwivrg author: Wang, Jian title: COVID-19 confirmed patients with negative antibodies results date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-298002-jvnwivrg.txt cache: ./cache/cord-298002-jvnwivrg.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298002-jvnwivrg.txt' === file2bib.sh === id: cord-295445-f4p00yaw author: Wang, Hao title: Differential removal of human pathogenic viruses from sewage by conventional and ozone treatments date: 2018-02-01 pages: extension: .txt txt: ./txt/cord-295445-f4p00yaw.txt cache: ./cache/cord-295445-f4p00yaw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295445-f4p00yaw.txt' === file2bib.sh === id: cord-297432-2edncbgn author: Helleberg, Marie title: Persistent COVID-19 in an Immunocompromised Patient Temporarily Responsive to Two Courses of Remdesivir Therapy date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-297432-2edncbgn.txt cache: ./cache/cord-297432-2edncbgn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297432-2edncbgn.txt' === file2bib.sh === id: cord-297646-49l6k5h2 author: Yu, Zhongjia title: Prevalence of intestinal parasites in companion dogs with diarrhea in Beijing, China, and genetic characteristics of Giardia and Cryptosporidium species date: 2017-11-18 pages: extension: .txt txt: ./txt/cord-297646-49l6k5h2.txt cache: ./cache/cord-297646-49l6k5h2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297646-49l6k5h2.txt' === file2bib.sh === id: cord-296979-8r851j4t author: Zhong, Ying title: Host genes regulate transcription of sperm-introduced hepatitis B virus genes in embryo date: 2017-10-31 pages: extension: .txt txt: ./txt/cord-296979-8r851j4t.txt cache: ./cache/cord-296979-8r851j4t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296979-8r851j4t.txt' === file2bib.sh === id: cord-299672-dq1y1gkc author: Leung, Ting Fan title: Multiplex Molecular Detection of Respiratory Pathogens in Children With Asthma Exacerbation date: 2010-02-28 pages: extension: .txt txt: ./txt/cord-299672-dq1y1gkc.txt cache: ./cache/cord-299672-dq1y1gkc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299672-dq1y1gkc.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 13707 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-298049-gabjdkx9 author: Gomez, D.E. title: Detection of Bovine Coronavirus in Healthy and Diarrheic Dairy Calves date: 2017-09-15 pages: extension: .txt txt: ./txt/cord-298049-gabjdkx9.txt cache: ./cache/cord-298049-gabjdkx9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298049-gabjdkx9.txt' === file2bib.sh === id: cord-299944-1e44usl6 author: Gardner, Shea N. title: Multiplex Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes date: 2014-08-03 pages: extension: .txt txt: ./txt/cord-299944-1e44usl6.txt cache: ./cache/cord-299944-1e44usl6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-299944-1e44usl6.txt' === file2bib.sh === id: cord-300243-5q67tnx4 author: Priya, A. Kokila title: Prevalence of enteropathogens and their antibiotic sensitivity pattern in puppies with hemorrhagic gastroenteritis date: 2017-08-04 pages: extension: .txt txt: ./txt/cord-300243-5q67tnx4.txt cache: ./cache/cord-300243-5q67tnx4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-300243-5q67tnx4.txt' === file2bib.sh === id: cord-296819-gztmidn2 author: Sambri, Vittorio title: Diagnosis of West Nile Virus Human Infections: Overview and Proposal of Diagnostic Protocols Considering the Results of External Quality Assessment Studies date: 2013-09-25 pages: extension: .txt txt: ./txt/cord-296819-gztmidn2.txt cache: ./cache/cord-296819-gztmidn2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296819-gztmidn2.txt' === file2bib.sh === id: cord-301254-093yih5n author: Brittain-Long, Robin title: Prospective evaluation of a novel multiplex real-time PCR assay for detection of fifteen respiratory pathogens—Duration of symptoms significantly affects detection rate date: 2010-01-18 pages: extension: .txt txt: ./txt/cord-301254-093yih5n.txt cache: ./cache/cord-301254-093yih5n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301254-093yih5n.txt' === file2bib.sh === id: cord-014976-546zaoxn author: nan title: Publication only date: 2006-03-08 pages: extension: .txt txt: ./txt/cord-014976-546zaoxn.txt cache: ./cache/cord-014976-546zaoxn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 7 resourceName b'cord-014976-546zaoxn.txt' === file2bib.sh === id: cord-300685-bcjnujlj author: Poon, Leo L M title: Rapid Diagnosis of a Coronavirus Associated with Severe Acute Respiratory Syndrome (SARS) date: 2003-06-01 pages: extension: .txt txt: ./txt/cord-300685-bcjnujlj.txt cache: ./cache/cord-300685-bcjnujlj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300685-bcjnujlj.txt' === file2bib.sh === id: cord-300316-r54ksiy3 author: Moesker, F.M. title: Diagnostic performance of influenza viruses and RSV rapid antigen detection tests in children in tertiary care date: 2016-03-25 pages: extension: .txt txt: ./txt/cord-300316-r54ksiy3.txt cache: ./cache/cord-300316-r54ksiy3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300316-r54ksiy3.txt' === file2bib.sh === id: cord-300508-po2zolo8 author: Inoue, Gen title: Experience of an Orthopaedic Surgery Department Early During the COVID-19 Outbreak in Japan Including Real-Time Polymerase Chain Reaction Assay Results for SARS-CoV-2 date: 2020-10-24 pages: extension: .txt txt: ./txt/cord-300508-po2zolo8.txt cache: ./cache/cord-300508-po2zolo8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300508-po2zolo8.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 14902 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 14852 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 14610 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-291916-5yqc3zcx author: Hozhabri, Hossein title: The Global Emergency of Novel Coronavirus (SARS-CoV-2): An Update of the Current Status and Forecasting date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-291916-5yqc3zcx.txt cache: ./cache/cord-291916-5yqc3zcx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291916-5yqc3zcx.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 15188 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 15045 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-298051-ej8qxkce author: Louten, Jennifer title: Detection and Diagnosis of Viral Infections date: 2016-05-06 pages: extension: .txt txt: ./txt/cord-298051-ej8qxkce.txt cache: ./cache/cord-298051-ej8qxkce.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-298051-ej8qxkce.txt' === file2bib.sh === id: cord-300999-20c17smt author: Xiao, Yong title: Exploration of turn-positive RT-PCR results and factors related to treatment outcome in COVID-19: A retrospective cohort study date: 2020-09-13 pages: extension: .txt txt: ./txt/cord-300999-20c17smt.txt cache: ./cache/cord-300999-20c17smt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-300999-20c17smt.txt' === file2bib.sh === id: cord-302189-3xab3yxc author: Tillmann, Ramona Liza title: Sensitive Commercial NASBA Assay for the Detection of Respiratory Syncytial Virus in Clinical Specimen date: 2007-12-26 pages: extension: .txt txt: ./txt/cord-302189-3xab3yxc.txt cache: ./cache/cord-302189-3xab3yxc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302189-3xab3yxc.txt' === file2bib.sh === id: cord-300313-w8njg569 author: Clifford, S. title: Strategies to reduce the risk of SARS-CoV-2 re-introduction from international travellers date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-300313-w8njg569.txt cache: ./cache/cord-300313-w8njg569.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300313-w8njg569.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 15422 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-301695-zl7cjs1k author: Wang, Ji title: Identification of Histoplasma causing an unexplained disease cluster in Matthews Ridge, Guyana date: 2019-12-31 pages: extension: .txt txt: ./txt/cord-301695-zl7cjs1k.txt cache: ./cache/cord-301695-zl7cjs1k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301695-zl7cjs1k.txt' === file2bib.sh === id: cord-301167-101lnq4f author: Liu, Quanjun title: Microarray-in-a-Tube for Detection of Multiple Viruses date: 2007-02-01 pages: extension: .txt txt: ./txt/cord-301167-101lnq4f.txt cache: ./cache/cord-301167-101lnq4f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301167-101lnq4f.txt' === file2bib.sh === id: cord-302871-x3mjov5l author: Ribeiro, Juliane title: Extra-intestinal detection of canine kobuvirus in a puppy from Southern Brazil date: 2016-11-25 pages: extension: .txt txt: ./txt/cord-302871-x3mjov5l.txt cache: ./cache/cord-302871-x3mjov5l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-302871-x3mjov5l.txt' === file2bib.sh === id: cord-301430-gzou8b9k author: Beier, D. title: Establishment of a new bovine leukosis virus producing cell line date: 2004-08-17 pages: extension: .txt txt: ./txt/cord-301430-gzou8b9k.txt cache: ./cache/cord-301430-gzou8b9k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301430-gzou8b9k.txt' === file2bib.sh === id: cord-301066-62qe4fb0 author: Chiu, Susan S. title: Human Coronavirus NL63 Infection and Other Coronavirus Infections in Children Hospitalized with Acute Respiratory Disease in Hong Kong, China date: 2005-06-15 pages: extension: .txt txt: ./txt/cord-301066-62qe4fb0.txt cache: ./cache/cord-301066-62qe4fb0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301066-62qe4fb0.txt' === file2bib.sh === id: cord-298697-v1qdizwx author: Chang, Jia Jin Marc title: Takeaways from Mobile DNA Barcoding with BentoLab and MinION date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-298697-v1qdizwx.txt cache: ./cache/cord-298697-v1qdizwx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298697-v1qdizwx.txt' === file2bib.sh === id: cord-300338-duhyb754 author: Urashima, Mitsuyoshi title: BCG Vaccination and Mortality of COVID-19 across 173 Countries: An Ecological Study date: 2020-08-03 pages: extension: .txt txt: ./txt/cord-300338-duhyb754.txt cache: ./cache/cord-300338-duhyb754.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300338-duhyb754.txt' === file2bib.sh === id: cord-292928-a4bn30ul author: Ghosh, Bipasha title: Review of bioaerosols in indoor environment with special reference to sampling, analysis and control mechanisms date: 2015-10-03 pages: extension: .txt txt: ./txt/cord-292928-a4bn30ul.txt cache: ./cache/cord-292928-a4bn30ul.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-292928-a4bn30ul.txt' === file2bib.sh === id: cord-302207-ljpfgih2 author: Lichtmannsperger, Katharina title: Molecular characterization of Giardia intestinalis and Cryptosporidium parvum from calves with diarrhoea in Austria and evaluation of point-of-care tests date: 2019-07-12 pages: extension: .txt txt: ./txt/cord-302207-ljpfgih2.txt cache: ./cache/cord-302207-ljpfgih2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-302207-ljpfgih2.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 16373 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-298805-ntpm68cg author: Otašević, S. title: Non-culture based assays for the detection of fungal pathogens date: 2018-03-29 pages: extension: .txt txt: ./txt/cord-298805-ntpm68cg.txt cache: ./cache/cord-298805-ntpm68cg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-298805-ntpm68cg.txt' === file2bib.sh === id: cord-301102-jbjysyqm author: Priestnall, Simon L. title: Quantification of mRNA encoding cytokines and chemokines and assessment of ciliary function in canine tracheal epithelium during infection with canine respiratory coronavirus (CRCoV) date: 2009-01-15 pages: extension: .txt txt: ./txt/cord-301102-jbjysyqm.txt cache: ./cache/cord-301102-jbjysyqm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301102-jbjysyqm.txt' === file2bib.sh === id: cord-298998-n5rhhzc9 author: Vashee, Sanjay title: Cloning, Assembly, and Modification of the Primary Human Cytomegalovirus Isolate Toledo by Yeast-Based Transformation-Associated Recombination date: 2017-10-04 pages: extension: .txt txt: ./txt/cord-298998-n5rhhzc9.txt cache: ./cache/cord-298998-n5rhhzc9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298998-n5rhhzc9.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 16708 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 16705 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 17016 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-303289-qoukiqr7 author: Hemida, M. G. title: Coronavirus infections in horses in Saudi Arabia and Oman date: 2017-03-13 pages: extension: .txt txt: ./txt/cord-303289-qoukiqr7.txt cache: ./cache/cord-303289-qoukiqr7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303289-qoukiqr7.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 14727 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-301823-fbeb1nw1 author: Sridhar, Sushmita title: A blueprint for the implementation of a validated approach for the detection of SARS-Cov2 in clinical samples in academic facilities date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-301823-fbeb1nw1.txt cache: ./cache/cord-301823-fbeb1nw1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301823-fbeb1nw1.txt' === file2bib.sh === id: cord-303818-z3js3mr4 author: Chen, Huixin title: Development and Evaluation of a SYBR Green–Based Real-Time Multiplex RT-PCR Assay for Simultaneous Detection and Serotyping of Dengue and Chikungunya Viruses date: 2015-10-11 pages: extension: .txt txt: ./txt/cord-303818-z3js3mr4.txt cache: ./cache/cord-303818-z3js3mr4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-303818-z3js3mr4.txt' === file2bib.sh === id: cord-302713-h3aoag4y author: Jauréguiberry, Stéphane title: Clinical and Microbiological Evaluation of Travel‐Associated Respiratory Tract Infections in Travelers Returning From Countries Affected by Pandemic A(H1N1) 2009 Influenza date: 2011-12-08 pages: extension: .txt txt: ./txt/cord-302713-h3aoag4y.txt cache: ./cache/cord-302713-h3aoag4y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302713-h3aoag4y.txt' === file2bib.sh === id: cord-302819-oj33i2ma author: Pasick, J title: Investigation into the Role of Potentially Contaminated Feed as a Source of the First-Detected Outbreaks of Porcine Epidemic Diarrhea in Canada date: 2014-08-07 pages: extension: .txt txt: ./txt/cord-302819-oj33i2ma.txt cache: ./cache/cord-302819-oj33i2ma.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-302819-oj33i2ma.txt' === file2bib.sh === id: cord-305025-pqye1ebh author: Sharifi, Majid title: Rapid diagnostics of coronavirus disease 2019 in early stages using nanobiosensors: challenges and opportunities date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-305025-pqye1ebh.txt cache: ./cache/cord-305025-pqye1ebh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305025-pqye1ebh.txt' === file2bib.sh === id: cord-302296-7ge92p69 author: Lilleeng, Einar title: Comparison of intestinal gene expression in Atlantic cod (Gadus morhua) fed standard fish meal or soybean meal by means of suppression subtractive hybridization and real-time PCR date: 2007-07-03 pages: extension: .txt txt: ./txt/cord-302296-7ge92p69.txt cache: ./cache/cord-302296-7ge92p69.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302296-7ge92p69.txt' === file2bib.sh === id: cord-302503-7s9f8wje author: Fu, Yuguang title: Rapid and efficient detection methods of pathogenic swine enteric coronaviruses date: 2020-05-19 pages: extension: .txt txt: ./txt/cord-302503-7s9f8wje.txt cache: ./cache/cord-302503-7s9f8wje.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-302503-7s9f8wje.txt' === file2bib.sh === id: cord-303588-bwllypvq author: Ababneh, Mustafa title: High-resolution melting curve analysis for infectious bronchitis virus strain differentiation date: 2020-03-03 pages: extension: .txt txt: ./txt/cord-303588-bwllypvq.txt cache: ./cache/cord-303588-bwllypvq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303588-bwllypvq.txt' === file2bib.sh === id: cord-302486-z36hcvrx author: Cobo, Fernando title: Diagnostic approaches for viruses and prions in stem cell banks date: 2006-03-30 pages: extension: .txt txt: ./txt/cord-302486-z36hcvrx.txt cache: ./cache/cord-302486-z36hcvrx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-302486-z36hcvrx.txt' === file2bib.sh === id: cord-303665-l57e54hu author: Lahrich, S. title: Review on the contamination of wastewater by COVID-19 virus: Impact and treatment date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-303665-l57e54hu.txt cache: ./cache/cord-303665-l57e54hu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-303665-l57e54hu.txt' === file2bib.sh === id: cord-306396-wci56l0c author: Kim, Jayoung title: Evaluation of an Immunochromatographic Assay for the Rapid and Simultaneous Detection of Rotavirus and Adenovirus in Stool Samples date: 2014-04-08 pages: extension: .txt txt: ./txt/cord-306396-wci56l0c.txt cache: ./cache/cord-306396-wci56l0c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306396-wci56l0c.txt' === file2bib.sh === id: cord-305462-2wz1f6k6 author: Beckham, J. David title: Respiratory viral infections in patients with chronic, obstructive pulmonary disease date: 2004-09-22 pages: extension: .txt txt: ./txt/cord-305462-2wz1f6k6.txt cache: ./cache/cord-305462-2wz1f6k6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305462-2wz1f6k6.txt' === file2bib.sh === id: cord-304044-i1ikf96b author: Wu, Yue title: Inhibition of white spot syndrome virus in Litopenaeus vannamei shrimp by sequence-specific siRNA date: 2007-10-03 pages: extension: .txt txt: ./txt/cord-304044-i1ikf96b.txt cache: ./cache/cord-304044-i1ikf96b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-304044-i1ikf96b.txt' === file2bib.sh === id: cord-302459-grs2x26l author: Matin, Farhana title: A Plasma Biomarker Panel of Four MicroRNAs for the Diagnosis of Prostate Cancer date: 2018-04-27 pages: extension: .txt txt: ./txt/cord-302459-grs2x26l.txt cache: ./cache/cord-302459-grs2x26l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-302459-grs2x26l.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 18677 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 18971 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 18402 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 18671 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 18942 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-023017-k6edtg58 author: nan title: AASLD Abstracts (pp. 282A–382A) date: 2006-02-10 pages: extension: .txt txt: ./txt/cord-023017-k6edtg58.txt cache: ./cache/cord-023017-k6edtg58.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-023017-k6edtg58.txt' === file2bib.sh === id: cord-304913-qb9zeazk author: Thibivilliers, Sandra title: Generation of Phaseolus vulgaris ESTs and investigation of their regulation upon Uromyces appendiculatus infection date: 2009-04-27 pages: extension: .txt txt: ./txt/cord-304913-qb9zeazk.txt cache: ./cache/cord-304913-qb9zeazk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304913-qb9zeazk.txt' === file2bib.sh === id: cord-305399-98sqovwb author: Li, Hao title: Development of a reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for the detection of porcine pegivirus date: 2019-04-22 pages: extension: .txt txt: ./txt/cord-305399-98sqovwb.txt cache: ./cache/cord-305399-98sqovwb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305399-98sqovwb.txt' === file2bib.sh === id: cord-305059-8z54lw2d author: Qu, Jie-Ming title: Chapter 4 Diagnosis of COVID-19 date: 2021-12-31 pages: extension: .txt txt: ./txt/cord-305059-8z54lw2d.txt cache: ./cache/cord-305059-8z54lw2d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-305059-8z54lw2d.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 18223 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 19049 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 19130 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 19241 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-305872-66vij492 author: Caasi, Donna Ria J. title: A multi-target, non-infectious and clonable artificial positive control for routine PCR-based assays date: 2013-09-05 pages: extension: .txt txt: ./txt/cord-305872-66vij492.txt cache: ./cache/cord-305872-66vij492.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305872-66vij492.txt' === file2bib.sh === id: cord-305475-lhi0hcki author: Risku, Minna title: Human bocavirus types 1, 2 and 3 in acute gastroenteritis of childhood date: 2012-05-24 pages: extension: .txt txt: ./txt/cord-305475-lhi0hcki.txt cache: ./cache/cord-305475-lhi0hcki.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305475-lhi0hcki.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 19562 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 19386 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-307070-tqxvu3pu author: Iqbal, Phool title: Should We Rely on Screening Tests for Further Management Alone in Polymerase Chain Reaction Negative COVID-19 Patients? A Case Series date: 2020-09-20 pages: extension: .txt txt: ./txt/cord-307070-tqxvu3pu.txt cache: ./cache/cord-307070-tqxvu3pu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307070-tqxvu3pu.txt' === file2bib.sh === id: cord-306682-01q775up author: Vijgen, Leen title: Identification of six new polymorphisms in the human coronavirus 229E receptor gene (aminopeptidase N/CD13)() date: 2004-06-22 pages: extension: .txt txt: ./txt/cord-306682-01q775up.txt cache: ./cache/cord-306682-01q775up.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-306682-01q775up.txt' === file2bib.sh === id: cord-307261-0a3iztns author: Hayden, Randall T. title: Comparison of two broadly multiplexed PCR systems for viral detection in clinical respiratory tract specimens from immunocompromised children date: 2012-01-30 pages: extension: .txt txt: ./txt/cord-307261-0a3iztns.txt cache: ./cache/cord-307261-0a3iztns.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307261-0a3iztns.txt' === file2bib.sh === id: cord-306605-mnafslqw author: Gibson, CS title: Fetal exposure to herpesviruses may be associated with pregnancy‐induced hypertensive disorders and preterm birth in a Caucasian population date: 2008-02-06 pages: extension: .txt txt: ./txt/cord-306605-mnafslqw.txt cache: ./cache/cord-306605-mnafslqw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-306605-mnafslqw.txt' === file2bib.sh === id: cord-300399-21xozruq author: Jayamohan, Harikrishnan title: SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations date: 2020-10-18 pages: extension: .txt txt: ./txt/cord-300399-21xozruq.txt cache: ./cache/cord-300399-21xozruq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-300399-21xozruq.txt' === file2bib.sh === id: cord-305657-ayqxesiv author: Kalra, Mannudeep K. title: Chest CT practice and protocols for COVID-19 from radiation dose management perspective date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-305657-ayqxesiv.txt cache: ./cache/cord-305657-ayqxesiv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305657-ayqxesiv.txt' === file2bib.sh === id: cord-305336-wxiazglk author: Li, Ji Lian title: Systemic Spread and Propagation of a Plant-Pathogenic Virus in European Honeybees, Apis mellifera date: 2014-01-21 pages: extension: .txt txt: ./txt/cord-305336-wxiazglk.txt cache: ./cache/cord-305336-wxiazglk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305336-wxiazglk.txt' === file2bib.sh === id: cord-305694-qzf425lw author: Andrés-Lasheras, Sara title: Preliminary studies on isolates of Clostridium difficile from dogs and exotic pets date: 2018-03-09 pages: extension: .txt txt: ./txt/cord-305694-qzf425lw.txt cache: ./cache/cord-305694-qzf425lw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305694-qzf425lw.txt' === file2bib.sh === id: cord-307068-360qs3ov author: Hagiwara, Masanori title: Loop‐mediated isothermal amplification method for detection of human papillomavirus type 6, 11, 16, and 18 date: 2007-03-26 pages: extension: .txt txt: ./txt/cord-307068-360qs3ov.txt cache: ./cache/cord-307068-360qs3ov.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307068-360qs3ov.txt' === file2bib.sh === id: cord-306829-88nihy7q author: Sharif, Saeed title: Diagnostic Methods for Feline Coronavirus: A Review date: 2010-07-28 pages: extension: .txt txt: ./txt/cord-306829-88nihy7q.txt cache: ./cache/cord-306829-88nihy7q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-306829-88nihy7q.txt' === file2bib.sh === id: cord-307602-2cmgu7rf author: McErlean, P. title: Characterisation of a newly identified human rhinovirus, HRV-QPM, discovered in infants with bronchiolitis date: 2007-05-07 pages: extension: .txt txt: ./txt/cord-307602-2cmgu7rf.txt cache: ./cache/cord-307602-2cmgu7rf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307602-2cmgu7rf.txt' === file2bib.sh === id: cord-306278-c4q4la5c author: Esposito, Susanna title: Epidemiology and Clinical Characteristics of Respiratory Infections Due to Adenovirus in Children Living in Milan, Italy, during 2013 and 2014 date: 2016-04-05 pages: extension: .txt txt: ./txt/cord-306278-c4q4la5c.txt cache: ./cache/cord-306278-c4q4la5c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-306278-c4q4la5c.txt' === file2bib.sh === id: cord-307702-n74wvika author: Durant, Thomas J S title: Impact of COVID-19 Pandemic on Laboratory Utilization date: 2020-07-14 pages: extension: .txt txt: ./txt/cord-307702-n74wvika.txt cache: ./cache/cord-307702-n74wvika.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-307702-n74wvika.txt' === file2bib.sh === id: cord-308315-g6udfu2a author: Decaro, Nicola title: Characterisation of bubaline coronavirus strains associated with gastroenteritis in water buffalo (Bubalus bubalis) calves date: 2010-10-26 pages: extension: .txt txt: ./txt/cord-308315-g6udfu2a.txt cache: ./cache/cord-308315-g6udfu2a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-308315-g6udfu2a.txt' === file2bib.sh === id: cord-308945-i2agpvhk author: Phipps, William S title: SARS-CoV-2 Antibody Responses Do Not Predict COVID-19 Disease Severity date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-308945-i2agpvhk.txt cache: ./cache/cord-308945-i2agpvhk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308945-i2agpvhk.txt' === file2bib.sh === id: cord-306135-pt4jsr6d author: Chan, Kamfai title: A Rapid and Low-Cost PCR Thermal Cycler for Infectious Disease Diagnostics date: 2016-02-12 pages: extension: .txt txt: ./txt/cord-306135-pt4jsr6d.txt cache: ./cache/cord-306135-pt4jsr6d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-306135-pt4jsr6d.txt' === file2bib.sh === id: cord-307758-a4sgt66g author: Hong, Ching-Ye title: Acute respiratory symptoms in adults in general practice date: 2004-06-17 pages: extension: .txt txt: ./txt/cord-307758-a4sgt66g.txt cache: ./cache/cord-307758-a4sgt66g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-307758-a4sgt66g.txt' === file2bib.sh === id: cord-304058-i8cywew0 author: Pfefferle, Susanne title: Reverse genetic characterization of the natural genomic deletion in SARS-Coronavirus strain Frankfurt-1 open reading frame 7b reveals an attenuating function of the 7b protein in-vitro and in-vivo date: 2009-08-24 pages: extension: .txt txt: ./txt/cord-304058-i8cywew0.txt cache: ./cache/cord-304058-i8cywew0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-304058-i8cywew0.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 20871 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 21047 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 21466 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-306780-9xelf8oh author: Dale, Timothy D. title: Enhancement of wildlife disease surveillance using multiplex quantitative PCR: development of qPCR assays for major pathogens in UK squirrel populations date: 2016-07-28 pages: extension: .txt txt: ./txt/cord-306780-9xelf8oh.txt cache: ./cache/cord-306780-9xelf8oh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-306780-9xelf8oh.txt' === file2bib.sh === id: cord-310096-a242g5kg author: Yokota, I. title: Mass screening of asymptomatic persons for SARS-CoV-2 using saliva date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-310096-a242g5kg.txt cache: ./cache/cord-310096-a242g5kg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310096-a242g5kg.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 21345 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-309540-4pk5tq5w author: Brandsma, E. title: Rapid, sensitive and specific SARS coronavirus-2 detection: a multi-center comparison between standard qRT-PCR and CRISPR based DETECTR. date: 2020-07-29 pages: extension: .txt txt: ./txt/cord-309540-4pk5tq5w.txt cache: ./cache/cord-309540-4pk5tq5w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-309540-4pk5tq5w.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 21359 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 21627 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 1526 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-308344-ao9z00t7 author: Diep, Nguyen Van title: Novel Porcine Epidemic Diarrhea Virus (PEDV) Variants with Large Deletions in the Spike (S) Gene Coexist with PEDV Strains Possessing an Intact S Gene in Domestic Pigs in Japan: A New Disease Situation date: 2017-01-17 pages: extension: .txt txt: ./txt/cord-308344-ao9z00t7.txt cache: ./cache/cord-308344-ao9z00t7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308344-ao9z00t7.txt' === file2bib.sh === id: cord-307338-4nta9b6w author: Slomka, Marek J. title: Original Article: Real time reverse transcription (RRT)‐polymerase chain reaction (PCR) methods for detection of pandemic (H1N1) 2009 influenza virus and European swine influenza A virus infections in pigs date: 2010-08-17 pages: extension: .txt txt: ./txt/cord-307338-4nta9b6w.txt cache: ./cache/cord-307338-4nta9b6w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-307338-4nta9b6w.txt' === file2bib.sh === id: cord-309107-2xzam3x9 author: Emmler, Laura title: Feline coronavirus with and without spike gene mutations detected by real-time RT-PCRs in cats with feline infectious peritonitis date: 2019-11-15 pages: extension: .txt txt: ./txt/cord-309107-2xzam3x9.txt cache: ./cache/cord-309107-2xzam3x9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-309107-2xzam3x9.txt' === file2bib.sh === id: cord-310501-ro55cqxw author: de Castro, Alessandra MMG title: Detection of porcine circovirus genotypes 2a and 2b in aborted foetuses from infected swine herds in the State of São Paulo, Brazil date: 2012-05-03 pages: extension: .txt txt: ./txt/cord-310501-ro55cqxw.txt cache: ./cache/cord-310501-ro55cqxw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310501-ro55cqxw.txt' === file2bib.sh === id: cord-308655-zntwwqod author: Dabisch-Ruthe, Mareike title: Comparison of three multiplex PCR assays for the detection of respiratory viral infections: evaluation of xTAG respiratory virus panel fast assay, RespiFinder 19 assay and RespiFinder SMART 22 assay date: 2012-07-24 pages: extension: .txt txt: ./txt/cord-308655-zntwwqod.txt cache: ./cache/cord-308655-zntwwqod.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-308655-zntwwqod.txt' === file2bib.sh === id: cord-308422-ueyaw8pd author: Wong, Christopher W title: Optimization and clinical validation of a pathogen detection microarray date: 2007-05-28 pages: extension: .txt txt: ./txt/cord-308422-ueyaw8pd.txt cache: ./cache/cord-308422-ueyaw8pd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-308422-ueyaw8pd.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 22025 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 22112 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 22187 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-311204-fc12f845 author: Zhou, Ling title: Full-length genomic characterization and molecular evolution of canine parvovirus in China date: 2016-04-02 pages: extension: .txt txt: ./txt/cord-311204-fc12f845.txt cache: ./cache/cord-311204-fc12f845.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311204-fc12f845.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 22181 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-310748-ao29zx1u author: Banner, Lisa R. title: Random nature of coronavirus RNA recombination in the absence of selection pressure date: 1991-11-30 pages: extension: .txt txt: ./txt/cord-310748-ao29zx1u.txt cache: ./cache/cord-310748-ao29zx1u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310748-ao29zx1u.txt' === file2bib.sh === id: cord-311439-y9jwu38r author: Bao, Changjun title: Possible Spread of adenovirus type 3 from poultry to humans: indirect evidence from an outbreak in China date: 2007-09-30 pages: extension: .txt txt: ./txt/cord-311439-y9jwu38r.txt cache: ./cache/cord-311439-y9jwu38r.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-311439-y9jwu38r.txt' === file2bib.sh === id: cord-307874-0obomty2 author: Pardon, Bart title: Bovine Respiratory Disease Diagnosis: What Progress Has Been Made in Infectious Diagnosis? date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-307874-0obomty2.txt cache: ./cache/cord-307874-0obomty2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307874-0obomty2.txt' === file2bib.sh === id: cord-311410-lgqup9ug author: Ayers, M. title: A single tube RT-PCR assay for the detection of mosquito-borne flaviviruses date: 2006-05-02 pages: extension: .txt txt: ./txt/cord-311410-lgqup9ug.txt cache: ./cache/cord-311410-lgqup9ug.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311410-lgqup9ug.txt' === file2bib.sh === id: cord-311801-m2otfdjw author: Wang, Pei title: Combination of Serological Total Antibody and RT-PCR Test for Detection of SARS-CoV-2 Infections date: 2020-06-15 pages: extension: .txt txt: ./txt/cord-311801-m2otfdjw.txt cache: ./cache/cord-311801-m2otfdjw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311801-m2otfdjw.txt' === file2bib.sh === id: cord-304720-0lgup7yj author: Robbins, R.C. title: Swine Diseases and Disorders date: 2014-08-21 pages: extension: .txt txt: ./txt/cord-304720-0lgup7yj.txt cache: ./cache/cord-304720-0lgup7yj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 10 resourceName b'cord-304720-0lgup7yj.txt' === file2bib.sh === id: cord-311639-zij2wbzs author: Kim, Hyun Soo title: Evaluation of the SD Bioline Norovirus rapid immunochromatography test using fecal specimens from Korean gastroenteritis patients date: 2012-08-30 pages: extension: .txt txt: ./txt/cord-311639-zij2wbzs.txt cache: ./cache/cord-311639-zij2wbzs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311639-zij2wbzs.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 23090 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 23075 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-312024-qdgqif5j author: Talbot, H. Keipp title: The Diagnosis of Viral Respiratory Disease in Older Adults date: 2010-02-01 pages: extension: .txt txt: ./txt/cord-312024-qdgqif5j.txt cache: ./cache/cord-312024-qdgqif5j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312024-qdgqif5j.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 23072 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-312139-g1hczx54 author: Liu, Wei title: Non-specific Primers Reveal False-negative Risk in Detection of COVID-19 Infections date: 2020-04-11 pages: extension: .txt txt: ./txt/cord-312139-g1hczx54.txt cache: ./cache/cord-312139-g1hczx54.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312139-g1hczx54.txt' === file2bib.sh === id: cord-310771-tnwfp1je author: Revilla-Fernández, Sandra title: The use of endogenous and exogenous reference RNAs for qualitative and quantitative detection of PRRSV in porcine semen date: 2005-02-23 pages: extension: .txt txt: ./txt/cord-310771-tnwfp1je.txt cache: ./cache/cord-310771-tnwfp1je.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310771-tnwfp1je.txt' === file2bib.sh === id: cord-313375-rs3jjiuj author: Panning, Marcus title: Singleplex real-time RT-PCR for detection of influenza A virus and simultaneous differentiation of A/H1N1v and evaluation of the RealStar influenza kit date: 2010-11-13 pages: extension: .txt txt: ./txt/cord-313375-rs3jjiuj.txt cache: ./cache/cord-313375-rs3jjiuj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313375-rs3jjiuj.txt' === file2bib.sh === id: cord-313107-6cfenpxm author: Singh, Anirudh K. title: Evaluation of pooled sample analysis strategy in expediting case detection in areas with emerging outbreaks of COVID-19: A pilot study date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-313107-6cfenpxm.txt cache: ./cache/cord-313107-6cfenpxm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313107-6cfenpxm.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 23559 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-312161-egwo19oc author: Aw, Tiong Gim title: Detection of pathogens in water: from phylochips to qPCR to pyrosequencing date: 2011-12-05 pages: extension: .txt txt: ./txt/cord-312161-egwo19oc.txt cache: ./cache/cord-312161-egwo19oc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312161-egwo19oc.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 23272 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-312222-aw5849rc author: Österdahl, Marc F. title: Detecting SARS-CoV-2 at point of care: preliminary data comparing loop-mediated isothermal amplification (LAMP) to polymerase chain reaction (PCR) date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-312222-aw5849rc.txt cache: ./cache/cord-312222-aw5849rc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312222-aw5849rc.txt' === file2bib.sh === id: cord-311982-wkg56xeq author: Dye, Charlotte title: Genomic RNA sequence of feline coronavirus strain FCoV C1Je date: 2007-06-17 pages: extension: .txt txt: ./txt/cord-311982-wkg56xeq.txt cache: ./cache/cord-311982-wkg56xeq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311982-wkg56xeq.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 23696 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 23770 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-312197-d5d8amk7 author: Edmond, Karen title: New Approaches to Preventing, Diagnosing, and Treating Neonatal Sepsis date: 2010-03-09 pages: extension: .txt txt: ./txt/cord-312197-d5d8amk7.txt cache: ./cache/cord-312197-d5d8amk7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-312197-d5d8amk7.txt' === file2bib.sh === id: cord-314386-cxq9v218 author: Nitsche, Andreas title: SARS Coronavirus Detection date: 2004-07-17 pages: extension: .txt txt: ./txt/cord-314386-cxq9v218.txt cache: ./cache/cord-314386-cxq9v218.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314386-cxq9v218.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 23923 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 23919 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-312240-0k8y86pf author: Schlaberg, Robert title: Viral Pathogen Detection by Metagenomics and Pan-Viral Group Polymerase Chain Reaction in Children With Pneumonia Lacking Identifiable Etiology date: 2017-05-01 pages: extension: .txt txt: ./txt/cord-312240-0k8y86pf.txt cache: ./cache/cord-312240-0k8y86pf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312240-0k8y86pf.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 24080 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 24188 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-316173-ocdlh310 author: LIU, Dafei title: One-step triplex PCR/RT-PCR to detect canine distemper virus, canine parvovirus and canine kobuvirus date: 2018-01-23 pages: extension: .txt txt: ./txt/cord-316173-ocdlh310.txt cache: ./cache/cord-316173-ocdlh310.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-316173-ocdlh310.txt' === file2bib.sh === id: cord-315476-7rdiesav author: Peret, Teresa C. T. title: Characterization of Human Metapneumoviruses Isolated from Patients in North America date: 2002-06-01 pages: extension: .txt txt: ./txt/cord-315476-7rdiesav.txt cache: ./cache/cord-315476-7rdiesav.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315476-7rdiesav.txt' === file2bib.sh === id: cord-312456-6lxc2rj2 author: Soltan, Mohamed A. title: Comparison of electron microscopy, ELISA, real time RT-PCR and insulated isothermal RT-PCR for the detection of Rotavirus group A (RVA) in feces of different animal species date: 2016-05-11 pages: extension: .txt txt: ./txt/cord-312456-6lxc2rj2.txt cache: ./cache/cord-312456-6lxc2rj2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312456-6lxc2rj2.txt' === file2bib.sh === id: cord-309083-ew9cwiw0 author: Su, Hang title: Cyprinid viral diseases and vaccine development date: 2018-09-07 pages: extension: .txt txt: ./txt/cord-309083-ew9cwiw0.txt cache: ./cache/cord-309083-ew9cwiw0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-309083-ew9cwiw0.txt' === file2bib.sh === id: cord-314051-dr27bsvt author: Lother, Sylvain A. title: Preoperative SARS-CoV-2 screening: Can it really rule out COVID-19? date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-314051-dr27bsvt.txt cache: ./cache/cord-314051-dr27bsvt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314051-dr27bsvt.txt' === file2bib.sh === id: cord-312996-qzu8pkyt author: Iles, R. K. title: A clinical MALDI-ToF Mass spectrometry assay for SARS-CoV-2: Rational design and multi-disciplinary team work. date: 2020-08-22 pages: extension: .txt txt: ./txt/cord-312996-qzu8pkyt.txt cache: ./cache/cord-312996-qzu8pkyt.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312996-qzu8pkyt.txt' === file2bib.sh === id: cord-317129-wa1j2f6b author: Zhang, Jia title: De Novo synthesis of PCR templates for the development of SARS diagnostic assay date: 2003 pages: extension: .txt txt: ./txt/cord-317129-wa1j2f6b.txt cache: ./cache/cord-317129-wa1j2f6b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317129-wa1j2f6b.txt' === file2bib.sh === id: cord-314069-8dxzf2ip author: Dongliu, Yuan title: Outbreak of acute febrile respiratory illness caused by human adenovirus B P14H11F14 in a military training camp in Shandong China date: 2016-06-28 pages: extension: .txt txt: ./txt/cord-314069-8dxzf2ip.txt cache: ./cache/cord-314069-8dxzf2ip.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314069-8dxzf2ip.txt' === file2bib.sh === id: cord-314986-uhpe69k0 author: Cai, Quan title: A model based on CT radiomic features for predicting RT-PCR becoming negative in coronavirus disease 2019 (COVID-19) patients date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-314986-uhpe69k0.txt cache: ./cache/cord-314986-uhpe69k0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-314986-uhpe69k0.txt' === file2bib.sh === id: cord-311748-yr2ep7uf author: Kahyaoglu, L. N. title: 11 New approaches in microbial pathogen detection date: 2013-12-31 pages: extension: .txt txt: ./txt/cord-311748-yr2ep7uf.txt cache: ./cache/cord-311748-yr2ep7uf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-311748-yr2ep7uf.txt' === file2bib.sh === id: cord-314937-jrxu65bl author: Kuwelker, K. title: High attack rates of SARS-CoV-2 infection through household-transmission: a prospective study date: 2020-11-04 pages: extension: .txt txt: ./txt/cord-314937-jrxu65bl.txt cache: ./cache/cord-314937-jrxu65bl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-314937-jrxu65bl.txt' === file2bib.sh === id: cord-313506-6bb4q7nv author: Sano, Akiko title: Physiological Level Production of Antigen-Specific Human Immunoglobulin in Cloned Transchromosomic Cattle date: 2013-10-24 pages: extension: .txt txt: ./txt/cord-313506-6bb4q7nv.txt cache: ./cache/cord-313506-6bb4q7nv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-313506-6bb4q7nv.txt' === file2bib.sh === id: cord-316250-w0nl88jz author: Yang, Falong title: Selection of reference genes for quantitative real-time PCR analysis in chicken embryo fibroblasts infected with avian leukosis virus subgroup J date: 2013-10-07 pages: extension: .txt txt: ./txt/cord-316250-w0nl88jz.txt cache: ./cache/cord-316250-w0nl88jz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316250-w0nl88jz.txt' === file2bib.sh === id: cord-318013-5om35tu8 author: Marie, Tré-Hardy title: The role of serology for COVID-19 control: Population, kinetics and test performance do matter date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-318013-5om35tu8.txt cache: ./cache/cord-318013-5om35tu8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318013-5om35tu8.txt' === file2bib.sh === id: cord-315780-uhi66unn author: Paton, David title: Detection of transmissible gastroenteritis virus by RT-PCR and differentiation from porcine respiratory coronavirus date: 1997-07-31 pages: extension: .txt txt: ./txt/cord-315780-uhi66unn.txt cache: ./cache/cord-315780-uhi66unn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315780-uhi66unn.txt' === file2bib.sh === id: cord-315949-7id5mitl author: Sentilhes, Anne‐Charlotte title: Respiratory virus infections in hospitalized children and adults in Lao PDR date: 2013-06-25 pages: extension: .txt txt: ./txt/cord-315949-7id5mitl.txt cache: ./cache/cord-315949-7id5mitl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315949-7id5mitl.txt' === file2bib.sh === id: cord-317049-q3bvmkf7 author: Forde, Justin J. title: Yield and Implications of Pre-Procedural COVID-19 PCR Testing on Routine Endoscopic Practice date: 2020-05-25 pages: extension: .txt txt: ./txt/cord-317049-q3bvmkf7.txt cache: ./cache/cord-317049-q3bvmkf7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-317049-q3bvmkf7.txt' === file2bib.sh === id: cord-314201-6njwigco author: Maher-Sturgess, Sheryl L title: Universal primers that amplify RNA from all three flavivirus subgroups date: 2008-01-24 pages: extension: .txt txt: ./txt/cord-314201-6njwigco.txt cache: ./cache/cord-314201-6njwigco.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314201-6njwigco.txt' === file2bib.sh === id: cord-313676-6rebpe57 author: De la Torre, David I. title: Enteric Virus Diversity Examined by Molecular Methods in Brazilian Poultry Flocks date: 2018-03-29 pages: extension: .txt txt: ./txt/cord-313676-6rebpe57.txt cache: ./cache/cord-313676-6rebpe57.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313676-6rebpe57.txt' === file2bib.sh === id: cord-315541-tirod4t6 author: Henriques, Ana Margarida title: Development and validation of a real-time PCR for the detection and quantification of porcine circovirus type 2 date: 2018-07-17 pages: extension: .txt txt: ./txt/cord-315541-tirod4t6.txt cache: ./cache/cord-315541-tirod4t6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-315541-tirod4t6.txt' === file2bib.sh === id: cord-316295-x636ux34 author: Roth, Bernhard title: Isolation of influenza viruses in MDCK 33016PF cells and clearance of contaminating respiratory viruses date: 2012-01-11 pages: extension: .txt txt: ./txt/cord-316295-x636ux34.txt cache: ./cache/cord-316295-x636ux34.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316295-x636ux34.txt' === file2bib.sh === id: cord-316343-u1uup5da author: Luo, Yun title: Longitudinal Surveillance of Betacoronaviruses in Fruit Bats in Yunnan Province, China During 2009–2016 date: 2018-02-01 pages: extension: .txt txt: ./txt/cord-316343-u1uup5da.txt cache: ./cache/cord-316343-u1uup5da.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-316343-u1uup5da.txt' === file2bib.sh === id: cord-318991-tw7wgpsi author: Nair, A. title: A British Society of Thoracic Imaging statement: considerations in designing local imaging diagnostic algorithms for the COVID-19 pandemic date: 2020-05-31 pages: extension: .txt txt: ./txt/cord-318991-tw7wgpsi.txt cache: ./cache/cord-318991-tw7wgpsi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318991-tw7wgpsi.txt' === file2bib.sh === id: cord-312223-qgwzgazd author: Shafagati, Nazly title: The Use of NanoTrap Particles as a Sample Enrichment Method to Enhance the Detection of Rift Valley Fever Virus date: 2013-07-04 pages: extension: .txt txt: ./txt/cord-312223-qgwzgazd.txt cache: ./cache/cord-312223-qgwzgazd.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312223-qgwzgazd.txt' === file2bib.sh === id: cord-316932-fia1w9jt author: Ireland, D. C. title: Improved detection of rhinoviruses in nasal and throat swabs by seminested RT‐PCR date: 2005-12-07 pages: extension: .txt txt: ./txt/cord-316932-fia1w9jt.txt cache: ./cache/cord-316932-fia1w9jt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-316932-fia1w9jt.txt' === file2bib.sh === id: cord-316309-8xe7cg8q author: Lee, Wah Heng title: LOMA: A fast method to generate efficient tagged-random primers despite amplification bias of random PCR on pathogens date: 2008-09-10 pages: extension: .txt txt: ./txt/cord-316309-8xe7cg8q.txt cache: ./cache/cord-316309-8xe7cg8q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316309-8xe7cg8q.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26121 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26137 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26144 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-320085-n9i54wzh author: Pfefferle, Susanne title: Evaluation of a quantitative RT-PCR assay for the detection of the emerging coronavirus SARS-CoV-2 using a high throughput system date: 2020-03-05 pages: extension: .txt txt: ./txt/cord-320085-n9i54wzh.txt cache: ./cache/cord-320085-n9i54wzh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320085-n9i54wzh.txt' === file2bib.sh === id: cord-318341-0827d8to author: Kaushik, Sulochana title: In-vitro and in silico activity of Cyamopsis tetragonoloba (Gaur) L. supercritical extract against the dengue-2 virus date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-318341-0827d8to.txt cache: ./cache/cord-318341-0827d8to.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318341-0827d8to.txt' === file2bib.sh === id: cord-318392-r9bbomvk author: Woo, Patrick CY title: Coronavirus HKU15 in respiratory tract of pigs and first discovery of coronavirus quasispecies in 5′-untranslated region date: 2017-06-21 pages: extension: .txt txt: ./txt/cord-318392-r9bbomvk.txt cache: ./cache/cord-318392-r9bbomvk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318392-r9bbomvk.txt' === file2bib.sh === id: cord-316537-f5rto51t author: Loens, Katherine title: Mycoplasma pneumoniae: Current Knowledge on Nucleic Acid Amplification Techniques and Serological Diagnostics date: 2016-03-31 pages: extension: .txt txt: ./txt/cord-316537-f5rto51t.txt cache: ./cache/cord-316537-f5rto51t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-316537-f5rto51t.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26617 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26608 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26631 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26809 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-321361-6bkrt49b author: Chang, De title: Reply to Suri et al.: COVID-19 Real-Time RT-PCR: Does Positivity on Follow-up RT-PCR Always Imply Infectivity? date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-321361-6bkrt49b.txt cache: ./cache/cord-321361-6bkrt49b.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-321361-6bkrt49b.txt' === file2bib.sh === id: cord-320769-qcpua9ck author: Park, Su-Jin title: Molecular epidemiology of bovine toroviruses circulating in South Korea date: 2008-01-25 pages: extension: .txt txt: ./txt/cord-320769-qcpua9ck.txt cache: ./cache/cord-320769-qcpua9ck.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-320769-qcpua9ck.txt' === file2bib.sh === id: cord-319392-zg7gkf0j author: Yi, Li title: Development of a combined canine distemper virus specific RT-PCR protocol for the differentiation of infected and vaccinated animals (DIVA) and genetic characterization of the hemagglutinin gene of seven Chinese strains demonstrated in dogs date: 2011-11-18 pages: extension: .txt txt: ./txt/cord-319392-zg7gkf0j.txt cache: ./cache/cord-319392-zg7gkf0j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319392-zg7gkf0j.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26973 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 27390 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 27410 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-321076-kont2sff author: Yeo, Wee Song title: Cohort PCR Testing: A Strategic Method for Rapid SARS-CoV-2 Screening date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-321076-kont2sff.txt cache: ./cache/cord-321076-kont2sff.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-321076-kont2sff.txt' === file2bib.sh === id: cord-321074-7jfy8cn6 author: Caruso, Damiano title: Quantitative Chest CT analysis in discriminating COVID-19 from non-COVID-19 patients date: 2020-10-12 pages: extension: .txt txt: ./txt/cord-321074-7jfy8cn6.txt cache: ./cache/cord-321074-7jfy8cn6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321074-7jfy8cn6.txt' === file2bib.sh === id: cord-320617-ucm7wx8b author: B’Krong, Nguyen Thi Thuy Chinh title: Enterovirus serotypes in patients with central nervous system and respiratory infections in Viet Nam 1997–2010 date: 2018-04-12 pages: extension: .txt txt: ./txt/cord-320617-ucm7wx8b.txt cache: ./cache/cord-320617-ucm7wx8b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320617-ucm7wx8b.txt' === file2bib.sh === id: cord-320002-25ivll3q author: Mathew, Joseph L. title: Etiology of community acquired pneumonia among children in India: prospective, cohort study date: 2015-10-21 pages: extension: .txt txt: ./txt/cord-320002-25ivll3q.txt cache: ./cache/cord-320002-25ivll3q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320002-25ivll3q.txt' === file2bib.sh === id: cord-320787-dwyyjq6o author: La Rosa, Giuseppina title: First detection of SARS-CoV-2 in untreated wastewaters in Italy date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-320787-dwyyjq6o.txt cache: ./cache/cord-320787-dwyyjq6o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320787-dwyyjq6o.txt' === file2bib.sh === id: cord-321443-89o13sox author: Umazume, Takeshi title: Survey on the use of personal protective equipment and COVID‐19 testing of pregnant women in Japan date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-321443-89o13sox.txt cache: ./cache/cord-321443-89o13sox.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-321443-89o13sox.txt' === file2bib.sh === id: cord-321284-0y69n1ea author: El Kholy, A. A. title: The use of multiplex PCR for the diagnosis of viral severe acute respiratory infection in children: a high rate of co-detection during the winter season date: 2016-06-10 pages: extension: .txt txt: ./txt/cord-321284-0y69n1ea.txt cache: ./cache/cord-321284-0y69n1ea.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-321284-0y69n1ea.txt' === file2bib.sh === id: cord-014527-nvzfpntu author: nan title: Research Communications of the 25th ECVIM‐CA Congress date: 2015-11-09 pages: extension: .txt txt: ./txt/cord-014527-nvzfpntu.txt cache: ./cache/cord-014527-nvzfpntu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 16 resourceName b'cord-014527-nvzfpntu.txt' === file2bib.sh === id: cord-319970-1gu0a6cb author: Edin, Alicia title: Development and Laboratory Evaluation of a Real-Time PCR Assay for Detecting Viruses and Bacteria of Relevance for Community-Acquired Pneumonia date: 2015-03-13 pages: extension: .txt txt: ./txt/cord-319970-1gu0a6cb.txt cache: ./cache/cord-319970-1gu0a6cb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 7 resourceName b'cord-319970-1gu0a6cb.txt' === file2bib.sh === id: cord-319460-n4ezxnjc author: Bertasio, Cristina title: Porcine Epidemic Diarrhea Virus Shedding and Antibody Response in Swine Farms: A Longitudinal Study date: 2016-12-15 pages: extension: .txt txt: ./txt/cord-319460-n4ezxnjc.txt cache: ./cache/cord-319460-n4ezxnjc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319460-n4ezxnjc.txt' === file2bib.sh === id: cord-319845-oob2ktnz author: Proença-Modena, José Luiz title: Detection of Human Bocavirus mRNA in Respiratory Secretions Correlates with High Viral Load and Concurrent Diarrhea date: 2011-06-20 pages: extension: .txt txt: ./txt/cord-319845-oob2ktnz.txt cache: ./cache/cord-319845-oob2ktnz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-319845-oob2ktnz.txt' === file2bib.sh === id: cord-319921-uxtydu60 author: Meli, Marina L. title: Feline Leukemia Virus and Other Pathogens as Important Threats to the Survival of the Critically Endangered Iberian Lynx (Lynx pardinus) date: 2009-03-09 pages: extension: .txt txt: ./txt/cord-319921-uxtydu60.txt cache: ./cache/cord-319921-uxtydu60.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-319921-uxtydu60.txt' === file2bib.sh === id: cord-321855-7b1c2xdh author: Alshami, Alanoud title: Silent disease and loss of taste and smell are common manifestations of SARS-COV-2 infection in a quarantine facility: Saudi Arabia date: 2020-10-30 pages: extension: .txt txt: ./txt/cord-321855-7b1c2xdh.txt cache: ./cache/cord-321855-7b1c2xdh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-321855-7b1c2xdh.txt' === file2bib.sh === id: cord-320547-law20pmw author: Luchsinger, Vivian title: Comparison of Luminex xTAG® RVP fast assay and real time RT‐PCR for the detection of respiratory viruses in adults with community‐acquired pneumonia date: 2016-02-02 pages: extension: .txt txt: ./txt/cord-320547-law20pmw.txt cache: ./cache/cord-320547-law20pmw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320547-law20pmw.txt' === file2bib.sh === id: cord-324012-q2ilk6gs author: Inui, Ken title: A field‐deployable insulated isothermal RT‐PCR assay for identification of influenza A (H7N9) shows good performance in the laboratory date: 2019-09-05 pages: extension: .txt txt: ./txt/cord-324012-q2ilk6gs.txt cache: ./cache/cord-324012-q2ilk6gs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324012-q2ilk6gs.txt' === file2bib.sh === id: cord-319685-dw0qsl4s author: Porter, Emily title: Amino acid changes in the spike protein of feline coronavirus correlate with systemic spread of virus from the intestine and not with feline infectious peritonitis date: 2014-04-25 pages: extension: .txt txt: ./txt/cord-319685-dw0qsl4s.txt cache: ./cache/cord-319685-dw0qsl4s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319685-dw0qsl4s.txt' === file2bib.sh === id: cord-320854-ybah03kr author: Kongprajug, Akechai title: Suppression of PmRab11 inhibits YHV infection in Penaeus monodon date: 2017-05-17 pages: extension: .txt txt: ./txt/cord-320854-ybah03kr.txt cache: ./cache/cord-320854-ybah03kr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-320854-ybah03kr.txt' === file2bib.sh === id: cord-321181-bqdsfgdc author: Garitano, Ignacio title: Estimando el número de casos de COVID-19 mediante una herramienta web: resultados de la primera semana del proyecto "Covid-19 Trends" en Euskadi date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-321181-bqdsfgdc.txt cache: ./cache/cord-321181-bqdsfgdc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-321181-bqdsfgdc.txt' === file2bib.sh === id: cord-322184-kgv9f58a author: Sohn, Yujin title: Assessing Viral Shedding and Infectivity of Asymptomatic or Mildly Symptomatic Patients with COVID-19 in a Later Phase date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-322184-kgv9f58a.txt cache: ./cache/cord-322184-kgv9f58a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-322184-kgv9f58a.txt' === file2bib.sh === id: cord-313439-cadyykks author: Felten, Sandra title: Diagnosis of Feline Infectious Peritonitis: A Review of the Current Literature date: 2019-11-15 pages: extension: .txt txt: ./txt/cord-313439-cadyykks.txt cache: ./cache/cord-313439-cadyykks.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313439-cadyykks.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 29333 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 29143 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-322937-lakdi3x8 author: Kang, Xiao-ping title: A duplex real-time RT-PCR assay for detecting H5N1 avian influenza virus and pandemic H1N1 influenza virus date: 2010-06-02 pages: extension: .txt txt: ./txt/cord-322937-lakdi3x8.txt cache: ./cache/cord-322937-lakdi3x8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322937-lakdi3x8.txt' === file2bib.sh === id: cord-321514-knyw023l author: Bénet, Thomas title: Severity of Pneumonia in Under 5-Year-Old Children from Developing Countries: A Multicenter, Prospective, Observational Study date: 2017-07-12 pages: extension: .txt txt: ./txt/cord-321514-knyw023l.txt cache: ./cache/cord-321514-knyw023l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-321514-knyw023l.txt' === file2bib.sh === id: cord-323700-5awng7h1 author: Goggin, Rachel K. title: Comparative Viral Sampling in the Sinonasal Passages; Different Viruses at Different Sites date: 2018-09-19 pages: extension: .txt txt: ./txt/cord-323700-5awng7h1.txt cache: ./cache/cord-323700-5awng7h1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323700-5awng7h1.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 29277 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-322234-1zyy536y author: Lorusso, Alessio title: One-step real-time RT-PCR for pandemic influenza A virus (H1N1) 2009 matrix gene detection in swine samples date: 2009-12-17 pages: extension: .txt txt: ./txt/cord-322234-1zyy536y.txt cache: ./cache/cord-322234-1zyy536y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-322234-1zyy536y.txt' === file2bib.sh === id: cord-322391-tumpiid5 author: Freymuth, François title: Detection of viral, Chlamydia pneumoniae and Mycoplasma pneumoniae infections in exacerbations of asthma in children date: 1999-08-31 pages: extension: .txt txt: ./txt/cord-322391-tumpiid5.txt cache: ./cache/cord-322391-tumpiid5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-322391-tumpiid5.txt' === file2bib.sh === id: cord-322657-q4aeood2 author: Jartti, Tuomas title: Respiratory Picornaviruses and Respiratory Syncytial Virus as Causative Agents of Acute Expiratory Wheezing in Children date: 2004-06-17 pages: extension: .txt txt: ./txt/cord-322657-q4aeood2.txt cache: ./cache/cord-322657-q4aeood2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322657-q4aeood2.txt' === file2bib.sh === id: cord-322987-zv58s79r author: Zali, Alireza title: Correlation between Low-Dose Chest Computed Tomography and RT-PCR Results for the Diagnosis of COVID-19: A Report of 27824 Cases in Tehran, Iran date: 2020-09-21 pages: extension: .txt txt: ./txt/cord-322987-zv58s79r.txt cache: ./cache/cord-322987-zv58s79r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322987-zv58s79r.txt' === file2bib.sh === id: cord-322524-bq9ok8h1 author: Belongia, Edward A title: Clinical Features, Severity, and Incidence of RSV Illness During 12 Consecutive Seasons in a Community Cohort of Adults ≥60 Years Old date: 2018-11-27 pages: extension: .txt txt: ./txt/cord-322524-bq9ok8h1.txt cache: ./cache/cord-322524-bq9ok8h1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322524-bq9ok8h1.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 30384 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-320938-f526k9q1 author: Chen, Hongjun title: Partial and Full PCR-Based Reverse Genetics Strategy for Influenza Viruses date: 2012-09-28 pages: extension: .txt txt: ./txt/cord-320938-f526k9q1.txt cache: ./cache/cord-320938-f526k9q1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320938-f526k9q1.txt' === file2bib.sh === id: cord-324531-lpoelp91 author: Artesi, Maria title: A Recurrent Mutation at Position 26340 of SARS-CoV-2 Is Associated with Failure of the E Gene Quantitative Reverse Transcription-PCR Utilized in a Commercial Dual-Target Diagnostic Assay date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-324531-lpoelp91.txt cache: ./cache/cord-324531-lpoelp91.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324531-lpoelp91.txt' === file2bib.sh === id: cord-323963-whv88ggl author: Fan, Xiaofeng title: Efficient amplification and cloning of near full-length hepatitis C virus genome from clinical samples date: 2006-08-11 pages: extension: .txt txt: ./txt/cord-323963-whv88ggl.txt cache: ./cache/cord-323963-whv88ggl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-323963-whv88ggl.txt' === file2bib.sh === id: cord-325068-j1lfq60o author: Pene, Frédéric title: Coronavirus 229E-Related Pneumonia in Immunocompromised Patients date: 2003-10-01 pages: extension: .txt txt: ./txt/cord-325068-j1lfq60o.txt cache: ./cache/cord-325068-j1lfq60o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325068-j1lfq60o.txt' === file2bib.sh === id: cord-325736-gs9d8y55 author: Marin, J title: Persistence of Viruses in Upper Respiratory Tract of Children with Asthma date: 2000-07-31 pages: extension: .txt txt: ./txt/cord-325736-gs9d8y55.txt cache: ./cache/cord-325736-gs9d8y55.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325736-gs9d8y55.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 30379 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 29279 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 30129 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-322566-ye27nqj2 author: Huang, Yuxiang title: Stable Internal Reference Genes for Normalizing Real-Time Quantitative PCR in Baphicacanthus cusia under Hormonal Stimuli and UV Irradiation, and in Different Plant Organs date: 2017-05-03 pages: extension: .txt txt: ./txt/cord-322566-ye27nqj2.txt cache: ./cache/cord-322566-ye27nqj2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-322566-ye27nqj2.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 30104 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-327105-7dsgs2sd author: Zóka, András title: Distinct changes in the real-time PCR detectability of certain SARS-CoV-2 target sequences date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-327105-7dsgs2sd.txt cache: ./cache/cord-327105-7dsgs2sd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-327105-7dsgs2sd.txt' === file2bib.sh === id: cord-321432-qi2knswx author: Gardner, Shea N title: A microbial detection array (MDA) for viral and bacterial detection date: 2010-11-25 pages: extension: .txt txt: ./txt/cord-321432-qi2knswx.txt cache: ./cache/cord-321432-qi2knswx.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-321432-qi2knswx.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 31327 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 31319 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-324094-23kzr8rq author: Parida, M. M. title: Rapid and real-time detection technologies for emerging viruses of biomedical importance date: 2008-11-01 pages: extension: .txt txt: ./txt/cord-324094-23kzr8rq.txt cache: ./cache/cord-324094-23kzr8rq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-324094-23kzr8rq.txt' === file2bib.sh === id: cord-325014-n7mnhk2v author: Gujski, Mariusz title: Prevalence of Current and Past SARS-CoV-2 Infections among Police Employees in Poland, June–July 2020 date: 2020-10-11 pages: extension: .txt txt: ./txt/cord-325014-n7mnhk2v.txt cache: ./cache/cord-325014-n7mnhk2v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325014-n7mnhk2v.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 31328 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-325529-pid58g2r author: Ben-Ami, Roni title: Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-325529-pid58g2r.txt cache: ./cache/cord-325529-pid58g2r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325529-pid58g2r.txt' === file2bib.sh === id: cord-328409-px92ff89 author: Hornuss, Daniel title: COVID-19-assoziierte Pneumonie trotz persistierend negativen PCR-Tests aus oropharyngealen Abstrichen date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-328409-px92ff89.txt cache: ./cache/cord-328409-px92ff89.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328409-px92ff89.txt' === file2bib.sh === id: cord-325113-sou8xyld author: Kuiper, Johannes W. P. title: Detection of SARS-CoV-2 from raw patient samples by coupled high temperature reverse transcription and amplification date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-325113-sou8xyld.txt cache: ./cache/cord-325113-sou8xyld.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-325113-sou8xyld.txt' === file2bib.sh === id: cord-325101-9qslo6qh author: Gizzi, Aline Baumann da Rocha title: Presence of infectious agents and co-infections in diarrheic dogs determined with a real-time polymerase chain reaction-based panel date: 2014-01-16 pages: extension: .txt txt: ./txt/cord-325101-9qslo6qh.txt cache: ./cache/cord-325101-9qslo6qh.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325101-9qslo6qh.txt' === file2bib.sh === id: cord-325969-9zhmmvdg author: To, Kelvin KW title: Additional molecular testing of saliva specimens improves the detection of respiratory viruses date: 2017-06-07 pages: extension: .txt txt: ./txt/cord-325969-9zhmmvdg.txt cache: ./cache/cord-325969-9zhmmvdg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-325969-9zhmmvdg.txt' === file2bib.sh === id: cord-325124-0hxan9rw author: Li, Chenyu title: Highly sensitive and full-genome interrogation of SARS-CoV-2 using multiplexed PCR enrichment followed by next-generation sequencing date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-325124-0hxan9rw.txt cache: ./cache/cord-325124-0hxan9rw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325124-0hxan9rw.txt' === file2bib.sh === id: cord-327259-7o7fs4yb author: Correa, I. A. title: Boosting SARS-CoV-2 qRT-PCR detection combining pool sample strategy and mathematical modeling date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-327259-7o7fs4yb.txt cache: ./cache/cord-327259-7o7fs4yb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327259-7o7fs4yb.txt' === file2bib.sh === id: cord-327675-uo839gvc author: Salamatian, Iman title: In vitro Acquisition and Retention of Low-Pathogenic Avian Influenza H9N2 by Musca domestica (Diptera: Muscidae) date: 2019-10-11 pages: extension: .txt txt: ./txt/cord-327675-uo839gvc.txt cache: ./cache/cord-327675-uo839gvc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-327675-uo839gvc.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 32018 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 31678 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 32910 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 32634 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-329052-jan20ljs author: Gombar, Saurabh title: Persistent detection of SARS-CoV-2 RNA in patients and healthcare workers with COVID-19 date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-329052-jan20ljs.txt cache: ./cache/cord-329052-jan20ljs.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329052-jan20ljs.txt' === file2bib.sh === id: cord-329395-4k8js9v2 author: Ratcliff, Jeremy title: Evaluation of Different PCR Assay Formats for Sensitive and Specific Detection of SARS-CoV-2 RNA date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-329395-4k8js9v2.txt cache: ./cache/cord-329395-4k8js9v2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329395-4k8js9v2.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 32753 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-326130-wm3l1849 author: Van Pelt, Amelia title: Evaluation of COVID-19 Testing Strategies for Repopulating College and University Campuses: A Decision Tree Analysis date: 2020-11-03 pages: extension: .txt txt: ./txt/cord-326130-wm3l1849.txt cache: ./cache/cord-326130-wm3l1849.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326130-wm3l1849.txt' === file2bib.sh === id: cord-327682-i3uim0zi author: Santti, Juhana title: Molecular detection and typing of human picornaviruses date: 1999-08-25 pages: extension: .txt txt: ./txt/cord-327682-i3uim0zi.txt cache: ./cache/cord-327682-i3uim0zi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-327682-i3uim0zi.txt' === file2bib.sh === id: cord-326122-5m1727m1 author: Wishaupt, Jérôme O. title: PCR testing for Paediatric Acute Respiratory Tract Infections date: 2014-08-04 pages: extension: .txt txt: ./txt/cord-326122-5m1727m1.txt cache: ./cache/cord-326122-5m1727m1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-326122-5m1727m1.txt' === file2bib.sh === id: cord-328373-cubp1cc1 author: Jiang, Yanfang title: Digital PCR is a sensitive new technique for SARS-CoV-2 detection in clinical applications date: 2020-11-04 pages: extension: .txt txt: ./txt/cord-328373-cubp1cc1.txt cache: ./cache/cord-328373-cubp1cc1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-328373-cubp1cc1.txt' === file2bib.sh === id: cord-327024-1k5jucae author: Zhang, Qingshui title: Isolation and characterization of an astrovirus causing fatal visceral gout in domestic goslings date: 2018-04-19 pages: extension: .txt txt: ./txt/cord-327024-1k5jucae.txt cache: ./cache/cord-327024-1k5jucae.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-327024-1k5jucae.txt' === file2bib.sh === id: cord-328206-iylw1bvw author: Yu, Daojun title: Simultaneous Detection and Differentiation of Human Papillomavirus Genotypes 6, 11, 16 and 18 by AllGlo Quadruplex Quantitative PCR date: 2012-11-09 pages: extension: .txt txt: ./txt/cord-328206-iylw1bvw.txt cache: ./cache/cord-328206-iylw1bvw.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-328206-iylw1bvw.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-325611-tu1bn4hu author: Pérez-Sautu, Unai title: Target-independent high-throughput sequencing methods provide evidence that already known human viral pathogens play a main role in respiratory infections with unexplained etiology date: 2019-07-23 pages: extension: .txt txt: ./txt/cord-325611-tu1bn4hu.txt cache: ./cache/cord-325611-tu1bn4hu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325611-tu1bn4hu.txt' === file2bib.sh === id: cord-327344-8gi1wb76 author: Gambarino, Stefano title: Development of a RT Real-Time PCR for the Detection and Quantification of Human Rhinoviruses date: 2009-03-17 pages: extension: .txt txt: ./txt/cord-327344-8gi1wb76.txt cache: ./cache/cord-327344-8gi1wb76.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-327344-8gi1wb76.txt' === file2bib.sh === id: cord-328961-waxtb759 author: Pratelli, Annamaria title: PCR assay for the detection and the identification of atypical canine coronavirus in dogs date: 2002-10-01 pages: extension: .txt txt: ./txt/cord-328961-waxtb759.txt cache: ./cache/cord-328961-waxtb759.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328961-waxtb759.txt' === file2bib.sh === id: cord-327069-vjlisnui author: Driscoll, Amanda J. title: Standardization of Laboratory Methods for the PERCH Study date: 2017-06-15 pages: extension: .txt txt: ./txt/cord-327069-vjlisnui.txt cache: ./cache/cord-327069-vjlisnui.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-327069-vjlisnui.txt' === file2bib.sh === id: cord-324321-y96x8x3h author: Cai, Yingyun title: Down-regulation of transcription of the proapoptotic gene BNip3 in cultured astrocytes by murine coronavirus infection date: 2003-11-10 pages: extension: .txt txt: ./txt/cord-324321-y96x8x3h.txt cache: ./cache/cord-324321-y96x8x3h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-324321-y96x8x3h.txt' === file2bib.sh === id: cord-327894-b0bsseui author: Pecellín, Lidia Gestoso title: Recomendaciones y uso de los diferentes tipos de test para detección de infección por SARS-COV-2 date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-327894-b0bsseui.txt cache: ./cache/cord-327894-b0bsseui.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327894-b0bsseui.txt' === file2bib.sh === id: cord-331455-dfnn9mrf author: Shah, Aditya S. title: The utility of chest computed tomography (CT) and RT-PCR screening of asymptomatic patients for SARS-CoV-2 prior to semiurgent or urgent hospital procedures date: 2020-07-16 pages: extension: .txt txt: ./txt/cord-331455-dfnn9mrf.txt cache: ./cache/cord-331455-dfnn9mrf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331455-dfnn9mrf.txt' === file2bib.sh === id: cord-329643-hhk900c1 author: Skalina, K. A. title: Extended Storage of SARS-CoV2 Nasopharyngeal Swabs Does Not Negatively Impact Results of Molecular-Based Testing date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-329643-hhk900c1.txt cache: ./cache/cord-329643-hhk900c1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329643-hhk900c1.txt' === file2bib.sh === id: cord-329564-tmi1u224 author: Arashiro, Takeshi title: COVID-19 in 2 Persons with Mild Upper Respiratory Tract Symptoms on a Cruise Ship, Japan date: 2020-06-17 pages: extension: .txt txt: ./txt/cord-329564-tmi1u224.txt cache: ./cache/cord-329564-tmi1u224.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329564-tmi1u224.txt' === file2bib.sh === id: cord-328795-rs1sd42z author: Falsey, Ann R. title: Rhinoviruses date: 2016-10-24 pages: extension: .txt txt: ./txt/cord-328795-rs1sd42z.txt cache: ./cache/cord-328795-rs1sd42z.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328795-rs1sd42z.txt' === file2bib.sh === id: cord-329517-3yn80r9h author: Yang, Jin-Long title: Development of a fluorescent quantitative real-time polymerase chain reaction assay for the detection of Goose parvovirus in vivo date: 2009-09-15 pages: extension: .txt txt: ./txt/cord-329517-3yn80r9h.txt cache: ./cache/cord-329517-3yn80r9h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-329517-3yn80r9h.txt' === file2bib.sh === id: cord-328526-es8t6t0j author: Hoppes, Sharman title: The Isolation, Pathogenesis, Diagnosis, Transmission, and Control of Avian Bornavirus and Proventricular Dilatation Disease date: 2010-08-02 pages: extension: .txt txt: ./txt/cord-328526-es8t6t0j.txt cache: ./cache/cord-328526-es8t6t0j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-328526-es8t6t0j.txt' === file2bib.sh === id: cord-330602-g0xaonxv author: Sugiura, Hiroaki title: Prescription Surveillance and Polymerase Chain Reaction Testing to Identify Pathogens during Outbreaks of Infection date: 2013-02-07 pages: extension: .txt txt: ./txt/cord-330602-g0xaonxv.txt cache: ./cache/cord-330602-g0xaonxv.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-330602-g0xaonxv.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 34282 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 34341 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 34336 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 34430 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-332024-jk983q4p author: Briese, Thomas title: Diagnostic System for Rapid and Sensitive Differential Detection of Pathogens date: 2005-02-17 pages: extension: .txt txt: ./txt/cord-332024-jk983q4p.txt cache: ./cache/cord-332024-jk983q4p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-332024-jk983q4p.txt' === file2bib.sh === id: cord-325137-6c6er06a author: Moser, Lindsey A. title: A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses date: 2016-06-07 pages: extension: .txt txt: ./txt/cord-325137-6c6er06a.txt cache: ./cache/cord-325137-6c6er06a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325137-6c6er06a.txt' === file2bib.sh === id: cord-329162-6w8qcv1c author: Ayginin, Andrey A. title: The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels date: 2018-08-12 pages: extension: .txt txt: ./txt/cord-329162-6w8qcv1c.txt cache: ./cache/cord-329162-6w8qcv1c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 12 resourceName b'cord-329162-6w8qcv1c.txt' === file2bib.sh === id: cord-323987-gh1m05gi author: Dziąbowska, Karolina title: Detection Methods of Human and Animal Influenza Virus—Current Trends date: 2018-10-18 pages: extension: .txt txt: ./txt/cord-323987-gh1m05gi.txt cache: ./cache/cord-323987-gh1m05gi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-323987-gh1m05gi.txt' === file2bib.sh === id: cord-331413-fejho1of author: Nakayama, Eiichi title: Rapid optimization of antimicrobial chemotherapy given to pediatric patients with community-acquired pneumonia using PCR techniques with serology and standard culture date: 2007-12-31 pages: extension: .txt txt: ./txt/cord-331413-fejho1of.txt cache: ./cache/cord-331413-fejho1of.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-331413-fejho1of.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 34495 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-331496-5xak7z6b author: Garnett, Emily title: Clinical Validation and Performance Evaluation of the Automated Vitros Total Anti–SARS-CoV-2 Antibodies Assay for Screening of Serostatus in COVID-19 date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-331496-5xak7z6b.txt cache: ./cache/cord-331496-5xak7z6b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-331496-5xak7z6b.txt' === file2bib.sh === id: cord-331475-mmcu18c8 author: Sahu, Amit Ranjan title: Selection and validation of suitable reference genes for qPCR gene expression analysis in goats and sheep under Peste des petits ruminants virus (PPRV), lineage IV infection date: 2018-10-29 pages: extension: .txt txt: ./txt/cord-331475-mmcu18c8.txt cache: ./cache/cord-331475-mmcu18c8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-331475-mmcu18c8.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 35178 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-331616-arnuoufn author: Blank, Walter A. title: Virus PCR Assay Panels: An Alternative to the Mouse Antibody Production Test date: 2004 pages: extension: .txt txt: ./txt/cord-331616-arnuoufn.txt cache: ./cache/cord-331616-arnuoufn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-331616-arnuoufn.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 34977 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 34593 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 34970 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-333216-fdwmsnz9 author: Gonzalez, J. E. title: ESTIMATING PREVALENCE AND TIME COURSE OF SARS-CoV-2 BASED ON NEW HOSPITAL ADMISSIONS AND PCR TESTS date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-333216-fdwmsnz9.txt cache: ./cache/cord-333216-fdwmsnz9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333216-fdwmsnz9.txt' === file2bib.sh === id: cord-332522-adul9nzf author: Wu, Qingfa title: Development of Taqman RT-nested PCR system for clinical SARS-CoV detection date: 2004-04-02 pages: extension: .txt txt: ./txt/cord-332522-adul9nzf.txt cache: ./cache/cord-332522-adul9nzf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332522-adul9nzf.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 35897 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-333261-knj2rrut author: Albright, Catherine J. title: An exercise in molecular epidemiology: Human rhinovirus prevalence and genetics date: 2011-11-11 pages: extension: .txt txt: ./txt/cord-333261-knj2rrut.txt cache: ./cache/cord-333261-knj2rrut.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333261-knj2rrut.txt' === file2bib.sh === id: cord-333453-v3gap8kj author: Dima, Mirabela title: First neonates with severe acute respiratory syndrome coronavirus 2 infection in Romania: Three case reports date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-333453-v3gap8kj.txt cache: ./cache/cord-333453-v3gap8kj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333453-v3gap8kj.txt' === file2bib.sh === id: cord-332042-bqtflk7r author: LeBlanc, J. J. title: Validation of the Seegene RV15 multiplex PCR for the detection of influenza A subtypes and influenza B lineages during national influenza surveillance in hospitalized adults date: 2019-07-02 pages: extension: .txt txt: ./txt/cord-332042-bqtflk7r.txt cache: ./cache/cord-332042-bqtflk7r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332042-bqtflk7r.txt' === file2bib.sh === id: cord-334090-66d8c75g author: Seger, Waleed title: Genotyping of infectious bronchitis viruses from broiler farms in Iraq during 2014-2015 date: 2016-02-18 pages: extension: .txt txt: ./txt/cord-334090-66d8c75g.txt cache: ./cache/cord-334090-66d8c75g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334090-66d8c75g.txt' === file2bib.sh === id: cord-331932-oujdl459 author: Lung, O. title: Multiplex PCR and Microarray for Detection of Swine Respiratory Pathogens date: 2015-12-12 pages: extension: .txt txt: ./txt/cord-331932-oujdl459.txt cache: ./cache/cord-331932-oujdl459.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-331932-oujdl459.txt' === file2bib.sh === id: cord-331740-yjt3q9ph author: Jones, R. M. title: Development and Validation of RT‐PCR Tests for the Detection and S1 Genotyping of Infectious Bronchitis Virus and Other Closely Related Gammacoronaviruses Within Clinical Samples date: 2011-04-07 pages: extension: .txt txt: ./txt/cord-331740-yjt3q9ph.txt cache: ./cache/cord-331740-yjt3q9ph.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-331740-yjt3q9ph.txt' === file2bib.sh === id: cord-331558-6rqd3fmj author: Sun, Chuan-bin title: Role of the Eye in Transmitting Human Coronavirus: What We Know and What We Do Not Know date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-331558-6rqd3fmj.txt cache: ./cache/cord-331558-6rqd3fmj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-331558-6rqd3fmj.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 36400 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 36252 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-335085-7pxkhgbq author: Dessau, R. B. title: Coronaviruses in spinal fluid of patients with acute monosymptomatic optic neuritis date: 2009-01-29 pages: extension: .txt txt: ./txt/cord-335085-7pxkhgbq.txt cache: ./cache/cord-335085-7pxkhgbq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-335085-7pxkhgbq.txt' === file2bib.sh === id: cord-333413-8buawes0 author: Liebing, J. title: Health status of free-ranging ring-necked pheasant chicks (Phasianus colchicus) in North-Western Germany date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-333413-8buawes0.txt cache: ./cache/cord-333413-8buawes0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333413-8buawes0.txt' === file2bib.sh === id: cord-334688-0i1pu8wc author: Martos Pérez, F. title: Comorbidity and prognostic factors on admission in a COVID-19 cohort of a general hospital date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-334688-0i1pu8wc.txt cache: ./cache/cord-334688-0i1pu8wc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334688-0i1pu8wc.txt' === file2bib.sh === id: cord-335459-tq4fwigw author: Chen, Hui Juan title: Early chest CT features of patients with 2019 novel coronavirus (COVID-19) pneumonia: relationship to diagnosis and prognosis date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-335459-tq4fwigw.txt cache: ./cache/cord-335459-tq4fwigw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335459-tq4fwigw.txt' === file2bib.sh === id: cord-335323-p7cv79ig author: DeSerres, Joshua J. title: Best Practice Guidelines for the Management of Acute Craniomaxillofacial Trauma During the COVID-19 Pandemic date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-335323-p7cv79ig.txt cache: ./cache/cord-335323-p7cv79ig.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335323-p7cv79ig.txt' === file2bib.sh === id: cord-332053-df44guu7 author: Malka, Jonathan title: The Effect of Viral Infection on Exhaled Nitric Oxide in Children with Acute Asthma Exacerbations date: 2015-07-26 pages: extension: .txt txt: ./txt/cord-332053-df44guu7.txt cache: ./cache/cord-332053-df44guu7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332053-df44guu7.txt' === file2bib.sh === id: cord-339278-9luefzyo author: Zayet, Souheil title: Contribution of anosmia and dysgeusia for diagnostic of COVID-19 in outpatients date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-339278-9luefzyo.txt cache: ./cache/cord-339278-9luefzyo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339278-9luefzyo.txt' === file2bib.sh === id: cord-336671-vfq5ft08 author: Ai, Jing-Wen title: Era of molecular diagnosis for pathogen identification of unexplained pneumonia, lessons to be learned date: 2020-03-16 pages: extension: .txt txt: ./txt/cord-336671-vfq5ft08.txt cache: ./cache/cord-336671-vfq5ft08.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336671-vfq5ft08.txt' === file2bib.sh === id: cord-333805-xmqs2ax7 author: Romoli, Michele title: A systematic review of neurological manifestations of SARS‐CoV‐2 infection: the devil is hidden in the details date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-333805-xmqs2ax7.txt cache: ./cache/cord-333805-xmqs2ax7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333805-xmqs2ax7.txt' === file2bib.sh === id: cord-335393-4buooi2d author: Xiang, Yangxi title: Comparative transcriptome analysis reveals the role of p53 signalling pathway during red‐spotted grouper nervous necrosis virus infection in Lateolabrax japonicus brain cells date: 2019-01-18 pages: extension: .txt txt: ./txt/cord-335393-4buooi2d.txt cache: ./cache/cord-335393-4buooi2d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335393-4buooi2d.txt' === file2bib.sh === id: cord-335359-4rcj75tc author: Jia, Bei title: Evaluation of a PCR-electrospray ionization mass spectrometry platform for detection and identification of fungal pathogens directly from prospectively collected bronchoalveolar lavage specimens date: 2020-01-15 pages: extension: .txt txt: ./txt/cord-335359-4rcj75tc.txt cache: ./cache/cord-335359-4rcj75tc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335359-4rcj75tc.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 36693 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 36982 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 37290 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-337701-56tmg38b author: Xiao, Yan title: Comparison of three TaqMan Real-Time Reverse Transcription-PCR assays in detecting SARS-CoV-2 date: 2020-07-06 pages: extension: .txt txt: ./txt/cord-337701-56tmg38b.txt cache: ./cache/cord-337701-56tmg38b.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337701-56tmg38b.txt' === file2bib.sh === id: cord-336975-28mtmw2z author: Sadeghi, Christine D title: Twelve years' detection of respiratory viruses by immunofluorescence in hospitalised children: impact of the introduction of a new respiratory picornavirus assay date: 2011-02-07 pages: extension: .txt txt: ./txt/cord-336975-28mtmw2z.txt cache: ./cache/cord-336975-28mtmw2z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336975-28mtmw2z.txt' === file2bib.sh === id: cord-335784-v7nbck0n author: Barak, N. title: Lessons from applied large-scale pooling of 133,816 SARS-CoV-2 RT-PCR tests date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-335784-v7nbck0n.txt cache: ./cache/cord-335784-v7nbck0n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-335784-v7nbck0n.txt' === file2bib.sh === id: cord-323029-7hqp8xuq author: Bognár, Zsófia title: Aptamers against Immunoglobulins: Design, Selection and Bioanalytical Applications date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-323029-7hqp8xuq.txt cache: ./cache/cord-323029-7hqp8xuq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323029-7hqp8xuq.txt' === file2bib.sh === id: cord-336453-cbq0ui4p author: Machitori, Akihiro title: Computed tomography surveillance helps tracking COVID-19 outbreak date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-336453-cbq0ui4p.txt cache: ./cache/cord-336453-cbq0ui4p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336453-cbq0ui4p.txt' === file2bib.sh === id: cord-339995-0pbknb32 author: Feng, Hao title: A case report of COVID-19 with false negative RT-PCR test: necessity of chest CT date: 2020-04-07 pages: extension: .txt txt: ./txt/cord-339995-0pbknb32.txt cache: ./cache/cord-339995-0pbknb32.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-339995-0pbknb32.txt' === file2bib.sh === id: cord-337003-7ygcfzii author: Mehrbod, Parvaneh title: Association of IFITM3 rs12252 polymorphisms, BMI, diabetes, and hypercholesterolemia with mild flu in an Iranian population date: 2017-11-09 pages: extension: .txt txt: ./txt/cord-337003-7ygcfzii.txt cache: ./cache/cord-337003-7ygcfzii.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337003-7ygcfzii.txt' === file2bib.sh === id: cord-338607-22f04uqe author: Verbeek, A. title: Genomic relationship between turkey and bovine enteric coronaviruses identified by hybridization with BCV or TCV specific cDNA probes date: 1991 pages: extension: .txt txt: ./txt/cord-338607-22f04uqe.txt cache: ./cache/cord-338607-22f04uqe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338607-22f04uqe.txt' === file2bib.sh === id: cord-340788-p02v46xu author: Zitek, Tony title: The Appropriate Use of Testing for COVID-19 date: 2020-04-13 pages: extension: .txt txt: ./txt/cord-340788-p02v46xu.txt cache: ./cache/cord-340788-p02v46xu.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-340788-p02v46xu.txt' === file2bib.sh === id: cord-340336-u59l0taa author: Perchetti, Garrett A. title: Multiplexing primer/probe sets for detection of SARS-CoV-2 by qRT-PCR date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-340336-u59l0taa.txt cache: ./cache/cord-340336-u59l0taa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340336-u59l0taa.txt' === file2bib.sh === id: cord-337198-4sors3bg author: Clementi, Nicola title: Combined Prophylactic and Therapeutic Use Maximizes Hydroxychloroquine Anti-SARS-CoV-2 Effects in vitro date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-337198-4sors3bg.txt cache: ./cache/cord-337198-4sors3bg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-337198-4sors3bg.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 38380 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-338899-qt17jhg0 author: Lakshmi, Vemu title: Clinical Features and Molecular Diagnosis of Chikungunya Fever from South India date: 2008-05-01 pages: extension: .txt txt: ./txt/cord-338899-qt17jhg0.txt cache: ./cache/cord-338899-qt17jhg0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338899-qt17jhg0.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 38906 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 38950 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 38228 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 38476 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 38781 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 38905 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 97296 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-339419-b6tr2zyx author: Lee, Thomas Ming-Hung title: DNA-based bioanalytical microsystems for handheld device applications date: 2006-01-18 pages: extension: .txt txt: ./txt/cord-339419-b6tr2zyx.txt cache: ./cache/cord-339419-b6tr2zyx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339419-b6tr2zyx.txt' === file2bib.sh === id: cord-333524-a6p6ma8r author: Khan, Pavana title: Isothermal SARS-CoV-2 Diagnostics: Tools for Enabling Distributed Pandemic Testing as a Means of Supporting Safe Reopenings date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-333524-a6p6ma8r.txt cache: ./cache/cord-333524-a6p6ma8r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333524-a6p6ma8r.txt' === file2bib.sh === id: cord-340046-kgbvld0y author: Houspie, Lieselot title: Exhaled breath condensate sampling is not a new method for detection of respiratory viruses date: 2011-03-04 pages: extension: .txt txt: ./txt/cord-340046-kgbvld0y.txt cache: ./cache/cord-340046-kgbvld0y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340046-kgbvld0y.txt' === file2bib.sh === id: cord-339976-tg2jkss7 author: Wang, Haibin title: Detection and Monitoring of SARS Coronavirus in the Plasma and Peripheral Blood Lymphocytes of Patients with Severe Acute Respiratory Syndrome date: 2004-07-01 pages: extension: .txt txt: ./txt/cord-339976-tg2jkss7.txt cache: ./cache/cord-339976-tg2jkss7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339976-tg2jkss7.txt' === file2bib.sh === id: cord-340627-xyvzgkxl author: Ornaghi, Sara title: Performance of an extended triage questionnaire to detect suspected cases of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection in obstetric patients: Experience from two large teaching hospitals in Lombardy, Northern Italy date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-340627-xyvzgkxl.txt cache: ./cache/cord-340627-xyvzgkxl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340627-xyvzgkxl.txt' === file2bib.sh === id: cord-339973-kj56zi59 author: Coleman, Kristen K. title: Bioaerosol Sampling for Respiratory Viruses in Singapore’s Mass Rapid Transit Network date: 2018-11-30 pages: extension: .txt txt: ./txt/cord-339973-kj56zi59.txt cache: ./cache/cord-339973-kj56zi59.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-339973-kj56zi59.txt' === file2bib.sh === id: cord-338942-q4neat3x author: Zhang, Haoqing title: LAMP-on-a-chip: Revising microfluidic platforms for loop-mediated DNA amplification date: 2019-01-31 pages: extension: .txt txt: ./txt/cord-338942-q4neat3x.txt cache: ./cache/cord-338942-q4neat3x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338942-q4neat3x.txt' === file2bib.sh === id: cord-339656-u0cpklsv author: de Groot-Mijnes, Jolanda D.F. title: Identification of New Pathogens in the Intraocular Fluid of Patients With Uveitis date: 2010-11-30 pages: extension: .txt txt: ./txt/cord-339656-u0cpklsv.txt cache: ./cache/cord-339656-u0cpklsv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-339656-u0cpklsv.txt' === file2bib.sh === id: cord-005147-mvoq9vln author: nan title: Autorenregister date: 2017-02-23 pages: extension: .txt txt: ./txt/cord-005147-mvoq9vln.txt cache: ./cache/cord-005147-mvoq9vln.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 9 resourceName b'cord-005147-mvoq9vln.txt' === file2bib.sh === id: cord-342344-jjnf4yje author: Mello, C. J. title: Absolute quantification and degradation evaluation of SARS-CoV-2 RNA by droplet digital PCR date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-342344-jjnf4yje.txt cache: ./cache/cord-342344-jjnf4yje.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342344-jjnf4yje.txt' === file2bib.sh === id: cord-344745-sgkq1l93 author: Selim, Karim title: Molecular characterization of infectious bronchitis viruses isolated from broiler and layer chicken farms in Egypt during 2012 date: 2013-11-18 pages: extension: .txt txt: ./txt/cord-344745-sgkq1l93.txt cache: ./cache/cord-344745-sgkq1l93.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344745-sgkq1l93.txt' === file2bib.sh === id: cord-340883-zf8jbhdl author: He, Zhongping title: Using patient-collected clinical samples and sera to detect and quantify the severe acute respiratory syndrome coronavirus (SARS-CoV) date: 2007-03-27 pages: extension: .txt txt: ./txt/cord-340883-zf8jbhdl.txt cache: ./cache/cord-340883-zf8jbhdl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340883-zf8jbhdl.txt' === file2bib.sh === id: cord-338205-sy91rnse author: Li, Chenxi title: Laboratory Diagnosis of Coronavirus Disease-2019 (COVID-19) date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-338205-sy91rnse.txt cache: ./cache/cord-338205-sy91rnse.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-338205-sy91rnse.txt' === file2bib.sh === id: cord-343377-6muareue author: Kidszun, André title: Viral Infections in Neonates with Suspected Late-Onset Bacterial Sepsis—A Prospective Cohort Study date: 2016-05-16 pages: extension: .txt txt: ./txt/cord-343377-6muareue.txt cache: ./cache/cord-343377-6muareue.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343377-6muareue.txt' === file2bib.sh === id: cord-342380-lihz7h1k author: Meguid Kassem, Abdel title: SARS-CoV-2 infection among healthcare workers of a gastroenterological service in a tertiary care facility date: 2020-07-21 pages: extension: .txt txt: ./txt/cord-342380-lihz7h1k.txt cache: ./cache/cord-342380-lihz7h1k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-342380-lihz7h1k.txt' === file2bib.sh === id: cord-343441-z849jvq5 author: Li, Yan title: Simultaneous detection of hemagglutinin and neuraminidase genes of novel influenza A (H7N9) by duplex real-time reverse transcription polymerase chain reaction date: 2013-09-01 pages: extension: .txt txt: ./txt/cord-343441-z849jvq5.txt cache: ./cache/cord-343441-z849jvq5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-343441-z849jvq5.txt' === file2bib.sh === id: cord-324944-ixh3ykrc author: Mitsakakis, Konstantinos title: Diagnostic tools for tackling febrile illness and enhancing patient management date: 2018-12-05 pages: extension: .txt txt: ./txt/cord-324944-ixh3ykrc.txt cache: ./cache/cord-324944-ixh3ykrc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-324944-ixh3ykrc.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 40546 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-342568-3sj235rm author: Bald-Blume, Niklas title: Development of a molecular assay for the general detection of tospoviruses and the distinction between tospoviral species date: 2017-02-11 pages: extension: .txt txt: ./txt/cord-342568-3sj235rm.txt cache: ./cache/cord-342568-3sj235rm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-342568-3sj235rm.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 40405 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 40557 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 40531 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 40683 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 40435 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 40654 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-345312-i7soyabu author: Wabe, Nasir title: The impact of rapid molecular diagnostic testing for respiratory viruses on outcomes for emergency department patients date: 2019-03-05 pages: extension: .txt txt: ./txt/cord-345312-i7soyabu.txt cache: ./cache/cord-345312-i7soyabu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-345312-i7soyabu.txt' === file2bib.sh === id: cord-342383-ckswlo9o author: Pawlowski, C. title: Exploratory analysis of immunization records highlights decreased SARS-CoV-2 rates in individuals with recent non-COVID-19 vaccinations date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-342383-ckswlo9o.txt cache: ./cache/cord-342383-ckswlo9o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342383-ckswlo9o.txt' === file2bib.sh === id: cord-344751-i4qnrtjq author: Van Praet, Jens T. title: Comparison of four commercial SARS-CoV-2 IgG immuno-assays in RT-PCR negative patients with suspect CT findings date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-344751-i4qnrtjq.txt cache: ./cache/cord-344751-i4qnrtjq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344751-i4qnrtjq.txt' === file2bib.sh === id: cord-341141-bgrgzfoo author: Hou, Peili title: Rapid detection of infectious bovine Rhinotracheitis virus using recombinase polymerase amplification assays date: 2017-12-13 pages: extension: .txt txt: ./txt/cord-341141-bgrgzfoo.txt cache: ./cache/cord-341141-bgrgzfoo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-341141-bgrgzfoo.txt' === file2bib.sh === id: cord-338582-o976nab9 author: Dahlhausen, Bob title: Future Veterinary Diagnostics date: 2010-09-19 pages: extension: .txt txt: ./txt/cord-338582-o976nab9.txt cache: ./cache/cord-338582-o976nab9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-338582-o976nab9.txt' === file2bib.sh === id: cord-343784-zgvxl4h3 author: Cho, Chi Hyun title: Evaluation of the AdvanSure™ real-time RT-PCR compared with culture and Seeplex RV15 for simultaneous detection of respiratory viruses date: 2014-05-31 pages: extension: .txt txt: ./txt/cord-343784-zgvxl4h3.txt cache: ./cache/cord-343784-zgvxl4h3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343784-zgvxl4h3.txt' === file2bib.sh === id: cord-343860-2j7nbryv author: Thiberville, S.D. title: The viral etiology of an influenza‐like illness during the 2009 pandemic date: 2012-05-14 pages: extension: .txt txt: ./txt/cord-343860-2j7nbryv.txt cache: ./cache/cord-343860-2j7nbryv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343860-2j7nbryv.txt' === file2bib.sh === id: cord-342476-0rupk21u author: van Rijn, Anneloes L. title: The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease date: 2019-10-24 pages: extension: .txt txt: ./txt/cord-342476-0rupk21u.txt cache: ./cache/cord-342476-0rupk21u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-342476-0rupk21u.txt' === file2bib.sh === id: cord-339456-82iks0xf author: Mikel, P. title: Methods for Preparation of MS2 Phage-Like Particles and Their Utilization as Process Control Viruses in RT-PCR and qRT-PCR Detection of RNA Viruses From Food Matrices and Clinical Specimens date: 2015-02-25 pages: extension: .txt txt: ./txt/cord-339456-82iks0xf.txt cache: ./cache/cord-339456-82iks0xf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-339456-82iks0xf.txt' === file2bib.sh === id: cord-346958-9eeqlkoq author: Caruso, Damiano title: Chest CT Features of COVID-19 in Rome, Italy date: 2020-04-03 pages: extension: .txt txt: ./txt/cord-346958-9eeqlkoq.txt cache: ./cache/cord-346958-9eeqlkoq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-346958-9eeqlkoq.txt' === file2bib.sh === id: cord-344782-ond1ziu5 author: Zhang, Jing title: Identification of a novel nidovirus as a potential cause of large scale mortalities in the endangered Bellinger River snapping turtle (Myuchelys georgesi) date: 2018-10-24 pages: extension: .txt txt: ./txt/cord-344782-ond1ziu5.txt cache: ./cache/cord-344782-ond1ziu5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-344782-ond1ziu5.txt' === file2bib.sh === id: cord-348914-6wzqitun author: Ahouach, B. title: Cutaneous lesions in a patient with COVID‐19: are they related? date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-348914-6wzqitun.txt cache: ./cache/cord-348914-6wzqitun.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-348914-6wzqitun.txt' === file2bib.sh === id: cord-346436-p61mpc6t author: Onodera, Kenji title: Selection for 3′-End Triplets for Polymerase Chain Reaction Primers date: 2007 pages: extension: .txt txt: ./txt/cord-346436-p61mpc6t.txt cache: ./cache/cord-346436-p61mpc6t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346436-p61mpc6t.txt' === file2bib.sh === id: cord-348209-rkkhv4mw author: Noerz, Dominik title: Clinical evaluation of a SARS-CoV-2 RT-PCR assay on a fully automated system for rapid on-demand testing in the hospital setting date: 2020-04-11 pages: extension: .txt txt: ./txt/cord-348209-rkkhv4mw.txt cache: ./cache/cord-348209-rkkhv4mw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-348209-rkkhv4mw.txt' === file2bib.sh === id: cord-344889-1y4ieamp author: Cameron, Robert J. title: Virus infection in exacerbations of chronic obstructive pulmonary disease requiring ventilation date: 2006-05-24 pages: extension: .txt txt: ./txt/cord-344889-1y4ieamp.txt cache: ./cache/cord-344889-1y4ieamp.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-344889-1y4ieamp.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 42151 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 42295 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-345211-4ivqlsgt author: Murdoch, David R. title: How recent advances in molecular tests could impact the diagnosis of pneumonia date: 2016-03-07 pages: extension: .txt txt: ./txt/cord-345211-4ivqlsgt.txt cache: ./cache/cord-345211-4ivqlsgt.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345211-4ivqlsgt.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 42291 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-346467-a0r4xh1c author: Cornelissen, Jan B. W. J. title: Mycoplasma detection by triplex real-time PCR in bronchoalveolar lavage fluid from bovine respiratory disease complex cases date: 2017-04-08 pages: extension: .txt txt: ./txt/cord-346467-a0r4xh1c.txt cache: ./cache/cord-346467-a0r4xh1c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-346467-a0r4xh1c.txt' === file2bib.sh === id: cord-346325-grt67p73 author: Reilev, M. title: Characteristics and predictors of hospitalization and death in the first 9,519 cases with a positive RT-PCR test for SARS-CoV-2 in Denmark: A nationwide cohort date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-346325-grt67p73.txt cache: ./cache/cord-346325-grt67p73.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-346325-grt67p73.txt' === file2bib.sh === id: cord-347462-yz67t10x author: Chan, Tak Yeung title: A Comparative Study of Clinical Features and Outcomes in Young and Older Adults with Severe Acute Respiratory Syndrome date: 2004-07-19 pages: extension: .txt txt: ./txt/cord-347462-yz67t10x.txt cache: ./cache/cord-347462-yz67t10x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347462-yz67t10x.txt' === file2bib.sh === id: cord-340481-i3qrxnpr author: Pozo, Francisco title: Aplicación de los métodos moleculares al diagnóstico y el estudio epidemiológico de las infecciones respiratorias causadas por virus date: 2008-07-31 pages: extension: .txt txt: ./txt/cord-340481-i3qrxnpr.txt cache: ./cache/cord-340481-i3qrxnpr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-340481-i3qrxnpr.txt' === file2bib.sh === id: cord-349745-zlhu1jit author: Konrad, Regina title: Rapid establishment of laboratory diagnostics for the novel coronavirus SARS-CoV-2 in Bavaria, Germany, February 2020 date: 2020-03-05 pages: extension: .txt txt: ./txt/cord-349745-zlhu1jit.txt cache: ./cache/cord-349745-zlhu1jit.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349745-zlhu1jit.txt' === file2bib.sh === id: cord-347443-0evqo01m author: Litwin, Christine M. title: Seasonality and prevalence of respiratory pathogens detected by multiplex PCR at a tertiary care medical center date: 2013-07-24 pages: extension: .txt txt: ./txt/cord-347443-0evqo01m.txt cache: ./cache/cord-347443-0evqo01m.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347443-0evqo01m.txt' === file2bib.sh === id: cord-346859-r1v6ir8u author: Mallett, Sue title: At what times during infection is SARS-CoV-2 detectable and no longer detectable using RT-PCR-based tests? A systematic review of individual participant data date: 2020-11-04 pages: extension: .txt txt: ./txt/cord-346859-r1v6ir8u.txt cache: ./cache/cord-346859-r1v6ir8u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346859-r1v6ir8u.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 43308 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 43161 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 43229 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-349070-bqv03u2e author: Jiang, Shih Sheng title: Sensitive and Quantitative Detection of Severe Acute Respiratory Syndrome Coronavirus Infection by Real-Time Nested Polymerase Chain Reaction date: 2004-01-15 pages: extension: .txt txt: ./txt/cord-349070-bqv03u2e.txt cache: ./cache/cord-349070-bqv03u2e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-349070-bqv03u2e.txt' === file2bib.sh === id: cord-346574-u28y1ttw author: Chen, Keyan title: Development and evaluation of an immunochromatographic strip for rapid detection of porcine hemagglutinating encephalomyelitis virus date: 2012-08-24 pages: extension: .txt txt: ./txt/cord-346574-u28y1ttw.txt cache: ./cache/cord-346574-u28y1ttw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346574-u28y1ttw.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 43135 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-349775-zwslhjju author: Brittain-Long, Robin title: Access to a polymerase chain reaction assay method targeting 13 respiratory viruses can reduce antibiotics: a randomised, controlled trial date: 2011-04-26 pages: extension: .txt txt: ./txt/cord-349775-zwslhjju.txt cache: ./cache/cord-349775-zwslhjju.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-349775-zwslhjju.txt' === file2bib.sh === id: cord-349562-ivu632j2 author: Hernes, S. S. title: Swabbing for respiratory viral infections in older patients: a comparison of rayon and nylon flocked swabs date: 2010-09-18 pages: extension: .txt txt: ./txt/cord-349562-ivu632j2.txt cache: ./cache/cord-349562-ivu632j2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349562-ivu632j2.txt' === file2bib.sh === id: cord-351643-8ce807ub author: Poon, LLM title: Rapid detection of reassortment of pandemic H1N1/2009 influenza virus date: 2010-08-01 pages: extension: .txt txt: ./txt/cord-351643-8ce807ub.txt cache: ./cache/cord-351643-8ce807ub.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-351643-8ce807ub.txt' === file2bib.sh === id: cord-351125-asrezu1f author: Lee, Sangmin title: Identification of Cystoisospora ohioensis in a Diarrheal Dog in Korea date: 2018-08-31 pages: extension: .txt txt: ./txt/cord-351125-asrezu1f.txt cache: ./cache/cord-351125-asrezu1f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351125-asrezu1f.txt' === file2bib.sh === id: cord-350890-ajxvjkmq author: Hsieh, Yi-Fan title: A real-time convective PCR machine in a capillary tube instrumented with a CCD-based fluorometer date: 2013-07-05 pages: extension: .txt txt: ./txt/cord-350890-ajxvjkmq.txt cache: ./cache/cord-350890-ajxvjkmq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350890-ajxvjkmq.txt' === file2bib.sh === id: cord-351038-k2m6woow author: Arun Krishnan, R. title: COVID-19: Current Trends in Invitro Diagnostics date: 2020-06-27 pages: extension: .txt txt: ./txt/cord-351038-k2m6woow.txt cache: ./cache/cord-351038-k2m6woow.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-351038-k2m6woow.txt' === file2bib.sh === id: cord-352554-hsbyznex author: Lee, Yeon Joo title: Quality of Ribonucleic Acid Extraction for Real-Time Reverse Transcription-PCR (rRT-PCR) of SARS-CoV-2: Importance of Internal Control Monitoring date: 2020-11-01 pages: extension: .txt txt: ./txt/cord-352554-hsbyznex.txt cache: ./cache/cord-352554-hsbyznex.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-352554-hsbyznex.txt' === file2bib.sh === id: cord-346054-k84rcpav author: Niespodziana, Katarzyna title: PreDicta chip-based high resolution diagnosis of rhinovirus-induced wheeze date: 2018-06-18 pages: extension: .txt txt: ./txt/cord-346054-k84rcpav.txt cache: ./cache/cord-346054-k84rcpav.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346054-k84rcpav.txt' === file2bib.sh === id: cord-349838-p6vfzbla author: Algwaiz, Ghada title: Real-world issues and potential solutions in HCT during the COVID-19 pandemic: Perspectives from the WBMT and the CIBMTR's Health Services and International Studies Committee date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-349838-p6vfzbla.txt cache: ./cache/cord-349838-p6vfzbla.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349838-p6vfzbla.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 44124 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-346989-604gho1u author: Chen-Harris, Haiyin title: Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs date: 2013-02-12 pages: extension: .txt txt: ./txt/cord-346989-604gho1u.txt cache: ./cache/cord-346989-604gho1u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-346989-604gho1u.txt' === file2bib.sh === id: cord-344749-omzhhr0k author: Kaya, Sariye Irem title: Electrochemical virus detections with nanobiosensors date: 2020-02-14 pages: extension: .txt txt: ./txt/cord-344749-omzhhr0k.txt cache: ./cache/cord-344749-omzhhr0k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344749-omzhhr0k.txt' === file2bib.sh === id: cord-352640-fycwhyfv author: Goel, Ashish title: Profile of Patients Suspected to be COVID-19: A Retrospective Analysis of Early Pandemic Data date: 2020-08-29 pages: extension: .txt txt: ./txt/cord-352640-fycwhyfv.txt cache: ./cache/cord-352640-fycwhyfv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-352640-fycwhyfv.txt' === file2bib.sh === id: cord-350807-qdq96723 author: Reckziegel, Maria title: Viruses and atypical bacteria in the respiratory tract of immunocompromised and immunocompetent patients with airway infection date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-350807-qdq96723.txt cache: ./cache/cord-350807-qdq96723.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-350807-qdq96723.txt' === file2bib.sh === id: cord-351100-llyl97ry author: Cariani, Lisa title: Time Length of Negativization and Cycle Threshold Values in 182 Healthcare Workers with Covid-19 in Milan, Italy: An Observational Cohort Study date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-351100-llyl97ry.txt cache: ./cache/cord-351100-llyl97ry.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351100-llyl97ry.txt' === file2bib.sh === id: cord-351854-5s03f0pp author: Ben-Ami, Roni title: Pooled RNA extraction and PCR assay for efficient SARS-CoV-2 detection date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-351854-5s03f0pp.txt cache: ./cache/cord-351854-5s03f0pp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351854-5s03f0pp.txt' === file2bib.sh === id: cord-352894-88c46evj author: Yoon, Soon‐Seek title: Comparison of the diagnostic methods on the canine adenovirus type 2 infection date: 2010-06-02 pages: extension: .txt txt: ./txt/cord-352894-88c46evj.txt cache: ./cache/cord-352894-88c46evj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-352894-88c46evj.txt' === file2bib.sh === id: cord-352720-z1cvjc2y author: Díaz-Corvillón, Pilar title: Routine screening for SARS CoV-2 in unselected pregnant women at delivery date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-352720-z1cvjc2y.txt cache: ./cache/cord-352720-z1cvjc2y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352720-z1cvjc2y.txt' === file2bib.sh === id: cord-345475-ttrcmtu4 author: de Oliveira, Luisa Abruzzi title: Reference Genes for the Normalization of Gene Expression in Eucalyptus Species date: 2011-12-24 pages: extension: .txt txt: ./txt/cord-345475-ttrcmtu4.txt cache: ./cache/cord-345475-ttrcmtu4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-345475-ttrcmtu4.txt' === file2bib.sh === id: cord-353499-os328w9o author: Yang, H. S. title: Routine laboratory blood tests predict SARS-CoV-2 infection using machine learning date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-353499-os328w9o.txt cache: ./cache/cord-353499-os328w9o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353499-os328w9o.txt' === file2bib.sh === id: cord-004675-n8mlxe7p author: nan title: 2019 CIS Annual Meeting: Immune Deficiency & Dysregulation North American Conference date: 2019-02-26 pages: extension: .txt txt: ./txt/cord-004675-n8mlxe7p.txt cache: ./cache/cord-004675-n8mlxe7p.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 7 resourceName b'cord-004675-n8mlxe7p.txt' === file2bib.sh === id: cord-353246-q9qpec7t author: Nijhuis, R. H. T. title: Comparison of ePlex Respiratory Pathogen Panel with Laboratory-Developed Real-Time PCR Assays for Detection of Respiratory Pathogens date: 2017-05-23 pages: extension: .txt txt: ./txt/cord-353246-q9qpec7t.txt cache: ./cache/cord-353246-q9qpec7t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353246-q9qpec7t.txt' === file2bib.sh === id: cord-350593-bvmg7f15 author: McDonald, R.S. title: Proportional mouse model for aerosol infection by influenza date: 2012-08-21 pages: extension: .txt txt: ./txt/cord-350593-bvmg7f15.txt cache: ./cache/cord-350593-bvmg7f15.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350593-bvmg7f15.txt' === file2bib.sh === id: cord-353573-y9jro9gt author: You, Huey-Ling title: Simultaneous detection of respiratory syncytial virus and human metapneumovirus by one-step multiplex real-time RT-PCR in patients with respiratory symptoms date: 2017-03-27 pages: extension: .txt txt: ./txt/cord-353573-y9jro9gt.txt cache: ./cache/cord-353573-y9jro9gt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353573-y9jro9gt.txt' === file2bib.sh === id: cord-353253-kk2q71vg author: Itokawa, Kentaro title: Disentangling primer interactions improves SARS-CoV-2 genome sequencing by multiplex tiling PCR date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-353253-kk2q71vg.txt cache: ./cache/cord-353253-kk2q71vg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353253-kk2q71vg.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-352872-y1qh5nig author: Herpe, Guillaume title: Efficacy of Chest CT for COVID-19 Pneumonia in France date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-352872-y1qh5nig.txt cache: ./cache/cord-352872-y1qh5nig.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352872-y1qh5nig.txt' === file2bib.sh === id: cord-353241-ityhcak7 author: Zhu, Hanliang title: IoT PCR for pandemic disease detection and its spread monitoring date: 2020-01-15 pages: extension: .txt txt: ./txt/cord-353241-ityhcak7.txt cache: ./cache/cord-353241-ityhcak7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-353241-ityhcak7.txt' === file2bib.sh === id: cord-356370-jjl1hbeb author: Sahajpal, Nikhil Shri title: Role of clinical laboratories in response to the COVID-19 pandemic date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-356370-jjl1hbeb.txt cache: ./cache/cord-356370-jjl1hbeb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-356370-jjl1hbeb.txt' === file2bib.sh === id: cord-351492-8jv7ip67 author: Urwin, S. G. title: FebriDx point-of-care test in patients with suspected COVID-19: a pooled diagnostic accuracy study date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-351492-8jv7ip67.txt cache: ./cache/cord-351492-8jv7ip67.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351492-8jv7ip67.txt' === file2bib.sh === id: cord-354035-i3sl2r0k author: Wylie, Kristine M. title: The Virome of the Human Respiratory Tract date: 2016-12-10 pages: extension: .txt txt: ./txt/cord-354035-i3sl2r0k.txt cache: ./cache/cord-354035-i3sl2r0k.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354035-i3sl2r0k.txt' === file2bib.sh === id: cord-354103-4dldgqzf author: Grubic, Andrew D title: COVID-19 outbreak and surgical practice: The rationale for suspending non-urgent surgeries and role of testing modalities date: 2020-06-27 pages: extension: .txt txt: ./txt/cord-354103-4dldgqzf.txt cache: ./cache/cord-354103-4dldgqzf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354103-4dldgqzf.txt' === file2bib.sh === id: cord-355874-nz6eqcdb author: Wang, Le title: A GeXP-Based Assay for Simultaneous Detection of Multiple Viruses in Hospitalized Children with Community Acquired Pneumonia date: 2016-09-14 pages: extension: .txt txt: ./txt/cord-355874-nz6eqcdb.txt cache: ./cache/cord-355874-nz6eqcdb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355874-nz6eqcdb.txt' === file2bib.sh === id: cord-355988-4eldkteb author: SAMPATH, RANGARAJAN title: Rapid Identification of Emerging Infectious Agents Using PCR and Electrospray Ionization Mass Spectrometry date: 2007-04-23 pages: extension: .txt txt: ./txt/cord-355988-4eldkteb.txt cache: ./cache/cord-355988-4eldkteb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355988-4eldkteb.txt' === file2bib.sh === id: cord-355102-jcyq8qve author: Avila, Eduardo title: Hemogram data as a tool for decision-making in COVID-19 management: applications to resource scarcity scenarios date: 2020-06-29 pages: extension: .txt txt: ./txt/cord-355102-jcyq8qve.txt cache: ./cache/cord-355102-jcyq8qve.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355102-jcyq8qve.txt' === file2bib.sh === id: cord-355014-los6q1k4 author: Ai, J. title: Analysis of factors associated early diagnosis in coronavirus disease 2019 (COVID-19) date: 2020-04-14 pages: extension: .txt txt: ./txt/cord-355014-los6q1k4.txt cache: ./cache/cord-355014-los6q1k4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-355014-los6q1k4.txt' === file2bib.sh === id: cord-354773-u86bdmvf author: Suo, Tao title: ddPCR: a more accurate tool for SARS-CoV-2 detection in low viral load specimens date: 2020-06-07 pages: extension: .txt txt: ./txt/cord-354773-u86bdmvf.txt cache: ./cache/cord-354773-u86bdmvf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-354773-u86bdmvf.txt' === file2bib.sh === id: cord-356007-6b0w36l9 author: Alanazi, Khalid H. title: Scope and extent of healthcare-associated Middle East respiratory syndrome coronavirus transmission during two contemporaneous outbreaks in Riyadh, Saudi Arabia, 2017 date: 2018-12-31 pages: extension: .txt txt: ./txt/cord-356007-6b0w36l9.txt cache: ./cache/cord-356007-6b0w36l9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-356007-6b0w36l9.txt' === file2bib.sh === id: cord-350398-w75flrwv author: Sampath, Rangarajan title: Comprehensive Biothreat Cluster Identification by PCR/Electrospray-Ionization Mass Spectrometry date: 2012-06-29 pages: extension: .txt txt: ./txt/cord-350398-w75flrwv.txt cache: ./cache/cord-350398-w75flrwv.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-350398-w75flrwv.txt' === file2bib.sh === id: cord-353353-njvalb44 author: Lau, Susanna K. P. title: Identification of Novel Rosavirus Species That Infects Diverse Rodent Species and Causes Multisystemic Dissemination in Mouse Model date: 2016-10-13 pages: extension: .txt txt: ./txt/cord-353353-njvalb44.txt cache: ./cache/cord-353353-njvalb44.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353353-njvalb44.txt' === file2bib.sh === id: cord-354733-qxivrhj8 author: Gniazdowski, V. title: Repeat COVID-19 Molecular Testing: Correlation with Recovery of Infectious Virus, Molecular Assay Cycle Thresholds, and Analytical Sensitivity date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-354733-qxivrhj8.txt cache: ./cache/cord-354733-qxivrhj8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354733-qxivrhj8.txt' === file2bib.sh === id: cord-353810-mf753ae9 author: Tan, Cedric Chih Shen title: A novel method for the capture-based purification of whole viral native RNA genomes date: 2019-04-08 pages: extension: .txt txt: ./txt/cord-353810-mf753ae9.txt cache: ./cache/cord-353810-mf753ae9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-353810-mf753ae9.txt' === file2bib.sh === id: cord-355489-tkvfneje author: Mendez, Jairo A title: Phylogenetic history demonstrates two different lineages of dengue type 1 virus in Colombia date: 2010-09-14 pages: extension: .txt txt: ./txt/cord-355489-tkvfneje.txt cache: ./cache/cord-355489-tkvfneje.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355489-tkvfneje.txt' === file2bib.sh === id: cord-022889-lv6fy6e6 author: Dávalos, Alberto title: Literature review of baseline information on non‐coding RNA (ncRNA) to support the risk assessment of ncRNA‐based genetically modified plants for food and feed date: 2019-08-07 pages: extension: .txt txt: ./txt/cord-022889-lv6fy6e6.txt cache: ./cache/cord-022889-lv6fy6e6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 10 resourceName b'cord-022889-lv6fy6e6.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-352562-qfb478sf author: Yamamoto, Lidia title: SARS-CoV-2 infections with emphasis on pediatric patients: a narrative review date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-352562-qfb478sf.txt cache: ./cache/cord-352562-qfb478sf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-352562-qfb478sf.txt' === file2bib.sh === id: cord-346308-9h2fk9qt author: Kaur, Rajwinder title: Microbiology of hospital wastewater date: 2020-05-01 pages: extension: .txt txt: ./txt/cord-346308-9h2fk9qt.txt cache: ./cache/cord-346308-9h2fk9qt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-346308-9h2fk9qt.txt' === file2bib.sh === id: cord-006860-a3b8hyyr author: nan title: 40th Annual Meeting of the GTH (Gesellschaft für Thrombose- und Hämostaseforschung) date: 1996 pages: extension: .txt txt: ./txt/cord-006860-a3b8hyyr.txt cache: ./cache/cord-006860-a3b8hyyr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 8 resourceName b'cord-006860-a3b8hyyr.txt' === file2bib.sh === id: cord-007890-bie1veti author: nan title: ECC-4 Abstracts date: 2002-04-16 pages: extension: .txt txt: ./txt/cord-007890-bie1veti.txt cache: ./cache/cord-007890-bie1veti.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 23 resourceName b'cord-007890-bie1veti.txt' === file2bib.sh === id: cord-267671-ys43n672 author: Whary, Mark T. title: Biology and Diseases of Mice date: 2015-07-10 pages: extension: .txt txt: ./txt/cord-267671-ys43n672.txt cache: ./cache/cord-267671-ys43n672.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 7 resourceName b'cord-267671-ys43n672.txt' === file2bib.sh === id: cord-341434-2xrdv92m author: Nowland, Megan H. title: Biology and Diseases of Rabbits date: 2015-07-10 pages: extension: .txt txt: ./txt/cord-341434-2xrdv92m.txt cache: ./cache/cord-341434-2xrdv92m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-341434-2xrdv92m.txt' === file2bib.sh === id: cord-353190-7qcoxl81 author: Nicklas, Werner title: Viral Infections of Laboratory Mice date: 2012-05-17 pages: extension: .txt txt: ./txt/cord-353190-7qcoxl81.txt cache: ./cache/cord-353190-7qcoxl81.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-353190-7qcoxl81.txt' === file2bib.sh === id: cord-315598-qwh72inx author: Mendoza, Jose Luis Accini title: ACTUALIZACION DE LA DECLARACIÓN DE CONSENSO EN MEDICINA CRITICA PARA LA ATENCIÓN MULTIDISCIPLINARIA DEL PACIENTE CON SOSPECHA O CONFIRMACIÓN DIAGNÓSTICA DE COVID-19 date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-315598-qwh72inx.txt cache: ./cache/cord-315598-qwh72inx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 9 resourceName b'cord-315598-qwh72inx.txt' === file2bib.sh === id: cord-023364-ut56gczm author: nan title: EDUCATION DAY MONDAY: PLENARY SESSION 1 MONDAY: PARALLEL SESSIONS date: 2005-06-08 pages: extension: .txt txt: ./txt/cord-023364-ut56gczm.txt cache: ./cache/cord-023364-ut56gczm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 23 resourceName b'cord-023364-ut56gczm.txt' === file2bib.sh === id: cord-022501-9wnmdvg5 author: nan title: P1460 – P1884 date: 2015-12-28 pages: extension: .txt txt: ./txt/cord-022501-9wnmdvg5.txt cache: ./cache/cord-022501-9wnmdvg5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 22 resourceName b'cord-022501-9wnmdvg5.txt' === file2bib.sh === id: cord-023026-2r84ndzv author: nan title: Posters date: 2013-06-14 pages: extension: .txt txt: ./txt/cord-023026-2r84ndzv.txt cache: ./cache/cord-023026-2r84ndzv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 16 resourceName b'cord-023026-2r84ndzv.txt' === file2bib.sh === id: cord-023346-8sqbqjm1 author: nan title: MONDAY: POSTERS date: 2005-06-08 pages: extension: .txt txt: ./txt/cord-023346-8sqbqjm1.txt cache: ./cache/cord-023346-8sqbqjm1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 21 resourceName b'cord-023346-8sqbqjm1.txt' === file2bib.sh === id: cord-023354-f2ciho6o author: nan title: TUESDAY PLENARY SESSION 3 TUESDAY: POSTERS date: 2005-06-08 pages: extension: .txt txt: ./txt/cord-023354-f2ciho6o.txt cache: ./cache/cord-023354-f2ciho6o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 13 resourceName b'cord-023354-f2ciho6o.txt' === file2bib.sh === id: cord-023095-4dannjjm author: nan title: Research Abstract Program of the 2011 ACVIM Forum Denver, Colorado, June 15–18, 2011 date: 2011-05-03 pages: extension: .txt txt: ./txt/cord-023095-4dannjjm.txt cache: ./cache/cord-023095-4dannjjm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 10 resourceName b'cord-023095-4dannjjm.txt' === file2bib.sh === id: cord-006230-xta38e7j author: nan title: Deutsche Gesellschaft für Experimentelle und Klinische Pharmakologie und Toxikologie e.V. date: 2012-02-22 pages: extension: .txt txt: ./txt/cord-006230-xta38e7j.txt cache: ./cache/cord-006230-xta38e7j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 12 resourceName b'cord-006230-xta38e7j.txt' === file2bib.sh === id: cord-008777-i2reanan author: nan title: ECB12: 12th European Congess on Biotechnology date: 2005-07-19 pages: extension: .txt txt: ./txt/cord-008777-i2reanan.txt cache: ./cache/cord-008777-i2reanan.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 15 resourceName b'cord-008777-i2reanan.txt' === file2bib.sh === id: cord-014794-yppi30a0 author: nan title: 19th European Congress of Pathology, Ljubljana, Slovenia, September 6-11, 2003 date: 2003-07-31 pages: extension: .txt txt: ./txt/cord-014794-yppi30a0.txt cache: ./cache/cord-014794-yppi30a0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 23 resourceName b'cord-014794-yppi30a0.txt' === file2bib.sh === id: cord-001521-l36f1gp7 author: nan title: Oral and Poster Manuscripts date: 2011-04-08 pages: extension: .txt txt: ./txt/cord-001521-l36f1gp7.txt cache: ./cache/cord-001521-l36f1gp7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 28 resourceName b'cord-001521-l36f1gp7.txt' === file2bib.sh === id: cord-000718-7whai7nr author: nan title: ESP Abstracts 2012 date: 2012-08-22 pages: extension: .txt txt: ./txt/cord-000718-7whai7nr.txt cache: ./cache/cord-000718-7whai7nr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 15 resourceName b'cord-000718-7whai7nr.txt' === file2bib.sh === id: cord-022888-dnsdg04n author: nan title: Poster Sessions date: 2009-08-19 pages: extension: .txt txt: ./txt/cord-022888-dnsdg04n.txt cache: ./cache/cord-022888-dnsdg04n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 15 resourceName b'cord-022888-dnsdg04n.txt' === file2bib.sh === id: cord-031907-ilhr3iu5 author: nan title: ISEV2020 Abstract Book date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-031907-ilhr3iu5.txt cache: ./cache/cord-031907-ilhr3iu5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 18 resourceName b'cord-031907-ilhr3iu5.txt' === file2bib.sh === id: cord-015324-y44sfr0c author: nan title: Scientific Programme date: 2007-09-01 pages: extension: .txt txt: ./txt/cord-015324-y44sfr0c.txt cache: ./cache/cord-015324-y44sfr0c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 14 resourceName b'cord-015324-y44sfr0c.txt' === file2bib.sh === id: cord-023211-kt5gt26t author: nan title: Poster Session Abstracts date: 2007-08-29 pages: extension: .txt txt: ./txt/cord-023211-kt5gt26t.txt cache: ./cache/cord-023211-kt5gt26t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 18 resourceName b'cord-023211-kt5gt26t.txt' === file2bib.sh === id: cord-010092-uftc8inx author: nan title: Abstract of 29th Regional Congress of the ISBT date: 2019-06-07 pages: extension: .txt txt: ./txt/cord-010092-uftc8inx.txt cache: ./cache/cord-010092-uftc8inx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 20 resourceName b'cord-010092-uftc8inx.txt' === file2bib.sh === id: cord-010119-t1x9gknd author: nan title: Abstract Presentations from the AABB Annual Meeting San Diego, CA ctober 7‐10, 2017 date: 2017-09-04 pages: extension: .txt txt: ./txt/cord-010119-t1x9gknd.txt cache: ./cache/cord-010119-t1x9gknd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 20 resourceName b'cord-010119-t1x9gknd.txt' === file2bib.sh === id: cord-015394-uj7fe5y6 author: nan title: Scientific Abstracts date: 2008-12-23 pages: extension: .txt txt: ./txt/cord-015394-uj7fe5y6.txt cache: ./cache/cord-015394-uj7fe5y6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 29 resourceName b'cord-015394-uj7fe5y6.txt' === file2bib.sh === id: cord-022940-atbjwpo5 author: nan title: Poster Sessions date: 2016-09-07 pages: extension: .txt txt: ./txt/cord-022940-atbjwpo5.txt cache: ./cache/cord-022940-atbjwpo5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 19 resourceName b'cord-022940-atbjwpo5.txt' === file2bib.sh === id: cord-005453-4057qib7 author: nan title: The 45th Annual Meeting of the European Society for Blood and Marrow Transplantation: Physicians – Poster Session date: 2019-07-03 pages: extension: .txt txt: ./txt/cord-005453-4057qib7.txt cache: ./cache/cord-005453-4057qib7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 38 resourceName b'cord-005453-4057qib7.txt' === file2bib.sh === id: cord-005460-ezrn8cva author: nan title: Physicians – Poster Session date: 2017-07-28 pages: extension: .txt txt: ./txt/cord-005460-ezrn8cva.txt cache: ./cache/cord-005460-ezrn8cva.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 39 resourceName b'cord-005460-ezrn8cva.txt' Que is empty; done keyword-pcr-cord === reduce.pl bib === id = cord-000322-8ctsa9sd author = Ninove, Laetitia title = RNA and DNA Bacteriophages as Molecular Diagnosis Controls in Clinical Virology: A Comprehensive Study of More than 45,000 Routine PCR Tests date = 2011-02-09 pages = extension = .txt mime = text/plain words = 2892 sentences = 130 flesch = 46 summary = Subsequently, T4 and MS2 ICs were evaluated in routine real-time PCR or RT-PCR virological diagnostic tests, using a series of 8,950 clinical samples (representing 36 distinct specimen types) sent to our laboratory for the detection of a variety of DNA and RNA viruses. It represents a valuable strategy for enhancing the quality of routine molecular diagnosis in laboratories that use in-house designed diagnostic systems, which can conveniently be associated to the use of specific synthetic ECs. The high rate of inhibitors observed in a variety of specimen types should stimulate the elaboration of improved technical protocols for the extraction and amplification of nucleic acids. Monitoring rt-PCR and rt-RT-PCR assays and validation of the results rely on the use of relevant external or internal controls (ECs or ICs) [1, 2] and commercial kits including such control systems are being increasingly improved for the molecular diagnosis of a number of pathogens such as HIV, hepatitis viruses, influenza viruses etc.. cache = ./cache/cord-000322-8ctsa9sd.txt txt = ./txt/cord-000322-8ctsa9sd.txt === reduce.pl bib === id = cord-000235-782iew86 author = Kapoor, A title = Human bocaviruses are highly diverse, dispersed, recombination prone, and prevalent enteric infections date = 2010-06-01 pages = extension = .txt mime = text/plain words = 4182 sentences = 228 flesch = 54 summary = The multiple species and high degree of genetic diversity seen among the human bocaviruses found in feces relative to the highly homogeneous HBoV1 suggest that this world-wide distributed respiratory pathogen may have recently evolved from an enteric bocavirus, perhaps after acquiring an expanded tropism favoring the respiratory track. Most PCR-positive stool samples contained HBoV2B (76 of 101), making this genotype the most commonly detected enteric human bocavirus (Table 1) . Based on the phylogenetic clustering observed for a large number of partial VP1 sequences ( Figure 1 ) and the distances among full genomes (Table 2) , we propose for future classification that HBoV strains showing 18% protein and 110% nucleotide difference in the complete VP1 gene should be considered different species, whereas those showing 11.5% protein and 15% nucleotide difference should be considered different genotypes. cache = ./cache/cord-000235-782iew86.txt txt = ./txt/cord-000235-782iew86.txt === reduce.pl bib === id = cord-000113-d0eur1hq author = Fooks, Anthony R. title = Emerging Technologies for the Detection of Rabies Virus: Challenges and Hopes in the 21st Century date = 2009-09-29 pages = extension = .txt mime = text/plain words = 6937 sentences = 319 flesch = 38 summary = The advent of molecular biology and new technological initiatives that combine advances in biology with other disciplines will support the development of techniques capable of high throughput testing with a low turnaround time for rabies diagnosis. The advent of molecular biology and new technological initiatives that combine advances in biology with other disciplines will support the development of techniques capable of high throughput testing with a low turnaround time for rabies diagnosis. Another method for the detection of rabies virus antigen from postmortem samples is a recently developed rapid immunodiagwww.plosntds.org nostic test (RIDT) based on the principles of immunochromatography [13] . Development of RT-LAMP assays for use in diagnosis and surveillance is challenged by the considerable sequence variation observed within the rabies virus genome [44] that can frustrate specific primer design. Currently, high-throughput rabies virus molecular detection methods augment standard diagnostic tests or are in the process of development and refinement for use alone. cache = ./cache/cord-000113-d0eur1hq.txt txt = ./txt/cord-000113-d0eur1hq.txt === reduce.pl bib === id = cord-000664-085v7n6k author = Cordey, Samuel title = Pilot Evaluation of RT-PCR/Electrospray Ionization Mass Spectrometry (PLEX-ID/Flu assay) on Influenza-Positive Specimens date = 2012-05-09 pages = extension = .txt mime = text/plain words = 2027 sentences = 100 flesch = 43 summary = The PLEX-ID/Flu assay has been recently developed to enable the detection and typing of influenza viruses based on the RT-PCR/electrospray ionization mass spectrometry technology. Taken together, and although our results need to be confirmed by further prospective studies, the PLEX-ID/Flu assay detected positively and gave a typing result for 93% of all NPS detected positively by real-time RT-PCR, thus suggesting a potential role for influenza virus surveillance among other techniques. The typing performance of the PLEX-ID/Flu assay versus the Sanger-based sequencing method was then compared for all influenza specimens with low viral loads (C T values 30; 19 influenza A and 18 influenza B-positive NPS; Table 2 ). Based on a selection of positive NPS collected in Switzerland during the 2010-2011 influenza season, this study suggests that the PLEX-ID/Flu assay is a convenient platform for the detection, typing, and subtyping (lineage characterization for influenza B) of circulating influenza viruses. cache = ./cache/cord-000664-085v7n6k.txt txt = ./txt/cord-000664-085v7n6k.txt === reduce.pl bib === id = cord-000180-howix091 author = MacLeod, Iain J. title = Binding of Herpes Simplex Virus Type-1 Virions Leads to the Induction of Intracellular Signalling in the Absence of Virus Entry date = 2010-03-05 pages = extension = .txt mime = text/plain words = 6788 sentences = 316 flesch = 49 summary = By taking advantage of the entry-defective phenotype of glycoprotein-deficient HSV-1 virus particles, the results presented here show that binding of virions to cellular receptors on the plasma membrane is sufficient to stimulate a change in cellular gene expression. As induction of the NF-kB reporter construct occurred within one hour of inoculation with DgH virions and peaked at around two-and-a-half hours post-inoculation, then the transcripts previHFFs were stimulated with 1000 particles/cell of DgB, DgD or DgH HSV-1 for six hours and a cDNA microarray corresponding to targets of 19 signalling pathways was used to detect changes in cellular gene expression when compared to mock-infected. Real-time PCR confirmed that changes in transcription associated with the NF-kB, JAK/STAT, JAK/Src and PI3K pathways were modulated as a result of virion binding, all of which required gD on the envelope surface To demonstrate that signalling occurred at physiologically relevant multiplicities of infection, HFFs were inoculated with either 1000, 100, 10 or 1 particles per cell of entry-defective HSV-1. cache = ./cache/cord-000180-howix091.txt txt = ./txt/cord-000180-howix091.txt === reduce.pl bib === id = cord-000010-prsvv6l9 author = Qin, Jian title = Studying copy number variations using a nanofluidic platform date = 2008-08-18 pages = extension = .txt mime = text/plain words = 4986 sentences = 250 flesch = 51 summary = Copy number variations (CNVs) in the human genome are conventionally detected using high-throughput scanning technologies, such as comparative genomic hybridization and high-density single nucleotide polymorphism (SNP) microarrays, or relatively low-throughput techniques, such as quantitative polymerase chain reaction (PCR). We have developed a new technology to study copy numbers using a platform known as the digital array, a nanofluidic biochip capable of accurately quantitating genes of interest in DNA samples. Other existing technologies, such as quantitative polymerase chain reaction (PCR), are limited because of their inability to reliably distinguish less than a twofold difference in copy number of a particular gene in DNA samples (11) (12) (13) . In this study we demonstrate the use of a unique integrated nanofluidic system, the digital array, in the study of CNVs. The digital array (14, 15) is able to accurately quantitate DNA samples based on the fact that single DNA molecules are randomly distributed in more than 9000 reaction chambers and then PCR amplified. cache = ./cache/cord-000010-prsvv6l9.txt txt = ./txt/cord-000010-prsvv6l9.txt === reduce.pl bib === id = cord-000483-zgapjjjw author = Faux, Cassandra E. title = Usefulness of Published PCR Primers in Detecting Human Rhinovirus Infection date = 2011-02-17 pages = extension = .txt mime = text/plain words = 1668 sentences = 83 flesch = 48 summary = We conducted a preliminary comparison of the relative sensitivity of a cross-section of published human rhinovirus (HRV)–specific PCR primer pairs, varying the oligonucleotides and annealing temperature. We conducted a preliminary comparison of the relative sensitivity of a cross-section of published HRV-specifi c PCR primer pairs (most of which were fi rst published before HRV-C was reported), independent of most variables described above, by testing a panel of 57 clinical specimen nucleic acid extracts from combined nose and throat swabs from preschool children with colds and infl uenza-like illnesses in Melbourne, Australia. Five primer pairs, including real-time PCR (rtPCR) pair 5, did not amplify the HEVs, a positive feature for HRV-specifi c studies. We next selected 4 frequently published primer pairs (1, 5, 7, and 8) to examine 44 picornavirus-positive specimens (39 HRVs, 3 HEVs, and 2 untypeable picornaviruses) from nonhospitalized children with acute asthma exacerbation (6) . cache = ./cache/cord-000483-zgapjjjw.txt txt = ./txt/cord-000483-zgapjjjw.txt === reduce.pl bib === id = cord-001455-n7quwr4s author = Rapin, Noreen title = Activation of Innate Immune-Response Genes in Little Brown Bats (Myotis lucifugus) Infected with the Fungus Pseudogymnoascus destructans date = 2014-11-12 pages = extension = .txt mime = text/plain words = 3719 sentences = 198 flesch = 50 summary = title: Activation of Innate Immune-Response Genes in Little Brown Bats (Myotis lucifugus) Infected with the Fungus Pseudogymnoascus destructans Using tissue samples collected at the termination of an experiment to explore the pathogenesis of White Nose Syndrome in Little Brown Bats, we determined if hibernating bats infected with the fungus Pseudogymnoascus destructans could respond to infection by activating genes responsible for innate immune and stress responses. We found that bats responded to infection with a significant increase in lungs of transcripts for Cathelicidin (an anti-microbial peptide) as well as the immune modulators tumor necrosis factor alpha and interleukins 10 and 23. We used samples collected during the experiment to address the question: Can hibernating bats respond to infection by activating genes responsible for innate immune and stress responses? We determined levels of transcripts for several immune and stress response genes (Table 1) in lungs from infected and control bats. cache = ./cache/cord-001455-n7quwr4s.txt txt = ./txt/cord-001455-n7quwr4s.txt === reduce.pl bib === id = cord-006960-9pho3hk6 author = Prakash, R. title = Droplet Microfluidic Chip Based Nucleic Acid Amplification and Real-Time Detection of Influenza Viruses date = 2013-12-27 pages = extension = .txt mime = text/plain words = 6279 sentences = 286 flesch = 51 summary = In this work, we have utilized electro-actuation based DMF technology, integrated with suitably tailored resistive micro-heaters and temperature sensors, to achieve chip based real-time, quantitative PCR (qRT-PCR). Performance of the integrated DMF device was analyzed in real-time chip based qRT-PCR detection of in-vitro synthesized influenza A and C virus RNAs during 30-35 PCR cycles. Among the contact temperature control methods, the micro-fabricated resistive heaters/RTDs have smaller power requirement, faster thermal response and higher heating ramp rates and are therefore preferred for the proposed qRT-PCR micro-device. Mixing of the influenza C RNA sample and the off-chip prepared PCR reagents, followed by the RT reaction and thermal cycling over Micro-electrode 1, is shown in Figure 7 . This article demonstrates the design and micro-fabrication of integrated droplet microfluidic device, with nano-textured superhydrophobic top surface, that is capable of electro-handling of PCR samples/reagents, facilitating chip based mixing/sample preparation and chip based qRT-PCR amplification and detection of influenza viruses. cache = ./cache/cord-006960-9pho3hk6.txt txt = ./txt/cord-006960-9pho3hk6.txt === reduce.pl bib === id = cord-002852-m4l2l2r1 author = Munyua, Peninah M. title = Detection of influenza A virus in live bird markets in Kenya, 2009–2011 date = 2012-04-19 pages = extension = .txt mime = text/plain words = 3991 sentences = 240 flesch = 60 summary = authors: Munyua, Peninah M.; Githinji, Jane W.; Waiboci, Lilian W.; Njagi, Leonard M.; Arunga, Geoffrey; Mwasi, Lydia; Murithi Mbabu, R.; Macharia, Joseph M.; Breiman, Robert F.; Kariuki Njenga, M.; Katz, Mark A. Background Surveillance for influenza viruses within live bird markets (LBMs) has been recognized as an effective tool for detecting circulating avian influenza viruses (AIVs). Efforts should be made to promote practices that could limit the maintenance and transmission of AIVs in LBMs. Influenza A viruses are zoonotic pathogens that infect a variety of domestic poultry such as chickens, turkeys, ducks, and geese. 2, 4, 5 Surveillance for influenza viruses within live bird markets (LBMs) has been recognized as an effective tool for detecting circulating influenza subtypes in the poultry population. 7, 8 Influenza viruses have also been detected in various environmental specimens collected in contaminated areas in LBMs including drinking water troughs, and surfaces in the delivery, holding and slaughter areas in markets. cache = ./cache/cord-002852-m4l2l2r1.txt txt = ./txt/cord-002852-m4l2l2r1.txt === reduce.pl bib === id = cord-000750-l9ozvlae author = Betts, Corinne title = Pip6-PMO, A New Generation of Peptide-oligonucleotide Conjugates With Improved Cardiac Exon Skipping Activity for DMD Treatment date = 2012-08-14 pages = extension = .txt mime = text/plain words = 6521 sentences = 337 flesch = 46 summary = We have previously reported impressive heart activity including high-splicing efficiency and dystrophin restoration following a single administration of an arginine-rich cell-penetrating peptide (CPPs) conjugated to a phosphorodiamidate morpholino oligonucleotide (PMO): Pip5e-PMO. We have previously reported impressive heart activity including high-splicing efficiency and dystrophin restoration following a single administration of an arginine-rich cell-penetrating peptide (CPPs) conjugated to a phosphorodiamidate morpholino oligonucleotide (PMO): Pip5e-PMO. These changes affect the levels of exon skipping and dystrophin restoration in multiple muscle groups, including the heart, following a single, low dose intravenous injection of the corresponding Pip6-PMO conjugates. Therefore, considering the results overall, mdx mice treated with each of the four 5-aa core Pip6-PMOs (Pip6a-, Pip6b-, Pip6e-, and Pip6f-PMO) appear to demonstrate improved dystrophin production and exon skipping in TA, quadriceps, and heart muscles compared with the previous lead candidate, Pip5e-PMO. cache = ./cache/cord-000750-l9ozvlae.txt txt = ./txt/cord-000750-l9ozvlae.txt === reduce.pl bib === id = cord-003047-3ejfxj6r author = Bai, Jianfa title = Comparison data of a two-target real-time PCR assay with and without an internal control in detecting Salmonella enterica from cattle lymph nodes date = 2018-04-22 pages = extension = .txt mime = text/plain words = 1095 sentences = 66 flesch = 60 summary = title: Comparison data of a two-target real-time PCR assay with and without an internal control in detecting Salmonella enterica from cattle lymph nodes Data was generated by the duplex qPCR assay on 138 enriched cattle lymph node samples without the internal control, and compared with data on the same samples tested by the triplex qPCR assay that has Similar threshold cycle (Ct) data were generated with and without the use of the 18S rRNA gene as internal control. Real-time PCR (qPCR) test data on 138 culture-enriched cattle lymph node samples for Salmonella enterica detections is shown in Table 1 . One Table 1 Real-time PCR threshold cycle (Ct) data on 138 Salmonella-positive cattle lymph node samples with and without the 18S rRNA internal control. A multiplex real-time PCR assay, based on invA and pagC genes, for the detection and quantification of Salmonella enterica from cattle lymph nodes cache = ./cache/cord-003047-3ejfxj6r.txt txt = ./txt/cord-003047-3ejfxj6r.txt === reduce.pl bib === id = cord-001134-8ljgxnhf author = Lin, Chao-Nan title = Comparison of viremia of type II porcine reproductive and respiratory syndrome virus in naturally infected pigs by zip nucleic acid probe-based real-time PCR date = 2013-09-12 pages = extension = .txt mime = text/plain words = 2978 sentences = 165 flesch = 52 summary = title: Comparison of viremia of type II porcine reproductive and respiratory syndrome virus in naturally infected pigs by zip nucleic acid probe-based real-time PCR In this study, we developed a sensitive and specific zip nucleic acid probe-based real-time PCR assay to evaluate the viremia of natural PRRSV-infected pigs in Taiwan. CONCLUSIONS: ZNA probe-based real-time PCR can be a useful tool to diagnose symptomatic and asymptomatic PRRSV-infected pigs. ZNA probe-based real-time PCR amplification and the limit of detection Tenfold serial plasmid dilutions (10 1 to 10 6 copies/μl) were tested and used to construct the standard curve by plotting the logarithm of the plasmid copy number against the measured quantification cycles (Cq) values. However, this is first study to report the viral load using serum samples in asymptomatic PRRSV-infected pigs using ZNA probebased real-time PCR. Development of a onestep real-time quantitative PCR assay based on primer-probe energy transfer for the detection of porcine reproductive and respiratory syndrome virus cache = ./cache/cord-001134-8ljgxnhf.txt txt = ./txt/cord-001134-8ljgxnhf.txt === reduce.pl bib === id = cord-005309-147erliy author = Senanayake, Savithra D. title = Precise large deletions by the PCR-based overlap extension method date = 1995 pages = extension = .txt mime = text/plain words = 859 sentences = 44 flesch = 59 summary = The authors describe an efficient method for generating large deletions (>200 nts) of precise length using the PCR-based method of gene splicing by overlap extension (1). Gene splicing by overlap extension or gene SOEing (1) is a powerful PCR-based technique for generating recombinant DNA molecules. A cloned 2231 nt subgenomic defective-interfering RNA of the bovine coronavirus in the pGEM3Zf(-) vector (Promega), containing an in-frame reporter sequence and called pDrepl (4) ( Fig. 1 ) was used for large deletion mutagenesis. GT3', the "universal" primer for pGEM vectors, and primer B, 5'CTTACCAGGAGTAAAAGA CATTGTGACCTATGGGTGGGCC3', which anneals to bases 192-213 and 502-519 in the genome-sense (plus) strand of pDrepl and forms the deletion, were used in the first round of PCR. Oligonucleotidedirected mutagenesis: A simple method using two oligonucleotide primers and a single-stranded DNA template cache = ./cache/cord-005309-147erliy.txt txt = ./txt/cord-005309-147erliy.txt === reduce.pl bib === id = cord-002376-970934vm author = Mikel, Pavel title = Preparation of MS2 Phage-Like Particles and Their Use As Potential Process Control Viruses for Detection and Quantification of Enteric RNA Viruses in Different Matrices date = 2016-12-01 pages = extension = .txt mime = text/plain words = 6581 sentences = 311 flesch = 52 summary = The quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay is nowadays considered as the gold standard method for detection and quantification of enteric RNA viruses such as hepatitis A virus (HAV), hepatitis E virus (HEV) or human noroviruses (NoV) (Mattison et al., 2009; Blaise-Boisseau et al., 2010; Di Pasquale et al., 2010; Vasickova et al., 2012; Hennechart-Collette et al., 2014) . The present article is a followup study of a previously published theoretical concept (Mikel et al., 2015) and describes a method of preparation of MS2 PLP carrying a specific control sequence and their use as a PCV in RT-qPCR detection and quantification of enteric RNA viruses in swab, liver tissue, serum, feces, and vegetable samples. MS2 PLP were added in the amount of 5 × 10 6 particles to the different types of matrices (swabs, liver tissue, serum, feces, and leafy green vegetables) to reveal their ability to serve as PCV in the RT-qPCR detection of enteric RNA viruses. cache = ./cache/cord-002376-970934vm.txt txt = ./txt/cord-002376-970934vm.txt === reduce.pl bib === id = cord-000715-zl1s82yi author = Shulman, Lester M. title = Evaluation of Four Different Systems for Extraction of RNA from Stool Suspensions Using MS-2 Coliphage as an Exogenous Control for RT-PCR Inhibition date = 2012-07-16 pages = extension = .txt mime = text/plain words = 4786 sentences = 248 flesch = 50 summary = These samples were selected from among archived stool samples previously tested for enterovirus and MS2 after extraction by QIAamp Viral RNA Mini Kit. A sufficient number of samples with high, intermediate, and low levels of inhibitors were chosen for re-analysis to enable comparison between extraction procedures at each of these levels of inhibition. Analysis of variance ( Fig. 3 , part 2), indicated that there was no significant difference (paired t-test, P.0.05) between the inhibition of rRT-PCR of the MS2 external control and the added enterovirus (P.0.05) for protocols A, C, and D. Stool suspensions (N = 185) prepared for routine analysis of clinical stool samples sent to the Central Virology Laboratory (CVL) at Chaim Sheba Medical Center in Israel were used to evaluate the efficiency of four different RNA extraction systems in excluding inhibitors of rRT-PCR. cache = ./cache/cord-000715-zl1s82yi.txt txt = ./txt/cord-000715-zl1s82yi.txt === reduce.pl bib === id = cord-000830-jiy4cp4n author = Cobo, Fernando title = Application of Molecular Diagnostic Techniques for Viral Testing date = 2012-11-30 pages = extension = .txt mime = text/plain words = 7969 sentences = 385 flesch = 39 summary = The use of amplification techniques such as polymerase chain reaction, real-time polymerase chain reaction or nucleic acid sequence-based amplification for virus detection, genotyping and quantification have some advantages like high sensitivity and reproducibility, as well as a broad dynamic range. The use of amplification techniques such as polymerase chain reaction (PCR), real-time PCR or nucleic acid sequence-based amplification (NASBA) [3] for virus detection, genotyping and quantification have some advantages like high sensitivity and reproducibility, as well as a broad dynamic range [4, 5] . NASBA assays could identify active infection by detecting viral messenger RNA (mRNA) but the most widely used tests in clinical virus diagnosis are quantitative real-time PCR techniques [8] . Some real-time PCR assays such as LightCycler parvovirus B19 quantitative assay (Roche Diagnostics, Indianapolis, IN) and ABI TaqMan (Applied Biosystems) have been developed for detecting B19 nucleic acids in association with infection during pregnancy or assessing the prevalence of the virus DNA in blood products [62, 63] . cache = ./cache/cord-000830-jiy4cp4n.txt txt = ./txt/cord-000830-jiy4cp4n.txt === reduce.pl bib === id = cord-001843-ceatyj3o author = Huang, Yong title = Ultrasensitive Detection of RNA and DNA Viruses Simultaneously Using Duplex UNDP-PCR Assay date = 2015-11-06 pages = extension = .txt mime = text/plain words = 5184 sentences = 231 flesch = 50 summary = PCV2 DNA and TGEV RNA were simultaneously released from the serum sample by boiling with lysis buffer, then magnetic beads and gold nanoparticles coated with single and/or duplex specific probes for TGEV and PCV2 were added to form a sandwich-like complex with nucleic acids released from viruses. This duplex UNDP-PCR assay could detect TGEV (RNA virus) and PCV2 (DNA virus) from large-scale serum samples simultaneously without the need for DNA/RNA extraction, purification and reverse transcription of RNA, and showed a significantly increased positive detection rate for PCV2 (29%) and TGEV (11.7%) preclinical infection than conventional duplex PCR/RT-PCR. The duplex UNDP-PCR assay is suitable for simultaneous detection of RNA and DNA viruses in early viral infection, providing an effective approach for diagnosis of swine diseases. The duplex UNDP-PCR assay developed in this study provided a useful tool for simultaneous detection of RNA (TGEV) and DNA viruses (PCV2) without the need for viral nucleic acid extraction, purification and reverse transcription. cache = ./cache/cord-001843-ceatyj3o.txt txt = ./txt/cord-001843-ceatyj3o.txt === reduce.pl bib === id = cord-007427-iqwojhq2 author = Dedkov, Vladimir G. title = Development and Evaluation of a One-Step Quantitative RT-PCR Assay for Detection of Lassa Virus date = 2019-06-03 pages = extension = .txt mime = text/plain words = 4043 sentences = 213 flesch = 53 summary = Based on sequencing data, LASV-specific assay was developed using synthetic MS2-phage-based armored RNA particles, RNA from Lassa virus strain Josiah, and further, evaluated in field conditions using samples from patients and Mastomys natalensis rodents. Viral RNAs were examined for Lassa immediately after extraction by the staff of the Virology Laboratory of Hemorrhagic Fevers Research Project of Gamal Abdel Nasser University of Conakry, Guinea and were then used to assess diagnostic sensitivity and specificity. In addition, LOD was assessed using a series of 10-fold dilutions of ARPs. For this purpose, eight LASV sequences of a maximal number of mismatches in the targeting region of L gene were selected (including a sequence of the strain Josiah, which was also used for the generation of the positive controls) and generated for the production of ARPs as described above (Table 2 ) . cache = ./cache/cord-007427-iqwojhq2.txt txt = ./txt/cord-007427-iqwojhq2.txt === reduce.pl bib === id = cord-003505-qr6ukfti author = Tabraue-Chávez, Mavys title = A colorimetric strategy based on dynamic chemistry for direct detection of Trypanosomatid species date = 2019-03-06 pages = extension = .txt mime = text/plain words = 5655 sentences = 331 flesch = 50 summary = In this work, we have developed a novel colorimetric molecular assay that integrates nucleic acid analysis by dynamic chemistry (ChemNAT) with reverse dot-blot hybridization in an array format for a rapid and easy discrimination of Leishmania major and Trypanosoma cruzi. Once the abasic PNA probes hybridize with target sequences, the SMART-C-Biotin dynamic incorporation takes place, enabling the unequivocal identification of the parasite present in the amplicon sample, because of the unique colorimetric pattern that each Trypanosomatid amplicon generates. DNA amplicon products were denatured and then together with the dynamic chemistry reaction reagents added directly into the internal column of the Spin-Tube that supports the nylon membrane for the color-development assay (Fig. 4) . 20 ng of human gDNA were used as PCR template for its amplification with the set of primers described in our study and neither colorimetric signals nor bands were detected using the Spin-Tube and capillary electrophoresis analysis respectively (Fig. 5 , column 2: 2A and 2B), hence probing the specificity when human gDNA is present. cache = ./cache/cord-003505-qr6ukfti.txt txt = ./txt/cord-003505-qr6ukfti.txt === reduce.pl bib === id = cord-000736-6f8vyziv author = Pripuzova, Natalia title = Development of Real-Time PCR Array for Simultaneous Detection of Eight Human Blood-Borne Viral Pathogens date = 2012-08-17 pages = extension = .txt mime = text/plain words = 6818 sentences = 328 flesch = 54 summary = FINDINGS: We developed a real-time PCR array capable of simultaneously detecting eight human viral pathogens: human immunodeficiency virus types 1 and 2 (HIV-1 and -2), hepatitis B virus (HBV), hepatitis C virus (HCV), human T-cell leukemia virus-1 and -2 (HTLV-1 and -2), vaccinia virus (VACV) and West Nile virus (WNV). The analytical sensitivity of each primer set was determined in the single virus testing using FDA/CBER panels (kindly provided by Dr. Stephen Kerby, FDA/CBER) consisting of various amounts of the viruses (0-1,000 genome copies/ml) spiked into the ''normal'' human plasma. The results of sensitivity testing of the real-time PCR array primer sets specific for HIV-1, HIV-2, HBV, HCV, and WNV the with FDA/CBER analytical plasma panels. Tm and C(t) values obtained with primer sets specific for HIV-1, HCV, or HBV in testing of 17 human clinical samples in the format of PCR array targeting eight different viruses. cache = ./cache/cord-000736-6f8vyziv.txt txt = ./txt/cord-000736-6f8vyziv.txt === reduce.pl bib === id = cord-001787-lj1nd922 author = Liu, Ying title = Enhancing production of ergosterol in Pichia pastoris GS115 by over-expression of 3-hydroxy-3-methylglutaryl CoA reductase from Glycyrrhiza uralensis date = 2014-04-02 pages = extension = .txt mime = text/plain words = 3105 sentences = 174 flesch = 56 summary = title: Enhancing production of ergosterol in Pichia pastoris GS115 by over-expression of 3-hydroxy-3-methylglutaryl CoA reductase from Glycyrrhiza uralensis pastoris strains containing different copy numbers of the GuHMGR gene were obtained and the content of ergosterol was analyzed by HPLC. In this study, we investigated how copy number variation (CNV) of the GuHMGR gene affects the formation of ergosterol. pastoris strains containing different copy numbers of the GuHMGR gene were induced to express the gene; P. pastoris strains was 1.07-2.51 times higher than in the negative control but with increase in the copy number of GuHMGR gene; the content of ergosterol showed an increasing-decreasingincreasing pattern. pastoris strain containing 44 copies of the GuHMGR gene. In this study, the dependence of the content of ergosterol on the copy number of the GuHMGR gene suggests that an increase in the latter could lead to an increase in the production of GA in G. cache = ./cache/cord-001787-lj1nd922.txt txt = ./txt/cord-001787-lj1nd922.txt === reduce.pl bib === id = cord-000979-cav9n18w author = Hoppe, Sebastian title = Rapid Identification of Novel Immunodominant Proteins and Characterization of a Specific Linear Epitope of Campylobacter jejuni date = 2013-05-29 pages = extension = .txt mime = text/plain words = 10056 sentences = 595 flesch = 50 summary = title: Rapid Identification of Novel Immunodominant Proteins and Characterization of a Specific Linear Epitope of Campylobacter jejuni The innovative approach presented herein of generating cDNAs of prokaryotes in combination with a microarray platform rendering time-consuming purification steps obsolete has helped to illuminate novel immunodominant proteins of C.jejuni. Additionally, the structure and antigenicity of the proteins and epitopes were modelled to analyze the suitability of the identified sequences for future applications like diagnostic tools or vaccine development. For a summary of the predicted characteristics, see S9: Transmembrane and antigenic potential of three potential epitope sites for cj0920c.Further, specificity control assays revealed that these signals do not drop significantly when using antibodies to Salmonella enterica indicative of nonspecific binding to occur, see S10: Specific vs. jejuni and were able to determine the important residue involved in antibody binding as well as modelling the epitope's accessibility within the full-length protein. cache = ./cache/cord-000979-cav9n18w.txt txt = ./txt/cord-000979-cav9n18w.txt === reduce.pl bib === id = cord-001858-nmi39n6h author = Petriccione, Milena title = Reference gene selection for normalization of RT-qPCR gene expression data from Actinidia deliciosa leaves infected with Pseudomonas syringae pv. actinidiae date = 2015-11-19 pages = extension = .txt mime = text/plain words = 5567 sentences = 286 flesch = 50 summary = title: Reference gene selection for normalization of RT-qPCR gene expression data from Actinidia deliciosa leaves infected with Pseudomonas syringae pv. Primer sequence (5′-3′) BestKeeper and the deltaCt method) were used to evaluate the stability of expression of selected RGs. The analyses were performed for three comparison groups considering both low-and high-dose bacterial inocula in the leaves and their combined dataset. In kiwifruit leaves with a high dose of bacterial inoculum, BestKeeper revealed that only the expression of TUB overcame the stability threshold; CYP and GAPDH were considered to be the most stable genes, with SD values of 0.50 and 0.61, respectively (Table 3 ). The expression of three genes encoding the reactive oxygen species (ROS) scavenging enzymes ascorbate peroxidase (APX), superoxide dismutase (SOD) and catalase (CAT), induced during the systemic infection of kiwifruit leaves with PSA, were chosen to further validate the reliability of the selected RGs for the normalization of RT-qPCR data. cache = ./cache/cord-001858-nmi39n6h.txt txt = ./txt/cord-001858-nmi39n6h.txt === reduce.pl bib === id = cord-001655-uqw74ra0 author = Stenglein, Mark D. title = Widespread Recombination, Reassortment, and Transmission of Unbalanced Compound Viral Genotypes in Natural Arenavirus Infections date = 2015-05-20 pages = extension = .txt mime = text/plain words = 8100 sentences = 479 flesch = 48 summary = The sets of viral genotypes ranged from that which would be expected for a straightforward co-infection by 2 virus strains in snake #45, to more complex combinations such as that in snake #33, which contained the sequences of 1 S and 10 distinct L segments. We applied homogenates from samples to cultures of boa constrictor-derived JK cells and monitored levels of virus RNA by qRT-PCR using genotype-discriminating primers. Thus, sequences of multiple viral genotypes Recombinant genome segments with unusual organizations. Virus populations replicate as stable ensembles in culture: (A) Liver homogenate from snake #38 was applied to cultures of JK cells and replication was monitored by measuring supernatant viral RNA levels using qRT-PCR and genotype-specific primers. Although we detected many instances of snake tissues containing multiple viral genotypes, our results do not prove that individual cells in these animals were multiply infected. cache = ./cache/cord-001655-uqw74ra0.txt txt = ./txt/cord-001655-uqw74ra0.txt === reduce.pl bib === id = cord-007066-zn10rnrm author = Park, Noh Jin title = Characterization of RNA in Saliva date = 2006-06-01 pages = extension = .txt mime = text/plain words = 4637 sentences = 285 flesch = 62 summary = RNA can enter the oral cavity through various routes, including saliva secretions from the 3 major salivary glands (the parotid, submandibular, and sublingual glands) and minor glands, gingival crevice fluid (GCF), and desquamated oral epithelial cells. It is therefore possible that the RPS9 PCR products in panels B and C of Fig. 1 are produced from both RPS9 and RPS9P2 mRNAs. Previous expression-based microarray analysis showed that 185 different transcripts were consistently detected in the supernatants of 10 healthy human saliva samples (6 ) . Although individual variations exist, we detected ␤-actin mRNA in all 3 major salivary glands, GCF, and desquamated oral epithelial cells ( Fig. 2A) , suggesting that RNA enters the oral cavity from different sites. In addition to the saliva samples, we also measured RNA-macromolecule associations in serum and found that ϳ8% and Ͻ1% of ␤-actin mRNA could be detected in serum filtered through 0.45 and 0.22 m pores, respectively (see Fig. 1c in the online Data Supplement). cache = ./cache/cord-007066-zn10rnrm.txt txt = ./txt/cord-007066-zn10rnrm.txt === reduce.pl bib === id = cord-004003-rlgzgyzn author = Lee, Jeewon title = Applying a Linear Amplification Strategy to Recombinase Polymerase Amplification for Uniform DNA Library Amplification date = 2019-11-12 pages = extension = .txt mime = text/plain words = 3386 sentences = 200 flesch = 51 summary = Thus, to amplify the size-variable DNA library uniformly, we introduced a linear amplification strategy with RPA and successfully improved the uniformity. Also, the average percentages of bases in the uniform range (uniformity value between 0.5 and 1.5) about the triplet experiment was improved from 56.3 and 49.2% by two-primer RPA to 73.6 and 75.7% by linear RPA for the small and large DNA libraries, respectively (Figures 2b and S5) . Taken together, the data show that RPA uniformly amplifies DNA libraries of the same size and has different amplification preferences than PCR. However, during the experiment, an accelerated small-sized DNA amplification by two-primer RPA reaction caused lower uniformity compared to PCR. It was noted that during the analysis, different amplification preferences were found between the PCR and RPA amplified oligo library sequencing data. Taken together, we show that single-primer linear RPA can be one of the alternative methods to PCR for DNA library amplification. cache = ./cache/cord-004003-rlgzgyzn.txt txt = ./txt/cord-004003-rlgzgyzn.txt === reduce.pl bib === id = cord-004810-g0y7ied0 author = Lee, S. K. title = S1 glycoprotein gene analysis of infectious bronchitis viruses isolated in Korea date = 2003-11-13 pages = extension = .txt mime = text/plain words = 3750 sentences = 190 flesch = 59 summary = The S1 glycoprotein gene of IBV isolates were amplified by reverse transcriptase – polymerase chain reaction (RT-PCR) and analyzed by restriction fragment length polymorphism (RFLP) analysis. And these IBV isolates showed different patterns from each other and non-Korean IBV isolates in reverse transcriptase-polymerase chain reaction-restriction fragment length polymorphism (RT-PCR-RFLP) analysis [29] . Amplified S1 genes were first classified by RFLP analysis and then the representative strains were cloned, sequenced and compared to other non-Korean published IBV sequences. Phylogenetic trees were constructed from the nucleotide and deduced amino acid sequences of the S1 glycoprotein genes of Korean IBV isolates and non-Korean IBV strains (Fig. 3) . Korean IBV K281-01 and K210-02 isolates formed distinct clusters that were related to non-Korean IBV Ark99, Ark DPI, Gray and JMK strains although K281-01 and K210-02 isolates were classified into the Arkansas type by PCR-RFLP analysis. cache = ./cache/cord-004810-g0y7ied0.txt txt = ./txt/cord-004810-g0y7ied0.txt === reduce.pl bib === id = cord-003850-in7he5o4 author = Xiu, Leshan title = Simultaneous detection of eleven sexually transmitted agents using multiplexed PCR coupled with MALDI-TOF analysis date = 2019-08-28 pages = extension = .txt mime = text/plain words = 5471 sentences = 286 flesch = 45 summary = Therefore, the aim of the current study was to develop a sensitive, multitarget, and high-throughput method that can detect various agents responsible for STIs. METHODS: We developed and tested a 23-plex PCR coupled with matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) assay (sexually transmitted infection-mass spectrometry, STI-MS) that simultaneously targets 11 different agents, including 8 most common clinical pathogens related to STIs (HSV-1, HSV-2, Neisseria gonorrhoeae, Chlamydia trachomatis, Treponema pallidum, Trichomonas vaginalis, Mycoplasma genitalium, and Haemophilus ducreyi) and 3 controversial microorganisms as pathogens (Mycoplasma hominis, Ureaplasma urealyticum, and Ureaplasma parvum). 3 In this study, the MassARRAY System (Agena Bioscience, Inc., San Diego, CA, USA), a detection platform combining endpoint multiplex-PCR with matrixassisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), was utilized to develop a sexually transmitted infection assay (STI-MS) that can simultaneously detect and identify common clinical pathogens implicated in STIs, including herpes simplex virus types 1 and 2 (HSV-1 and HSV-2), Neisseria gonorrhoeae, Chlamydia trachomatis, Treponema pallidum, Trichomonas vaginalis, Mycoplasma genitalium, and Haemophilus ducreyi. cache = ./cache/cord-003850-in7he5o4.txt txt = ./txt/cord-003850-in7he5o4.txt === reduce.pl bib === id = cord-011966-7k2cxy8a author = Jang, Seong Sik title = The Epidemiological Characteristics of the Korean Bat Paramyxovirus between 2016 and 2019 date = 2020-06-04 pages = extension = .txt mime = text/plain words = 2997 sentences = 190 flesch = 58 summary = Phylogenetic analysis based on the partial nucleotide sequences of RdRp, F, and HN proteins suggested that the viruses belonged to the proposed genus Shaanvirus. The Hendra and Nipah viruses are emerging bat-borne infectious agents that are highly pathogenic paramyxoviruses, which have caused outbreaks of respiratory and neurological diseases in humans and domesticated mammals [13, 14] . In 2016, 121 bat fecal samples were collected and four positive samples were identified based on RT-semi-nested PCR using consensus primers targeting the RdRp region. Based on the partial RdRp, F, and HN nucleotide sequences, the Korean bat paramyxoviruses belonged to the proposed genus shaanvirus. The phylogenetic analysis based on partial RdRp nucleotide sequences indicated that Korean bat paramyxoviruses belonged to the unclassified proposed genera Shaanvirus (Figure 2 ). In addition, the phylogenetic analysis based on the partial nucleotide sequences of RdRp, F, and HN proteins suggested that the viruses belonged to the proposed genus Shaanvirus. cache = ./cache/cord-011966-7k2cxy8a.txt txt = ./txt/cord-011966-7k2cxy8a.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-011322-olvqgs85 author = El-Senousy, Waled M. title = Clinical and Environmental Surveillance of Rotavirus Common Genotypes Showed High Prevalence of Common P Genotypes in Egypt date = 2020-04-11 pages = extension = .txt mime = text/plain words = 9515 sentences = 482 flesch = 53 summary = The objective of this study was to compare the prevalence of human rotavirus group A common G and P genotypes in human Egyptian stool specimens and raw sewage samples to determine the most common genotypes for future vaccine development. Also, previous studies reported that rotavirus group A was the most frequent RNA enteric viruses in Egyptian clinical specimens and aquatic environment and was the most resistant one to sewage and water treatment processes (El-Senousy et al. The present study was conducted to estimate the burden of rotavirus gastroenteritis as well as to compare the prevalence of rotavirus common G and P genotypes among children ≤ 5 years of age visiting Abo El-Reech hospital (from Oct. 2015 to Sep. 2017 ) and in raw sewage samples collected from WWTPs in Greater Cairo during winter and autumn months in the same period to determine the most common G and P genotypes for future vaccine development. cache = ./cache/cord-011322-olvqgs85.txt txt = ./txt/cord-011322-olvqgs85.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-007068-vcfs41eb author = Moradi, Tony title = Use of Procalcitonin and a Respiratory Polymerase Chain Reaction Panel to Reduce Antibiotic Use via an Electronic Medical Record Alert date = 2019-10-22 pages = extension = .txt mime = text/plain words = 3669 sentences = 197 flesch = 38 summary = We sought to determine whether an automated electronic medical record best practice alert (BPA) based on procalcitonin and respiratory polymerase chain reaction (PCR) results could help reduce inappropriate antibiotic use in patients with likely viral respiratory illness. In the study group, a BPA alerted providers of the diagnostic results suggesting viral infection and prompted them to reassess the need for antibiotics. CONCLUSIONS: The automated antimicrobial stewardship BPA effectively reduced antibiotic use and discharge prescribing rates when diagnostics suggested viral respiratory tract infection, without a higher rate for reinitiation of antibiotics after discontinuation. The aim of our study was to determine if antibiotic use could be reduced by deploying an automated antimicrobial stewardship provider alert that prompted antibiotic de-escalation if 3 criteria were met: PCT <0.25 ng/mL, virus detected on respiratory PCR, and active use of systemic antibiotics. cache = ./cache/cord-007068-vcfs41eb.txt txt = ./txt/cord-007068-vcfs41eb.txt === reduce.pl bib === id = cord-005752-tur57xd9 author = Linden, Saara title = Parechovirus infection preceding Guillain–Barré syndrome date = 2012-05-12 pages = extension = .txt mime = text/plain words = 1307 sentences = 87 flesch = 49 summary = Since the near global eradication of poliomyelitis, Guillain-Barré syndrome (GBS) has become the most common cause of acute neuromuscular paralysis. Recent Campylobacter jejuni infection is discovered in 30 % of GBS patients (Poropatich et al. In this case report, we describe a 36-year-old male Finnish patient with GBS, who had a parechovirus infection preceding the neurological illness. Picornavirus PCR was positive from a stool sample taken on the day following hospitalization. Our patient had a mild clinical parechovirus infection preceding GBS. jejuni infection preceding GBS include serological evidence of C. jejuni IgG antibody titer≥1:2,000 by ELISA test) and a definite history of diarrhea within the previous 3 weeks of GBS onset (Kuwabara et al. It remains unproven whether HPeV had any causative role in triggering autoimmunity in our patient, but no other acute or recent microbial infections were detected. Epidemiology and clinical associations of human parechovirus respiratory infections cache = ./cache/cord-005752-tur57xd9.txt txt = ./txt/cord-005752-tur57xd9.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-014942-4hk0veck author = Boone, Stephanie A. title = The Prevalence of Human Parainfluenza Virus 1 on Indoor Office Fomites date = 2010-02-09 pages = extension = .txt mime = text/plain words = 3437 sentences = 199 flesch = 54 summary = The objective of this study was to evaluate the potential role of fomites in human parainfluenza virus 1 (HPIV1) transmission by assessing the occurrence of HPIV1 on surfaces in an adult setting (office). Data revealed a statistically significant difference between the percentage of HPIV1 positive fomites in office cubicles and conference rooms (Chi-square P < 0.011, Fisher's Exact P = 0.054). A study conducted at the San Francisco University Medical Center during the 2002 influenza season found HPIV1 in healthy adults with respiratory infections after using polymerase chain reaction (PCR) for diagnosis (Louie et al. The offices sampled in Arizona indicated a greater variation in the total percentage of HPIV1 positive surfaces per building (Fig. 3) . Potential role of hands in the spread of respiratory viral infections: Studies with human Parainfluenza virus 3 and Rhinovirus 14 cache = ./cache/cord-014942-4hk0veck.txt txt = ./txt/cord-014942-4hk0veck.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-010027-r0tl01kq author = nan title = Dublin Pathology 2015. 8th Joint Meeting of the British Division of the International Academy of Pathology and the Pathological Society of Great Britain & Ireland date = 2015-09-15 pages = extension = .txt mime = text/plain words = 36299 sentences = 2004 flesch = 47 summary = Further profiling of other T cell populations may help to further understand this expression which may act as a biomarker or provide a therapeutic target Biomarkers that are able to distinguish stage II and III colon cancer patients at high risk of developing disease recurrence, who may benefit from adjuvant chemotherapy, are still lacking. *AM supported by the NIHR and the Academy of Medical Sciences ABSTRACTS S·17 Assessment of HER2 Status on Needle Core Biopsy of Breast Cancer: Impact of Histopathological Concordance P M Pigera; AHS Lee; IO Ellis; EA Rakha; Z Hodi Nottingham City Hospital, Nottingham, UK One of the key recommendations introduced in the ASCO/CAP update guideline recommendation on HER2 testing is the novel concept of "histopathological concordance." It is proposed that certain tumour morphological features such as histologic type and grade should trigger repeating a molecular test in cases of "discordance". cache = ./cache/cord-010027-r0tl01kq.txt txt = ./txt/cord-010027-r0tl01kq.txt === reduce.pl bib === id = cord-009376-a35a92gh author = Lovatt, Archie title = Applications of quantitative PCR in the biosafety and genetic stability assessment of biotechnology products date = 2002-01-07 pages = extension = .txt mime = text/plain words = 9214 sentences = 523 flesch = 48 summary = Applications of Q-PCR within biotechnology are discussed with particular emphasis on the following areas of biosafety and genetic stability testing: (a) determination of the biodistribution of gene therapy vectors in animals; (b) quantification of the residual DNA in final product therapeutics; (c) detection of viral and bacterial nucleic acid in contaminated cell banks and final products; (d) quantification of the level of virus removal in process validation viral clearance studies; (e) specific detection of retroviral RT activity in vaccines with high sensitivity; and (f) transgene copy number determination for monitoring genetic stability during production. We are developing Q-PCR assays for these repeat regions for rodent and primate residual DNA to obtain sensitivity in the fg range, however, one advantage of using a gene such as ␤-actin is gene stability, as this target should not undergo copy number changes within a stable cell line. cache = ./cache/cord-009376-a35a92gh.txt txt = ./txt/cord-009376-a35a92gh.txt === reduce.pl bib === === reduce.pl bib === id = cord-007564-ljqrxjvv author = Leroy, O. title = 04 – Apport des explorations microbiologiques au diagnostic des infections des voies respiratoires basses date = 2006-11-13 pages = extension = .txt mime = text/plain words = 13542 sentences = 1229 flesch = 54 summary = Trentetrois examens directs et 46 Ces données montrent que l'examen direct et la culture de l'expectoration dès lors qu'ils sont correctement effectués chez un patient sans antibiothérapie sont fréquemment positifs au cours des PAC à pneumocoque les plus graves, c'est-à-dire bactériémiques. Ces données ne doivent pas toutefois faire perdre de vue, comme le souligne Pesola [37] que dans plus de 10 % des cas, les PAC ont une étiologie plurimicrobienne et qu'il n'est peut être pas raisonnable de focaliser l'antibiothérapie uniquement sur le pneumocoque en cas de test positif. À partir d'échantillons provenant du tractus respiratoire inférieur (expectoration, voire prélèvements endoscopiques) ou supérieur (prélèvement nasopharyngé), un certain nombre de techniques ont été mises au point pour le diagnostic des infections liées à des germes tels que Chlamydia pneumoniae, Mycoplasma pneumoniae ou Legionella spp. cache = ./cache/cord-007564-ljqrxjvv.txt txt = ./txt/cord-007564-ljqrxjvv.txt === reduce.pl bib === id = cord-013589-3l8kar3k author = Doummar, Diane title = Biallelic PDE2A variants: a new cause of syndromic paroxysmal dyskinesia date = 2020-05-28 pages = extension = .txt mime = text/plain words = 4136 sentences = 249 flesch = 47 summary = A homozygous missense variant leading to drastic decrease of PDE2A enzymatic activity was reported in one patient with childhood-onset choreodystonia preceded by paroxysmal dyskinesia and associated with cognitive impairment and interictal EEG abnormalities. The phenotype of the two oldest patients, aged 9 and 26, was characterized by childhood-onset refractory paroxysmal dyskinesia initially misdiagnosed as epilepsy due to interictal EEG abnormalities. Together with previously reported case, our three patients confirm that biallelic PDE2A variants are a cause of childhood-onset refractory paroxysmal dyskinesia with cognitive impairment, sometimes associated with choreodystonia and interictal baseline EEG abnormalities or epilepsy. reported a missense homozygous variant in PDE2A in a patient with cognitive impairment, interictal EEG abnormalities, and childhoodonset chorea [8] . indicate that biallelic variants in PDE2A leading to loss of function are involved in heterogeneous phenotypes characterized by early-onset paroxysmal hyperkinetic movement disorders associated with cognitive impairment and possibly epilepsy. cache = ./cache/cord-013589-3l8kar3k.txt txt = ./txt/cord-013589-3l8kar3k.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-004133-32w6g7qk author = Walker, Faye M. title = Advances in Directly Amplifying Nucleic Acids from Complex Samples date = 2019-09-30 pages = extension = .txt mime = text/plain words = 13585 sentences = 664 flesch = 42 summary = Studies were included if they involved direct amplification and detection of genetic material from one of six representative sample types: blood, dried blood spot, serum and plasma, saliva and sputum, swabs, urine, and stool. However, it is important to note that the sensitivity does not necessarily suffer in much more concentrated samples-in Liu et al.'s highly robust two-step amplification process with direct hairpin assembly and HCR-based detection of SNP DNA sequences in 50% (v/v) serum, they achieved a very low LOD of 100 pg [119] . However, it is important to note that the sensitivity does not necessarily suffer in much more concentrated samples-in Liu et al.'s highly robust two-step amplification process with direct hairpin assembly and HCR-based detection of SNP DNA sequences in 50% (v/v) serum, they achieved a very low LOD of 100 pg [119] . cache = ./cache/cord-004133-32w6g7qk.txt txt = ./txt/cord-004133-32w6g7qk.txt === reduce.pl bib === id = cord-006450-si5168pb author = Jouneau, S. title = Which patients should be tested for viruses on bronchoalveolar lavage fluid? date = 2012-12-14 pages = extension = .txt mime = text/plain words = 3119 sentences = 154 flesch = 38 summary = The variables associated with positive viral tests on univariate analysis were immunosuppression [human immunodeficiency virus (HIV), corticosteroids >10 mg/day for ≥3 weeks, or other immunosuppressive therapy], ground-glass attenuations on computed tomography (CT) scanning, late-onset ventilator-associated pneumonia (VAP), and durations of (i) hospital stay, (ii) intensive care unit (ICU) stay, and (iii) mechanical ventilation before BAL (p < 0.01 for each comparison). The variables significantly associated with positive viral tests on univariate analysis were immunosuppression (i.e., HIV infection, corticosteroids >10 mg/day for ≥3 weeks, and/or other immunosuppressive therapy), ground-glass attenuations on chest CT scans, late-onset ventilator-associated pneumonia (VAP), and durations of (i) hospital stay, (ii) ICU stay, and (iii) mechanical ventilation before BAL was performed (p<0.01 for each comparison). This advocates for the systematic use of PCR techniques for viral tests in BALF, in accordance with previous studies [27, 28] , in the situations where viruses may reasonably be suspected (i.e., acute lower tract respiratory disease in immunocompromised patients and/or patients with unexplained bilateral ground-glass attenuations on CT scan). cache = ./cache/cord-006450-si5168pb.txt txt = ./txt/cord-006450-si5168pb.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-002178-ggtxuulg author = Mauk, Michael G. title = Integrated Microfluidic Nucleic Acid Isolation, Isothermal Amplification, and Amplicon Quantification date = 2015-10-20 pages = extension = .txt mime = text/plain words = 5753 sentences = 257 flesch = 39 summary = A portable, miniaturized POC NAAT with performance comparable to conventional PCR (polymerase-chain reaction)-based tests in clinical laboratories can be realized with a disposable, palm-sized, plastic microfluidic chip in which: (1) nucleic acids (NAs) are extracted from relatively large (~mL) volume sample lysates using an embedded porous silica glass fiber or cellulose binding phase ("membrane") to capture sample NAs in a flow-through, filtration mode; (2) NAs captured on the membrane are isothermally (~65 °C) amplified; (3) amplicon production is monitored by real-time fluorescence detection, such as with a smartphone CCD camera serving as a low-cost detector; and (4) paraffin-encapsulated, lyophilized reagents for temperature-activated release are pre-stored in the chip. cache = ./cache/cord-002178-ggtxuulg.txt txt = ./txt/cord-002178-ggtxuulg.txt === reduce.pl bib === id = cord-002560-pue5q5wp author = Moreno, Paloma S. title = Characterisation of the canine faecal virome in healthy dogs and dogs with acute diarrhoea using shotgun metagenomics date = 2017-06-01 pages = extension = .txt mime = text/plain words = 5137 sentences = 265 flesch = 50 summary = Recently, due to the advent of molecular enrichment protocols, high throughput sequencing and new metagenomic analytical methods we are now able to explore, identify and characterise viruses from different biological and environmental samples with a greater capacity [2, [5] [6] [7] [8] [9] [10] [11] In studies of human faeces, the virome has been shown to include viruses that infect eukaryotic organisms and viruses that infect prokaryotes (bacteriophages) [2, 5, [12] [13] [14] [15] [16] [17] [18] . Another eukaryotic viral family found in one healthy dog sample was Parvoviridae, genetic analysis of the 3 contigs/singletons showed a coverage of approximately 3.5% of the complete genome of canine parvovirus reference sequence (NC_001539), or 9.3% of the polyprotetin Ns1-Ns2. Nucleic acids from a single faecal sample from a dog with acute diarrhoea (DD1), which had 18 contigs/singletons of canine astrovirus (after tBLASTx analysis) was used to determine the complete genome sequence. cache = ./cache/cord-002560-pue5q5wp.txt txt = ./txt/cord-002560-pue5q5wp.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-007047-7ty9mxa9 author = Reller, L. Barth title = Implications of New Technology for Infectious Diseases Practice date = 2006-11-15 pages = extension = .txt mime = text/plain words = 4095 sentences = 190 flesch = 38 summary = Problems with currently available molecular assays include a lack of knowledge about the extent of microbial nucleic acid in "normal" hosts, concentration of agent material in small volume samples, lack of microbiologist expertise, lack of adequate reimbursement, and difficulty with validation based on conventional methods. Infectious diseases clinicians have relied on these expert workers, and Reliable molecular diagnostic tests are not readily available for many infectious agents Commercial tests should only be used for validated specimen types Transportation problems, low concentrations of infectious agent, primer binding site genetic changes, final assay volume, inhibition, contamination, nonspecific amplification, and operator error lead to false-negative and false-positive amplification results Genomic bacterial sequencing is subject to error because of sequence homology among different bacteria, database problems, and mutations A number of nucleic acid hybridization and amplification methods are now in use, including direct probe hybridization (AdvanDx FISH for Staphylococcus aureus [AdvanDx] and GenProbe for group A streptococci [GenProbe]), hybrid capture (Digene for human papillomavirus; Digene), PCR, branched-chain DNA (bDNA; Bayer Diagnostics), and transcription-mediated amplification (Probe-Tec for Chlamydia and N. cache = ./cache/cord-007047-7ty9mxa9.txt txt = ./txt/cord-007047-7ty9mxa9.txt === reduce.pl bib === === reduce.pl bib === id = cord-002757-upwe0cpj author = Sullivan, Kathleen E. title = Emerging Infections and Pertinent Infections Related to Travel for Patients with Primary Immunodeficiencies date = 2017-08-07 pages = extension = .txt mime = text/plain words = 24212 sentences = 1364 flesch = 40 summary = The first section addresses general considerations, the second section profiles specific infections organized according to mechanism of transmission, and the third section focuses on unique phenotypes and unique susceptibilities in patients with PIDDs. This review does not address most parasitic diseases. In developing countries where polio is still endemic and oral polio vaccine is essential for eradicating the disease, it is of utmost importance that all PIDD patients and family members should not receive live oral polio (OPV) because of the reported prolonged excretion of the virus for months and even years [24] . As for host factors, although severe and fatal cases have been described in healthy immunocompetent hosts [129, 130] , there is evidence to suggest that children under the age of 10 [130] and immunocompromised hosts either secondary to hematologic malignancies, immunosuppressant treatment for organ transplantation, or HIV infection are at a greater risk to develop more severe disease with higher case fatality rates [131, 132] . cache = ./cache/cord-002757-upwe0cpj.txt txt = ./txt/cord-002757-upwe0cpj.txt === reduce.pl bib === === reduce.pl bib === id = cord-001521-l36f1gp7 author = nan title = Oral and Poster Manuscripts date = 2011-04-08 pages = extension = .txt mime = text/plain words = 183363 sentences = 11362 flesch = 53 summary = The IC 50 values determined in functional NI assays provide valuable information for detection of resistant viruses, but should not be used to draw direct correlations with drug concentrations needed to inhibit virus replication in the infected human host, as clinical data to support such inferences are inadequate. • Standardized reagents and protocols • Choice of detection technology • Simple instrumentation requirements • High sensitivity for use with low virus concentrations • Compatibility with batch-mode processing and largescale assay throughput • Broad specificity of influenza detection • Flexibility in assay format • Additional NA assay applications -cell-based viral assays, screening for new NIs, detection of NA from other organisms Functional neuraminidase inhibition assays enable detection of any resistance mutation and are extremely important in conjunction with sequence-based screening assays for global monitoring of virus isolates for NI resistance mutations, including known and new mutations. Such new assays need to include methods to measure local antibodies and virus-specific lymphocytes, especially in the case of live attenuated influenza vaccines, because of their potential to induce such broad-based immune responses. cache = ./cache/cord-001521-l36f1gp7.txt txt = ./txt/cord-001521-l36f1gp7.txt === reduce.pl bib === id = cord-010235-hu6o1ggc author = Atmar, Robert L. title = Nonculturable agents of viral gastroenteritis date = 1997-12-01 pages = extension = .txt mime = text/plain words = 3989 sentences = 190 flesch = 43 summary = (3) provided the first clear demonstration of the causal relationship between a virus (Norwalk virus [NV] ) and gastroenteritis by using immune electron microscopy (IEM) to detect the presence of viral particles in the stools of individuals from an epidemic outbreak of gastroenteritis. This article describes the structure and genome organization of the human caliciviruses that cause gastroenteritis, the clinical and epidemiologic features of these viruses, and new methods for the laboratory diagnosis of infection with these viruses. The inability to cultivate the HuCVs and establish neutralization assays has prevented the definition of specific serotypes; however, at least five different serotypes are thought to exist based on early human cross-challenge studies and comparisons of the IEM and enzyme-linked immunosorbent assay (ELISA) reactivities of several prototype virus strains. cache = ./cache/cord-010235-hu6o1ggc.txt txt = ./txt/cord-010235-hu6o1ggc.txt === reduce.pl bib === === reduce.pl bib === id = cord-005147-mvoq9vln author = nan title = Autorenregister date = 2017-02-23 pages = extension = .txt mime = text/plain words = 86573 sentences = 4356 flesch = 45 summary = Using whole-exome sequencing and trio-based de novo analysis, we identified a novel heterozygous de novo frameshift variant in the leukemia inhibitory factor receptor (LIFR) gene causing instability of the mRNA in a patient presenting with bilateral CAKUT and requiring kidney transplantation at one year of age. Loss of cdkl5 associated with deficient mammalian target of rapamycin (mTOR) signaling in mice and human cells We and other groups have shown that mutations in the X-linked cyclin-dependent kinase-like 5 (CDKL5) gene cause a severe neurodevelopmental disorder with clinical features including intellectual disability, early-onset intractable seizures and autism, that are closely related to those present in Rett syndrome (RTT) patients. Functional characterization of novel GNB1 mutations as a rare cause of global developmental delay Over the past years, prioritization strategies that combined the molecular predictors of sequence variants from exomes and genomes of patients with rare Mendelian disorders with computer-readable phenotype information became a highly effective method for detecting disease-causing mutations. cache = ./cache/cord-005147-mvoq9vln.txt txt = ./txt/cord-005147-mvoq9vln.txt === reduce.pl bib === === reduce.pl bib === id = cord-014976-546zaoxn author = nan title = Publication only date = 2006-03-08 pages = extension = .txt mime = text/plain words = 51926 sentences = 2983 flesch = 53 summary = In order to evaluate if malignant and non malignant hematological diseases quantitatively and qualitatively affect BM derived MSCs, bone marrow from children with acute lymphoblastic leukemia (ALL diagnosis n=9, different phases of treatment n=29, end of therapy n=10), idiopathic thrombocytopenic purpura (n=16), autoimmune neutropenia (n=12) and control patients (solid tumors without BM involvement, n=30) was harvested and the mononuclear cell (MNC) fraction isolated. Case: In our hospital a total of 3 patients with relapsed Hodgkin's disease underwent reduced-intensity conditioning (RIC) allogeneic stem cell transplantation (allo-SCT) from an HLA-identical sibling. We report a case of a young male patient of 19 years old with aggressive MS who was treated with a high-dose immunosuppressive regimen (HDIS) using myeloablation followed by autologous blood stem cell transplantation (ASCT) that has induced a dramatic and long-lasting remission of the disease. cache = ./cache/cord-014976-546zaoxn.txt txt = ./txt/cord-014976-546zaoxn.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-015763-5lx179pa author = Thellier, D. title = Quels prélèvements aux urgences pour le diagnostic microbiologique d’une infection pulmonaire communautaire grave du sujet immunocompétent ? date = 2014-09-23 pages = extension = .txt mime = text/plain words = 5181 sentences = 450 flesch = 51 summary = Keywords Severe community acquired pneumonia · Microbial diagnosis La pneumonie communautaire grave (PCG) est la première cause de sepsis sévère et de choc septique rencontrée aux urgences [1] . Ainsi, puisque les pathogènes responsables et l'antibiothérapie à instaurer sont connus, l'utilité de réaliser des prélèvements microbiologiques systématiques chez tous les patients admis aux urgences pour une pneumonie communautaire peut se discuter. Toutefois, cette relation entre la gravité de l'infection et la fréquence de positivité de l'hémoculture lorsqu'elle est appréciée non plus par le lieu d'admission du patient mais par un élément objectif tel que le Pneumonia Severity Index (PSI, score de Fine) ou le CURB-65 apparaît plus difficile à établir, tant les études sur le sujet rapportent des résultats discordants. Ces données ne doivent pas toutefois faire perdre de vue que les pneumonies ayant une étiologie pluri microbienne dans plus de 10 % des cas il n'est peutêtre pas raisonnable de focaliser l'antibiothérapie uniquement sur le pneumocoque en cas de test positif. cache = ./cache/cord-015763-5lx179pa.txt txt = ./txt/cord-015763-5lx179pa.txt === reduce.pl bib === id = cord-016020-awanrm9u author = Fox, Julie D. title = Respiratory Pathogens date = 2007 pages = extension = .txt mime = text/plain words = 4603 sentences = 220 flesch = 30 summary = In addition, despite the well-recognized association of viral infections with upper and lower respiratory tract infections, the current diagnostic virology procedures do not provide an answer rapidly enough to with parainfluenza virus type 4, human coronaviruses, rhinoviruses, and some enteroviruses would not ordinarily be identified without RNA detection methods. Published diagnostic methods for detection of respiratory pathogen DNA or RNA directly from clinical specimens utilize target amplification procedures such as polymerase chain reaction (PCR) or nucleic acid sequence-based amplification (NASBA).Although direct detection methods based on nucleic acid hybridization would be theoretically possible, the amount of target nucleic acid in specimens may be minimal and such methods would lack sensitivity compared to amplification methods, unless the organism was propagated before analysis. Thus, the molecular amplification procedures reported for direct detection of respiratory pathogens in clinical samples include PCR (e.g., Reference 19 and Figure 41 assays have utilized bacterial ribosomal RNA (rRNA; e.g., Reference 22 ). cache = ./cache/cord-016020-awanrm9u.txt txt = ./txt/cord-016020-awanrm9u.txt === reduce.pl bib === id = cord-015941-4fz79wzf author = Hu, Yuan title = Molecular Techniques for Blood and Blood Product Screening date = 2018-11-10 pages = extension = .txt mime = text/plain words = 7210 sentences = 381 flesch = 50 summary = Through the application of molecular biology, biological and biochemical analyses have been revolutionized, and nucleic acid, gene-based techniques have been developed to screen blood and plasma donations for evidence of very recent and earlier viral infections that might otherwise be missed by conventional serologic testing. Because NAT detects a virus's genetic material instead of waiting for the body's response, the formation of antibodies, as with many current tests, it offers the opportunity to reduce the window period during which an infecting agent is undetectable by traditional tests [21] , thus further improving blood safety. One reason for this is that currently available blood screening technologies detect core antibodies or surface antigens, which appear up to 8 weeks after infection. The anti-HBc test developed in 1987 detects an antibody to the hepatitis B virus that is produced during and after infection. Detection of HIV-1 and HCV infections among antibody-negative blood donors by nucleic acid-amplification testing cache = ./cache/cord-015941-4fz79wzf.txt txt = ./txt/cord-015941-4fz79wzf.txt === reduce.pl bib === id = cord-004675-n8mlxe7p author = nan title = 2019 CIS Annual Meeting: Immune Deficiency & Dysregulation North American Conference date = 2019-02-26 pages = extension = .txt mime = text/plain words = 86427 sentences = 5050 flesch = 46 summary = However, the mean infusion rate per site was similar between patients aged <18 years ( XMEN disease (X-linked Immunodeficency with Magnesium defect, Epstein-Barr virus infection and Neoplasia) is a primary immune deficiency caused by mutations in MAGT1 and characterized by chronic infection with Epstein-Barr virus (EBV), EBV-driven lymphoma, CD4 T-cell lymphopenia, and dysgammaglobulinemia. We present the case of a 1-year old Hispanic infant with a pathogenic variant in MAGT1 gene that clinically manifested with early Pneumocystis jirovecii and cytomegalovirus (CMV) interstitial pneumonia, and EBV chronic infection with good response to intravenous immunoglobulins supplementation without hematopoietic stem cell transplantation or gene therapy. Chief, Laboratory of Clinical Immunology and Microbiology, IDGS, DIR, NIAID, NIH, Bethesda, MD, USA Hypomorphic Recombination Activating Gene 1 (RAG1) mutations result in residual T-and B-cell development in both humans and mice and have been found in patients presenting with delayed-onset combined immune deficiency with granulomas and/or autoimmunity (CID-G/AI). cache = ./cache/cord-004675-n8mlxe7p.txt txt = ./txt/cord-004675-n8mlxe7p.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-017767-zj1h5ixf author = Shieh, Wun-Ju title = Advanced Pathology Techniques for Detecting Emerging Infectious Disease Pathogens date = 2012-04-05 pages = extension = .txt mime = text/plain words = 5249 sentences = 247 flesch = 35 summary = Although general practice of pathology is largely oriented toward diagnosis of neoplastic diseases, pathologists have been increasingly called upon to make diagnoses from tissue samples collected by cytology, biopsy, and autopsy procedures in response to the challenge of emerging infections [1] [2] [3] [4] . Immunolocalization of antigens by IHC provides histomorphologic correlation between the infectious pathogen and host tissue responses, which is not only crucial for diagnosis but also important to study the pathogenesis of those emerging infections [ 19, 21, 39, 40 ] . PCR ampli fi cation undoubtedly is the most sensitive method available to detect microbial organisms in tissue specimens and has become a common practice in many pathology laboratories. These differential 16S rRNA gene PCR assays provide more speci fi c information regarding the bacteria identity and are very useful for detecting bacterial pathogens in tissue samples in conjunction with histopathologic evaluation, special stains, and IHC. cache = ./cache/cord-017767-zj1h5ixf.txt txt = ./txt/cord-017767-zj1h5ixf.txt === reduce.pl bib === === reduce.pl bib === id = cord-015683-a9a82of4 author = Gupta, Varsha title = Molecular Diagnostics date = 2016-10-23 pages = extension = .txt mime = text/plain words = 4774 sentences = 294 flesch = 52 summary = Molecular diagnostics such as Western blot , ELISA , PCR , DNA, and protein microarrays are 7 revolutionizing the clinical practice of infectious diseases. Molecular diagnostics such as Western blot , ELISA , PCR , DNA, and protein microarrays are 7 revolutionizing the clinical practice of infectious diseases. Binding of another antigen-specifi c antibody linked with enzyme results in color formation upon addition of the substrate 9.2 Diagnosis of Bacterial, Viral, and Parasitic Diseases peptide may react in some assays but not in others as some regions of a peptide may be more immunogenic than others. Because of the specifi city, homogeneity, and unlimited availability of the MAbs, vast amount of work has been carried out on the production/development The immuno-diagnoses of protozoan and parasitic diseases have signifi cantly been improved by MAb technology because the tests involving MAb as diagnostic reagents overcome the limitations of polyclonal antibodies. The sensitivity and specifi city of a PCR assay is dependent on target genes, primer sequences, PCR techniques, DNA extraction procedures, and PCR product detection methods. cache = ./cache/cord-015683-a9a82of4.txt txt = ./txt/cord-015683-a9a82of4.txt === reduce.pl bib === id = cord-016000-le22pknc author = Saikumar, G. title = Porcine Circovirus date = 2019-06-06 pages = extension = .txt mime = text/plain words = 9651 sentences = 527 flesch = 45 summary = Porcine circovirus (PCV) infections associated with post-weaning multisystemic wasting syndrome (PMWS) are characterized by weight loss, respiratory distress, jaundice, etc. Later on in 1991, a novel PCV associated with a sporadic disease called as post-weaning multisystemic wasting syndrome (PMWS), characterized by weight loss, respiratory distress, jaundice, etc., was reported from Saskatchewan, Canada (Harding 1996; Clark 1997) . Genetic characterization of type 2 porcine circovirus (PCV-2) from pigs with postweaning multisystemic wasting syndrome in different geographic regions of North America and development of a differential PCR-restriction fragment length polymorphism assay to detect and differentiate between infections with PCV-1 and PCV-2 Mycoplasma hyopneumoniae bacterins and porcine circovirus type 2 (PCV2) infection: induction of postweaning multisystemic wasting syndrome (PMWS) in the gnotobiotic swine model of PCV2-associated disease Porcine circovirus type 2 (PCV2) distribution and replication in tissues and immune cells in early infected pigs cache = ./cache/cord-016000-le22pknc.txt txt = ./txt/cord-016000-le22pknc.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-017363-dmb42kna author = Vemulapalli, Ramesh title = Real-Time Reverse Transcription Polymerase Chain Reaction for Rapid Detection of Transmissible Gastroenteritis Virus date = 2015-09-10 pages = extension = .txt mime = text/plain words = 1069 sentences = 86 flesch = 63 summary = Transmissible gastroenteritis (TGE) is a highly contagious disease of pigs caused by the TGE virus (TGEV). Rapid detection of the virus in the affected pigs' feces is critical for controlling the disease outbreaks. The real-time RT-PCR assay described in this chapter can quickly detect the presence of TGEV in fecal samples with high sensitivity and specificity. The assay, along with the RNA extraction method described here, can be established in any molecular diagnostic laboratory for detection of TGEV in pig fecal samples [ 6 -8 ] . It is recommended that the nucleic acid extraction, preparation of master mix, and real-time PCR amplifi cation are performed in three physically separated areas. In our experience, RNA extracted from pig fecal samples using the following method is suitable for TGEV detection using the real-time RT-PCR assay. A real-time TaqMan ® RT-PCR assay with an internal amplifi cation control for rapid detection of transmissible gastroenteritis virus in swine fecal samples cache = ./cache/cord-017363-dmb42kna.txt txt = ./txt/cord-017363-dmb42kna.txt === reduce.pl bib === id = cord-016417-3cwwmyv9 author = Sluijter, J. P. G. title = Quantitative Real-Time PCR date = 2006 pages = extension = .txt mime = text/plain words = 3110 sentences = 174 flesch = 53 summary = In this chapter, we focus on the newest advancements in reverse transcription polymerase chain reaction (rt-pcr) technology, the real-time PCR or quantitative PCR, using small amounts of RNA to determine expression levels.We discuss the technique in general and describe two different approaches. Traditional methods to quantify mRNA expression levels are Northern blotting, in situ hybridization, ribonuclease protection, cDNA arrays, and reverse transcription polymerase chain reaction (rt-pcr). PCR amplification of your target DNA will increase the number of probes that hybridize with the complementary template. Accumulation of the released reporter molecules during the amplification cycles results in an increasing fluorescent signal and is correlated to the amount of the target DNA present. When the probe binds to the target sequence this will result in a separation of the reporter and quencher molecule and the fluorescent signal can be monitored. Amplification in a real-time PCR will increase the target DNA and therefore also the observed fluorescent signal. cache = ./cache/cord-016417-3cwwmyv9.txt txt = ./txt/cord-016417-3cwwmyv9.txt === reduce.pl bib === id = cord-017331-ru7mvfc0 author = Samanta, Indranil title = Infectious Diseases date = 2017-02-25 pages = extension = .txt mime = text/plain words = 37735 sentences = 2273 flesch = 45 summary = The chapter includes history, etiology, susceptible hosts, transmission, pathogenesis, clinical symptoms, lesion, diagnosis, zoonosis, Treatment and control strategy of Tuberculosis, Salmonellosis, Chlamydiosis, Campylobacteriosis, Lyme disease, other bacterial infection, Newcastle disease, Avian Influenza infection, West Nile Virus infection, Usutu virus infection, Avian Borna Virus infection, Beak and feather disease, other viral infection, Toxoplasmosis, Giardiasis, Cryptosporidiosis, other parasitic infection, Cryptococcosis, Aspergillosis, Other fungal infections. Clinical samples include faeces or cloacal swabs, blood/serum of live birds and affected tissues, such as liver, spleen, heart, intestine/caeca, lung, esophagus/crop, brain and kidney in 10% buffered formalin. Non-specific clinical symptoms such as neurological signs (head between legs), depression, ruffled feathers, and standing at the bottom of the cage are observed in pet birds with AIV infection (Fig. 2.13) . The virus is detected in brain, heart, liver, kidney, lungs, and intestinal tissues of laboratory mice and naturally infected birds. cache = ./cache/cord-017331-ru7mvfc0.txt txt = ./txt/cord-017331-ru7mvfc0.txt === reduce.pl bib === id = cord-017948-fqhl1qb4 author = Hu, Yuan title = Molecular Techniques for Blood and Blood Product Screening date = 2012-04-05 pages = extension = .txt mime = text/plain words = 7304 sentences = 372 flesch = 54 summary = Currently, nucleic acid testing techniques have been developed to screen blood and plasma products for evidence of very recent viral infections that could be missed by conventional serologic tests. Through the application of molecular biology, biological and biochemical analyses have been revolutionized, and nucleic acid, gene-based techniques have been developed to screen blood and plasma donations for evidence of very recent and earlier viral infections that might otherwise be missed by conventional serologic testing. Because NAT detects a virus's genetic material instead of waiting for the body's response, the formation of antibodies, as with many current tests, it offers the opportunity to reduce the window period during which an infecting agent is undetectable by traditional tests [ 19 ] , thus further improving blood safety. Detection of HIV-1 and HCV infections among antibody-negative blood donors by nucleic acid-ampli fi cation testing cache = ./cache/cord-017948-fqhl1qb4.txt txt = ./txt/cord-017948-fqhl1qb4.txt === reduce.pl bib === id = cord-006860-a3b8hyyr author = nan title = 40th Annual Meeting of the GTH (Gesellschaft für Thrombose- und Hämostaseforschung) date = 1996 pages = extension = .txt mime = text/plain words = 90660 sentences = 5152 flesch = 50 summary = Dept of Pediatrics, University Hospitals Kiel and Mtinster, Germany Resistance to activated protein C (APCR), in the majority of cases associated with the Arg 506 Gin point mutation in the factor V gene is present in more than 50 % of patients < 60 years of age with unexplained thrombophilia. The regular APC resistance test is not applicable to plasma from Orally anticoagulated (OAC) or heparinized patients due to decreased levels of vitamin K-dependent clotting factors and to thrombin inhibition by antithrombin, respectively. On admission an extensive coagulation screen yielded the following results (n/normal, t/elevated, I/reduced, +/positive, -/negative): PT t, aPTT t, Tr n, factor II, V, VIII n, factor VII, IX, XI, XII /,, fibrinogan t, ATIII n, protein C, S *, activated protein C sensitivity ratio 1.92 ($), FV-Leidenmutation PCR -, fibrinolytic system n, TAT t, Ft÷2 t, lupus anticoagulant +, heparin induced platelet antibodies +; no diagnosis of a specific autoimmuna disorder could be made. cache = ./cache/cord-006860-a3b8hyyr.txt txt = ./txt/cord-006860-a3b8hyyr.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-020568-c5425959 author = Blatny, Janet Martha title = Detecting and Responding to Bioterrorism date = 2007 pages = extension = .txt mime = text/plain words = 3480 sentences = 204 flesch = 42 summary = The avian flu outbreak in several Asian countries killing approximately 50 million chickens has revealed the need for establishing rapid molecular diagnostics for mass screening of the Biological threat agents may be difficult to detect and identify quickly and reliable both from a civilian (public health) and a military point of view. Real-time PCR is the most commonly used nucleic acid-based method for specific and sensitive identification of biological threat agents. Internal controls may consist of either a plasmid or a DNA fragment in which the amplified DNA sequence is Several real-time PCR assays have been outlined for a number of biological threat agents, and commercial kits containing the specific reagents are available. An essential part of bioterrorism preparedness and response includes the design of efficient and reliable systems for detection and identification of biological threat agents. Classical microbiology, immunoassays, and nucleic acid-based methods, including molecular forensics, are laboratory approaches for detecting, identifying, and verifying various biological threat agents. cache = ./cache/cord-020568-c5425959.txt txt = ./txt/cord-020568-c5425959.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-017072-qwe1ne3q author = Poritz, Mark A. title = Multiplex PCR for Detection and Identification of Microbial Pathogens date = 2018-11-10 pages = extension = .txt mime = text/plain words = 7205 sentences = 299 flesch = 41 summary = Multiplex respiratory panels have the potential to improve patient management and lower overall healthcare costs by improving use of influenza antivirals, reducing inappropriate use of antibiotics and antivirals, reducing use of healthcare resource (e.g., additional laboratory or imaging procedures), informing appropriate infection control practices, and reducing length of hospital, emergency department, and intensive care unit (ICU) stay. In another study evaluating adult patients with a positive influenza result on a multiplex respiratory panel, Rappo [21] reported a significantly lower odds ratio for hospital admission (p = 0.046), a reduced length of stay (p = 0.040), reductions in antimicrobial duration (p = 0.032), and a reduction in the number of chest radiographs (p = 0.005). As with the individual molecular assays and the MALDI-TOF identification, numerous studies have shown that use of multiplex molecular blood culture panels dramatically reduces the time to organism identification [29] [30] [31] [32] which drives more appropriate pathogen-directed therapy. A retrospective study of the impact of rapid diagnostic testing on time to pathogen identification and antibiotic use for children with positive blood cultures cache = ./cache/cord-017072-qwe1ne3q.txt txt = ./txt/cord-017072-qwe1ne3q.txt === reduce.pl bib === === reduce.pl bib === id = cord-018721-othar2uv author = Schwab, Stefan title = Infektionen date = 2012-03-17 pages = extension = .txt mime = text/plain words = 13415 sentences = 1662 flesch = 40 summary = Zusammenfassend kann aufgrund der zur Verfügung stehenden Daten die Gabe von Dexamethason bei erwachsenen Patienten mit Verdacht auf eine bakterielle Meningitis (d. Für Entwicklungsländer mit eingeschränkter medizinischer Versorgung und einem hohen Anteil HIV-positiver Patienten konnte keine Wirksamkeit für Dexamethason bei der bakteriellen Meningitis nachgewiesen werden [32] , [33] , [34] . HIV-positive Patienten mit intrakraniellen Tuberkulomen können im Rahmen des "immune reconstitution syndrome" (IRIS) eine durchaus dramatische klinisch neurologische Verschlechterung erfahren, mit Zunahme der neurologi-z Diagnostik Die Untersuchung des Liquor cerebrospinalis ist für die Diagnose einer chronischen Meningitis unverzichtbar, der Liquor ist typischerweise klar, bei deutlich erhöhtem Eiweiß auch xanthochrom wirkend. Da bei der Pathogenese dieser Enzephalitis auch Autoimmunmechanismen eine wichtige Rolle spielen, scheint unter einer kombinierten Th erapie mit Aciclovir und Dexamethason die Rate von Patienten mit schlechtem Outcome geringer zu sein als unter alleiniger Th erapie mit Aciclovir [158] . cache = ./cache/cord-018721-othar2uv.txt txt = ./txt/cord-018721-othar2uv.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-017543-60q9iecq author = Tian, Wei-Chang title = Microfluidic Applications in Biodefense date = 2008-08-23 pages = extension = .txt mime = text/plain words = 16557 sentences = 831 flesch = 37 summary = Sections cover microscale sample preparation methods; immunomagnetic separations and immunoassays; proteomics; polymerase chain reaction (PCR), quantitative PCR (qPCR) and other nucleic acid amplification methods; DNA microarrays, microelectrophoresis, and finally integrated Lab-on-a-Chip systems. The intent of JBAIDS Block III, Next Generation Diagnostics (NGD), is to establish a new system incorporating the capabilities of Block I and Block II capabilities (Table 10 .1) and adding immunoassay capabilities and the ability to identify up to 50 agents including toxins in 15 minutes using automated, miniaturized sample preparation integrated with analysis for nucleic acids and proteins, in a hand held or smaller format. They will need to be completely automated or simple to use; incorporate advanced technologies including sample preparation starting from primary samples (aerosols, blood, etc.), molecular detection, automation, microfluidics, and bioinformatics; reduce reagent consumption and space requirements; and provide cost and performance advantages compared to present systems. cache = ./cache/cord-017543-60q9iecq.txt txt = ./txt/cord-017543-60q9iecq.txt === reduce.pl bib === === reduce.pl bib === id = cord-017199-dn413uud author = Heineman, M.J. title = 21 Infecties, ziekte en zwangerschap date = 2016 pages = extension = .txt mime = text/plain words = 36456 sentences = 3453 flesch = 61 summary = Aan zwangeren met een positieve kweekuitslag of aan vrouwen van wie nog geen uitslag bekend is, moeten intrapartum profylactisch antibiotica intraveneus worden toegediend, bij voorkeur 2 miljoen IE penicilline G, of anders 2 g amoxicilline/ampicilline, zo mogelijk te geven minstens vier uur voor de te verwachten partus en daarna à 4 uur de helft tot de baby geboren is. Dit kan via seksueel contact, maar vaak blijkt de bron van infectie een kind uit het gezin te zijn dat door contact met andere geïnfecteerde kinderen besmet is geraakt. Onafhankelijke risicofactoren voor hiv-overdracht zijn: primo-infectie tijdens zwangerschap of lactatie, vroeggeboorte, andere geslachtsziekten wanneer die leiden tot ulceratie van de genitaliën, vitamine-A-deficiëntie, langer dan vier uur gebroken vliezen, invasieve diagnostiek bij het kind voor de geboorte en een vaginale geboorte. Bij gezonde zwangeren is de D-dimeer plasmaspiegel rondom de bevalling en vier weken post partum dermate verhoogd dat deze bepaling tijdens zwangerschap en kraambed niet kan worden gebruikt voor het vaststellen van een tromboembolisch proces. cache = ./cache/cord-017199-dn413uud.txt txt = ./txt/cord-017199-dn413uud.txt === reduce.pl bib === id = cord-018865-melttpiq author = Yu, Tian-fei title = Express Transmissible Gastroenteritis Virus Spike Gene B and C Antigen Sites in Multiple Expression Systems date = 2012 pages = extension = .txt mime = text/plain words = 2186 sentences = 126 flesch = 53 summary = In order to illuminate the antigenicity of porcine transmissible gastroenteritis virus (TGEV) spike protein B and C antigen sites, the truncated spike gene including B and C antigen sites of Chinese isolate TH-98 was expressed respectively in E.coli, baculovirus and pichia pastoris expression systems. Dot-ELISA assays based on these three recombinant proteins were developed to detect TGEV antibodies and could avoid antibody cross-reaction from PRCV theoretically. The recombinant B and C antigen sites protein expressed into the yeast culture supernatant was identified on the bases of its molecular weight. When the amount of spotting is 50ng, the recombinant B and C antigen sites protein expressed into the yeast culture supernatant show the positive reaction in contrast with the GS115 cells transformed with pPIC9K plasmids (Fig. 2. Antigenic variation among transmissible gastroenteritis virus (TGEV) and porcine respiratory coronavirus strains detected with monoclonal antibodies to the S protein of TGEV cache = ./cache/cord-018865-melttpiq.txt txt = ./txt/cord-018865-melttpiq.txt === reduce.pl bib === id = cord-018944-du42ho11 author = Shin, Jeong Hwan title = Nucleic Acid Extraction and Enrichment date = 2018-11-10 pages = extension = .txt mime = text/plain words = 6857 sentences = 355 flesch = 41 summary = [6, 7] as follows: (1) extraction should be simple and rapid and should show high sensitivity and specificity; (2) it is preferred that there be no requirements for specialized equipment or special knowledge and skills; (3) the final nucleic acid should be pure and easy to modify for various amplification techniques; (4) the reagents and their product should be harmless; and (5) the process of preparation should resist contamination with other specimens. Although the phenolchloroform method is relatively easy compared with the CsCl/EtBr gradient and is very useful for the extraction of nucleic acids, it also is problematic for the clinical microbiology laboratory because phenol has important limitations due to its being toxic, caustic, and flammable [5, 15, 16] . In recent years, it has become possible to extract viral nucleic acid from clinical specimens having cellular components, and there have been trials of these commercially available kits to detect various clinically important viruses [30] [31] [32] . cache = ./cache/cord-018944-du42ho11.txt txt = ./txt/cord-018944-du42ho11.txt === reduce.pl bib === id = cord-021052-qydc404w author = Fernandez-Flores, Angel title = Aportaciones de la anatomía patológica en el diagnóstico de las infecciones cutáneas: una perspectiva histórica date = 2015-11-02 pages = extension = .txt mime = text/plain words = 4484 sentences = 462 flesch = 59 summary = Las té cnicas de Romanovsky fueron introducidas en 1891 con un uso principal en la identificació n de pará sitos en hematología.El avance en este caso se centró en que los microorganismos podían verse en su contexto tisular. Gracias a ello, en 1950 se realizaron las primeras observaciones de un virus al microscopio electró nico mediante sombreado de los viriones, pero fue en 1960 cuando se difundió el uso del microscopio electró nico en virología 20 para enfermedades que hasta ese momento se diagnosticaban con cultivo, a veces no concluyente. Un magnífico ejemplo lo representaron los anticuerpos contra el herpesvirus humano 8 (HHV8) y contra el virus del carcinoma de cé lulas de Merkel. De otro, el virus tambié n fue detectado en tejido no tumoral de pacientes tanto con carcinoma de cé lulas de Merkel como sin é l 51 . cache = ./cache/cord-021052-qydc404w.txt txt = ./txt/cord-021052-qydc404w.txt === reduce.pl bib === id = cord-017867-8cn4c6cu author = Collántes-Fernández, Esther title = Trichomonas date = 2017-11-08 pages = extension = .txt mime = text/plain words = 24060 sentences = 1231 flesch = 48 summary = In addition, the OIE Terrestrial Manual also provides recommendations for PCR analyses, which can be applied in combination either with or after culture as an ancillary test or-more often-direct as the primary test to examine bovine samples-i.e., preputial material, uterine or vaginal secretions, or abomasal content of aborted fetuses. In bovine tritrichomonosis cultivation became an important diagnostic tool, because parasite numbers in bovine samples-e.g., preputial smegma or cervico-vaginal mucus-are usually too low to be detected by direct microscopy and a multiplication of parasites after a few days of cultivation increases the chance to find infected bulls. Sensitivity and specificity of culture and PCR of smegma samples of bulls experimentally infected with Tritrichomonas foetus Evaluation of a PCR test for the diagnosis of Tritrichomonas foetus infection in bulls: effects of sample collection method, storage and transport medium on the test Comparison of sampling and culture methods for the diagnosis of Tritrichomonas foetus infection in bulls cache = ./cache/cord-017867-8cn4c6cu.txt txt = ./txt/cord-017867-8cn4c6cu.txt === reduce.pl bib === === reduce.pl bib === id = cord-022034-o27mh4wz author = OLANO, JUAN P. title = Distinguishing Tropical Infectious Diseases from Bioterrorism date = 2009-05-15 pages = extension = .txt mime = text/plain words = 10720 sentences = 642 flesch = 41 summary = They include presence of disease outbreaks of the same illness in noncontiguous areas, disease outbreaks with zoonotic impact, different attack rates in different environments (indoor versus outdoor), presence of large epidemics in small populations, increased number of unexplained deaths, unusually high severity of a disease for a particular pathogen, unusual clinical manifestations owing to route of transmission for a given pathogen, presence of a disease (vector-borne or not) in an area not endemic for that particular disease, multiple epidemics with different diseases in the same population, a case of a disease by an uncommon agent (smallpox, viral hemorrhagic fevers, inhalational anthrax), unusual strains of microorganisms when compared to conventional strains circulating in the same affected areas, and genetically homogenous organisms isolated from different locations. cache = ./cache/cord-022034-o27mh4wz.txt txt = ./txt/cord-022034-o27mh4wz.txt === reduce.pl bib === id = cord-008777-i2reanan author = nan title = ECB12: 12th European Congess on Biotechnology date = 2005-07-19 pages = extension = .txt mime = text/plain words = 151383 sentences = 7577 flesch = 43 summary = Mollerup Department of Chemical Engineering, Building 229, DTU, 2800 Lyngby, Denmark A variety of factors that govern the properties of proteins are utilized in the development of chromatographic processes for the recovery of biological products including the binding and release of protons, the non-covalent association with non-polar groups (often hydrophobic interactions), the association of small ions (ion exchange) and the highly specific antigen-antibody interaction (affinity interactions). Such fermenters will be needed in order to meet the increasing pressure on costs for low price commodity type products such as single cell protein or food and technical grade enzymes, and to meet the demands of the new wave of white biotech, in which bio-produced chemicals must be made at prices competitive with those of the traditional chemical industry. The presentation will focus on use of the sensitive sandwich hybridization technology for the quantitative analysis of process relevant marker genes in different kind of microbial cell cultures with a focus on the production of recombinant proteins. cache = ./cache/cord-008777-i2reanan.txt txt = ./txt/cord-008777-i2reanan.txt === reduce.pl bib === id = cord-022310-yc6xtw0s author = Lappin, Michael R. title = Microbiology and Infectious Disease date = 2011-12-15 pages = extension = .txt mime = text/plain words = 14109 sentences = 913 flesch = 39 summary = 47 Because of these findings, it is currently recommended to combine serologic test results with those of blood culture or PCR assay results when evaluating clinically ill cats for bartonellosis. Because serologic test results do not accurately correlate with presence of bacteremia and individual culture or PCR assay results can be falsely negative, there is no indication for testing healthy cats for Bartonella spp. T. gondii-specific IgM is detectable in serum by ELISA in approximately 80% of subclinically ill cats 2 to 4 weeks after experimental induction of toxoplasmosis; these titers generally are negative less than 16 weeks after infection. The author, however, has demonstrated IgG antibody titers greater than 1 : 16,384 in subclinically ill cats 5 years after experimental induction In chronic disease or asymptomatic carriers, demonstration of organisms is unreliable, and a tentative diagnosis is based on clinical signs and a positive titer. gondii-specific antibodies can also be detected in the serum, CSF, and aqueous humor of healthy, infected animals, one cannot assay results in clinically ill dogs, E. cache = ./cache/cord-022310-yc6xtw0s.txt txt = ./txt/cord-022310-yc6xtw0s.txt === reduce.pl bib === === reduce.pl bib === id = cord-021402-wq770ik9 author = Relford, Roberta L. title = New Diagnostic Tools for Infectious Disease date = 2009-05-15 pages = extension = .txt mime = text/plain words = 3166 sentences = 157 flesch = 36 summary = The most common laboratory methodologies used to identify an infectious agent include visualization of the organism via cytology/biopsy, isolation of the agent in microbiological culture, immunodiagnostics/serology, and nucleic acid technology. Fluorescent antibody and immunoblot assays are performed in commercial laboratories, whereas numerous patient-side rapid ELISA and latex agglutination kits are available for antigen detection. Until the introduction of nucleic acid amplification by the PCR, detection of an organism's DNA or RNA often was impossible because of the small amount of antigen present in a sample. In the ELISA and IFA antibody assays, a specific antigen from the infectious agent in question is fixed to a solid surface (microtiter plate or glass slide, respectively) and the patient's serum is added. The SVN assay evaluates the ability of antibodies in a patient's serum to prevent the infection of culture cells or embryonated eggs with a known specific virus. cache = ./cache/cord-021402-wq770ik9.txt txt = ./txt/cord-021402-wq770ik9.txt === reduce.pl bib === id = cord-021596-5s8lksxp author = Colegrove, Kathleen M. title = Pinnipediae date = 2018-10-26 pages = extension = .txt mime = text/plain words = 10418 sentences = 613 flesch = 39 summary = Hepatic hemosiderosois is seen frequently in several pinniped species including young northern elephant and harbor seals, Hawaiian monk seals, northern fur seals, and CSLs. Mild chronic cholecystitis and portal hepatitis are common findings in wild pinnipeds secondary to trematode infection and trematode-associated pigment accumulation can occur. is most commonly reported in free-ranging pinnipeds including CSLs, harbor, and northern elephant seals along the Pacific coast of North America (Colegrove et al., 2005b; Gulland et al., 1996b) . pinnipedii has not been reported for any phocid species; however, the potential host range is broad and transmission from infected fur seals and sea lions has been described for zoo species, domestic cattle, and humans (Cousins et al., 2003; Kiers et al., 2008; Loeffler et al., 2014; Moser et al., 2008; Thompson et al., 1993; Thorel et al., 1998) . Harbor seals are the most commonly reported species to develop severe fatal disease with infection, and in California subadults and adults are primarily affected (Barbosa et al., 2015; Miller, 2008) . cache = ./cache/cord-021596-5s8lksxp.txt txt = ./txt/cord-021596-5s8lksxp.txt === reduce.pl bib === id = cord-000718-7whai7nr author = nan title = ESP Abstracts 2012 date = 2012-08-22 pages = extension = .txt mime = text/plain words = 166497 sentences = 12847 flesch = 49 summary = Method: We analyzed consecutive gastric cancer cases in terms of AMACR immunohistochemical expression and clinical/pathological characteristics and followed patients' postoperative history. Results: Histological, immunohistochemical and molecular examination revealed non-neoplastic lymphadenopathy with atypical paracortical T-cell hyperplasia with immunoblastic reaction in the former and burnt-out histiocytic pattern in the latter, both falling into a broad spectrum of reactive lymph node changes associated with Still's disease. Method: We have thus collected, from our two Institutions a large number (45 cases) of cancers showing the histological definition of adenosquamous carcinomas according to the WHO criteria and performed gene analysis for k-RAS (codons 12, 13) and EGFR (codons 18, 19 and 21) mutations. Objective: We previously identified amplified fibroblast growth factor 1 (FGFR1) as a therapeutic target for small molecule inhibitor (SMI) therapy in squamous cell lung cancer (L-SCC), resulting in currently running clinical trials treating patients with stage III disease. cache = ./cache/cord-000718-7whai7nr.txt txt = ./txt/cord-000718-7whai7nr.txt === reduce.pl bib === id = cord-023134-y665agnh author = nan title = Oral Research Communications of the 22(nd) ECVIM‐CA Congress date = 2012-11-20 pages = extension = .txt mime = text/plain words = 29595 sentences = 1548 flesch = 50 summary = Doppler echocardiographic indices of diastolic function of the right ventricle are good prognostic markers during left ventricular (LV) failure secondary to ischemic and dilated cardiomyopathy.The aims of the present study were: to assess LV and RV diastolic function by conventional Doppler and pulsed-wave tissue Doppler imaging (PW-TDI) in dogs with mitral valve disease (MVD), with or without pulmonary hypertension (PH); to test if echocardiographic parameters of LV and RV diastolic dysfunction correlate to the Doppler-estimated pulmonary artery systolic pressure (PASP).114 dogs were prospectively evaluated, including 86 dogs with MVD. The aims of the present study were to assess whether diabetic cats have pathological evidence of islet inflammation or pancreatitis and to define islet lesions in comparison to a well-matched control population.Formalin-fixed, paraffin-embedded pancreatic samples were collected from post-mortem examination performed on diabetic and control cats died due to any disease at the Clinic for Small Animal Internal Medicine, University of Zurich (Switzerland) between 1997 and 2009. cache = ./cache/cord-023134-y665agnh.txt txt = ./txt/cord-023134-y665agnh.txt === reduce.pl bib === id = cord-022053-idft1p6d author = Pecora, Nicole title = New Technologies for the Diagnosis of Infection date = 2017-07-21 pages = extension = .txt mime = text/plain words = 11496 sentences = 610 flesch = 40 summary = Organisms commonly identified this way include spirochetes, mycobacteria, DNA viruses, Aspergillus, Candida, and Toxoplasma, although special reference laboratories (e.g., The Infectious Disease Pathology Branch at the Centers for Disease Control and Prevention) have a wide range of antibodies for common to exotic pathogens for tissue confirmation. These include highly sensitive probes for use in direct specimens, to alternative amplification methods, rapid assays of single targets, and multiplexed systems that allow for the detection of many organisms in one assay. Application of RNA-ISH to Aspergillus and Candida in FFPE showed less sensitivity than real-time PCR with sequencing (gold standard), although some FISH-positive, PCRnegative cases with obvious fungal elements were seen, suggesting refinements of this technique may be valuable for rapid identification of these common organisms, especially if mucormycosis is in the differential. Comparative evaluation of the Bruker Biotyper and Vitek MS matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry systems for identification of yeasts of medical importance cache = ./cache/cord-022053-idft1p6d.txt txt = ./txt/cord-022053-idft1p6d.txt === reduce.pl bib === id = cord-021772-5v4gor2v author = Levine, Gwendolyn J. title = Cerebrospinal Fluid and Central Nervous System Cytology date = 2019-05-31 pages = extension = .txt mime = text/plain words = 12646 sentences = 768 flesch = 46 summary = 45, 46 In a recent study of 106 canine CSF samples without pleocytosis (TNCC <5/μL) but containing at least 500 RBCs/μL, the mean percentage of neutrophils (45.2% versus 5.7%), percentage of samples with eosinophils present (36.8% versus 6.8%), and mean protein concentration (40 mg/dL versus 26 mg/dL) were found to be significantly increased in the samples with blood contamination when compared with controls. 4 A study of cats with CNS cryptococcosis showed organisms in 9 of 11 of the CSF samples, and a majority of cases (9 of 10) had neutrophilic pleocytosis and increased protein concentration (8 of 10). A case series of five cats showed CSF ranging from normal to marked neutrophilic pleocytosis with moderately elevated protein concentration and variable correlation to clinical outcome. 85 A study of eight dogs with natural infection (confirmed by CNS tissue-PCR and histopathology) showed lymphocytic pleocytosis in all samples and normal protein concentrations. cache = ./cache/cord-021772-5v4gor2v.txt txt = ./txt/cord-021772-5v4gor2v.txt === reduce.pl bib === === reduce.pl bib === id = cord-014527-nvzfpntu author = nan title = Research Communications of the 25th ECVIM‐CA Congress date = 2015-11-09 pages = extension = .txt mime = text/plain words = 89238 sentences = 4996 flesch = 52 summary = A negative outcome was associated with higher fecal S100A12 concentrations in CE dogs, but the response to different forms of treatment and fecal S100A12 has not been reported, and this information will be important to further evaluate the utility of fecal S100A12 as a biomarker for gastrointestinal disease. Statistical analysis was performed using non-parametric 2-or multiple-group comparisons, the likelihood ratio to evaluate the association between groups of dogs and response to treatment, and a receiver operating characteristic curve to calculate sensitivity and specificity at the optimum cut-off concentration. The objectives of this study were to describe pulmonary transit time and myocardial perfusion normalized to heart rate (nPTT and nMP, respectively), evaluated by means of contrast echocardiography, in dogs with stable stage C ACVIM myxomatous mitral valve disease (MMVD), and to assess short-term effects of pimobendan on these parameters. cache = ./cache/cord-014527-nvzfpntu.txt txt = ./txt/cord-014527-nvzfpntu.txt === reduce.pl bib === === reduce.pl bib === id = cord-023017-k6edtg58 author = nan title = AASLD Abstracts (pp. 282A–382A) date = 2006-02-10 pages = extension = .txt mime = text/plain words = 65796 sentences = 3553 flesch = 51 summary = 14/55 (25%) patients in AC who did not discontinue by week 24 received ribavirin dose reduction in comparison to 31/108 ( The clinical outcome in response to combination therapy for treatment of chronic hepatitis C virus (HCV) infection appears to be different for Caucasian versus African American patients. Over the period of combination therapy, most patients in which serum virus titers were reduced to non detectable levels had significant increases in T cell responses to HCV proteins. CHRONIC Background: Recent large prospective trials demonstrated that the combination therapy of interferon (1FN)-alphalribavirin significantly increased the ratio of a sustained virological response in patients with chronic hepatitis C in comparison with IFN monotherapy, especially in patients with high HCV-RNA titer and genotype lb. Results: Patients with chronic HCV infection showed higher MxA gene expression levels than healthy controls, indicating that hepatitis C virus induces IFN production. cache = ./cache/cord-023017-k6edtg58.txt txt = ./txt/cord-023017-k6edtg58.txt === reduce.pl bib === id = cord-023308-af5nihyi author = nan title = COPD SIG: Poster Session 2 date = 2008-03-12 pages = extension = .txt mime = text/plain words = 30159 sentences = 1761 flesch = 53 summary = Results Data indicate splice variant expression in dendritic cells from asthmatic patients is influenced by asthma severity. Methods Randomized controlled trials (RCTs) of GORD treatment in adults or children that reported asthma health outcomes and had symptomatic GORD were included and assessed in accordance with the standard Cochrane systematic review process. Results 11 male (44%) and 14 female (56%) patients with moderate to severe persistent asthma (mean age 44 years, SD = 11) participated. Methods A comprehensive range of intracellular T-cell and monocyte proand anti-inflammatory cytokines/chemokines was investigated in peripheral blood from 5 OSA patients and 5 aged-matched control subjects (with no evidence of sleep problems) using multiparameter flow cytometry. Methods Following completion of a 12-month exercise study, which included a supervised program (Intervention, n = 18) and control group (Control, n = 17), COPD subjects [mean age (SD): 66 (8); mean FEV1 (% predicted) = 56% (19)] were asked to complete a questionnaire. cache = ./cache/cord-023308-af5nihyi.txt txt = ./txt/cord-023308-af5nihyi.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-007890-bie1veti author = nan title = ECC-4 Abstracts date = 2002-04-16 pages = extension = .txt mime = text/plain words = 85992 sentences = 5665 flesch = 50 summary = Effects of Interferon alpha plus ribavirine therapy on frequencies of HCV, HIV and CMV specific CD4-T-cell responses in peripheral blood of HIV/HCV coinfected patients after 6 months of treatment SoA9.5 Methods: Two groups of patients with chronic HCV infection were studied: 26 HIV coinfected progressors with antiretroviral therapy and 13 HIV-negative controls. In order to assess the local temporal trend of antibiotic sensitivity of the most common urinary tract bacterial pathogen, all urine-cultured Escherichia coli isolates were reviewed as to susceptibility profile, and specimen source (community-versus hospital-acquired infection). Methods: A total of 87 penicillin resistant clinical strains isolated from patients at Hacettepe Children's Hospital, Ankara, Turkey between 1999 and 2001 were tested for their in vitro susceptibility to various antibiotics that are commonly used in the treatment of respiratory tract infections. cache = ./cache/cord-007890-bie1veti.txt txt = ./txt/cord-007890-bie1veti.txt === reduce.pl bib === id = cord-022889-lv6fy6e6 author = Dávalos, Alberto title = Literature review of baseline information on non‐coding RNA (ncRNA) to support the risk assessment of ncRNA‐based genetically modified plants for food and feed date = 2019-08-07 pages = extension = .txt mime = text/plain words = 96011 sentences = 5041 flesch = 51 summary = This report suggests that some plant ncRNAs (e.g miRNAs and siRNAs) show higher stability as compared to other ncRNAs due to peculiar chemical characteristics (2'‐O‐methylation at 3' end).However, ingested or administered ncRNA must overcome many extracellular and cellular barriers to reach the intended target tissue or functional location in sufficient amount to exert any biological effect. Finally, the publications reporting the outcome of two EFSA procurements aiming respectively at investigating and summarising the state of knowledge on the mode-of-action of dsRNA and miRNA pathways, the potential for non-target gene regulation by dsRNA-derived siRNAs or miRNAs, the determination of siRNA pools in plant tissues and the importance of individual siRNAs for silencing 6 ; and reviewing relevant scientific information on RNA interference that could serve as baseline information for the environmental risk assessment of RNAi-based GM plants ) 7 were also used. cache = ./cache/cord-022889-lv6fy6e6.txt txt = ./txt/cord-022889-lv6fy6e6.txt === reduce.pl bib === id = cord-014794-yppi30a0 author = nan title = 19th European Congress of Pathology, Ljubljana, Slovenia, September 6-11, 2003 date = 2003-07-31 pages = extension = .txt mime = text/plain words = 158059 sentences = 9041 flesch = 44 summary = These parts were in a high percentage associated with fibrosis and lymphocyte rich areas and showed a higher mitotic activity than usual PTCs. Discussion The differences in the occurrence of TCV and TCmorphology between the presented series and previously reported cases might result from until now not clearly defined tall cell morphology as well as from similarities to PTCs, such as the oxyphilic variant, which is extremely rare in our series, and maybe also from often described squamous changes within PTCs. Due to these data it is not clear which tumor parts have relevance for prognosis and which tumors should be treated more aggressively than others. The aims of this study were to characterize the group of patients with BSOT and evaluate the significance of various molecular markers expression versus serous papillary ovarian carcinomas (SPOC) Material and methods We analyzed a total of 102 cases including: 64 cystadenoma, 10 borderline and 28 cystadenocarcinoma. cache = ./cache/cord-014794-yppi30a0.txt txt = ./txt/cord-014794-yppi30a0.txt === reduce.pl bib === id = cord-006230-xta38e7j author = nan title = Deutsche Gesellschaft für Experimentelle und Klinische Pharmakologie und Toxikologie e.V. date = 2012-02-22 pages = extension = .txt mime = text/plain words = 135419 sentences = 7042 flesch = 43 summary = Here, we will present our analysis of Ca 2+ signaling following stimulation of the FcεRI receptor and application of secretagogues that are supposed to affect Ca 2+ -dependent mast cell activation such as adenosine, endothelin-1, substance P and compound 48/80 in BMMCs and PMCs derived from mouse lines with inactivation of TRPC1, TRPC3, TRPC4, TRPC5 or TRPC6 since specific antagonists are still lacking for these TRP channels. These data indicate that increased PP2A activity is associated with modified gene expression in TG hearts possibly affecting stress response and regulation of cell signalling. As demonstrated by qPCR and Western blot experiments, mesangial cells showed a marked time-and dose-dependent upregulation of CSE mRNA and protein levels after treatment with platelet-derived growth factor (PDGF-BB). The transcription factor cAMP response element (CRE)-binding protein (CREB) plays a critical role in regulating gene expression in response to activation of the cAMPdependent signaling pathway, which is implicated in the pathophysiology of heart failure. cache = ./cache/cord-006230-xta38e7j.txt txt = ./txt/cord-006230-xta38e7j.txt === reduce.pl bib === id = cord-023830-w218ogsk author = Perlin, David title = Rapid Detection of Bioterrorism Pathogens date = 2008-09-10 pages = extension = .txt mime = text/plain words = 6048 sentences = 292 flesch = 38 summary = The inadequacy of phenotypic-based diagnostic assays is illustrated graphically by the ''gold standard'' public health laboratory-testing algorithm that was in place for positive identification of Bacillus anthracis from environmental samples during the October 2001 anthrax outbreak (Fig. 16.1a) . Genomic differences between microbes offer an alternative to culturing for detection and identification of pathogens by providing species-specific DNA targets that can be accurately resolved by molecular methodology. Polymerase chain reaction (PCR)-based amplification of highly conserved ribosomal RNA (rRNA) genes, intergenic sequences, and specific toxin genes is currently the most reliable approach for identification of bacterial, fungal and many viral pathogenic agents. Most importantly, these genetic probing systems offer rapid turn around time (1-6 h) and are suitable for high throughput, automated multiplex operations critical for use in clinical diagnostic laboratories. Rapid diagnostic assays in the genomic biology era: detection and identification of infectious disease and biological weapon agents cache = ./cache/cord-023830-w218ogsk.txt txt = ./txt/cord-023830-w218ogsk.txt === reduce.pl bib === id = cord-023698-wvk200j0 author = Hammerschlag, Margaret R. title = Chlamydia pneumoniae date = 2014-10-31 pages = extension = .txt mime = text/plain words = 10016 sentences = 533 flesch = 38 summary = Because the organism has been difficult to grow and because of the lack of a commercially available other diagnostic assay, most original associations with respiratory diseases have been use of serology with the microimmunofluorescence (MIF) test. 38, 39 For an example of the complexity of this issue, consider that two multicenter pneumonia treatment studies in children showed that although 7% to 13% of the patients in the study had positive culture results and 7% to 18% met the serologic criteria with the MIF test for acute infection, they were not the same patients. pneumoniae infection is that the MIF method used to detect serum antibodies is not standardized; recent studies have shown substantial interlaboratory variation in the performance of these tests. Multicenter comparison trial of DNA extraction methods and PCR assays for detection of Chlamydia pneumoniae in endarterectomy specimens Multicenter comparison trial of DNA extraction methods and PCR assays for detection of Chlamydia pneumoniae in endarterectomy specimens cache = ./cache/cord-023698-wvk200j0.txt txt = ./txt/cord-023698-wvk200j0.txt === reduce.pl bib === === reduce.pl bib === id = cord-025634-31n5fvex author = Zhuge, Shurui title = The prevalence of occult HBV infection in immunized children with HBsAg-positive parents: a hospital-based analysis date = 2020-05-29 pages = extension = .txt mime = text/plain words = 3985 sentences = 216 flesch = 52 summary = title: The prevalence of occult HBV infection in immunized children with HBsAg-positive parents: a hospital-based analysis BACKGROUND AND OBJECT: The risk of occult HBV infection (OBI) in children whose mothers are HBV carriers has received more widespread attention, but there were few reports to focus on the children with HBsAg-positive parents. In this study, we aimed at exploring the prevalence of OBI in hepatitis B-vaccinated children with HBV-positive mothers and/or fathers, trying to identify the risk factors of OBI. Forty-six [14.10% (95% CI 10.3-17.9%)] HBsAg-negative children were detected HBV DNA positive by nested PCR, which were confirmed through sequencing analysis. To our acknowledgement, this is the first study to explore the prevalence of OBI among hepatitis B vaccinated children with HBsAg-positive parents lived in HBV highly endemic areas. There is an equal potential risk of occult HBV infection in children with the HBsAg-positive father and mother. cache = ./cache/cord-025634-31n5fvex.txt txt = ./txt/cord-025634-31n5fvex.txt === reduce.pl bib === id = cord-024080-eh3ztsv5 author = Dheda, Keertan title = Diagnosis of COVID-19: Considerations, Controversies and Challenges in South Africa date = 2020-04-17 pages = extension = .txt mime = text/plain words = 3953 sentences = 214 flesch = 44 summary = Recent data from infections in special contexts such as cruise liners (9) and in close contacts of COVID-19 patients (10) have demonstrated that SARS-CoV-2-specific RT-PCR may be positive in the early phase of the disease, and that viral shedding in the asymptomatic phase and in the early prodromal phase can be considerable. (19) This false negativity phenomenon may be due to several factors, including a low viral load below the detection limit of the assay, low sample volume or cellular mass during acquisition, sampling location (upper versus lower respiratory tract), sample degradation during transport or storage, sample processing methodology and the timing of sampling in relation to the stage of the disease (RT-PCR positivity may progressively increase during the course of the disease). In patients with more severe diseases, including those with lower respiratory tract infection, but also in individuals with mild disease, high viral loads can be detected often for several days after the resolution of symptoms. cache = ./cache/cord-024080-eh3ztsv5.txt txt = ./txt/cord-024080-eh3ztsv5.txt === reduce.pl bib === id = cord-025232-5itrsfmk author = Yan, Yuqian title = Construction and Characterization of a Novel Recombinant Attenuated and Replication-Deficient Candidate Human Adenovirus Type 3 Vaccine: “Adenovirus Vaccine Within an Adenovirus Vector” date = 2020-05-26 pages = extension = .txt mime = text/plain words = 5669 sentences = 312 flesch = 45 summary = The strategy of using a clinically approved and replication-defective HAdV-5 vector provides a novel approach to develop universal adenovirus vaccine candidates against all the other types of adenoviruses causing ARDs and perhaps other adenovirus-associated diseases. In this study, the commercially-available and gene therapy use approved replication-defective HAdV-5 vector was used to construct a recombinant attenuated human adenovirus type 3 vaccine (Ginn et al. The complete hexon gene of HAdV-3 GZ01 was cloned into the AdEasy TM Adenoviral Vector, and this type-specific antigen was expressed when the recombinant adenovirus vaccine was inoculated into mice. The recombinant vaccine is expected to be used in the prevention of ARD outbreaks caused by HAdV-3 infections, and to serve as a model using adenovirus vectors for the construction of other vaccines against additional important serotypes of adenoviral respiratory pathogens. Mice were either inoculated with HAdV-3 wild-type strain GZ01 or immunized with the rAd3H recombinant vaccine by either the intranasal route or intramuscular route, respectively, to assess the antibody titer. cache = ./cache/cord-025232-5itrsfmk.txt txt = ./txt/cord-025232-5itrsfmk.txt === reduce.pl bib === id = cord-027498-cfzfgzqi author = Hattori, Takeshi title = Older age is associated with sustained detection of SARS-CoV-2 in nasopharyngeal swab samples date = 2020-06-21 pages = extension = .txt mime = text/plain words = 841 sentences = 49 flesch = 56 summary = Currently, the standard for diagnosis of Severe Acute Respiratory Syndrome-Coronavirus-2 (SARSinfection is a positive result based on a polymerase chain reaction (PCR) test from nasopharyngeal swab samples. Although her clinical symptoms and radiological findings resolved within a few days, PCR results from nasopharyngeal swab samples remained positive for 50 days after the onset. We specifically hypothesized that old age could be a risk for prolonged duration of positive PCR results from nasopharyngeal swab samples. In our analysis, older age is significantly associated with prolonged duration of positive PCR tests from nasopharyngeal swab samples, irrespective of the disease severity and the used of medication ( Figure 1 ). In summary, we demonstrated that old age is significantly associated with prolonged duration of positive PCR results from nasopharyngeal swab samples; this is the case regardless of disease severity. cache = ./cache/cord-027498-cfzfgzqi.txt txt = ./txt/cord-027498-cfzfgzqi.txt === reduce.pl bib === id = cord-029183-3aotgq6m author = Monard, Céline title = Multicenter evaluation of a syndromic rapid multiplex PCR test for early adaptation of antimicrobial therapy in adult patients with pneumonia date = 2020-07-14 pages = extension = .txt mime = text/plain words = 5858 sentences = 301 flesch = 37 summary = We evaluated the relevance of a new syndromic rapid multiplex PCR test (rm-PCR) on respiratory samples to guide empirical antimicrobial therapy in adult patients with community-acquired pneumonia (CAP), hospital-acquired pneumonia (HAP), and ventilator-acquired pneumonia (VAP). CONCLUSIONS: Use of a syndromic rm-PCR test has the potential to reduce unnecessary antimicrobial exposure and increase the appropriateness of empirical antibiotic therapy in adult patients with pneumonia. Therefore, in pneumonia patients, international guidelines state that an attempt should be made to obtain respiratory samples and recommend to start early empirical treatment while awaiting for the results of culture and antimicrobial susceptibility testing (AST) [3] . The BioFire® FilmArray® Pneumonia Panel (bioMerieux S.A., Marcy-l'Etoile, France) is a novel assay able to simultaneously identify 27 of the most common pathogens involved in lower respiratory tract infections (semi-quantitative results for 11 Gram-negative and 4 Gram-positive bacteria, qualitative results for 3 atypical bacteria and 9 viruses) as well as 7 antibiotic resistance genes (Fig. 1) . cache = ./cache/cord-029183-3aotgq6m.txt txt = ./txt/cord-029183-3aotgq6m.txt === reduce.pl bib === id = cord-029710-ythz9ax0 author = Homayounieh, Fatemeh title = CT Radiomics, Radiologists and Clinical Information in Predicting Outcome of Patients with COVID-19 Pneumonia date = 2020-07-23 pages = extension = .txt mime = text/plain words = 3090 sentences = 166 flesch = 44 summary = PURPOSE: To compare prediction of disease outcome, severity, and patient triage in COVID-19 pneumonia with whole lung radiomics, radiologists' interpretation, and clinical variables. CONCLUSION: Radiomics from non-contrast chest CT were superior to radiologists' assessment of extent and type of pulmonary opacities in predicting COVID-19 pneumonia outcome, disease severity, and patient triage. We compared prediction of disease outcome, severity, and patient triage in COVID-19 pneumonia with whole lung radiomics, radiologists' interpretation, and clinical variables. Although prior studies have reported on the ability of visual severity score of COVID-19 pneumonia on chest CT [16, 18, 20] , we found that such qualitative assessment was not as useful as radiomics in predicting ICU admission or patient outcome (recovery versus death). Another limitation of our study pertains to the fact that some patients may have been admitted to the hospital based on severity of symptoms, other comorbidities (such as immunodeficiencies) or positive CT findings rather than an extensive lung changes related to COVID-19 pneumonia. cache = ./cache/cord-029710-ythz9ax0.txt txt = ./txt/cord-029710-ythz9ax0.txt === reduce.pl bib === id = cord-029775-mntcor5d author = Oka, Tomoichiro title = Polymerase chain reaction primer sets for the detection of genetically diverse human sapoviruses date = 2020-07-27 pages = extension = .txt mime = text/plain words = 1827 sentences = 100 flesch = 58 summary = For the initial reactivity test, double-stranded DNA fragments (gBlocks® Gene Fragments) including the sequence targeted by the PCR primers (approximately 1700 bp each) of the human sapovirus genotypes GI.1 (GenBank accession number X86560), GI.2 (AB614356), GI.3 (AB623037), GI.4 (AJ606693), GI.5 (DQ366345), GI.6 (AJ606694), GI.7 (AB522390), GII.1 (AJ249939), GII.2 (AY237420), GII.3 (AB630068), GII.4 (AB522397), GII.5 (LC190463), GII.6 (AY646855), GII.7 (AB630067), GII.8 (KX894315), GIV.1 (DQ058829), GV.1 (DQ366344), and GV.2 (AB775659) were synthesized (Integrated DNA Technologies, Coralville, IA), and 1.0 × 10 4 copies of these fragments were used. The target regions of HuSaV-F1, -F2, and -F3 recently designed as forward primers in a broadly reactive real-time PCR for human sapoviruses [11] are similar to those of SV-F13 and SV-F14 (Fig. 2) , and the sapovirus-specific sequence of M13R-HuSaV5498R (5′-CCCCANCCNGCVHACAT-3′) ( [11] are shown in parentheses. The assay including two primers (M13F-HuSaV-5159F and M13R-HuSaV-5498R) generated similar-sized PCR products (approximately 380 bp) for all of the sapovirus genotypes tested (Fig. 1A, right panel, and Fig. 1B) . cache = ./cache/cord-029775-mntcor5d.txt txt = ./txt/cord-029775-mntcor5d.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-032134-mvj7i1er author = Ballauff, Antje title = Funktions- und Laboruntersuchungen date = 2013 pages = extension = .txt mime = text/plain words = 9299 sentences = 1365 flesch = 49 summary = Bei Durchführung des Tests wird nach Verzicht auf ballaststoffreiche Kost für 3 Tage sowie nach einer Nüchternperiode von je nach Alter 8-12 Stunden und nach Mundspülung mit Wasser oder desinfizierender Lösung (morgens nicht Zähneputzen wegen Kohlenhydraten in der Zahnpasta) der Basalwert durch Gewinn von 1-2 Atemproben vor der Gabe der Testsubstanz ermittelt. Andererseits hat der EHEC-Ausbruch im Mai / Juni 2011 in Norddeutschland in eigenen vergleichenden Studien gezeigt, dass die Amplifikation von Zielsequenzen der Shiga-Toxin kodierenden Gene mittels PCR direkt im Stuhl das mit Abstand sensitivste und schnellste Verfahren zum frühen Nachweis oder Ausschluss einer EHEC-Infektion ist (Bialek et al., unveröffentlichtes Manuskript; Robert Koch Institut 2011b) . Nur bei der Amöbenruhr, verursacht durch Entamoeba histolytica, finden sich temperatursensible Trophozoiten im blutig-schleimigen Stuhl, die nur bei noch "warmer" Stuhlprobe mikroskopisch nachweisbar und identifizierbar sind, so dass eine Probe entweder direkt im Labor entnommen werden sollte oder diese warm zu transportieren ist. cache = ./cache/cord-032134-mvj7i1er.txt txt = ./txt/cord-032134-mvj7i1er.txt === reduce.pl bib === === reduce.pl bib === id = cord-034689-se1hdn61 author = Smith, David L. title = A Characteristic Chest Radiographic Pattern in the Setting of COVID-19 Pandemic date = 2020-09-03 pages = extension = .txt mime = text/plain words = 2913 sentences = 156 flesch = 48 summary = CONCLUSION: The presence of patchy and/or confluent, bandlike ground glass opacity or consolidation in a peripheral and mid-to-lower lung zone distribution on a chest radiograph obtained in the setting of pandemic COVID-19 is highly suggestive of SARS-CoV-2 infection and should be used in conjunction with clinical judgement to make a diagnosis. The characteristic COVID-19 pattern ( Fig. 2-4) was defined in accordance with the prevailingly accepted chest imaging findings of COVID-19 in recent literature [2, 12, 20, 24, 25, [27] [28] [29] including the presence of bilateral "patchy" or "confluent, bandlike" ground glass opacity or consolidation in a peripheral and mid-to-lower lung zone distribution. The presence of bilateral "patchy" and/or "confluent, bandlike" ground glass opacity or consolidation in a peripheral and mid-to-lower lung zone distribution on a chest radiograph obtained in the setting of pandemic COVID-19 is highly suggestive of SARS-CoV-2 infection and should be used in conjunction with clinical judgement to make a diagnosis, especially when rapid and reliable serologic testing is lacking. cache = ./cache/cord-034689-se1hdn61.txt txt = ./txt/cord-034689-se1hdn61.txt === reduce.pl bib === id = cord-034746-uxhpufnv author = Nusshag, Christian title = Glomerular filtration barrier dysfunction in a self-limiting, RNA virus-induced glomerulopathy resembles findings in idiopathic nephrotic syndromes date = 2020-11-05 pages = extension = .txt mime = text/plain words = 3642 sentences = 194 flesch = 36 summary = We therefore analyzed standard markers of glomerular proteinuria (e.g. immunoglobulin G [IgG]), urinary nephrin excretion (podocyte injury) and serum levels of the soluble urokinase plasminogen activator receptor (suPAR), a proposed pathomechanically involved molecule in INS, in PUUV-infected patients. On admission, patients suffering from hantavirus infection showed significantly increased urinary nephrin, IgG, α1-MG and serum suPAR levels compared to healthy controls (Fig. 3A ). Though, urinary biomarker levels decreased in both groups over time, patients with severe PCR showed significantly higher levels of nephrin, IgG, ACR and PCR during the first 48 h after admission ( Table 2 ). Our data show a strong association between urinary nephrin levels and the extent of (non-selective) glomerular proteinuria, suggesting that hantavirus infection causes a pronounced podocyte damage and subsequent impairment of the GFB. To date, one other study showed significantly elevated blood suPAR levels and their association with hantavirus disease severity but did not include nephrinuria and the extent of proteinuria in their analysis 19 . cache = ./cache/cord-034746-uxhpufnv.txt txt = ./txt/cord-034746-uxhpufnv.txt === reduce.pl bib === === reduce.pl bib === id = cord-023026-2r84ndzv author = nan title = Posters date = 2013-06-14 pages = extension = .txt mime = text/plain words = 138458 sentences = 6513 flesch = 40 summary = Thus, this work provides the basis to identify molecular pathways regulated by distinct niche/environmental signals and involved in the heterogeneity of adult OPCs. Multiple sclerosis (MS) is a chronic inflammatory and neurodegenerative demyelinating disease of the central nervous system (CNS) characterized by inflammation, which leads to formation of demyelinating areas due to loss of oligodendrocytes, astrogliosis and, finally, axonal degeneration. Taken together, these results demonstrate the important role of miR-200b in modulating the MAPK pathway via c-Jun which in turn affects different aspects of the inflammatory process accompanying microglia activation including cytokine response, NO production, phagocytosis and neuronal cell death. For this purpose, coronal cryostat free-floating sections from the brain of both adult transgenic mice and their corresponding wild-type (Wt) littermates, were processed for the study of astrocytes using GFAP immunohistochemistry and microglia using antibodies against Iba1 and several markers commonly related to the activated phenotype of these microglial cells, such as CD16/32 (Fc receptor), F4/80, CD11b, CD206, CD150 and MHC-II. cache = ./cache/cord-023026-2r84ndzv.txt txt = ./txt/cord-023026-2r84ndzv.txt === reduce.pl bib === id = cord-023346-8sqbqjm1 author = nan title = MONDAY: POSTERS date = 2005-06-08 pages = extension = .txt mime = text/plain words = 130043 sentences = 7330 flesch = 54 summary = • enhancement of automation/computerisation; • process control to provide an 'error-free pathway'; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody 'combi' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas' disease infection (for retrieval of otherwise wasted blood); • European Union's in vitro diagnostics directive: this has caused some problems and reduced flexibility. cache = ./cache/cord-023346-8sqbqjm1.txt txt = ./txt/cord-023346-8sqbqjm1.txt === reduce.pl bib === id = cord-048470-33mqfj2t author = Takano, T title = Quantitative measurement of thyroglobulin mRNA in peripheral blood of patients after total thyroidectomy date = 2001-07-17 pages = extension = .txt mime = text/plain words = 3040 sentences = 146 flesch = 54 summary = Previous studies have reported the clinical usefulness of reverse transcription-polymerase chain reaction (RT-PCR) detection of thyroglobulin (TG) mRNA in the peripheral blood of patients with differentiated thyroid carcinoma. To evaluate this usefulness, we measured TG mRNA in the peripheral blood of patients diagnosed with thyroid carcinoma after total thyroidectomy by real-time quantitative RT-PCR using glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA as an internal control. Recent reports have demonstrated that the reverse transcription-polymerase chain reaction (RT-PCR) can be used to detect circulating cancer cells in the peripheral blood of patients with malignancies such as prostate cancer (Ghossein et al, 1995) and neuroblastoma (Mattano et al, 1992) . As such, we measured TG mRNA in the peripheral blood of patients after total thyroidectomy and determined the expression levels of TG mRNA by real time-quantitative RT-PCR using GAPDH mRNA as an internal control. cache = ./cache/cord-048470-33mqfj2t.txt txt = ./txt/cord-048470-33mqfj2t.txt === reduce.pl bib === === reduce.pl bib === id = cord-048359-lz37rh82 author = Li, Jin title = s-RT-MELT for rapid mutation scanning using enzymatic selection and real time DNA-melting: new potential for multiplex genetic analysis date = 2007-06-01 pages = extension = .txt mime = text/plain words = 6258 sentences = 299 flesch = 49 summary = Subsequently, melting curve analysis, on conventional or nano-technology real-time PCR platforms, detects the samples that contain mutations in a high-throughput and closed-tube manner. Following denaturation and re-annealing of PCR products that leads to formation of cross-hybridized sequences at the positions of mutations ( Figure 1A ) the sample is exposed to Surveyor TM endonuclease that recognizes base pair mismatches or small loops with high specificity (28) and generates a break on both DNA strands 3 0 to the mismatch. Finally, because the amplified mutated sequences contain defined primers at their ends, direct sequencing of enzymatically selected PCR products is readily possible following the real-time melting step, enabling sequencing of low-level mutations identified by Surveyor TM . Here we enabled Surveyor TM , an endonuclease that recognizes selectively mismatches formed by mutations and small deletions following 'cross-hybridized sequence' formation, to generate mutation-specific DNA fragments that are amplified and screened via differential melting curve analysis. cache = ./cache/cord-048359-lz37rh82.txt txt = ./txt/cord-048359-lz37rh82.txt === reduce.pl bib === id = cord-022501-9wnmdvg5 author = nan title = P1460 – P1884 date = 2015-12-28 pages = extension = .txt mime = text/plain words = 128256 sentences = 7808 flesch = 51 summary = Methods: Using published data on (1) the prevalence of MRSA and other bacterial pathogens causing cSSSI in the US, (2) the in-vitro susceptibility rates of commonly used regimens in cSSSI in the US in relation to the most pervasive pathogens identified above, and (3) estimated costs of failure of initial, empiric treatment from a recent study of a large US multi-hospital database, we developed a model to predict the expected clinical and economic impact of increasing prevalence of MRSA. Small outbreaks of VEB-1 ESBL producing Acinetobacter baumannii in Belgian nursing homes and hospitals through cross-border transfer of patients from northern France Methods: From 01/04 to 03/05, all Belgian acute hospitals were invited to report cases of nosocomial infections/colonisations due to MDR Ab isolates presenting a resistance profile similar to the French epidemic strain (resistance to all agents except carbapenems and colistin) and to send such isolates to the reference laboratory for phenotypic confirmation and for genotypic characterization (PCR of VEB-1 and class 1 Integron, PFGE typing). cache = ./cache/cord-022501-9wnmdvg5.txt txt = ./txt/cord-022501-9wnmdvg5.txt === reduce.pl bib === id = cord-102511-7zgd45fl author = Khodakov, Dmitriy title = Donut PCR: a rapid, portable, multiplexed, and quantitative DNA detection platform with single-nucleotide specificity date = 2020-05-05 pages = extension = .txt mime = text/plain words = 4279 sentences = 214 flesch = 44 summary = Here, we present the Donut PCR platform that features high multiplexing, rapid turnaround times, single nucleotide discrimination, and precise quantitation of DNA targets in a portable, affordable, and battery-powered instrument using closed consumables that minimize contamination. Here, we present the Donut PCR platform for DNA detection that combines scalable and massive multiplexing, rapid turnaround times, single nucleotide discrimination, and precise quantitation in a portable, affordable, and batterypowered instrument using closed consumables that minimize contamination risks ( Table 1 ). By engineering a donut-shaped reaction chamber in the PCR chip, we remove most of the dead volume, and are able to achieve similar PCR specificity on human genomic DNA as the commercial Bio-Rad CFX96 instrument (Fig. 2a) . The Donut PCR platform presented here achieves rapid, sensitive, and quantitative detection of many DNA targets from a single sample using a closed, portable, and affordable instrument. cache = ./cache/cord-102511-7zgd45fl.txt txt = ./txt/cord-102511-7zgd45fl.txt === reduce.pl bib === id = cord-023354-f2ciho6o author = nan title = TUESDAY PLENARY SESSION 3 TUESDAY: POSTERS date = 2005-06-08 pages = extension = .txt mime = text/plain words = 130046 sentences = 7333 flesch = 54 summary = • enhancement of automation/computerisation; • process control to provide an 'error-free pathway'; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody 'combi' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas' disease infection (for retrieval of otherwise wasted blood); • European Union's in vitro diagnostics directive: this has caused some problems and reduced flexibility. cache = ./cache/cord-023354-f2ciho6o.txt txt = ./txt/cord-023354-f2ciho6o.txt === reduce.pl bib === id = cord-103163-0rreoh4o author = Smith, Sydni Caet title = Reovirus RNA recombination is sequence directed and generates internally deleted defective genome segments during passage date = 2020-10-22 pages = extension = .txt mime = text/plain words = 8965 sentences = 456 flesch = 46 summary = We determined the titers and RNA segment profiles of reovirus (rsT1L and rsT3D I ) and rotavirus (rsSA11) laboratory strains that had been rescued by reverse genetics then serially passaged ten times, each in triplicate lineages, in cultured cells. The two reoviruses accumulated non-canonical RNAs that retain 5′ and 3′ termini and feature one or more large internal deletions, while the rotavirus rarely accumulated such DVGs. Analyses of next-generation RNA-sequencing data sets from purified rsT1L reovirus RNA revealed many junctions, with hot spots for recombination in specific viral gene segments. Taken together, lin1 RNA profiles suggest non-canonical RNA species that differ in length but have identical termini to the parental segments accumulate variably during reovirus and rotavirus serial passage in cultured cells. cache = ./cache/cord-103163-0rreoh4o.txt txt = ./txt/cord-103163-0rreoh4o.txt === reduce.pl bib === id = cord-022888-dnsdg04n author = nan title = Poster Sessions date = 2009-08-19 pages = extension = .txt mime = text/plain words = 188640 sentences = 9313 flesch = 45 summary = Methods: Phospho-specific Western blot analyses were performed to verify the functionality of the different IFN-g pathway components, intra-and extracellular flow cytometry experiments were employed to determine the expression of antigen processing components and HLA class I cell surface antigens, quantitative real time-PCR experiments to confirm the absence of JAK2 and presence of pathway relevant molecules as well as, genomic PCR and chromosome typing technique to prove the deletion of JAK2. In order to accomplish these objectives we induced priming or tolerance of ovalbumin (OVA 323-339 peptide)-specific T cells from DO11.10 TCR transgenic mice in vitro or, following adoptive transfer of near physiologically relevant numbers of such cells into recipients, in vivo and correlated functional outcome (via proliferation and cytokine readout assays or antibody production) with E3 ubiquitin-protein ligases expression and the ubiquitination status of the TCR signalling machinery. cache = ./cache/cord-022888-dnsdg04n.txt txt = ./txt/cord-022888-dnsdg04n.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-023364-ut56gczm author = nan title = EDUCATION DAY MONDAY: PLENARY SESSION 1 MONDAY: PARALLEL SESSIONS date = 2005-06-08 pages = extension = .txt mime = text/plain words = 130049 sentences = 7334 flesch = 54 summary = • enhancement of automation/computerisation; • process control to provide an 'error-free pathway'; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody 'combi' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas' disease infection (for retrieval of otherwise wasted blood); • European Union's in vitro diagnostics directive: this has caused some problems and reduced flexibility. cache = ./cache/cord-023364-ut56gczm.txt txt = ./txt/cord-023364-ut56gczm.txt === reduce.pl bib === id = cord-103563-7a3wdduq author = Nunez-Bajo, Estefania title = Ultra-Low-Cost Integrated Silicon-based Transducer for On-Site, Genetic Detection of Pathogens date = 2020-03-25 pages = extension = .txt mime = text/plain words = 4535 sentences = 211 flesch = 44 summary = Unlike other silicon-based technologies, TriSilix can be produced at wafer-scale in a standard laboratory; we have developed a series of methodologies based on metal-assisted chemical (wet) etching, electroplating, thermal bonding and laser-cutting to enable a cleanroom-free low-cost fabrication that does not require processing in an advanced semiconductor foundry. To create an ultra-low-cost device, the architecture proposed exploits the intrinsic properties of silicon and integrates three modes of operation in a single chip: i) electrical (Joule) heater, ii) temperature sensor (i.e. thermistor) with a negative temperature coefficient that can provide the precise temperature of the sample solution during reaction and iii) electrochemical sensor for detecting target NA. Using TriSilix, the sample solution can be maintained at a single, specific temperature (needed for isothermal amplification of NA such as Recombinase Polymerase Amplification (RPA) or cycled between different temperatures (with a precision of ±1.3°C) for Polymerase Chain Reaction (PCR) while the exact concentration of amplicons is measured quantitatively and in real-time electrochemically. cache = ./cache/cord-103563-7a3wdduq.txt txt = ./txt/cord-103563-7a3wdduq.txt === reduce.pl bib === id = cord-023095-4dannjjm author = nan title = Research Abstract Program of the 2011 ACVIM Forum Denver, Colorado, June 15–18, 2011 date = 2011-05-03 pages = extension = .txt mime = text/plain words = 134226 sentences = 6834 flesch = 51 summary = The purpose of this study was to determine the short-term effects of ivabradine on heart rate (HR), blood pressure, left ventricular (LV) systolic and diastolic function, left atrial (LA) performance, and clinical tolerance in healthy cats after repeated oral doses. The goal of this study was to investigate the relationship between heart rate and ECG time intervals to body mass in apparently healthy horses and ponies and to calculate normal ranges for different weight groups. This study aimed to investigate the prevalence of hypercoagulability in PLN dogs based on thromboelastography (TEG), and to determine whether hypercoagulability in these patients could be predicted by clinical assessments that identify systemic hypertension (systolic blood pressure 4 160 mmHg), hypoalbuminemia (serum albumin o 2.7 mg/dl), antithrombin activity (o 70%), and degree of proteinuria (urine protein:creatinine ratio [UPC] ! cache = ./cache/cord-023095-4dannjjm.txt txt = ./txt/cord-023095-4dannjjm.txt === reduce.pl bib === id = cord-140318-xtx8hl14 author = Martin, Alexandra title = High-sensitivity COVID-19 group testing by digital PCR date = 2020-06-03 pages = extension = .txt mime = text/plain words = 4252 sentences = 213 flesch = 58 summary = Methods: We implemented RT-dPCR based COVID-19 group testing on commercially available system and assay (Naica System from Stilla Technologies) and investigated the sensitivity of the method in real life conditions of a university hospital in Paris, France, in May 2020. The results for SARS-CoV-2 detection by RT-dPCR in groups of 8 samples, detailed in Tables 1 and 2 , are in concordance with the reference individual RT-PCR testing for 52 groups (corresponding for 416 samples), out of which 32 were RT-PCR negative groups and 20 groups contained at least one RT-PCR+ sample. In this work, we assessed the sensitivity and specificity of group testing combined with digital PCR for SARS-CoV-2 detection. cache = ./cache/cord-140318-xtx8hl14.txt txt = ./txt/cord-140318-xtx8hl14.txt === reduce.pl bib === id = cord-158252-l43ztxsl author = Pawlowski, Colin title = Longitudinal laboratory testing tied to PCR diagnostics in COVID-19 patients reveals temporal evolution of distinctive coagulopathy signatures date = 2020-05-21 pages = extension = .txt mime = text/plain words = 6126 sentences = 221 flesch = 35 summary = We found that compared to COVIDneg at the time of clinical presentation and diagnostic testing, COVIDpos patients tended to have higher plasma fibrinogen levels and similarly low platelet counts, with approximately 25% of patients in both cohorts showing outright thrombocytopenia. To this end, we instituted a holistic data science platform across an academic health care system that enables machine intelligence to augment the curation of phenotypes and outcomes from 15.2 million EHR clinical notes and associated 3 million lab tests from 1,192 COVID-19positive (COVIDpos) and 47,344 confirmed COVID-19-negative (COVIDneg) patients over a retrospectively defined 2-month observation period straddling the date of the PCR test (see Methods). Conversely, platelet counts were lower in the COVIDpos cohort at the time of clinical presentation but tended to increase over the subsequent 10 days to levels significantly higher than those in COVIDneg patients (Cohen's D = 0.361, BH-adjusted Mann-Whitney p-value = 0.008, Table 2, Figure 2B ). cache = ./cache/cord-158252-l43ztxsl.txt txt = ./txt/cord-158252-l43ztxsl.txt === reduce.pl bib === id = cord-103787-qhftb6d7 author = Garcia, Elizabeth P. title = Scalable Transcriptional Analysis Routine—Multiplexed Quantitative Real-Time Polymerase Chain Reaction Platform for Gene Expression Analysis and Molecular Diagnostics date = 2005-10-31 pages = extension = .txt mime = text/plain words = 7354 sentences = 355 flesch = 47 summary = Scalable transcriptional analysis routine (STAR) represents a novel integration of reverse transcriptase-polymerase chain reaction and capillary electrophoresis that allows detection of dozens of gene transcripts in a multiplexed format using amplicon size as an identifier for each target. Scalable transcriptional analysis routine (STAR) represents a novel integration of reverse transcriptase-polymerase chain reaction and capillary electrophoresis that allows detection of dozens of gene transcripts in a multiplexed format using amplicon size as an identifier for each target. We have developed STAR (scalable transcription analysis routine), a gene expression analysis platform that represents an innovative integration of real-time multiplex PCR and capillary electrophoresis (CE), allowing the simultaneous quantitative measurement of multiple targets in a single sample with high sensitivity. In a typical STAR experiment (diagrammatically shown in Figure 1A ), a PCR reaction is set up in a single tube containing the analyte, common PCR reagents (eg, DNA polymerase, dNTPs), and, for each target to be amplified, gene-specific primers where at least one of each pair is labeled with a fluorophore. cache = ./cache/cord-103787-qhftb6d7.txt txt = ./txt/cord-103787-qhftb6d7.txt === reduce.pl bib === id = cord-252198-gs52k4lq author = Onions, David title = Validation of the safety of MDCK cells as a substrate for the production of a cell-derived influenza vaccine date = 2010-09-30 pages = extension = .txt mime = text/plain words = 6592 sentences = 290 flesch = 41 summary = We conclude that the theoretical risks arising from manufacturing seasonal influenza vaccine using MDCK-33016PF cells are reduced to levels that are effectively zero by the multiple, orthogonal processes used during production. In order to quantitatively assess potential risks represented by adventitious viruses, data were collected about growth properties of various relevant viruses in MDCK-33016PF cells, about the virus inactivating and virus clearance of the vaccine manufacturing process, and about the detection limits of applied PCR methods to detect adventitious viruses. Combining all data on the virus growth in MDCK-33016PF cells, on the inactivation or process removal of various model viruses, and with consideration of applicable detection limits for virus exclusion tests, a process-specific risk assessment was made using quantitative data relative to infectious doses. First a rigorous analysis of the MDCK-33016PF cells was undertaken to exclude the presence of infectious oncogenic viruses or infectious oncogenic viral genomes; secondly the manufacturing process was shown to be capable of inactivating potential virus contaminants at very high levels. cache = ./cache/cord-252198-gs52k4lq.txt txt = ./txt/cord-252198-gs52k4lq.txt === reduce.pl bib === === reduce.pl bib === id = cord-254064-qxgpehuy author = Chacko, J. title = Hydroxychloroquine in COVID-19: A systematic review and meta-analysis date = 2020-05-19 pages = extension = .txt mime = text/plain words = 4034 sentences = 289 flesch = 57 summary = In spite of several observational studies and a few randomized controlled trials, the effect of hydroxychloroquine on patients with COVID 19 infection remains unclear. Conclusions Our meta-analysis does not suggest improvement in clinical progression, mortality, or viral clearance by RT PCR among patients with COVID 19 infection who are treated with hydroxychloroquine. Hence, we performed a systematic review and meta-analysis of available controlled studies to evaluate the safety and efficacy of hydroxychloroquine in the treatment of COVID-19 infection. Studies were considered eligible if they included patients who received hydroxychloroquine alone or in combination with other specific treatment modalities for COVID-19 infection and were compared with a control group. Data on at least one of the following outcomes had to be available for inclusion in the meta-analysis: (i) mortality, (ii) clinical progress, (iii) results of the reverse transcription-polymerase chain reaction (RT-PCR) test after the commencement of treatment, (iv) changes on computed tomography (CT) imaging of the chest, and (iv) adverse clinical events. cache = ./cache/cord-254064-qxgpehuy.txt txt = ./txt/cord-254064-qxgpehuy.txt === reduce.pl bib === === reduce.pl bib === id = cord-253502-v2hh3w3r author = Leung, C.W. title = Clinical picture, diagnosis, treatment and outcome of severe acute respiratory syndrome (SARS) in children date = 2004-11-05 pages = extension = .txt mime = text/plain words = 8625 sentences = 524 flesch = 45 summary = authors: Leung, C.W.; Chiu, W.K. title: Clinical picture, diagnosis, treatment and outcome of severe acute respiratory syndrome (SARS) in children [5] [6] [7] [8] [9] [10] [11] Superspreading events including a major hospital outbreak, in-flight transmission on board commercial PAEDIATRIC RESPIRATORY REVIEWS (2004) Summary Children are susceptible to infection by SARS-associated coronavirus (SARS-CoV) but the clinical picture of SARS is milder than in adults. cache = ./cache/cord-253502-v2hh3w3r.txt txt = ./txt/cord-253502-v2hh3w3r.txt === reduce.pl bib === id = cord-252268-o63ep08b author = Carolan, Louise A. title = TaqMan real time RT-PCR assays for detecting ferret innate and adaptive immune responses date = 2014-09-01 pages = extension = .txt mime = text/plain words = 6643 sentences = 358 flesch = 52 summary = As this equation relies on consistency between samples in the RNA quantity assayed, and the optimum reaction efficiency, as well as minimal fluctuation in the expression of housekeeping genes (endogenous controls) (Peters et al., 2007; Mane et al., 2008; Bruder et al., 2010) , these parameters were optimized using RNA extracted from cultured ferret lymph node cells stimulated with mitogens or with influenza virus. To test the ability of ferret leukocytes to produce mRNA cytokines and chemokines, lymph node cells from naïve ferrets were cultured with various mitogens known to activate T and B lymphocyte and macrophage/monocyte responses (Fig. 5) and with live or heat inactivated influenza virus (Fig. 6 ) and the cytokine and chemokine expression profiles were determined (summarized in (ConA) or Phytohaemagglutinin (PHA), which act by cross linking T cell receptors via sugars on the surface of human T lymphocytes (Chilson and Kelly-Chilson, 1989) , induced similar cytokine profiles, increasing expression of IL2, IL4, IL6, IL10, IL17, Granzyme A, TNF␣ and IFN␥, most with high fold changes, consistent with effective stimulation of T lymphocytes (Fig. 5) . cache = ./cache/cord-252268-o63ep08b.txt txt = ./txt/cord-252268-o63ep08b.txt === reduce.pl bib === === reduce.pl bib === id = cord-252347-vnn4135b author = Lee, Wai-Ming title = A Diverse Group of Previously Unrecognized Human Rhinoviruses Are Common Causes of Respiratory Illnesses in Infants date = 2007-10-03 pages = extension = .txt mime = text/plain words = 5672 sentences = 271 flesch = 51 summary = METHODS AND FINDINGS: To directly type HRVs in nasal secretions of infants with frequent respiratory illnesses, we developed a sensitive molecular typing assay based on phylogenetic comparisons of a 260-bp variable sequence in the 5' noncoding region with homologous sequences of the 101 known serotypes. The degenerate primers EV292 and EV222 for PCR amplification of NIm-1A region were not sensitive enough for direct detection of small amount of HRV in original clinical samples (data not shown), and high titer infected cell lysates of cultured isolates were needed to produce enough PCR product for cloning and sequencing. This new assay had 3 key components: sensitive pan-HRV primers and semi-nested PCR to amplify P1-P2 region from cDNA prepared from original clinical specimens, a sequence database of 260-bp P1-P2 region of 5'NCR of all 101 HRV serotypes to serve as standard references for HRV identification, and phylogenetic tree reconstruction of the new P1-P2 sequences and the 101 homologous reference sequences. cache = ./cache/cord-252347-vnn4135b.txt txt = ./txt/cord-252347-vnn4135b.txt === reduce.pl bib === === reduce.pl bib === id = cord-252694-36ijqwge author = Heidinger, Benedikt H. title = Radiologische Manifestationen von Lungenerkrankungen bei COVID-19 date = 2020-09-08 pages = extension = .txt mime = text/plain words = 2948 sentences = 368 flesch = 39 summary = Der Referenzstandard für die Diagnose von COVID-19 ist eine positive "reverse transcription polymerase chain reaction" (RT-PCR) eines Nasen-/ Rachenabstriches oder einer Probe tiefen Bronchialsekrets [4] . Mehrere medizinische und radiologische Fachgesellschaften haben Empfehlungen für die Anwendung der verschiedenen Bildgebungsmodalitäten bei Patienten mit Verdacht auf oder bereits nachgewiesener SARS-CoV-2 publiziert [5] [6] [7] [8] [9] [10] . Sollten sich COVID-19-typische Lungenveränderungen als Zufallsbefund bei respiratorisch asymptomatischen Patienten zeigen, ist eine Bestätigung der Diagnose mittels RT-PCR notwendig [7, 8] . Im Thoraxröntgen untypisch für COVID-19 sind Kavitationen und Pleuraergüsse, die hinweisend auf Komplikationen oder andere Diagnosen wie beispielswei-se eine kardiale Dekompensation sein können [19] . Besteht jedoch eine hohe klinische Vortestwahrscheinlichkeit für COVID-19, beispielsweise bei typischen klinischen Symptomen und bekanntem Kontakt zu einer SARS-CoV2-positiven Person oder einer hohen Erkrankungsprävalenz in der Bevölkerung, sind diese jedoch als wahrscheinlich für das Vorliegen einer COVID-19-Pneumonie zu werten. cache = ./cache/cord-252694-36ijqwge.txt txt = ./txt/cord-252694-36ijqwge.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-254101-613aftc1 author = Wang, Ping title = Establishment of a transgenic mouse model with liver-specific expression of secretory immunoglobulin D date = 2012-04-14 pages = extension = .txt mime = text/plain words = 4387 sentences = 239 flesch = 60 summary = In this study, we generated by fusion PCR a vector to express high levels of chimeric secretory IgD (csIgD) specifically in the liver. Hyperimmunoglobulinemia D syndrome (HIDS), also called receptor-associated periodic syndrome or etiocholanolone fever, is characterized by high serum levels of immunoglobulin D (IgD) and recurrent febrile attacks, and may also include arthritis, lymphadenopathy, hepatosplenomegaly, and skin rash [1-3]. The resulting plasmids, designated en-pAlb-csIgD-H and en-pAlb-cKappa, were under control of the mouse Alb regulatory sequences to direct gene expression specifically in the liver. This indicates that the inflammation in the transgenic mice is caused by increased sIgD rather than by Mvk mutation. Skin ulcers in transgenic mice with high expression of sIgD may be caused by excessive immune activation. An albumin enhancer located 10-kb upstream functions along with its promoter to direct efficient, liver-specific expression in transgenic mice High level expression of a functional human/mouse chimeric anti-CD20 monoclonal antibody in milk of transgenic mice cache = ./cache/cord-254101-613aftc1.txt txt = ./txt/cord-254101-613aftc1.txt === reduce.pl bib === id = cord-254115-hwy962a4 author = Reslova, Nikol title = xMAP Technology: Applications in Detection of Pathogens date = 2017-01-25 pages = extension = .txt mime = text/plain words = 11354 sentences = 530 flesch = 40 summary = xMAP multiplex assays are currently available in various nucleic acid and immunoassay formats, enabling simultaneous detection and typing of pathogenic viruses, bacteria, parasites and fungi and also antigen or antibody interception. High-throughput multiplex detection techniques are designed for the rapid, sensitive and specific testing of large numbers of analytes (nucleic acid assays, immunoassays, enzyme assays, or receptor-ligands) in a single biological sample. Although PCR allows multiplex amplification of several targets in a single run xMAP as a methodology represents a significant step forward, and was designed with the aim of creating a high-throughput bioassay platform, enabling rapid, cost-effective, and simultaneous analysis of multiple analytes within a single biological sample. In direct DNA hybridization (DDH), allele-specific primer extension (ASPE), single base chain extension (SBCE), and Oligonucleotide ligation assay (OLA) all the target DNA sequences are amplified in multiplex PCR prior to hybridization to microspheres. cache = ./cache/cord-254115-hwy962a4.txt txt = ./txt/cord-254115-hwy962a4.txt === reduce.pl bib === id = cord-255871-dau9tz6u author = Lee, Mi-Kyung title = Survey of Clinical Laboratory Practices for 2015 Middle East Respiratory Syndrome Coronavirus Outbreak in the Republic of Korea date = 2015-12-18 pages = extension = .txt mime = text/plain words = 2610 sentences = 130 flesch = 48 summary = BACKGROUND: It is crucial to understand the current status of clinical laboratory practices for the largest outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infections in the Republic of Korea to be well prepared for future emerging infectious diseases. The number of MERS-CoV rRT-PCR tests performed was collected from 32 medical institutions and five referral medical laboratories. A total of 27,009 MERS-CoV rRT-PCR tests were performed at 32 medical institutions (N = 11,502) and five referral medical laboratories (N = 15,507) (Table 1 and Fig. 1 ). The proportion of medical institutions was significantly underestimated because one tertiary care hospital submitted responses for the survey but not the specimen list, and the numbers of MERS-CoV rRT-PCR tests and positive specimens at this institution would have been predominant in the reporting medical institutions. Table 2 shows the current status of clinical laboratories in medical institutions with respect to their response to the outbreak of MERS-CoV infections. cache = ./cache/cord-255871-dau9tz6u.txt txt = ./txt/cord-255871-dau9tz6u.txt === reduce.pl bib === id = cord-252604-1u14i4v1 author = Smith, Alvin W. title = Vesivirus viremia and seroprevalence in humans date = 2006-03-22 pages = extension = .txt mime = text/plain words = 5270 sentences = 266 flesch = 53 summary = To test the possibility that sera may contain Vesivirus genomes, as suggested by the clinical evidence of viremia in cases of Vesivirus illness, including humans [Smith et al., 1998a] , three complementary methods targeting three Vesivirus genomic regions were utilized to detect Vesivirus RNA in serum ( Fig. 1 ): dot blot for the ORF1 3C protease region, reverse transcriptionpolymerase chain reaction (RT-PCR) for the 3 0 terminal region of ORF1 encoding a portion of the viral RNA polymerase or for a portion of the viral capsid protein, and nucleotide sequencing of RT-PCR amplicons. cache = ./cache/cord-252604-1u14i4v1.txt txt = ./txt/cord-252604-1u14i4v1.txt === reduce.pl bib === === reduce.pl bib === id = cord-255026-fdp6mies author = Belák, Sándor title = Molecular diagnosis of viral diseases, present trends and future aspects: A view from the OIE Collaborating Centre for the Application of Polymerase Chain Reaction Methods for Diagnosis of Viral Diseases in Veterinary Medicine date = 2007-07-26 pages = extension = .txt mime = text/plain words = 5342 sentences = 225 flesch = 40 summary = The experiences of an OIE-Collaborating Centre and of two EU project consortia are summarised on the diagnostic application of gel-based PCR, general PCR systems, phylogeny, molecular epidemiology, real-time PCR (TaqMan, Molecular Beacons, Primer-Probe Energy Transfer), amplification without thermocycling (Invader), multiplex PCR, nucleic acid extraction and pipetting robotics, automation and quality control, including internal controls. cache = ./cache/cord-255026-fdp6mies.txt txt = ./txt/cord-255026-fdp6mies.txt === reduce.pl bib === id = cord-255545-nycdhdsd author = Schoenike, Barry title = Quantitative sense-specific determination of murine coronavirus RNA by reverse transcription polymerase chain reaction date = 1999-03-10 pages = extension = .txt mime = text/plain words = 6170 sentences = 265 flesch = 48 summary = In theory, sense-specific measurement of viral RNAs may be achieved by reverse transcription polymerase chain reaction (RT-PCR) assays which utilize primers of defined polarity during the RT step. Key RT-PCR parameters which were optimized include the design of tagged primers, DNase treatment of in vitro transcribed RNA standards, specification of temperature differences between RT and PCR annealing steps, and use of competitive RNA templates for quantitative assays. In fact, several studies have demonstrated that RT-PCR assays based on specific RNA template recognition by RT primers of defined polarity will not reliably distinguish between viral RNAs of positive or negative sense. Despite the findings above, many published research reports are based on conventional RT-PCR assays, relying on the polarity of primers added to the RT step in putative sense-specific measurements of viral RNAs; rarely are control reactions performed to rigorously show that this method is in fact sense-specific. cache = ./cache/cord-255545-nycdhdsd.txt txt = ./txt/cord-255545-nycdhdsd.txt === reduce.pl bib === id = cord-255019-iie8wxb4 author = Chen, Xin title = Acute lower respiratory tract infections by human metapneumovirus in children in Southwest China: A 2‐year study date = 2010-06-25 pages = extension = .txt mime = text/plain words = 4005 sentences = 234 flesch = 50 summary = title: Acute lower respiratory tract infections by human metapneumovirus in children in Southwest China: A 2‐year study Specimens were collected over a 2‐year period from children hospitalized with acute lower respiratory tract infections (ALRTI) and analyzed for the presence of hMPV using real‐time RT‐PCR assays. 2, 3 Human metapneumovirus (hMPV) was first isolated in 2001 from nasopharyngeal aspirates (NPAs) obtained from children with acute lower respiratory tract infections (ALRTI) in the Netherlands. The validated assay was then used to detect the presence of hMPV in NPAs from pediatric patients presenting at a large teaching children's hospital located in southwest China over a period of 2 years. NPAs from pediatric patients presenting with ALRTI in the daytime were collected at the Respiratory Ward, Children's Hospital of Chongqing Medical University, on three fixed days each week over a 2-year period from April 2006 to March 2008. cache = ./cache/cord-255019-iie8wxb4.txt txt = ./txt/cord-255019-iie8wxb4.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-254250-l0v602x9 author = Hooper, Chantelle title = A Novel RNA Virus, Macrobrachium rosenbergii Golda Virus (MrGV), Linked to Mass Mortalities of the Larval Giant Freshwater Prawn in Bangladesh date = 2020-10-02 pages = extension = .txt mime = text/plain words = 6440 sentences = 309 flesch = 48 summary = title: A Novel RNA Virus, Macrobrachium rosenbergii Golda Virus (MrGV), Linked to Mass Mortalities of the Larval Giant Freshwater Prawn in Bangladesh De novo virus assembly revealed a 29 kb single-stranded positive-sense RNA virus with similarities in key protein motif sequences to yellow head virus (YHV), an RNA virus that causes mass mortalities in marine shrimp aquaculture, and other viruses in the Nidovirales order. rnaSPAdes assembly of combined libraries produced 38,826 contigs; 23 contigs, of average length 4560 bp, had similarity in protein sequence to YHV or gill-associated virus (GAV), but when the trimmed reads were aligned against the YHV genome (accession number GCA_003972805.1), no alignment was seen. rosenbergii were negative: MrNV and XSV, the causative agents of white tail disease [9, 10] ; MrTV, a virus associated with mass larval mortalities in China [15] , Spiroplasma eriocheiris [8] , and WSSV-shown to be able to infect M. cache = ./cache/cord-254250-l0v602x9.txt txt = ./txt/cord-254250-l0v602x9.txt === reduce.pl bib === id = cord-255975-ymw9avlm author = Ho, Yen‐Peng title = Advances in mass spectrometry for the identification of pathogens date = 2011-05-09 pages = extension = .txt mime = text/plain words = 15945 sentences = 814 flesch = 35 summary = The direct analysis of whole pathogenic microbial cells with matrix‐assisted laser desorption/ionization MS without sample separation reveals specific biomarkers for taxonomy, and has the advantages of simplicity, rapidity, and high‐throughput measurements. Matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) allows the fast and accurate identification and subtyping of bacterial species (Seng et al., 2009; Stevenson, Drake, & Murray, 2010) , fungi (Marinach-Patrice et al., 2009 , 2010 Santos et al., 2010) , and viruses Franco et al., 2010) . Direct bacterial profiling with MALDI-TOFMS is based mainly on a comparison of specific mass spectra of the proteins, peptides, and other cellular components that are obtained from microbial cells. The development of a matrix-assisted laser desorption/ionization mass spectrometry-based method for the protein fingerprinting and identification of Aeromonas species using whole cells On-probe sample pretreatment for direct analysis of lipids in gram-positive bacterial cells by matrix-assisted laser desorption ionization mass spectrometry Universal sample preparation method for characterization of bacteria by matrix-assisted laser desorption ionization-time of flight mass spectrometry cache = ./cache/cord-255975-ymw9avlm.txt txt = ./txt/cord-255975-ymw9avlm.txt === reduce.pl bib === id = cord-256130-zhlvvuj4 author = Nordén, Rickard title = Quantification of Torque Teno Virus and Epstein-Barr Virus Is of Limited Value for Predicting the Net State of Immunosuppression After Lung Transplantation date = 2018-03-06 pages = extension = .txt mime = text/plain words = 4853 sentences = 230 flesch = 47 summary = Here, we evaluated quantification of torque teno virus (TTV) and Epstein-Barr virus (EBV) as biomarkers for defining the net state of immunosuppression in lung-transplanted patients. The aim of the present study was to evaluate levels of TTV and EBV in relation to the frequency of infectious events and acute rejections over time in a prospective manner in a single-center cohort of lung-transplanted patients. The total nucleic acid content was isolated from serum or whole blood samples and analyzed for TTV-, EBV-, and CMV-DNA load by real-time PCR. Comparison of TTV-and EBV-DNA levels in lung transplant recipients who received either Tacrolimus-or Cyclosporinebased therapy revealed that Cyclosporine-treated patients had significantly lower TTV-DNA levels in serum at month 6 post-LTx and onwards, compared with the Tacrolimustreated patients (Figure 1 ). However, we found no association between either TTV-or EBV-DNA load and infectious events or acute rejections, which suggests a limited clinical applicability as biomarkers predicting short-term outcomes related to the net state of immunosuppression. cache = ./cache/cord-256130-zhlvvuj4.txt txt = ./txt/cord-256130-zhlvvuj4.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-256244-f5zsy56p author = Funakoshi, Yu title = Enterovirus D68 respiratory infection in a children's hospital in Japan in 2015 date = 2019-08-22 pages = extension = .txt mime = text/plain words = 3854 sentences = 231 flesch = 47 summary = Mycoplasma pneumonia was tested for using the loop-mediated isothermal amplification method (Eiken Chemical, Tokyo, Japan) 15 when physicians in charge considered it as a potential etiologic pathogen based on patient age and symptoms regardless of the patient's eligibility for this study. We encountered an outbreak of EV-D68 in the autumn of 2015 (September-October), in which the number of patients with respiratory symptoms who required treatment for wheezing increased dramatically compared with previous years. 19, 29, 30 In the present study, EV-D68 infection with a history of asthma was not associated with either severity (defined as ICU admission, magnesium sulfate use, or ventilation support) nor prolonged hospitalization. In contrast to previous research, asthma history was not associated with the risk of developing severe respiratory infections in the present study. Two cases of acute severe flaccid myelitis associated with enterovirus D68 infection in children cache = ./cache/cord-256244-f5zsy56p.txt txt = ./txt/cord-256244-f5zsy56p.txt === reduce.pl bib === id = cord-257284-dash9udv author = Decaro, Nicola title = Development and validation of a real-time PCR assay for specific and sensitive detection of canid herpesvirus 1 date = 2010-07-30 pages = extension = .txt mime = text/plain words = 3138 sentences = 149 flesch = 52 summary = The detection limit was 10(1) and 1.20 × 10(1) DNA copies per 10 μl(−1) of template for standard DNA and a CHV-1-positive kidney sample, respectively: about 1-log higher than a gel-based PCR assay targeting the thymidine kinase gene. Unlike other CHV-1-specific diagnostic methods, this quantitative assay permits simultaneous detection and quantitation of CHV-1 DNA in a wide range of canine tissues and body fluids, thus providing a useful tool for confirmation of a clinical diagnosis, for the study of viral pathogenesis and for evaluation of the efficacy of vaccines and antiviral drugs. To evaluate the detection limits of the real-time PCR assay, 10fold dilutions of the plasmid DNA, ranging from 10 9 to 10 0 copies, were made in a CHV-1-negative kidney homogenate and tested subsequently. The development and validation of a real-time PCR assay for detection and absolute quantitation of CHV-1 DNA in tissue samples and body fluids of dogs are described. cache = ./cache/cord-257284-dash9udv.txt txt = ./txt/cord-257284-dash9udv.txt === reduce.pl bib === id = cord-254506-cxdklz4u author = Castellvi, J. title = Impact On Clinical Practice Of The Preoperative Screening Of Covid-19 Infection In Surgical Oncological Patients. Prospective Cohort Study date = 2020-08-11 pages = extension = .txt mime = text/plain words = 1850 sentences = 131 flesch = 52 summary = The aim of this study was to describe the impact on clinical practice of sequential preoperative screening for COVID-19-infection in deciding whether to proceed or postpone surgery. Sequential preoperative screening for COVID-19-infection: two-time medical history (telematic and face-to-face), PCR and chest CT, 48 hours before of surgical intervention. Conclusion preoperative screening for COVID-19-infection using medical history and PCR helped the surgeon to decide whether to go ahead or postpone surgery in oncological patients. Three preoperative screening tests have been proposed: a detailed history, a COVID-19 PCR determination and a chest radiological imaging (CT or Xray), despite not having any control studies available [6] [7] [8] [9] [10] [11] [12] . Therefore, our working hypothesis is that sequential preoperative screening: clinical (detailed history), PCR and radiology (chest CT) of COVID-19 infection and pneumonia will identify symptomatic and asymptomatic infected patients. cache = ./cache/cord-254506-cxdklz4u.txt txt = ./txt/cord-254506-cxdklz4u.txt === reduce.pl bib === === reduce.pl bib === id = cord-256931-wj0esjwi author = Gelfer, Gita title = The clinical impact of the detection of potential etiologic pathogens of community-acquired pneumonia date = 2015-08-05 pages = extension = .txt mime = text/plain words = 4850 sentences = 280 flesch = 49 summary = The etiology of community-acquired pneumonia (CAP) is determined in less than half of the patients based on cultures of sputum and blood plus testing urine for the antigens of Streptococcus pneumoniae and Legionella pneumophila. A common core diagnostic test bundle was applied to all patients in the study: i.e., 2 blood cultures; sputum culture and sensitivity; serum PCT level; and urine antigen testing for L. If a respiratory virus was detected and the serum PCT was above 0.5 ng/mL and/or a bacterial pathogen was found in the sputum culture, the patient was assumed to have a dual infection with the identified virus and bacteria. If a respiratory virus was detected, an associated bacterial infection was deemed present if a bacterial pathogen was identified by culture or PCR or urine antigens or if the serum PCT concentration was N0.5 ng/mL. cache = ./cache/cord-256931-wj0esjwi.txt txt = ./txt/cord-256931-wj0esjwi.txt === reduce.pl bib === id = cord-256982-t6urqus7 author = Wellinghausen, Nele title = Evaluation of the SARS-CoV-2-IgG response in outpatients by five commercial immunoassays date = 2020-09-16 pages = extension = .txt mime = text/plain words = 2514 sentences = 131 flesch = 51 summary = The sensitivity in serum samples, collected at a median of 24 days after onset of symptoms, detected by the Anti-SARS-CoV-2-ELISA IgG (Euroimmun), EDI™ Novel Coronavirus COVID-19 IgG ELISA (Epitope Diagnostics), Liaison(®) SARS-CoV-2 S1/S2 IgG (Diasorin), SARS-CoV-2 IgG on the Architect™ i2000 (Abbott), and Elecsys(®) Anti-SARS-CoV-2 (IgM/IgA/IgG) on the cobas™ e801 (Roche) was 84.3%, 78.4%, 74.5%, 86.3%, and 88.2%, respectively. Our results show significant individual differences of the IgG response against SARS-CoV-2, additionally confirmed in three patients with follow-up serum samples and seven asymptomatic but PCR-positive contact persons. In conclusion, our study shows that commercially available immunoassays detect SARS-CoV-2-IgG or total antibodies in outpatients with a satisfying sensitivity, but lower than that reported for hospitalized patients. A comparison of five commercial immunoassays in serum samples taken at least ten days after onset of symptoms from 51 PCR-confirmed COVID-19 outpatients revealed an overall sensitivity of the assays from 74.5% to 88.2%. cache = ./cache/cord-256982-t6urqus7.txt txt = ./txt/cord-256982-t6urqus7.txt === reduce.pl bib === === reduce.pl bib === id = cord-256456-rg366bk2 author = Kulcsar, Gabor title = Testing for viral contaminants of veterinary vaccines in Hungary date = 2010-05-31 pages = extension = .txt mime = text/plain words = 2801 sentences = 147 flesch = 50 summary = Contrary to group 1, group 2 agents like Torque Teno virus (TTV) or RD114, a replication-competent feline γ-retrovirus, have only recently been recognised and their role as contaminants needs further investigation. Since 2007, 12 batches of live Aujeszky's disease vaccines have been tested for Pestivirus by reverse transcriptase-polymerase chain reaction (RT-PCR), in the framework of the Official Control Authority Batch Release (OCABR). In addition, 27 poultry vaccines, from eight different manufacturers, used in Hungary between 1996 and 2009 were randomly selected and examined by PCR for the presence of chicken anaemia virus (CAV) and egg drop syndrome virus (EDSV). Contrary to the wellknown Group 1 agents, Group 2 contains new potential contaminants, such as TTV and/or RD114 virus, recently found to be present in vaccines. Swine Torque Teno virus detection in pig commercial vaccines, enzymes for laboratory use and human drugs containing components of porcine origin cache = ./cache/cord-256456-rg366bk2.txt txt = ./txt/cord-256456-rg366bk2.txt === reduce.pl bib === === reduce.pl bib === id = cord-255983-3dq99xz9 author = Do, Lien Anh Ha title = A sensitive real-time PCR for detection and subgrouping of human respiratory syncytial virus date = 2012-01-17 pages = extension = .txt mime = text/plain words = 4267 sentences = 193 flesch = 50 summary = The quantitative assay was compared to a commercial conventional multiplex PCR method (Seeplex TM RV detection kit, Seegene, Inc., Seoul, Korea) (Kim et al., 2009; Roh et al., 2008) respiratory samples from a study (Do et al., 2011) on acute respiratory infection in children at the Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam. All samples were analyzed in parallel by the commercial multiplex Seeplex TM RV detection kit (Seegene, Inc., Seoul, Korea) according to the manufacturer's instructions, to determine the presence of 12 respiratory viruses: human RSV subgroups A and B (RSV A, RSV B); influenza virus A (InfV A); influenza virus B (InfV B); human coronaviruses (229E, OC43), human metapneumovirus (hMPV), parainfluenza virus 1, 2 and 3 (PIV1, 2, 3), human rhinovirus (hRV A) and adenovirus (AdV) (Kim et al., 2009; Roh et al., 2008) and by the newly developed RSV LNA real-time RT-PCR. cache = ./cache/cord-255983-3dq99xz9.txt txt = ./txt/cord-255983-3dq99xz9.txt === reduce.pl bib === === reduce.pl bib === id = cord-257521-1amcsgmj author = Hirsilä, Maija title = Detection by Reverse Transcription–Polymerase Chain Reaction of Influenza C in Nasopharyngeal Secretions of Adults with a Common Cold date = 2001-04-15 pages = extension = .txt mime = text/plain words = 2297 sentences = 116 flesch = 53 summary = All 7 patients had a significant increase in antibody titers between serum samples collected during the acute and convalescent phases of the illness. Only 1 of the 7 patients from whom these samples were obtained was still positive by PCR at the first control visit 1 week later, but a signal was detected only with the NS-1 primer pair. A у8-fold increase between acute-and convalescent-phase serum samples was found in all 7 individuals with PCR-positive results (table 2). All 7 individuals with PCR-positive results had a у8-fold increase in antibody titers between serum samples collected during the acute and convalescent phases of the illness. In addition, 1 study participant with PCR-negative results also had a significant increase in antibody titer (patient 160; table 2). NPAs obtained from the 7 patients with RT-PCR-positive results at the first control visit 1 week after study entry also were tested. cache = ./cache/cord-257521-1amcsgmj.txt txt = ./txt/cord-257521-1amcsgmj.txt === reduce.pl bib === id = cord-256702-lwxt4587 author = Song, Lingjie title = A case of SARS-CoV-2 carrier for 32 days with several times false negative nucleic acid tests date = 2020-04-06 pages = extension = .txt mime = text/plain words = 2037 sentences = 144 flesch = 57 summary = title: A case of SARS-CoV-2 carrier for 32 days with several times false negative nucleic acid tests After the onset of clinical symptoms, chest CT results showed patchy ground-glass opacity (GGO) in her lungs, but it took a total of nine nucleic acid tests to confirm the diagnosis, among which the first eight RT-PCR results were negative or single-target positive. Although the nucleic acid test was negative or single-target positive, the low number of white blood cells and lymphocytes in laboratory tests, and GGO in the lungs by CT examination indicated SARS-CoV-2 infection. https://doi.org/10.1101/2020.03.31.20045401 doi: medRxiv preprint pathogenic nucleic acid genomes from samples of asymptomatic and occult infected patients is also conducive to studying the virus mutations in the pathogenic genes providing a basis for subsequent virus tracing and epidemiological investigations. We report the epidemiological history and clinical information of a patient with negative (or single-target positive) SARS-CoV-2 infection with multiple RT-PCR tests. cache = ./cache/cord-256702-lwxt4587.txt txt = ./txt/cord-256702-lwxt4587.txt === reduce.pl bib === id = cord-256338-ovj63ith author = bhattacharya, b. title = SARS-CoV-2 RT-PCR profile in 298 Indian COVID-19 patients : a retrospective observational study date = 2020-06-20 pages = extension = .txt mime = text/plain words = 2146 sentences = 141 flesch = 60 summary = title: SARS-CoV-2 RT-PCR profile in 298 Indian COVID-19 patients : a retrospective observational study Currently as per the revised government of India guidelines asymptomatic or mildly symptomatic patients can be discharged 10 days after symptom onset and the strategy of repeat RT-PCR testing has been done away with. Cases with laboratory confirmed diagnosis of COVID-19, made by positive SARS-CoV-2 RT-PCR on nasopharyngeal samples, were enrolled regardless of symptomatology. The mean duration from 1st and last positive RT-PCR assays between symptomatic and asymptomatic patients were 13·01±4·63 and 13·93±5·42 days respectively; and the difference was not statistically significant with p value <0·05 (p=0·39). This study was conducted in the initial part of pandemic in India, which, to the best of our knowledge provides the largest data on SARS-CoV-2 RNA detection in naso-pharyngeal and oro-pharyngeal samples in symptomatic or asymptomatic COVID-19 cases. Profile of RT-PCR for SARS-CoV-2: a preliminary study from 56 COVID-19 patients cache = ./cache/cord-256338-ovj63ith.txt txt = ./txt/cord-256338-ovj63ith.txt === reduce.pl bib === === reduce.pl bib === id = cord-257398-fmkfo5ju author = Meng, Qing-Bin title = Clinical application of combined detection of SARS-CoV-2-specific antibody and nucleic acid date = 2020-10-06 pages = extension = .txt mime = text/plain words = 3231 sentences = 190 flesch = 49 summary = In the present study, we collected clinical data from 652 suspected COVID-19 patients and 206 non-COVID-19 patients to investigate the diagnostic value of SARS-CoV-2 IgM/IgG antibody test kits with colloidal gold immunoassays and nucleic acid RT-PCR test kits. As recently reported, a rapid IgM/IgG October 6, 2020 Volume 8 Issue 19 combined antibody test was used for the diagnosis of SARS-CoV-2 infection, showing 88.66% sensitivity and 90.63% specificity [15] . Of the 415 suspected COVID-19 patients who were negative for the SARS-CoV-2 nucleic acid tests, 366 patients were positive for the SARS-CoV-2specific IgM and/or IgG antibody tests with a positive detection rate of 88.2%. Of the 415 suspected COVID-19 patients who were negative for the SARS-CoV-2 nucleic acid tests, 366 patients were positive for the SARS-CoV-2specific IgM and/or IgG antibody tests with a positive detection rate of 88.2%. cache = ./cache/cord-257398-fmkfo5ju.txt txt = ./txt/cord-257398-fmkfo5ju.txt === reduce.pl bib === id = cord-258008-t78svobg author = Bruijnesteijn van Coppenraet, L.E.S. title = Comparison of two commercial molecular assays for simultaneous detection of respiratory viruses in clinical samples using two automatic electrophoresis detection systems date = 2010-08-05 pages = extension = .txt mime = text/plain words = 3519 sentences = 181 flesch = 49 summary = Two molecular assays were compared with real-time RT-PCR and viral culture for simultaneous detection of common viruses from respiratory samples: a multiplex ligation-dependant probe amplification (MLPA) and a dual priming oligonucleotide system (DPO). A panel of 168 culture-positive and negative samples was tested by the molecular assays for the presence of influenza A and B virus, respiratory syncytial virus, human metapneumovirus, rhinovirus, coronaviruses, parainfluenza viruses and adenovirus. Both molecular assays are comparable with real-time RT-PCR, more sensitive than viral culture and can detect dual infections easily. In this study, two commercial molecular assays, both designed for simultaneous detection of the most common viruses from a variety of respiratory samples, were compared with real-time RT-PCR and viral culture: a multiplex ligation-dependant probe amplification (MLPA) and a dual priming oligonucleotide system (DPO). Defined as true positives were samples that yielded positive viral detections by more than one method (culture, DPO, MLPA or real-time RT-PCR). cache = ./cache/cord-258008-t78svobg.txt txt = ./txt/cord-258008-t78svobg.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-258819-4boe6t1v author = Waller, Joseph V. title = The Limited Sensitivity of Chest Computed Tomography Relative to Reverse Transcription Polymerase Chain Reaction for Severe Acute Respiratory Syndrome Coronavirus-2 Infection: A Systematic Review on COVID-19 Diagnostics date = 2020-06-16 pages = extension = .txt mime = text/plain words = 4443 sentences = 226 flesch = 49 summary = title: The Limited Sensitivity of Chest Computed Tomography Relative to Reverse Transcription Polymerase Chain Reaction for Severe Acute Respiratory Syndrome Coronavirus-2 Infection: A Systematic Review on COVID-19 Diagnostics OBJECTIVES: Several studies suggest the sensitivity of chest computed tomography (CT) is far greater than that of reverse transcription polymerase chain reaction (RT-PCR) in diagnosing COVID-19 patients, and therefore, CT should be included as a primary diagnostic tool. The quality assessment tool QUADAS-2 was used to stratify studies according to their risk of bias, and exclusion criteria included not providing the information deemed relevant for such a stratification, such as not indicating if the patients were symptomatic or asymptomatic, or identifying the source of the specimen for the reference standard, RT-PCR (eg, nasal, oropharyngeal, etc). A recent study by Li and colleagues 18 tested a cohort of patients assumed to have SARS-CoV-2 infection owing to CT findings consistent with a viral pneumonia and reported an RT-PCR sensitivity of 27.5% (n = 610). cache = ./cache/cord-258819-4boe6t1v.txt txt = ./txt/cord-258819-4boe6t1v.txt === reduce.pl bib === id = cord-258250-zueo1xfa author = Hirotsu, Yosuke title = Comparison of Automated SARS-CoV-2 Antigen Test for COVID-19 Infection with Quantitative RT-PCR using 313 Nasopharyngeal Swabs Including from 7 Serially Followed Patients date = 2020-08-12 pages = extension = .txt mime = text/plain words = 3105 sentences = 184 flesch = 55 summary = title: Comparison of Automated SARS-CoV-2 Antigen Test for COVID-19 Infection with Quantitative RT-PCR using 313 Nasopharyngeal Swabs Including from 7 Serially Followed Patients In summary, the LUMIPULSE antigen test can rapidly identify SARS-CoV-2-infected individuals with moderate to high viral loads and may be helpful for monitoring viral clearance in hospitalized patients. To date, 11 million individuals have been infected with SARS-CoV-2 and 0.52 million patients have died from coronavirus disease 2019 (COVID-19) [2] . We compared the quantitative RT-PCR (RT-qPCR) results for viral load with the CLEIA results for antigen level following testing of 313 nasopharyngeal swabs. We used 100 µL of the supernatant per sample of thawed viral transport media from each nasopharyngeal swab to measure the antigen level with the LUMIPULSE SARS-CoV-2 Ag kit (Fujirebio) on the LUMIPULSE G600II automated immunoassay analyzer (Fujirebio) based on the CLEIA method. We next examined the relationship between the SARS-CoV-2 viral loads (as determined by RT-qPCR) and the antigen levels (Fig 2) . cache = ./cache/cord-258250-zueo1xfa.txt txt = ./txt/cord-258250-zueo1xfa.txt === reduce.pl bib === id = cord-257600-0plhquk9 author = Calles, Antonio title = Outcomes of COVID-19 in Patients With Lung Cancer Treated in a Tertiary Hospital in Madrid date = 2020-09-16 pages = extension = .txt mime = text/plain words = 6981 sentences = 353 flesch = 47 summary = Differences in health-care systems, in the incidence and prevalence of SARS-CoV-2 infection by geographic regions, and patient access to intensive support care -including MVand treatment with antivirals or anti-IL6/IL1 agents may ultimately influence outcomes in patients with lung cancer affected by COVID-19. We aimed to describe the clinical characteristics of lung cancer patients with COVID-19 attended in a tertiary hospital in Madrid, one of the most hit regions by coronavirus in the world so far, and analyze factors associated with worse outcome, including type of treatment receiving at the time of COVID-19 diagnosis. We performed SARS-CoV-2 RT-PCR to every suspicious case and included all lung cancer patients attended at our hospital (emergency room, hospitalization, ambulatory office, day care area). Data from Wuhan, in China, showed that active cancer treatment received in the 14 days before SARS-CoV-2 infection had an increase on the risk of severe outcomes of COVID-19 (HR 4.079, 95%CI, 1.086-15.322; p = 0.037) (9) . cache = ./cache/cord-257600-0plhquk9.txt txt = ./txt/cord-257600-0plhquk9.txt === reduce.pl bib === id = cord-260457-m1jbpo5l author = Allander, Tobias title = Human Bocavirus and Acute Wheezing in Children date = 2007-04-01 pages = extension = .txt mime = text/plain words = 3713 sentences = 209 flesch = 49 summary = We investigated the presence of human bocavirus by quantitative polymerase chain reaction of nasopharyngeal aspirate specimens and selected serum samples obtained from 259 children (median age, 1.6 years) who had been hospitalized for acute expiratory wheezing. Human bocavirus DNA was frequently detected in serum specimens obtained from patients with acute wheezing, suggesting systemic infection. Results suggest a model for bocavirus infection in which high viral loads are potentially associated with respiratory symptoms and low viral loads indicate asymptomatic shedding. Of the 293 children who were randomized, 259 children (median age, 1.6 years; range, 3 months to 15 years) who had sufficient sample material available for complete virus diagnostic evaluation (nasopharyngeal aspirate specimens were used for PCR [for 16 viruses], virus culture [for 9 viruses], and antigen detection [for 7 viruses]; acute-and convalescent-phase serum samples were used for serologic testing [for 7 viruses]) were included in the present study. cache = ./cache/cord-260457-m1jbpo5l.txt txt = ./txt/cord-260457-m1jbpo5l.txt === reduce.pl bib === id = cord-258021-xhx74vr6 author = Waterer, Grant W. title = Diagnosing Viral and Atypical Pathogens in the Setting of Community-Acquired Pneumonia date = 2016-12-21 pages = extension = .txt mime = text/plain words = 4405 sentences = 223 flesch = 38 summary = This review focuses principally on the diagnosis of Legionella, Mycoplasma, and influenza infections, but also covers recent publications on the cutting edge of diagnostic tools likely to transform the field of infectious diseases over the coming decade. 28 Recently, there has been interest in antigen detection assays for the diagnosis of M pneumoniae because these offer the potential for point-of-care testing, but so far these have yet to enter the clinical mainstream. 73 A single study from Taiwan indicates that PCR-electrospray ionization mass spectrometry has promise for the detection of multiple viruses in the setting of respiratory tract infection but this was done retrospectively rather than in real time. Comparison of the performance of direct fluorescent antibody staining, a point-of-care rapid antigen test and virus isolation with that of RT-PCR for the detection of novel 2009 influenza A (H1N1) virus in respiratory specimens cache = ./cache/cord-258021-xhx74vr6.txt txt = ./txt/cord-258021-xhx74vr6.txt === reduce.pl bib === id = cord-258724-1qhen1bj author = Young, Barnaby E title = Viral dynamics and immune correlates of COVID-19 disease severity date = 2020-08-28 pages = extension = .txt mime = text/plain words = 3612 sentences = 253 flesch = 52 summary = METHODS: We evaluated these characteristics and established their association with clinical severity in a prospective observational cohort study of 100 patients with PCR-confirmed SARS-CoV-2 infection (mean age 46 years, 56% male, 38% with comorbidities). In this multi-pronged study, we describe the serologic evolution, inflammatory response and pattern of viral shedding and viability in patients with virologically confirmed COVID-19 in Singapore, and analyse the contributions these make to severe infections. Serum collected during the acute and convalescent phases of infection were tested for SARS-CoV-2 receptor binding domain specific IgM and IgG using capture ELISA (details in Supplementary Appendix). The central role of the immune response to SARS-CoV-2 in COVID-19 was evident from the strong correlation between disease severity and levels of IgG/IgM and inflammatory immune mediators in our cohort. Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study cache = ./cache/cord-258724-1qhen1bj.txt txt = ./txt/cord-258724-1qhen1bj.txt === reduce.pl bib === id = cord-259324-g8kv4pvq author = Ko, Suk-Min title = Expression of the protective antigen for PEDV in transgenic duckweed, Lemna minor date = 2011-10-28 pages = extension = .txt mime = text/plain words = 2332 sentences = 121 flesch = 50 summary = In this study, we assessed the feasibility of producing a protective antigen for the PEDV spike protein 1 using duckweed, Lemna minor. Transgene integration and expression of the PEDV spike protein 1 gene were confirmed by genomic PCR and RT-PCR and western blot analysis of transgenic Lemna, respectively. In this study, we report the stable transformation and expression of a protective antigen for PEDV in Lemna minor with potential for use as an effective complement to the diets of animals. Fronds were then blotted onto sterile filter paper, and co-cultivated with Agrobacterium tumefaciens strain EHA105 harboring the PEDV spike protein 1 gene fused to a c-myc tag for 72 h on antibiotic-free ½MS1BA medium. PCR products of the expected size (330 bp) corresponding to primers designed on the internal PEDV spike protein 1 gene were detected from kanamycin-resistant Lemna, whereas no DNA band corresponding to the target gene was detected in untransformed wild-type Lemna. cache = ./cache/cord-259324-g8kv4pvq.txt txt = ./txt/cord-259324-g8kv4pvq.txt === reduce.pl bib === id = cord-259590-ot933axv author = Fielding, Burtram C title = Human coronavirus NL63: a clinically important virus? date = 2011-03-02 pages = extension = .txt mime = text/plain words = 4014 sentences = 238 flesch = 51 summary = In this article, the current knowledge of human coronavirus HCoV-NL63, with special reference to the clinical features, prevalence and seasonal incidence, and coinfection with other respiratory viruses, will be discussed. In this article, the current knowledge of human coronavirus HCoV-NL63, with special reference to the clinical features, prevalence and seasonal incidence, and coinfection with other respiratory viruses, will be discussed. A recent comprehen sive 2year populationbased study, using data from different countries, on children under 3 years of age with lower respiratory tract infec tion (LRTI) shows that HCoVNL63 infections peak in winter months. Another study reports that HCoVNL63, when compared with other respiratory viruses, is the virus secondmost com monly associated with young children (median age 13 months) hospitalized with croup [17] . A novel pancoronavirus RTPCR assay: frequent detection of human coronavirus NL63 in children hospitalized with respiratory tract infections in Belgium cache = ./cache/cord-259590-ot933axv.txt txt = ./txt/cord-259590-ot933axv.txt === reduce.pl bib === id = cord-259458-o2yts5pq author = O’Grady, Kerry‐Ann F. title = Successful application of a simple specimen transport method for the conduct of respiratory virus surveillance in remote Indigenous communities in Australia date = 2011-03-21 pages = extension = .txt mime = text/plain words = 3636 sentences = 176 flesch = 49 summary = This study assessed the sensitivity of a simple method for transporting respiratory samples from a remote setting for viral PCR compared with frozen specimens. To inform the design of surveillance and intervention studies addressing respiratory infections in remote communities, we compared the sensitivity of a simple, cost-efficient method for transporting respiratory samples from a remote setting for viral real-time PCR with transport using frozen specimens. Given the sensitivity and specificity of real-time PCR diagnosis, we considered a specimen from either nostril positive for any virus to represent a true-positive, similar to previous studies (Lambert et al. Determining the aetiology and burden of viral respiratory infections in remote communities has to date been limited by the inability to store and transport clinical specimens requiring freezing ⁄ refrigeration to urban laboratories. We propose that this method, combining standard clinic refrigeration and weekly surface mailing of specimens combined with real-time PCR, can be used for viral respiratory research in remote locations. cache = ./cache/cord-259458-o2yts5pq.txt txt = ./txt/cord-259458-o2yts5pq.txt === reduce.pl bib === id = cord-259823-ia1g5dt4 author = Gowin, Ewelina title = Assessment of the Usefulness of Multiplex Real-Time PCR Tests in the Diagnostic and Therapeutic Process of Pneumonia in Hospitalized Children: A Single-Center Experience date = 2017-01-15 pages = extension = .txt mime = text/plain words = 3883 sentences = 198 flesch = 43 summary = British, American, and Polish guidelines state that, in children hospitalized due to pneumonia, microbiological examinations should include blood cultures, the detection of the presence of viruses with the use of PCR (Polymerase Chain Reaction) or immunofluorescence in material collected from the nasopharynx (smear or upper respiratory aspirate), the assessment of antibodies against Mycoplasma and Chlamydophila in classes IgM and IgG, and the comparison of antibody levels in the acute phase of the disease and during convalescence [4] [5] [6] . achieved positive results of multiplex real-time PCR tests detecting only viral factors in 76% of cases in a group of children below the age of six with symptoms of respiratory tract infection and the dominant pathogen was RSV [12] . cache = ./cache/cord-259823-ia1g5dt4.txt txt = ./txt/cord-259823-ia1g5dt4.txt === reduce.pl bib === id = cord-023211-kt5gt26t author = nan title = Poster Session Abstracts date = 2007-08-29 pages = extension = .txt mime = text/plain words = 221224 sentences = 11772 flesch = 52 summary = Previous studies performed using fluorescence halide efflux measurements and short-circuit current voltage clamp have shown that treatment with PPARγ (peroxisome proliferator activated receptor gamma) agonists, such as pioglitazone and FLL (FMOC-L-leucine), resulted in an increased biosynthesis and trafficking of ∆F508-CFTR to the cell surface. Physiology, School of Medical Sciences, University of Bristol, Bristol, United Kingdom Recent progress in the development of small molecule correctors and potentiators capable of restoring CFTR function have increased the need for pre-clinical test models including cultured airway epithelial cells from human CF patients as well as CF mouse models. Clinical studies have linked increased sputum and peripheral blood neutrophil MPO activity with increased airflow obstruction in cystic fibrosis (CF) patients of the same age, gender, airway bacterial flora, and CFTR genotype. Because patients expressing low levels of normal CFTR mRNA (5-20%) have mild disease symptoms, these studies demonstrate that the incorporation of the ciliated cell-specific FOXJ1 promoter into gene therapy vectors may be useful for treatment of CF. cache = ./cache/cord-023211-kt5gt26t.txt txt = ./txt/cord-023211-kt5gt26t.txt === reduce.pl bib === id = cord-260404-leifaqda author = Ishak, Anthony M. title = Prevalence of Mycoplasma haemofelis, ‘Candidatus Mycoplasma haemominutum’, Bartonella species, Ehrlichia species, and Anaplasma phagocytophilum DNA in the blood of cats with anemia date = 2006-07-17 pages = extension = .txt mime = text/plain words = 3401 sentences = 143 flesch = 44 summary = In this retrospective study, we used polymerase chain reaction (PCR) assays to determine the prevalence rates of Mycoplasma haemofelis, 'Candidatus M haemominutum', A phagocytophilum, Ehrlichia species, and Bartonella species DNA in the blood of cats with anemia and a control group of healthy cats. The purpose of this study was to determine whether there were differences in prevalence rates of M haemofelis, 'Candidatus M haemominutum', A phagocytophilum, Ehrlichia species, and Bartonella species DNA in the blood of healthy cats and retrovirus-negative cats with anemia that did not have an apparent non-infectious (ie, blood loss, chronic disease) cause for their anemia. In this study, we reviewed the laboratory submission forms and medical records to attempt to eliminate cats with known causes of anemia including neoplasia, FeLV, FIV, suspected FIP, blood loss, chronic renal failure, bone marrow disease, other chronic diseases (eg, neoplasia), endocrinopathies, and previous cytologic evidence of hemoplasmosis to allow for selection of cases that were likely to have anemia from previously unrecognized infectious diseases or primary immune-mediated anemia. cache = ./cache/cord-260404-leifaqda.txt txt = ./txt/cord-260404-leifaqda.txt === reduce.pl bib === id = cord-259988-3s7b5ovi author = Decaro, Nicola title = Virological and molecular characterization of a mammalian orthoreovirus type 3 strain isolated from a dog in Italy date = 2005-08-10 pages = extension = .txt mime = text/plain words = 3336 sentences = 191 flesch = 57 summary = A mammalian orthoreovirus (MRV) strain was isolated from a pup with fatal diarrhea, which had a concurrent infection by canine parvovirus type 2. Assignment of the isolated virus to MRV-3 was confirmed by type-specific RT-PCR assays, targeting the S1 gene, and by subsequent sequence analysis of the PCR product. A total of 110 fecal samples, 56 nasal and 31 ocular swabs from dogs with diarrhea or nasal/ocular discharge were tested by a nested-PCR assay specific for reoviruses, and no sample was found to contain MRV RNA, a finding that is apparently in contrast with the seroprevalence (25.77%) observed in dogs. In the present study, the isolation and molecular characterization of a MRV-3 strain from a dog with diarrhea are reported. By the type-specific RT-PCR assays the isolate was recognized as MRV-3 (Fig. 5) , and therefore designated T3/ canine/Italy/Decaro/2004 (T3D/04), according to the conventional system used to identify MRV strains. cache = ./cache/cord-259988-3s7b5ovi.txt txt = ./txt/cord-259988-3s7b5ovi.txt === reduce.pl bib === id = cord-259422-5ex12eun author = Graat, Judith M title = A prospective, community-based study on virologic assessment among elderly people with and without symptoms of acute respiratory infection date = 2003-12-11 pages = extension = .txt mime = text/plain words = 3897 sentences = 196 flesch = 42 summary = title: A prospective, community-based study on virologic assessment among elderly people with and without symptoms of acute respiratory infection METHODS: In a 1-year community-based study, we prospectively investigated the possible virologic cause of acute respiratory infections in 107 symptomatic case episodes and 91 symptom-free control periods. Therefore, in this prospective, community-based study, we investigated the presence of known respiratory viruses in elderly persons both with and without symptoms of an acute upper respiratory tract infection. Second, we compared the clinical characteristics of the persons suffering from an acute respiratory infection, during episodes with positive and negative virologic laboratory diagnosis. Cases who reported their symptoms after 3 days to the study nurse were excluded for virologic assessment to overcome false negative test results. Preliminary results of a Dutch study being performed in persons consulting their general practitioner for signs and symptoms of an acute respiratory infection, showed a positive virologic assessment in 19% of the controls [16] . cache = ./cache/cord-259422-5ex12eun.txt txt = ./txt/cord-259422-5ex12eun.txt === reduce.pl bib === id = cord-260231-vayxg23a author = Hsien Koh, Tse title = Epidemiology of Clostridium difficile infection in a large teaching hospital in Singapore date = 2007-08-31 pages = extension = .txt mime = text/plain words = 3314 sentences = 224 flesch = 58 summary = Summary Aims We undertook this study to define the incidence of toxigenic Clostridium difficile in our hospital and to characterise the isolates. Detection of tcdA and tcdB genes was carried out for A2B+ strains by polymerase chain reaction (PCR).The minimum inhibitory concentrations (MICs) of metronidazole, vancomycin and clindamycin for all isolates were tested using the Etest. All unformed stool from SGH inpatients sent to the Department of Pathology from 1 October 2002 to 28 February 2003 was tested for the presence of TcdA and TcdB using the Premier Toxin A and B enzyme immunoassay (EIA) kit (Meridian Diagnostics, USA) following the manufacturer's instructions. Combining the numbers of toxigenic strains and culture negative/direct toxin positive specimens, the incidence of CDAD was 3.2 cases per 1000 admissions or discharges and 53.8 cases per 100 000 patient days. Clindamycin resistant strains of Clostridium difficile isolated from cases of C. cache = ./cache/cord-260231-vayxg23a.txt txt = ./txt/cord-260231-vayxg23a.txt === reduce.pl bib === id = cord-259886-j0bpp7iw author = Cho, Hyejin title = Positive control synthesis method for COVID-19 diagnosis by one-step real-time RT-PCR date = 2020-10-12 pages = extension = .txt mime = text/plain words = 2319 sentences = 136 flesch = 53 summary = SPT oligonucleotides contain probe binding and virus-irrelevant regions as templates for detecting SARS-CoV-2 genes (RdRP, E, and N SARS-CoV-2) by real-time RT-PCR was performed in a concentration-dependent manner. Therefore, this approach may be integrated into the molecular diagnosis of COVID-19 and provides a general method for preparing positive controls for diagnosing emerging RNA virus infections. Therefore, a new preparation design that provides contamination-free positive controls for COVID-19 real-time RT-PCR testing is urgently needed. Here, we present a new approach for producing synthetic positive controls using synthetic positive template (SPT) oligonucleotides that contain probe binding and virusirrelevant regions as templates for detecting SARS-CoV-2 genes by real-time RT-PCR. We performed multiplex real-time RT-PCR using an SPT (positive control) as a template in a concentration-dependent manner, to determine the limit of detection (LOD) for individual SARS-CoV-2 genes. In previous studies, the Uni-Control method for preparing real-time RT-PCR positive controls has been developed as a generic approach for diagnosing viral infections [22] . cache = ./cache/cord-259886-j0bpp7iw.txt txt = ./txt/cord-259886-j0bpp7iw.txt === reduce.pl bib === id = cord-260168-rb7j94dh author = Gu, Jiang title = H5N1 infection of the respiratory tract and beyond: a molecular pathology study date = 2007-09-27 pages = extension = .txt mime = text/plain words = 6291 sentences = 369 flesch = 51 summary = Negative controls also included an unrelated antisense probe against the fragment of the polymerase gene (R1AB) of the severe acute respiratory syndrome-associated coronavirus (SARS-CoV), 20 as well as H5N1 in-situ hybridisation probes to tissues (including lung and tracheal) obtained from seven adults who died from infectious lung diseases other than H5N1 infl uenza (four, SARS; one, purulent bronchitis; two, pneumonia), one adult who died from a non-infectious disease (gastric ulcer), one pregnant woman who died from an amniotic embolism, and one aborted fetus. Presence of viral sequences and antigens in the CNS is consistent with the recent isolation of H5N1 virus from cerebrospinal fl uid of a boy who died from encephalitis 6 with neurological symptoms commonly seen in patients with H5N1 infl uenza (Gao Zh, unpublished), including the two cases in this study. cache = ./cache/cord-260168-rb7j94dh.txt txt = ./txt/cord-260168-rb7j94dh.txt === reduce.pl bib === id = cord-258768-bjjfkfgg author = McElligott, Susan title = Detection and genetic characterization of canine parvoviruses and coronaviruses in southern Ireland date = 2010-11-24 pages = extension = .txt mime = text/plain words = 4380 sentences = 220 flesch = 53 summary = Two hundred fifty samples were collected in total, Fig. 2 Phylogenetic tree based on partial S gene nucleotide sequences of CCoVs described in this study and reference strains. As a result of RNA recombination, insertions, deletions and a high susceptibility to frequent mutation, coronaviruses can mutate rapidly, leading to new genotypes (CCoV-I), biotypes (pantropic CCoV) and host variants (canine respiratory coronavirus), all of which may present possible difficulties regarding successful vaccination of dogs. As a result of this study, it can be concluded that although it appears that the viral evolution of CPV type 2 is not yet a significant problem for the canine population in Ireland, vaccine efficacy may need to be re-evaluated by the animal healthcare industry, as it is a possibility that the new CPV-2c strain will eventually emerge into the population as a result of importing dogs from other parts of the world. cache = ./cache/cord-258768-bjjfkfgg.txt txt = ./txt/cord-258768-bjjfkfgg.txt === reduce.pl bib === id = cord-260700-u12aa739 author = Kainulainen, Leena title = Recurrent and persistent respiratory tract viral infections in patients with primary hypogammaglobulinemia date = 2010-06-10 pages = extension = .txt mime = text/plain words = 3686 sentences = 248 flesch = 46 summary = title: Recurrent and persistent respiratory tract viral infections in patients with primary hypogammaglobulinemia OBJECTIVE: We conducted a prospective 12-month follow-up study of respiratory tract infections in 12 adult patients with primary hypogammaglobulinemia. METHODS: Nasal swab samples and induced sputum samples were taken at the onset of acute respiratory tract infection and every 3 months thereafter. CONCLUSIONS: Despite adequate immunoglobulin replacement therapy, patients with primary hypogammaglobulinemia have increased susceptibility to respiratory tract viral infections. Using modern diagnostic techniques, we wanted to study the occurrence of respiratory tract infections, especially viral infections, in patients with primary hypogammaglobulinemia who were receiving regular immunoglobulin replacement therapy. If the spouse of the patient had acute symptoms of respiratory tract infection, she or he took nasal swabs at home according to the instructions of the research nurse and sent the vials by post. First, despite adequate immunoglobulin replacement therapy, most patients with primary hypogammaglobulinemia had increased susceptibility to respiratory tract viral infections. cache = ./cache/cord-260700-u12aa739.txt txt = ./txt/cord-260700-u12aa739.txt === reduce.pl bib === id = cord-260728-4w23kwzu author = Timmermans, Ans title = Human Sentinel Surveillance of Influenza and Other Respiratory Viral Pathogens in Border Areas of Western Cambodia date = 2016-03-30 pages = extension = .txt mime = text/plain words = 7411 sentences = 381 flesch = 50 summary = Real-time reverse transcriptase (rRT) PCR for influenza was performed on combined nasal and throat specimens followed by viral culture, antigenic analysis, antiviral susceptibility testing and full genome sequencing for phylogenetic analysis. Between May 2010 and December 2012, we collected specimens and surveillance data for influenza and other viral respiratory pathogens from a subset of outpatients presenting with influenza-like-illness (ILI) at four sentinel sites-located in five health centers and hospitals in Battambang, Oddar Meanchey, Pailin and Banteay Meanchey provinces in Cambodia (Fig 1) . A subset of 164 culture-negative specimens (collected between May 2010 and April 2012), where we found a higher proportion (5.6%) of non-polio enteroviruses in children less than 5 years old as compared with previous studies (1%) in Cambodia [2] , were tested for enterovirus and rhinovirus by two separate nested RT-PCR methods adapted from Coiras et al., 2004 and Singh et al., 2002 [29,30] , one for simultaneous detection of pan-enteroviruses and rhinoviruses, and the other specific for enterovirus 71 (EV71). cache = ./cache/cord-260728-4w23kwzu.txt txt = ./txt/cord-260728-4w23kwzu.txt === reduce.pl bib === id = cord-259747-sl9q63oc author = Remmelink, Myriam title = Unspecific post-mortem findings despite multiorgan viral spread in COVID-19 patients date = 2020-08-12 pages = extension = .txt mime = text/plain words = 4541 sentences = 244 flesch = 48 summary = BACKGROUND: Post-mortem studies can provide important information for understanding new diseases and small autopsy case series have already reported different findings in COVID-19 patients. IHC revealed positive cells with a heterogeneous distribution in the lungs of 11 of the 17 (65%) patients; RT-PCR yielded a wide distribution of SARS-CoV-2 in different tissues, with 8 patients showing viral presence in all tested organs (i.e., lung, heart, spleen, liver, colon, kidney, and brain). In this post-mortem study, we included the first 17 adult patients (> 18 years) who died in our hospital (either in a COVID-19 unit or an intensive care unit) from March 13, 2020, with confirmed SARS-CoV-2 infection (i.e., positive RT-PCR assay on nasopharyngeal swab and/or bronchoalveolar lavage specimen). This post-mortem study showed several histopathological abnormalities in COVID-19 non-survivors; however, none of the findings was specific for direct viral injury, even though SARS-CoV-2 was detected in all examined organs using RT-PCR. cache = ./cache/cord-259747-sl9q63oc.txt txt = ./txt/cord-259747-sl9q63oc.txt === reduce.pl bib === id = cord-260647-7bjhobg7 author = Coudray-Meunier, Coralie title = A Novel High-Throughput Method for Molecular Detection of Human Pathogenic Viruses Using a Nanofluidic Real-Time PCR System date = 2016-01-29 pages = extension = .txt mime = text/plain words = 5581 sentences = 278 flesch = 48 summary = A nanofluidic real-time PCR system was used to develop novel high-throughput methods for qualitative molecular detection (RT-qPCR array) and quantification of human pathogenic viruses by digital RT-PCR (RT-dPCR). The aim of this study was to develop real time RT-PCR assays for detection of a total of 19 human enteric viruses (including 3 genogroupes of norovirus and 4 coronaviruses) and two control process viruses (mengovirus and murine norovirus) generally used for monitoring the recovery of viral foodstuff extraction methods. The sensitivity of conventional qPCR assays targeting 21 viral genomes was compared to the quantitative digital RT-PCR array and to the qualitative nanofluidic real-time PCR array performed on Fluidigm's BioMark System. Similarly, by testing genomes from viruses in stools and RNA from virus production in cells, the limit of detection (LOD) as determined by RT-dPCR was respectively 1.5 to 3.4 log 10 and 1.6 to 2.1 log 10 lower than the expected copy numbers calculated via the standard curve by RT-qPCR. cache = ./cache/cord-260647-7bjhobg7.txt txt = ./txt/cord-260647-7bjhobg7.txt === reduce.pl bib === id = cord-260431-eksl7pp8 author = Sun, Heting title = Isolation and Identification of Feline Herpesvirus Type 1 from a South China Tiger in China date = 2014-02-28 pages = extension = .txt mime = text/plain words = 2523 sentences = 140 flesch = 55 summary = In the present study, we used molecular methods, virus isolation, TEM examination and an animal challenge experiment to diagnose the cause of death of the South China tiger, and for the first time, we confirmed the infection with FHV-1 in the captive tiger population in China. The phylogenetic tree based on the TK gene sequences showed that the isolate investigated in this study, was closely related to the ten isolates of FHV-1 ( Figure 2 ), a result consistent with the alignment analysis. By PCR/RT-PCR, the only virus detected in the trachea homogenates was FHV-1, which was confirmed afterwards by virus isolation, the TEM examination of cell cultures showing CPE, and a challenge experiment in cats. In this study, the authors described the first occurrence of feline herpesvirus type 1 (FHV-1) in a South China tiger in China. cache = ./cache/cord-260431-eksl7pp8.txt txt = ./txt/cord-260431-eksl7pp8.txt === reduce.pl bib === id = cord-260690-h5pjv2dw author = Druce, Julian title = Laboratory diagnosis and surveillance of human respiratory viruses by PCR in Victoria, Australia, 2002–2003 date = 2004-11-12 pages = extension = .txt mime = text/plain words = 3803 sentences = 201 flesch = 45 summary = A total of 333 additional respiratory specimens, including 20 from asymptomatic laboratory staff was used to validate the PCR assays for influenza A virus (H1 and H3 subtypes), influenza B virus, RSV, parainfluenza viruses (at least one of types 1-3), picornaviruses (a mixture of enteroviruses and rhinoviruses), and adenoviruses (each of different serotype) (Table III) . The process included the design and evaluation of primers; optimization of nucleic acid extraction conditions; establishment of optimum PCR amplification conditions; evaluation of applicable specimen types; determination of assay sensitivity compared to conventional assays; specificity testing using clinical material likely to be negative (including asymptomatic staff volunteers); or material previously shown to be positive for respiratory viruses by conventional assays or by sequencing of an amplified product where no other confirmatory method was available. cache = ./cache/cord-260690-h5pjv2dw.txt txt = ./txt/cord-260690-h5pjv2dw.txt === reduce.pl bib === id = cord-260250-t48y27wg author = Decaro, Nicola title = Quantitation of canine coronavirus RNA in the faeces of dogs by TaqMan RT-PCR date = 2004-05-07 pages = extension = .txt mime = text/plain words = 3322 sentences = 157 flesch = 51 summary = A TaqMan(®) fluorogenic reverse transcriptase-polymerase chain reaction (RT-PCR) assay was developed for the detection and quantitation of canine coronavirus (CCoV) RNA in the faeces of naturally or experimentally infected dogs. The CCoV fluorogenic RT-PCR assay, which targeted the ORF5 (M gene), was more sensitive than a conventional RT-PCR assay targeting the same gene, showing a detection limit of 10 copies of CCoV standard RNA, and was linear from 10 to 10(8) copies, allowing quantitation of samples with a wide range of CCoV RNA loads. As shown in Table 2 , the detec-tion limit of the TaqMan RT-PCR was 1-2 log higher than that of conventional RT-PCR, ranging around 10 1 copies/l and 10 −1.50 TCID 50 /50 l for standard RNA and CCoV strain, respectively, with a detection rate of 100% for each positive dilution. The results of the conventional amplification and real-time analysis carried out on the faecal samples of the CCoV experimentally infected dog are summarized in Fig. 3 . cache = ./cache/cord-260250-t48y27wg.txt txt = ./txt/cord-260250-t48y27wg.txt === reduce.pl bib === id = cord-260481-twk5kvd3 author = Täufer, Matthias title = Rapid, large-scale, and effective detection of COVID-19 via non-adaptive testing date = 2020-08-18 pages = extension = .txt mime = text/plain words = 3854 sentences = 226 flesch = 64 summary = More precisely, assuming knowledge about the overall incidence rate, we calculate explicit error bounds on the number of false positives which scale favourably with pool size and sample multiplicity. then in any multipooling strategy with pool size n and multiplicity k, the probability of a positive test being a false positive does not exceed fp . Table 1 : Probability of a positive result being a false positive and the compression k/n compared to individual testing for pool size n = 31, incidence ρ ≤ 0.01 and different multiplicities k. If we choose k = 4 and accept fp = 1.2% as the k fp k/n 3 0.17 0.049 4 0.012 0.066 5 0.0007 0.082 Table 2 : Probability of a positive result being a false positive and the compression k/n compared to individual testing for pool size n = 31, incidence ρ ≤ 0.01 and different multiplicities k. cache = ./cache/cord-260481-twk5kvd3.txt txt = ./txt/cord-260481-twk5kvd3.txt === reduce.pl bib === id = cord-015324-y44sfr0c author = nan title = Scientific Programme date = 2007-09-01 pages = extension = .txt mime = text/plain words = 197618 sentences = 12774 flesch = 53 summary = In order to further validate this approach, we performed a prospective randomized open-label multicenter trial in 41 low-risk pediatric renal transplant recipients (12 f, 29 m; mean age 10.1 yrs; range, 3.4 to 17.8) on CsA (target trough level 100-200 ng/ml), MMF (1200 mg/m 2 per day) and methylprednisolone (3) (4) mg/m 2 per day), who were randomly assigned >1 year posttransplant to continue steroids or to withdraw over a period of 3 months. We evaluated MMF in 15 children with LN, 11 F/4 M, mean age: 12.4±3.9 yrs, proteinuria >3 g/day, decreased C3 and increased anti-dsDNA serum levels, normal renal function. Patients and methods: 91 children and adolescents (60 male, 31 female, mean age at transplantation 9.7±5.2 years) with stable renal function and observation period exceeding 6 months were included. cache = ./cache/cord-015324-y44sfr0c.txt txt = ./txt/cord-015324-y44sfr0c.txt === reduce.pl bib === id = cord-261134-zarq507s author = Pulford, David title = Amplification refractory mutation system PCR assays for the detection of variola and Orthopoxvirus date = 2004-02-13 pages = extension = .txt mime = text/plain words = 3799 sentences = 215 flesch = 50 summary = PCR assays that can identify the presence of variola virus (VARV) sequences in an unknown DNA sample were developed using principles established for the amplification refractory mutation system (ARMS). When a variola virus specific primer was used with a consensus primer in an ARMS assay with different Orthopoxvirus genomes, a PCR product was only amplified from variola virus DNA. Incorporating a second consensus primer into the assay produced a multiplex PCR that provided Orthopoxvirus generic and variola-specific products with variola virus DNA. The variola virus specific primers did not produce amplicons with either assay format when tested with 50 other Orthopoxvirus DNA samples. These multiplex assays employ three primers; two consensus primers generate an amplicon diagnostic of an Old World Orthopoxvirus and the third primer simultaneously binds to a variola-specific polymorphism and initiates extension of a shorter PCR product to detect the presence of variola virus. cache = ./cache/cord-261134-zarq507s.txt txt = ./txt/cord-261134-zarq507s.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-261089-aul4ifso author = Yuan, Wen title = Development of a duplex real-time RT-PCR for the simultaneous detection and differentiation of Theiler’s murine encephalomyelitis virus and rat theilovirus date = 2016-07-07 pages = extension = .txt mime = text/plain words = 4522 sentences = 214 flesch = 52 summary = The aim of this study is to develop a rapid, sensitive and specific duplex real-time RT-PCR assay for the simultaneous detection of TMEV and RTV, and provide a useful tool for the routine health monitoring of these two viruses in laboratory rodents and for the screening of contaminated biological materials. In addition, twenty cecum content and spleen samples collected from eight specific pathogen free (SPF) mouse strains (BALB/c, C57BL/6, DBA, FVB, 129, ICR, KM and NIH) and two rat strains (SD and Wistar) were used to evaluate specificity of the duplex real-time RT-PCR assay, these animals were reared under barrier colonies and were confirmed as serology negative for TMEV and RTV by a commercial ELISA kit (XpressBio, Maryland, USA). The specificity of the duplex real-time RT-PCR assay was determined by evaluation of RNA extracted from positive cultures of the following rodent viral pathogens: TMEV, RTV, MHV, Reo-3, RCV, Sendai, PVM, MNV and LCMV, and from twenty cecum content and spleen samples of ten SPF rodent strains. cache = ./cache/cord-261089-aul4ifso.txt txt = ./txt/cord-261089-aul4ifso.txt === reduce.pl bib === id = cord-261237-0hbijukt author = Hou, Peili title = Development of a recombinase polymerase amplification combined with lateral-flow dipstick assay for detection of bovine ephemeral fever virus date = 2017-12-26 pages = extension = .txt mime = text/plain words = 4858 sentences = 254 flesch = 51 summary = title: Development of a recombinase polymerase amplification combined with lateral-flow dipstick assay for detection of bovine ephemeral fever virus In this study, we described the development of lateral-flow dipstick isothermal recombinase polymerase amplification (LFD-RPA) assays for detection of BEFV. In this study, we aimed to develop the lateral flow dipsticks recombinase polymerase amplification (LFD-RPA) assays for rapid detection of BEFV. The results of those assays showed that a total of 83 clinical specimens were tested positive by conventional RT-PCR, while the similar performance that 96 specimens were detected positive by BEFV RPA nucleic acid amplification assays on LFD within 5 min, and 95 specimens were positive with the C t values below 35 using the real-time qPCR assay. As the applications of LFD-RPA, conventional RT-PCR and real time qPCR methods for detection BEFV genomes from clinical samples (Table 2) , the results clearly indicated the potential benefits of the developed assay over PCR-based methods. cache = ./cache/cord-261237-0hbijukt.txt txt = ./txt/cord-261237-0hbijukt.txt === reduce.pl bib === id = cord-261279-6mef38eo author = Chu, Daniel K W title = Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia date = 2020-01-31 pages = extension = .txt mime = text/plain words = 2971 sentences = 178 flesch = 54 summary = RESULTS: Using RNA extracted from cells infected by SARS coronavirus as a positive control, these assays were shown to have a dynamic range of at least seven orders of magnitude (2x10(−4)-2000 TCID(50)/reaction). In this study, we report the development of RT-PCR assays to detect this novel virus in human clinical specimens. Two monoplex real-time RT-PCR assays targeting the ORF1b and N gene regions of 2019-nCoV were designed based on the first publicly available sequence in Genbank (Accession number: MN908947). Viral RNA from cells infected by SARS coronavirus or DNA plasmids containing the target sequences were positive in the assays as expected. In addition, the N gene RT-PCR assay was found to be more sensitive in detecting 2019-nCoV RNA in the studied clinical samples. cache = ./cache/cord-261279-6mef38eo.txt txt = ./txt/cord-261279-6mef38eo.txt === reduce.pl bib === id = cord-261735-03hvi4el author = Rodrigues, R. title = Development of a one step real time RT-PCR assay to detect and quantify Dugbe virus date = 2011-06-14 pages = extension = .txt mime = text/plain words = 2637 sentences = 159 flesch = 60 summary = A one-step real time quantitative RT-PCR (qRT-PCR) assay was developed to detect all published Dugbe virus (DUGV) genomes of the Nairovirus genus. Frequently detected in tick-borne virus surveys in Africa (Guilherme et al., 1996) , DUGV is a tri-segmented single-stranded negative RNA enveloped virus and is considered endemic in arid regions (Burt et al., 1996) . The aim of this study was to develop a sensitive, specific and rapid one-step quantitative real time RT-PCR assay (qRT-PCR) to detect DUGV in infected cell supernatants, ticks or serum samples. The specificity was evaluated by using RNA extracted from supernatants from CCHFV, Hazara virus, Coronavirus and Influenza A virus infected cells. Among the 498 captured ticks, one Dugbe virus RNA was detected in one tick using the qRT-PCR assay (0.2%). In conclusion, a sensitive and specific qRT-PCR assay was developed to detect and quantify DUGV RNAs in infected cell supernatants, extracts from ticks and potentially sera. cache = ./cache/cord-261735-03hvi4el.txt txt = ./txt/cord-261735-03hvi4el.txt === reduce.pl bib === id = cord-015394-uj7fe5y6 author = nan title = Scientific Abstracts date = 2008-12-23 pages = extension = .txt mime = text/plain words = 242330 sentences = 15267 flesch = 52 summary = Studies involving immunohistochemical analysis of normal ovaries have shown that granulosa cells express significantly higher levels of the activator protein-1 (AP-1) transcription factor, cFos compared to theca cells, where cFos expression is virtually absent. Following acute hypoxia (0.5% O2) for one to six hours, RhoA mRNA, total protein and activation (RhoA-GTP) levels were analysed, using semi-quantitative PCRs and western blot, and compared to normoxic non-pregnant human uterine smooth muscle control cells. Since there is an urgent need for non-invasive methods for determination of fetal (F) and placental (P) function, this study was designed to evaluate the genes differently and commonly expressed in P tissue and leukocytes in maternal (M) and F circulation.Material and Methods. The current study: 1) localized IL-6 mRNA levels in preeclamptic versus normal decidual sections; 2) evaluated mechanisms regulating IL-6 synthesis by targeting intracellular signaling pathways with specific inhibitors; 3) identified potential IL-6 targets by immunolocalizing the IL-6 receptor (IL-6R) to specific cell types in placental bed biopsies. cache = ./cache/cord-015394-uj7fe5y6.txt txt = ./txt/cord-015394-uj7fe5y6.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-263417-jgu8kc5k author = Yan, Yong title = A multiplex liquid-chip assay based on Luminex xMAP technology for simultaneous detection of six common respiratory viruses date = 2017-06-17 pages = extension = .txt mime = text/plain words = 4657 sentences = 189 flesch = 45 summary = We utilized one-step multiplex reverse transcription-PCR (RT-PCR) and Luminex xMAP technology to develop a respiratory multiplex liquid-chip assay (rMLA) for simultaneous detection of 6 common respiratory viruses, including influenza virus type A (FluA) and type B (FluB), para-influenza virus type 3 (PIV-3), respiratory syncytial virus (RSV), human metapneumovirus (MPV) and a threatening virus to China, Middle East Respiratory Syndrome coronavirus (MERS-CoV). In this study, one-step multiplex reverse transcription-PCR(RT-PCR) and Luminex xMAP technology were utilized to develop a respiratory multiplex LiquiChip assay (rMLA) for the detection of 6 common respiratory viruses in Jiaxing, including influenza virus type A (FluA) and B (FluB), parainfluenza virus type 3 (PIV-3), respiratory syncytial virus (RSV) and human metapneumovirus (MPV), as well as a potentially threatening virus, MERS-CoV [29] . The analytical sensitivities of the Luminex-based rMLA and multiplex real-time RT-PCR assay developed in this study were assessed by testing in duplicate 10-fold serial dilutions of positive standards ranging from 10 6 to 10 1 copies/μl of viral RNA transcripts for each target. cache = ./cache/cord-263417-jgu8kc5k.txt txt = ./txt/cord-263417-jgu8kc5k.txt === reduce.pl bib === id = cord-262826-2usqmujy author = She, Rosemary C. title = Performance of diagnostic tests to detect respiratory viruses in older adults date = 2010-07-31 pages = extension = .txt mime = text/plain words = 2874 sentences = 147 flesch = 45 summary = For this population, there has not been a comprehensive comparison of current modalities for detection of respiratory viruses (i.e., direct fluorescent antibody testing [DFA], culture, multiplex nucleic acid amplification, and rapid antigen assays), and test performance is likely to differ because adults are known to shed fewer virus particles than children during RTI (Hall et al., 1976) . Although many studies have examined the utility of the various methods used for diagnosis of respiratory virus infections, to our knowledge, none have systematically and concurrently examined the performance characteristics of DFA, culture, rapid antigen testing, and PCR on an older adult population (Barenfanger et al., 2000; Falsey et al., 1996 Falsey et al., , 1995 Lam et al., 2007; Templeton et al., 2004) . The data in this study indicate that multiplexed RT-PCR is highly sensitive in detecting respiratory viruses in older adults compared to DFA, culture, and rapid antigen testing. cache = ./cache/cord-262826-2usqmujy.txt txt = ./txt/cord-262826-2usqmujy.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-261823-pgluidj8 author = Wang, Ji title = Novel One-Step Single-Tube Nested Quantitative Real-Time PCR Assay for Highly Sensitive Detection of SARS-CoV-2 date = 2020-05-22 pages = extension = .txt mime = text/plain words = 3581 sentences = 183 flesch = 60 summary = In this study, we have developed and evaluated a novel one-step single-tube nested quantitative real-time PCR (OSN-qRT-PCR) assay for the highly sensitive detection of SARS-CoV-2 targeting the ORF1ab and N genes. 7−10 In this study, we developed and evaluated an OSN-qRT-PCR assay for the highly sensitive detection of SARS-CoV-2, targeting the ORF1ab and N genes on the basis of a commercial qRT-PCR kit for SARS-CoV-2 (Sansure, Hunan, China). Compared to this qRT-PCR kit, the OSN-qRT-PCR assay revealed higher sensitivity and specificity, showing better suitability to clinical applications for the detection of SARS-CoV-2 in patients with low viral load. Compared to this qRT-PCR kit, the OSN-qRT-PCR assay revealed higher sensitivity and specificity, showing better suitability to clinical applications for the detection of SARS-CoV-2 in patients with low viral load. Collectively, the OSN-qRT-PCR assay has advantages of high sensitivity and easy applicability for the detection of SARS-CoV-2 in clinical samples. cache = ./cache/cord-261823-pgluidj8.txt txt = ./txt/cord-261823-pgluidj8.txt === reduce.pl bib === id = cord-263134-0p4zy5t2 author = de Paz, Hector David title = Molecular isothermal techniques for combating infectious diseases: towards low-cost point-of-care diagnostics date = 2014-07-23 pages = extension = .txt mime = text/plain words = 6474 sentences = 304 flesch = 34 summary = This review describes the landscape of molecular isothermal diagnostic techniques for infectious diseases, their characteristics, current state of development, and available products, with a focus on new directions towards point-of-care applications. Advances in microfluidics and miniaturization of signal detectors have allowed the integration of molecular diagnostics into microscale lab-on-achip devices that perform all necessary PCR steps automatically, from sample intake to cell lysis, DNA extraction, purification and amplification. This review describes the state-ofthe-art and new directions in the development of isothermal amplification technologies for diagnosis of infectious diseases with particular focus on those susceptible to be integrated in inexpensive molecular POC tests. • Loop-mediated isothermal amplification, smart amplification process & signal mediated amplification of RNA technology, helicasedependent amplification, strand displacement amplification, recombinase polymerase amplification and nicking and extension amplification reaction are isothermal techniques with mid/high tolerance to inhibitory compounds that allow the use of raw samples without any pretreatment step, which may be an interesting feature for PCR-based point-of-care (POC) testing. cache = ./cache/cord-263134-0p4zy5t2.txt txt = ./txt/cord-263134-0p4zy5t2.txt === reduce.pl bib === id = cord-259717-e8ljkv2y author = Holtz, Lori R. title = Geographic variation in the eukaryotic virome of human diarrhea date = 2014-11-01 pages = extension = .txt mime = text/plain words = 6748 sentences = 349 flesch = 49 summary = Viromes from Northern Territory children contained more viral families per sample than viromes from Melbourne, which could be attributed largely to an increased number of sequences from the families Adenoviridae and Picornaviridae (genus enterovirus). Viromes from Northern Territory children contained more viral families per sample than viromes from Melbourne, which could be attributed largely to an increased number of sequences from the families Adenoviridae and Picornaviridae (genus enterovirus). Because previous metagenomic studies demonstrated significant virus diversity in patients with diarrhea (Finkbeiner et al., 2008) we focused this study on comparing the eukaryotic virus populations in stools of children with diarrhea collected from two different locations, Melbourne, Australia and the Northern Territory, Australia. In order to independently confirm the sequencing results, we used PCR to define the prevalence of the most frequently detected viruses for which pan-family or pan-genus primers could be used including: adenovirus, astrovirus, enterovirus, norovirus, and rotavirus. cache = ./cache/cord-259717-e8ljkv2y.txt txt = ./txt/cord-259717-e8ljkv2y.txt === reduce.pl bib === === reduce.pl bib === id = cord-263763-a8wgvgz2 author = Çelik, Ersin title = Treatment Approach to Coronavirus Disease (COVID-19) Seen Early After Open Heart Surgery. Case Report date = 2020-07-02 pages = extension = .txt mime = text/plain words = 1535 sentences = 90 flesch = 50 summary = Here, we present our approach to a 54-year-old male patient who had coronary artery bypass (CABG) surgery diagnosed as high probability coronavirus disease 2019 (COVID-19) in early postoperative period. We aimed to present our approach to high probability COVID-19 pneumonia which developed on early postoperative period in our patient after coronary artery bypass grafting (CABG) operation, which was not reported in the literature before. After consultations applied by chest physicians and infectious disease departments of our hospital, COVID-19 was evaluated as a high probability due to the laboratory tests, radiological findings, and clinical course. Having considered our patient as high risk, without waiting for the RT-PCR result, we started the specific treatment for COVID-19 immediately, by evaluating clinical, laboratory, and radiology findings. Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: a report of 1024 cases cache = ./cache/cord-263763-a8wgvgz2.txt txt = ./txt/cord-263763-a8wgvgz2.txt === reduce.pl bib === id = cord-031907-ilhr3iu5 author = nan title = ISEV2020 Abstract Book date = 2020-07-15 pages = extension = .txt mime = text/plain words = 200999 sentences = 11528 flesch = 44 summary = L.M., and the National Institutes of Health (R35GM119623) to T.R.G. The addition of a size exclusion chromatography step to various urinary extracellular vesicle concentrating methods reveals differences in the small RNA profile Introduction: Urinary extracellular vesicles (EVs) and their RNA cargo are a novel source of biomarkers for various diseases, however non-vesicular RNA (e.g. associated with proteins) is also present within urine. We then evaluated efficiency of heart targeting for eAAV9 or eAAV6 and standard AAV9 or AAV6 encoding for EGFP, mCherry or firefly luciferase in different human cell lines in vitro, in black mouse and in passive immunity nude mouse model in vivo using flow cytometry, confocal microscopy, Langendorff perfusion system and Methods: HLHS patients (n = 3) after Glenn procedure and swine (n = 3) after PAB were given RV injections of allogeneic/xenogeneic MSCs. Donor-specific, HLA-I+, exosomes were isolated from plasma. cache = ./cache/cord-031907-ilhr3iu5.txt txt = ./txt/cord-031907-ilhr3iu5.txt === reduce.pl bib === id = cord-261160-g92zhv19 author = Rowland, Raymond R.R title = Lymphoid tissue tropism of porcine reproductive and respiratory syndrome virus replication during persistent infection of pigs originally exposed to virus in utero date = 2003-10-30 pages = extension = .txt mime = text/plain words = 6383 sentences = 322 flesch = 48 summary = title: Lymphoid tissue tropism of porcine reproductive and respiratory syndrome virus replication during persistent infection of pigs originally exposed to virus in utero Even though PRRSV-specific antibody appears as early as 5 days post-infection and is followed by serum neutralizing activity and cell-mediated immunity Molitor, 1997, 1999; Rowland et al., 1999 Rowland et al., , 2001 persistently infected pigs can continue to shed virus. The purpose of this study was to further understand persistent infection in congenitally infected pigs by characterizing the course of clinical disease, sites of virus replication and the capacity to transmit virus in a group of pigs exposed to PRRSV in utero. Analysis of virus and antibody in blood and/or umbilical cords from the 28 live neonates showed that at least 20 or 74% were virus isolation (VI) or RT-PCR positive for PRRSV at the time of farrowing indicating that in utero infection was successful. cache = ./cache/cord-261160-g92zhv19.txt txt = ./txt/cord-261160-g92zhv19.txt === reduce.pl bib === id = cord-261329-k1p7fo0e author = Nidzworski, Dawid title = Detection and differentiation of virulent and avirulent strains of Newcastle disease virus by real-time PCR date = 2010-12-28 pages = extension = .txt mime = text/plain words = 3156 sentences = 199 flesch = 58 summary = A rapid diagnostic method based on the melting curve SYBR Green I real-time PCR analysis was developed to detect and differentiate Newcastle disease virus (NDV) strains. The results obtained in this study demonstrate the possible applications for melting curve real-time PCR analysis in laboratory practice for the diagnosis and differentiation of avirulent and virulent strains of Newcastle disease virus. (2005) described a SYBR Green I real-time PCR melting curve analysis assay for differentiation, although the differences in the Tm values between the three genotypes were not very significant and could cause false characterization of the virus. Using the SYBR Green I real-time PCR melting peak analysis, it was possible to detect and differentiate virulent and avirulent strains of Newcastle disease virus. In this study, a method for the rapid detection and differentiation of Newcastle disease virus by SYBR Green I melting-curve analysis was described. cache = ./cache/cord-261329-k1p7fo0e.txt txt = ./txt/cord-261329-k1p7fo0e.txt === reduce.pl bib === id = cord-263279-afdmegq0 author = Uhteg, Katharine title = Comparing the analytical performance of three SARS-CoV-2 molecular diagnostic assays date = 2020-04-26 pages = extension = .txt mime = text/plain words = 3175 sentences = 186 flesch = 51 summary = Of the first assays that were available for validations were the CDC COVID-19 RT-PCR panel assay (IDT, Coralville, IA) as well as the RealStar® SARS-CoV-2 RT-PCR (Altona Diagnostics, Hamburg, Germany), and both were initially validated for clinical use at the Johns Hopkins Hospital Medical Microbiology laboratory. To compare the analytical performance of the three assays, positive and negative SARS-CoV-2 clinical specimens (using the RealStar® SARS-CoV-2 as the reference method as this assay was the first to be offered in house for clinical diagnosis) were tested by the CDC COVID-19 RT-PCR and/ or the ePlex® SARS-CoV-2 assays. Comparing the performance of the CDC COVID-19 RT-PCR to the RealStar® SARS-CoV-2 included testing 20 positive and 48 negative clinical NP specimens. In this study, we compared the analytical performance of three different molecular assays for the detection of SARS-CoV-2; the RealStar® SARS-CoV-2 RT-PCR, ePlex® SARS-CoV-2, and the CDC COVID-19 RT-PCR tests. cache = ./cache/cord-263279-afdmegq0.txt txt = ./txt/cord-263279-afdmegq0.txt === reduce.pl bib === id = cord-264071-hg0qslyx author = Camelo-Castillo, Anny title = Nasopharyngeal Microbiota in Children With Invasive Pneumococcal Disease: Identification of Bacteria With Potential Disease-Promoting and Protective Effects date = 2019-01-28 pages = extension = .txt mime = text/plain words = 7151 sentences = 335 flesch = 39 summary = Principal coordinate analysis revealed three different microbiota profiles: microbiota A, dominated by the genus Dolosigranulum (44.3%); Microbiota B, mostly represented by Streptococcus (36.9%) and Staphylococcus (21.3%) and a high diversity of anaerobic genera including Veillonella, Prevotella and Porphyromonas; and Microbiota C, mainly containing Haemophilus (52.1%) and Moraxella (31.4%). To test this hypothesis, the objective of the present study was to characterize the nasopharyngeal microbiota profiles in two groups of children: (i) children with invasive pneumococcal disease (IPD), considered as a case group whose nasopharyngeal microbiota was suffering an important disturbance; and (ii) a matched control group of healthy children representative of a healthy nasopharyngeal niche. Sequence files and metadata for all samples used in this study are stored in the MG-RAST server to be publicly available by accessing the project Invasive Pneumococcal Disease (IPD) in children is associated with a highly diverse nasopharyngeal microbiota: a case-control study, ID mgp80930. cache = ./cache/cord-264071-hg0qslyx.txt txt = ./txt/cord-264071-hg0qslyx.txt === reduce.pl bib === id = cord-260866-bzdd4f5h author = Barceló, Damià title = Wastewater-Based Epidemiology to Monitor COVID-19 Outbreak: Present and Future Diagnostic Methods to be in Your Radar date = 2020-09-14 pages = extension = .txt mime = text/plain words = 4676 sentences = 249 flesch = 50 summary = Paper-based devices would be certainly one of the best measurement solutions for the rapid and onsite detection of COVID-19 in sewage waters and humans as well [2, 16] and also the use of other biomarkers of exposure [1] . Detection of SARS-CoV-2 in sewage has been employed as a complementary method to clinical test .It is an early warning indicator of virus spreading in communities, covering both symptomatic and asymptomatic cases. Hopefully at certain moment applications to detect SARS-CoV-2 and other viruses in wastewater will be developed based on these LOC/POCT systems that will enable simple, fast and sensitive virus detection. PCR platforms like RT-qPCR are still the most widely used methods for SARS-Cov-2 detection in waste waters. Sewage sensors, such as paper-based and smartphones for SARS-CoV2 detection at the population level have as well a clear potential for early warning of COVID-19 pandemic. cache = ./cache/cord-260866-bzdd4f5h.txt txt = ./txt/cord-260866-bzdd4f5h.txt === reduce.pl bib === id = cord-263735-sos2ovng author = Li, K. title = Diagnostic performance of CT and its key signs for COVID-19: A systematic review and meta-analysis date = 2020-05-26 pages = extension = .txt mime = text/plain words = 5251 sentences = 310 flesch = 69 summary = Furthermore, several studies reported that CT had high sensitivity for COVID-19 [7, 9, 10] , but a recent study including 121 cases found 56% of patients had a normal CT finding in the early stage of infection [11] . Furthermore, there are 10 studies reported the diagnostic sensitivity of the initial PCR assay [7, 10, 11, 18, 22, 29, 32, [34] [35] [36] , while 5 of them mentioned the rate of missed diagnosis after the second tests [10, 22, 29, 32, 35] . For these 25 studies, the diagnostic sensitivity and specificity of CT for COVID-19 ranged from 69% to 100% and from 0% to 96%, with pooled estimates of 93% (95% CI, 89-96%) and 44% (95% CI, 27-62%) (Figure 4 ), respectively. For the 10 studies with repeated PCR assay, the pooled sensitivity of the initial RT-PCR test in diagnosis of COVID-19 was 76% (95% CI: 59-89%; I 2 =96%). cache = ./cache/cord-263735-sos2ovng.txt txt = ./txt/cord-263735-sos2ovng.txt === reduce.pl bib === id = cord-263567-6uacorpp author = Collignon, C. title = Polyarthrite associée à une leishmaniose chez un jeune chien date = 2009-03-31 pages = extension = .txt mime = text/plain words = 3626 sentences = 323 flesch = 58 summary = Lors du dernier examen, après deux mois de traitement, la PCR sur sang est négative, et seule une légère protéinurie persiste. La période d'incubation peut être extrêmement variable avant l'apparition de la maladie (trois à 12 mois à quatre à 15 ans, selon les auteurs) [1, [5] [6] [7] [8] ; dans une étude portant sur 390 chiens en Espagne, deux pics d'âges sont notés : trois et sept ans, et plus. En effet, une étude montre qu'en dépit d'une thérapeutique combinée (antimoniate de méglumine et allopurinol pendant un mois) en relais longue durée avec de l'allopurinol, les chiens cliniquement améliorés restent PCR positifs dans les tissus (moelle ou noeuds lymphatiques) [26] [27] [28] . Ainsi, il peut être intéressant d'arrêter l'antimoniate de méglumine dès que les signes cliniques ont disparu et que la PCR sur sang est négative, afin de diminuer les effets secondaires (surtout hépatiques et rénaux), liés à l'utilisation de cette molécule [29] , et de réduire le coût du traitement. cache = ./cache/cord-263567-6uacorpp.txt txt = ./txt/cord-263567-6uacorpp.txt === reduce.pl bib === id = cord-263426-l32gyiky author = Najafi, Hamideh title = Molecular and clinical study on prevalence of feline herpesvirus type 1 and calicivirus in correlation with feline leukemia and immunodeficiency viruses date = 2014 pages = extension = .txt mime = text/plain words = 3437 sentences = 200 flesch = 59 summary = In clinically normal cats, prevalence rates of FCV and FHV were about 50.00%, but FIV and FeLV rates (42.00% and 65.00% respectively) were higher compared to other studies. Feline herpesvirus1 (FHV-1), a double-stranded DNA virus, member of the Varicellovirus, genus of the subfamily Alphaherpesvirinae combine with, feline calicivirus (FCV) that is a single-stranded positive-sense RNA virus, in the family Caliciviridae, genus Vesivirus are considered as the main agents involved in upper respiratory tract diseases (URTD) in cats. 1 However, it is important to determine the prevalence of FHV-1 and FCV and evaluation of their clinical signs, especially in relation with FIV and FeLV, to identify agents involved in URTD in Iran. For better understanding the role of FIV and FeLV viruses in induction of FCV and FHV infections, the prevalence rates of these infections were investigated in healthy and diseased cats. Association between clinical signs in cats with URTD and infection with FIV, FeLV, FCV, FHV-1. cache = ./cache/cord-263426-l32gyiky.txt txt = ./txt/cord-263426-l32gyiky.txt === reduce.pl bib === === reduce.pl bib === id = cord-261867-6n0g3bz5 author = Evermann, James F. title = Canine Reproductive, Respiratory, and Ocular Diseases due to Canine Herpesvirus date = 2011-10-28 pages = extension = .txt mime = text/plain words = 8808 sentences = 468 flesch = 41 summary = Infection rates, based on serologic studies, are high enough to explain entry of CHV into multidog environments, either as an active infection or as the result of reactivation of latent virus in environments associated with natural, or pharmacologically induced immunosuppression. In fetal and neonatal dogs with primary CHV infection, severe intraocular lesions are frequently present concurrent with systemic viral disease. The results of this study showed that topical ocular prednisolone at the concentration and treatment regimen used did not result in detectable reactivation of CHV latency, based on a combination of recrudescent clinical signs, confocal microscopy findings, ocular infectious virus shedding, real-time PCR findings, and serologic response. Primary and recurrent CHV infection in mature dogs is associated with mucosal viral shedding that it detectable by PCR assay or virus isolation. Experimental recurrent ocular CHV infection induced by systemic corticosteroid administration to dogs recovered from primary ocular infection again resulted in viral shedding. cache = ./cache/cord-261867-6n0g3bz5.txt txt = ./txt/cord-261867-6n0g3bz5.txt === reduce.pl bib === id = cord-010092-uftc8inx author = nan title = Abstract of 29th Regional Congress of the ISBT date = 2019-06-07 pages = extension = .txt mime = text/plain words = 233304 sentences = 13171 flesch = 54 summary = Prospective testing of blood donations in endemic areas of the U.S. revealed 0.38% of donors were positive for Babesia DNA or antibodies (Moritz, NEJM, 2016) Aims: -To report results of ongoing Babesia clinical trial -To explain significance of Babesia as a TT infection Methods: In cobas â Babesia for use on the cobas â 6800/8800 Systems, is a qualitative polymerase chain reaction nucleic acid amplification test, developed to detect in whole blood (WB) donor samples the 4 Babesia species that cause human disease: B. In sensitivity analyses, there were two discrepant results for HIV testing, three for HCV, and five for anti-HBc. Summary/Conclusions: Elecsys â infectious disease parameters on the cobas e 801 analyser demonstrate high specificity/sensitivity for screening first-time blood donor samples, with similar clinical performance to other commercially available assays. cache = ./cache/cord-010092-uftc8inx.txt txt = ./txt/cord-010092-uftc8inx.txt === reduce.pl bib === id = cord-264261-98h1bmb2 author = Caruana, Giorgia title = Diagnostic strategies for SARS-CoV-2 infection and interpretation of microbiological results date = 2020-06-25 pages = extension = .txt mime = text/plain words = 1417 sentences = 99 flesch = 48 summary = It is recommended to use real-time RT-PCR for RNA viruses in order (i) to perform a rapid and accurate diagnostic, (ii) to guide patient care and management and (iii) to guide epidemiological strategies. IMPLICATIONS: Real-time RT-PCR remains the reference method for diagnosis of SARS-CoV-2 infection. On the other hand, notwithstanding its varying sensitivity according to the time of infection, serology represents a valid asset (i) to try to solve possible discrepancies between a highly suggestive clinical and radiological presentation and negative RT-PCR, (ii) to solve discrepancies between different PCR assays, and (iii) for epidemiological purposes. Improved molecular diagnosis of COVID-19 by the novel, highly sensitive 316 and specific COVID-19-RdRp/Hel real-time reverse transcription-polymerase chain 317 reaction assay validated in vitro and with clinical specimens Antibody responses to SARS-CoV-2 in patients of 373 novel coronavirus disease 2019 SARS-CoV-2 viral load in 413 upper respiratory specimens of infected patients cache = ./cache/cord-264261-98h1bmb2.txt txt = ./txt/cord-264261-98h1bmb2.txt === reduce.pl bib === id = cord-263976-b9shffb3 author = Shaukat, Shahzad title = Identification and characterization of unrecognized viruses in stool samples of non-polio acute flaccid paralysis children by simplified VIDISCA date = 2014-08-12 pages = extension = .txt mime = text/plain words = 3687 sentences = 183 flesch = 44 summary = One sequence independent method, Virus Discovery based on cDNA Amplified Fragment Length Polymorphism (VIDISCA) is capable of identifying viruses that would have remained unidentified in standard diagnostics or cell cultures. Therefore, a simplified VIDISCA protocol was developed, which lacks the last amplification round, and evaluated using viruses that were cultured from stool samples of acute flaccid paralysis children, and which had remained unrecognized on both cell culture and enterovirus specific real-time PCR. On the other hand, genetic analysis in ORF2 gene (capsid protein) showed that PAK-NIH-VS908 shared 99.7% nucleotide and 100% amino acid similarities with HAstV type 3 isolate IDH2211 (AB54844), a finding which matches with the results from VIDISCA and we conclude that the astrovirus is a recombinant, with a recombination site between ORF1a and ORF2. cache = ./cache/cord-263976-b9shffb3.txt txt = ./txt/cord-263976-b9shffb3.txt === reduce.pl bib === === reduce.pl bib === id = cord-262467-epqqd8n8 author = Chen, Jun title = COVID-19 infection: the China and Italy perspectives date = 2020-06-08 pages = extension = .txt mime = text/plain words = 7596 sentences = 384 flesch = 47 summary = The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the COVID-19 disease as originally shown in Wuhan, China, as early as documented from 1 December 2019 (ref. A recent prospective study failed to find antiviral activity or clinical benefit of this combination for the treatment of our hospitalized patients with severe COVID-19 (ref. More recently, a randomized, controlled study conducted in Wuhan, China also failed to identify beneficial effect of LPV/r beyond standard therapy in hospitalized patients with severe Covid-19 (ref. Clinical trials also showed that in patients with severe H1N1 influenza A, in the 2009 pandemic, therapy with convalescent plasma from patients who recovered, especially within 5 days of symptom onset, resulted in a lower viral load and lower mortality 66, 67 . The duration from onset of symptoms to viral clearance is significantly longer in severe and critical ill SARS-CoV-2infected patients compared with that in the mild cases 48 . cache = ./cache/cord-262467-epqqd8n8.txt txt = ./txt/cord-262467-epqqd8n8.txt === reduce.pl bib === id = cord-263570-6notzm6s author = Elia, Gabriella title = Detection of infectious canine parvovirus type 2 by mRNA real-time RT-PCR date = 2007-08-10 pages = extension = .txt mime = text/plain words = 3990 sentences = 224 flesch = 58 summary = The load and distribution of CPV-2 mRNA in samples from infected dogs were estimated in comparison with the load of virus DNA, as evaluated by real-time PCR. The analytic specificity of spliced CPV-2 mRNA detection by real-time RT-PCR was assessed by testing RNA and DNA preparations of other canine pathogens, including canine coronavirus types I and II (CCoVI, CCoVII) (Decaro et al., 2005d) , canine distemper virus (CDV) (Elia et al., 2006) , canine adenovirus (CAdV) (Decaro et al., 2006a) , reoviruses (Decaro et al., 2005b) and rotaviruses . To compare the amount of viral DNA in the tissue samples and in the infected cell cultures, a real-time PCR assay was used as described previously (Decaro et al., 2005c) . The newly developed real-time RT-PCR assay was applied to determine the viral mRNA loads in different tissues of CPV-2 naturally infected dogs. A real-time PCR assay for rapid detection and quantitation of canine parvovirus type 2 DNA in the feces of dogs cache = ./cache/cord-263570-6notzm6s.txt txt = ./txt/cord-263570-6notzm6s.txt === reduce.pl bib === id = cord-263118-6sf41rsj author = Landry, Marie L. title = Real-time PCR compared to Binax NOW and cytospin-immunofluorescence for detection of influenza in hospitalized patients date = 2008-07-18 pages = extension = .txt mime = text/plain words = 2586 sentences = 137 flesch = 56 summary = STUDY DESIGN: Binax NOW, cytospin-enhanced direct immunofluoroescence (DFA), and influenza A and B multiplex TaqMan RT-PCR were performed on 237 clinical samples. RESULTS: Binax NOW detected 70 (53.0%), cytospin-DFA detected 127 (96.2%), and TaqMan RT-PCR detected 132 (100%) influenza-positive samples. CONCLUSIONS: The accuracy of real-time RT-PCR should greatly improve the diagnosis of influenza in hospitals using simple rapid flu tests, but may have a more modest impact in hospitals with expertise in cytospin-DFA. In our hospital, cytospin-enhanced direct immunofluorescence (DFA) is performed on respiratory samples when Virology is open, and a rapid influenza test, Binax NOW, is used in the Core Laboratory when Virology is closed (Landry and Ferguson, 2000; Landry et al., 2004) . During the study period, reflex cultures were performed on 683 DFA-negative samples, but only three influenza A positives were detected. cache = ./cache/cord-263118-6sf41rsj.txt txt = ./txt/cord-263118-6sf41rsj.txt === reduce.pl bib === id = cord-264880-0tmd9knh author = Li, Zhao title = Picoliter Well Array Chip-Based Digital Recombinase Polymerase Amplification for Absolute Quantification of Nucleic Acids date = 2016-04-13 pages = extension = .txt mime = text/plain words = 5347 sentences = 260 flesch = 46 summary = We developed a picoliter well array (PWA) chip with 27,000 consistently sized picoliter reactions (314 pL) for isothermal DNA quantification using digital RPA (dRPA) at 39°C. To avoid thermal cycling, different isothermal amplification methods have been developed that rapidly amplify nucleic acids to detectable levels at a single temperature [42, 43] , such as loop-mediated amplification (LAMP) [44] , rolling circle amplification (RCA) [45] , helicasedependent amplification (HDA) [46] , nucleic acid sequence-based amplification (NASBA) [47] , recombinase polymerase amplification (RPA) [48] , transcription-mediated amplification (TMA) [49] , multiple displacement amplification (MDA) [50] , and strand-displacement amplification (SDA) [51] . Finally, we sealed the PWA chip in a homemade copper chamber filled with oil and successfully performed real-time dRPA on an isothermal incubation setup for the absolute quantification of serial dilutions of a Listeria monocytogenes gDNA stock solution. cache = ./cache/cord-264880-0tmd9knh.txt txt = ./txt/cord-264880-0tmd9knh.txt === reduce.pl bib === id = cord-265221-qtkwciym author = Bahadur, Gulam title = SARS-CoV-2: diagnostic and design conundrums, and the male factor infertility date = 2020-06-03 pages = extension = .txt mime = text/plain words = 3261 sentences = 182 flesch = 49 summary = It is essential to understand the limitations of both antibody and real time polymerase chain reaction (RT-PCR) tests in interpreting SARS-CoV-2 data in relation to semen and testicular tissues analyses without appropriate controls. raising equal concerns for embryo and fetal development (Colaco et al., 2020) .In males, ACE2 receptor sites have been reported in testicular tissue which then have the capability to harbour SARS-CoV-2 virus and eventual shedding into the semen and hence its implication in sexual transmission, early pregnancy or early in utero embryonic development. Studies analysing SARS-CoV-2 in seminal fluid or testicular biopsies have so far lacked appropriate controls and patients suffered from predominantly mild infections and tested several weeks after the infection, thereby increasing the complexity of result interpretation. Also no SARS-CoV-2 was detected in expressed prostatic secretion (EPS) of 18 confirmed Covid-19 infected patients and 5 strongly suspected cases but absent semen analyses. cache = ./cache/cord-265221-qtkwciym.txt txt = ./txt/cord-265221-qtkwciym.txt === reduce.pl bib === id = cord-262485-sx2q5ol4 author = Davda, Jayeshkumar Narsibhai title = An Inexpensive RT-PCR Endpoint Diagnostic Assay for SARS-CoV-2 Using Nested PCR: Direct Assessment of Detection Efficiency of RT-qPCR Tests and Suitability for Surveillance date = 2020-06-08 pages = extension = .txt mime = text/plain words = 3255 sentences = 193 flesch = 59 summary = The method employs real time quantitative reverse transcription polymerase chain reaction (RT-qPCR) of RNA extracted from nasopharyngeal (NP) swab samples, to measure amplification of a short segment of a viral gene in the course of a PCR reaction following reverse transcription of viral RNA. We developed and tested a RT-nPCR protocol comprising a multiplex primary RT-PCR for amplification of four SARS-CoV-2 amplicons and a control human RPP30 amplicon followed by a secondary nested PCR for individual amplicons 4 and visualization by agarose gel electrophoresis. Based on the experimentally measured false negative rate by RT-nPCR tests from this study we estimated that as many as 50% of positive samples may escape detection in single pass testing by RT-qPCR in an actual testing scenario. To detect the presence of SARS-CoV-2 in RNA isolated from NP swabs we performed a multiplex one-step RT-PCR on RNA from positive and negative samples using pooled primers for the four viral amplicons together with human RPP30 control. cache = ./cache/cord-262485-sx2q5ol4.txt txt = ./txt/cord-262485-sx2q5ol4.txt === reduce.pl bib === id = cord-263302-z5uhrta5 author = Zhang, Xuming title = Identification of a Noncanonical Signal for Transcription of a Novel Subgenomic mRNA of Mouse Hepatitis Virus: Implication for the Mechanism of Coronavirus RNA Transcription date = 2000-12-05 pages = extension = .txt mime = text/plain words = 7944 sentences = 411 flesch = 58 summary = Transfection of the reporter RNA into MHV-infected cells resulted in synthesis of a CAT-specific subgenomic mRNA detected by reverse transcription-polymerase chain reaction (RT-PCR). Further sequencing on cDNA clones derived from JHM2c mRNAs by reserve transcription-polymerase chain reaction (RT-PCR) has shown that the leader-body joining sites in subgenomic mRNA2-1 are more heterogeneous . When it was placed in front of the chloramphenicol acetyl-transferase (CAT) gene in the defective-interfering (DI) RNA-CAT reporter plasmid, the IG5-1, which is devoid of any known IRES sequence, can direct the synthesis of a subgenomic CAT-containing mRNA and expression of the CAT activity, thus confirming that the IG5-1 serves as a promoter for transcription of a subgenomic mRNA. To identify the minimal sequence required for subgenomic mRNA transcription, three deletions within the 140-nt sequence were made by PCR, and the deletion fragments were cloned into the DI RNA-CAT reporter vector in place of the wild-type, full-length (140-nt) se, and MHV-1 (F), respectively. cache = ./cache/cord-263302-z5uhrta5.txt txt = ./txt/cord-263302-z5uhrta5.txt === reduce.pl bib === === reduce.pl bib === id = cord-265978-i0fu8e0p author = Amer, Haitham M. title = Development of a SYBR Green I based real-time RT-PCR assay for detection and quantification of bovine coronavirus date = 2011-06-30 pages = extension = .txt mime = text/plain words = 4797 sentences = 227 flesch = 49 summary = In this report, a real-time RT-PCR system using SYBR Green I and melt curve analysis was developed for detection and quantification of BCoV in clinical samples. The reaction conditions were first optimized by testing variable concentrations of BCoV and internal control QPCR primer sets; MgCl 2 concentrations; template volumes and primer annealing Following amplification, a melt curve analysis was performed to verify the specificity of the amplified products by their specific melting temperatures (Tm). In order to determine the optimal conditions for developing a robust SYBR Green I based real-time qPCR assay that detects BCoV and internal control RNA simultaneously, different variables of the reaction were assessed. The competence of the developed real-time RT-PCR assay, for accurate detection of BCoV in clinical samples, was evaluated by analysis of 103 swab samples (68 fecal and 35 nasal) in comparison to the gel-based RT-PCR assay ( Table 4 ). cache = ./cache/cord-265978-i0fu8e0p.txt txt = ./txt/cord-265978-i0fu8e0p.txt === reduce.pl bib === === reduce.pl bib === id = cord-265258-2rmtsyns author = Domanska‐Blicharz, K. title = Specific detection of GII‐1 lineage of infectious bronchitis virus date = 2017-07-03 pages = extension = .txt mime = text/plain words = 3393 sentences = 170 flesch = 53 summary = The real-time RT-PCR assays seem to be effective tools for IBV-type identification and although S1 coding region is prone to mutations, methods aimed in this gene detection has been recently developed and used for GI-1 (Mass, Connecticut), GI-9 (Arkansas), GI-11 (SAI), G1-16 (ASAII) and GIV-1 (DE072/GA98) lineages (Acevedo et al. Here, we describe the development of a TaqMan probe-based real-time RT-PCR for the detection of GII-1 (D1466-like) IBV lineage. Moreover, the assay developed in the present study showed to be highly specific as no fluorescent signals were detected with other tested IBV lineages or chicken RNA viral pathogens. In conclusion, the TaqMan probe-based real-time RT-PCR assay described here is a time-saving, specific, sensitive and reliable method of detection of GII-1 lineage (D1466-like) of IBV which could successfully replace standard nested RT-PCR. Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens cache = ./cache/cord-265258-2rmtsyns.txt txt = ./txt/cord-265258-2rmtsyns.txt === reduce.pl bib === === reduce.pl bib === id = cord-022940-atbjwpo5 author = nan title = Poster Sessions date = 2016-09-07 pages = extension = .txt mime = text/plain words = 241182 sentences = 12746 flesch = 47 summary = We have studied the effect of inhibition of IRE1 (inositol requiring enzyme 1), which is a central mediator of endoplasmic reticulum stress and controls cell proliferation and tumor growth, on hypoxic regulation of the expression of different proliferation related genes in U87 glioma cells. Transient inhibition of Akt and mTOR protein kinase activation in tumor cells followed by reactivation of signaling pathway did not result in a time-dependent difference on EGFR, HER2 and HER3 expression levels. In our study we aimed to determine cytotoxic effect of RES in K562 human CML cell line and to evaluate the expressions of miRNAs that are associated with genetics of leukemia after treatment with RES; to investigate target genes of miRNAs which show significant expression alterations and molecular mechanisms of RES treatment. cache = ./cache/cord-022940-atbjwpo5.txt txt = ./txt/cord-022940-atbjwpo5.txt === reduce.pl bib === id = cord-266036-qhlo99l7 author = Axell-House, Dierdre B. title = The Estimation of Diagnostic Accuracy of Tests for COVID-19: A Scoping Review date = 2020-08-31 pages = extension = .txt mime = text/plain words = 5760 sentences = 318 flesch = 47 summary = OBJECTIVES: To assess the methodologies used in the estimation of diagnostic accuracy of SARS-CoV-2 real-time reverse transcription polymerase chain reaction (rRT-PCR) and other nucleic acid amplification tests (NAATs) and to evaluate the quality and reliability of the studies employing those methods. After its emergence in December 2019, the virus now known as SARS-CoV-2 was identified and sequenced in early January 2020, 1 allowing for the rapid development of diagnostic testing based on the detection of viral nucleic acid (i.e., real-time reverse transcription polymerase chain reaction [rRT-PCR]). Articles were included if they met the following criteria on screening: 1) Peer-reviewed publication, 2) Study evaluated diagnostic test accuracy of NAAT, 3) Diagnostic test performed on ≥10 patients, 4) Diagnostic/Clinical sensitivity, specificity, other correlative statistics, or test positive rate were either identified by name or were included in the publication as a numerical value and we could reproduce the calculations. cache = ./cache/cord-266036-qhlo99l7.txt txt = ./txt/cord-266036-qhlo99l7.txt === reduce.pl bib === === reduce.pl bib === id = cord-264944-7xj27r98 author = Koopmans, Marion title = Optimization of extraction and PCR amplification of RNA extracts from paraffin-embedded tissue in different fixatives date = 1993-07-31 pages = extension = .txt mime = text/plain words = 5182 sentences = 255 flesch = 54 summary = The method was compared to existing extraction techniques by studying the quality of the templates for reverse-transcriptase polymerase chain reaction amplification (RT-PCR), using virus-infected and mock-infected paraffin-embedded cell pellets as a model. The method was compared to existing extraction techniques by studying the quality of the templates for rcvcrsetranscriptase polymerase chain reaction amplification (RT-PCR), using virusinfected and mock-infected paraffin-embedded cell pellets as a model. In the work reported here we used paraffin-embedded torovirus-infected cell pellets to compare the effect of different fixatives and RNA extraction methods on RT-PCR amplification of tissue extracts. cache = ./cache/cord-264944-7xj27r98.txt txt = ./txt/cord-264944-7xj27r98.txt === reduce.pl bib === id = cord-265268-5xu9hj2n author = Ahmed, W. title = Evaluation of Glass Wool Filters and Hollow-Fiber Ultrafiltration Concentration Methods for qPCR Detection of Human Adenoviruses and Polyomaviruses in River Water date = 2016-08-13 pages = extension = .txt mime = text/plain words = 4942 sentences = 271 flesch = 51 summary = title: Evaluation of Glass Wool Filters and Hollow-Fiber Ultrafiltration Concentration Methods for qPCR Detection of Human Adenoviruses and Polyomaviruses in River Water Here, we compared the recovery efficiencies of human adenoviruses (HAdVs) and human polyomaviruses (HPyVs) from 10-L river water samples seeded with raw human wastewater (100 and 10 mL) using hollow-fiber ultrafiltration (HFUF) and glass wool filter (GWF) methods. Little has been documented on the recovery efficiencies of HFUF and GWF methods for concentrating HAdVs and HPyVs markers from environmental water samples seeded with raw human wastewater. HFUF method recovered significantly higher concentration of HAdVs (P = 0.004; P = 0.003) and HPyVs (P = 0.01; P = 0.009) compared to GWF method for river water samples seeded with 100 and 10 mL of human wastewater, respectively. cache = ./cache/cord-265268-5xu9hj2n.txt txt = ./txt/cord-265268-5xu9hj2n.txt === reduce.pl bib === id = cord-264392-he1vekrt author = Lambeth, L. S. title = Complete genome sequence of Nariva virus, a rodent paramyxovirus date = 2008-12-23 pages = extension = .txt mime = text/plain words = 4363 sentences = 204 flesch = 52 summary = This study confirmed the classification of NarPV as a member of the subfamily Paramyxovirinae and established the close genome organization and sequence relationship between the two rodent paramyxoviruses isolated almost a decade apart and from two locations separated by more than 15,000 km. This was then followed by PCR to fill in the ''gaps'' using specific primers designed from NarPV Nariva virus genome 201 sequences obtained from the cDNA subtraction or degenerate primers designed using highly conserved consensus sequences of known paramyxoviruses in the subfamily Paramyxovirinae. Overall comparison of deduced sizes and amino acid sequences of all proteins indicated that NarPV is most closely related to MosPV (Table 1) genome is significantly larger (16,650 nt) than that of NarPV due to the longer untranslated regions (UTRs) located at the 3 0 end of most genes ( Fig. 1b and Table 1 ). cache = ./cache/cord-264392-he1vekrt.txt txt = ./txt/cord-264392-he1vekrt.txt === reduce.pl bib === id = cord-266466-5sgfx7oq author = Mansour, Amani title = First Case of an Infant with COVID-19 in the Middle East date = 2020-04-03 pages = extension = .txt mime = text/plain words = 1504 sentences = 97 flesch = 55 summary = Here, we report the case of a 16-month-old female infant from Lebanon who presented with fever and severe diarrhea and tested positive for COVID-19. Her RT-PCR test was negative after five days of treatment, suggesting that children can clear the virus faster than adults. Most severe illness occurs in older adults but comparison with the pediatric population can be challenging as documented cases in infants and children have been scarce [3, 4] . On day 5, the RT-PCR test of the infant was negative, and the patient's symptoms had resolved. Uniquely, our patient presented with fever and diarrhea; cough and other respiratory symptoms were not reported. Similarly, previous research in children indicates that the RT-PCR test becomes negative within 12 days (range: 6-22) after the presentation of symptoms [6] . This is the first case reported from the Middle East on an infant presenting with fever and diarrhea that tested positive for COVID-19. cache = ./cache/cord-266466-5sgfx7oq.txt txt = ./txt/cord-266466-5sgfx7oq.txt === reduce.pl bib === id = cord-266156-xmf4emln author = Miller, Tyler E. title = Clinical sensitivity and interpretation of PCR and serological COVID‐19 diagnostics for patients presenting to the hospital date = 2020-08-28 pages = extension = .txt mime = text/plain words = 4329 sentences = 221 flesch = 45 summary = Our goal was to examine the clinical sensitivity of two most common SARS‐CoV‐2 diagnostic test modalities, polymerase chain reaction (PCR) and serology, over the disease course to provide insight into their clinical interpretation in patients presenting to the hospital. The goal of this study is to examine the clinical sensitivity and provide insights into the interpretation of the two most common SARS-CoV-2 diagnostic test modalities: polymerase chain reaction (PCR) and serology. Serologic analysis of IgM, IgA and IgG status was performed in a subset of the above SARS-CoV-2 PCR-positive patients for which we had excess material in the MGH core laboratories for clinical validation studies. To assess the sensitivity of our serology assay over time, we tested for IgM, IgG, and IgA antibodies against the RBD of SARS-CoV-2 spike protein in 157 SARS-CoV-2 PCR-positive patients using an in-house ELISA (Table 1) . cache = ./cache/cord-266156-xmf4emln.txt txt = ./txt/cord-266156-xmf4emln.txt === reduce.pl bib === === reduce.pl bib === id = cord-266150-wox7pnkr author = Torres, Juan Pablo title = SARS-CoV-2 antibody prevalence in blood in a large school community subject to a Covid-19 outbreak: a cross-sectional study date = 2020-07-10 pages = extension = .txt mime = text/plain words = 4202 sentences = 222 flesch = 53 summary = Once these forms were signed, a copy was emailed to participants for their records and they were directed to a secure survey that i) asked basic demographic questions, ii) requested information on any previous RT-PCR test for SARS-CoV-2 and potential contact with any Covid-19 positive cases, and iii) asked about symptoms experienced since the outbreak (date and duration in days of each symptom). Among students, antibody positive children were younger, had a higher PCR positivity rate (in those who underwent PCR testing during the outbreak), and were more likely to self-report contact with one or more confirmed cases, as compared to seronegative children ( Table 2 ). Overall, PCR testing and contact history was significantly higher in staff compared to students, which in addition to the higher antibody positivity observed in this study, support the more significant role of adults within the outbreak, in proportion to the overall population. cache = ./cache/cord-266150-wox7pnkr.txt txt = ./txt/cord-266150-wox7pnkr.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-266670-jxgywvwx author = Wong, Mark title = Chapter 13 Recent Advances and Future Needs in Environmental Virology date = 2007-09-06 pages = extension = .txt mime = text/plain words = 5842 sentences = 333 flesch = 39 summary = The standard method of detection of viral pathogens in environmental samples uses assays in mammalian cell culture. The standard method of detection of viral pathogens in environmental samples uses assays in mammalian cell culture. When realtime PCR quantitative results for adenoviruses in environmental samples were compared with conventional cell culture results, it was concluded that the real-time PCR method demonstrated higher quantities of adenoviruses in comparison with conventional techniques. Detection of astroviruses, enteroviruses, and adenovirus types 40 and 41 in surface waters collected and evaluated by the information collection rule and an integrated cell culture-nested PCR procedure Application of Real-Time PCR and Tissue Culture Assay for Adenovirus Detection in Two Southern California Urban Rivers Rapid and quantitative detection of human adenovirus DNA by real-time PCR Use of cell culture-PCR assay based on combination of A549 and BGMK cell lines and molecular identification as a tool to monitor infectious adenoviruses and enteroviruses in river water cache = ./cache/cord-266670-jxgywvwx.txt txt = ./txt/cord-266670-jxgywvwx.txt === reduce.pl bib === id = cord-268094-ubz0q7e9 author = Curland, N. title = Investigation into diseases in free-ranging ring-necked pheasants (Phasianus colchicus) in northwestern Germany during population decline with special reference to infectious pathogens date = 2018-02-06 pages = extension = .txt mime = text/plain words = 8168 sentences = 451 flesch = 46 summary = title: Investigation into diseases in free-ranging ring-necked pheasants (Phasianus colchicus) in northwestern Germany during population decline with special reference to infectious pathogens In the present study, carcasses of 258 deceased free-ranging pheasants of different age groups, predominantly adult pheasants, collected over a period of 4 years in the states of Lower Saxony, North Rhine–Westphalia and Schleswig-Holstein, were examined pathomorphologically, parasitologically, virologically and bacteriologically, with a focus set on infectious pathogens. In China, antibodies against infectious bursal disease virus (IBDV) were detected in 14 out of 40 samples of free-ranging pheasants (Gu et al. The aim of the present study was to elucidate pathogens in free-ranging pheasants during the current population decline in Northwestern Germany using pathomorphological, virological, microbiological and parasitological investigations. Non-purulent mostly perivascularly accentuated inflammations with different cellular compositions and gradual variable infiltrations of lymphocytes, plasma cells and macrophages were detected in 68 birds (68.7% of affected pheasants) (Fig. 2) . cache = ./cache/cord-268094-ubz0q7e9.txt txt = ./txt/cord-268094-ubz0q7e9.txt === reduce.pl bib === === reduce.pl bib === id = cord-268468-036i1082 author = Asif, Muhammad title = The role of biosensors in COVID-19 outbreak date = 2020-09-18 pages = extension = .txt mime = text/plain words = 3204 sentences = 189 flesch = 43 summary = In this review, the importance of biosensors including electrochemical, surface enhanced Raman scattering, field-effect transistor and surface plasmon resonance biosensors in the detection of SARS-CoV-2 has been underscored. In this outbreak, three different types of diagnosis tests are being used including (i) chest CT scan along with clinical indications, (ii) RNA detection using RT-PCR assay and (iii) lateral flow assays, full automatic chemiluminescence method, enzyme-linked immunosorbent assay (ELISA) for the determination of antibodies [5] . In this review, we have summarized the biosensor based technologies which are able to detect SARS-CoV-2 effectively. The peptide monolayer was successfully coated on SPR biosensor and further functionalized with virus nucleocapsid protein which was finally able to detect SARS-CoV-2 antibodies at nanomolar level. The sensing aptitude of the biosensor was evaluated employing antigen protein, self-cultured virus, and nasopharyngeal swab samples taken from people infected with COVID-19 pneumonia. cache = ./cache/cord-268468-036i1082.txt txt = ./txt/cord-268468-036i1082.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-268567-2xoubkxb author = Samannodi, Mohammed title = Compliance with international guidelines in adults with encephalitis date = 2020-04-14 pages = extension = .txt mime = text/plain words = 3278 sentences = 192 flesch = 43 summary = In this study, we are evaluating the work up, management and outcome of 241 adults with encephalitis based on the majority of current guidelines recommendations in literature [11] [12] [13] [14] . As summarized in (Supplemental Digital Content Table 1 ), all guidelines of encephalitis management have major parts in evaluating and managing patients with encephalitis; exposure evaluation, appropriate utilization of diagnostic and neurodiagnostic studies, and proportion and timing of empirical antibiotic and antiviral therapy [11] [12] [13] [14] [15] . The Infectious Disease Society of America (IDSA), British, Australian, International consortium, and French guidelines recommend that clinicians evaluate for potential exposures and risk factors and to perform appropriate utilization of diagnostic studies in patients with suspected encephalitis. Also, most of the guidelines recommends to repeat CSF HSV PCR in 3-7 days in undiagnosed cases of encephalitis in which patients have clinical features or neuroimaging findings of HSV encephalitis [11] [12] [13] [14] . cache = ./cache/cord-268567-2xoubkxb.txt txt = ./txt/cord-268567-2xoubkxb.txt === reduce.pl bib === id = cord-268977-hcg2rrhl author = Feikin, Daniel R. title = Etiology and Incidence of Viral and Bacterial Acute Respiratory Illness among Older Children and Adults in Rural Western Kenya, 2007–2010 date = 2012-08-24 pages = extension = .txt mime = text/plain words = 6440 sentences = 402 flesch = 53 summary = METHODOLOGY/PRINCIPAL FINDINGS: From March 1, 2007, to February 28, 2010, among a surveillance population of 21,420 persons >5 years old in rural western Kenya, we collected blood for culture and malaria smears, nasopharyngeal and oropharyngeal swabs for quantitative real-time PCR for ten viruses and three atypical bacteria, and urine for pneumococcal antigen testing on outpatients and inpatients meeting a ARI case definition (cough or difficulty breathing or chest pain and temperature >38.0°C or oxygen saturation <90% or hospitalization). CONCLUSIONS/SIGNFICANCE: Vaccination against influenza and pneumococcus (by potential herd immunity from childhood vaccination or of HIV-infected adults) might prevent much of the substantial ARI incidence among persons >5 years old in similar rural African settings. Compared with other regions, the mortality rate among older children and adults remains several-fold higher in sub-Saharan Africa, where acute respiratory infections (ARI) are a leading cause of this high mortality, as well as associated morbidity [1] . cache = ./cache/cord-268977-hcg2rrhl.txt txt = ./txt/cord-268977-hcg2rrhl.txt === reduce.pl bib === id = cord-268817-wx96wwpg author = Karp, Donna Grace title = Sensitive and Specific Detection of SARS-CoV-2 Antibodies Using a High-Throughput, Fully Automated Liquid-Handling Robotic System date = 2020-08-20 pages = extension = .txt mime = text/plain words = 3600 sentences = 182 flesch = 47 summary = Here, we present an ultrasensitive and high-throughput automated liquid biopsy assay based on the Hamilton Microlab ADAP STAR automated liquid-handling platform, which was developed and validated for the qualitative detection of total antibodies against spike protein 1 (S1) of SARS-CoV-2 that uses as little as 4 µL of serum. 6 In this study, we report the development and validation of a highly sensitive and specific SARS-CoV-2 total antibody assay on a Hamilton MicroLab STAR liquid-handling platform (Fig. 1) , based on the ADAP STAR assay-ready workstation. The successful implementation of the automated high-throughput ADAP SARS-CoV-2 total antibody assay solution as described herein can help meet the surge in demand for COVID-19 infection testing. To evaluate the assay's sensitivity, 57 serum specimens from COVID-19 patients were subjected to the ADAP SARS-CoV-2 total antibody analysis. cache = ./cache/cord-268817-wx96wwpg.txt txt = ./txt/cord-268817-wx96wwpg.txt === reduce.pl bib === === reduce.pl bib === id = cord-268721-n6dsc4ig author = Pawlowski, Colin title = Inference from longitudinal laboratory tests characterizes temporal evolution of COVID-19-associated coagulopathy (CAC) date = 2020-08-17 pages = extension = .txt mime = text/plain words = 6967 sentences = 296 flesch = 41 summary = . Summary of lab tests significantly different between COVID pos and propensity score-matched COVID neg cohorts during at least one clinical time window. Conversely, platelet counts were lower in the COVID pos cohort at the time of clinical presentation but tended to increase over the subsequent 10 days to levels significantly higher than those in COVID neg patients (Cohen's D = 0.229, BH-adjusted Mann-Whitney p-value = 3.6e-3, Table 2, Figure 3B ). This approach offers the advantage of increased granularity at the cost of sample size per time point, but we did identify similar lab tests as altered in COVID pos patients using each approach including the fibrinogen decline and platelet increase in the COVID pos cohort after diagnosis ( Figure 4 ). Our study focusing on COVID-19 patients with longitudinal lab data suggests that COVID-19 is indeed associated with modulation of coagulation related parameters such as platelet counts, fibrinogen levels, and clotting time ( Figure 2) . cache = ./cache/cord-268721-n6dsc4ig.txt txt = ./txt/cord-268721-n6dsc4ig.txt === reduce.pl bib === id = cord-268455-btuzihsy author = de Santiago, Javier title = COVID-19: gynecologic cancer surgery at a single center in Madrid date = 2020-07-07 pages = extension = .txt mime = text/plain words = 2968 sentences = 170 flesch = 46 summary = The aim of this study was to evaluate surgical treatment of gynecological cancer patients during the COVID-19 outbreak in our center. During this period, the hospital was divided into two separate areas, independent of each other, assisting COVID-19 cases and at the same time allocating resources to surgical care, follow-up, or ongoing treatments of patients with cancer. Our study showed that we were able to safely manage 126 gynecological cancer surgeries in the COVID free zone during the pandemic, avoiding delays or cancellations. The number of low complexity surgeries with short hospital stays included in the study may have influenced the risk of postoperative contagion, and the fact that the PCR test before surgery was not performed in half of the patients due to low availability could have reduced the diagnosis of the infection. This study, conducted in a partial COVID-19 free hospital, showed that with adequate preventive and protective measures, cancer surgery was possible and did not significantly compromise patients or healthcare workers. cache = ./cache/cord-268455-btuzihsy.txt txt = ./txt/cord-268455-btuzihsy.txt === reduce.pl bib === id = cord-267671-ys43n672 author = Whary, Mark T. title = Biology and Diseases of Mice date = 2015-07-10 pages = extension = .txt mime = text/plain words = 63666 sentences = 3678 flesch = 40 summary = Clinical Signs MCMV causes subclinical infection in adult immunocompetent mice, but experimental inoculation of neonates can cause lethal disease due to multisystemic necrosis and inflammation. Diagnosis Because infected mice do not manifest signs or lesions and the virus is very difficult to propagate in cell culture, detection and diagnosis rely on serology and molecular methods. Differential Diagnosis Reovirus infection must be differentiated from other diarrheal diseases of infant mice, including those caused by mouse coronaviruses, EDIM virus, Salmonella spp., or Clostridium piliforme. Epizootiology EDIM virus appears to be infectious only for mice and occurs episodically in mouse colonies, and infection is probably widespread geographically (Livingston and Riley, 2003; Pritchett-Corning LABORATORY ANIMAL MEDICINE et al., 2009) . Sentinel mouse surveillance, using soiled bedding, is an effective strategy for detecting MNV (Manuel et al., 2008) Differential Diagnosis The mild change in fecal consistency associated with MNV in adult mice may mimic rotavirus, coronavirus, Helicobacter spp., Citrobacter rodentium, or other enteric diseases. cache = ./cache/cord-267671-ys43n672.txt txt = ./txt/cord-267671-ys43n672.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-269194-b1wlr3t7 author = Engstrom-Melnyk, Julia title = Chapter 5 Clinical Applications of Quantitative Real-Time PCR in Virology date = 2015-12-31 pages = extension = .txt mime = text/plain words = 12542 sentences = 501 flesch = 36 summary = Complementing serologic testing by detecting infections within the pre-seroconversion window period and infections with immunovariant viruses, real-time PCR provides a highly valuable tool for screening, diagnosing, or monitoring diseases, as well as evaluating medical and therapeutic decision points that allows for more timely predictions of therapeutic failures than traditional methods and, lastly, assessing cure rates following targeted therapies. Beyond this, quantitative real-time PCR facilitates advancements in the quality of diagnostics by driving consensus management guidelines following standardisation to improve patient outcomes, pushing for disease eradication with assays offering progressively lower limits of detection, and rapidly meeting medical needs in cases of emerging epidemic crises involving new pathogens that may result in significant health threats. With the development and administration of newer drugs that target specific biological processes of HIV, routine and clinical monitoring of viral loads using a real-time quantitative PCR assay continues to be critical to predict treatment failure and early emergence of drug resistance mutations, within a timeframe that would increase subsequent treatment success. cache = ./cache/cord-269194-b1wlr3t7.txt txt = ./txt/cord-269194-b1wlr3t7.txt === reduce.pl bib === id = cord-269726-z0frgm7s author = Gidari, Anna title = Is recurrence possible in coronavirus disease 2019 (COVID-19)? Case series and systematic review of literature date = 2020-10-10 pages = extension = .txt mime = text/plain words = 6678 sentences = 441 flesch = 54 summary = Criteria for patients' selection were diagnosis of SARS-CoV-2 infection [5] ; the subsequent meeting of criteria for hospital discharge (improvement of symptoms and two negative swabs collected at least 24 h apart) [4] ; and a positive respiratory sample collected after discharge. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) Statement protocol [8] , a systematic review has been performed concerning the patients with a diagnosis of COVID-19 that, after clinical and virological recovery, presented a new positive respiratory sample (swab, sputum, saliva, tracheal aspirate, or BAL). The patient was discharged in good clinical conditions with indication to repeat quarantine and swab tests that came negative for SARS-CoV-2 (Allplex™ 2019-nCoV Assay) on April 27 and 28 (Fig. 1b) . cache = ./cache/cord-269726-z0frgm7s.txt txt = ./txt/cord-269726-z0frgm7s.txt === reduce.pl bib === id = cord-270579-rf933a0y author = van Kruijssen, Alida M. title = Detection of respiratory pathogens by real-time PCR in children with clinical suspicion of pertussis date = 2006-12-20 pages = extension = .txt mime = text/plain words = 513 sentences = 33 flesch = 55 summary = title: Detection of respiratory pathogens by real-time PCR in children with clinical suspicion of pertussis The use of a multiplex respiratory real-time PCR in patients clinically suspected of pertussis increases the number of pathogens detected. Pathogens were detected by PCR in 31 out of 38 (82%) cases and 10 out of 21 (48%) cases in Group I and Group II, respectively. PCR can also give falsenegative results and fewer diagnoses in those patients with pertussis could be due to the quality of the sample. Other pathogens were detected in 31 out of 38 patients with clinical diagnosis of pertussis. Other pathogens that cause a pertussis-like disease have previously been described using serological assays and Cherry et al. pertussis and other pathogens causing pertussis-like symptoms and use of this form of diagnosis might help in treatment and improve management of patients. Evaluation of real-time PCR for detection of and discrimination between Bordetella pertussis, Bordetella parapertussis, and Bordetella holmesii for clinical diagnosis cache = ./cache/cord-270579-rf933a0y.txt txt = ./txt/cord-270579-rf933a0y.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-270929-utn21ce1 author = Wise, Annabel G. title = Molecular characterization of a novel coronavirus associated with epizootic catarrhal enteritis (ECE) in ferrets date = 2006-05-25 pages = extension = .txt mime = text/plain words = 6092 sentences = 336 flesch = 57 summary = Using consensus PCR assays for the genus Coronavirus, followed by additional genomic sequencing and phylogenetic analyses, we provide the first molecular evidence that the virus associated with ECE in ferrets is a new coronavirus, tentatively designated as "ferret enteric coronavirus" (FECV). Table 1 shows the sequence identities between the N protein of FECV-MSU1 and those of porcine transmissible gastroenteritis virus (TGEV), canine coronavirus (CCV), feline coronavirus (FCoV), porcine epidemic diarrhea virus (PEDV), human coronavirus (HCoV) 229E, bovine coronavirus (BCV), mouse hepatitis virus (MHV), HCoV OC43, SARS virus, avian infectious bronchitis virus (IBV), and turkey coronavirus (TCoV). As with the analysis of the N protein sequence, phylogenetic analyses based upon these three other regions of the genome gave similar results, further supporting the classification of FECV as a member of group 1 coronaviruses with highest similarities to CCV, FCoV, and TGEV and more distantly related to PEDV and HcoV 229E. cache = ./cache/cord-270929-utn21ce1.txt txt = ./txt/cord-270929-utn21ce1.txt === reduce.pl bib === id = cord-271130-6s79q1c1 author = Filoni, Claudia title = Putative progressive and abortive feline leukemia virus infection outcomes in captive jaguarundis (Puma yagouaroundi) date = 2017-11-17 pages = extension = .txt mime = text/plain words = 6584 sentences = 337 flesch = 47 summary = title: Putative progressive and abortive feline leukemia virus infection outcomes in captive jaguarundis (Puma yagouaroundi) Thus, the aim of this study was to perform additional serological and molecular tests and monitor the population of jaguarundis at FPZSP for FeLV infection and development of FeLV-related diseases for 5 years (2003) (2004) (2005) (2006) (2007) . Two captive-born male jaguarundis, the geriatric #1 and the mature adult #4, presented serological and molecular FeLV test results similar to the progressive FeLV infection outcome in domestic cats [25] . Moreover, consistent with findings in domestic cats with a progressive FeLV infection, no antibodies to FeLV antigens were detected in jaguarundis #1 and #4. Two captive-born jaguarundis, #2 and #22, presented test results similar to those reported for domestic cats with abortive FeLV infection and seroconversion as the only marker of FeLV exposure [28] . cache = ./cache/cord-271130-6s79q1c1.txt txt = ./txt/cord-271130-6s79q1c1.txt === reduce.pl bib === id = cord-005460-ezrn8cva author = nan title = Physicians – Poster Session date = 2017-07-28 pages = extension = .txt mime = text/plain words = 287105 sentences = 15681 flesch = 56 summary = Still the optimal combination of immunosuppressive agents with PTCy should be elucidated for different types of SCTs. We report the 2-year update of the prospective NCT02294552 single-center trial that evaluated risk-adapted graft-versushost disease (GVHD) prophylaxis with PTCy in related, unrelated and haploidentical SCTs. 200 adult patients (median age 32 y.o., range: 18-62) with hematologic malignancies, including AML (47.5%), ALL (26.5%), CML (10.5%), MDS (4%), and lymphomas (11.5%), were enrolled in the study. Long-term follow-up from the prospective randomized phase III multicenter trial comparing a standard GvHD prophylaxis with cyclosporine A and methotrexate with or without additional pretransplant ATLG (Grafalon, previously ATG-FRESENIUS S) (given 20 mg/kg/day, days − 3 to − 1) in unrelated donor hematopoietic cell transplantation after myeloablative conditioning resulted in a significant reduction of acute and chronic GvHD without compromising relapse rate and survival [1, 2, 3] . cache = ./cache/cord-005460-ezrn8cva.txt txt = ./txt/cord-005460-ezrn8cva.txt === reduce.pl bib === id = cord-270964-kxze0470 author = Lau, Kwok-Kwong title = Possible Central Nervous System Infection by SARS Coronavirus date = 2004-02-17 pages = extension = .txt mime = text/plain words = 1556 sentences = 93 flesch = 57 summary = On day 22 of illness, generalized tonic-clonic convulsion developed in a 32-year-old woman with severe acute respiratory syndrome (SARS). In our patient, the occurrence of generalized convulsion with a positive RT-PCR for SARS-CoV in the CSF suggests possible infection of the central nervous system by SARS-CoV. The findings from our patient are not compatible with multiple sclerosis, and the PCR result suggests that the central nervous system (CNS) is affected by SARS-CoV. The possibility also remains that infection of the CNS never occurred, as suggested by the lack of focal neurologic deficit, normal CSF pressure, cell count, and biochemistry. Besides involvement of the lungs and possibly the CNS, no good alternative explanation exists for acute renal failure in this patient. Renal failure could possibly be caused by SARS-CoV involving the kidneys. Additionally, our patient had diarrhea from day 3 to day 20, with positive RT-PCR for SARS-CoV in stool specimens, suggesting involvement of the gastrointestinal tract as well. cache = ./cache/cord-270964-kxze0470.txt txt = ./txt/cord-270964-kxze0470.txt === reduce.pl bib === id = cord-271341-fszljnax author = Lei, Pinggui title = COVID-19 Carrier or Pneumonia: Positive Real-Time Reverse-Transcriptase Polymerase Chain Reaction but Negative or Positive Chest CT Results date = 2020-05-06 pages = extension = .txt mime = text/plain words = 1011 sentences = 59 flesch = 43 summary = title: COVID-19 Carrier or Pneumonia: Positive Real-Time Reverse-Transcriptase Polymerase Chain Reaction but Negative or Positive Chest CT Results Dear Editor, We have read the articles published in the Korean Journal of Radiology with great interest concerning the real-time reverse-transcriptase polymerase chain reaction (rRT-PCR) amplification of the viral deoxyribonucleic acid (DNA) and chest computed tomography (CT) results for screening or detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (1, 2) . Based on the aforementioned situation, patients with positive rRT-PCR but negative chest CT results should be classified as SARS-CoV-2 carriers. To the Editor, Thank you for your comments on our online article focusing on the false-negative results of real-time reversetranscriptase polymerase chain reaction (rRT-PCR) and the possible complementary approaches for screening coronavirus disease 2019 (COVID-19). With the rapid and extensive spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), patients with positive rRT-PCR but negative chest CT results emerged. cache = ./cache/cord-271341-fszljnax.txt txt = ./txt/cord-271341-fszljnax.txt === reduce.pl bib === id = cord-271339-wt5o9sgm author = Chen, Chao-Ju title = Optimization of the CDC Protocol of Molecular Diagnosis of COVID-19 for Timely Diagnosis date = 2020-05-21 pages = extension = .txt mime = text/plain words = 2084 sentences = 122 flesch = 57 summary = The real-time reverse transcriptase polymerase chain was one of the most quickly established methods in the novel viral pandemic and was considered as the gold standard for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To ensure the whole process of the COVID-19 diagnostic testing took place without a problem, we simultaneously added primers and a probe of human RNase P gene (RP gene) as an internal control in the same well with the RdRp gene assay according to the protocol from the U.S. CDC [6] (Figure 3 ). In the present report, we demonstrated our experience of relying on a protocol template from the Taiwan CDC to establish an optimized COVID-19 molecular diagnostic test within our routine services in a public health emergency. cache = ./cache/cord-271339-wt5o9sgm.txt txt = ./txt/cord-271339-wt5o9sgm.txt === reduce.pl bib === id = cord-010119-t1x9gknd author = nan title = Abstract Presentations from the AABB Annual Meeting San Diego, CA ctober 7‐10, 2017 date = 2017-09-04 pages = extension = .txt mime = text/plain words = 230193 sentences = 13234 flesch = 55 summary = Conclusion: The wide distribution in the concentration of bioactive lipids among 405 stored RBC units suggests that lipid degradation is highly donor-Background/Case Studies: To ensure availability of biological products to hospitals, blood banks have developed and validated multiple storage conditions for each of their products to maximize shelf life and quality. 1 The Department of Blood Transfusion, The PLA General Hospital, 2 The Department of Blood Transfusion, Air Force General Hospital, PLA Background/Case Studies: Recently, multi researches have reported that longer term-stored red blood cells(RBCs) units were associated with increased risks of clinically adverse events, especially in critically ill patients. Weak D types 1, 2 and 3 express all the major RhD epitopes and these patients can be managed as RhD-positive, which may lead to a reduction in unnecessary Rh immunoglobulin (RhIG) administration and conservation of RhD-negative RBCs. Study Design/Method: RHD genotyping was performed on all patient samples with weaker than expected or discrepant RhD typing results, utilizing a commercially available genotyping kit manufactured by Immucor (RHD BeadChip). cache = ./cache/cord-010119-t1x9gknd.txt txt = ./txt/cord-010119-t1x9gknd.txt === reduce.pl bib === id = cord-271504-t3y1w9ef author = Luo, Zichao title = Combating the Coronavirus Pandemic: Early Detection, Medical Treatment, and a Concerted Effort by the Global Community date = 2020-06-16 pages = extension = .txt mime = text/plain words = 14361 sentences = 795 flesch = 42 summary = A confirmed case should have at least one of the following criteria: (i) a positive result for 2019-nCoV nucleic acid, using real-time PCR tests from respiratory or blood samples; (ii) a high homogeneity between viral gene sequencing from respiratory or blood samples and known 2019-nCoV; and (iii) serum samples positive for IgM or IgG to 2019-nCoV, or seroconversion in IgG, or a fourfold or more significant increase in IgG antibody titer to 2019-nCoV in the recovery phase than in the acute phase [25] . Using blood samples taken from alleged COVID-19 patients, the researchers detected antibodies targeting the spike protein that prevented the virus from killing cells in laboratory tests. showed a promising in vitro inhibitory effect of this serine protease inhibitor in SARS-CoV and 2019-nCoV on human lung cells, showing potential as a viable option for COVID-19 treatment [113] . Given that antiviral drugs have previously demonstrated reasonable inhibition of coronaviruses and therapeutic efficacy against coronavirus outbreaks, umifenovir, chloroquine, hydroxychloroquine, lopinavir-ritonavir, and ribavirin have been recommended in the latest guidelines for diagnosis and treatment of COVID-19, updated on 17 February 2020 [189] . cache = ./cache/cord-271504-t3y1w9ef.txt txt = ./txt/cord-271504-t3y1w9ef.txt === reduce.pl bib === === reduce.pl bib === id = cord-271669-dkg6229j author = Han, Seung Beom title = Respiratory Viral Infections in Children and Adolescents with Hematological Malignancies date = 2019-01-01 pages = extension = .txt mime = text/plain words = 3774 sentences = 213 flesch = 41 summary = Because these conventional methods have low sensitivity for detecting rhinovirus and enterovirus, which are the most common causes of community-acquired respiratory viral infection (RVI), RVI was identified only in 6-22% of immune compromised children with respiratory symptoms in the past. 7, 10, 19, 23, [25] [26] [27] Even in rhinovirus infection, which causes milder respiratory illnesses compared to those of RSV, parainfluenza virus and influenza virus, mortality was significantly higher in patients with LRIs than that in those with URIs. 26 Therefore, the early detection of patients at risk of progression to LRIs and early application of proper management for LRIs are necessary to improve the outcome of RVI in immune compromised patients. Considering the confirmed RVI diagnosis in half of the immune compromised children and adolescents with respiratory symptoms in this study, the introduction of multiplex PCR tests for RV detection in this population should be encouraged, especially for patients complaining of rhinorrhea or sputum prominent over a cough. cache = ./cache/cord-271669-dkg6229j.txt txt = ./txt/cord-271669-dkg6229j.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-272696-1jg46veg author = Tang, An title = Detection of Novel Coronavirus by RT-PCR in Stool Specimen from Asymptomatic Child, China date = 2020-06-17 pages = extension = .txt mime = text/plain words = 1724 sentences = 93 flesch = 55 summary = We collected nasopharyngeal swab and sputum samples from the boy 15 days after the last close contact and tested these specimens for SARS-CoV-2 by using RT-PCRs targeting the open reading frame lab (ORF1ab) and nucleoprotein gene regions (4) . The boy we report had close contact with confirmed COVID-19 case-patients on several occasions before he showed an equivocal RT-PCR result for respiratory specimens and subsequently positive results for stool specimens. We report an asymptomatic child who was positive for a coronavirus by reverse transcription PCR in a stool specimen 17 days after the last virus exposure. We report an asymptomatic child who was positive for a coronavirus by reverse transcription PCR in a stool specimen 17 days after the last virus exposure. Timeline for detection of novel coronavirus by RT-PCR in stool specimen from asymptomatic child, China cache = ./cache/cord-272696-1jg46veg.txt txt = ./txt/cord-272696-1jg46veg.txt === reduce.pl bib === id = cord-271920-1dzkgt6w author = Carpenter, Christopher R. title = Diagnosing COVID‐19 in the Emergency Department: A Scoping Review of Clinical Exam, Labs, Imaging Accuracy and Biases date = 2020-06-16 pages = extension = .txt mime = text/plain words = 7248 sentences = 523 flesch = 48 summary = 3 As waves of COVID-19 patients present to ED's in coming months with symptoms or potential exposures, understanding the diagnostic accuracy and reliability of history, physical exam, routine labs, advanced imaging, and an evolving array of COVID-19 diagnostics will be essential knowledge to inform the timing of testing, optimal specimen and test selection, shared decision-making, and ultimately derivation of clinical instruments to guide disposition, follow-up, and shared The search strategy used a combination of standardized terms and key words, including but not limited to (Covid-19 OR Novel Coronavirus OR SARS-COV-2) AND (diagnosis OR polymerase chain reaction OR serology OR CRISPR-CAS OR sensitivity/specificity) (Appendix). 40,42 It is known, however, that false negatives are frequent, so current recommendations advise incorporating patient's exposure risk, clinical signs and symptoms, routine lab and imaging findings, serology, and (when available) CT results into real-time determination of COVID-19 status. cache = ./cache/cord-271920-1dzkgt6w.txt txt = ./txt/cord-271920-1dzkgt6w.txt === reduce.pl bib === id = cord-273343-als886fe author = McClenahan, Shasta D. title = Discovery of a Bovine Enterovirus in Alpaca date = 2013-08-12 pages = extension = .txt mime = text/plain words = 4596 sentences = 214 flesch = 51 summary = A cytopathic virus was isolated using Madin-Darby bovine kidney (MDBK) cells from lung tissue of alpaca that died of a severe respiratory infection. To identify the virus, the infected cell culture supernatant was enriched for virus particles and a generic, PCR-based method was used to amplify potential viral sequences. The new alpaca virus sequence was most similar to recently designated Enterovirus species F, previously bovine enterovirus (BEVs), viruses that are globally prevalent in cattle, although they appear not to cause significant disease. Analysis of the full polyprotein and the individual capsid, 2A protease, 3C protease, and polymerase proteins of the alpaca-infecting virus relative to sequences of other representative enteroviruses from bovine EV-E (BEV-A serotypes 1-4) and EV-F (BEV-B serotypes 1-4), and sequences from three unclassified EV-F viruses [16] , two from bovine sources (AY724744 and AY724745) [20] , and one from a capped langur (JX538037) [21] , possum, porcine (PEV), and human (HEV) hosts. cache = ./cache/cord-273343-als886fe.txt txt = ./txt/cord-273343-als886fe.txt === reduce.pl bib === id = cord-273179-bpnak9ov author = Ma, Fen-lian title = Quantitative detection of human Malawi polyomavirus in nasopharyngeal aspirates, sera, and feces in Beijing, China, using real-time TaqMan-based PCR date = 2017-08-14 pages = extension = .txt mime = text/plain words = 4116 sentences = 218 flesch = 60 summary = METHODS: We used real-time TaqMan-based PCR to detect MWPyV in the feces (n = 174) of children with diarrhea, nasopharyngeal aspirates (n = 887) from children with respiratory infections, and sera (n = 200) from healthy adults, and analyzed its clinical characteristics statistically. Therefore, in this study, we used realtime qPCR and DNA sequencing to investigate the presence of MWPyV in fecal samples from 174 children with diarrhea, nasopharyngeal aspirate (NPA) samples from 887 children with acute respiratory tract infections (ARIs), and sera from 200 healthy adults in China. In brief, the analysis of 1261 clinical samples only detected MWPyV in respiratory and fecal specimens from children, suggesting that the establishment of the primary infection occurs at an early age, and that the gastrointestinal and respiratory tracts are sites of viral persistence. cache = ./cache/cord-273179-bpnak9ov.txt txt = ./txt/cord-273179-bpnak9ov.txt === reduce.pl bib === id = cord-273608-dxx3p1x5 author = Deng, Jikui title = Respiratory virus multiplex RT-PCR assay sensitivities and influence factors in hospitalized children with lower respiratory tract infections date = 2013-04-11 pages = extension = .txt mime = text/plain words = 3461 sentences = 187 flesch = 51 summary = Total nucleic acids were extracted using the EZ1 system (Qiagen, Germany) and 17 respiratory viruses and genotypes including influenza A virus (FluA), FluB, parainfluenza virus 1 (PIV1), PIV2, PIV3, PIV4, respiratory syncytial virus (RSV), human metapneumovirus (hMPV), rhinoviruses (RhV), enteroviruses (EnV), human bocaviruses (hBoV), adenoviruses (AdV), four coronaviruses (229E, OC43, NL63 and HKU1), and FluA 2009 pandemic H1N1(H1N1-p) were detected and identified by the ResPlex II kit. In this study, we evaluated the ResPlex II V2.0 kit (Qiagen, Germany), which uses a target enriched multiplexing RT-PCR amplification coupled with a suspension array detection, for detection and identification of a panel of respiratory specimens in pediatric inpatients with LRTIs. Clinical accuracy of the ResPlex II assay was validated on a panel of prospectively collected consecutive nasopharyngeal swab (NPS) specimens in comparison to viral culture and a monoplex real-time TaqMan RT-PCR. cache = ./cache/cord-273608-dxx3p1x5.txt txt = ./txt/cord-273608-dxx3p1x5.txt === reduce.pl bib === id = cord-272955-kkkrkgg1 author = Belsy, Acosta title = Molecular characterization of adenoviral infections in Cuba: report of an unusual association of species D adenoviruses with different clinical syndromes date = 2009-03-12 pages = extension = .txt mime = text/plain words = 4219 sentences = 233 flesch = 39 summary = title: Molecular characterization of adenoviral infections in Cuba: report of an unusual association of species D adenoviruses with different clinical syndromes The objectives of this study were to identify and characterize members of different adenovirus species at the molecular level and to describe the correlation between viruses and clinical syndromes during a period of 4 years. Four isolates from clinical materials obtained from patients with encephalitis, acute flaccid paralysis and meningoencephalitis were identified as belonging to the species Human adenovirus D. In the present report, the nested PCR method used was able to detect different HAdVs in clinical samples and supernatant culture with a sensitive internal control system to assure the quality of reaction conditions in each individual tube. Human adenovirus DNA was detected in the supernatant of a cell culture infected with viruses obtained from fecal specimens taken from a patient with acute flaccid paralysis (AFP), as well as in two cases of meningoencephalitis. cache = ./cache/cord-272955-kkkrkgg1.txt txt = ./txt/cord-272955-kkkrkgg1.txt === reduce.pl bib === id = cord-273840-jjm7y07m author = Vabret, Astrid title = Detection of the New Human Coronavirus HKU1: A Report of 6 Cases date = 2006-03-01 pages = extension = .txt mime = text/plain words = 3057 sentences = 168 flesch = 54 summary = The clinical presentation of these 6 patients was as follows: 3 were admitted to the hospital for acute enteric disease resulting in severe dehydration associated with upper respiratory symptoms; 1 had fever, otitis, and febrile seizure; 1 had a sample obtained to investigate failure to thrive; and 1 had a sample obtained for exploration of X-linked agammaglobulinemia and hyperleucocytosis. Our results suggest that HCoV-HKU1 could be associated with respiratory and enteric diseases, and its detection can be related to a persistent asymptomatic infection in patients with poor underlying conditions. For 2 patients with results positive for detection of HCoV-HKU1 in respiratory specimens, stool samples obtained at the same time were available and have been tested. To eliminate cell culture contamination, the N gene HCoV-HKU1 RT-PCR was performed directly on the respiratory specimens obtained from the 6 patients. Patient 6, who tested positive for HCoV-HKU1, had an influenza C virus detected in the same clinical specimen. cache = ./cache/cord-273840-jjm7y07m.txt txt = ./txt/cord-273840-jjm7y07m.txt === reduce.pl bib === id = cord-273829-t5cuop5c author = Görgülü, Özkan title = rRT-PCR Results of a Covid-19 Diagnosed Geriatric Patient date = 2020-10-17 pages = extension = .txt mime = text/plain words = 1482 sentences = 89 flesch = 52 summary = Therefore, the COVID-19 pandemic control and filiation evaluation with the rRT-PCR test may produce false negative results. Patient with positive Covid-19 IgM Rapid Test performed on May 19, 2020, was subjected to the rRT-PCR test, repeated twice on the 19th of May which also resulted in positive. The nucleic acid test functions as the gold standard method for confirming the SARS-COV-2 infection; however, some recent studies have detected false negative results of real-time reverse transcriptase polymerase chain reaction (rRT-PCR) [4] . Similar to our case, there are case reports of reverse transcription-polymerase chain reaction (RT-PCR) test initially false negative and later positive in the literature [11] . Therefore, it can be argued that COVID-19 pandemic control and filiation evaluation with the rRT-PCR test may produce false negative results. A case report of COVID-19 with false negative RT-PCR test: necessity of chest CT cache = ./cache/cord-273829-t5cuop5c.txt txt = ./txt/cord-273829-t5cuop5c.txt === reduce.pl bib === id = cord-273846-l0elcfe8 author = Ganapathy, Kannan title = Effects of cold storage on detection of avian infectious bronchitis virus in chicken carcasses and local antibodies in tracheal washes date = 2005-02-24 pages = extension = .txt mime = text/plain words = 2440 sentences = 134 flesch = 59 summary = title: Effects of cold storage on detection of avian infectious bronchitis virus in chicken carcasses and local antibodies in tracheal washes In order to test the survivability of infectious bronchitis virus (IBV) in dead chicken carcasses during 24 h of cold storage, 7 week-old specific-pathogen-free chickens were infected with virulent IBV Massachusetts strain M41, and were killed humanely 10 days later. Trachea, lung, kidney and rectum were collected for virus isolation by tracheal organ culture (TOC) or embryonated chicken eggs (ECE), and detection by nested reverse-transcriptase polymerase chain reaction (RT-PCR). Diagnosis of infectious bronchitis virus (IBV) is confirmed by isolation of the virus using either chicken embryonated eggs (ECE) or tracheal organ culture (TOC) and detection by reverse-transcriptase polymerase chain reaction (RT-PCR) (Cavanagh and Naqi, 2003; Gelb and Jackwood, 1998) . The use of chicken tracheal organ cultures for the isolation and assay of avian infectious bronchitis virus cache = ./cache/cord-273846-l0elcfe8.txt txt = ./txt/cord-273846-l0elcfe8.txt === reduce.pl bib === id = cord-005453-4057qib7 author = nan title = The 45th Annual Meeting of the European Society for Blood and Marrow Transplantation: Physicians – Poster Session date = 2019-07-03 pages = extension = .txt mime = text/plain words = 275771 sentences = 16876 flesch = 56 summary = To compare the safety and efficacy of prophylactic DLI for prevention of relapse after allogeneic peripheral blood stem cell transplantation from haploidentical donors (HID-SCT) and matched-sibling donors (MSD-SCT) in patients with very high-risk acute myeloid leukemia (AML), we performed a retrospective, observational cohort study enrolled in 21 HID-SCT and 13 MSD-SCT recipients. The aim of this study is to identify the prognostic impact of pre-transplant TIM3 levels on early and late transplant related complications as well as post-transplant relapse and survival Methods: A total of 177 hematopoietic stem cell transplantation (HSCT) recipients with an initial diagnosis of acute leukemia [median age: 36(16-66) years; male/ female: 111/66] were included in the study. cache = ./cache/cord-005453-4057qib7.txt txt = ./txt/cord-005453-4057qib7.txt === reduce.pl bib === id = cord-273859-tr4s5i7h author = Luis García Garmendia, José title = DETECCIÓN VIRAL Y RESPUESTA SEROLÓGICA EN PACIENTES CRÍTICOS INTUBADOS CON SARS-CoV-2. IMPLICACIONES PARA RETIRADA DE AISLAMIENTO date = 2020-04-29 pages = extension = .txt mime = text/plain words = 1379 sentences = 139 flesch = 61 summary = En las formas clínicas menos graves, la detección de ARN viral es máxima durante las dos primeras semanas desde el inicio de los síntomas(4), y a partir de los 7-10 días se produce respuesta inmunológica de IgM y después de IgG (5) . El CDC propone como una pauta segura la determinación de 2 rRT-PCR negativas consecutivas para valorar la necesidad de aislamiento de los pacientes con COVID-19 (8). A estos pacientes se les hicieron 2 determinaciones de rRT-PCR de Coronavirus a partir de 21 días del inicio de síntomas, separadas por 24 h, para comprobar si persistía eliminación del virus. La detección del ARN viral mediante técnicas de rRT-PCR parece ser una forma adecuada de determinar la necesidad de aislamiento de los pacientes con SARS-CoV-2(8, 12). Seguimiento de negativización de rRT-PCR a coronavirus en 10 pacientes críticos con SARS-CoV-2 bajo ventilación mecánica. Seguimiento de negativización de rRT-PCR a coronavirus en 10 pacientes críticos con SARS-CoV-2 bajo ventilación mecánica. cache = ./cache/cord-273859-tr4s5i7h.txt txt = ./txt/cord-273859-tr4s5i7h.txt === reduce.pl bib === id = cord-274289-8g9tuyrc author = Liang, Xiao title = Evaluation of Fast Technology Analysis (FTA) Cards as an improved method for specimen collection and shipment targeting viruses associated with Bovine Respiratory Disease Complex date = 2014-06-15 pages = extension = .txt mime = text/plain words = 3438 sentences = 139 flesch = 42 summary = The study assessed the stability of nucleic acids stored on FTA cards at a temperature range representing the extremes of environmental heat (13 • to 46 • C) and cold specimen handling conditions (−7 • to −27 • C), and a timeframe from specimen collection to laboratory processing consistent with the expected extremes of diagnostic sample shipping (7-14 days). Bovine Coronavirus was the most prevalent virus detected by realtime PCR during this phase of the study, with 60% animals testing Table 2 Kappa values (95% CI) and percentage agreement for specimens collected into viral transport media compared to specimens collected onto FTA Cards. Bovine Respiratory Syncytial virus was detected using both the specimens in viral transport media and those on FTA Cards for 100% agreement; however the realtime PCR positive test result was for only one animal (Tables 1 and 2) . cache = ./cache/cord-274289-8g9tuyrc.txt txt = ./txt/cord-274289-8g9tuyrc.txt === reduce.pl bib === id = cord-274184-hm516x6p author = Elli, Luca title = Endoscopy during the Covid-19 outbreak: experience and recommendations from a single center in a high-incidence scenario date = 2020-04-27 pages = extension = .txt mime = text/plain words = 4843 sentences = 280 flesch = 50 summary = From the abovementioned reasons we must deduce that: -in high SARS-CoV-2 incidence areas where PCR assays are not extensively performed, Covid-19 cannot be ruled out by simple clinical examination or epidemiological link; -the greatest amount of efforts and precautions are required to minimize the spread of the disease and to preserve medical staff from infection. In our current situation, which is characterized by high incidence of Covid-19 and relative scarcity of surveillance assays in asymptomatic subjects, for the abovementioned reasons we recommend different modalities of individual protection based on a strict clinical and epidemiological stratification of patients with potential SARS-CoV-2 infection undergoing endoscopic examination. In this setting, regardless of the classification of patients (high/low-risk, , in order to prevent the medical staff from becoming infected, we suggest high-performance personal protection equipment, i.e. a N95 or FFP2/FFP3 respirator, a hairnet, a double pair of gloves, a disposable waterproof surgical gown, a face shield (which we prefer because it allows to protect, and then spare, respirators) or goggles, and work safety clogs (Table 1) . cache = ./cache/cord-274184-hm516x6p.txt txt = ./txt/cord-274184-hm516x6p.txt === reduce.pl bib === id = cord-274438-tgslabi2 author = Schnee, Sarah Valerie title = Performance of the Alere i RSV assay for point-of-care detection of respiratory syncytial virus in children date = 2017-12-13 pages = extension = .txt mime = text/plain words = 3123 sentences = 210 flesch = 56 summary = title: Performance of the Alere i RSV assay for point-of-care detection of respiratory syncytial virus in children False negative Alere i RSV test results mostly occurred in samples with low viral load (mean CT value 31.1; CI(95) 29.6 – 32.6). Mann-Whitney-U-test was applied to compare C T values in samples with true positive versus false negative Alere i RSV result. In comparison to the RT-PCR reference standard, the Alere i RSV test result was true positive in 213 and true negative in 278 samples, respectively. The Alere i RSV performed well in the point-of-care setting, and sensitive test results were obtained across all pediatric age groups within 13 min. Evaluation of Alere i RSV for rapid detection of respiratory syncytial virus in children hospitalized with acute respiratory tract infection Host and viral factors affecting clinical performance of a rapid diagnostic test for respiratory Syncytial virus in hospitalized children cache = ./cache/cord-274438-tgslabi2.txt txt = ./txt/cord-274438-tgslabi2.txt === reduce.pl bib === id = cord-274128-kgtr77e7 author = Hochstetter, Axel title = Lab-on-a-Chip Technologies for the Single Cell Level: Separation, Analysis, and Diagnostics date = 2020-04-29 pages = extension = .txt mime = text/plain words = 14656 sentences = 748 flesch = 49 summary = Given the vast adaptability of microfluidics to any kind of single or multi-cellular assay [63] , the ability to combine it with various light microscopy techniques [64] , image processing [65] , optical or acoustic traps [53] , generation of chemical gradients [66] , and even cell culture [4, [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] , any cellular or subcellular target seems to be possible for future on-chip diagnostics. If the sample is in the continuous phase, we can separate the target cells either using deterministic lateral displacement (DLD), ratchets, dean-flow, di-electrophoresis, surface acoustic waves (SAW), optical and acoustic tweezers or by using optical density/refractive index. cache = ./cache/cord-274128-kgtr77e7.txt txt = ./txt/cord-274128-kgtr77e7.txt === reduce.pl bib === id = cord-274567-xd37wxxf author = Monpoeho, S. title = Application of a Real-Time Polymerase Chain Reaction with Internal Positive Control for Detection and Quantification of Enterovirus in Cerebrospinal Fluid date = 2002-07-13 pages = extension = .txt mime = text/plain words = 3284 sentences = 161 flesch = 47 summary = title: Application of a Real-Time Polymerase Chain Reaction with Internal Positive Control for Detection and Quantification of Enterovirus in Cerebrospinal Fluid A quantitative real-time reverse transcriptase-polymerase chain reaction (RT-PCR) method based on TaqMan technology was developed to determine the presence and amount of enterovirus RNA. Amplification of the internal positive control was effective in all but two specimens, confirming the absence of PCR inhibitors and allowing the results of amplification to be validated. Detection of EVs by amplification of viral RNA from CSF using reverse transcriptase-polymerase chain reaction (RT-PCR) assay has already been reported [4, 5, 6 ]. The fluorogenic RT-PCR was applied to detection of EVs in the CSF of 104 patients presenting with signs of meningitis. Amplicor enterovirus polymerase chain reaction in patients with aseptic meningitis: a sensitive test limited by amplification inhibitors Comparison of use of cerebrospinal fluid, serum, and throat swab specimens in diagnosis of enteroviral acute neurological infection by a rapid RNA detection PCR assay cache = ./cache/cord-274567-xd37wxxf.txt txt = ./txt/cord-274567-xd37wxxf.txt === reduce.pl bib === id = cord-274127-12x5cc8i author = Jeong, Ji Hun title = Comparison of sputum and nasopharyngeal swabs for detection of respiratory viruses date = 2014-05-06 pages = extension = .txt mime = text/plain words = 2721 sentences = 148 flesch = 49 summary = Paired specimens of nasopharyngeal swabs and sputum were obtained from 154 subjects, and RNA was extracted and tested for 16 different respiratory viruses using the Anyplex II RV16 Detection kit (Seegene, Seoul, Korea). The detection rates of respiratory viruses from sputum samples were significantly higher than those from nasopharyngeal swabs in adults using real‐time multiplex RT‐PCR. The aim of this study was to compare the detection rates of respiratory viruses in paired nasopharyngeal swabs and sputum samples from adult patients with respiratory symptoms using multiplex real-time RT-PCR. The present study found that the overall detection rate from sputum samples in adults was significantly higher than from nasopharyngeal swabs using multiplex real-time RT-PCR. In conclusion, the detection rates of respiratory viruses from sputum samples are significantly higher than those from nasopharyngeal swabs in adults using multiple real-time RT-PCR. cache = ./cache/cord-274127-12x5cc8i.txt txt = ./txt/cord-274127-12x5cc8i.txt === reduce.pl bib === id = cord-274676-wtizb7hk author = Lee, Seung-Hun title = Multilocus typing of Cryptosporidium spp. in young calves with diarrhea in Korea date = 2016-10-15 pages = extension = .txt mime = text/plain words = 4374 sentences = 272 flesch = 56 summary = Cryptosporidium prevalence was assessed by PCR and ELISA, and molecular characterization was performed by targeting the 18S rRNA, heat-shock protein 70 (hsp70), and glycoprotein 60 (gp60) genes. Previous studies using different methods found variable prevalence rates of Cryptosporidium in cattle: 49.4% (39/79) in Hungary using IFA (Plutzer and Karanis, 2007) , 11.9% (68/571) in the United States using PCR (Fayer et al., 2006) , 75.0% (60/80) in Japan using PCR (Karanis et al., 2010) , 20.0% (15/60) in New Zealand using IFA (Shrestha et al., 2014) , 5.1% (150/2945) in China using PCR (Zhang et al., 2015) , 21.5-22.5% in Ireland using direct fluorescence antibody testing (Mirhashemi et al., 2016) , and 10.2% (49/480) in Egypt using microscopy with staining (Ibrahim et al., 2016) . In addition, the PCR and ELISA results showed the same statistically significant differences with respect to the higher prevalence in the central region and lower prevalence in the case of hemorrhagic diarrhea. In addition, a higher prevalence at the farm level than the individual level was observed, regardless of the PCR or ELISA results, indicating a wide distribution of Cryptosporidium in calves in Korea. cache = ./cache/cord-274676-wtizb7hk.txt txt = ./txt/cord-274676-wtizb7hk.txt === reduce.pl bib === id = cord-274828-67yeag50 author = Dybkær, Karen title = Identification of acute myeloid leukemia patients with diminished expression of CD13 myeloid transcripts by competitive reverse transcription polymerase chain reaction (RT-PCR) date = 2000-04-21 pages = extension = .txt mime = text/plain words = 6048 sentences = 342 flesch = 50 summary = In this study we determine surface expression and transcript levels of CD13 within mononuclear cells originating from 40 AML patients with median blast percent of 90% and four healthy controls. Mononuclear cells of bone marrow aspirations from 40 AML patients and four healthy controls were analysed by competitive RT-PCR, and content of CD13 and GAPDH transcripts were determined. For the 32 AML patients and the four healthy controls having intermediate to high values of normalised CD13 transcripts levels there was a linear correlation between normalised CD13 transcript levels and cell surface expression of CD13 (r = 0.59, P B 0.001, n = 36). Such differences of up to 200-fold variation in normalised transcript levels were found only for AML patients having less than 15% surface expression of CD13 antigen. The diversity of normalised CD13 transcript levels found for patients with less than 15% CD13 antigen on the surface of their mononuclear cells was not caused by limitations of the competitive RT-PCR method. cache = ./cache/cord-274828-67yeag50.txt txt = ./txt/cord-274828-67yeag50.txt === reduce.pl bib === === reduce.pl bib === id = cord-274656-dngumjns author = Mori, Masahiro title = Detection of mumps virus RNA in cerebrospinal fluid of patients with neuromyelitis optica date = 2011-04-06 pages = extension = .txt mime = text/plain words = 1985 sentences = 112 flesch = 49 summary = To investigate the relationship between NMO and viruses that have special affinity for the central nervous system, we performed a nested polymerase chain reaction (PCR) to detect mumps virus or enterovirus RNA in cerebrospinal fluid samples from 13 patients with MS, 8 with NMO and 20 with other neurological diseases (ONDs). The aim of this study was to investigate using nested polymerase chain reaction (PCR) the relationship between NMO and the two causative agents of polio-like disease, mumps virus [9] and enteroviruses, which have specific affinity for the central nervous system. PCR tests for detection of the mumps virus and the enterovirus genomes CSF samples were tested for the presence of the mumps virus and enterovirus genomes by a nested PCR method (PCR-FMU), as described elsewhere [13, 14] , blindly with respect to clinical information and the results of NMO-IgG or anti-aquaporin-4 antibody assays. cache = ./cache/cord-274656-dngumjns.txt txt = ./txt/cord-274656-dngumjns.txt === reduce.pl bib === id = cord-274707-mxh38hwd author = Laureano, Ana Flávia Santarine title = The different tests for the diagnosis of COVID-19 - A review in Brazil so far date = 2020 pages = extension = .txt mime = text/plain words = 3736 sentences = 204 flesch = 50 summary = The virus is now widespread and causing the current pandemic of COVID-19, a highly pathogenic viral pneumonia, commonly presented with fever and cough, which frequently lead to lower respiratory tract disease with poor clinical outcomes associated with older age and underlying health conditions. Most rapid tests use colloidal gold particles in a technique known as immunochromatography, also called lateral flow immunoassay, a type of sandwich assay that relies on a pair of antibodies used to recognize two independent epitopes of a protein, and therefore it can achieve high specificity (Zhou et al., 2012) . One of the first rapid tests (lateral flow immunoassay) for SARS-CoV-2 IgG and IgM immune responses was developed by professor's Feng Ye group at the National Clinical Research Centre for Respiratory Disease in Guangzhou, China. Development and Clinical Application of A Rapid IgM-IgG Combined Antibody Test for SARS-CoV-2 Infection Diagnosis cache = ./cache/cord-274707-mxh38hwd.txt txt = ./txt/cord-274707-mxh38hwd.txt === reduce.pl bib === id = cord-274805-b3mqkfhh author = Onodera, Kenji title = Selection for 3′ end triplets for polymerase chain reaction primers date = 2004-12-31 pages = extension = .txt mime = text/plain words = 2271 sentences = 112 flesch = 58 summary = We analyzed 3′ end triplets of PCR primer sequences obtained from refereed journal articles, to test those recommendations and to make empirical recommendations for primer design. The frequencies of the 64 possible 3′end triplets among 2137 PCR primers from the VirOligo database were not uniformly distributed. The analysis results revealed preferred and disfavored 3 0 end triplets in successful primer sequences, and led to recommendations for primer design based on experience rather than theory. Since the primer sequence data set contained 134 BHV-1, 237 BVDV and 121 FMV primers, these viruses were used to test whether genome compositions determined the 3 0 end triplet frequencies. Low GCC contents in the 3 0 end triplets of PCR primers were not frequently reported in the VirOligo database. We suggest that primer design software incorporate scores based on empirical frequencies of 3 0 end triplets, such as those reported here, into the evaluation of oligonucleotides as primers. cache = ./cache/cord-274805-b3mqkfhh.txt txt = ./txt/cord-274805-b3mqkfhh.txt === reduce.pl bib === id = cord-274568-flqc3jjd author = Naguib, Michael title = The use of radiological imaging alongside reverse transcriptase PCR in diagnosing novel coronavirus disease 2019: a narrative review date = 2020-07-08 pages = extension = .txt mime = text/plain words = 2821 sentences = 148 flesch = 49 summary = Many studies have reported high sensitivities of CT scans and suggested that they can be used in the diagnosis of COVID-19 alongside reverse transcriptase PCR. In this report, we will discuss the clinical relevance of each test and the current Centers for Disease Control and Prevention and American College of Radiology recommendations regarding the use of imaging in the diagnosis of COVID-19. Sensitivity of CT scans • Many studies have reported high sensitivity of CT scans and suggested its valuable use in aiding the diagnosis of novel coronavirus disease 2019 (COVID-19) alongside reverse transcriptase PCR. • Centers for Disease Control & Prevention and the American College of Radiology recommend against the use of CT as well as CXR for diagnosis and that reverse transcriptase PCR is the reference test for diagnosing of COVID-19. Discusses the importance of background chest computed tomography (CT) being used for diagnosis of novel coronavirus disease 2019 (COVID-19) alongside reverse transcriptase PCR. cache = ./cache/cord-274568-flqc3jjd.txt txt = ./txt/cord-274568-flqc3jjd.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-275275-wy8d6cw3 author = Rovida, Francesca title = Molecular detection of gastrointestinal viral infections in hospitalized patients date = 2013-09-12 pages = extension = .txt mime = text/plain words = 2595 sentences = 143 flesch = 50 summary = During the period April 2011 to April 2012, 689 stool samples from as many patients hospitalized at the Fondazione IRCCS Policlinico San Matteo of Pavia exhibiting gastrointestinal syndromes were examined for the presence of rotavirus, norovirus, astrovirus, adenovirus, rhinovirus, enterovirus, parechovirus, bocavirus, coronavirus, sapovirus, cosavirus, and aichi virus using polymerase chain reaction assays. Viral pathogens causing acute gastroenteritis include Rotavirus (RV), members of the Caliciviridae family such as Norovirus (NoV) and Sapovirus (SaV), Adenovirus (HAdV) and Astrovirus (HAstV) (Eckardt and Baumgart, 2011) . Overall, 689 stool samples stored in the period April 2011 to April 2012 from as many patients (356 pediatrics and 333 adults) with gastrointestinal syndromes hospitalized at the Fondazione IRCCS Policlinico San Matteo of Pavia (a teaching and university hospital with 50,000 admissions, 2,500,000 outpatients visits, and 94,000 emergency consultations per year) were systematically examined for the presence of gastroenteric viruses. cache = ./cache/cord-275275-wy8d6cw3.txt txt = ./txt/cord-275275-wy8d6cw3.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-275787-5s442sy2 author = Banerjee, Arinjay title = Generation and Characterization of Eptesicus fuscus (Big brown bat) kidney cell lines immortalized using the Myotis polyomavirus large T-antigen date = 2016-09-14 pages = extension = .txt mime = text/plain words = 5817 sentences = 347 flesch = 57 summary = title: Generation and Characterization of Eptesicus fuscus (Big brown bat) kidney cell lines immortalized using the Myotis polyomavirus large T-antigen Here we describe a method to establish and immortalize big brown bat (Eptesicus fuscus) kidney (Efk3) cells using the Myotis polyomavirus T-antigen. Cell clones expressed interferon beta in response to poly(I:C) stimulation and supported the replication of four different viruses, namely, vesicular stomatitis virus (VSV), porcine epidemic diarrhea coronavirus (PED-CoV), Middle-East respiratory syndrome coronavirus (MERS-CoV) and herpes simplex virus (HSV). The parental cell line and clones were capable of expressing IFN beta and supported the replication of viruses such as vesicular stomatitis virus (VSV; family Rhabdoviridae, genus Vesiculovirus), herpes simplex virus (HSV; family Herpesviridae, subfamily Alphaherpesvirinae, genus Herpesvirus), PED-CoV and MERS-CoV. Bat kidney cells were immortalized by using ViaFect (Promega, USA) to transfect cells with either 2.5 g of pcDNA3 (Invitrogen, USA) empty vector or plasmids expressing either SV40 large T-antigen (SV40Tag) or Myotis polyomavirus large T-antigen (MyPVTag). cache = ./cache/cord-275787-5s442sy2.txt txt = ./txt/cord-275787-5s442sy2.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-276739-84vf5bts author = Sakurai, Akira title = Rapid typing of influenza viruses using super high-speed quantitative real-time PCR date = 2011-08-22 pages = extension = .txt mime = text/plain words = 3311 sentences = 182 flesch = 54 summary = Using SHRT-PCR, 86 strains of influenza viruses isolated by the Tokyo Metropolitan Institute of Public Health were tested; the results showed 100% sensitivity and specificity for each influenza A and B virus, and swine-origin influenza virus. This method offers high sensitivity and selectivity, but generally requires approximately 2 h per run; therefore, qRT-PCR is not appropriate for rapid virus detection or subtyping in outbreaks of fast-spreading and/or highly pathogenic viruses at public health centers, hospitals, airports, and other public transportation hubs. The commercial reaction mixture was from the qRT-PCR kit, RNA-Direct TM SYBR ® Green Real-time PCR Master Mix (Toyobo, Osaka, Japan; http://www.toyobo.co.jp/e/). The SHRT-PCR system detects the highly conserved sequence of the corresponding viral genome, and the newly designed primer sets targeted for typing MP segments do not exhibit any cross reactions among other influenza viruses (Table 5 ). cache = ./cache/cord-276739-84vf5bts.txt txt = ./txt/cord-276739-84vf5bts.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-277125-s11obc7w author = Kim, Hyeong Rae title = An integrated system of air sampling and simultaneous enrichment for rapid biosensing of airborne coronavirus and influenza virus date = 2020-09-26 pages = extension = .txt mime = text/plain words = 3925 sentences = 240 flesch = 66 summary = This study employed an electrostatic air sampler to capture aerosolized test viruses (human coronavirus 229E (HCoV-229E), influenza A virus subtype H1N1 (A/H1N1), and influenza A virus subtype H3N2 (A/H3N2)) in a continuously flowing liquid (aerosol-to-hydrosol (ATH) enrichment) and a concanavalin A (ConA)-coated magnetic particles (CMPs)-installed fluidic channel for simultaneous hydrosol-to-hydrosol (HTH) enrichment. Even though a liquid sample obtained via the ATH collection of virus particles of very low concentration in air is "non-detectable" in real-time qRT-PCR analysis, we demonstrate that subsequent HTH enrichment can cause a "non-detectable" sample to become "detectable." Human coronavirus 229E (HCoV-229E), Influenza A virus subtype H1N1 (A/H1N1), and Influenza A virus subtype H3N2 (A/H3N2) J o u r n a l P r e -p r o o f 6 were used as test viruses. cache = ./cache/cord-277125-s11obc7w.txt txt = ./txt/cord-277125-s11obc7w.txt === reduce.pl bib === id = cord-277057-ww41t4k2 author = Sakthivel, Senthilkumar K. title = Comparison of fast-track diagnostics respiratory pathogens multiplex real-time RT-PCR assay with in-house singleplex assays for comprehensive detection of human respiratory viruses() date = 2012-07-11 pages = extension = .txt mime = text/plain words = 4952 sentences = 226 flesch = 49 summary = title: Comparison of fast-track diagnostics respiratory pathogens multiplex real-time RT-PCR assay with in-house singleplex assays for comprehensive detection of human respiratory viruses() Individual FTDRP assays for adenovirus, respiratory syncytial virus and rhinovirus showed the lowest comparative sensitivities with in-house assays, with most discrepancies occurring with specimens containing low virus loads and failed to detect some rhinovirus strains, even when abundant. This study reports the results of a comparison of the FTDRP multiplex assay with a panel of validated in-house singleplex real-time RT-PCR assays developed at the Centers for Disease Control and Prevention (CDC). These included 26 laboratory reference virus strains and field isolates and 265 geographically (U.S., Central and South America and Africa) and compositionally diverse specimens [nasopharyngeal and oropharyngeal swabs (223), nasal washes and aspirates (21), sputum (1), lung autopsy tissue (1) and unidentified (19)] collected from children and adults with acute respiratory illnesses (ARIs) acquired between 2008 and 2011 and previously testing positive for respiratory viruses by the in-house singleplex assays. cache = ./cache/cord-277057-ww41t4k2.txt txt = ./txt/cord-277057-ww41t4k2.txt === reduce.pl bib === id = cord-277265-p8pns7r9 author = Malik, Yashpal Singh title = Biotechnological innovations in farm and pet animal disease diagnosis date = 2019-09-20 pages = extension = .txt mime = text/plain words = 7286 sentences = 346 flesch = 37 summary = However, utilizing the principles of ELISA and PCR, several serological and molecular technologies have been developed to achieve higher sensitivity, rapid, and point-of-care (POC) detection such as lateral flow assays, biosensors, loop-mediated isothermal amplification, recombinase polymerase amplification, and molecular platforms for field-level detection of animal pathogens. Since then, biotechnological applications have been making significant contributions in the development of novel powerful diagnostic assays for the efficient diagnosis and control of animal infectious diseases. Presently, molecular detection-based methods such as polymerase chain reaction (PCR) or its variants, and serological methods such as enzyme-linked immunosorbent assay (ELISA), are being used worldwide for the accurate diagnosis of many animal diseases. Although, yet not been adopted for animal disease diagnosis, but novel platforms such as smartphonebased diagnosis (which expands nucleic acid-based detection assays toward POCD) like RT-LAMP and fluorescent lateral flow immunoassay (already developed for Zika virus and Dengue virus) provide exciting opportunities for veterinary diagnostics in the near future (Rong et al., 2019) . cache = ./cache/cord-277265-p8pns7r9.txt txt = ./txt/cord-277265-p8pns7r9.txt === reduce.pl bib === id = cord-277357-lpurk7pe author = González-González, Everardo title = Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection date = 2020-08-13 pages = extension = .txt mime = text/plain words = 3999 sentences = 211 flesch = 49 summary = title: Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection Here, we demonstrate the use of the miniPCR, a commercial compact and portable PCR device recently available on the market, in combination with a commercial well-plate reader as a diagnostic system for detecting genetic material of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of COVID-19. Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection containing the amplification products of each one of three experiments, where the three different sets of primers (namely N1, N2, and N3) were used to amplify the same range of concentrations of template. Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection others), we observe differences in the performance of each primer pair. cache = ./cache/cord-277357-lpurk7pe.txt txt = ./txt/cord-277357-lpurk7pe.txt === reduce.pl bib === === reduce.pl bib === id = cord-277359-za2hh71g author = Chae, Kum Ju title = Positive conversion of COVID-19 after two consecutive negative RT-PCR results: A role of low-dose CT date = 2020-06-09 pages = extension = .txt mime = text/plain words = 600 sentences = 39 flesch = 61 summary = , and we would like to discuss a role of low-dose CT in discharge decision based on our recent experience regarding the positive conversion of COVID-19 after two consecutive negative RT-PCR results. In order to discharge patients from the hospital, most guidelines include no fever for more than 3 days, improvement of symptoms, and two consecutive negative real-time polymerase chain reaction (RT-PCR) test results [2] . The patient therefore met the criteria for hospital discharge (absence of fever or symptoms and two negative RT-PCR results) established by the Korea Centers for Disease J o u r n a l P r e -p r o o f Control and Prevention [5] ; however, follow-up LDCT prior to discharge revealed newly developed multifocal GGOs in the lower lobes, which led to cancelation of discharge. With continued treatment, the patient was discharged after two consecutive negative RT-PCR results and near complete resolution of her previous pneumonia without new lesions on LDCT (Figure 1) . cache = ./cache/cord-277359-za2hh71g.txt txt = ./txt/cord-277359-za2hh71g.txt === reduce.pl bib === id = cord-279101-c763gzq2 author = Xu, Sen title = Identification and characterization of a novel L-type lectin (MjLTL2) from kuruma shrimp (Marsupenaeus japonicus) date = 2020-01-13 pages = extension = .txt mime = text/plain words = 4797 sentences = 291 flesch = 56 summary = title: Identification and characterization of a novel L-type lectin (MjLTL2) from kuruma shrimp (Marsupenaeus japonicus) MjLTL2 was upregulated following challenge of shrimp with Vibrio anguillarum and white spot syndrome virus (WSSV). A novel L-type lectin is required for the multiplication of white spot syndrome virus (WSSV) in red swamp crayfish Procambarus clakii [12] . anguillarum-challenged shrimps were also analyzed, and results indicated that MjLTL2 expression is upregulated 24-48 h after WSSV injection in hemocytes and the hepatopancreas ( Fig. 4B and C) ; by comparison, MjLTL2 is upregulated 6-24 h after V. Shrimps were injected with WSSV after MjLTL2 silencing, followed by total RNA extraction from hemocytes at 36 and 48 hpi. Our results revealed lower VP19, VP24, VP26, and VP28 mRNA expression in the hemocytes of MjLTL2 knockdown shrimps than in the control. The results of this study revealed that expression of MjLTL2 was upregulated from 24 to 48 hpi in hemocytes and hepatopancreas after WSSV injection. cache = ./cache/cord-279101-c763gzq2.txt txt = ./txt/cord-279101-c763gzq2.txt === reduce.pl bib === id = cord-277838-931sco95 author = Erles, Kerstin title = Detection of a group 2 coronavirus in dogs with canine infectious respiratory disease date = 2003-06-05 pages = extension = .txt mime = text/plain words = 5077 sentences = 270 flesch = 60 summary = Sequence analysis of four positive samples showed the presence of a coronavirus with high similarity to both bovine and human coronavirus (strain OC43) in their polymerase and spike genes, whereas there was a low similarity to comparable genes in the enteric canine coronavirus. This investigation sought to detect coronaviruses associated with CIRD in a large kenneled dog population with a history of endemic respiratory disease, using virus culture and PCR techniques as well as serology on paired serum samples. Of the group of dogs which developed respiratory disease, 17 were positive for antibodies to CRCV on the day of entry into the kennel and 64 were negative. Furthermore, serological analysis revealed that dogs with antibodies to CRCV on the day of entry into the kennel developed respiratory disease less frequently than dogs RT-PCR results from tracheal and lung samples of 119 dogs with different respiratory signs (none to severe) using a nested PCR directed against the coronavirus spike gene. cache = ./cache/cord-277838-931sco95.txt txt = ./txt/cord-277838-931sco95.txt === reduce.pl bib === id = cord-278176-o9glkhyv author = Houng, Huo-Shu H title = Development and evaluation of an efficient 3′-noncoding region based SARS coronavirus (SARS-CoV) RT-PCR assay for detection of SARS-CoV infections date = 2004-09-01 pages = extension = .txt mime = text/plain words = 4782 sentences = 226 flesch = 54 summary = The SARS-CoV cDNA preparations derived from viral RNA extract and the cloned recombinant plasmid both exhibit the identical amplification characteristics, i.e. amplification efficacy using the same PCR formulation developed in this study. The 3′-NCR based SARS-CoV assay demonstrated 100% diagnostic specificity testing samples of patients with acute respiratory disease from a non-SARS epidemic region. It was demonstrated that the RT-PCR assay with 91% amplification efficiency could be used for consistent detect ion of the SARS-CoV viral RNA extracted from samples containing as little as 0.005 pfu per reaction with an anticipated C T value of 40 cycles (data not shown). It was demonstrated in this study that the cloned pHCV1 plasmid could be used to replace viral cDNA as a stable and rational SARS-CoV copy number standard for the SARS-CoV RT-PCR assay. Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays cache = ./cache/cord-278176-o9glkhyv.txt txt = ./txt/cord-278176-o9glkhyv.txt === reduce.pl bib === id = cord-279229-2226jnfl author = Savan, R title = Loop‐mediated isothermal amplification: an emerging technology for detection of fish and shellfish pathogens date = 2005-11-22 pages = extension = .txt mime = text/plain words = 4188 sentences = 230 flesch = 45 summary = In this paper, we review a novel method of DNA amplification known as loop-mediated isothermal amplification (LAMP) of a target nucleic acid. Screening for KHV has become very important as trade of fancy carp is an easy route for geographical spread of the virus and a rapid and efficient system like LAMP is very Figure 2 Loop-mediated isothermal amplification reaction amplifying the haemolysin gene from Edwardsiella tarda isolates. Rapid detection of a fish iridovirus using loop-mediated isothermal amplification (LAMP) Rapid diagnosis of Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease (PKD) in salmonid fish by a novel DNA amplification method, loop-mediated isothermal amplification (LAMP) Rapid diagnosis of herpes simplex virus infection by a loop-mediated isothermal amplification method A loop mediated isothermal amplification (LAMP) method for detection of infectious hematopoietic necrosis virus (IHNV) in rainbow trout (Oncorhynchus mykiss) Rapid diagnosis of human herpesvirus 6 infection by a novel DNA amplification method, loop-mediated isothermal amplification cache = ./cache/cord-279229-2226jnfl.txt txt = ./txt/cord-279229-2226jnfl.txt === reduce.pl bib === id = cord-279223-qvih5qas author = Hascoët, Jean-Michel title = Case Series of COVID-19 Asymptomatic Newborns With Possible Intrapartum Transmission of SARS-CoV-2 date = 2020-09-29 pages = extension = .txt mime = text/plain words = 3057 sentences = 165 flesch = 50 summary = Another mother exhibited infection 6 weeks pre-delivery, confirmed by nasopharyngeal swab testing with positive RT-PCR, and positive antibody detection (IgM and IgG). Two additional mothers exhibited infection confirmed by positive RT-PCR testing at 28and 31-days pre-delivery but did not present detectable antibody reaction at the time of delivery. Thus, although the mother was considered cleared at 6 weeks after the onset of infection, which was confirmed by negative nasopharyngeal and stool SARS-CoV-2 RT-PCR tests after delivery, we tested stool and pharynx swab samples from asymptomatic baby-girl D. Two additional babies and their mothers were tested at birth because the mothers had symptomatic infection, documented with positive SARS-CoV-2 RT-PCR results, at 28 and 31 days before delivery, respectively. Despite the first newborn was asymptomatic and the screening performed as part of routine systematic testing, SARS-CoV-2 RNA detection through early nasopharyngeal sampling and the persistent detection of virus in stool strongly suggest possible vertical maternofetal infection. cache = ./cache/cord-279223-qvih5qas.txt txt = ./txt/cord-279223-qvih5qas.txt === reduce.pl bib === id = cord-281653-zogtpm7a author = Thurman, Kathleen A. title = Detection of Mycoplasma pneumoniae, Chlamydia pneumoniae, and Legionella spp. in clinical specimens using a single-tube multiplex real-time PCR assay() date = 2011-03-11 pages = extension = .txt mime = text/plain words = 3307 sentences = 195 flesch = 45 summary = A multiplex real-time PCR assay for the detection of Mycoplasma pneumoniae (MP181), Chlamydia (Chlamydophila) pneumoniae (CP-Arg), Legionella spp. This procedure may allow for a practical and efficient means to test respiratory clinical specimens for atypical pneumonia agents in health care settings and facilitate an appropriate public health response to outbreaks. Specific real-time PCR assays have been developed to provide a more rapid and reliable method for detecting respiratory pathogens in clinical specimens (Apfalter et al., 2003; Hayden et al., 2001; Mitchell et al., 2009; Winchell et al., 2008) . The current study reports the development and evaluation of a multiplex real-time PCR assay for simultaneous detection of 3 atypical bacterial pneumonia-causing organisms in clinical specimens. The sensitivity observed when testing clinical specimens with the multiplex assay was found to be significantly greater in 2 agent-specific assays (CP-Arg and Pan-Leg) and the RNase P. Development of a multiplex real-time quantitative PCR assay to detect Chlamydia pneumoniae, Legionella pneumophila and Mycoplasma pneumoniae in respiratory tract secretions cache = ./cache/cord-281653-zogtpm7a.txt txt = ./txt/cord-281653-zogtpm7a.txt === reduce.pl bib === id = cord-278635-vwdxr1bl author = Świętoń, Edyta title = Low pathogenic avian influenza virus isolates with different levels of defective genome segments vary in pathogenicity and transmission efficiency date = 2020-08-28 pages = extension = .txt mime = text/plain words = 5432 sentences = 295 flesch = 48 summary = In the present study we compared the clinical outcome, mortality and transmission in chickens and turkeys infected with the same infectious doses of H7N7 low pathogenic avian influenza virus containing different levels of defective gene segments (95/95(DVG-high) and 95/95(DVG-low)). Virions containing highly deleted forms of genome segments (defective viral genes-DVGs) are able to replicate only in the presence and at the expense of fully infectious virus, hence the term "defective interfering particles" (DIPs) [4] . To evaluate the effect of DIPs on the course of infection with low pathogenic avian influenza virus (LPAIV), a comparison of pathogenicity of two virus stocks of H7N7 LPAIV with different levels of defective genomes was performed in turkeys and chickens. Infected birds received the same infectious dose of the virus but with different amount of DVGs. The semiquantitative analysis of defective particles was done by a combination of RT-PCR, real time RT-PCR and whole genome sequencing and indicated significantly higher amount of truncated gene segments in 95/95(DVG-high). cache = ./cache/cord-278635-vwdxr1bl.txt txt = ./txt/cord-278635-vwdxr1bl.txt === reduce.pl bib === id = cord-277909-rn1dow26 author = Gunson, R.N. title = Practical experience of high throughput real time PCR in the routine diagnostic virology setting date = 2006-02-07 pages = extension = .txt mime = text/plain words = 6853 sentences = 342 flesch = 54 summary = In comparison to traditional gel-based PCR assays, real time PCR offers increased sensitivity and specificity in a rapid format (turn around time from sample receipt to result <5 h). Most of the published real time probe based PCR assays for viral diagnosis utilise either molecular beacons or dual labelled probes although more recent publications tend to favour the use of dual labelled probes. In real time PCR, the signal is detected early in the amplification process, and therefore the end-point variation seen in gel-based assays does not affect the result. Despite this we still perform an initial optimisation of both primer and probe concentrations to ensure we are running our real time PCR assays at their most sensitive and efficient. Some manufacturers are now producing real time reaction mixes specifically designed for use with multiplex assays, and provide guidelines on the optimal primer and probe concentrations to use. cache = ./cache/cord-277909-rn1dow26.txt txt = ./txt/cord-277909-rn1dow26.txt === reduce.pl bib === id = cord-279644-g9cr9m96 author = Abedi Kiasari, Bahman title = Merkel cell polyomavirus DNA in immunocompetent and immunocompromised patients with respiratory disease date = 2011-10-19 pages = extension = .txt mime = text/plain words = 2469 sentences = 147 flesch = 55 summary = To determine the prevalence of MCPyV in 305 respiratory samples from immunocompetent and immunocompromised patients and evaluate their contribution to respiratory diseases, specimens were screened for MCPyV using single, multiplex, or real‐time PCR; co‐infection with other viruses was examined. The aim of this study was to determine the prevalence of MCPyV in respiratory specimens collected from immunocompetent and immunocompromised patients and evaluate the possible of contribution of the virus in respiratory disease alone, or in combination with other respiratory viruses. MCPyV DNA was found in 3.27% of nasopharyngeal aspirate samples obtained from patients with respiratory tract disease as determined by both PCR assays (LT and VP1). Although samples tested in this study were only collected during the autumn and winter months, there was no Sequence data from positive specimens showed that the MCPyV found in respiratory specimens was similar to the sequence of viruses identified within Merkel cell carcinomas by Feng et al. cache = ./cache/cord-279644-g9cr9m96.txt txt = ./txt/cord-279644-g9cr9m96.txt === reduce.pl bib === === reduce.pl bib === id = cord-280442-jtvez46y author = Wu, Xuan title = Simultaneous and visual detection of infectious bronchitis virus and Newcastle disease virus by multiple LAMP and lateral flow dipstick date = 2019-11-01 pages = extension = .txt mime = text/plain words = 5308 sentences = 271 flesch = 55 summary = To evaluate this novel detection method, PCR assays (including conventional RT-PCR, qRT-PCR and nRT-PCR) and reverse-transcription LAMP (RT-LAMP) monitored by electrophoresis were also conducted and the specificity and sensitivity of the assays were compared with those of the mRT-LAMP-LFD assay. A total of 13 IBV strains, 7 NDV strains, and the PCR and LAMP target sequences of 6 NDV and 1 turkey coronavirus strains (TCoV) synthesized by Sangon Biotech (Shanghai, China) Co, as well as 6 other avian virus strains, were used for the determination of the specificities of RT-PCR and RT-LAMP assays. Statistical significance difference studies showed that the mean detection rates of mRT-LAMP-LFD were significantly higher than that of conventional RT-PCR assays when detecting IBV or NDV alone (P < 0.05). The mean IBV and NDV detection rates of different samples, detected by mRT-LAMP-LFD, were both 95%, and were significantly higher than those detected by conventional RT-PCR and qRT-PCR (P < 0.05, Figure 6B) . cache = ./cache/cord-280442-jtvez46y.txt txt = ./txt/cord-280442-jtvez46y.txt === reduce.pl bib === id = cord-279577-iwqr2d0r author = Kaur, Taranjit title = Descriptive epidemiology of fatal respiratory outbreaks and detection of a human‐related metapneumovirus in wild chimpanzees (Pan troglodytes) at Mahale Mountains National Park, Western Tanzania date = 2008-06-11 pages = extension = .txt mime = text/plain words = 6210 sentences = 301 flesch = 49 summary = title: Descriptive epidemiology of fatal respiratory outbreaks and detection of a human‐related metapneumovirus in wild chimpanzees (Pan troglodytes) at Mahale Mountains National Park, Western Tanzania Here, we provide the descriptive epidemiology on respiratory outbreaks that were observed in 2003, 2005 and 2006 in the M-Group at MMNP, and present our findings that the probable causative agent responsible for the fatal 2006 illness is a human-related paramyxovirus. Also, shown is 2006 plus presumed cases, where nine additional chimpanzees, although not observed with clinical signs, have not been seen since the time of the outbreak as follows: one on May 25 (day -8), six on June 5 (day 3), one on June 6 (day 4) and one on June 28 (day 26); they are presumed dead possibly in association with the respiratory illness [Hanamura et al., 2008] . Clinical signs of respiratory illness were observed in all age groups of the M-Group chimpanzees consistent with those reported in humans infected with hMPV. cache = ./cache/cord-279577-iwqr2d0r.txt txt = ./txt/cord-279577-iwqr2d0r.txt === reduce.pl bib === id = cord-281871-3j64de2i author = Sinagra, G title = Viral presence guided immunomodulation in lymphocytic myocarditis: An update date = 2020-07-19 pages = extension = .txt mime = text/plain words = 2743 sentences = 143 flesch = 32 summary = In patients with lymphocytic myocarditis and heart failure (HF) with severe left ventricular dysfunction or lifethreatening ventricular arrhythmias who do not respond to conventional treatments in the short term (i.e. 7-10 days), EMB may guide more advanced medical therapy, including immunosuppression and immunomodulation 1 state, "Immunosuppression should be started only after ruling out active infection on EMB by PCR," and, "Immunosuppression may be considered, on an individual basis, in infection-negative lymphocytic myocarditis refractory to standard therapy in patients with no contraindications to Accepted Article immunosuppression." 4 Accordingly, the latest version of the Cochrane bank analysis 5 reports, "Corticosteroids may have a role in treating myocarditis without viral evidence." The same recommendations have been reaffirmed in recent reviews 1, 6, 7 , where different international experts highlight the need for ruling out viral presence in EMB via PCR analysis before starting immunosuppression or immunomodulation in clinically suspected acute myocarditis patients presenting life-threatening scenarios. cache = ./cache/cord-281871-3j64de2i.txt txt = ./txt/cord-281871-3j64de2i.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-277659-afysef1e author = Hamilton, F. title = Kinetics and performance of the Abbott Architect SARS-CoV-2 IgG antibody assay date = 2020-07-04 pages = extension = .txt mime = text/plain words = 3096 sentences = 203 flesch = 53 summary = Objectives: To assess the performance (sensitivity and specificity) of the Abbott Architect SARS-CoV-2 IgG antibody assay across three clinical settings. Methods: Antibody testing was performed on three clinical cohorts of COVID-19 disease: hospitalised patients with PCR confirmation, hospitalized patients with a clinical diagnosis but negative PCR, and symptomatic healthcare workers (HCWs). To assess the performance (sensitivity and specificity) of the Abbott Architect SARS-CoV-2 IgG antibody assay across three clinical settings. Antibody testing was performed on three clinical cohorts of COVID-19 disease: hospitalised patients with PCR confirmation, hospitalized patients with a clinical diagnosis but negative PCR, and symptomatic healthcare workers (HCW's). In this paper, we report the kinetics and performance of this assay in three populations: confirmed (PCR +ve) and suspected COVID-19 patients, confirmed (PCR +ve) healthcare workers, and pre-pandemic controls with respiratory infection. The sensitivity of the Abbott SARS-CoV-2 IgG assay was estimated with 95% Confidence Intervals at different time points post symptom onset (DISCOVER patients) or first PCR positive result (healthcare workers). cache = ./cache/cord-277659-afysef1e.txt txt = ./txt/cord-277659-afysef1e.txt === reduce.pl bib === id = cord-281529-2rec51xg author = Haagmans, Bart L title = Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation date = 2013-12-17 pages = extension = .txt mime = text/plain words = 4032 sentences = 205 flesch = 57 summary = We tested for the presence of MERS-CoV in dromedary camels from a farm in Qatar linked to two human cases of the infection in October, 2013. 13 Both MERS-CoV spike protein binding antibodies and virus neutralising antibodies were reported in dromedary camels from diff erent regions, including Oman and Egypt, but no virus shedding could be detected and, therefore, the signifi cance of these observations remained an issue of debate. The camel MERS-CoV clustered with viral sequences obtained from the two human cases related to the farm and with a sequence from Hafr-Al-Batin as the next closest relative (fi gure 1). However, virological testing was unable to detect MERS-CoV viral sequences in camels, probably because only faecal and serum samples were analysed. Our report describes the fi rst detection of MERS-CoV in dromedary camels on a farm in Qatar that had been linked to human cases of the disease. cache = ./cache/cord-281529-2rec51xg.txt txt = ./txt/cord-281529-2rec51xg.txt === reduce.pl bib === id = cord-281162-2pu7x5rj author = Etemadi, Mohammad Reza title = Diversity of respiratory viruses detected among hospitalized children with acute lower respiratory tract infections at Hospital Serdang, Malaysia date = 2019-03-22 pages = extension = .txt mime = text/plain words = 4902 sentences = 280 flesch = 49 summary = The aim of this study was to use conventional and molecular detection methods to assess the epidemiology of respiratory viral infections in children less than five years of age that were hospitalized with ALRTIs. Methods: The cross-sectional study was designed to investigate the occurrence of respiratory viruses including respiratory syncytisl virus (RSV), human metapneumovirus (HMPV), influenza virus A and B (IFV-A and B), parainfluenzavirus 1, 2, 3 and 4 (PIV 1, 2, 3 and 4), human rhinoviruses (HRV), human enterovirus (HEV), human coronaviruses (HCoV) 229E and OC43, human bocavirus (HBoV) and human adenovirus (HAdV) in hospitalized children with ALRTIs, at Hospital Serdang, Malaysia, from June 16 to December 21, 2009. cache = ./cache/cord-281162-2pu7x5rj.txt txt = ./txt/cord-281162-2pu7x5rj.txt === reduce.pl bib === id = cord-281844-c0uhcatg author = Costa, Lusmaia D.C. title = Exacerbation of asthma and airway infection: is the virus the villain? date = 2014-12-31 pages = extension = .txt mime = text/plain words = 6547 sentences = 351 flesch = 45 summary = Abstract Objective To review the available literature on the association between acute viral respiratory tract infection and the onset of asthma exacerbations, identifying the most prevalent viruses, detection methods, as well as preventive and therapeutic aspects. Studies using reverse transcriptase polymerase chain reaction (RT-PCR) as the detection technique, isolated or combined with traditional methods, observed positivity for respiratory viruses in up to 92.2% of episodes of acute asthma exacerbation in children. Several authors have performed studies aiming to detect viruses in respiratory secretions of exacerbated asthma patients, showing a prevalence of viral identification that varies with several factors, such as patient age, time of the year, method of sample collection, and method of viral detection. The use of viral detection techniques with high sensitivity and specificity has increased the identification of some respiratory viruses in children with asthma exacerbation. cache = ./cache/cord-281844-c0uhcatg.txt txt = ./txt/cord-281844-c0uhcatg.txt === reduce.pl bib === id = cord-278833-wlhmcdcn author = Rutschke, Nils title = Hot start reverse transcriptase: an approach for improved real-time RT-PCR performance date = 2015-06-21 pages = extension = .txt mime = text/plain words = 2280 sentences = 134 flesch = 59 summary = FINDINGS: The hot start effect was investigated in a one-step real-time RT-PCR assay for the detection of Middle East respiratory syndrome coronavirus (MERS-CoV). CONCLUSIONS: The study demonstrates the potential of aptamer-dependent hot start RT for the improvement of diagnostic real-time RT-PCR assays. In the present study, the aptamer was analyzed in a one-step real-time RT-PCR assay for the detection of Middle East respiratory syndrome coronavirus (MERS-CoV) to investigate the potential of a hot start RT for improved real-time RT-PCR performance. The one-step real-time RT-PCR was performed in a 25-μL reaction mix containing 10 μL of RNA template, 1x PCR reaction buffer (altona Diagnostics GmbH), 2.4 mM MgCl 2 (Sigma-Aldrich), 240 μg/μL BSA (Roche), 1 U of Platinum® Taq DNA Polymerase high fidelity (Invitrogen), 156 U of SuperScript® III Reverse Transcriptase (Invitrogen). The analytic sensitivity was determined by analyzing a half-logarithmic serial dilution Table 1 Hit rate of 25 μM aptamer and without aptamer in real-time RT-PCR MERS-CoV assay. cache = ./cache/cord-278833-wlhmcdcn.txt txt = ./txt/cord-278833-wlhmcdcn.txt === reduce.pl bib === id = cord-280865-shwxhak9 author = Zhang, Dan title = Clinical evaluation of a panel of multiplex quantitative real-time reverse transcription polymerase chain reaction assays for the detection of 16 respiratory viruses associated with community-acquired pneumonia date = 2018-06-30 pages = extension = .txt mime = text/plain words = 2547 sentences = 118 flesch = 51 summary = title: Clinical evaluation of a panel of multiplex quantitative real-time reverse transcription polymerase chain reaction assays for the detection of 16 respiratory viruses associated with community-acquired pneumonia We developed a panel of multiplex quantitative real-time reverse transcription polymerase chain reaction (mqRT-PCR) assay consisting of seven internally controlled qRT-PCR assays to detect 16 different respiratory viruses. Given that the laboratories from all of the provincial and most municipal CDC laboratories in China have access to conventional real-time PCR instrumentation, in this study, we aimed to develop a multiplex quantitative real-time RT-PCR (mqRT-PCR) consisting of a panel of seven internally controlled qRT-PCR assays to detect 16 different respiratory viruses: human coronavirus (CoV) 229E, CoV NL63, CoV OC43, CoVHKU1, parainfluenza virus (PIV)1, PIV2, PIV3, PIV4, influenza virus (IV) types A and B, human respiratory syncytial virus (RSV) types A and B, human rhinovirus (HRV), human metapneumovirus (HMPV), human adenovirus (ADV), and human bocavirus (HBoV). cache = ./cache/cord-280865-shwxhak9.txt txt = ./txt/cord-280865-shwxhak9.txt === reduce.pl bib === id = cord-279551-py2awuav author = Willi, Barbara title = Clinical and molecular investigation of a canine distemper outbreak and vector-borne infections in a group of rescue dogs imported from Hungary to Switzerland date = 2015-07-16 pages = extension = .txt mime = text/plain words = 6264 sentences = 315 flesch = 53 summary = title: Clinical and molecular investigation of a canine distemper outbreak and vector-borne infections in a group of rescue dogs imported from Hungary to Switzerland In the present study, we describe a distemper outbreak in 15 rescue dogs that were imported from Hungary to Switzerland by an animal welfare organisation. Canine distemper virus (CDV) is one of the most important viral pathogens in domestic dogs and causes high morbidity and mortality worldwide, particularly in unvaccinated dogs or dogs with incomplete vaccination [1] . The study provides data on vaccination, medical history, clinical examinations and diagnostic imaging of the dogs and CDV testing, testing for canine parvovirus (CPV) and vector-borne infections. The vaccine-specific real-time reverse transcription (RT)quantitative (q)PCR was negative for all ten dogs that were tested, which supports the finding of infection with a wild-type CDV strain. cache = ./cache/cord-279551-py2awuav.txt txt = ./txt/cord-279551-py2awuav.txt === reduce.pl bib === id = cord-277804-ujabzic4 author = Yuk, Seong-su title = Comparison between dot-immunoblotting assay and clinical sign determination method for quantifying avian infectious bronchitis virus vaccine by titration in embryonated eggs date = 2016-01-21 pages = extension = .txt mime = text/plain words = 4146 sentences = 202 flesch = 53 summary = title: Comparison between dot-immunoblotting assay and clinical sign determination method for quantifying avian infectious bronchitis virus vaccine by titration in embryonated eggs In this study, we used a dot-immunoblotting assay (DIA) to measure the titers of IBV vaccines that originated from different pathogenic strains or attenuation methods in embryonated eggs, and we compared this assay to the currently used method, clinical sign evaluation. The aim of this study was to evaluate and compare the sensitivity and specificity of the DIA to the clinical sign determination method for detecting IBV in inoculated embryonated eggs during titration of IBV vaccines. Propagation of the inoculated virus was determined using real-time RT-PCR, DIA, and the EE index method, and the 50% egg infectious dose (EID 50 ) of the five vaccines was calculated based on the method of Reed and Muench (1938) . cache = ./cache/cord-277804-ujabzic4.txt txt = ./txt/cord-277804-ujabzic4.txt === reduce.pl bib === id = cord-282321-svoshzz8 author = Eboigbodin, Kevin title = Reverse transcription strand invasion based amplification (RT-SIBA): a method for rapid detection of influenza A and B date = 2016-04-11 pages = extension = .txt mime = text/plain words = 4409 sentences = 217 flesch = 48 summary = The RT-SIBA method includes a reverse transcriptase enzyme that allows one-step reverse transcription of RNA to complementary DNA (cDNA) and simultaneous amplification and detection of the cDNA by SIBA under isothermal reaction conditions. The RT-SIBA method includes a reverse transcriptase enzyme that allows a one-step reverse transcription of RNA to cDNA and simultaneous amplification and detection of the cDNA with SIBA under isothermal reaction conditions. The use of an Influenza A assay IO with no seeding region resulted in reactions with the longest detection time, suggesting that the seeding region is of vital importance for efficient amplification of the target DNA. The recombinasemediated target duplex separation and polymerase-mediated extension are the basis for exponential amplification conclusion, IOs for both influenza A and B assays used in the following experiments were designed to contain seeding regions consisting of a polyC sequence of 10 and 14 nucleotides in length, respectively. cache = ./cache/cord-282321-svoshzz8.txt txt = ./txt/cord-282321-svoshzz8.txt === reduce.pl bib === id = cord-281887-b511bjdy author = Ribeiro, Reitan title = Perioperative Cancer Care in the Context of Limited Resources during the COVID-19 Pandemic: Brazilian Society of Surgical Oncology Recommendations date = 2020-09-26 pages = extension = .txt mime = text/plain words = 4739 sentences = 234 flesch = 45 summary = DISCUSSION: The rational use of resources to reduce the risk of surgical cancer patients being operated on during the incubation period of a corona virus infection is important in this context. CONCLUSIONS: We present a protocol, focused on the patients' outcomes, for safe and rational use of resources to reduce the risk of surgical cancer patients being operated on during the virus incubation period, in the context of areas with limited resources. Our objective was to present the Brazilian Society of Surgical Oncology (BSSO) protocol for rational use of resources and for reducing the risk of surgical cancer patients being operated on during the coronavirus incubation period, in the context of areas with limited resources, and focused on patient outcomes. In light of all the previous considerations, Table 3 presents our suggested protocol for the rational use of resources to reduce the risk of surgical cancer patients from being operated on during the COVID-19 incubation period, in the context of areas with limited resources. cache = ./cache/cord-281887-b511bjdy.txt txt = ./txt/cord-281887-b511bjdy.txt === reduce.pl bib === id = cord-279576-wt4crton author = Fajardo, Álvaro title = Evaluation Of SYBR Green Real Time PCR For Detecting SARS-CoV-2 From Clinical Samples date = 2020-05-13 pages = extension = .txt mime = text/plain words = 4842 sentences = 263 flesch = 54 summary = Several methods based on real time reverse transcription polymerase chain reaction (RT-qPCR) for the detection of SARS-CoV-2 genomic RNA have been developed. The aim of the study was to set up an alternative molecular protocol to detect SARS-CoV-2 from clinical samples, without the need of TaqMan probes or post-PCR steps (i.e. gel electrophoresis), which can be implemented in case of difficulties to get specific reagents or kits because of the current pandemic situation. In order to select an appropriate amount of control vector to use in the comparison between the two real time qPCR methods, we prepared plasmids dilutions (107, 106, 105 and 104 copies/μL) and assayed them following both protocols: the probe-based One Step RT-qPCR developed by the University of Hong Kong Poon et al. The amplification data for the SYBR Green-based qPCR protocol showed that the ORF1b-nsp14 region was correctly amplified for all SARS-CoV-2 positive samples (1 to 7) (Fig. 3) . cache = ./cache/cord-279576-wt4crton.txt txt = ./txt/cord-279576-wt4crton.txt === reduce.pl bib === id = cord-280846-bbv6f5gf author = Greninger, Alexander L. title = A Metagenomic Analysis of Pandemic Influenza A (2009 H1N1) Infection in Patients from North America date = 2010-10-18 pages = extension = .txt mime = text/plain words = 8023 sentences = 327 flesch = 44 summary = To determine whether a pan-viral microarray assay was capable of identifying novel 2009 H1N1 in the absence of a priori sequence information, we used the Virochip to comprehensively screen for viruses in 29 nasopharyngeal swab samples from individuals with influenza-like illness. To further characterize the metagenomics of 2009 H1N1 infection in humans, we labeled the 17 influenza samples positive for 2009 H1N1 by Virochip with distinct molecular barcodes and analyzed them by paired-end deep sequencing on three lanes of an Illumina Genome Analyzer IIx. After trimming reads to remove barcodes and exclude low-complexity or primer sequences, 11,427,212 high-quality 60-bp sequence reads were subjected to an iterative BLASTN analysis pipeline (Fig. 1B) . After stratifying by originating location and corresponding method of sample processing (pre-DNase and/or post-DNase treatment), the percentage of total reads aligning to influenza was linearly correlated with calculated viral titers by realtime quantitative RT-PCR for sites in the United States (California) and Canada but not in Mexico (Fig. 5A ). cache = ./cache/cord-280846-bbv6f5gf.txt txt = ./txt/cord-280846-bbv6f5gf.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-279980-49yv65gm author = WANARATANA, S. title = The potential of house flies to act as a vector of avian influenza subtype H5N1 under experimental conditions date = 2010-12-01 pages = extension = .txt mime = text/plain words = 4317 sentences = 240 flesch = 58 summary = The objective of the present study was to determine the potential for house flies (Musca domestica L.) (Diptera: Muscidae) to harbour the avian influenza (AI) H5N1 virus. Before initiation of all experiments the adult stage flies were randomly selected and confirmed to be free of the AI H5N1 virus by the real-time reverse transcription-polymerase chain reaction (RRT-PCR) assay using specific primers and probes to the influenza A matrix (M) gene. The BHI washing fluid (W1) was inoculated into six 10-day-old embryonated chicken eggs to evaluate the presence of the AI H5N1 virus on the external surface of the house flies. The W2 washing fluid was inoculated into six 10-dayold embryonated chicken eggs to confirm the absence of the AI H5N1 virus on the external surface of house flies. Avian influenza (AI) H5N1 virus titre between house fly homogenates and W1 of the AI H5N1 virus exposed house flies at different times of post-exposure in embryonated chicken eggs. cache = ./cache/cord-279980-49yv65gm.txt txt = ./txt/cord-279980-49yv65gm.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-283309-ovx5fzsg author = Yang, Yong-Le title = Characterization of a novel bat-HKU2-like swine enteric alphacoronavirus (SeACoV) infection in cultured cells and development of a SeACoV infectious clone date = 2019-08-09 pages = extension = .txt mime = text/plain words = 5422 sentences = 271 flesch = 52 summary = Six subgenomic mRNAs containing the leader-body junction sites, including a bicistronic mRNA encoding the accessory NS7a and NS7b genes, were experimentally identified in SeACoV-infected cells. Anti-Ac (Nsp3) staining also resulted in detection of perinuclear foci at four time points, indicating localization to the viral replication-transcription complexes (Fig. 1C) , which was similar to the pattern of Nsp3 antibody observed in SARS-CoV-infected Vero cells (Prentice et al., 2004) . DMVs are membrane structures where viral genomic RNA is recognized by the host cell machinery and translated into non-structural proteins (ORF1ab), assembling into viral replication-transcription complexes (Gosert et al., 2002) , whereas LVCVs are large circular organelles that are thought to originate from Golgi compartments expanding to accommodate numerous precursor virions Positions of forward (LF) and reverse primers (S1-R, sgORF3-R, sgE-R, sgM-R, sgN-R and NS7a-R/NS7-R) used for PCR amplification of distinct subgenomic mRNAs (sgRNAs) are indicated by arrows under the genome. cache = ./cache/cord-283309-ovx5fzsg.txt txt = ./txt/cord-283309-ovx5fzsg.txt === reduce.pl bib === id = cord-283409-ynwgdz52 author = Baggett, Travis P. title = Clinical Outcomes, Costs, and Cost-effectiveness of Strategies for People Experiencing Sheltered Homelessness During the COVID-19 Pandemic date = 2020-10-20 pages = extension = .txt mime = text/plain words = 1741 sentences = 111 flesch = 44 summary = INTERVENTIONS: We assessed daily symptom screening with polymerase chain reaction (PCR) testing of screen-positives, universal PCR testing every 2 weeks, hospital-based COVID-19 care, alternate care sites [ACSs] for mild/moderate COVID-19, and temporary housing, each compared to no intervention. CONCLUSIONS & RELEVANCE: In this modeling study of simulated adults living in homeless shelters, daily symptom screening and ACSs were associated with fewer COVID-19 infections and decreased costs compared with no intervention. In addition, we provide details on the Clinical and Economic Analysis of COVID-19 interventions (CEACOV) model and management strategies for people experiencing sheltered homelessness. The effective magnitude of the transmission rate, however, changes over time as social interventions alter the daily average number of contacts between susceptible and infected individuals as well as the infectivity per contact. PCR-positive individuals with mild/moderate illness remain in temporary housing and are transferred to the hospital if they progress to severe or critical disease cache = ./cache/cord-283409-ynwgdz52.txt txt = ./txt/cord-283409-ynwgdz52.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-284313-rg3krh7d author = Wood, Lisa G. title = Persistent Airway Obstruction After Virus Infection Is Not Associated With Airway Inflammation date = 2007-02-28 pages = extension = .txt mime = text/plain words = 3828 sentences = 216 flesch = 44 summary = Abstract Background:This study examined the contribution of airway inflammation to the delayed lung function recovery that occurs in some people following virus-induced asthma exacerbations. In contrast, during exacerbation, subjects with persistent airway obstruction showed no differences in inflammatory cell counts compared to stable subjects with asthma, nor did cell counts change postexacerbation. Table 3 indicates that during the exacerbation the CCQ was elevated in both the airwayrecovery and the persistent-airway-obstruction groups; then, at 4 to 6 weeks postexacerbation, a similar improvement in virus symptoms was seen in both groups (percentage change in CCQ) [Fig 1] . The poor lung function (percent predicted FEV 1 ) observed during the acute episode significantly improved in the airway-recovery group, with values returning to levels of stable asthma patients postexacerbation. 11 Conversely, patients in the persistent-airway-obstruction group showed a lower airway inflammatory profile during exacerbations similar to those with stable asthma (Fig 2) , and this did not change significantly postexacerbation (Table 4 ). cache = ./cache/cord-284313-rg3krh7d.txt txt = ./txt/cord-284313-rg3krh7d.txt === reduce.pl bib === id = cord-284262-lddmo1sv author = Li, Linlin title = Circovirus in Tissues of Dogs with Vasculitis and Hemorrhage date = 2013-04-17 pages = extension = .txt mime = text/plain words = 4159 sentences = 218 flesch = 46 summary = We identified a canine circovirus in the liver of a dog that had necrotizing vasculitis and granulomatous lymphadenitis, both of which are described in PCV2-infected pigs (4) . A fourth sample cohort consisted of tissue samples from 21 necropsy cases of dogs whose clinical signs or microscopic lesions matched the sentinel animal (i.e., hemorrhagic diarrhea, vasculitis, and/or granulomatous disease); these samples were selected from the tissue archives of Anatomic Pathology at the UC Davis Veterinary Medical Teaching Hospital. To establish tissue distribution and investigate whether DogCV contributes to canine disease, we developed and validated an ISH oligomeric probe and examined the sentinel dog and dogs from 21 suspected, retrospective cases that included >2 of these 3 signs: vasculitis, hemorrhage, or granulomatous disease. We characterized the genome of multiple DogCV strains, determined DogCV prevalence in dog fecal and plasma samples and tissue distribution in infected animals, and detected paracrystalline arrays in inclusion bodies in macrophages. cache = ./cache/cord-284262-lddmo1sv.txt txt = ./txt/cord-284262-lddmo1sv.txt === reduce.pl bib === === reduce.pl bib === id = cord-284625-to6w5hm2 author = Duan, Xiaopei title = A retrospective study of the initial 25 COVID-19 patients in Luoyang, China date = 2020-05-26 pages = extension = .txt mime = text/plain words = 3347 sentences = 183 flesch = 55 summary = Given the concept of the early diagnosis and treatment of SARS-CoV-2, this article mainly focused on the 25 initial laboratory-confirmed patients in the Luoyang area, discussing their imaging features and clinical characteristics. From January 10 to February 8, 2020, 25 patients with laboratory-confirmed SARS-CoV-2 infection in the area of Luoyang, Henan Province, China, were enrolled in the study. In addition, COVID-19 patients were not found to have combined a On the admission day, the unenhanced CT scan shows diffuse bilateral multiple patchy GGO (white arrow), and the partial boundary is clear while some have unclear boundaries, which are especially significant in the lower lobes of both lungs; strip consolidative opacities (black arrow) are in the focal area. A woman who is the wife of the patient 3 and mother of patient 22 had two negative PCR results, but the lesions in her lung had the same progression, and the blood test also confirmed the SARS-CoV-2 infection. cache = ./cache/cord-284625-to6w5hm2.txt txt = ./txt/cord-284625-to6w5hm2.txt === reduce.pl bib === id = cord-284608-ba7wq52t author = Sias, Catia title = Alpha, Beta, gamma human PapillomaViruses (HPV) detection with a different sets of primers in oropharyngeal swabs, anal and cervical samples date = 2019-03-04 pages = extension = .txt mime = text/plain words = 5645 sentences = 281 flesch = 55 summary = title: Alpha, Beta, gamma human PapillomaViruses (HPV) detection with a different sets of primers in oropharyngeal swabs, anal and cervical samples BACKGROUND: Recent studies have shown a 13-fold increase of oropharyngeal cancer in the presence of HPV, while α-HPV detection seems to be rare in oral cavity in comparison to anal or cervical district, many novel β and γ types have been isolated in this anatomical site suggesting a wide tropism range. METHODS: We analysed the presence of HPV DNA in oropharyngeal (n = 124), anal (n = 186), cervical specimens (n = 43) from HIV positive and negative patients using FAP59/64 and MY09/11 primers. In this study, we analyzed the presence of HPV DNA in oral, anal, and cervical specimens collected from HIV positive and HIV negative individuals, living in the same geographic area (regione Lazio) by using MY09/11 [20, 21] FAP59/64 primers [22] . cache = ./cache/cord-284608-ba7wq52t.txt txt = ./txt/cord-284608-ba7wq52t.txt === reduce.pl bib === id = cord-284366-snajbvr9 author = Han, Zhiyong title = Discharged COVID‐19 Patients Testing Positive Again for SARS‐CoV‐2 RNA: A Minireview of Published Studies from China date = 2020-07-01 pages = extension = .txt mime = text/plain words = 2017 sentences = 133 flesch = 61 summary = [3] [4] [5] The diagnosis of COVID-19 considers clinical symptoms, GGO lesions in chest CT or Xray images, and positive RT-PCR test results for the presence of SARS-CoV-2 RNA in patient samples. For example, the guidelines of the National Health Commission of China state that patients must meet the following 4 benchmarks before they can be discharged: (i) be afebrile for at least 3 consecutive days, (ii) have significantly improved respiratory function, (iii) produce two negative SARS-CoV-2 RT-PCR test results at least 24 hours apart, and (iv) have significant improvement in lung GGO lesions determined by chest CT or X-ray imaging. In Table 1 , we summarize the information about patients who tested positive for SARS-CoV-2 RNA in post-discharge, follow-up examinations in China as described in the 12 published reports. Our analysis indicates that many of the discharged patients tested positive for SARS-CoV-2 RNA when feces or anal swabs were employed, even though they tested negative at the same time when nasopharyngeal or oropharyngeal or sputum samples were examined. cache = ./cache/cord-284366-snajbvr9.txt txt = ./txt/cord-284366-snajbvr9.txt === reduce.pl bib === id = cord-284423-fzz8g3rq author = Wang, Hui-yu title = Establishment and optimization of a liquid bead array for the simultaneous detection of ten insect-borne pathogens date = 2018-07-31 pages = extension = .txt mime = text/plain words = 4665 sentences = 236 flesch = 51 summary = This study aimed to establish a liquid bead array based on Luminex xMAP technology that was able to simultaneously detect multiple insect-borne pathogens. CONCLUSIONS: This optimized liquid array detection system was high-throughput and highly specific and sensitive in screening of the insect-borne pathogens. To date, multiple molecular detection methods have been established to detect insect-borne pathogens, including reverse transcriptase-polymerase chain reaction (PCR) [8] , real-time PCR [9] , a liquid bead array [10] and a microwell membrane array [11] . In this study, we established a method that was able to simultaneously detect multiple insect-borne pathogens rapidly and effectively, including bluetongue virus (BTV), epizootic hemorrhagic disease virus of deer (EHDV), Q-fever pathogen Coxiella burnetii (CB), African swine fever virus (ASFV), West Nile fever virus (WNV), Borrelia burgdorferi (BB), vesicular stomatitis virus (VSV), Rift Valley fever virus (RVFV), Ebola virus (EBV) and Schmallenberg virus (SBV). This study established a multiplexed PCR-coupled liquid array to simultaneously detect 10 types of insect-borne pathogens. cache = ./cache/cord-284423-fzz8g3rq.txt txt = ./txt/cord-284423-fzz8g3rq.txt === reduce.pl bib === === reduce.pl bib === id = cord-284372-v95fzp8n author = Coyle, Peter V title = A touchdown nucleic acid amplification protocol as an alternative to culture backup for immunofluorescence in the routine diagnosis of acute viral respiratory tract infections date = 2004-10-25 pages = extension = .txt mime = text/plain words = 4717 sentences = 224 flesch = 43 summary = title: A touchdown nucleic acid amplification protocol as an alternative to culture backup for immunofluorescence in the routine diagnosis of acute viral respiratory tract infections To overcome this problem we developed a diagnostic molecular strip which combined a generic nested touchdown protocol with in-house primer master-mixes that could recognise 12 common respiratory viruses. CONCLUSIONS: The touchdown protocol with pre-dispensed primer master-mixes was suitable for replacing virus culture for the diagnosis of respiratory viruses which were negative by immunofluorescence. To test the feasibility of its routine use we needed to clinically validate its performance in a routine setting on specimens tested in parallel with our standard immunofluorescence protocol for the diagnosis of acute virus respiratory infections. In conclusion the use of the touchdown protocol with pre-dispensed and quality checked primer master-mixes was suitable for replacing virus culture for the diagnosis of respiratory viruses for immunofluorescence negative specimens. cache = ./cache/cord-284372-v95fzp8n.txt txt = ./txt/cord-284372-v95fzp8n.txt === reduce.pl bib === id = cord-284367-cy61pjcb author = MULEYA, Walter title = Molecular Epidemiology of Paramyxoviruses in Frugivorous Eidolon helvum Bats in Zambia date = 2013-12-31 pages = extension = .txt mime = text/plain words = 1565 sentences = 92 flesch = 53 summary = In this study, we describe the detection of novel paramyxoviruses from the Eidolon helvum species of fruit bats. Semi-nested RT-PCR detected a total of 25 (8%) positive samples for paramyxoviruses which were then directly sequenced and analyzed using phylogenetic analysis. Our study identified novel Henipavirus-related and unrelated viruses using RT-PCR in fruit bats from Kansaka National Park and indicated the presence of similar Bat paramyxoviruses originating from wide geographic areas, suggesting the ability of bats to harbor and transmit viruses. This has been as a result of the high detection rate of previously unknown viral sequences in bats coupled with the emergence of pathogens, such as Hendra, Nipah, Severe acute respiratory syndrome (SARS)-Corona, Ebola and Marburg viruses, all of which are highly virulent and pose a great zoonotic risk [2, 3, 8, 9, 17] . The samples from Zambia formed clusters with the Henipavirus-related viruses and with the unclassified Bat paramyxoviruses (Fig. 1) . cache = ./cache/cord-284367-cy61pjcb.txt txt = ./txt/cord-284367-cy61pjcb.txt === reduce.pl bib === id = cord-284644-9k2oox64 author = Sharma, Vikrant title = Evaluation of clinical applicability of reverse transcription-loop-mediated isothermal amplification assay for detection and subtyping of Influenza A viruses date = 2017-12-15 pages = extension = .txt mime = text/plain words = 4489 sentences = 220 flesch = 49 summary = Optimized RT-LAMP assays were applied on clinical samples from patients having influenza like illness and results were compared with conventional one-step RT-PCR and real-time RT-PCR. CONCLUSIONS: RT-LAMP assay is rapid, sensitive, specific and cost effective method for detection of influenza A viruses than conventional one-step RT-PCR and it can serve as a good alternate for diagnosis and surveillance studies during influenza outbreaks in resource-limited setups of developing countries. The objectives of the current study were to (1) optimize RT-LAMP assay for detection of influenza A viruses and their subtypes (H1N1, H3N2 and pdm09/H1N1); (2) determine sensitivity and specificity of RT-LAMP assay; (3) clinical evaluation of RT-LAMP assay and conventional one-step RT-PCR in comparison to WHO recommended rRT-PCR taken as standard. Development and evaluation of reverse transcription loop-mediated isothermal amplification assay for rapid and real-time detection of the swine-origin influenza A H1N1 virus cache = ./cache/cord-284644-9k2oox64.txt txt = ./txt/cord-284644-9k2oox64.txt === reduce.pl bib === id = cord-286555-rz88g3ze author = Petrovan, Vlad title = Evaluation of Commercial qPCR Kits for Detection of SARS-CoV-2 in Pooled Samples date = 2020-07-11 pages = extension = .txt mime = text/plain words = 3527 sentences = 156 flesch = 55 summary = The most widely used molecular method approved by the World Health Organization (WHO) and the Centers for Disease Control and Prevention (CDC) to detect SARS-CoV-2 is the real-time reverse transcription polymerase chain reaction (qRT-PCR) [4] . The protocol for the COVID-19 PCR Diatheva Detection Kit used with Fast Gene Probe One Step Mix uses 5 µL of mix 1 mixed with 0.625 µL of mix 2, 9.375 µL of primer/probe mix, and 5 µL of RNA template, with a total volume of 20 µL. An initial interlaboratory validation was performed by the Molecular Pathology Laboratory from the University Emergency Hospital Bucharest, using the PowerCheck 2019-nCoV Real-Time PCR Kit. This study was conducted as part of a surveillance program for COVID-19 implemented by the Romanian government. To determine the analytical sensitivity of the COVID-19 commercial assays used in Romanian hospitals (PowerCheck Kogene 2019-nCoV, COVID-19 PCR Diatheva Detection Kit, and 2019-nCoV CDC EUA), we first evaluated their limit of detection (LOD) by performing 10-fold serial dilutions of the controls provided by the kits. cache = ./cache/cord-286555-rz88g3ze.txt txt = ./txt/cord-286555-rz88g3ze.txt === reduce.pl bib === id = cord-285587-rggfg60a author = Meligy, Bassant title = Detection of viral acute lower respiratory tract infection in hospitalized infants using real-time PCR date = 2015-12-30 pages = extension = .txt mime = text/plain words = 3534 sentences = 212 flesch = 50 summary = title: Detection of viral acute lower respiratory tract infection in hospitalized infants using real-time PCR Detection of viral acute lower respiratory tract infection in hospitalized infants using real-time PCR Introduction Viral pathogens account for a large proportion of community acquired pneumonia cases. 6, 7 The present study aims at investigating the epidemiology of viral infection using multiplex real time PCR, and exploring the clinical spectrum of the affected children in relation to viral type, during the winter season in hospitalized children with viral pneumonia. 19 Although RSV is well recognized as the main agent associated with severe ALRTIs, recent data indicate that other viruses may play a significant role in these clinical outcomes, RV seems to be of particular interest, as the most prevalent virus in respiratory illnesses even in the first years of life, being associated with severe acute bronchiolitis. Viral etiology of hospitalized acute lower respiratory infections in children under 5 years of age -a systematic review and metaanalysis cache = ./cache/cord-285587-rggfg60a.txt txt = ./txt/cord-285587-rggfg60a.txt === reduce.pl bib === id = cord-286096-h275nner author = Huijskens, Elisabeth G. W. title = Viral and bacterial aetiology of community‐acquired pneumonia in adults date = 2012-08-22 pages = extension = .txt mime = text/plain words = 3714 sentences = 192 flesch = 47 summary = Methods Between April 2008 and April 2009, 408 adult patients (aged between 20 and 94 years) with community‐acquired pneumonia were tested for the presence of respiratory pathogens using bacterial cultures, real‐time PCR for viruses and bacteria, urinary antigen testing for Legionella and Pneumococci and serology for the presence of viral and bacterial pathogens. All samples were tested using real-time PCR for the presence of respiratory viruses and bacteria including adenovirus (AdV), human bocavirus (hBoV), KI-and WU polyomaviruses (KIPyV and WUPyV), human metapneumovirus (hMPV), human rhinovirus (HRV), human coronaviruses (HCoV) (OC43, NL63, HKU and 229E), parainfluenza viruses (PIV), 1-4 influenza viruses A and B (InfA, InfB), respiratory syncytial virus (RSV), Legionella pneumophila, Mycoplasma pneumoniae, Chlamydophila psittaci, Chlamydophila pneumoniae, Coxiella burnetii and Streptococcus pneumoniae. This study revealed the viral and bacterial aetiology in 263 (64AE5%) of 408 patients with community-acquired pneumonia. cache = ./cache/cord-286096-h275nner.txt txt = ./txt/cord-286096-h275nner.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-284777-z7bd3a91 author = Sun, Ning title = Reverse transcription recombinase polymerase amplification with lateral flow dipsticks for detection of influenza A virus and subtyping of H1 and H3 date = 2018-10-27 pages = extension = .txt mime = text/plain words = 4298 sentences = 234 flesch = 54 summary = Three reverse transcription recombinase polymerase amplification assays with lateral flow dipsticks (RT-RPA-LFD) were developed for identification of the matrix and hemagglutinin (HA) genes to detect influenza A virus and distinguish subtypes H1 and H3. More recently, nucleic acid amplification tests (NAATs), such as reverse transcription polymerase chain reaction (RT-PCR) [12] [13] [14] [15] , real-time RT-PCR [16, 17] , and reverse transcription loop-mediated isothermal amplification (RT-LAMP) [18, 19] , have been used for rapid and sensitive diagnosis or subtyping of IAVs. Nevertheless, these methods require expensive equipment and/or skilled technicians, making them inappropriate for use in developing countries. In order to comprehensively evaluate the performance of RT-RPA-LFD, 28 positive throat swab specimens by matrix real-time RT-PCR were tested by RIDTs (Rapid influenza A virus antigen test kits, Guangzhou Wondfo Biotechnology Co., Ltd, China). cache = ./cache/cord-284777-z7bd3a91.txt txt = ./txt/cord-284777-z7bd3a91.txt === reduce.pl bib === id = cord-284376-plwyjhl8 author = Fu, Xinmiao title = Simulating and forecasting the cumulative confirmed cases of SARS-CoV-2 in China by Boltzmann function-based regression analyses date = 2020-05-31 pages = extension = .txt mime = text/plain words = 14726 sentences = 782 flesch = 49 summary = All specimens tested negative by direct examination for PJ, whereas 27 were positive by real-time PCR (BAL, n = 18; sputa, n = 7, and TA, n = 2); Following stringent clinical, microbiological and imaging criteria ( Table 1 ) , PJP was deemed to be the most probable diagnosis in 12 episodes occurring in unique patients. In contrast, corticosteroid use within the month before sampling was not different between The probability of Pneumocystis jirovecii (PJ) pneumonia (PJP) for each patient was retrospectively evaluated by an expert committee including infectious diseases and microbiology specialists at both centers, on the basis of (i) documented PJ presence in respiratory specimens by microscopy; (ii) compatibility of clinical signs and symptoms (at least 2 of the following: subtle onset of progressive dyspnea, pyrexia, nonproductive cough, hypoxaemia and chest pain), (iii) compatible (suggestive) radiological findings (chest radiograph and/or high-resolution computed tomographic scan detection of interstitial opacities and/or diffuse infiltration infiltrates); (iv) complete resolution of symptoms after a full course of anti-PJP treatment; (v) absence of alternative diagnosis. cache = ./cache/cord-284376-plwyjhl8.txt txt = ./txt/cord-284376-plwyjhl8.txt === reduce.pl bib === === reduce.pl bib === id = cord-287104-4k8pqbc0 author = Lee, J. Y. title = Development of Rapid and Specific Detection for the Human Aichivirus A Using the Loop-Mediated Isothermal Amplification from Water Samples date = 2019-04-04 pages = extension = .txt mime = text/plain words = 2019 sentences = 108 flesch = 53 summary = title: Development of Rapid and Specific Detection for the Human Aichivirus A Using the Loop-Mediated Isothermal Amplification from Water Samples In this study, developed a LAMP method to achieve a rapid, specific and highly sensitive detection of AiV-A. A newly developed method was more rapid (approximately 2–8 h), specific and equivalent detection of AiV-A than with the conventional PCRs. In addition, confirm system of positive LAMP reaction was developed by using the restriction enzyme Aci I and Hae III. A method for detecting AiV-A specific genes by using reverse transcription nested polymerase chain reaction (RT-PCR) assay, have been reported [15] [16] [17] . In this study, developed a rapid, specific and highly sensitive detection of AiV-A by using a LAMP assay. In this study, developed a LAMP assay that could rapid, specific, and sensitive detection of AiV-A from water samples. cache = ./cache/cord-287104-4k8pqbc0.txt txt = ./txt/cord-287104-4k8pqbc0.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-286360-wrrqb387 author = Pratelli, A title = Development of a nested PCR assay for the detection of canine coronavirus date = 1999-06-02 pages = extension = .txt mime = text/plain words = 1677 sentences = 97 flesch = 63 summary = A diagnostic test for canine coronavirus (CCV) infection based on a nested polymerase chain reaction (n-PCR) assay was developed and tested using the following coronavirus strains: CCV (USDA strain), CCV (45/93, field strain), feline infectious peritonitis virus (FIPV, field strain), trasmissible gastroenteritis virus (TGEV, Purdue strain), bovine coronavirus (BCV, 9WBL-77 strain), infectious bronchitis virus (IBV, M-41 strain) and fecal samples of dogs with CCV enteritis. The test described in the present study was able to amplify both CCV and TGEV strains and also gave positive results on fecal samples from CCV infected dogs. Recently a nested polymerase chain reaction (n-PCR) assay was developed for detection of feline infectious peritonitis virus (FIPV), a coronavirus closely related to CCV, in clinical specimens (Gamble et al., 1997) . PCR carried out with CCV1 and CCV2 primers specific for the target sequence 337 -746 of M gene revealed high sensitivity; tests performed on corresponding viral dilutions, which also were inoculated into cell cultures, gave positive results to the 10 − 4 dilution (approximately 10 -50 TCID 50 of virus). cache = ./cache/cord-286360-wrrqb387.txt txt = ./txt/cord-286360-wrrqb387.txt === reduce.pl bib === id = cord-286065-x0g67pnb author = Metzgar, David title = The IRIDICA BAC BSI Assay: Rapid, Sensitive and Culture-Independent Identification of Bacteria and Candida in Blood date = 2016-07-06 pages = extension = .txt mime = text/plain words = 5925 sentences = 240 flesch = 38 summary = We describe the analytical characteristics of the IRIDICA BAC BSI Assay and compare its pre-clinical performance to current standard-of-care methods in a collection of prospectively collected blood specimens from patients with symptoms of sepsis. During the clinical sample study, performed following the sterility and personal protective equipment recommendations of the manufacturer, 61 negative controls were tested and yielded no Other reportable organisms excluding potential contaminants (n = 550) 0 0 0 207 A These 11 culture-negative, IRIDICA BAC BSI Assay-positive detections were supported by later organism-specific ID data which identified the same species as agents of infection (as noted on the subjects' charts). The broad-spectrum nature of the IRIDICA BAC BSI Assay primers, paired with a signal analysis method capable of sensitive and specific detection and identification of one or more species signatures in samples with high background levels of human DNA, make it uniquely suited as a molecular test for bacterial and Candida DNA in blood samples. cache = ./cache/cord-286065-x0g67pnb.txt txt = ./txt/cord-286065-x0g67pnb.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-287466-ag5y781z author = Cowley, J.A. title = Nidoviruses of Fish and Crustaceans date = 2016-09-09 pages = extension = .txt mime = text/plain words = 17715 sentences = 760 flesch = 47 summary = As evidenced by the presence of genomic-length and sgmRNA-length replicativeintermediate double-stranded (ds)RNAs in shrimp cells infected with gill-associated virus (GAV) (Cowley et al., 2002a) , the type species okavirus (Cowley et al., 2012) , it is speculated that transcription termination of the antisense RNAs might occur at precise positions, resulting in common 3′-termini, and that these then act directly as promoters for transcription initiation of the genomic and sgmRNAs. In all other nidoviruses, however, and for the longest of the sgmRNAs transcribed by toroviruses, the (−) and (+) strand sgmRNAs are transcribed using a far more complex discontinuous process involving the splicing of a common "anti-leader" sequence derived from the genome 5′-terminus to each (−) strand sgmRNA that then acts as a universal promoter for transcribing each (+) strand sgmRNA (Pasternak et al., 2006; Sawicki et al., 2007; Smits et al., 2005; van Vliet et al., 2002) . Nidoviruses of aquatic species include the rod-shaped okaviruses GAV and yellow head virus (YHV) that primarily infect Penaeid shrimp (Longyant et al., 2005; Flegel, 2012; Flegel et al., 1997a; Cowley et al., 2000a Cowley et al., , 2002a Cowley and Walker, 2002; Sittidilokratna et al., 2008) and a morphologically similar virus with a ~22 kb ssRNA genome detected in diseased Chinese mitten crabs (Zhang and Bonami, 2007) . cache = ./cache/cord-287466-ag5y781z.txt txt = ./txt/cord-287466-ag5y781z.txt === reduce.pl bib === id = cord-287931-cxqzac4a author = Huang, Weiwei title = An easy operating pathogen microarray (EOPM) platform for rapid screening of vertebrate pathogens date = 2013-09-20 pages = extension = .txt mime = text/plain words = 5161 sentences = 256 flesch = 45 summary = RESULTS: Using multiple probes designed to specifically detect a microbial genus or species, EOPM can correctly identify known pathogens at the species or genus level in blinded testing. To facilitate the application of EOPM in multiple surveillance sites for infectious diseases, we designed software with a user-friendly interface, which is supported by a statistical analysis method based on a comprehensive microbial sequence identification database. Analysis of the enrichment results at the genus level revealed Cardiovirus as the number one match, showing significant enrichment ( The microarray raw data of other symptom-causing pathogens, such as streptococcus and mycoplasma, identified by EOPM in peripheral blood in infectious patients, were also submitted to the GEO database. These microarray platforms use long oligonucleotide probes (60-70-mer) and random PCR amplification, and have successfully identified unexpected pathogens in infectious disease outbreaks, even discovering novel viruses with homology to known species [8, 11] . cache = ./cache/cord-287931-cxqzac4a.txt txt = ./txt/cord-287931-cxqzac4a.txt === reduce.pl bib === id = cord-287447-5lzzobl3 author = Keyaerts, Els title = In vitro inhibition of severe acute respiratory syndrome coronavirus by chloroquine date = 2004-10-08 pages = extension = .txt mime = text/plain words = 2159 sentences = 130 flesch = 53 summary = Abstract We report on chloroquine, a 4-amino-quinoline, as an effective inhibitor of the replication of the severe acute respiratory syndrome coronavirus (SARS-CoV) in vitro. Glycyrrhizin (an active component of liquorice roots), niclosamide (an antihelminthic drug), nelfinavir (a human immunodeficiency deficiency virus (HIV) protease inhibitor), and SNAP (a nitric oxide donor) were reported to have an antiviral effect against SARS-CoV [12] [13] [14] [15] . In this study we report the in vitro antiviral activity of chloroquine against SARS-CoV Frankfurt 1 strain infection. The IC 50 of chloroquine inhibition of SARS-CoV replication in Vero E6 cells, 8.8 lM, is below (1000-fold) the plasma concentrations of chloroquine that are reached in human plasma, following treatment with chloroquine (for acute malaria) at a dose of 25 mg/kg over three days [27] . Our results show that chloroquine inhibits the replication of SARS-CoV in Vero E6 cells. cache = ./cache/cord-287447-5lzzobl3.txt txt = ./txt/cord-287447-5lzzobl3.txt === reduce.pl bib === id = cord-288253-wqrhiq08 author = Park, Jung-Eun title = Development of transgenic mouse model expressing porcine aminopeptidase N and its susceptibility to porcine epidemic diarrhea virus date = 2015-02-02 pages = extension = .txt mime = text/plain words = 5318 sentences = 289 flesch = 51 summary = Because the major pathological changes of the porcine coronaviruses (e.g., TGEV and PEDV) involves enteric diseases, we measured porcine APN expression in the small intestine by RT-PCR, immunoblotting, and IHC. An immunohistochemical analysis, with both anti-Flag and anti-porcine APN antibodies, clearly confirmed porcine APN expression in the brush borders of the absorptive cells in the small intestines of the mouse model (Fig. 4C) . For these purposes, many transgenic mouse models have been developed to study viral pathogenesis, immune responses, and vaccines (Darling et Both wild type and porcine APN transgenic mice were infected with PEDV (5X TCID5010 6 ) orally on day 0. Although significant clinical illness was not observed when the transgenic mice were infected with PEDV, their susceptibility to the virus was confirmed by the detection of viral RNA in various organs with RT-PCR and viral proteins in the small intestines with IHC. cache = ./cache/cord-288253-wqrhiq08.txt txt = ./txt/cord-288253-wqrhiq08.txt === reduce.pl bib === id = cord-288556-o8i6j3b2 author = Li, Yanpeng title = Virome of a Feline Outbreak of Diarrhea and Vomiting Includes Bocaviruses and a Novel Chapparvovirus date = 2020-05-04 pages = extension = .txt mime = text/plain words = 5872 sentences = 325 flesch = 53 summary = We characterized from fecal samples the genome of a novel chapparvovirus we named fechavirus that was shed by 8/17 affected cats and identified three different feline bocaviruses shed by 9/17 cats. Epidemiological investigation of disease signs, time of onset, and transfers of affected cats between three facilities support a possible role for this new chapparvovirus in a highly contagious feline diarrhea and vomiting disease. Here, we analyzed a multi-facility outbreak of vomiting and diarrhea in cats using the following approaches: a commercial feline diarrhea panel of PCR tests for known enteric pathogens; viral metagenomics; and follow-up PCRs. Multiple mammalian viruses of varied origins were detected. DNA was extracted from each individual fecal sample (and one pool of 3, cat#973-975) shown in Table 3 plus 4 vomit samples using the QIAamp MinElute Virus Spin Kit (Qiagen, Hilden, Germany), and PCR assays were used for the detection of different viral nucleic acids in each sample. cache = ./cache/cord-288556-o8i6j3b2.txt txt = ./txt/cord-288556-o8i6j3b2.txt === reduce.pl bib === id = cord-288306-0chcsqe7 author = Wang, Lihua title = Recent Advances in the Diagnosis of Classical Swine Fever and Future Perspectives date = 2020-08-15 pages = extension = .txt mime = text/plain words = 5833 sentences = 280 flesch = 41 summary = The wellestablished diagnostic methods of CSF such as virus isolation, fluorescent antibody test (FAT), antigen capture antibody enzyme-linked immunosorbent assay (ELISA), reverse-transcription polymerase chain reaction (RT-PCR), virus neutralization test (VNT), and antibody ELISA (Table 1) have been widely used and well described in the OIE Terrestrial Manual [17] . The well-established diagnostic methods of CSF such as virus isolation, fluorescent antibody test (FAT), antigen capture antibody enzyme-linked immunosorbent assay (ELISA), reverse-transcription polymerase chain reaction (RT-PCR), virus neutralization test (VNT), and antibody ELISA (Table 1 ) have been widely used and well described in the OIE Terrestrial Manual [17] . Evaluation of a multiplex real-time RT-PCR for quantitative and differential detection of wild-type viruses and C-strain vaccine of Classical swine fever virus The double-antigen ELISA concept for early detection of E rns -specific classical swine fever virus antibodies and application as an accompanying test for differentiation of infected from marker vaccinated animals cache = ./cache/cord-288306-0chcsqe7.txt txt = ./txt/cord-288306-0chcsqe7.txt === reduce.pl bib === id = cord-288327-r20zowty author = Coiras, M.T. title = Oligonucleotide array for simultaneous detection of respiratory viruses using a reverse‐line blot hybridization assay date = 2005-04-15 pages = extension = .txt mime = text/plain words = 5919 sentences = 286 flesch = 47 summary = Biotin‐labeled PCR products obtained with two multiplex reverse transcription (RT)‐polymerase chain reaction (PCR) assays described previously, which allow for the detection of fourteen different groups of respiratory viruses, were hybridized to the oligonucleotide array. Biotin-labeled PCR products obtained with two multiplex reverse transcription (RT)-polymerase chain reaction (PCR) assays described previously, which allow for the detection of fourteen different groups of respiratory viruses, were hybridized to the oligonucleotide array. To evaluate the validity of this method for routine diagnosis was performed a comparative analysis using reference strains from a wide range of respiratory viruses, viral isolates and clinical specimens that have been analyzed by both nested PCR and RLB assays. In conclusion, a RT-PCR-RLB method has been developed for simultaneous detection and typing of a wide range of respiratory viruses, based on the hybridization of biotinylated PCR products, obtained with two multiplex RT-PCR assays described previously, to an array of oligonucleotides that are immobilized and orientated on a nylon membrane. cache = ./cache/cord-288327-r20zowty.txt txt = ./txt/cord-288327-r20zowty.txt === reduce.pl bib === id = cord-288692-v471648u author = Yip, Shea Ping title = Use of Dual TaqMan Probes to Increase the Sensitivity of 1-Step Quantitative Reverse Transcription-PCR: Application to the Detection of SARS Coronavirus date = 2005-10-01 pages = extension = .txt mime = text/plain words = 2387 sentences = 117 flesch = 51 summary = title: Use of Dual TaqMan Probes to Increase the Sensitivity of 1-Step Quantitative Reverse Transcription-PCR: Application to the Detection of SARS Coronavirus We designed a 1-step real-time quantitative RT-PCR assay for SARS-CoV with the use of 2 TaqMan probes, instead of 1 probe, hybridizing to the same PCR product to further improve the sensitivity. In conclusion, we report the use of dual TaqMan probes for quantification purposes and apply it to the detection of Clinical Chemistry 51, No. 10, 2005 SARS-CoV with a detection limit of 1 copy RNA per reaction. Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays Quantitation of severe acute respiratory syndrome coronavirus genome by real-time polymerase chain reaction assay using minor groove binder DNA probe technology Sensitive and quantitative detection of severe acute respiratory syndrome coronavirus infection by real-time nested-polymerase chain reaction cache = ./cache/cord-288692-v471648u.txt txt = ./txt/cord-288692-v471648u.txt === reduce.pl bib === id = cord-287843-snra23sy author = Lee, Wan‐Ji title = Prevalence and molecular epidemiology of human coronavirus HKU1 in patients with acute respiratory illness date = 2012-11-14 pages = extension = .txt mime = text/plain words = 2715 sentences = 157 flesch = 56 summary = In this study, a Taq-Man 1 -based real-time polymerase chain reaction (PCR) method that targets the HCoV-HKU1 open reading frame (ORF) 1a and ORF 1b genes with high sensitivity and specificity was developed and evaluated. Fifty HCoV-HKU1-positive cases were detected (2.5%) out of 1,985 clinical specimens using real-time PCR assays targeting ORF 1a and ORF 1b. To circumvent these limitations, a quantitative real-time PCR was developed and targeted a study group of 1,985 throat swab specimens collected from patients with an acute respiratory illness from January 2007 to May 2008. The aim of the real-time PCR assays developed in this study was to detect both of the HCoV-HKU1 ORF 1a and ORF 1b genes. One limitation of this study was that because clinical specimens were chosen from negative cases of acute respiratory illness in the ARI-Net laboratory surveillance system [Chun et al., 2009] , dual or multiple infections of HCoV-HKU1 with other respiratory viruses could not be detected. cache = ./cache/cord-287843-snra23sy.txt txt = ./txt/cord-287843-snra23sy.txt === reduce.pl bib === id = cord-288962-jgtoehcr author = Andréoletti, Laurent title = Differential detection of rhinoviruses and enteroviruses RNA sequences associated with classical immunofluorescence assay detection of respiratory virus antigens in nasopharyngeal swabs from infants with bronchiolitis date = 2000-06-06 pages = extension = .txt mime = text/plain words = 3704 sentences = 186 flesch = 36 summary = To define the role of enteroviruses and human rhinoviruses as etiological agents in childhood bronchiolitis, clinical aspirates from 84 infants admitted to hospital with symptoms of obstructive bronchiolitis were tested by picornavirus RT‐PCR assay, adenovirus PCR assay and classical immunofluorescence antigen detection of common respiratory viral agents. In summary, combination of molecular and classical detection assays of common viruses can be used to demonstrate enterovirus and human rhinovirus respiratory infection in childhood bronchiolitis, and provides an improved approach to obtain new insights into concomitant viral respiratory tract infection in infants. To investigate the role of enteroviruses and human rhinoviruses as etiological agent in bronchiolitis, 84 nasopharyngeal aspirates were tested by picornavirus RT-PCR assay, classical immunofluorescence antigens detection of respiratory syncytial viruses, influenza viruses, parainfluenza viruses, coronaviruses, and adenovirus PCR assay. cache = ./cache/cord-288962-jgtoehcr.txt txt = ./txt/cord-288962-jgtoehcr.txt === reduce.pl bib === id = cord-289050-9w7ks01n author = Donoso, Alejandro F. title = Fatal hemorrhagic pneumonia caused by human metapneumovirus in an immunocompetent child date = 2008-08-25 pages = extension = .txt mime = text/plain words = 1780 sentences = 119 flesch = 50 summary = 5, 6 The aim of the present study was to report the case of a pediatric, immunocompetent patient who presented with severe acute respiratory distress syndrome (ARDS), for whom there was a fatal outcome, and in whom hMPV was the only etiologic agent found even on post-mortem necropsy. Human metapneumovirus could be more severe in patients with underlying medical conditions such as chronic lung disease caused by prematurity, cardiac disease, and immunodefi ciency. The accumulation of cases, however, and comprehensive microbiological analysis including (RT-) PCR for other respiratory viruses are needed to confi rm that infection with hMPV alone can result in such severe lung disease. We believe that the present case should warn us about the occasional role of hMPV as an agent of severe lung infection in children without a predisposing condition. Human metapneumovirus detection in patients with severe acute respiratory syndrome cache = ./cache/cord-289050-9w7ks01n.txt txt = ./txt/cord-289050-9w7ks01n.txt === reduce.pl bib === id = cord-289017-vwye3pk9 author = Comach, Guillermo title = Sentinel Surveillance of Influenza-Like Illness in Two Hospitals in Maracay, Venezuela: 2006–2010 date = 2012-09-11 pages = extension = .txt mime = text/plain words = 6262 sentences = 301 flesch = 47 summary = CONCLUSIONS/SIGNIFICANCE: Influenza viruses were the most commonly detected viral organisms among patients with acute febrile respiratory illnesses presenting at two hospitals in Maracay, Venezuela. Recent prospective studies, which utilized more sensitive methods for detecting respiratory viruses such as multiplex polymerase chain reaction (PCR), have similarly demonstrated that the highest rates of viral respiratory infection occur among children and the frequency of infection tends to decrease with age due to increasing acquired immunity [8] . On the other hand, the percentage of influenza viruses (not including pH1N1) detected in our study during a similar period of time, but in different years accounted for the significant differences found in both studies: a) the collection, preservation and further processing of respiratory samples, and b) the type of cells and IFA reagents used for virus isolation and identification. In contrast, a prospective study of ILI among Brazilian adults, which utilized viral isolation and RT-PCR testing on respiratory samples, detected rhinoviruses in 19.6% of patients [14] . cache = ./cache/cord-289017-vwye3pk9.txt txt = ./txt/cord-289017-vwye3pk9.txt === reduce.pl bib === id = cord-289114-ifnk41oq author = Singh, Angaraj title = Effect of pre‐existing diseases on COVID‐19 infection and role of new sensors and biomaterials for its detection and treatment date = 2020-10-28 pages = extension = .txt mime = text/plain words = 6894 sentences = 470 flesch = 54 summary = The SARS-CoV-2 infected patients with the cardiovascular problem have a higher fatality rate as compared to general COVID-19 patients. The ACE-2 has been suggested as a medicine for the treatment of diabetes because it reduces inflammation .Therefore, the diabetes and COVID-19 patients treated with ACE-2 have higher risk of infection (Zachary, 2020) . Although, the specific drug for SARS-CoV-2 is not discovered till date, the medical observers are attempting with different antiviral drugs for the treatment of COVID-19 infection . All rights reserved patients demonstrated that the combination of a new antiviral drug remdesivir and chloroquine slowed down the growth of SARS-CoV-2 (Abdul et al., 2017) . Convalescent plasma therapy has been observed as a better alternative for the treatment of severely infected COVID-19 patients. A research report suggested that plasma treatment is more effective at the initial stage (within 14 days of symptoms) of COVID-19 infection. cache = ./cache/cord-289114-ifnk41oq.txt txt = ./txt/cord-289114-ifnk41oq.txt === reduce.pl bib === id = cord-288701-nx9fg4yn author = Mari, Viviana title = Multiplex real-time RT-PCR assay for bovine viral diarrhea virus type 1, type 2 and HoBi-like pestivirus date = 2015-12-17 pages = extension = .txt mime = text/plain words = 4827 sentences = 227 flesch = 53 summary = The aim of the present study was to develop a multiplex real-time RT-PCR assay, based on the TaqMan technology, for the rapid and unambiguous characterisation of all bovine pestiviruses, including the emerging HoBi-like strains. Analysis of field samples tested positive for BVDV-1, BVDV-2 or HoBi-like virus by a nested PCR protocol revealed that the developed TaqMan assay had equal or higher sensitivity and was able to discriminate correctly the viral species in all tested samples, whereas a real-time RT-PCR assay previously developed for HoBi-like pestivirus detection showed cross-reactivity with few high-titre BVDV-2 samples. To overcome these limitations, we have developed a multiplex real-time RT-PCR assay for simultaneous detection of the different species of bovine pestiviruses, including the emerging HoBi-like group, allowing a rapid, sensitive and specific diagnosis of pestivirus infection and characterisation of the viral species. cache = ./cache/cord-288701-nx9fg4yn.txt txt = ./txt/cord-288701-nx9fg4yn.txt === reduce.pl bib === id = cord-289200-6yhz1a23 author = Yang, Ziyi title = Vertical Transmission of Severe Acute Respiratory Syndrome Coronavirus 2: A Systematic Review date = 2020-05-13 pages = extension = .txt mime = text/plain words = 1898 sentences = 123 flesch = 50 summary = Two authors independently and systematically searched these databases using the following MeSH terms: "pregnancy," "infant, newborn," "COVID-19," and "severe acute respiratory syndrome coronavirus 2." We also performed a manual search in Google Scholar and the websites of key journals in the related field. Indeed, breastfeeding may not be safe until COVID-19 is ruled out or until both mother and neonate clear As there is no evidence to support the possibility of intrauterine vertical transmission, the timing of delivery should not be based solely on the condition that a pregnant patient is infected but should be individualized in each case; that is, obstetricians may consider maternal and fetal wellbeing, gestational age, and other concomitant conditions to determine the time of delivery. The currently available evidence does not support the possibility of intrauterine vertical transmission of SARS-CoV-2 infection during the third trimester of pregnancy. cache = ./cache/cord-289200-6yhz1a23.txt txt = ./txt/cord-289200-6yhz1a23.txt === reduce.pl bib === === reduce.pl bib === id = cord-289216-g4kqi560 author = Malecki, M. title = Analysis of external quality assessment samples revealed crucial performance differences between commercial RT-PCR assays for SARS-CoV-2 detection when taking extraction methods and real-time-PCR instruments into account date = 2020-09-23 pages = extension = .txt mime = text/plain words = 1927 sentences = 127 flesch = 51 summary = title: Analysis of external quality assessment samples revealed crucial performance differences between commercial RT-PCR assays for SARS-CoV-2 detection when taking extraction methods and real-time-PCR instruments into account The aim of this study was to compare the performance of the overall analytical matrix including the extraction kit (BD MAX, Promega, Qiagen), the PCR instrument (Agilent Mx3005P, BD MAX, Qiagen Rotor-Gene, Roche Cobas z 480) and the RT-PCR assay (Altona Diagnostics, CerTest Biotec, R-Biopharm AG) using predefined samples from proficiency testing organizers. In this study, two diagnostic laboratories of a tertiary care hospital equipped with different PCR systems validated the available kits on the respective systems for SARS-CoV-2 testing. In order to evaluate the performance of analytical components used for SARS-CoV-2 diagnostic we compared three commercially available RT-PCR kits, six extraction kits and four PCR cyclers in all possible combinations using predefined EQA samples. cache = ./cache/cord-289216-g4kqi560.txt txt = ./txt/cord-289216-g4kqi560.txt === reduce.pl bib === id = cord-290513-ygqin14x author = Stevens, Barry J. title = Reporting radiographers’ interpretation and use of the British Society of Thoracic Imaging’s coding system when reporting COVID-19 chest x-rays date = 2020-06-18 pages = extension = .txt mime = text/plain words = 2443 sentences = 139 flesch = 51 summary = title: Reporting radiographers' interpretation and use of the British Society of Thoracic Imaging's coding system when reporting COVID-19 chest x-rays Methodology Retrospective review of CXR reports by radiographers for suspected COVID-19 patients attending the Emergency Department (ED) of a hospital in the UK. The criteria for inclusion were; adult patients attending the ED with the diagnostic question querying COVID-19, with a BSTI code in the report and an initial RT-PCR swab result. The fact that the reporting team and Radiologist arbiter reached agreement that the 18 false negative reports with code CVCX0 all had normal appearances, despite returning a positive RT-PCR result, corroborates findings from previous work suggesting that there may be no radiographic features in early or mild disease 7,10,21 . Correlation of Chest CT and RT-PCR Testing in Coronavirus Disease 2019 (COVID-19) in China: A Report of 1014 Cases cache = ./cache/cord-290513-ygqin14x.txt txt = ./txt/cord-290513-ygqin14x.txt === reduce.pl bib === id = cord-290540-r0d6oaez author = Rottier, Peter J.M. title = The molecular dynamics of feline coronaviruses date = 1999-09-01 pages = extension = .txt mime = text/plain words = 3820 sentences = 200 flesch = 56 summary = Special attention is given to the genetic dynamics of the viruses as these now allow us to begin to understand the origin of the different phenotypes, in particular the genesis of virulence during persistent infection. The conclusion from these experiments is that feline coronaviruses may persist in the lower intestinal tract where the virus continues to replicate at low levels. Conceivably, the persisting virus confers to its host resistance against superinfection by the closely related feline coronaviruses, which were infecting the other cats. The idea was that'feline enteric coronaviruses' are indeed restricted in tropism, while'FIP viruses' would cross the epithelium, infect macrophages and go systemically. The result of all these studies is that generally there is no protection when an antibody response to the spike protein is induced there is rather an enhancement of the infection, with an'early death' phenomenon. Detection of feline coronavirus RNA in feces, tissues and body fluids of naturally infected cats by reverse transcriptase PCR cache = ./cache/cord-290540-r0d6oaez.txt txt = ./txt/cord-290540-r0d6oaez.txt === reduce.pl bib === id = cord-289745-qtorq2qq author = Esper, Frank title = Evidence of a Novel Human Coronavirus That Is Associated with Respiratory Tract Disease in Infants and Young Children date = 2005-02-15 pages = extension = .txt mime = text/plain words = 3627 sentences = 205 flesch = 53 summary = We sought to determine whether novel human coronaviruses (HCoVs) are circulating in New Haven, Connecticut, and, if so, whether they are associated with respiratory tract disease in infants and young children. To determine whether novel HCoVs are circulating and, if so, whether they are responsible for respiratory tract disease in children, we developed a strategy to screen for previously unknown HCoVs. Our initial assumption was that all CoVs must have conserved functions and that these conserved functions are reflected in the genome. These specimens, which were obtained from both ambulatory and hospitalized patients, were screened for presence of human metapneumovirus (hMPV) by use of an RT-PCR-based approach described elsewhere [12, 13] and were submitted to the Clinical Virology Laboratory, Yale-New Haven Hospital, for diagnostic testing. The novel HCoV identified in New Haven and The Netherlands was associated with both upper and lower respiratory tract disease in infants and young children. cache = ./cache/cord-289745-qtorq2qq.txt txt = ./txt/cord-289745-qtorq2qq.txt === reduce.pl bib === id = cord-289744-suiqh3gv author = Lafolie, Jérémy title = Assessment of blood enterovirus PCR testing in paediatric populations with fever without source, sepsis-like disease, or suspected meningitis: a prospective, multicentre, observational cohort study date = 2018-10-30 pages = extension = .txt mime = text/plain words = 4727 sentences = 239 flesch = 48 summary = The aim of our multicentre study was to assess detection of enterovirus by PCR in blood specimens of newborn babies, infants, and children with fever without source, sepsis-like disease, or suspected meningitis. Evidence before this study We searched PubMed up to Feb 7, 2018, for papers reporting paediatric enterovirus diseases and enterovirus PCR testing or molecular detection of viruses in cerebrospinal fluid (CSF) or blood specimens of patients with aseptic meningitis, sepsis and sepsis-like disease, or fever without source. Our study of 360 patients with laboratory findings of enterovirus infection is, as far as we are aware, the largest prospective, multicentre, observational study to assess PCR testing for enterovirus in both blood and CSF samples from newborn babies (aged ≤28 days) and infants (aged >28 days to ≤2 years) with fever without source, sepsis-like disease, or suspected meningitis, and children (aged >2 years to ≤16 years) with suspected meningitis. cache = ./cache/cord-289744-suiqh3gv.txt txt = ./txt/cord-289744-suiqh3gv.txt === reduce.pl bib === id = cord-291026-99cit4ig author = Lung, O. title = Insulated Isothermal Reverse Transcriptase PCR (iiRT‐PCR) for Rapid and Sensitive Detection of Classical Swine Fever Virus date = 2015-01-27 pages = extension = .txt mime = text/plain words = 4566 sentences = 206 flesch = 55 summary = In this study, we describe validation of a new probe‐based insulated isothermal reverse transcriptase PCR (iiRT‐PCR) assay for rapid detection of classical swine fever virus (CSFV) on a compact, user‐friendly device (POCKIT (™) Nucleic Acid Analyzer) that does not need data interpretation by the user. Archived viral nucleic acid from 18 laboratory-amplified non-CSF viruses including eight other pestiviruses (BVDV 1-Hastings, Singer and NY1 strains; BVDV 2-Ames 125c, 890, 24515 strains; BDV-Coos Bay; HoBi atypical pestivirus), African swine fever virus-Lisbon, swine vesicular disease virus-ITL 19/92, porcine respiratory and reproductive syndrome virus-YNL, swine influenza virus (H3N2), porcine circovirus 1 (PCV1, derived from infectious clone based on GenBank accession no. The iiRT-PCR assay accurately detected all CSFV RNA samples which represented all three genotypes, and eight of 11 subgenotypes that were available for testing and gave negative results for three BVDV type 1 strains, three BVDV type 2 strains, BDV, HoBi atypical pestivirus, ASFV and nine other viruses that affect livestock. cache = ./cache/cord-291026-99cit4ig.txt txt = ./txt/cord-291026-99cit4ig.txt === reduce.pl bib === id = cord-291954-wormplcu author = Sakulkonkij, Parichart title = A family cluster of diagnosed coronavirus disease 2019 (COVID‐19) kidney transplant recipient in Thailand date = 2020-08-08 pages = extension = .txt mime = text/plain words = 4424 sentences = 304 flesch = 48 summary = A novel betacoronavirus, the seventh member of coronaviruses, which is shown to infect humans and lately named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes an ongoing outbreak of respiratory illness that began in December 2019 in China called coronavirus disease 2019 . On admission, a nasopharyngeal and throat swabs for SARS-CoV-2 reverse transcription-polymerase chain reaction (RT-PCR) revealed a positive result, other laboratory findings included white blood cell count (WBC) 2480 cells/mm 3 , lymphocyte (L) 18%, neutrophil (N) 78%, and C-reactive protein (CRP) 62.7 mg/L. Although acute hypoxemic respiratory failure from COVID-19 in elderly and KT recipients in our cohort seemed to be prominent, early investigation in high-risk populations, prompt initiation of potential therapy, and intensive supportive care are important to prevent adverse consequences and mortality. Case report of COVID-19 in a kidney transplant recipient: Does immunosuppression alter the clinical presentation? cache = ./cache/cord-291954-wormplcu.txt txt = ./txt/cord-291954-wormplcu.txt === reduce.pl bib === id = cord-289612-4x5t4c5u author = Alsuliman, Tamim title = COVID-19 paraclinical diagnostic tools: Updates and future trends date = 2020-06-20 pages = extension = .txt mime = text/plain words = 7353 sentences = 387 flesch = 48 summary = Laboratory-confirmed SARS-CoV-2 infection requires the detection of viral nucleic acid in respiratory tract samples by the use of real-time reverse-transcription polymerase chain reaction (rRT-PCR) assay. In the course of this phase, upper respiratory specimens were tested by RT-PCR for viral RNA and the majority of the patients showed positive results for SARS-CoV-2. These results contrast with another German smaller study by Wolfel et al., conducted on 9 COVID-19 patients, with no discernible difference in viral loads or detection rates when comparing nasal and throat swabs [38] . found that 66.67% of laboratory-confirmed COVID-19 patients were tested positive for SARS-CoV-2 RNA in stool specimens. enrolled a total of 173 confirmed cases of COVID-19 by the use of rRT-PCR on samples from the respiratory track reported that the seroconversion sequentially appeared for the total antibody (Ab), IgM and then IgG, with a median time of 11, 12 and 14 days, respectively. Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: a report of 1014 cases cache = ./cache/cord-289612-4x5t4c5u.txt txt = ./txt/cord-289612-4x5t4c5u.txt === reduce.pl bib === id = cord-289735-iw3uq2z9 author = Tsou, P. title = Association between multiple respiratory viral infections and pediatric intensive care unit admission among infants with bronchiolitis date = 2019-11-25 pages = extension = .txt mime = text/plain words = 3864 sentences = 193 flesch = 37 summary = BACKGROUND: It is unclear whether multiple respiratory viral infections are associated with more severe bronchiolitis requiring pediatric intensive care unit (PICU) admission. Other viruses frequently found in children with bronchiolitis include rhinovirus, Background: It is unclear whether multiple respiratory viral infections are associated with more severe bronchiolitis requiring pediatric intensive care unit (PICU) admission. To address these issues, we conducted a case-control study and performed a multivariable regression analysis to determine the association between severe bronchiolitis resulting in PICU admission and the number of viral co-infections among previously healthy infants hospitalized for acute bronchiolitis, while accounting for confounders. As controls, the same number of neonates (<28 days; n = 20) and infants (n = 135) were randomly selected among the 890 patients (age 1 year) with bronchiolitis admitted to the general pediatric unit, and for whom PCR was performed during the same study period, using a random sampling method. cache = ./cache/cord-289735-iw3uq2z9.txt txt = ./txt/cord-289735-iw3uq2z9.txt === reduce.pl bib === id = cord-290456-cgrn5c36 author = Soliman, Mohamed A. R. title = Endoscopic endonasal skull base surgery during the COVID-19 pandemic: A developing country perspective date = 2020-09-25 pages = extension = .txt mime = text/plain words = 4102 sentences = 241 flesch = 51 summary = [16] e aim of this study is to present the current situation from a developing country perspective in dealing with emergency endoscopic endonasal skull base surgeries at the time of the COVID-19 pandemic in terms of preoperative patients' screening, surgical techniques, and intraoperative PPE utilization. e survey consisted of 12 questions designed to explore three domains; patients' information (age, clinical manifestations [neurological and COVID-19 related], diagnosis, preoperative COVID-19 screening, and COVID-19 symptoms during the first 3 weeks postsurgery), surgical team information (age, chronic medical conditions, and COVID-19 symptoms during the first 3 weeks postsurgery), and operative information (PPE utilization and basal craniectomy). ere was only one surgeon who developed a high-grade fever, malaise, and bony aches in the first 3 days after surgery who had undergone two nasopharyngeal swabs with RT-PCR testing 1 week apart and both came back negative representing 2.1% of the surgical team members [ Figure 2c ]. cache = ./cache/cord-290456-cgrn5c36.txt txt = ./txt/cord-290456-cgrn5c36.txt === reduce.pl bib === === reduce.pl bib === id = cord-291860-dw1sfzqx author = van Boheemen, Sander title = Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients date = 2019-12-16 pages = extension = .txt mime = text/plain words = 5398 sentences = 276 flesch = 40 summary = Herein, were studied the performance of an in-house mNGS protocol for routine diagnostics of viral respiratory infections with potential for automated pan-pathogen detection. Herein, were studied the performance of an in-house mNGS protocol for routine diagnostics of viral respiratory infections with potential for automated pan-pathogen detection. Clinical sensitivity was analyzed using the optimized procedure, which in short consisted of total nucleic acid extraction, including internal controls (1:100 dilution); the adapted New England Biolabs Next library preparation protocol, including fragmentation with zinc, for combined RNA and DNA detection (see Library Preparation); and sequencing of 10 million reads (Illumina NextSeq 500). The Centrifuge default settings, with NCBI's nucleotide database and assignment of sequence reads to a maximum of five labels per sequence, resulted in various spurious classifications ( Figure 4) [eg, Lassa virus ( Figure 5 ), evidently highly unlikely to be present in patient samples from the Netherlands with respiratory complaints]. cache = ./cache/cord-291860-dw1sfzqx.txt txt = ./txt/cord-291860-dw1sfzqx.txt === reduce.pl bib === id = cord-291958-g4jlg9pw author = Silva, Camila S title = Human Respiratory Coronaviruses Detected In Patients with Influenza-Like Illness in Arkansas, USA date = 2014-03-26 pages = extension = .txt mime = text/plain words = 4255 sentences = 221 flesch = 57 summary = Our study aim was to investigate the molecular epidemiology of human CoV strains circulating in Arkansas, their genetic variability and their association with reported influenza-like symptoms. Samples were pre-screened, using a quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) multiprobe for coronavirus, and subjected to confirmatory pancoronavirus and/or strain-specific reverse transcriptase (RT)-PCR followed by sequence analysis. RNAs positive for CoV by qRT-PCR were analyzed by one-step RT-PCR, using degenerate primers for the ORF1b [20] and specific primers (Table 1) for the spike and nucleocapsid genes of human alphacoronavirus (NL63 and 229E) and betacoronavirus (OC43 and HKU1). Among the 3 feline-like samples (based on ORF1b phylogenetic analysis), two were amplified and sequenced using primers to the S region, one was shown to share the highest identity with the OC43 strain (95.9% identity) and another shared the highest identity to feline CoV (83.8% identity) ( Figure 2 ). cache = ./cache/cord-291958-g4jlg9pw.txt txt = ./txt/cord-291958-g4jlg9pw.txt === reduce.pl bib === id = cord-291029-oldket3n author = Sefers, Susan E. title = QIAamp MinElute Virus kit effectively extracts viral nucleic acids from cerebrospinal fluids and nasopharyngeal swabs() date = 2005-07-21 pages = extension = .txt mime = text/plain words = 3532 sentences = 182 flesch = 53 summary = The QIAamp MinElute Virus kit (Qiagen Inc., Valencia, CA) was compared to the two existing methods currently used in our laboratory, IsoQuick (Orca Research Inc., Bothell, WA) for DNA extraction and RNAzol B (Leedo Laboratories Inc., Houston, TX) for RNA extraction, of viral nucleic acids. In this study, we have chosen both nasopharyngeal swab (NPS) and cerebrospinal fluid (CSF) specimens submitted for influenza A virus, enterovirus and herpesvirus testing to validate the MinElute nucleic acid extraction system. Nucleic acid recovery rates between the MinElute and RNAzol B were further determined by quantitating HIV-1 or CMV viral loads in extracted RNA or DNA specimens using a real-time TaqMan PCR. The MinElute kits possessed an equivalent sensitivity in nucleic acid recovery and detection, in comparison to the IsoQuick and RNAzol B, for both DNA and RNA extraction. cache = ./cache/cord-291029-oldket3n.txt txt = ./txt/cord-291029-oldket3n.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-291360-z19ri377 author = Lan, Fan-Yun title = COVID-19 symptoms predictive of healthcare workers’ SARS-CoV-2 PCR results date = 2020-06-26 pages = extension = .txt mime = text/plain words = 4339 sentences = 251 flesch = 52 summary = Of 509 HCWs with initial negative SARS-CoV-2 assays, nine had symptom progression and positive re-tests, yielding an estimated negative predictive value of 98.2% (95% CI: 96.8–99.0%) for the exclusion of clinically relevant COVID-19. CONCLUSIONS: Symptom and temperature reports are useful screening tools for predicting SARS-CoV-2 assay results in HCWs. Anosmia/ageusia, fever, and myalgia were the strongest independent predictors of positive assays. Therefore, we investigated the presenting symptoms most predictive of positive/negative SARS-CoV-2 RT-PCR results among HCWs. Since March 9, 2020, the occupational health service of a Massachusetts community healthcare system has implemented a staff "hotline" system to maintain a viable/healthy workforce and operational continuity during the pandemic. The clinical COVID-19 attack rate during the study period was calculated as: (the number of initial positive SARS-CoV-2 assays + the number of false negatives) divided by the system's estimated total HCW population (n = 4600). cache = ./cache/cord-291360-z19ri377.txt txt = ./txt/cord-291360-z19ri377.txt === reduce.pl bib === === reduce.pl bib === id = cord-291281-ygrh8ces author = Durner, J. title = Critical Questions when Interpreting Coronavirus PCR Diagnostics date = 2020-06-14 pages = extension = .txt mime = text/plain words = 1912 sentences = 121 flesch = 57 summary = In contrast to other PCR examinations, or laboratory medical analyses, currently SARS-CoV-2 diagnostic information about the device or the detection limit / sensitivity is not usually provided by the laboratory. Using a protocol without purification of viral RNA, i.e. the Munich Extraction Protocol (MEP) [2] , we could show that the type of transport medium had little influence on the detection sensitivity of SARS-CoV-2 in the PCR (Table 1) . By using this system, the sensitivity could be increased by at least one more dilution step compared to the use of commercial purification methods in PCR (Table 3) . . https://doi.org/10.1101/2020.06.11.20127241 doi: medRxiv preprint Table 1 Comparison of different types of transport media for their influence on the detectability of SARS-CoV-2. . https://doi.org/10.1101/2020.06.11.20127241 doi: medRxiv preprint Table 2 Comparison of different purification systems for their influence on the detectability of SARS-CoV-2 (Cp = crossing point). cache = ./cache/cord-291281-ygrh8ces.txt txt = ./txt/cord-291281-ygrh8ces.txt === reduce.pl bib === id = cord-292031-weiwksh6 author = Ramírez-Castillo, Flor Yazmín title = Waterborne Pathogens: Detection Methods and Challenges date = 2015-05-21 pages = extension = .txt mime = text/plain words = 7358 sentences = 378 flesch = 36 summary = Quantitative microbial risk assessment (QMRA) is a helpful tool to evaluate the scenarios for pathogen contamination that involve surveillance, detection methods, analysis and decision-making. Molecular techniques, such as nucleic acid amplification procedures, offer sensitive and analytical tools for detecting a variety of pathogens, including new emerging strains, present the possibility of automation, and real-time analysis to provide information for microbial risk assessment purposes [33] . Limitations of DNA based methods such as PCR include the inability to discriminate between viable from non-viable cells that both contain DNA, the low concentration of several pathogens in water such as Cryptosporidium, Giardia and viruses, and the lack of data to indicate the real infectious risk to a population. Oligonucleotide microarrays are a powerful genomic technology that is widely utilized to monitor gene expression under different cell growth conditions, detecting specific mutations in DNA sequences and characterizing microorganisms in environmental samples [76] . cache = ./cache/cord-292031-weiwksh6.txt txt = ./txt/cord-292031-weiwksh6.txt === reduce.pl bib === id = cord-292281-fui9all6 author = Pratelli, A. title = High‐cell‐passage canine coronavirus vaccine providing sterilising immunity date = 2007-09-14 pages = extension = .txt mime = text/plain words = 3532 sentences = 177 flesch = 54 summary = Clinical Significance: This study showed the efficacy of a high‐cell‐passage canine coronavirus vaccine in preventing infection of dogs by virulent virus and, specifically, its ability to induce sterilising immunity. Faecal samples collected from the vaccinated and control dogs were tested by virus isolation and PCR assays. After challenge with field strain 144/ 01, the vaccinated dogs did not develop clinical signs, and virus isolation and PCR did not detect viral shedding. In a recent study, it was found that the inactivated vaccine had poor efficacy in reducing faecal shedding of CCoV following infection with a field strain of the virus (Pratelli and others 2003b) . After challenge at 14 dpsv, protection from CCoV infection was complete because no viral shedding was observed by either virus isolation or PCR tests. The present study has shown the efficacy of a high-cell-passage CCoV vaccine in preventing infection of dogs by virulent virus and, specifically, its ability to induce sterilising immunity. cache = ./cache/cord-292281-fui9all6.txt txt = ./txt/cord-292281-fui9all6.txt === reduce.pl bib === id = cord-291961-usl8z6ep author = Zheng, Wen-zhi title = Human polyomavirus type six in respiratory samples from hospitalized children with respiratory tract infections in Beijing, China date = 2015-10-13 pages = extension = .txt mime = text/plain words = 2915 sentences = 162 flesch = 54 summary = METHODS: The VP1 gene of HPyV6 was detected with an established TaqMan real-time PCR from nasopharyngeal aspirate specimens collected from hospitalized children with respiratory tract infections. All 15 HPyV6-positive patients were diagnosed with lower respiratory tract infections, and their viral loads ranged from 1.38 to 182.42 copies/μl nasopharyngeal aspirate specimen. CONCLUSIONS: The prevalence of HPyV6 was 1.7 % in nasopharyngeal aspirate specimens from hospitalized children with respiratory tract infections, as analyzed by real-time PCR. Previous studies have indicated that a number of HPyVs are associated with human diseases, such as progressive multifocal leukoencephalopathy (JCPyV), hemorrhagic cystitis (BKPyV), Merkel cell carcinoma (MCPyV), and trichodysplasia spinulosa (TSPyV) [3, 7, 9, [17] [18] [19] . Because initial infections with most HPyVs occur in infancy, the prevalence of HPyV6 in NPAs from children was detected with real-time PCR. The detection rate for HPyV6 by real-time PCR assay was 1.7 % in 887 NPA samples collected from hospitalized children with RTI. cache = ./cache/cord-291961-usl8z6ep.txt txt = ./txt/cord-291961-usl8z6ep.txt === reduce.pl bib === id = cord-291916-5yqc3zcx author = Hozhabri, Hossein title = The Global Emergency of Novel Coronavirus (SARS-CoV-2): An Update of the Current Status and Forecasting date = 2020-08-05 pages = extension = .txt mime = text/plain words = 16737 sentences = 847 flesch = 45 summary = cache = ./cache/cord-291916-5yqc3zcx.txt txt = ./txt/cord-291916-5yqc3zcx.txt === reduce.pl bib === id = cord-292172-aqsc9fbl author = Al Amin, Md. title = Screening of commercial meat products from supermarket chains for feline derivatives using SP-PCR-RLFP and lab-on-a-chip date = 2020-06-09 pages = extension = .txt mime = text/plain words = 4852 sentences = 308 flesch = 63 summary = Hence this paper documented the application of species specific polymerase chain reaction-restriction fragment length polymorphism (SP-PCR-RFLP) assay targeting a short-fragments (69 bp) of mitochondrial cytochrome b (cytb) gene to screen feline meat in commercial meat products using lab-on-a-chip. Thus, total 378 samples of two types (chicken and beef) with three commercial meat products (frankfurter, nuggets and meatball) of total six (6) different brands purchased from total six (6) supermarket located at Kedah, Penang and Kuala Lumpur of Malaysia (Fig. 4) were negative for feline meat detection using feline SP-PCR based on lab-on-a-chip (Table 4 ). Henceforward, the amazing stability and established sensitivity of this assay initiates its J o u r n a l P r e -p r o o f application for the screening of larger quantity of samples of three major commercial meat products (frankfurters, nuggets and meatballs) of total six brands from different supermarket chains across Malaysia (three-states) for feline species detection. cache = ./cache/cord-292172-aqsc9fbl.txt txt = ./txt/cord-292172-aqsc9fbl.txt === reduce.pl bib === id = cord-292347-d7xq7x5g author = Carter, Linda J. title = Assay Techniques and Test Development for COVID-19 Diagnosis date = 2020-04-30 pages = extension = .txt mime = text/plain words = 3426 sentences = 227 flesch = 51 summary = 375 While RT-PCR-based viral RNA detection has been widely 376 used in diagnosis of COVID-19, it cannot be used to monitor 377 the progress of the disease stages and cannot be applied to 378 broad identification of past infection and immunity. 46,47 410 The determination of SARS-CoV-2 exposure relies largely 411 on the detection of either IgM or IgG antibodies that are 412 specific for various viral antigens including, but not exclusively, 413 the spike glycoprotein (S1 and S2 subunits, receptor-binding 414 domain) and nucleocapsid protein. While RT-PCR has been 571 the dominant technique for detection of viral RNA, other 572 nucleic acid assays including isothermal amplification assays, 573 hybridization microarray assays, amplicon-based metagenomics 574 sequencing, and the cutting-edge CRISPR-related technologies 575 are also under development or have resulted in approved 576 tests. cache = ./cache/cord-292347-d7xq7x5g.txt txt = ./txt/cord-292347-d7xq7x5g.txt === reduce.pl bib === id = cord-292312-cwrqorn1 author = Sales, M. J. T. title = Fernando de Noronha: how an island controlled the community transmission of COVID-19 in Brazil date = 2020-10-27 pages = extension = .txt mime = text/plain words = 4329 sentences = 250 flesch = 56 summary = Conclusion: Despite high levels of COVID-19 in Pernambuco, continued exposure through the provision of essential services from the mainland, and lack of direction from national authorities, FNA was able to implement a series of prevention measures unique in Brazil that contained the epidemic on the island. These included imposing a lockdown, promoting physical distancing and providing emergency assistance to the neediest families; enhancing testing for Sars-Cov-2, including monitoring of arriving travelers, restricting access to the island and the initiation of the cohort study described here to estimate the incidence and prevalence of Covid-19. First we reviewed data extracted from the following sources: 1) demographic and socioeconomic data from the Brazilian Institute of Geography and Statistics 8 ; 2) state and district decrees and 4 ordinances; 3) number of cases and deaths from COVID-19 reported by the Pernambuco State Health Department; 4) flights and passengers from the National Aviation Agency 5 ; and 5) information provided by local authorities and residents. cache = ./cache/cord-292312-cwrqorn1.txt txt = ./txt/cord-292312-cwrqorn1.txt === reduce.pl bib === === reduce.pl bib === id = cord-292772-xdic7rcy author = Petini, Matteo title = Nested–polymerase chain reaction detection of Pneumocystis carinii f. sp. canis in a suspected immunocompromised Cavalier King Charles spaniel with multiple infections date = 2019-04-26 pages = extension = .txt mime = text/plain words = 2467 sentences = 158 flesch = 45 summary = Bordetella bronchiseptica, Mycoplasma spp., and Pneumocystis carinii were identified by polymerase chain reaction testing, and Klebsiella pneumonia was cultured from the bronchoalveolar lavage fluid. canis in a suspected immunocompromised Cavalier King Charles Spaniel with concurrent pulmonary and urinary tract infections involving four different pathogens, and highlights the importance of the use of polymerase chain reaction testing to detect canine Pneumocystis spp. 1 In the veterinary literature, there are many published cases of confirmed canine pneumocystosis-most of which described cases of young to middle-age dogs with suspected immunodeficiency, with the Miniature Dachshund, and the Cavalier King Charles Spaniel (CKCS) breeds most commonly reported. This case report, in the authors' opinion, highlights four points about the diagnosis and clinical presentation of dogs with Pneumocystis spp. Second, the detection of the fungal pathogen was achieved through PCR testing of a BAL sample which was negative with microscopic visualization for Pneumocystis spp. cache = ./cache/cord-292772-xdic7rcy.txt txt = ./txt/cord-292772-xdic7rcy.txt === reduce.pl bib === id = cord-292828-29jbf9ik author = Alsaleh, Asma N title = Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control date = 2014-01-09 pages = extension = .txt mime = text/plain words = 3915 sentences = 185 flesch = 45 summary = title: Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control We therefore investigated the impact of sample collection quality and the presence of visible mould in samples upon respiratory virus detection by real-time polymerase chain reaction (PCR) assays. Quality control measures, including monitoring human DNA loads using ERV3 as a marker for epithelial cell components in samples should be undertaken to optimize the validity of real-time PCR results for respiratory virus investigations in community-based studies. Importantly, when using highly sensitive polymerase chain reaction (PCR) assays the detection rates for respiratory viruses are similar in both anterior nasal swab specimens and samples collected by the more traditional method of nasopharyngeal aspiration [18, 19] . The ORChID project is an ongoing comprehensive community-based study using PCR assays to detect respiratory viruses in anterior nasal swab specimens taken weekly by parents from their infants throughout the first 2-years of life. cache = ./cache/cord-292828-29jbf9ik.txt txt = ./txt/cord-292828-29jbf9ik.txt === reduce.pl bib === === reduce.pl bib === id = cord-292575-vsswxwdi author = Hammou, Rahma Ait title = Chapter 7 Scientific Advances in the Diagnosis of Emerging and Reemerging Viral Human Pathogens date = 2020-12-31 pages = extension = .txt mime = text/plain words = 8496 sentences = 402 flesch = 39 summary = It is in this context that this chapter aims to discuss the various scientific advances, particularly molecular, in terms of diagnosis of these diseases; the new discoveries in the role of nanotechnologies and nanobiosensors; and also the implication of biomarkers, especially microRNAs (miRNAs), since it was reported that a single miRNA has the ultimate capacity to target multiple genes simultaneously. The availability of nucleic acidÀbased technology, such as real-time PCR, along with conventional staining and culture methods and immunoassays, can provide laboratories of many sizes with a comprehensive and responsible approach for the detection of both commonly encountered and emerging or reemerging pathogens. As is the case for SARS, agents of bioterrorism, and the other pathogens, rapid diagnostic methods, such as real-time PCR, and microarray will likely play a major role in the early and sensitive detection of emerging and reemerging infectious diseases encountered in the future. cache = ./cache/cord-292575-vsswxwdi.txt txt = ./txt/cord-292575-vsswxwdi.txt === reduce.pl bib === id = cord-292742-mio4przi author = McAloose, Denise title = From People to Panthera: Natural SARS-CoV-2 Infection in Tigers and Lions at the Bronx Zoo date = 2020-10-13 pages = extension = .txt mime = text/plain words = 6364 sentences = 309 flesch = 47 summary = KEYWORDS One Health, Panthera leo, Panthera tigris, SARS-CoV-2, in situ hybridization, lion, rRT-PCR, tiger, virus isolation, whole-genome sequencing, zoo, zoonotic infection C oronaviruses are a recognized cause of disease in humans and animals (1) . Subsequent to confirmation of SARS-CoV-2 infection in the animals, an epidemiologic investigation of zoo staff identified 10 zoo keepers and two managers who provided care for and had close (Յ1.8-m) but not direct contact with the tigers or lions between 16 March 2020 (the date on which the zoo was closed to the public due to the pandemic) and 27 March to 3 April 2020 (timeline of disease onset in the animals). Nine complete SARS-CoV-2 genome sequences (from four tigers, three lions, and two keepers) and eight full-length S gene sequences (from seven symptomatic animals and one asymptomatic animal) were generated directly from respiratory and/or fecal samples (Data Sets 3 and 4). cache = ./cache/cord-292742-mio4przi.txt txt = ./txt/cord-292742-mio4przi.txt === reduce.pl bib === === reduce.pl bib === id = cord-292928-a4bn30ul author = Ghosh, Bipasha title = Review of bioaerosols in indoor environment with special reference to sampling, analysis and control mechanisms date = 2015-10-03 pages = extension = .txt mime = text/plain words = 16757 sentences = 730 flesch = 39 summary = This review also provides the information on the concentration levels of various airborne microorganisms in different indoor environments, their associated health effects as well as various bioaerosol control mechanisms worked upon till now. A recently developed electrostatic precipitator had no charging unit in the inlet while the physical collection efficiency strongly depended on the precipitation voltage which eventually depended on the charge present on the airborne microbes naturally due to aerosolization (Kunkel, 1950; Flagan, 2001 ) thereby making collection possible by differentiating between the positively and negatively charged microorganisms by adding a signature to the bioaerosol particle sampled (Lee et al., 2004a; ; Lee et al., 2004b) . Whole genome sequencing has also been applied to study the airborne microbial community in various indoor and outdoor environments of NYC after collecting air samples using a Wet Cyclone Portable Air Sampler at the flow rate of 450 L/min (Yooseph et al., 2013) . cache = ./cache/cord-292928-a4bn30ul.txt txt = ./txt/cord-292928-a4bn30ul.txt === reduce.pl bib === id = cord-293234-ouykx6g5 author = Puig-Barberà, J. title = Effectiveness of the 2010–2011 seasonal influenza vaccine in preventing confirmed influenza hospitalizations in adults: A case–case comparison, case-control study date = 2012-08-24 pages = extension = .txt mime = text/plain words = 4417 sentences = 226 flesch = 44 summary = title: Effectiveness of the 2010–2011 seasonal influenza vaccine in preventing confirmed influenza hospitalizations in adults: A case–case comparison, case-control study INTRODUCTION: We estimated influenza vaccine effectiveness (IVE) to prevent laboratory-confirmed influenza-related hospitalizations in patients 18 years old or older during the 2010–2011 influenza season. Using a prospective case-case comparison approach, we have estimated seasonal influenza vaccine effectiveness (IVE) to prevent laboratory confirmed influenza-related hospitalizations in adults. When restricting the comparison, between cases and controls, by the presence of high-risk conditions, the differences that remained significant were age, 23-valent pneumococcal vaccination, and having been vaccinated with the previous or current season influenza vaccines (Table 2) . When restricted to those 60 years old or older, age and influenza vaccination with the previous or current seasonal influenza vaccine remained as significant differences between cases and controls ( Table 2 ). cache = ./cache/cord-293234-ouykx6g5.txt txt = ./txt/cord-293234-ouykx6g5.txt === reduce.pl bib === id = cord-293590-0xn6mqh6 author = Peña, Andrea A title = An evaluation of potential reference genes for stability of expression in two salmonid cell lines after infection with either Piscirickettsia salmonis or IPNV date = 2010-04-14 pages = extension = .txt mime = text/plain words = 3724 sentences = 187 flesch = 48 summary = FINDINGS: The expression stability of five commonly used housekeeping genes [beta-actin (ACTB), elongation factor 1-alpha (EF1A), ubiquitin (UBQ), glyceraldehyd-3-phosphate dehydrogenase (GAPDH) and tubulin alpha (TUBA)] were monitored in salmonid cell lines CHSE-214 and RTS11 after infection with two of the most fastidious fish pathogens, the facultative bacterium Piscirickettsia salmonis and the aquabirnavirus IPNV (Infectious Pancreatic Necrosis Virus). CONCLUSION: Based on the data presented here with the cell culture models CHSE-214 and RTS11, we suggest the initial choice of UBQ, ACTB and EF1A as reference genes in qRT-PCR assays for studying the effect of P. Prior validation of the selected reference gene candidates (ACTB, EF1A, GAPDH, UBQ and TUBA), general expression levels based on mean qPCR threshold cycle (Ct) values in control CHSE-214 and RTS11 cells were determined, since extremely high or low expression levels might preclude their usefulness as internal controls ( Figure 3) . cache = ./cache/cord-293590-0xn6mqh6.txt txt = ./txt/cord-293590-0xn6mqh6.txt === reduce.pl bib === id = cord-293629-1cno01un author = Vila Estapé, Jordi title = Métodos moleculares de diagnóstico de infecciones respiratorias. ¿Ha cambiado el esquema diagnóstico? date = 2016-07-31 pages = extension = .txt mime = text/plain words = 5051 sentences = 363 flesch = 41 summary = En este artículo se pretende hacer una revisión de las diversas técnicas de biología molecular aplicadas al diagnóstico de las infecciones respiratorias, centrándose fundamentalmente en la neumonía, y analizar el impacto que pueden tener en el manejo del paciente con infección respiratoria aguda. En este artículo se pretende hacer una revisión de las diversas técnicas de biología molecular aplicadas al diagnóstico de las infecciones respiratorias, centrándose fundamentalmente en la neumonía, y analizar el impacto que pueden tener en el manejo del paciente con infección respiratoria aguda. En los últimos años se han realizado estudios sobre el impacto de las técnicas moleculares en el manejo y pronóstico de pacientes con infecciones respiratorias, así como de coste-efectividad de su implantación en los laboratorios de microbiología clínica. Aplicación de los métodos moleculares al diagnóstico y el estudio epidemiológico de las infecciones respiratorias causadas por virus cache = ./cache/cord-293629-1cno01un.txt txt = ./txt/cord-293629-1cno01un.txt === reduce.pl bib === id = cord-293421-0ksn0fc7 author = Rodriguez, J. M. title = Detection of animal pathogens by using the polymerasechain reaction (PCR) date = 1997-05-31 pages = extension = .txt mime = text/plain words = 9106 sentences = 559 flesch = 49 summary = Summary The polymerase chain reaction (PCR) is a nucleic acid-based technique that enables the rapid and sensitive detection of specific micro-organisms. Althougla PCR has some shortcomings, such as the problems caused by contaminants and inhibitors or the lack of suitable sequences for designing specific primers, the outstanding research effort focused on tiffs technique, together with the remarkable development of molecular biology have minimized the deficiencies and allowed its increased general use as a diagnostic tool. Sensitive studies using reference strains of BVDV fi-om persistently infected carriers have shown that reverse transo-iption (RT)-PCR has greater sensitivity than other tests, including enzyme-linked immunosorbent assay (ELISA) (Horner el aL, 1995) ; unfortunately, cost currently makes this technique unsuitahle for large-scale testing but it should be valuahle as a coniirmatm T test in cases where ELISA resuhs are in the 'suspicious range' or where the viral titre is low, such as in batches of foetal bovine serum. Comparison of polymerase chain reaction and virus isolation for detection of epizootic hemorrhagic disease in clinical samples from naturally infected deer cache = ./cache/cord-293421-0ksn0fc7.txt txt = ./txt/cord-293421-0ksn0fc7.txt === reduce.pl bib === id = cord-293849-p3j2keyo author = Renaud, Christian title = Comparison of FilmArray Respiratory Panel and laboratory-developed real-time reverse transcription–polymerase chain reaction assays for respiratory virus detection date = 2012-12-31 pages = extension = .txt mime = text/plain words = 3288 sentences = 153 flesch = 47 summary = Eighty-four respiratory viruses identified by laboratory-developed real-time reverse transcription–PCR assays (LDA) or by viral cultures were mixed and tested by FilmArray to assess its performance. The cost of each reagent pouch was approximately 6-fold higher than the cost per sample of the reagents needed to perform the laboratory-developed multiplexed real-time RT-PCR assays for detection of 12 respiratory viruses. The sensitivity of the FilmArray Respiratory Panel assay was comparable to our LDA for detection of 12 respiratory viruses in clinical samples and in dilutions of positive control mixes. In the analysis of 34 positive mixed clinical specimens, the FilmArray had results similar to those in another study comparing FilmArray with real-time PCR assays, identifying 90% of the 80 viruses detected by our LDA (Pierce et al., 2012) . In other situations, use of multiplexed Table 4 Results of laboratory-developed real-time RT-PCR assays and FilmArray Respiratory Panel assay for dilutions of the influenza positive mix control. cache = ./cache/cord-293849-p3j2keyo.txt txt = ./txt/cord-293849-p3j2keyo.txt === reduce.pl bib === id = cord-294138-h7sfd1wa author = McIver, David J. title = Coronavirus surveillance of wildlife in the Lao People’s Democratic Republic detects viral RNA in rodents date = 2020-06-01 pages = extension = .txt mime = text/plain words = 2780 sentences = 130 flesch = 56 summary = Both countries were involved in the United States Agency for International Development's (USAID) Emerging Pandemic Threats PREDICT program, and surveillance of bats in wildlife markets in rural areas in Laos using family-level PCR assays revealed the presence of CoV RNA in 41 animals [5] . Considering the significant interactions of wildlife and especially rodents with humans in Laos, we were interested in investigating the presence of CoVs in these animals, which can be primary or intermediate hosts for CoVs with zoonotic potential. Since there are abundant contact opportunities for wildlife pathogens and humans in Laos, and considering that coronavirus-zoonotic events can involve intermediate hosts, as in the cases of SARS and MERS, we focused our screening on non-bat species potentially capable of playing that role. It is worth noting that we targeted rodents most likely to be in contact with humans and transmit virus and found fewer CoV-RNA-positive animals than in other studies of rodents in the region or elsewhere. cache = ./cache/cord-294138-h7sfd1wa.txt txt = ./txt/cord-294138-h7sfd1wa.txt === reduce.pl bib === id = cord-293966-5c466xvz author = Fehr, Anthony R. title = Bacterial Artificial Chromosome-Based Lambda Red Recombination with the I-SceI Homing Endonuclease for Genetic Alteration of MERS-CoV date = 2019-09-14 pages = extension = .txt mime = text/plain words = 3813 sentences = 229 flesch = 62 summary = Quickly after the identification of Middle East respiratory syndrome-CoV (MERS-CoV), both in vitro ligation and BAC-based reverse genetic technologies were engineered for MERS-CoV to study its basic biological properties, develop live-attenuated vaccines, and test antiviral drugs. Here, I will describe how lambda red recombination can be used with the MERS-CoV BAC to quickly and efficiently introduce virtually any type of genetic modification (point mutations, insertions, deletions) into the MERS-CoV genome and recover recombinant virus. In the method described here, this recognition site is engineered on a plasmid (pEP-KanS) just outside of the positive selection marker, and its cleavage with the I-SceI enzyme allows for the removal of the positive selection marker by intramolecular Red recombination utilizing sequence duplication introduced in the original PCR primers. Using 1 μL of the BAC DNA, use the external primers located 100-200 bp outside the region of homology you previously designed to test for the insertion of Kan r -I-SceI by PCR. cache = ./cache/cord-293966-5c466xvz.txt txt = ./txt/cord-293966-5c466xvz.txt === reduce.pl bib === id = cord-294335-qnu19ru5 author = Yousaf, Anna R title = A prospective cohort study in non-hospitalized household contacts with SARS-CoV-2 infection: symptom profiles and symptom change over time date = 2020-07-28 pages = extension = .txt mime = text/plain words = 3221 sentences = 179 flesch = 50 summary = We assessed symptoms reported by household contacts on the collection date of their first RT-PCRpositive NP specimen (Figure 1 , Subset A), and categorized symptoms as constitutional (fever, chills, myalgia, or fatigue), upper respiratory (runny nose, nasal congestion, or sore throat), lower respiratory (cough, difficulty breathing, shortness of breath, wheezing, or chest pain), neurologic (headache, loss of taste, or loss of smell), and gastrointestinal (nausea/vomiting, diarrhea, or abdominal pain). We identified and prospectively followed household contacts who were asymptomatic at the time they initially tested positive for SARS-CoV-2 by PCR ( Figure 1 , Subset B) to see if they developed symptoms during the study period. The symptom profiles and demographic characteristics of our cohort of SARS-CoV-2 RT-PCR positive household contacts differ from those described in inpatient populations [3] [4] [5] 12] . cache = ./cache/cord-294335-qnu19ru5.txt txt = ./txt/cord-294335-qnu19ru5.txt === reduce.pl bib === id = cord-294155-94skyx5f author = Terrosi, Chiara title = Human bocavirus detection in an atopic child affected by pneumonia associated with wheezing date = 2007-08-07 pages = extension = .txt mime = text/plain words = 1360 sentences = 82 flesch = 52 summary = HBoV was detected in respiratory samples by PCR, but its aetiologic role in the pathogenesis of acute respiratory infectious diseases is still unclear. CONCLUSIONS: Detection of HboV, as the only microbial agent, in samples from children with wheezing and acute respiratory diseases supports the assumption that this emerging virus could have an aetiologic role in the pathogenesis of respiratory diseases. A new parvovirus, the human bocavirus (HBoV), has recently been discovered by the application of random PCR/cloning technique on respiratory samples (Allender et al., 2005) . In this report, we describe a case of pneumonia and severe wheezing associated with HBoV DNA in the pharyngeal swab sample from a child. The detection of HBoV in the nasopharyngeal swab in a child with a clinical picture of pneumonia supports the assumption that this virus has a causative role in respiratory diseases. Human bocavirus DNA detected by quantitative real-time PCR in two children hospitalized for lower respiratory tract infection cache = ./cache/cord-294155-94skyx5f.txt txt = ./txt/cord-294155-94skyx5f.txt === reduce.pl bib === id = cord-294947-g4ntyddb author = Zhu, Yu title = Establishment of a nanoparticle-assisted RT-PCR assay to distinguish field strains and attenuated strains of porcine epidemic diarrhea virus date = 2016-06-10 pages = extension = .txt mime = text/plain words = 2849 sentences = 154 flesch = 54 summary = title: Establishment of a nanoparticle-assisted RT-PCR assay to distinguish field strains and attenuated strains of porcine epidemic diarrhea virus In this study, a nanoparticle-assisted polymerase chain reaction (nanoparticle-assisted RT-PCR) assay targeting the ORF3 of PEDV was developed to distinguish PEDV field strains from attenuated strains by using a specific pair of primers. The nanoparticle-assisted RT-PCR assay we describe here can be used to distinguish field strains from vaccine strains of PEDV, and it shows promise for reducing economic loss due to PEDV infection. The results showed that the nanoparticle-assisted RT-PCR assay could distinguish PEDV field strains from the attenuated strain in samples from infected pigs. The present study demonstrated that an effective nanoparticle-assisted RT-PCR assay targeting the ORF3 gene of PEDV was able to distinguish field strains from attenuated vaccine strains. Development of a nanoparticle-assisted PCR assay for detection of porcine epidemic diarrhea virus cache = ./cache/cord-294947-g4ntyddb.txt txt = ./txt/cord-294947-g4ntyddb.txt === reduce.pl bib === === reduce.pl bib === id = cord-294546-0otd1heg author = Prendki, V. title = Accuracy of comprehensive PCR analysis of nasopharyngeal and oropharyngeal swabs for CT-scan-confirmed pneumonia in elderly patients: a prospective cohort study date = 2019-01-12 pages = extension = .txt mime = text/plain words = 3021 sentences = 169 flesch = 39 summary = CONCLUSION: Comprehensive molecular testing of NPS increases the number of pathogens detected compared with routine methods, but results are poorly predictive of the presence of pneumonia. showed in a randomized controlled trial (107 individuals with lower respiratory tract infections, mean age 65 years) that PCR for viruses and atypical bacteria in nasopharyngeal and oropharyngeal swabs (NPS) allowed the identification of additional pathogens but did not reduce antibiotic use or costs [7] . Individuals admitted to hospital for suspected pneumonia had NPS collected at inclusion for the detection of multiple bacterial and viral pathogens using multiplex PCR (comprehensive molecular testing), in addition to routine testing. Demographic data, co-morbidities, vital signs, clinical findings, severity scores, results of standard laboratory tests, blood, sputum and urine cultures, urinary antigen detection, PCR for respiratory viruses on NPS, and antimicrobial therapy administered were recorded prospectively. cache = ./cache/cord-294546-0otd1heg.txt txt = ./txt/cord-294546-0otd1heg.txt === reduce.pl bib === id = cord-295296-jtjx1vgd author = Tiwari, Shashi Kant title = `In-silico primer designing and PCR for detection of novel coronavirus-19 date = 2020-10-23 pages = extension = .txt mime = text/plain words = 569 sentences = 43 flesch = 67 summary = title: 'In-silico primer designing and PCR for detection of novel coronavirus-19 Novel corona virus (2019-nCoV or COVID-19) pandemic has been considered as a major public health emergency in the world of this century. Novel corona virus (2019-nCoV or COVID-19) pandemic has been considered as a major public health emergency in the world of this century. qRT-PCR primer and probe were designed within conserved region from whole genome, RNA dependent RNA polymerase (RdRP) and envelope to detect SARS-CoV2 from COVID-19 virus isolated from Wuhan, China (Gene bank No: NC_045512, MT072668.1and MT111896.1 respectively). All these sets of primers of COVID-19 were highly specific and any of the primer set either syber green based or Taqman probe based may be useful for commercial one step RT-PCR based kit development for the molecular diagnosis of COVID-19 viruses. The assay based on one step qRT-PCR detection will be sensitive, rapid and specific to detect COVID-19 viruses in mouth swab, nasal swab, cache = ./cache/cord-295296-jtjx1vgd.txt txt = ./txt/cord-295296-jtjx1vgd.txt === reduce.pl bib === id = cord-295401-3p6q92x4 author = Gueudin, M title = Quantitation of respiratory syncytial virus RNA in nasal aspirates of children by real-time RT-PCR assay date = 2003-02-18 pages = extension = .txt mime = text/plain words = 3975 sentences = 206 flesch = 60 summary = title: Quantitation of respiratory syncytial virus RNA in nasal aspirates of children by real-time RT-PCR assay RSV and GAPDH were quantified in nasal aspirates from 75 children hospitalised for acute respiratory tract disease: 31 (41.3%) were positive according to the immunofluorescence assay (IFA), 34 (45.3%) were culture-positive and 42 (56%) were positive according to our real-time RT-PCR method. RNA and DNA extracted from cell cultures infected with different respiratory viruses were screened by the real-time RT-PCR for RSV to assess the specificity of this assay. Of the 42 samples found to be positive by the real-time RT-PCR assay for RSV, six could not be quantitated as the number of RSV RNA copies contained was below the detection limit of the technique; two of these six samples were also culturepositive. The sensitivity of the real-time RT-PCR assay for RSV on clinical samples was 56%, which is significantly higher than the sensitivity of conventional techniques for the detection of RSV in nasal aspirates. cache = ./cache/cord-295401-3p6q92x4.txt txt = ./txt/cord-295401-3p6q92x4.txt === reduce.pl bib === id = cord-296109-kco85lqn author = Vanuytsel, Kim title = Rapid Implementation of a SARS-CoV-2 Diagnostic qRT-PCR Test with Emergency Use Authorization at a Large Academic Safety-Net Hospital date = 2020-05-19 pages = extension = .txt mime = text/plain words = 2499 sentences = 132 flesch = 47 summary = Furthermore, vulnerable populations such as those served by Boston Medical Center (BMC), the largest safety net hospital in New England, represent a high-risk group across multiple dimensions, including a higher prevalence of pre-existing conditions and substance use disorders, lower health maintenance, unstable housing, and a propensity for rapid community spread, highlighting the urgent need for expedient and reliable in-house testing. In the United States, significant delays in the rapid development and distribution of diagnostic testing for SARS-CoV-2 infection have prevented adequate COVID-19 patient care and public health management of the pandemic (Sharfstein et al., 2020) , impacting the timely mapping of the dynamics of viral spread in the general population, and more topically, the conservation of personal protective equipment. Subsequently, we implemented a quantitative, real-time reverse transcriptase polymerase chain reaction (qRT-PCR)-based assay to detect viral SARS-CoV-2 RNA from nasopharyngeal swabs, based on guidelines from the Centers for Disease Control and Prevention (CDC) and the FDA for use with in-house testing of BMC patient samples ( Figure 1 ) (CDC, 2020; Wang et al., 2020a). cache = ./cache/cord-296109-kco85lqn.txt txt = ./txt/cord-296109-kco85lqn.txt === reduce.pl bib === id = cord-295445-f4p00yaw author = Wang, Hao title = Differential removal of human pathogenic viruses from sewage by conventional and ozone treatments date = 2018-02-01 pages = extension = .txt mime = text/plain words = 6889 sentences = 284 flesch = 48 summary = Previous studies conducted in wastewater treatment plants have shown that ozone disinfection might be highly efficient in inactivating bacteria and bacteriophages after conventional sewage treatments (Kim et al., 1999; Tyrrell et al., 1995) , but knowledge regarding its effect for reducing human enteric viruses is relatively scarce. The four concentrated water samples (incoming sewage, conventionally treated, ozone treated, and outlet water) from each of the three weeks were also analyzed by qPCR for 14 common enteric viruses (adenovirus, astrovirus, hepatitis A virus, hepatitis E virus, norovirus GI, norovirus GII, norovirus GIV, parechovirus, sapovirus, aichivirus, mengovirus, torovirus, enterovirus, and rotavirus). However, in this study some viruses that were undetectable in the ozone-treated samples reoccurred in the outlet water, including parvovirus, norovirus GII, human feces pecovirus, parvovirus-like virus, gokushovirus, and HAdV-F41, although the amounts were significantly lower compared with raw sewage. cache = ./cache/cord-295445-f4p00yaw.txt txt = ./txt/cord-295445-f4p00yaw.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-296392-2u9mz6d3 author = Sarıgül, Figen title = Investigation of compatibility of severe acute respiratory syndrome coronavirus 2 reverse transcriptase-PCR kits containing different gene targets during coronavirus disease 2019 pandemic date = 2020-08-26 pages = extension = .txt mime = text/plain words = 3891 sentences = 209 flesch = 51 summary = title: Investigation of compatibility of severe acute respiratory syndrome coronavirus 2 reverse transcriptase-PCR kits containing different gene targets during coronavirus disease 2019 pandemic This value being higher than 0.73 coefficient obtained through comparison of RdRps of the two kits only, showed that inclusion of a secondary biomarker by Diagnovital improved the correlation of different kits. In this study, we investigated the compatibility between the two different SARS-CoV-2 PCR kits produced in Turkey during the COVID-19 pandemic. Nevertheless, the strong correlation of the two kit results suggested that two different RNA targeting gene assays were appropriate as suggested by WHO in the diagnosis of COVID-19 disease [20] . showed that similar results were found; the PCR kit with two different genes of the SARS-CoV-2 had a higher yield than the other two kits performing one gene analysis [21] . cache = ./cache/cord-296392-2u9mz6d3.txt txt = ./txt/cord-296392-2u9mz6d3.txt === reduce.pl bib === id = cord-296979-8r851j4t author = Zhong, Ying title = Host genes regulate transcription of sperm-introduced hepatitis B virus genes in embryo date = 2017-10-31 pages = extension = .txt mime = text/plain words = 6753 sentences = 322 flesch = 49 summary = Eighteen healthy donors were randomly divided into six groups, and their sperm samples were used to fertilize zona-free hamster oocytes in vitro and assess the effects of the silencing of five target genes (CSH2, EIF4G2, PCBD2, PSG4 and TTN) and a control gene (ESRRG) on transcription of HBV s and x genes by real-time quantitative (q)RT-PCR. Eighteen healthy donors were randomly divided into six groups, and their sperm sample were used to fertilize zona-free hamster oocytes in vitro and assess the effects of the silencing of five target genes (CSH2, EIF4G2, PCBD2, PSG4 and TTN) and a control gene (ESRRG) on transcription of HBV S and X genes in two-cell embryos using real time qRT-PCR and 2 − CT method. cache = ./cache/cord-296979-8r851j4t.txt txt = ./txt/cord-296979-8r851j4t.txt === reduce.pl bib === id = cord-296736-jsm6o5pq author = Chidlow, Glenys R. title = An Economical Tandem Multiplex Real-Time PCR Technique for the Detection of a Comprehensive Range of Respiratory Pathogens date = 2009-06-08 pages = extension = .txt mime = text/plain words = 4131 sentences = 183 flesch = 43 summary = title: An Economical Tandem Multiplex Real-Time PCR Technique for the Detection of a Comprehensive Range of Respiratory Pathogens The aim of this study was to modify real-time PCR assays to facilitate the rapid screening of respiratory samples for a comprehensive range of viral and bacterial pathogens. This tandem multiplex real-time PCR assay, in combination with the semi-nested picornavirus and human metapneumovirus PCR assays, tests for 35 respiratory agents from a sample volume of 180µL compared to 720 µL required for the individual assays. Further work is planned to incorporate the picornavirus and human metapneumovirus assays into the tandem multiplex real-time PCR assay, but so far we have been unable to design or use published real-time PCR primers and probes that detect all types of these viruses with the same sensitivity as our nested assays. A tandem multiplex real-time assay is presented which detects a comprehensive range of respiratory pathogens from a specimen sample of 180µL. Multiplex real-time PCR assay for detection of Influenza and human respiratory syncytial viruses cache = ./cache/cord-296736-jsm6o5pq.txt txt = ./txt/cord-296736-jsm6o5pq.txt === reduce.pl bib === === reduce.pl bib === id = cord-298051-ej8qxkce author = Louten, Jennifer title = Detection and Diagnosis of Viral Infections date = 2016-05-06 pages = extension = .txt mime = text/plain words = 11204 sentences = 602 flesch = 57 summary = Cell lines can be infected with patient samples to allow viral replication within the cells; observable cytopathic effects can help to identify the identity of the virus. Infected cells can also be used for immunofluorescence assays, which use fluorescently labeled virus-specific antibodies to identify viruses in fixed cells or tissues. In the process of PCR, DNA (including any viral DNA present) is isolated from the clinical specimen, generally blood cells or tissue, and added to a tube containing primers, DNA polymerase, and nucleotides ( Fig. 7.14) . The diagnostic techniques described in this chapter identify the presence of a virus in a sample, or even the amount of viral nucleic acid, but these assays cannot determine the amount of virus present that is capable of productively infecting cells. Fluorescently labeled antibodies bind to viral antigens present in infected cells. cache = ./cache/cord-298051-ej8qxkce.txt txt = ./txt/cord-298051-ej8qxkce.txt === reduce.pl bib === id = cord-297396-r1p7xn3a author = Ng, Ming-Yen title = Development and Validation of Risk Prediction Models for COVID-19 Positivity in a Hospital Setting date = 2020-09-15 pages = extension = .txt mime = text/plain words = 3251 sentences = 182 flesch = 53 summary = OBJECTIVES: To develop:(1) two validated risk prediction models for COVID-19 positivity using readily available parameters in a general hospital setting; (2) nomograms and probabilities to allow clinical utilisation.  Developed two simple-to use nomograms for identifying COVID-19 positive patients  Probabilities are provided to allow healthcare leaders to decide suitable cut-offs  Variables are age, white cell count, chest x-ray appearances and contact history  Model variables are easily available in the general hospital setting. To develop: (1) two validated risk prediction models for COVID-19 positivity using readily available parameters in a general hospital setting; (2) nomograms and probabilities to allow clinical utilisation. Thus, a COVID-19 prediction model based on clinical, laboratory and radiological findings which presents the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) would allow public healthcare systems to decide a suitable strategy on prioritizing tests when such RT-PCR availability is constrained. cache = ./cache/cord-297396-r1p7xn3a.txt txt = ./txt/cord-297396-r1p7xn3a.txt === reduce.pl bib === id = cord-296819-gztmidn2 author = Sambri, Vittorio title = Diagnosis of West Nile Virus Human Infections: Overview and Proposal of Diagnostic Protocols Considering the Results of External Quality Assessment Studies date = 2013-09-25 pages = extension = .txt mime = text/plain words = 6732 sentences = 304 flesch = 42 summary = title: Diagnosis of West Nile Virus Human Infections: Overview and Proposal of Diagnostic Protocols Considering the Results of External Quality Assessment Studies This paper reviews the presently available methods to achieve the laboratory diagnosis of West Nile virus infections in humans, discussing the most prominent advantages and disadvantages of each in light of the results obtained during four different External Quality Assessment studies carried out by the European Network for 'Imported' Viral Diseases (ENIVD). For the routine detection of WNV RNA using molecular techniques there are two distinct diagnostic settings: the first involves blood and organ donation screening from subjects living in an area where WNV circulation is known to be occurring, and the second involves the identification of viral genomes in serum, plasma and CSF samples from patients presenting with a clinical picture typical of WNV infection [21] . cache = ./cache/cord-296819-gztmidn2.txt txt = ./txt/cord-296819-gztmidn2.txt === reduce.pl bib === id = cord-297646-49l6k5h2 author = Yu, Zhongjia title = Prevalence of intestinal parasites in companion dogs with diarrhea in Beijing, China, and genetic characteristics of Giardia and Cryptosporidium species date = 2017-11-18 pages = extension = .txt mime = text/plain words = 4599 sentences = 244 flesch = 52 summary = title: Prevalence of intestinal parasites in companion dogs with diarrhea in Beijing, China, and genetic characteristics of Giardia and Cryptosporidium species In this study, we performed a survey of intestinal parasites in fecal specimens (n = 485) collected from outpatient pet dogs with diarrhea in Beijing, China, for the entire year of 2015 by microscopic examination (all parasites) and SSU rRNA-based nested PCR detection (Giardia and Cryptosporidium). Smears were examined microscopically for the presence of common parasites by observing eggs of helminthes (e.g., Toxocara canis [canine ascariasis] and Trichuris vulpis [canine whipworm]) and oocysts or trophozoites of protozoa (e.g., coccidia, Giardia duodenalis and trichomonads Tritrichomonas foetus/Pentatrichomonas hominis). We collected a total of 485 fecal specimens in year 2015 from outpatient dogs with diarrhea, in which 124 specimens were parasite-positive by wet mount microscopic examination and/ or PCR detection (i.e., an overall positive rate at 25.6%, n = 124) ( Table 1 , Fig. 1a ). cache = ./cache/cord-297646-49l6k5h2.txt txt = ./txt/cord-297646-49l6k5h2.txt === reduce.pl bib === id = cord-298991-5qae0ege author = Aiello, Francesco title = Coronavirus disease 2019 (SARS-CoV-2) and colonization of ocular tissues and secretions: a systematic review date = 2020-05-18 pages = extension = .txt mime = text/plain words = 3143 sentences = 183 flesch = 50 summary = SARS-CoV-2 may use ocular structure as an additional transmission route, as demonstrated by the COVID-19 patients' conjunctival secretion and tears positivity to reverse transcriptase-PCR SARS-CoV-2-RNA assay. This systematic review will firstly attempt to analyse the current knowledge on SARS-CoV-2 colonization of ocular and periocular tissues and secretions (i.e., cornea, conjunctiva, lacrimal sac, and tears), in order elucidate if conjunctival transmission occurs, and secondarily aims to propose a potential diagnostic tool in the evaluation of suspected, infected patients. Due to the scant evidence, both original articles, editorials, letters, and reviews providing evidence (i.e., prevalence, anecdotal report) about SARS-CoV-2 colonization of ocular and periocular tissues and secretions were all included in the study. This systematic review analysed 252 SARS-CoV-2infected patients globally who underwent conjunctival swab, and demonstrates the prevalence of ocular conjunctivitis complicating the course of COVID-19 to be as high as 32% (12 patients out 38) , differently as what Lu et al. cache = ./cache/cord-298991-5qae0ege.txt txt = ./txt/cord-298991-5qae0ege.txt === reduce.pl bib === id = cord-296593-ox6x53vj author = Sonoo, M. title = Correlation between PCR Examination Rate among the Population and the Containment of Pandemic of COVID-19 date = 2020-05-16 pages = extension = .txt mime = text/plain words = 1081 sentences = 81 flesch = 58 summary = We investigated the relation between PCR examination rate among population and the success of containment of COVID-19. We investigated the relation between PCR examination rate among population and the success of containment of COVID-19. Close inspection of individual countries suggested that the social distancing is the largest factor to achieve containment, and the contribution of broad PCR tests is smaller. Close inspection of individual countries suggested that the social distancing is the largest factor to achieve containment, and the contribution of broad PCR tests is smaller. . https://doi.org/10.1101/2020.05.13.20100982 doi: medRxiv preprint Coronavirus disease 2019 (COVID-19) pandemic is now a worldwide peril and its control is an emergent issue. Trajectory analysis of new coronavirus COVID-19 cases and deaths by country No reuse allowed without permission.(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. cache = ./cache/cord-296593-ox6x53vj.txt txt = ./txt/cord-296593-ox6x53vj.txt === reduce.pl bib === id = cord-298462-xpx3orvs author = Lin, Feng title = Quantification of human bocavirus in lower respiratory tract infections in China date = 2007-01-31 pages = extension = .txt mime = text/plain words = 1455 sentences = 82 flesch = 52 summary = A quantitative PCR method was established to quantify human bocavirus (HBoV) genomic copies in clinical specimens from children with lower respiratory tract infections (LRTI) in China. Recently, a reliable quantitative PCR (Q-PCR) method has been developed to detect HBoV genomic copies in clinical samples, and this has demonstrated a presence of HBoV DNA in children with pneumonia-like symptoms in Thailand [14] . In this study, we used a Q-PCR with the amplicon targeted to the NS coding region of HBoV to detect the presence of HBoV DNA in children with respiratory tract infection in China. All 7 positive samples were either sputum or aspirated sputum, indicating a significant presence of HBoV DNA in lower respiratory tract. HBoV (Human bocavirus); LTRI (Lower respiratory tract infection); Q-PCR (Quantitative polymerase chain reaction). Detection of human bocavirus in Japanese children with lower respiratory tract infections cache = ./cache/cord-298462-xpx3orvs.txt txt = ./txt/cord-298462-xpx3orvs.txt === reduce.pl bib === id = cord-299537-lbx1plqx author = Wang, Wei title = Molecular monitoring of causative viruses in child acute respiratory infection in endemo-epidemic situations in Shanghai date = 2010-09-19 pages = extension = .txt mime = text/plain words = 3998 sentences = 227 flesch = 53 summary = METHODS: A 2-year surveillance program of children presenting with acute respiratory infections (ARIs) was carried out to characterize the viral etiology and to assess whether using gene amplification and sequencing could be a reliable approach to monitor virus introduction and spread in a population subgroup. RESULTS: Using multiplex RT-PCR, 15 different respiratory viruses were detected within the 486 nasopharyngeal positive samples collected among 817 children aged <9-year old who presented with ARI during October 2006 to September 2008. CONCLUSIONS: This study supports the usefulness of multiplex RT-PCR for virus detection and co-infection, and for implementation of a molecular monitoring system for endemic and epidemic viral respiratory infections. In the present 2-year study, we used a five-tube mRT-PCR assay we implemented in the Pasteur Institute network in the Asian region (http://www.pasteur-international.org/ip/easysite/ pasteur-international/activites-scientifiques/projets/tous-lesprojets/sisea), which covered 17 common respiratory viruses, 10 to identify viruses in nasopharyngeal specimens in 817 children with Table 1 Criteria of patient enrollment. cache = ./cache/cord-299537-lbx1plqx.txt txt = ./txt/cord-299537-lbx1plqx.txt === reduce.pl bib === id = cord-299585-fkg8d6ym author = Wang, Leyi title = Development of a triplex real-time RT-PCR assay for detection and differentiation of three US genotypes of porcine hemagglutinating encephalomyelitis virus date = 2019-04-05 pages = extension = .txt mime = text/plain words = 2722 sentences = 132 flesch = 55 summary = title: Development of a triplex real-time RT-PCR assay for detection and differentiation of three US genotypes of porcine hemagglutinating encephalomyelitis virus In the present study, we report the development of a triplex real-time RT-PCR assay for detection and differentiation of three PHEV genotypes, 1, 2, and 3. The triplex real-time RT-PCR provides a rapid and sensitive method to detect and differentiate all three US genotypes of PHEV from clinical samples. Porcine hemagglutinating encephalomyelitis virus (PHEV) is one of six known porcine coronaviruses (CoVs) causing diseases in pigs (Gong et al., 2017; Wang and Zhang, 2016) . The triplex rRT-PCR developed in the present study will fulfill this purpose and can be used to monitor PHEV of different genetic genotypes and differentiate between them. The detection limit of the triplex rRT-PCR assay was determined by testing 10-fold serially diluted positive PHEV RNAs (15SW1362 and 15SW25049) and plasmid DNAs (pCR 2.1-15SW1582-N, pCR 2.1-15SW1362-NS2, and pCR 2.1-15SW25049-NS2) in duplicate. cache = ./cache/cord-299585-fkg8d6ym.txt txt = ./txt/cord-299585-fkg8d6ym.txt === reduce.pl bib === id = cord-298600-cnolne6k author = Majeed, Talal title = The Role of the Computed Tomography (CT) Thorax in the Diagnosis of COVID-19 for Patients Presenting with Acute Surgical Emergencies. A Single Institute Experience date = 2020-10-20 pages = extension = .txt mime = text/plain words = 3221 sentences = 164 flesch = 48 summary = Our aim was to determine the diagnostic accuracy in terms of sensitivity and specificity of CT chest in diagnosing and confirming COVID-19 infection in patients presenting with acute surgical and medical pathologies. Patients admitted for acute surgical emergencies were treated according to RCS guidelines and subjected to RT-PCR test and/or CT scan of the thorax. Patients admitted for acute surgical emergencies were treated according to RCS guidelines and subjected to RT-PCR test and/or CT scan of the thorax. CT imaging was found to have a high false positive rate making it an unreliable tool for a definitive diagnosis in the presence of concomitant respiratory pathologies, but with a strong negative predictive value at 82.4% makes it a useful tool for the exclusion of COVID-19 infection and can be helpful in surgical decision making for asymptomatic patients (Table 1 ).In our study, more than 70% of all acute surgical presentations which are normally treated surgically were treated conservatively with good outcome. cache = ./cache/cord-298600-cnolne6k.txt txt = ./txt/cord-298600-cnolne6k.txt === reduce.pl bib === === reduce.pl bib === id = cord-298049-gabjdkx9 author = Gomez, D.E. title = Detection of Bovine Coronavirus in Healthy and Diarrheic Dairy Calves date = 2017-09-15 pages = extension = .txt mime = text/plain words = 4538 sentences = 257 flesch = 62 summary = OBJECTIVES: To investigate the detection rates of bovine coronavirus (BCoV) in feces of healthy and diarrheic calves and to describe the usefulness of a pancoronavirus reverse transcriptase (RT) PCR (PanCoV‐RT‐PCR) assay to identify BCoV in samples of diarrheic calves. The objectives of this study were to investigate the detection rates of BCoV in feces of healthy and diarrheic dairy calves and to describe the usefulness of a PanCoV-RT-PCR assay to identify BCoV in nasal and fecal samples of a group of calves from a dairy farm suffering an outbreak of diarrhea. The results of this study demonstrated a positive association between BCoV and diarrhea in dairy calves as detection rates of this agent were higher in diarrheic calves than in farm-, season-, aged-matched nondiarrheic calves. cache = ./cache/cord-298049-gabjdkx9.txt txt = ./txt/cord-298049-gabjdkx9.txt === reduce.pl bib === === reduce.pl bib === id = cord-298002-jvnwivrg author = Wang, Jian title = COVID-19 confirmed patients with negative antibodies results date = 2020-09-22 pages = extension = .txt mime = text/plain words = 1499 sentences = 92 flesch = 59 summary = CASE PRESENTATIONS: We present two cases of confirmed COVID-19 patients and characterize their initial symptoms, chest CT results, medication, and laboratory test results in detail (including RT-PCR, IgM/ IgG, cytokine and blood cell counts). CONCLUSION: Both of patients with confirmed COVID-19 pneumonia failed to produce either IgM or IgG even 40 to 50 days after their symptoms onset. During the outbreak of coronavirus 2019 (COVID-19) [1] [2] [3] , a small proportion of confirmed COVID-19 patients fail to produce IgM or IgG antibodies against SARS-CoV-2 even 40 days or longer periods of time after onset of their initial symptoms. From January 30 to March 15, 310 of COVID-19 patients who were positive for SARS-CoV-2 real time reverse-transcription PCR (RT-PCR) testing and received IgM and IgG detection at Wuhan Union Hospital (Wuhan, China) were enrolled. In this study, two patients with confirmed COVID-19 failed to produce either IgM or IgG even 40 to 50 days after their symptoms onset. cache = ./cache/cord-298002-jvnwivrg.txt txt = ./txt/cord-298002-jvnwivrg.txt === reduce.pl bib === id = cord-298998-n5rhhzc9 author = Vashee, Sanjay title = Cloning, Assembly, and Modification of the Primary Human Cytomegalovirus Isolate Toledo by Yeast-Based Transformation-Associated Recombination date = 2017-10-04 pages = extension = .txt mime = text/plain words = 9327 sentences = 440 flesch = 48 summary = Using an early passage of the human CMV isolate Toledo, we first applied transformation-associated recombination (TAR) to clone 16 overlapping fragments covering the entire Toledo genome in Saccharomyces cerevisiae. Since next-generation sequence analysis revealed that the low-passage-number isolate represented a mixture of parental and fibroblast-adapted genomes, we selectively modified individual DNA fragments of fibroblast-adapted Toledo (Toledo-F) and again used TAR assembly to recreate parental Toledo (Toledo-P). IMPORTANCE The genomes of large DNA viruses, such as human cytomegalovirus (HCMV), are difficult to manipulate using current genetic tools, and at this time, it is not possible to obtain, molecular clones of CMV without extensive tissue culture. IMPORTANCE The genomes of large DNA viruses, such as human cytomegalovirus (HCMV), are difficult to manipulate using current genetic tools, and at this time, it is not possible to obtain, molecular clones of CMV without extensive tissue culture. cache = ./cache/cord-298998-n5rhhzc9.txt txt = ./txt/cord-298998-n5rhhzc9.txt === reduce.pl bib === id = cord-297432-2edncbgn author = Helleberg, Marie title = Persistent COVID-19 in an Immunocompromised Patient Temporarily Responsive to Two Courses of Remdesivir Therapy date = 2020-07-23 pages = extension = .txt mime = text/plain words = 2390 sentences = 139 flesch = 46 summary = A man in his fifties treated with chemoimmunotherapy for chronic lymphocytic leukemia experienced a 9-week course of COVID-19 with high fever and severe viral pneumonia. Recently, preliminary results of the Adaptive COVID-19 Treatment Trial (ACTT), a multicenter randomized controlled trial of remdesivir versus placebo for treatment of coronavirus disease 2019 (COVID-19) in hospitalized patients, demonstrated that remdesivir reduced time to recovery, in particular for those not yet having experienced respiratory failure with need for assisted ventilation [1] . We here report the clinical course and findings in an immunocompromised patient with remission of COVID-19 during treatment with remdesivir but relapse soon after discontinuation. We present a case of severe COVID-19 in a patient with B-and T-lymphocyte impairment secondary to CLL treated with chemoimmunotherapy 3 months prior to the SARS-CoV-2 infection. The course and findings in this clinical case suggest that remdesivir has a rapid onset of action and can suppress, but may not eradicate, SARS-CoV-2 in immunocompromised patients. cache = ./cache/cord-297432-2edncbgn.txt txt = ./txt/cord-297432-2edncbgn.txt === reduce.pl bib === id = cord-298805-ntpm68cg author = Otašević, S. title = Non-culture based assays for the detection of fungal pathogens date = 2018-03-29 pages = extension = .txt mime = text/plain words = 9284 sentences = 402 flesch = 34 summary = Therefore, in order to overcome the limitations, many researchers have focused on the development of new immunological and molecular based rapid assays that could enable early diagnosis of infection and accurate identification of fungal pathogens causing superficial and invasive infection. Therefore, in order to overcome the limitations, many researchers have focused on the development of new immunological and molecular based rapid assays that could enable early diagnosis of infection and accurate identification of fungal pathogens causing superficial and invasive infection. As for the use of GM in diagnosis of invasive aspergilosis, recently published data suggest that detection of this Aspergillus Ag in blood and parallel PCR diagnostics provide very high sensitivity of 99% with specificity of 64% which influence 100% negative predictive value in high risk patients and enable the consideration of no-existing invasive aspergillosis in these patients and no need for antifungal therapy. cache = ./cache/cord-298805-ntpm68cg.txt txt = ./txt/cord-298805-ntpm68cg.txt === reduce.pl bib === id = cord-299672-dq1y1gkc author = Leung, Ting Fan title = Multiplex Molecular Detection of Respiratory Pathogens in Children With Asthma Exacerbation date = 2010-02-28 pages = extension = .txt mime = text/plain words = 3642 sentences = 221 flesch = 51 summary = Conclusions Respiratory viral infections are commonly found in children with asthma exacerbation, with HRV being the most important pathogen in our patients. Our primary outcome was the difference in detection rate for any respiratory pathogen between children with asthma with acute exacerbation and controls (ie, stable asthma). Secondary outcomes consisted of differences in the clinical severity of asthma exacerbation, lung function parameters, and fractional exhaled nitric oxide concentration (FeNO) in relation to patients with different respiratory pathogens. HRV infection was associated with asthma exacerbation in the children, which is consistent with FeNO was the only parameter that differed between patients with and without HRV, being signifi cantly lower in the former group ( P 5 .018). Identifi cation of viral and atypical bacterial pathogens in children hospitalized with acute respiratory infections in Hong Kong by multiplex PCR assays cache = ./cache/cord-299672-dq1y1gkc.txt txt = ./txt/cord-299672-dq1y1gkc.txt === reduce.pl bib === id = cord-298697-v1qdizwx author = Chang, Jia Jin Marc title = Takeaways from Mobile DNA Barcoding with BentoLab and MinION date = 2020-09-24 pages = extension = .txt mime = text/plain words = 7206 sentences = 395 flesch = 56 summary = One of the most common applications of MinION is for nanopore-based DNA barcoding in situ for species identification and discovery, yet the existing sample capability is limited (n ≤ 10). We also tested the performance of the newly released R10.3 nanopore flow cell for DNA barcoding, and showed that the barcodes generated were ~99.9% accurate when compared to Illumina references. For the field sequencing phase, an additional 31 samples were collected and subjected to QE-based DNA extraction on the BentoLab. While we did not run the gel check in situ to save time, a postliminary amplification check on agarose back at the laboratory revealed 20 observable gel bands. For the field sequencing phase, an additional 31 samples were collected and subjected to QE-based DNA extraction on the BentoLab. While we did not run the gel check in situ to save time, a postliminary amplification check on agarose back at the laboratory revealed 20 observable gel bands. cache = ./cache/cord-298697-v1qdizwx.txt txt = ./txt/cord-298697-v1qdizwx.txt === reduce.pl bib === id = cord-300243-5q67tnx4 author = Priya, A. Kokila title = Prevalence of enteropathogens and their antibiotic sensitivity pattern in puppies with hemorrhagic gastroenteritis date = 2017-08-04 pages = extension = .txt mime = text/plain words = 2997 sentences = 172 flesch = 50 summary = The aim of the study was to identify the prevalence of common enteropathogens and the antibiotic sensitivity pattern in puppies reported with HGE. Fecal polymerase chain reaction (PCR) assay was employed to screen and compare the enteropathogens in puppies with hemorrhagic diarrhea and healthy control. The potential enteropathogenic bacteria associated with bacterial gastroenteritis in dogs include Clostridium difficile, Clostridium perfringens, Escherichia coli, Campylobacter jejuni, and Salmonella sp. Fecal samples collected from all the puppies during the study period were screened by polymerase chain reaction (PCR) for the common enteropathogens, including the bacteria, their toxins and viruses. The cpa (alpha toxin) and cpe (enterotoxin) genes corresponding to the Clostridium perfringens were tested to show amplification with a molecular length of 400 and 233 bp [14] . difficile toxin B, enteric CCoV and Rotavirus were found negative in 62 puppies with hemorrhagic diarrhea screened samples. cache = ./cache/cord-300243-5q67tnx4.txt txt = ./txt/cord-300243-5q67tnx4.txt === reduce.pl bib === id = cord-299737-r34d0rx7 author = Grant, Paul R title = Extraction-free COVID-19 (SARS-CoV-2) diagnosis by RT-PCR to increase capacity for national testing programmes during a pandemic date = 2020-04-08 pages = extension = .txt mime = text/plain words = 1383 sentences = 78 flesch = 63 summary = The standard molecular diagnostic test is a multistep process involving viral RNA extraction and real-time quantitative reverse transcriptase PCR (qRT-PCR). We have developed a simplified qRT-PCR assay that removes the need for an RNA extraction process and can be run on a real-time thermal cycler. The standard molecular diagnostic test for this virus is a multistep process involving viral RNA extraction and real-time quantitative reverse transcriptase PCR (qRT-PCR). Using the same primers and probes, we have now developed a qRT-PCR that can be run on a real-time thermal cycler without the need for an RNA extraction process. Direct addition of samples to the qRT-PCR without extraction with a diagnostic sensitivity of 98.0%, specificity of 100% and accuracy of 98.8% compared to the method on the Panther Fusion. Many laboratories use real-time thermal cyclers, so this method can be used to increase national screening capacity without the need for other specialized equipment or RNA extraction reagents. cache = ./cache/cord-299737-r34d0rx7.txt txt = ./txt/cord-299737-r34d0rx7.txt === reduce.pl bib === === reduce.pl bib === id = cord-299944-1e44usl6 author = Gardner, Shea N. title = Multiplex Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes date = 2014-08-03 pages = extension = .txt mime = text/plain words = 4147 sentences = 175 flesch = 52 summary = The major difference is that it begins with a consensus sequence containing degenerate bases and selects primers with fewer than 3 or 4 degenerate bases, so that in the end a majority of strains are amplified, 2 Advances in Bioinformatics Table 1 : Summary of average lengths, number of sequences, and percentage of conserved bases in a multiple sequence alignment (with MUSCLE [5] ), and number of tiled primers required for the short and long amplicon settings. The method here differs in that it takes the full multiple sequence alignment as input rather than a consensus, and it seeks to automatically design a minimal, degenerate set of multiplex compatible primers to amplify all the strains for a given region in a single reaction. The run tiled primers process can be summarized as follows: split a multiple sequence alignment into overlapping regions, and for each region design a degenerate multiplex set of primers that in combination amplify that region in all strains with as few primers as possible. cache = ./cache/cord-299944-1e44usl6.txt txt = ./txt/cord-299944-1e44usl6.txt === reduce.pl bib === id = cord-300285-su2fueox author = Gajurel, Kiran title = Persistently positive severe acute respiratory syndrome coronavirus 2 (SARS‐COV2) nasopharyngeal PCR in a kidney transplant recipient date = 2020-07-27 pages = extension = .txt mime = text/plain words = 384 sentences = 27 flesch = 54 summary = title: Persistently positive severe acute respiratory syndrome coronavirus 2 (SARS‐COV2) nasopharyngeal PCR in a kidney transplant recipient Severe acute respiratory syndrome coronavirus 2 (SARS-COV2 ) infection is usually diagnosed by a positive PCR test in respiratory samples. While the respiratory PCR may remain positive for 2-3 weeks in the general population there have been occasional reports of persistent and recurrent positive SARS-COV2 PCR beyond 4 weeks despite clinical resolution 1-6 . This is particularly relevant in transplant recipients who carry a significant mortality and morbidity associated with SARS COV2 infection. 8 Here, we would like to share our experience of a Follow-up NP SARS COV2 PCR, however, remained intermittently positive for 57 days after the first positive test (Table 1) . Quantifying the prevalence of SARS-CoV-2 long-term shedding among non-hospitalized COVID-19 patients Case report: viral shedding for 60 days in a woman with COVID-19 cache = ./cache/cord-300285-su2fueox.txt txt = ./txt/cord-300285-su2fueox.txt === reduce.pl bib === id = cord-300313-w8njg569 author = Clifford, S. title = Strategies to reduce the risk of SARS-CoV-2 re-introduction from international travellers date = 2020-07-24 pages = extension = .txt mime = text/plain words = 7266 sentences = 363 flesch = 51 summary = To mitigate SARS-CoV-2 transmission risks from international travellers, many countries currently use a combination of up to 14 days of self-quarantine on arrival and testing for active infection. Due to differences in COVID-19 prevalence and estimated travel volume in July 2020, the expected numbers of infectious entries per week in a no-intervention scenario (apart from self-reporting of symptoms and syndromic screening at departure) from the USA are approximately double that of the EU (up to 28 and up to 12, respectively). While the acceptable number of infected travellers entering the community will depend on the local context of SARS-CoV-2 transmission we find that for travellers arriving from low prevalence destinations the absolute risk of seeding new outbreaks is likely low and hence either testing and/or quarantine-based strategies may do little to further reduce such risk, particularly when many infectious arrivals are asymptomatic cases. cache = ./cache/cord-300313-w8njg569.txt txt = ./txt/cord-300313-w8njg569.txt === reduce.pl bib === id = cord-300338-duhyb754 author = Urashima, Mitsuyoshi title = BCG Vaccination and Mortality of COVID-19 across 173 Countries: An Ecological Study date = 2020-08-03 pages = extension = .txt mime = text/plain words = 5672 sentences = 250 flesch = 44 summary = We therefore aimed to explore whether recent BCG vaccine coverage is associated with COVID-19 morbidity and/or mortality rates, using linear regression models to explore associations between the two continuous random variables adjusted for a variety of potential confounders, such as median age and body mass index (BMI) in individual countries through this ecological study. As a result, '≥60 years of age' (p < 0.001) and 'BCG vaccine coverage' (p = 0.002) remained significant factors associated with COVID-19 mortality, even after adjustment for morbidity and PCR-tests. As a result, '≥60 years of age' (p < 0.001) and 'BCG vaccine coverage' (p = 0.002) remained significant factors associated with COVID-19 mortality, even after adjustment for morbidity and PCR-tests. cache = ./cache/cord-300338-duhyb754.txt txt = ./txt/cord-300338-duhyb754.txt === reduce.pl bib === id = cord-300316-r54ksiy3 author = Moesker, F.M. title = Diagnostic performance of influenza viruses and RSV rapid antigen detection tests in children in tertiary care date = 2016-03-25 pages = extension = .txt mime = text/plain words = 3350 sentences = 201 flesch = 56 summary = authors: Moesker, F.M.; van Kampen, J.J.A.; Aron, G.; Schutten, M.; van de Vijver, D.A.M.C.; Koopmans, M.P.G.; Osterhaus, A.D.M.E.; Fraaij, P.L.A. title: Diagnostic performance of influenza viruses and RSV rapid antigen detection tests in children in tertiary care OBJECTIVES: Comparing diagnostic performances of BinaxNow Influenza AB(®) (BNI) and BinaxNow RSV(®) (BNR), to those of real-time reverse transcriptase PCR (RT-PCR), virus isolation and direct immunofluorescence (D-IF) in paediatric patients. Comparing diagnostic performances of two RADTs, BinaxNow Influenza AB ® (BNI) and BinaxNow RSV ® (BNR), with those of RT-PCR in samples of paediatric patients attending our tertiary care centre with ARTIs for a period of almost eight consecutive years. The main outcomes of this study were the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the BNI and BNR rapid test results compared to RT-PCR during the total study period and during viral season (October 1st through March 31st). cache = ./cache/cord-300316-r54ksiy3.txt txt = ./txt/cord-300316-r54ksiy3.txt === reduce.pl bib === id = cord-300399-21xozruq author = Jayamohan, Harikrishnan title = SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations date = 2020-10-18 pages = extension = .txt mime = text/plain words = 13003 sentences = 770 flesch = 44 summary = This review paper examines current molecular diagnostic tools (Fig. 1) , such as amplification-based (including CRISPR-Cas based), antibody and antigen tests, and sequencing, utilized for the detection of SARS-CoV-2. In addition, we also discuss sample preparation aspects that are relevant to wider utilization and point-of-care (POC) deployment of COVID-19 diagnostic tests (PCR, isothermal amplification, and sequencing-including library preparation). RT-PCR broadly involves four steps-lysis of SARS-CoV-2 in the sample, purification of the viral RNA, reverse transcription to complementary DNA (cDNA), and amplification of specific regions of the cDNA, and finally, optical detection of the amplified cDNA. The assay can detect the virus from respiratory swab samples with sensitivity comparable to that of the US Centers for Disease Control and Prevention (CDC) SARS-CoV-2 real-time RT-PCR assay in 30-40 min. Evaluation of novel antigen-based rapid detection test for the diagnosis of SARS-CoV-2 in respiratory samples cache = ./cache/cord-300399-21xozruq.txt txt = ./txt/cord-300399-21xozruq.txt === reduce.pl bib === id = cord-300685-bcjnujlj author = Poon, Leo L M title = Rapid Diagnosis of a Coronavirus Associated with Severe Acute Respiratory Syndrome (SARS) date = 2003-06-01 pages = extension = .txt mime = text/plain words = 2425 sentences = 115 flesch = 54 summary = The detection of live virus (4 ) and the detection of high copy numbers of viral sequence from NPA samples in the current study clearly support that the concept that cough and sneeze droplets from SARS patients are a major route of spread of this infectious agent. Interestingly, two of four available stool samples from the SARS patients in this study were positive in the assay (data not shown). RNA samples from this study were subjected to nested reverse transcription-PCR (4 ), and no evidence of metapneumovirus infection was detected in any of the patients in this study (data not shown), suggesting that the novel coronavirus is the key player in the pathogenesis of SARS. The PCR products from all 23 positive cases in this study had the same melting point, strongly suggesting that there was no viral sequence variation in the target region of samples collected at the two Hong Kong hospitals during the 1-month period of patient accrual. cache = ./cache/cord-300685-bcjnujlj.txt txt = ./txt/cord-300685-bcjnujlj.txt === reduce.pl bib === id = cord-300508-po2zolo8 author = Inoue, Gen title = Experience of an Orthopaedic Surgery Department Early During the COVID-19 Outbreak in Japan Including Real-Time Polymerase Chain Reaction Assay Results for SARS-CoV-2 date = 2020-10-24 pages = extension = .txt mime = text/plain words = 3942 sentences = 182 flesch = 49 summary = With the need to develop an approach to manage orthopaedic surgeries, we aimed to evaluate the most current data on all the surgical cases in our department including the results of the reverse-transcriptase polymerase chain reaction (RT-PCR) assay for infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We also examined the results of PT-PCR for SARS-CoV-2, which was principally performed for all the surgical candidates in our department beginning May 13, and investigated their laboratory test results before surgery, their clinical signs and symptoms, which were reported to be related with COVID-19. evaluated 66 orthopaedic healthcare workers exposed to one patient who became positive for SARS-CoV-2 infection one week after admission, and reported that the RT-PCR assays were negative for all 66 healthcare workers, although 14 (21%) manifested clinical signs/symptoms suggestive of COVID-19, including cough (6.1%), sore throat (4.5%), nasal congestion (4.5%), dyspnoea (3.0%), fever (1.5%), headache, and myalgias (1.5%) [19] . cache = ./cache/cord-300508-po2zolo8.txt txt = ./txt/cord-300508-po2zolo8.txt === reduce.pl bib === id = cord-300999-20c17smt author = Xiao, Yong title = Exploration of turn-positive RT-PCR results and factors related to treatment outcome in COVID-19: A retrospective cohort study date = 2020-09-13 pages = extension = .txt mime = text/plain words = 3382 sentences = 181 flesch = 52 summary = title: Exploration of turn-positive RT-PCR results and factors related to treatment outcome in COVID-19: A retrospective cohort study In the recurrent group, white blood cell, Neutrophils, prothrombin time, activated partial thromboplastin time, CD3, CD4, CD8, ratio of CD4/CD8, IgG and C4 complement were of significant difference among the baseline, negative and turn-positive time points. Due to a lack of specific antiviral treatments and vaccines, identifying and isolating as many potential patients as possible, especially for those with earlyonset of symptoms, is of great importance for the prevention and control of COVID-19 [2] , Real-time reverse-transcriptase polymerase-chain-reaction (RT-PCR) assay is a nucleic acid detection-based approach to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which confer an advantage to rapid detection and specificity [3, 4] . As such, we attempt to review the details of 116 COVID-19 patients in Renmin Hospitals of Wuhan University and thus, perform cause analysis of RT-PCR turn-positive and the effective screening factors related to treatment outcome in COVID-19. cache = ./cache/cord-300999-20c17smt.txt txt = ./txt/cord-300999-20c17smt.txt === reduce.pl bib === id = cord-301066-62qe4fb0 author = Chiu, Susan S. title = Human Coronavirus NL63 Infection and Other Coronavirus Infections in Children Hospitalized with Acute Respiratory Disease in Hong Kong, China date = 2005-06-15 pages = extension = .txt mime = text/plain words = 3944 sentences = 220 flesch = 56 summary = In 2001 and 2002, we performed prospective clinical and virological studies of children (age, р18 years) with acute respiratory tract infection who were admitted to Queen Mary Hospital (Hong Kong, China). We studied a systematic sample of children (age, р18 years) with acute respiratory infection admitted to Queen Mary Hospital during the period from August 2001 to March 2002. One child with HCoV-NL63 upper respiratory tract infection had positive results of only the consensus primer PCR, so no viral load could be measured. We documented that human coronavirus infection was a significant cause of hospitalization for children aged р18 years, accounting for 4.4% of all admissions for acute respiratory infections. A previous study showed that 8.2% of children aged !18 months who were admitted to a Chicago, Illinois, hospital with lower respiratory tract diseases had serological evidence of HCoV-229E or HCoV-OC43 infection [13] . cache = ./cache/cord-301066-62qe4fb0.txt txt = ./txt/cord-301066-62qe4fb0.txt === reduce.pl bib === id = cord-301102-jbjysyqm author = Priestnall, Simon L. title = Quantification of mRNA encoding cytokines and chemokines and assessment of ciliary function in canine tracheal epithelium during infection with canine respiratory coronavirus (CRCoV) date = 2009-01-15 pages = extension = .txt mime = text/plain words = 6022 sentences = 296 flesch = 48 summary = title: Quantification of mRNA encoding cytokines and chemokines and assessment of ciliary function in canine tracheal epithelium during infection with canine respiratory coronavirus (CRCoV) This study aimed to quantify pro-inflammatory cytokine mRNAs following infection of canine air-interface tracheal cultures with CRCoV. This study aimed to quantify pro-inflammatory cytokine mRNAs following infection of canine air-interface tracheal cultures with CRCoV. The quantification of canine IL-6, IL-8 and TNF-a mRNA copies in CRCoV-inoculated cultures was presented as the logarithm of the fold change relative to control-inoculated cultures in the same dog at the same time point. In response to LPS, mRNA levels of TNF-a, IL-6 and IL-8 in cultures, were significantly increased from 24 h post-inoculation, relative to controls, indicating that the assay was sensitive enough to detect changes in cytokine mRNAs within this system. IHC revealed coronavirus antigen positive intra-cytoplasmic staining of ciliated epithelial and goblet cells within canine tracheas of both CRCoV-inoculated cultures and from naturally infected cases of CIRD. cache = ./cache/cord-301102-jbjysyqm.txt txt = ./txt/cord-301102-jbjysyqm.txt === reduce.pl bib === id = cord-301254-093yih5n author = Brittain-Long, Robin title = Prospective evaluation of a novel multiplex real-time PCR assay for detection of fifteen respiratory pathogens—Duration of symptoms significantly affects detection rate date = 2010-01-18 pages = extension = .txt mime = text/plain words = 2860 sentences = 160 flesch = 48 summary = OBJECTIVES: The aim of the present study was to evaluate the diagnostic performance and clinical use of a novel multiplex PCR method in adults with community-acquired respiratory viral infection, and the impact of duration of symptoms on detection rates. CONCLUSIONS: Duration of symptoms significantly affects the detection rate of respiratory pathogens by multiplex real-time PCR in nasopharyngeal swab samples from adult patients with respiratory infections. The aim of the present study was to evaluate the diagnostic performance and clinical use of a novel multiplex PCR method in adults with community-acquired respiratory viral infection, and the impact of duration of symptoms on detection rates. All patients still positive for the same agent on follow-up had a higher Ct-value (corresponding to a lower Table 2 Follow-up (10 ± 2 days after initial visit) test result from analysis with real-time PCR of nasopharyngeal/throat swab specimens. cache = ./cache/cord-301254-093yih5n.txt txt = ./txt/cord-301254-093yih5n.txt === reduce.pl bib === id = cord-301430-gzou8b9k author = Beier, D. title = Establishment of a new bovine leukosis virus producing cell line date = 2004-08-17 pages = extension = .txt mime = text/plain words = 4086 sentences = 248 flesch = 58 summary = In addition, earlier investigations demonstrated that contamination of the BLV antigen-producing cell culture systems by bovine viral diarrhea virus (BVDV) may give rise to misinterpretation of serological test results after BVDV vaccination of cattle. Investigations of a panel of well-characterised sera by agar gel immunodiffusion (AGID) and capture ELISA (cELISA) tests using antigen prepared from this new cell line in comparison with antigen of the well-known cell line FLK/BLV yielded comparable results. Standard and field sera were investigated in parallel with a commercially available test kit (Riemser Rinderleukose Test Kit, RTAM/Germany) in order to compare sensitivity and specificity of the antigens from the cell lines PO714 and FLK/BLV. Comparative investigations of sera from cattle infected with BLV of different provirus subtypes with antigen from both cell lines using the gp51 cELISA. cache = ./cache/cord-301430-gzou8b9k.txt txt = ./txt/cord-301430-gzou8b9k.txt === reduce.pl bib === id = cord-301167-101lnq4f author = Liu, Quanjun title = Microarray-in-a-Tube for Detection of Multiple Viruses date = 2007-02-01 pages = extension = .txt mime = text/plain words = 3248 sentences = 177 flesch = 48 summary = Methods: We developed a novel PCR assay, the microarray-in-a-tube system, which integrates multiple PCR processes and DNA microarrays for multiple virus detection. A 5 × 5 oligonucleotide microarray for detecting 4 respiratory tract viruses (severe acute respiratory syndrome–associated coronavirus, influenza A virus, influenza B virus, and enterovirus) with inner controls was arranged on the inner surface of a specially designed Eppendorf cap with a flat, optically transparent window. We aimed to develop a microarray-in-a-tube that integrates RT-PCR and a DNA microarray for detecting and distinguishing 4 viruses causing human acute respiratory tract infection, SARS coronavirus, influenza A and B viruses, and enterovirus. The system (Fig. 1 ) has 3 parts, which include an optically transparent plastic cap with an oligonucleotide microarray on the inner surface, a black inner vessel that contains hybridization solution, and the body of the Eppendorf tube. cache = ./cache/cord-301167-101lnq4f.txt txt = ./txt/cord-301167-101lnq4f.txt === reduce.pl bib === id = cord-301823-fbeb1nw1 author = Sridhar, Sushmita title = A blueprint for the implementation of a validated approach for the detection of SARS-Cov2 in clinical samples in academic facilities date = 2020-10-21 pages = extension = .txt mime = text/plain words = 6118 sentences = 309 flesch = 51 summary = Here we describe our experience in establishing a COVID-19 diagnostics laboratory in an academic containment level 2 (CL2) research facility (UK) in which we validated and established a real-time PCR workflow to detect SARS-CoV2 in nose and throat swabs from HCWs. We developed an assay and workflow over eight working days (set-up to validation to screening) that can produce a quantitative diagnostic result ~4 hours after swabbing. Establishing and validating the workflow in our setting Establishing a workflow for SARS-Cov2 qRT-PCR Upon the decision to rapidly establish the qRT-PCR assay we identified several challenges, and these included: a) establishment and validation of a method suitable for diagnostic reporting, b) safe extraction of nucleic acid from a highly transmissible virus, c) accessing reagents required for performing extractions and amplifications, d) establishing a "clean" diagnostic workflow to minimise the risk of contamination, and e) creating a system in which HCWs could be swabbed and the data reported confidentially within a specified timeframe. cache = ./cache/cord-301823-fbeb1nw1.txt txt = ./txt/cord-301823-fbeb1nw1.txt === reduce.pl bib === === reduce.pl bib === id = cord-302189-3xab3yxc author = Tillmann, Ramona Liza title = Sensitive Commercial NASBA Assay for the Detection of Respiratory Syncytial Virus in Clinical Specimen date = 2007-12-26 pages = extension = .txt mime = text/plain words = 1777 sentences = 90 flesch = 45 summary = Thereby, NASBA turned out to be the most sensitive method with a total number of 80 RSV positive samples out of a cohort of 251 nasopharyngeal washings from patients suffering from clinical symptoms, followed by the inhouse RT-PCR (62/251) and ELISA (52/251). Despite an increasing number of newly detected respiratory pathogen the human Respiratory syncytial virus (RSV) remains the single most prevalent etiologic agent in pediatric viral respiratory tract infection [1, 2, 3] . In relation to the positive test results obtained with the NucliSENSH EasyQ NASBA, the relative sensitivity of the RT-PCR was 77,5% compared to 65% obtained with the NOWH RSV ELISA. The results showed that from the three tested methods for molecular diagnosis of RSV the NucliSENSH EasyQ NASBA (bioMerieux, Nürtingen, Germany) detected the most RSV positive samples in a cohort of 251 nasopharyngeal samples of pediatric patients hospitalized with respiratory disease. cache = ./cache/cord-302189-3xab3yxc.txt txt = ./txt/cord-302189-3xab3yxc.txt === reduce.pl bib === id = cord-301695-zl7cjs1k author = Wang, Ji title = Identification of Histoplasma causing an unexplained disease cluster in Matthews Ridge, Guyana date = 2019-12-31 pages = extension = .txt mime = text/plain words = 3068 sentences = 165 flesch = 53 summary = Though NGS had a longer turnaround time (24 hours), it worked well with different sample types (lung tissue, brain tissue and serum from deceased cases and plasma from a severe case) and was more sensitive than nanopore sequencing. The data generated by the Ion Torrent platform were aligned with the genomic database of Histoplasma, and specific reads were found in the serum and mixed brain and lung tissue from the deceased patients and in the plasma from the severe case ( Figure 5 ) [16] . In this case, NGS also identified specific fragments of Histoplasma in all tested samples (lung, brain and blood serum) from the deceased patients, which consolidated the identification of Histoplasma as the causative pathogen, indicating higher detection sensitivity by NGS than nanopore sequencing. We conclude that Histoplasma was the causative pathogen of this disease cluster based on epidemiologic, clinical, pathological and nucleic acid evidence. cache = ./cache/cord-301695-zl7cjs1k.txt txt = ./txt/cord-301695-zl7cjs1k.txt === reduce.pl bib === id = cord-302296-7ge92p69 author = Lilleeng, Einar title = Comparison of intestinal gene expression in Atlantic cod (Gadus morhua) fed standard fish meal or soybean meal by means of suppression subtractive hybridization and real-time PCR date = 2007-07-03 pages = extension = .txt mime = text/plain words = 6481 sentences = 351 flesch = 57 summary = The selected clones were sequences showing similarity to the following genes: fatty acid binding protein (FABP, clone ID GH4A-F142), putative transmembrane 4 superfamily member protein (TM4, clone ID GH4A-F103), polypeptide N-acetylgalactosaminyltransferase (ppGaNTase, clone ID GH4A-F107), Aminopeptidase M (Alanyl aminopeptidase)(CD13)/Aminopeptidase N (APN, clone ID GH4A-F77), transcobalamin I precursor (TCI, clone ID GH4A-F84), Sec61-alpha (SEC61, clone ID GH4A-F137), F-box protein 44 (F-BOX, clone ID GH4A-F138), glutathione peroxidase (GPx, clone ID GH4A-F127), peroxiredoxin 4 (Prx4, clone ID GH4A-F167), cytochrome P450 3A40 (CYP3A40, clone ID GH4A-F166), ras-related nuclear protein (Ran, clone ID GH4A-F53), and 14-3-3B2 protein (14-3-3, clone ID GH4A-F159). Mean normalized calibrated ratios from real-time PCR of 12 clones, selected based on their similarity to genes involved in processes such as protein-and lipid metabolism, growth and antioxidant functions, showed that expression of 4 out of the 12 clones tested were significantly up regulated (P b 0.05) in intestine from cod fed SBM compared to intestines from cod fed FM. cache = ./cache/cord-302296-7ge92p69.txt txt = ./txt/cord-302296-7ge92p69.txt === reduce.pl bib === === reduce.pl bib === id = cord-302207-ljpfgih2 author = Lichtmannsperger, Katharina title = Molecular characterization of Giardia intestinalis and Cryptosporidium parvum from calves with diarrhoea in Austria and evaluation of point-of-care tests date = 2019-07-12 pages = extension = .txt mime = text/plain words = 4491 sentences = 241 flesch = 52 summary = title: Molecular characterization of Giardia intestinalis and Cryptosporidium parvum from calves with diarrhoea in Austria and evaluation of point-of-care tests Validation of two immunochromatographic point-of-care tests resulted in a sensitivity of 29.2% and 77.6%; a specificity of 98.4% and 91.1% for the detection of Giardia intestinalis and Cryptosporidium parvum, respectively. It was hypothesized that diarrhoeic calves from Austria harbour Giardia and Cryptosporidium genotypes/subtypes which have the potential to cause human infection, and that immunochromatographic point-of-care tests are valid methods for the detection of these parasites in calf faeces. This is in sharp contrast to a previous study on the possible causes of diarrhoea in calves from Austria which only detected 4.4-6.1% Giardia-and 11.7-25.6% Cryptosporidium-positive samples by sugar-flotation [19, 37] . In Southern Germany 101/110 Giardia intestinalis-positive faecal samples from calves were positive for genotype assemblage E, eight for A and one had a mixed infection with A and E [13] . cache = ./cache/cord-302207-ljpfgih2.txt txt = ./txt/cord-302207-ljpfgih2.txt === reduce.pl bib === id = cord-302503-7s9f8wje author = Fu, Yuguang title = Rapid and efficient detection methods of pathogenic swine enteric coronaviruses date = 2020-05-19 pages = extension = .txt mime = text/plain words = 6349 sentences = 295 flesch = 51 summary = In October 2010, a severe PED outbreak caused by a highly virulent PEDV variant emerged in southern China with high mortality ranging from 70 to 100%; the result was devastating damage to the pig farm industry and tremendous economic losses, and later, the PEDV variant spreads to other countries, e.g., USA, Canada, and Mexico ( For the early and rapid detection of PEDV, different types of PCR methods have been developed. A TaqMan probe-based real-time PCR to differentiate porcine epidemic diarrhea virus virulent strains from attenuated vaccine strains Development and evaluation of a duplex real-time RT-PCR for detection and differentiation of virulent and variant strains of porcine epidemic diarrhea viruses from the United States Development of a TaqMan-based real-time RT-PCR assay for the detection of SADS-CoV associated with severe diarrhea disease in pigs cache = ./cache/cord-302503-7s9f8wje.txt txt = ./txt/cord-302503-7s9f8wje.txt === reduce.pl bib === id = cord-302486-z36hcvrx author = Cobo, Fernando title = Diagnostic approaches for viruses and prions in stem cell banks date = 2006-03-30 pages = extension = .txt mime = text/plain words = 7276 sentences = 347 flesch = 41 summary = Viral and prion contamination of cell cultures and "feeder" cells, which is a common risk in all biotechnological products derived from the cell lines, is the most challenging and potentially serious outcome to address, due to the difficulty involved in virus and prion detection and the potential to cause serious disease in recipients of these cell products. The use of bovine fetal serum in stem cell cultures requires an urgent need for a risk assessment for Transmissible Spongiform Encephalopathies (TSEs) by means of a sensitive and specific test in all products derived from ruminants (U.S. Food and Drugs Administration, 1999; Directive 2004/C 24/ 03). This panel of tests should necessarily include reverse transcriptase detection as a general test for retroviruses, electron microscopy that can detect different kinds of viral particles and characterize many unknown isolates present in cell cultures and molecular techniques like PCR (conventional or real-time) and RT-PCR tests to include all the viruses that we know pose a risk to the product. cache = ./cache/cord-302486-z36hcvrx.txt txt = ./txt/cord-302486-z36hcvrx.txt === reduce.pl bib === id = cord-302459-grs2x26l author = Matin, Farhana title = A Plasma Biomarker Panel of Four MicroRNAs for the Diagnosis of Prostate Cancer date = 2018-04-27 pages = extension = .txt mime = text/plain words = 8311 sentences = 413 flesch = 48 summary = In this study we profiled 372 cancer-associated miRNAs in plasma collected before (~60% patients) and after/during commencement of treatment (~40% patients), from age-matched prostate cancer patients and healthy controls, and observed elevated levels of 4 miRNAs miR-4289, miR-326, miR-152-3p and miR-98-5p, which were validated in an independent cohort. Analysis of published miRNA transcriptomic data from clinical samples in the TCGA dataset demonstrated low expression of miR-152-3p in tumour compared to adjacent non-malignant tissues (p = 0.001) (Wilcoxon test, p ≤ 0.05) (Fig. 4) Figure S3) . Similarly, other groups have assessed the diagnostic performance of plasma or serum miRNAs in patients with localised or metastatic prostate cancer, BPH and healthy controls, and in most instances the specificity and sensitivity of the miRNA biomarkers have outperformed the accuracy of the PSA test 23, 28, 29 . cache = ./cache/cord-302459-grs2x26l.txt txt = ./txt/cord-302459-grs2x26l.txt === reduce.pl bib === === reduce.pl bib === id = cord-302819-oj33i2ma author = Pasick, J title = Investigation into the Role of Potentially Contaminated Feed as a Source of the First-Detected Outbreaks of Porcine Epidemic Diarrhea in Canada date = 2014-08-07 pages = extension = .txt mime = text/plain words = 7941 sentences = 363 flesch = 55 summary = On the SDPP sample that was tested, the following N gene rRT-PCR results were observed: C t of 35.84 for PBS supernatant after 10 000 g, C t of 36.74 for the PBS pellet after 10 000 g, C t of 38.83 for the PBS + Nonidet P-40 Comparison of S protein gene sequences obtained from bioassay piglets versus those of field cases. No significant difference was observed in the kinetics of N gene rRT-PCR positivity in animals that were inoculated with the three SDPP samples that were tested, suggesting that each contained infectious virus. Negative contrast staining electron microscopy of fecal samples collected at 4 dpi from the SDPP-inoculated piglets and the positive control group piglets showed the presence of virus-like particles consistent with coronavirus virions. Similar virus-like particles were also found in the content of the small intestine of a SDPP-inoculated piglet at 7 dpi and a positive control group contact piglet at 5 days post-contact. cache = ./cache/cord-302819-oj33i2ma.txt txt = ./txt/cord-302819-oj33i2ma.txt === reduce.pl bib === id = cord-302871-x3mjov5l author = Ribeiro, Juliane title = Extra-intestinal detection of canine kobuvirus in a puppy from Southern Brazil date = 2016-11-25 pages = extension = .txt mime = text/plain words = 2586 sentences = 129 flesch = 45 summary = This study presents the pathological, immunohistochemical, and molecular findings associated with the extra-intestinal detection of canine kobuvirus (CaKV) in a 5-month-old Chihuahua puppy, that had a clinical history of bloody-tinged feces. There are few descriptions of coinfection due to CaKV and other viral agents: a recent study identified CaKV in association with a several agents including canine herpesvirus type 1 (CaHV-1), canine distemper virus (CDV), canine parvovirus (CPV), and canine adenovirus A types 1 (CAdV-1) and 2 (CAdV-2) in diarrheic and non-diarrheic dogs from Korea [19] . Furthermore, widespread viral dissemination was demonstrated in multiple tissues as CaKV nucleic acids were detected in the liver, lung, brain, and tonsils of this Fig. 2 Phylogenetic analysis of a partial nucleotide sequence (nt 201) of the RdRp gene (a) and partial region of the VP1 protein (nt 303) of canine kobuvirus (CaKV) (b). cache = ./cache/cord-302871-x3mjov5l.txt txt = ./txt/cord-302871-x3mjov5l.txt === reduce.pl bib === id = cord-303665-l57e54hu author = Lahrich, S. title = Review on the contamination of wastewater by COVID-19 virus: Impact and treatment date = 2020-09-10 pages = extension = .txt mime = text/plain words = 5849 sentences = 329 flesch = 48 summary = Under these circumstances, the passive, but effective, method of sewage or wastewater monitoring can be used to trace and track the presence of SARS-CoV-2, through their genetic material RNA, and screen entire community. Since wastewater contains viruses that are repelled by everyone, regardless of their health, monitoring for viruses in wastewater and environmental waters that receive effluent from wastewater treatment plants (WWTPs) can determine the true prevalence and molecular epidemiology of gastroenteritis viruses and the risks to human health (Guan et al., 2020; Huang et al., 2020; Wang et al., 2020a) in a given geographical area rather than clinical research (Prevost et al., 2015; Kazama et al., 2017) . Therefore, the safety of drinking water and wastewater depends on the appropriate selection of the disinfectant dose and contact time in the treated environment, which are very important analytical techniques and methods that can detect viruses. Understanding how the virus breaks down in the aquatic environment is also critical to assessing risks to human health at present; the stability of the SARS-CoV-2 genome in wastewater is unclear. cache = ./cache/cord-303665-l57e54hu.txt txt = ./txt/cord-303665-l57e54hu.txt === reduce.pl bib === id = cord-302713-h3aoag4y author = Jauréguiberry, Stéphane title = Clinical and Microbiological Evaluation of Travel‐Associated Respiratory Tract Infections in Travelers Returning From Countries Affected by Pandemic A(H1N1) 2009 Influenza date = 2011-12-08 pages = extension = .txt mime = text/plain words = 3012 sentences = 184 flesch = 51 summary = title: Clinical and Microbiological Evaluation of Travel‐Associated Respiratory Tract Infections in Travelers Returning From Countries Affected by Pandemic A(H1N1) 2009 Influenza BACKGROUND: Although acute respiratory tract infections (RTI) have been recognized as a significant cause of illness in returning travelers, few studies have specifically evaluated the etiologies of RTI in this population. Patients were included if they presented with signs suggestive of RTI that had occurred during travel or <7 days after their return from countries endemic for influenza virus A(H1N1) 2009. At the virology laboratory, the first step of the diagnostic evaluation was to identify influenza A(H1N1) 2009 virus infection by means of real-time reverse transcription-PCR (RT-PCR), as previously described 11 to assess whether or not the patient should remain isolated. In a study performed at San Francisco University Medical Center during the influenza season, a viral agent was identified (through shell vial assay and PCR) in 103 (39%) of the patients with RTI. cache = ./cache/cord-302713-h3aoag4y.txt txt = ./txt/cord-302713-h3aoag4y.txt === reduce.pl bib === id = cord-303289-qoukiqr7 author = Hemida, M. G. title = Coronavirus infections in horses in Saudi Arabia and Oman date = 2017-03-13 pages = extension = .txt mime = text/plain words = 2807 sentences = 151 flesch = 61 summary = We carried out RT‐PCR on 306 nasal and 315 rectal swabs and tested 243 sera for antibodies to detect coronavirus infections in apparently healthy horses in Saudi Arabia and Oman. RNA extracts were tested for evidence of conserved coronavirus nucleic acid genetic sequences using previously reported RT-PCR assays (Chu et al., 2014) , RTqPCR assay for MERS-CoV upE gene (Corman et al., 2012) , RTqPCR assay for ECoV (Miszczak et al., 2014) , and a RTqPCR assay for HKU23 reported below. T A B L E 5 Cross-neutralization titres (denoted as reciprocal titres) for Middle East respiratory coronavirus (MERS-CoV), bovine coronavirus (BCoV) and equine coronavirus (ECoV) in hyperimmune or naturally infected sera known to be positive for different coronaviruses NR460pig antiserum to porcine respiratory coronavirus 1,200 a <20 <20 <20 <20 Similarly, a BCoV immune serum from an experimentally infected gnotobiotic calf showed detectable, but 16-fold reduced antibody titre with ECoV but no cross-reaction with MERS-CoV. cache = ./cache/cord-303289-qoukiqr7.txt txt = ./txt/cord-303289-qoukiqr7.txt === reduce.pl bib === id = cord-303588-bwllypvq author = Ababneh, Mustafa title = High-resolution melting curve analysis for infectious bronchitis virus strain differentiation date = 2020-03-03 pages = extension = .txt mime = text/plain words = 3137 sentences = 159 flesch = 58 summary = MATERIALS AND METHODS: In this study, qRT-PCR was conducted on a partial fragment S1 gene followed by a high resolution melting curve analysis (qRT-PCR/HRM) on 23 IBV-positive samples in Jordan. Although the third cluster contained the highest number of samples, it displayed no similarity to any of the reference vaccine strains, and, after comparing them with the sequencing results, we found that the samples in the third cluster were similar to the variant II-like (IS-1494-06) IBV field strain. CONCLUSION: Our developed qRT-PCR/HRM curve analysis was able to detect and rapidly identify novel and vaccine-related IBV strains as confirmed by S1 gene nucleotide sequences, making it a rapid and cost-effective tool. High-resolution melting (HRM) curve analysis is a newly established PCR-based technique that has been used to differentiate related strains of the same animal or avian virus [16] [17] [18] [19] . Those 22 samples, along with the five IBV vaccine reference strains, were subjected to qRT-PCR targeting the S1 gene followed with HRM curve analysis. cache = ./cache/cord-303588-bwllypvq.txt txt = ./txt/cord-303588-bwllypvq.txt === reduce.pl bib === id = cord-304058-i8cywew0 author = Pfefferle, Susanne title = Reverse genetic characterization of the natural genomic deletion in SARS-Coronavirus strain Frankfurt-1 open reading frame 7b reveals an attenuating function of the 7b protein in-vitro and in-vivo date = 2009-08-24 pages = extension = .txt mime = text/plain words = 9548 sentences = 514 flesch = 53 summary = title: Reverse genetic characterization of the natural genomic deletion in SARS-Coronavirus strain Frankfurt-1 open reading frame 7b reveals an attenuating function of the 7b protein in-vitro and in-vivo To study the role of ORF 7b in the context of virus replication, we cloned a full genome cDNA copy of Frankfurt-1 in a bacterial artificial chromosome downstream of a T7 RNA polymerase promoter. In the context of viral host switching, it is interesting that several SARS-CoV proteins encoded on subgenomic (sg) RNAs seem to be dispensable for virus replication in cultured cells of primate or rodent origin, as well as in rodent models [17] [18] [19] . Both BACs were sequenced, confirming presence of all marker mutations and absence of any further mutations (refer to Influence on apoptosis and type I interferon induction by overexpression of ORF 7a, ORF 7b, and ORF 7b with the Frankfurt-1-specific deletion Interferon beta promoter-specific reporter gene expression (y-axis), shown as the factor of induction as compared to the mock-transfected, non-superinfected control (see below). cache = ./cache/cord-304058-i8cywew0.txt txt = ./txt/cord-304058-i8cywew0.txt === reduce.pl bib === id = cord-305025-pqye1ebh author = Sharifi, Majid title = Rapid diagnostics of coronavirus disease 2019 in early stages using nanobiosensors: challenges and opportunities date = 2020-09-28 pages = extension = .txt mime = text/plain words = 3583 sentences = 226 flesch = 44 summary = The rapid outbreak of coronavirus disease 2019 (COVID-19) around the world is a tragic and shocking event that demonstrates the unpreparedness of humans to develop quick diagnostic platforms for novel infectious diseases. In conclusion, it can be deduced that as rapid COVID-19 detection infection can play a vital role in disease control and treatment, this review may be of great help for controlling the COVID-19 outbreak by providing some necessary information for the development of portable, accurate, selectable and simple nanobiosensors. Detection of severe acute respiratory syndrome (SARS) coronavirus nucleocapsid 637 protein in human serum using a localized surface plasmon coupled fluorescence fiber-optic 638 RNA as a control for multiplex real-time reverse transcription-PCR detection of influenza 790 virus and severe acute respiratory syndrome coronavirus Development and evaluation of a novel loop-mediated isothermal amplification 829 method for rapid detection of severe acute respiratory syndrome coronavirus Rapid COVID-19 detection causative virus (SARS-CoV-2) in human 933 nasopharyngeal swab specimens using field-effect transistor-based biosensor cache = ./cache/cord-305025-pqye1ebh.txt txt = ./txt/cord-305025-pqye1ebh.txt === reduce.pl bib === id = cord-304044-i1ikf96b author = Wu, Yue title = Inhibition of white spot syndrome virus in Litopenaeus vannamei shrimp by sequence-specific siRNA date = 2007-10-03 pages = extension = .txt mime = text/plain words = 4733 sentences = 304 flesch = 58 summary = Here, we described specific silencing of five white spot syndrome virus (WSSV) genes in Litopenaeus vannamei in vivo with sequence-specific siRNAs. These genes included DNA polymerase (dnapol), ribonucleotide reductase small subunit (rr2), thymidine kinase and thymidylate kinase (tk-tmk), vp24 and vp28. control for interference action of siRNAs. Delivery of the selected sequence-specific siRNAs resulted in increase of survival rate of shrimp infected by WSSV, as compared to the virus injected controls (Fig. 1) . To examine if treatment of specific and mutant siRNAs resulted in a reduced expression level of the selected WSSV genes in shrimp in vivo, semiquantitative and highly sensitive RT-PCR analyses were used to compare the relative silencing effects. The results showed that sequence-specific siRNAs significantly inhibited replication of WSSV relative to that of positive controls and the mutant siRNA injected group at 24 h during experiment (Fig. 3) . Our data strongly indicated that sequence-specific siRNAs significantly inhibited expression of target genes and viral replication to protect shrimp from WSSV. cache = ./cache/cord-304044-i1ikf96b.txt txt = ./txt/cord-304044-i1ikf96b.txt === reduce.pl bib === === reduce.pl bib === id = cord-304720-0lgup7yj author = Robbins, R.C. title = Swine Diseases and Disorders date = 2014-08-21 pages = extension = .txt mime = text/plain words = 12872 sentences = 837 flesch = 44 summary = The industry significance, etiology, epidemiology, pathogenesis, clinical signs, postmortem and histpathologic lesions, diagnostic testing, and generic treatment, control, and prevention are described. Important history to understand from caretakers includes: age of pigs affected, duration of clinical signs, morbidity rate, mortality rate, treatments administered, response to treatments, and any other important information regarding previous diagnoses or disease in the affected group of animals. Records include but are not limited to: where the animals originated from; number in the herd; age; daily mortality; number treated; name of treatment, route of delivery and dose; feed and water usage; high-low temperatures; and vaccinations received or administered. Postweaning infections result in a high morbidity but low mortality; most significant economic losses at this time are caused by reduced average daily gain, market weights, and overall system efficiency. Postweaning infections result in a high morbidity but low mortality; most significant economic losses at this time are caused by reduced average daily gain, market weights, and overall system efficiency. cache = ./cache/cord-304720-0lgup7yj.txt txt = ./txt/cord-304720-0lgup7yj.txt === reduce.pl bib === === reduce.pl bib === id = cord-303818-z3js3mr4 author = Chen, Huixin title = Development and Evaluation of a SYBR Green–Based Real-Time Multiplex RT-PCR Assay for Simultaneous Detection and Serotyping of Dengue and Chikungunya Viruses date = 2015-10-11 pages = extension = .txt mime = text/plain words = 3836 sentences = 196 flesch = 51 summary = title: Development and Evaluation of a SYBR Green–Based Real-Time Multiplex RT-PCR Assay for Simultaneous Detection and Serotyping of Dengue and Chikungunya Viruses In the present study, we aimed to develop and evaluate a SYBR Green Iebased multiplex real-time RT-PCR assay to detect, differentiate, and quantify DENV and CHIKV and simultaneously to serotype DENV based on Tm analysis of the PCR amplicon. A set of 22 serum samples from CHIKV-infected patients and 30 from uninfected individuals were collected at the National University Hospital, Singapore, with informed consent, to evaluate the clinical sensitivity and specificity of the real-time RT-PCR assay. To our knowledge, this is the first SYBR Green Iebased real-time RT-PCR assay reported that is able to detect, quantify, differentiate, and serotype DENV and CHIKV simultaneously. Establishment of one-step SYBR green-based real time-PCR assay for rapid detection and quantification of chikungunya virus infection Development of group-and serotype-specific one-step SYBR green I-based real-time reverse transcription-PCR assay for dengue virus cache = ./cache/cord-303818-z3js3mr4.txt txt = ./txt/cord-303818-z3js3mr4.txt === reduce.pl bib === id = cord-304913-qb9zeazk author = Thibivilliers, Sandra title = Generation of Phaseolus vulgaris ESTs and investigation of their regulation upon Uromyces appendiculatus infection date = 2009-04-27 pages = extension = .txt mime = text/plain words = 6680 sentences = 344 flesch = 52 summary = RESULTS: A subtractive bean cDNA library composed of 10,581 unisequences was constructed and enriched in sequences regulated by either bean rust race 41, a virulent strain, or race 49, an avirulent strain on cultivar Early Gallatin carrying the resistance gene Ur-4. Plant gene expression was similar for both race 41 and 49 during the first 48 hours of the infection process but varied significantly at the later time points (72–96 hours after inoculation) mainly due to the presence of the Avr4 gene in the race 49 leading to a hypersensitive response in the bean plants. The stability of the expression level of the 3 remaining genes, TC127, cons6 and cons7 was evaluated by qRT-PCR on cDNAs from bean uninfected or infected with bean rust race 41 or 49 at 6, 12, 24, 48, 72, and 96 hours after inoculation (HAI). cache = ./cache/cord-304913-qb9zeazk.txt txt = ./txt/cord-304913-qb9zeazk.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-305059-8z54lw2d author = Qu, Jie-Ming title = Chapter 4 Diagnosis of COVID-19 date = 2021-12-31 pages = extension = .txt mime = text/plain words = 5054 sentences = 271 flesch = 45 summary = If any one of the following pathogenic or serological tests is positive, the patient is confirmed as COVID-19: (1) positive RT-PCR results for SARS-CoV-2 nucleic acid; (2) viral gene sequencing highly homologous to the known SARS-CoV-2; or (3) serum samples positive for SARS-CoV-2-specific IgM and IgG antibodies. The fifth edition of the program was specially designed for Hubei to establish the diagnostic criteria of "clinical diagnosis cases," which include clinical compliance with the characteristics of viral pneumonia, such as corresponding clinical symptoms and imaging CT findings, especially the multiple lobes exudative ground-glass shadow and intermittent consolidation, normal or decreased total count of white blood cells in laboratory examination, and reduced lymphocyte count. The methods are: (1) real-time fluorescence RT-PCR detection of SARS-CoV-2 nucleic acid positive and (2) viral gene sequencing, highly homologous with the known novel coronavirus. cache = ./cache/cord-305059-8z54lw2d.txt txt = ./txt/cord-305059-8z54lw2d.txt === reduce.pl bib === id = cord-305462-2wz1f6k6 author = Beckham, J. David title = Respiratory viral infections in patients with chronic, obstructive pulmonary disease date = 2004-09-22 pages = extension = .txt mime = text/plain words = 3215 sentences = 191 flesch = 43 summary = OBJECTIVES: The purpose of the present study was to apply reverse transcription-PCR (RT-PCR) assays to clinical specimens collected from patients with acute respiratory illness and chronic obstructive pulmonary disease (COPD). METHODS: One hundred and ninety-four samples from two different study cohorts were analysed using RT-PCR assays for picornaviruses, coronaviruses 229E and OC43, influenza A and B viruses, respiratory syncytial virus, parainfluenza types 1–3 viruses, and human metapneumovirus and a PCR assay for adenoviruses. 11 The number of respiratory viral infections identified in asthmatic patients with acute exacerbations of disease increase significantly when RT-PCR assays are used in addition to other diagnostic methods. 3 In order to extend our understanding of the prevalence of respiratory viral infection in acute respiratory illnesses in patients with COPD, we used RT-PCR assays to evaluate samples from the previous two prospective studies for evidence of respiratory virus infection. cache = ./cache/cord-305462-2wz1f6k6.txt txt = ./txt/cord-305462-2wz1f6k6.txt === reduce.pl bib === === reduce.pl bib === id = cord-305336-wxiazglk author = Li, Ji Lian title = Systemic Spread and Propagation of a Plant-Pathogenic Virus in European Honeybees, Apis mellifera date = 2014-01-21 pages = extension = .txt mime = text/plain words = 6907 sentences = 319 flesch = 50 summary = In the present study, we showed that a plant-pathogenic RNA virus, tobacco ringspot virus (TRSV), could replicate and produce virions in honeybees, Apis mellifera, resulting in infections that were found throughout the entire body. While intracellular life cycle, species-level genetic variation, and pathogenesis of the virus in honeybee hosts remain to be determined, the increasing prevalence of TRSV in conjunction with other bee viruses from spring toward winter in infected colonies was associated with gradual decline of host populations and winter colony collapse, suggesting the negative impact of the virus on colony survival. Conventional RT-PCR was performed on RNA samples extracted from adult bees, Varroa mites, different tissues, and bee bread collected from the same colony for the presence and distribution of TRSV. cache = ./cache/cord-305336-wxiazglk.txt txt = ./txt/cord-305336-wxiazglk.txt === reduce.pl bib === === reduce.pl bib === id = cord-306396-wci56l0c author = Kim, Jayoung title = Evaluation of an Immunochromatographic Assay for the Rapid and Simultaneous Detection of Rotavirus and Adenovirus in Stool Samples date = 2014-04-08 pages = extension = .txt mime = text/plain words = 2736 sentences = 142 flesch = 46 summary = BACKGROUND: We evaluated the analytical and clinical performances of the SD BIOLINE Rota/Adeno Rapid kit (SD Rota/Adeno Rapid; Standard Diagnostics, Inc., Korea), an immunochromatographic assay (ICA), for the simultaneous detection of rotaviruses and adenoviruses in human stool samples. METHODS: We tested 400 clinical stool samples from patients with acute gastroenteritis and compared the ICA results with the results obtained by using ELISA, enzyme-linked fluorescent assays (ELFA), PCR, and multiplex reverse transcription-PCR (mRT-PCR). In this study, we evaluated the analytical and clinical performance of this ICA for the detection of rotaviruses and adenoviruses and compared the results with those of other tests, including ELISA, enzyme-linked fluorescent assays (ELFA), real-time PCR, and multiplex reverse transcription-PCR (mRT-PCR) assays. The SD Rota/Adeno Rapid test is a one-step lateral flow ICA that simultaneously detects group A rotavirus and adenovirus in stool samples. cache = ./cache/cord-306396-wci56l0c.txt txt = ./txt/cord-306396-wci56l0c.txt === reduce.pl bib === id = cord-306135-pt4jsr6d author = Chan, Kamfai title = A Rapid and Low-Cost PCR Thermal Cycler for Infectious Disease Diagnostics date = 2016-02-12 pages = extension = .txt mime = text/plain words = 6292 sentences = 284 flesch = 56 summary = Many molecular diagnostic assays are developed based on using thermal cyclers to carry out polymerase chain reaction (PCR) and reverse-transcription PCR for DNA and RNA amplification and detection, respectively. This thermos thermal cycler (TTC) uses a very simple design that performs PCR amplification based on the "archaic" method of hand-transferring reaction tubes through a series of water baths, minimizing the temperature ramping time needed for PCR tubes to reach thermal equilibrium (Fig 1) . The TTC RT-PCR was performed using protocols similar to the HIV test, with PCR tubes transferred between three thermoses (reverse transcription, denaturation, and annealing/extension) and an optional room-temperature water bath. The gel photo in Fig 3 shows that the TTC can produce multiplexed amplicons with the correct sizes and that the yield is similar to a three-step reaction performed in the commercial cycler with same number of PCR cycles. cache = ./cache/cord-306135-pt4jsr6d.txt txt = ./txt/cord-306135-pt4jsr6d.txt === reduce.pl bib === id = cord-305399-98sqovwb author = Li, Hao title = Development of a reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for the detection of porcine pegivirus date = 2019-04-22 pages = extension = .txt mime = text/plain words = 2854 sentences = 136 flesch = 56 summary = A simple and accurate reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay was developed and evaluated for the detection of porcine pegivirus (PPgV). The results indicated that RT-LAMP assay developed in this study could be a highly specific, sensitive, and cost-effective alternative for a rapid detection of PPgV in field settings. The final volume of 25 μl reaction mixtures for RT-LAMP was prepared, which contained 1 μl of Bst DNA polymerase (NEB, USA) (8000 U/ml), 2.5 μl of 10 × Isothermal Amplification Buffer, 5 μl of Betaine (5 M), 1 μl of MgSO 4 (100 mM), 5 μl of dNTP (2.5 mM), 2 μl of each inner primers FIP and BIP (10 μmol), 0.25 μl of each outer primers F3 and B3 (10 μmol), 0.25 μl of each loop primers LF and LB (10 μmol), 1.25 μl of AMV reverse transcriptase (TaKaRa, China) (40 U/μl), 2 μl of RNA template, and the sterile distilled water was set as a negative control template. cache = ./cache/cord-305399-98sqovwb.txt txt = ./txt/cord-305399-98sqovwb.txt === reduce.pl bib === id = cord-305694-qzf425lw author = Andrés-Lasheras, Sara title = Preliminary studies on isolates of Clostridium difficile from dogs and exotic pets date = 2018-03-09 pages = extension = .txt mime = text/plain words = 4542 sentences = 253 flesch = 48 summary = CONCLUSIONS: The results obtained in this study suggest the implementation of antimicrobial susceptibility surveillance programs to assess the prevalence of metronidazole resistance in dogs; molecular studies to elucidate C. difficile in canine enteric disease is still unclear due to the presence of toxigenic strains or their toxins in asymptomatic animals and the failure to reproduce CDI in healthy dogs with and without antibiotic treatment [9, 10] . difficile, molecular characterisation of the strains obtained (i.e. tpi housekeeping and toxin genes detection by PCR, identification of non-toxigenic strains, and PCR-ribotyping) and antimicrobial susceptibility testing was performed as described elsewhere [21] . Since the ribotypes found in dogs are also commonly found in humans, it is possible Fig. 2 Metronidazole susceptibility test of Clostridium difficile D24 strain after 48 h of incubation. Antibiotic resistance patterns and PCR-ribotyping of Clostridium difficile strains isolated from swine and dogs in Italy cache = ./cache/cord-305694-qzf425lw.txt txt = ./txt/cord-305694-qzf425lw.txt === reduce.pl bib === id = cord-305872-66vij492 author = Caasi, Donna Ria J. title = A multi-target, non-infectious and clonable artificial positive control for routine PCR-based assays date = 2013-09-05 pages = extension = .txt mime = text/plain words = 4830 sentences = 228 flesch = 47 summary = To test this concept, artificial positive controls (APCs) for use in PCR were synthesized to contain primer sequences targeting four viruses (Barley yellow dwarf virus, Soilborne wheat mosaic virus, Triticum mosaic virus and Wheat streak mosaic virus) pathogenic to wheat and, as internal control, the plant mitochondrial nad5 gene. Plasmid construct-based synthetic controls harboring a custom and de novo designed insert can enhance technologies such as polymerase chain reaction (PCR) to improve biosafety, speed of processing and overall detection without compromising sensitivity and specificity. The Plot ΔG or energy dot plot contains the Table 1 Primers used for designing the APC synthetic inserts, performing PCR of the targets within APCs, and RT-PCR of in vivo reference positive controls a . PCR products from APCs may differ in size from those generated by traditionally-used positive controls (Fig. 2) due to the discrepancy in the lengths between the annealing sites of the target sequences in vivo and the arrangement of primer sequences in the APC template (Table 1) . cache = ./cache/cord-305872-66vij492.txt txt = ./txt/cord-305872-66vij492.txt === reduce.pl bib === === reduce.pl bib === id = cord-305475-lhi0hcki author = Risku, Minna title = Human bocavirus types 1, 2 and 3 in acute gastroenteritis of childhood date = 2012-05-24 pages = extension = .txt mime = text/plain words = 3575 sentences = 195 flesch = 59 summary = We studied 878 stool specimens from children with acute gastroenteritis and 112 controls (43 children with unspecified fever, 33 with respiratory tract infection and 36 healthy children) for known HBoVs. The same specimens were previously studied for rotaviruses, noroviruses, sapoviruses, adenoviruses, coronaviruses and aichivirus. As in the case of the respiratory tract, simultaneous presence of HBoV1 with other, previously established gastroenteritis viruses is common in faecal specimens (10, 12, 13) , and no clear connection between HBoV1 and AGE of children has been established (11, 13, 14) . We did a thorough work-up of most of the established gastroenteritis viruses including rotaviruses, noroviruses, sapoviruses, enteric adenoviruses, coronaviruses and aichivirus (astroviruses or bacterial pathogens were not studied) and found co-infections in 81.2% of all bocavirus-positive AGE cases. Human bocavirus in children hospitalized for acute gastroenteritis: a case-control study cache = ./cache/cord-305475-lhi0hcki.txt txt = ./txt/cord-305475-lhi0hcki.txt === reduce.pl bib === id = cord-306278-c4q4la5c author = Esposito, Susanna title = Epidemiology and Clinical Characteristics of Respiratory Infections Due to Adenovirus in Children Living in Milan, Italy, during 2013 and 2014 date = 2016-04-05 pages = extension = .txt mime = text/plain words = 4660 sentences = 220 flesch = 48 summary = To evaluate the predominant human adenovirus (HAdV) species and types associated with pediatric respiratory infections, nasopharyngeal swabs were collected from otherwise healthy children attending an emergency room in Milan, Italy, due to a respiratory tract infection from January 1 to February 28 of two subsequent years, 2013 and 2014. To evaluate the circulation of the different HAdV types and the possible relationship between viral load, viral genetic characteristics, and the severity of infection, nasopharyngeal swabs were collected from otherwise healthy children consecutively attending the Emergency Room of the Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Italy, due to a respiratory tract infection. However, further studies are needed to identify the potential pathogenetic role of the different species and types of HAdV and the importance of viral load in the severity of infection. cache = ./cache/cord-306278-c4q4la5c.txt txt = ./txt/cord-306278-c4q4la5c.txt === reduce.pl bib === id = cord-306605-mnafslqw author = Gibson, CS title = Fetal exposure to herpesviruses may be associated with pregnancy‐induced hypertensive disorders and preterm birth in a Caucasian population date = 2008-02-06 pages = extension = .txt mime = text/plain words = 4772 sentences = 281 flesch = 49 summary = Objective To investigate the role of fetal viral infection in the development of a range of adverse pregnancy outcomes (APOs), including pregnancy‐induced hypertensive disorders (PIHD), antepartum haemorrhage (APH), birthweight <10th percentile (small for gestational age, SGA) and preterm birth (PTB). Main outcome measure Odds ratios and 95% CIs for specific APOs. Results For both term and PTBs, the risk of developing PIHD was increased in the presence of DNA from Herpes PCR group B viruses (OR 3.57, 95% CI 1.10–11.70), CMV (OR 3.89, 95% CI 1.67–9.06), any herpesvirus (OR 5.70, 95% CI 1.85–17.57) and any virus (OR 5.17, 95% CI 1.68–15.94). 2, 3 It has been postulated that fetal viral infection in utero may increase the risk of adverse pregnancy outcomes (APOs), such as pregnancy-induced hypertensive disorders (PIHD), birthweight <10th percentile (small for gestational age, SGA) and preterm birth (PTB). This study investigated the role of fetal exposure to viral infection (detected through the presence of viral nucleic acids in newborn screening cards) in APOs, including SGA, PIHD, antepartum haemorrhage (APH) and PTB. cache = ./cache/cord-306605-mnafslqw.txt txt = ./txt/cord-306605-mnafslqw.txt === reduce.pl bib === id = cord-305657-ayqxesiv author = Kalra, Mannudeep K. title = Chest CT practice and protocols for COVID-19 from radiation dose management perspective date = 2020-07-03 pages = extension = .txt mime = text/plain words = 3958 sentences = 197 flesch = 49 summary = Out of concern over the use of CT and associated radiation doses to patients with suspected or known COVID-19 infection, the International Atomic Energy Agency (IAEA) organized a survey and a webinar to discuss CT practice and protocol optimization for COVID-19 pneumonia on April 9, 2020. When these assays have limited availability, diagnostic imaging (chest radiographs or CT) can be used in patients with at least moderate to severe clinical features supportive of COVID-19 pneumonia. Although there are no specific publications or guidance on this matter, in pregnant patients with suspected complications or worsening respiratory status, a chest CT may be indicated and, when necessary, performed with single-phase, non-contrast, lowdose CT protocol. Most national and international organizations recommend against routine use of diagnostic imaging for the diagnosis of COVID-19 pneumonia unless there is a lack of availability or access to RT-PCR or immunoassays in patients with moderate to severe disease, worsening respiratory status, or a suspicion of cardiopulmonary complications. cache = ./cache/cord-305657-ayqxesiv.txt txt = ./txt/cord-305657-ayqxesiv.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-306780-9xelf8oh author = Dale, Timothy D. title = Enhancement of wildlife disease surveillance using multiplex quantitative PCR: development of qPCR assays for major pathogens in UK squirrel populations date = 2016-07-28 pages = extension = .txt mime = text/plain words = 6931 sentences = 371 flesch = 54 summary = However, comparatively few wildlife epidemiological studies use quantitative PCR (qPCR) for pathogen detection, even fewer employ an internal control, to ensure confidence in negative results, and PCR's ability to multiplex and therefore detect several targets in a single reaction is underutilised. Tests on infected squirrel tissue demonstrate that simple swab samples (particularly from distal antebrachial skin) are sufficient to detect and identify the relative quantity of SQPV DNA in both squirrel species, while rectal swabs and blood cell pellets can be used to reliably indicate SADV infection. As grey squirrels appear asymptomatic, lower infection loads are recorded, and thus it is essential to use the more sensitive qPCR assays when screening for SQPV presence as part of a wildlife disease management programme for red squirrels. cache = ./cache/cord-306780-9xelf8oh.txt txt = ./txt/cord-306780-9xelf8oh.txt === reduce.pl bib === id = cord-307261-0a3iztns author = Hayden, Randall T. title = Comparison of two broadly multiplexed PCR systems for viral detection in clinical respiratory tract specimens from immunocompromised children date = 2012-01-30 pages = extension = .txt mime = text/plain words = 4052 sentences = 206 flesch = 48 summary = title: Comparison of two broadly multiplexed PCR systems for viral detection in clinical respiratory tract specimens from immunocompromised children Samples were de-identified and assayed in parallel using two different, broadly multiplexed PCR systems: ResPlex™ II Panel v2.0 (ResPlex), Qiagen, Hilden, Germany and FilmArray(®) Respiratory Panel (FilmArray), Idaho Technology Inc., Salt Lake City, UT. Two broadly multiplexed PCR systems were compared to each other and to a panel of laboratory developed tests for the detection of respiratory viral pathogens in clinical respiratory tract specimens from pediatric immunocompromised children. FilmArray detected viral targets: adenovirus, bocavirus, coronavirus 229E, HKU1, NL63, OC43, enterovirus, hMPV, human rhinovirus, influenza virus types A and B, parainfluenza viruses 1, 2, 3 and 4, and RSV. The current study, to our knowledge, is the first reported that compares the FilmArray with the ResPlex II v2.0 for the direct detection of viral agents in clinical respiratory tract specimens from immunocompromised children. cache = ./cache/cord-307261-0a3iztns.txt txt = ./txt/cord-307261-0a3iztns.txt === reduce.pl bib === id = cord-306829-88nihy7q author = Sharif, Saeed title = Diagnostic Methods for Feline Coronavirus: A Review date = 2010-07-28 pages = extension = .txt mime = text/plain words = 3829 sentences = 209 flesch = 48 summary = Infection with FCoV can result in a diverse range of signs from clinically inapparent infections to a highly fatal disease called feline infectious peritonitis (FIP). The currently available serological tests have low specificity and sensitivity for detection of active infection and cross-react with FCoV strains of low pathogenicity, the feline enteric coronaviruses (FECV). Therefore, a quantitative real-time RT-PCR assay that could determine the amount of viral mRNA in blood may be able to better differentiate FCoV-positive healthy cats from FIP cases. Detection of feline coronaviruses by culture and reverse transcriptase-polymerase chain reaction of blood samples from healthy cats and cats with clinical feline infectious peritonitis Protein electrophoresis on effusions from cats as a diagnostic test for feline infectious peritonitis Detection of feline coronavirus RNA in feces, tissues, and body fluids of naturally infected cats by reverse transcriptase PCR Detection of feline coronavirus RNA in feces, tissues, and body fluids of naturally infected cats by reverse transcriptase PCR cache = ./cache/cord-306829-88nihy7q.txt txt = ./txt/cord-306829-88nihy7q.txt === reduce.pl bib === id = cord-307068-360qs3ov author = Hagiwara, Masanori title = Loop‐mediated isothermal amplification method for detection of human papillomavirus type 6, 11, 16, and 18 date = 2007-03-26 pages = extension = .txt mime = text/plain words = 3332 sentences = 194 flesch = 56 summary = A new method was developed for detection of human papillomavirus (HPV) by loop‐mediated isothermal amplification (LAMP), which was compared with the polymerase chain reaction (PCR), and real‐time PCR for specificity and sensitivity. In order to evaluate the reliability of HPV type‐specific LAMP detecting HPV DNA from clinical samples, tissue specimens were obtained from 27 patients with external genital polypoid lesions. In this study, a LAMP-based HPV typespecific DNA amplification method was developed and were compared its specificity and sensitivity with PCR and real-time PCR. Type-specific real-time PCR was used to measure the quantity of the DNAs of HPV-6, -11, -16, and -18 in each sample. The sensitivity of HPV-6, -11, -16, and -18 type-specific LAMP determined by turbidity assay were 1,000 copies/tube (Fig. 3) . The sensitivity of amplification of LAMP for detection of viral DNA was nearly the same as that of real-time PCR. cache = ./cache/cord-307068-360qs3ov.txt txt = ./txt/cord-307068-360qs3ov.txt === reduce.pl bib === === reduce.pl bib === id = cord-307602-2cmgu7rf author = McErlean, P. title = Characterisation of a newly identified human rhinovirus, HRV-QPM, discovered in infants with bronchiolitis date = 2007-05-07 pages = extension = .txt mime = text/plain words = 3269 sentences = 172 flesch = 50 summary = BACKGROUND: Human rhinoviruses (HRVs) are some of the earliest identified and most commonly detected viruses associated with acute respiratory tract infections (ARTIs) and yet the molecular epidemiology and genomic variation of individual serotypes remains undefined. RESULTS: Phylogenetic studies of complete coding sequences defined HRV-QPM as a novel member the genus Rhinovirus residing within the previously described HRV-A2 sub-lineage. CONCLUSIONS: We present the molecular characterisation and preliminary clinical impact of a newly identified HRV along with sequences representing additional new HRVs. Acute respiratory tract infections (ARTIs) are a leading cause of human morbidity worldwide and are most frequently viral in origin. We further investigated one of these putative viruses and herein present the complete polyprotein coding sequence of a novel HRV, HRV-QPM, which was first detected in an infant with bronchiolitis. cache = ./cache/cord-307602-2cmgu7rf.txt txt = ./txt/cord-307602-2cmgu7rf.txt === reduce.pl bib === id = cord-306682-01q775up author = Vijgen, Leen title = Identification of six new polymorphisms in the human coronavirus 229E receptor gene (aminopeptidase N/CD13)() date = 2004-06-22 pages = extension = .txt mime = text/plain words = 2965 sentences = 166 flesch = 54 summary = In this study we examined whether polymorphisms could be detected in the HCoV-229E binding domain of APN in a Caucasian population of 100 unrelated, healthy individuals, assuming that these mutations could be of importance in HCoV-229E attachment to human cells. A total of 100 healthy unrelated Belgian individuals were screened for polymorphisms in the human aminopeptidase N domain that is essential for its HCoV-229E receptor activity. All individuals were heterozygous for these polymorphisms, which have no apparent functional consequence, as they are located in a non-coding intron region of the APN gene. In our search for polymorphisms in the APN domain that is essential for its HCoV-229E receptor function, we identified seven polymorphisms, of which four were located in the non-coding intron 3. Three polymorphisms in APN exon 4 (C956T, G978T and G987A) in association with an intron 3 variation (C389T), were identified at a relatively high allele frequency (8.5%) in our Belgian population. cache = ./cache/cord-306682-01q775up.txt txt = ./txt/cord-306682-01q775up.txt === reduce.pl bib === id = cord-307070-tqxvu3pu author = Iqbal, Phool title = Should We Rely on Screening Tests for Further Management Alone in Polymerase Chain Reaction Negative COVID-19 Patients? A Case Series date = 2020-09-20 pages = extension = .txt mime = text/plain words = 2758 sentences = 150 flesch = 49 summary = However, improvement was observed in the clinical condition of the patients who were managed as per COVID-19 protocol based upon the clinical signs and symptoms after correlating with diagnostic chest imaging studies. The infectious disease team advised testing with COVID-19 serology (immunoglobulin (Ig) M and IgG antibodies through lateral flow assay), the results of which were positive, indicating recent infection. The infectious disease team was consulted and based upon his clinical presentation and previous investigations, the patient was maintained on the local management protocol for COVID-19 infection. Moreover, biomarkers such as CRP, ferritin, lymphocyte counts, lactate dehydrogenase, and N-terminal pro b-type natriuretic peptide, along with radiological findings in CXR or features such as unilateral or bilateral pneumonia, ground-glass opacities, or consolidations in a chest CT scan, can suggest COVID-19 infection even in such patients where RT-PCR alone is negative [4] . cache = ./cache/cord-307070-tqxvu3pu.txt txt = ./txt/cord-307070-tqxvu3pu.txt === reduce.pl bib === id = cord-307338-4nta9b6w author = Slomka, Marek J. title = Original Article: Real time reverse transcription (RRT)‐polymerase chain reaction (PCR) methods for detection of pandemic (H1N1) 2009 influenza virus and European swine influenza A virus infections in pigs date = 2010-08-17 pages = extension = .txt mime = text/plain words = 7990 sentences = 469 flesch = 62 summary = Fifteen of these specimens (six swabs and nine tissues) were shown to be Avian influenza viruses, with highly pathogenic (HP) H5 and H7 isolates indicated positive for H1N1v by non-RRT PCR approaches (Table 3) , i.e. amplification of RNA extracted from the clinical specimen by conventional RT PCR using primers that had been designed specifically for the HA gene of current H1N1v isolates, available at: http://www.who.int/csr/resources/publications/swineflu/GenomePrimers_20090512.pdf Amplicons were electrophoresed in 2% agarose and stained with RedSafeÔ (iNtRON Biotechnology, Kyungki-Do, Korea) for visualisation, excised and purified from agarose using the QIAquick Ò Gel Extraction Kit (Qiagen, Crawley, UK). These test results with archived tissue specimens obtained from the field reinforced the observation that the ''perfect match'' M gene RRT PCR is the most sensitive for detecting contemporary European and UK SIVs. All 31 archived UK tissue samples from SIV-positive pigs were negative by the ''H1-118'' RRT PCR assay (Table 2) . cache = ./cache/cord-307338-4nta9b6w.txt txt = ./txt/cord-307338-4nta9b6w.txt === reduce.pl bib === id = cord-307758-a4sgt66g author = Hong, Ching-Ye title = Acute respiratory symptoms in adults in general practice date = 2004-06-17 pages = extension = .txt mime = text/plain words = 3927 sentences = 241 flesch = 56 summary = Community studies have shown that ∼30% of patients with acute respiratory tract symptoms have no identifiable infective aetiology. The purpose of this study was to determine the infective aetiology in patients who presented to primary care doctors with acute respiratory symptoms. Data collection was through interview using structured questionnaire, physical examination, throat swabs for bacterial culture and nasal swabs for virus identification by immunofluorescence (IF) and polymerase chain reaction (PCR). The main objective of our study was therefore to determine the aetiological cause in patients who presented with acute respiratory symptoms in nine primary care clinics in Singapore, using bacterial culture, IF and PCR. To our knowledge, this is the first practice-based study on the aetiological diagnosis of a large group of patients presenting with URTI in primary care clinics in Asia, using IF and PCR as identification methods. cache = ./cache/cord-307758-a4sgt66g.txt txt = ./txt/cord-307758-a4sgt66g.txt === reduce.pl bib === id = cord-307702-n74wvika author = Durant, Thomas J S title = Impact of COVID-19 Pandemic on Laboratory Utilization date = 2020-07-14 pages = extension = .txt mime = text/plain words = 2811 sentences = 162 flesch = 44 summary = METHODS: We performed a retrospective assessment of laboratory test order and specimen container utilization at a single, urban tertiary care medical center. We performed a retrospective assessment of laboratory test order and specimen container utilization at a single, urban tertiary care medical center. Total testing volumes were calculated during the first and last two-weeks of the observation period and used as reference points to examine the absolute and relative differences in test order volume between the pre-pandemic and COVID-19 surge periods. Total testing volumes were calculated during the first and last two-weeks of the observation period and used as reference points to examine the absolute and relative differences in test order volume between the pre-pandemic and COVID-19 surge periods. While volume increases were seen for laboratory tests related to COVID-19 diagnostics and management, including some with limited evidence to support their use, overall testing volumes decreased substantially. cache = ./cache/cord-307702-n74wvika.txt txt = ./txt/cord-307702-n74wvika.txt === reduce.pl bib === id = cord-308344-ao9z00t7 author = Diep, Nguyen Van title = Novel Porcine Epidemic Diarrhea Virus (PEDV) Variants with Large Deletions in the Spike (S) Gene Coexist with PEDV Strains Possessing an Intact S Gene in Domestic Pigs in Japan: A New Disease Situation date = 2017-01-17 pages = extension = .txt mime = text/plain words = 4179 sentences = 193 flesch = 52 summary = title: Novel Porcine Epidemic Diarrhea Virus (PEDV) Variants with Large Deletions in the Spike (S) Gene Coexist with PEDV Strains Possessing an Intact S Gene in Domestic Pigs in Japan: A New Disease Situation Among 17 PEDV samples isolated from individual pigs, all of them contained at least two distinct genotypes with large genomic deletions, and 94.1% of them were found to consist of strains with an intact S gene. In this study, variants with large deletions in the S gene were found in eight primary and nine recurrent outbreaks from 16 pig farms, and they mostly (94.1%) coexisted with PEDV strains with an intact S gene. Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene New porcine epidemic diarrhoea virus variant with a large deletion in the spike gene identified in domestic pigs cache = ./cache/cord-308344-ao9z00t7.txt txt = ./txt/cord-308344-ao9z00t7.txt === reduce.pl bib === id = cord-308315-g6udfu2a author = Decaro, Nicola title = Characterisation of bubaline coronavirus strains associated with gastroenteritis in water buffalo (Bubalus bubalis) calves date = 2010-10-26 pages = extension = .txt mime = text/plain words = 3701 sentences = 172 flesch = 50 summary = Recently, a coronavirus strain (179/07-11) was isolated from water buffalo (Bubalus bubalis) and the virus which displayed a strict genetic and biological relatedness with bovine coronavirus (BCoV) was referred to as bubaline coronavirus (BuCoV). There are multiple genetic and antigenic evidences that several subgroup 2a CoVs, such as HCoV-OC43, HECoV-4408, PHEV and CRCoV, have arisen as consequence of trans-species infections caused by BCoV (Zhang et al., 1994; Vijgen et al., 2005 Vijgen et al., , 2006 Erles et al., Veterinary Microbiology 145 (2010) [245] [246] [247] [248] [249] [250] [251] Recently, a coronavirus strain (179/07-11) was isolated from water buffalo (Bubalus bubalis) and the virus which displayed a strict genetic and biological relatedness with bovine coronavirus (BCoV) was referred to as bubaline coronavirus (BuCoV). Recently, another bovine-like CoV, which was referred to as bubaline coronavirus (BuCoV), was isolated from water buffalo (Bubalus bubalis) calves with fatal gastroenteritis in Italy (Decaro et al., 2008d) . cache = ./cache/cord-308315-g6udfu2a.txt txt = ./txt/cord-308315-g6udfu2a.txt === reduce.pl bib === id = cord-308655-zntwwqod author = Dabisch-Ruthe, Mareike title = Comparison of three multiplex PCR assays for the detection of respiratory viral infections: evaluation of xTAG respiratory virus panel fast assay, RespiFinder 19 assay and RespiFinder SMART 22 assay date = 2012-07-24 pages = extension = .txt mime = text/plain words = 5799 sentences = 312 flesch = 48 summary = title: Comparison of three multiplex PCR assays for the detection of respiratory viral infections: evaluation of xTAG respiratory virus panel fast assay, RespiFinder 19 assay and RespiFinder SMART 22 assay METHODS: The analytical sensitivity of three multiplex PCR assays, RespiFinder-19, RespiFinder-SMART-22 and xTAG-Respiratory-Virus-Panel-Fast-Assay (RVP), were compared to monoplex real-time PCR with quantified standardized control material. RESULTS: To compare the analytical sensitivity of the multiplex assays, samples were inoculated with 13 different quantified viruses in the range of 10(1) to 10(5) copies/ml. This study presents the first comparison of the analytical sensitivity of three novel multiplex PCR methods, the RespiFinder-19 assay, RespiFinder-SMART(Single tube Multiplex Amplification in Real-Time)-22 assay (both PathoFinder, Maastricht, Netherlands) and the xTAG Respiratory Virus Panel Fast Assay (Abbott Molecular, Wiesbaden, Germany), with quantified virus control material. Previous studies with clinical samples showed that the sensitivity and specificity of the RVP assay was 78.8% and 99.6%, respectively, compared to real-time PCR-methods, that are currently declared as the gold standard [21] . cache = ./cache/cord-308655-zntwwqod.txt txt = ./txt/cord-308655-zntwwqod.txt === reduce.pl bib === id = cord-307874-0obomty2 author = Pardon, Bart title = Bovine Respiratory Disease Diagnosis: What Progress Has Been Made in Infectious Diagnosis? date = 2020-05-23 pages = extension = .txt mime = text/plain words = 7061 sentences = 388 flesch = 43 summary = Evidence-based guidelines for precise interpretation of microbiologic tests results are lacking; however, approaches that have been practically useful for the management of bovine respiratory disease outbreaks are presented. However, naturally resistant to fluoroquinolones 71 Escherichia coli, Gallibacterium anatis, Enterobacter hormaechei, staphylococci, streptococci, fungi Secondary Single reports on cattle-specific strains isolated in pure culture in an outbreak of pneumonia in calves 52, [72] [73] [74] Multiple other bacterial species can be detected in the bovine respiratory tract. 10, 35, 54 However, with current knowledge on the interpretation of DNS results at the individual or group level, samples of the lower respiratory tract are likely a better option to evaluate potential involvement of opportunistic pathogens. In the example where the pathogen is causing the disease in 100% of affected calves, the risk of not finding an infected animal after sampling n cases is (1-Se)n , where Se is the test sensitivity. cache = ./cache/cord-307874-0obomty2.txt txt = ./txt/cord-307874-0obomty2.txt === reduce.pl bib === id = cord-308945-i2agpvhk author = Phipps, William S title = SARS-CoV-2 Antibody Responses Do Not Predict COVID-19 Disease Severity date = 2020-07-15 pages = extension = .txt mime = text/plain words = 3167 sentences = 174 flesch = 50 summary = METHODS: A total of 967 subjects were tested for IgG antibodies reactive to SARS-CoV-2, including 172 suspected cases of SARS-CoV-2, 656 plasma samples from healthy donors, 49 sera from patients with rheumatic disease, and 90 specimens from individuals positive for polymerase chain reaction (PCR)–based respiratory viral panel. Long et al 8 have described a variable antiviral IgM and IgG immune response to SARS-CoV-2 infection in a Chinese population in which seroconversion in a group of 285 patients from 3 hospitals showed IgG positivity for all cases beyond 17 to 19 days. The goals of this study were to ascertain key performance metrics of analytical specificity and cross-reactivity for a SARS-CoV-2 IgG serologic assay, perform a detailed cross-sectional and serial assessment of IgG and IgM antibody responses in suspected COVID-19 patients, and determine their relation to disease severity. SARS-CoV-2 IgG antibody results agreed with the PCR-negative samples for 96 of 97 (99%) of cases, including 55 instances of patients with new or acute-on-chronic symptoms suspicious for COVID-19 and with known time of onset. cache = ./cache/cord-308945-i2agpvhk.txt txt = ./txt/cord-308945-i2agpvhk.txt === reduce.pl bib === id = cord-308422-ueyaw8pd author = Wong, Christopher W title = Optimization and clinical validation of a pathogen detection microarray date = 2007-05-28 pages = extension = .txt mime = text/plain words = 6487 sentences = 298 flesch = 43 summary = Here, we report the results of a systematic investigation of the complex relationships between viral amplification efficiency, hybridization signal output, target-probe annealing specificity, and reproducibility of pathogen detection using a custom designed microarray platform. The array was designed to detect up to 35 RNA viruses using 40-mer probes tiled at an average 8-base resolution across the full length of each genome (53,555 probes; Figure S1 and Table S1 in Additional data file 1). We next hypothesized that amplification efficiency scoring could be used to select an optimal tag sequence (that is, for the RT-PCR primers) for achieving uniformly high AES Table 1 Binning of probes into specific pathogen signature probe sets across viral genomes, thus globally maximizing PCR efficiency (see supplemental methods in Additional data file 1 and [25] ). cache = ./cache/cord-308422-ueyaw8pd.txt txt = ./txt/cord-308422-ueyaw8pd.txt === reduce.pl bib === === reduce.pl bib === id = cord-309107-2xzam3x9 author = Emmler, Laura title = Feline coronavirus with and without spike gene mutations detected by real-time RT-PCRs in cats with feline infectious peritonitis date = 2019-11-15 pages = extension = .txt mime = text/plain words = 4623 sentences = 228 flesch = 54 summary = title: Feline coronavirus with and without spike gene mutations detected by real-time RT-PCRs in cats with feline infectious peritonitis This study investigated the presence of FCoV with and without S gene mutations in cats with FIP using two different real-time RT-PCRs on different samples obtained under clinical conditions. METHODS: Fine-needle aspirates (FNAs) and incisional biopsies (IBs) of popliteal and mesenteric lymph nodes, liver, spleen, omentum and kidneys (each n = 20), EDTA blood (n = 13), buffy coat smears (n = 13), serum (n = 11), effusion (n = 14), cerebrospinal fluid (n = 16), aqueous humour (n = 20) and peritoneal lavage (n = 6) were obtained from 20 cats with FIP diagnosed by immunohistochemistry. This study investigated the presence of FCoV with and without S gene mutations in different tissue and body fluid samples from cats with IHC-confirmed FIP via realtime RT-PCR. cache = ./cache/cord-309107-2xzam3x9.txt txt = ./txt/cord-309107-2xzam3x9.txt === reduce.pl bib === id = cord-309540-4pk5tq5w author = Brandsma, E. title = Rapid, sensitive and specific SARS coronavirus-2 detection: a multi-center comparison between standard qRT-PCR and CRISPR based DETECTR. date = 2020-07-29 pages = extension = .txt mime = text/plain words = 4283 sentences = 268 flesch = 54 summary = Recent advances in CRISPR-based diagnostics suggest that DETECTR, a combination of isothermal reverse transcriptase loop mediated amplification (RT-LAMP) and subsequent Cas12 bystander nuclease activation by amplicon targeting ribonucleoprotein complexes, could be a faster and cheaper alternative to qRT-PCR without sacrificing sensitivity/specificity. Isothermal reverse transcriptase loop mediated isothermal amplification (RT-LAMP) in combination with Cas12 detection does not need expensive specialised equipment, is highly sensitive and specific, has a short TAT and is easy to implement and therefore could be used as an alternative for qRT-PCR (5, 6) . Since DETECTR depends on both signal amplification by RT-LAMP and reporter degradation after Cas12-dependent amplicon recognition, the assay produces a binary readout and is potentially more sensitive and specific compared to qRT-PCR (5, 6) . In this manuscript we describe the development of an in-house SARS-CoV-2 DETECTR assay, compare its performance with routine diagnostic qRT-PCR on almost 400 patient samples of three Dutch hospitals, thereby providing a first field test of this novel Cas12-mediated SARS-CoV-2 detection tool. cache = ./cache/cord-309540-4pk5tq5w.txt txt = ./txt/cord-309540-4pk5tq5w.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-309083-ew9cwiw0 author = Su, Hang title = Cyprinid viral diseases and vaccine development date = 2018-09-07 pages = extension = .txt mime = text/plain words = 11167 sentences = 585 flesch = 43 summary = In this review, authors summarized six major cyprinid viral diseases, including koi herpesvirus disease (KHVD), spring viraemia of carp (SVC), grass carp hemorrhagic disease (GCHD), koi sleepy disease (KSD), carp pox disease (CPD) and herpesviral haematopoietic necrosis (HPHN). Challenge experiment reveals that the oral recombinant subunit vaccine can protect 50%-60% grass carp from infection and generate immunity against GCRV [199] . Oral vaccination is an effective way to induce mucosal immunity [215] and this strategy has shown a successful induction of the antiviral responses against viral diseases in different fish species [165] . Gene expression analysis of common carp (Cyprinus carpio L.) lines during cyprinid herpesvirus 3 infection yields insights into differential immune responses Recombinant lactobacillus expressing G protein of spring viremia of carp virus (SVCV) combined with ORF81 protein of koi herpesvirus (KHV): a promising way to induce protective immunity against SVCV and KHV infection in cyprinid fish via oral vaccination cache = ./cache/cord-309083-ew9cwiw0.txt txt = ./txt/cord-309083-ew9cwiw0.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-310096-a242g5kg author = Yokota, I. title = Mass screening of asymptomatic persons for SARS-CoV-2 using saliva date = 2020-08-14 pages = extension = .txt mime = text/plain words = 1956 sentences = 131 flesch = 49 summary = Methods We conducted a mass-screening study to compare the utility of nucleic acid amplification, such as reverse transcriptase polymerase chain reaction (RT-PCR) testing, using NPS and saliva samples from each individual in two cohorts of asymptomatic persons: the contact tracing cohort and the airport quarantine cohort. We conducted a mass-screening study to compare the utility of nucleic acid amplification, such as reverse transcriptase polymerase chain reaction (RT-PCR) testing, using NPS and saliva samples from each individual in two cohorts of asymptomatic persons: the contact tracing cohort and the airport quarantine cohort. Currently, the diagnosis of COVID-19 is made by the detection of the nucleic acids of SARS-CoV-2 typically by real-time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) testing of specimens collected by nasopharyngeal swabs (NPS) [5, 6] . We conducted a mass-screening study to determine and compare the sensitivity and specificity of nucleic acid amplification using paired samples (self-collected saliva and NPS) for the detection of SARS-CoV-2 in two cohorts of asymptomatic individuals. cache = ./cache/cord-310096-a242g5kg.txt txt = ./txt/cord-310096-a242g5kg.txt === reduce.pl bib === === reduce.pl bib === id = cord-310501-ro55cqxw author = de Castro, Alessandra MMG title = Detection of porcine circovirus genotypes 2a and 2b in aborted foetuses from infected swine herds in the State of São Paulo, Brazil date = 2012-05-03 pages = extension = .txt mime = text/plain words = 2212 sentences = 127 flesch = 58 summary = title: Detection of porcine circovirus genotypes 2a and 2b in aborted foetuses from infected swine herds in the State of São Paulo, Brazil FINDINGS: Samples of 168 aborted foetuses or mummified foetuses from five farrow-to-finish swine farms known to be infected with PCV2 and located in the State of São Paulo were tested for PCV2 by polymerase chain reaction (PCR). CONCLUSIONS: The findings indicate that the frequency of PCV2 infections in aborted porcine foetuses from the State of São Paulo is rather low (10.7%) and that co-infection with other pathogens is common and may be involved in PCV2 associated reproductive failure. Given the distribution of the virus in swine populations worldwide and the impact of PCV2 associated reproductive failure on swine herd economy, the aim of this study was to identify genotypes of PCV2 involved in reproductive failure in State of São Paulo, Brazil and to investigate the level of co-infections of foetuses with other pathogens. cache = ./cache/cord-310501-ro55cqxw.txt txt = ./txt/cord-310501-ro55cqxw.txt === reduce.pl bib === id = cord-311439-y9jwu38r author = Bao, Changjun title = Possible Spread of adenovirus type 3 from poultry to humans: indirect evidence from an outbreak in China date = 2007-09-30 pages = extension = .txt mime = text/plain words = 4299 sentences = 219 flesch = 50 summary = We describe an outbreak of acute respiratory infection due to adenovirus type 3 that occurred in one county of Jiangsu Province, China, during the period from April 18 th to July 4 th 2004. Pharyngeal swab specimens from children and adolescent patients who were diagnosed with acute upper respiratory tract infections at Township A health care hospital during the outbreak from April through July 2005 were cultured for adenovirus. An infection caused by adenovirus type 3 was verified by entire gene sequence testing to 10 Nested PCR amplification products of positive specimens (from nine patients) in the laboratory of the National CDC of China. Eighteen paired patient serums(acute and convalescent) were used to test neutralization titer with the isolate adenovirus type 3 viral strain simultaneously. This investigation demonstrated that acute respiratory infection caused by adenovirus type 3 caused the outbreak that occurred in over seventy schools in ten townships in 2004. cache = ./cache/cord-311439-y9jwu38r.txt txt = ./txt/cord-311439-y9jwu38r.txt === reduce.pl bib === id = cord-310771-tnwfp1je author = Revilla-Fernández, Sandra title = The use of endogenous and exogenous reference RNAs for qualitative and quantitative detection of PRRSV in porcine semen date = 2005-02-23 pages = extension = .txt mime = text/plain words = 5933 sentences = 297 flesch = 51 summary = A method was developed for qualitative and quantitative detection of the seminal cell-associated PRRSV RNA in relation to endogenous and exogenous reference RNAs. As endogenous control for one-step real-time reverse transcription (RT)-PCR UBE2D2 mRNA was selected. Particularly for the analysis of persistent infections associated with low copy numbers of PRRSV RNA, UBE2D2 mRNA is an ideal control due to its low expression in seminal cells and its detection in all samples analysed (n = 36). For the development of one-step real-time RT-PCR for four endogenous reference RNAs (HPRT, UBE2D2, PPIA, and HMBS) appropriate target regions were selected and the assay conditions were optimised for amplification efficiency. One-step real-time RT-PCR assays for PRRSV-1 and -2 RNA allowed quantitation with optimal efficiency (Fig. 1a ; standard curves for two additional viremic pigs infected with PRRSV-1 (data not shown)) as achieved for endogenous and Fig. 1 . cache = ./cache/cord-310771-tnwfp1je.txt txt = ./txt/cord-310771-tnwfp1je.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-311204-fc12f845 author = Zhou, Ling title = Full-length genomic characterization and molecular evolution of canine parvovirus in China date = 2016-04-02 pages = extension = .txt mime = text/plain words = 2229 sentences = 138 flesch = 65 summary = Canine parvovirus type 2 (CPV-2) can cause acute haemorrhagic enteritis in dogs and myocarditis in puppies. Some faecal samples were negative for the CPV-2 antigen based on a colloidal gold test strip but were positive based on PCR, and a viral strain was isolated from one such sample. Identification of CPV-2 with cell culture and IPMA Feline kidney cell line F81 was obtained from the American Type Culture Collection, USA and was used to isolate viruses from clinical samples and to observe cytopathic effects associated with viral replication. Cloning the full-length genomic sequence of CPV-2 DNA and RNA were extracted from the homogenized samples (faeces from infected dogs) with the TIANamp Virus DNA/RNA Kit (Beijing TIANGEN Biotech Company, Beijing, China) according to the manufacturer's protocol. One viral strain was isolated from the faeces of dogs that tested negative in the colloidal gold test strip but positive with PCR. cache = ./cache/cord-311204-fc12f845.txt txt = ./txt/cord-311204-fc12f845.txt === reduce.pl bib === id = cord-310748-ao29zx1u author = Banner, Lisa R. title = Random nature of coronavirus RNA recombination in the absence of selection pressure date = 1991-11-30 pages = extension = .txt mime = text/plain words = 2839 sentences = 155 flesch = 52 summary = Our results showed that within a 1-kb region of the peplomer gene, RNA recombination occurred at almost every potential crossover site. To study RNA recombination in the absence of selection pressure, we developed a polymer-ase chain reaction (PCR) assay using two primers specific for the potential recombinant viruses which have a crossover site between the two primers. Only recombinant RNAs which had a crossover between the two primers and contained A59-specific sequences on the 5'-side and JHM-DL-specific sequences on the 3'-side could be detected by this PCR approach. DNA sequence analysis of 35 cloned PCR products showed that the crossover sites were almost randomly distributed throughout the nearly 1-kb region of the peplomer gene studied ( Fig. 2A) . Analysis of 53 recombinant clones revealed that, similar to the intracellular recombinants, the crossover sites in the viral recombinant RNAs were almost randomly distributed over the 1 -kb region of the peplomer gene (Fig. 2B) . cache = ./cache/cord-310748-ao29zx1u.txt txt = ./txt/cord-310748-ao29zx1u.txt === reduce.pl bib === id = cord-311410-lgqup9ug author = Ayers, M. title = A single tube RT-PCR assay for the detection of mosquito-borne flaviviruses date = 2006-05-02 pages = extension = .txt mime = text/plain words = 3106 sentences = 157 flesch = 52 summary = In this study we present the design and validation of a single tube RT-PCR assay using a pair of consensus primers for the detection of mosquito-borne flaviviruses. For specificity studies, several viral samples were used, including clinical samples found to contain CMV and EBV DNA by PCR testing, as described (Johnson et al., 2000) ; a clinical isolate of influenza virus from the 2004-2005 season, typed as H3 by sequencing of the hemagglutinin gene; echovirus 11 from the laboratory collection at the Hospital for Sick Children; hepatitis C virus RNA was obtained by in vitro transcription of the infectious clone pCV-H77C (Yanagi et al., 1997) (the clone was kindly provided by Dr. J. Coupled with sequencing, it could detect with great sensitivity and identify several mosquito-borne flaviviruses including WNV, Kunjin, SLE, YFV and dengue fever viruses. cache = ./cache/cord-311410-lgqup9ug.txt txt = ./txt/cord-311410-lgqup9ug.txt === reduce.pl bib === id = cord-311639-zij2wbzs author = Kim, Hyun Soo title = Evaluation of the SD Bioline Norovirus rapid immunochromatography test using fecal specimens from Korean gastroenteritis patients date = 2012-08-30 pages = extension = .txt mime = text/plain words = 3674 sentences = 175 flesch = 52 summary = This study was performed to evaluate the analytical and clinical performance of a newly developed rapid ICG test (SD Bioline Norovirus test) for detecting human norovirus genogroups GI and GII in stool specimens. In samples with negative ICG and positive real-time PCR results, 200 L of fecal suspension was mixed with 200 L diluent (1:1 dilution) instead of 1 mL diluent, and the test was repeated. In this study, therefore, in the case of samples with negative ICG and positive real-time PCR results, 200 L of fecal suspension was mixed with 200 L diluent instead of 1 mL diluent (total dilution titer was 1:10-1:20 dilution, which is similar to that of the original procedure of this assay using stool), and the test was repeated. Evaluation of rapid immunochromatography test for the detection of norovirus infection: comparison with ELISA and real time quantitative reverse transcription PCR assays cache = ./cache/cord-311639-zij2wbzs.txt txt = ./txt/cord-311639-zij2wbzs.txt === reduce.pl bib === id = cord-311748-yr2ep7uf author = Kahyaoglu, L. N. title = 11 New approaches in microbial pathogen detection date = 2013-12-31 pages = extension = .txt mime = text/plain words = 8020 sentences = 381 flesch = 48 summary = In recent years, polymerase chain reaction (PCR)-based methods in particular, have become the gold standard for virus detection in food due to their high sensitivity, specifi city and potential to detect even a single virus particle (Bosch et al. In recent years, qRT-PCR has been widely used in food virology as the most promising nucleic acid detection method, since it offers several advantages over conventional RT-PCR, including high sensitivity, the possibility of simultaneous amplifi cation, detection and quantifi cation of the target nucleic acids in a single step, and with minimum risk of carry-over contamination through the use of a closed system (Mackay et al. The challenges associated with the detection of foodborne viruses, such as PCR inhibitors and low virus concentrations in foods, affect the effi ciency of realtime assay adversely, therefore, for process control (PC) an internal amplifi cation control (IAC), which is extracted and amplifi ed with the target sequence, is crucial in the evaluation of PCR and to prevent false negatives (Di Pasquale et al. cache = ./cache/cord-311748-yr2ep7uf.txt txt = ./txt/cord-311748-yr2ep7uf.txt === reduce.pl bib === id = cord-311801-m2otfdjw author = Wang, Pei title = Combination of Serological Total Antibody and RT-PCR Test for Detection of SARS-CoV-2 Infections date = 2020-06-15 pages = extension = .txt mime = text/plain words = 2724 sentences = 184 flesch = 62 summary = The purpose of this study was to investigate the feasibility of serological total antibody tests combined with RT-PCR for detection of SARS-CoV-2. Serum samples and throat swabs were collected from 375 patients for total antibody testing against SARS-CoV-2 and RT-PCR analysis, respectively. This study supported the advantage of the combined method for detection of SARS-CoV-2 with a high degree of sensitivity and specificity, as a useful tool for accurate diagnosis and timely treatment of suspected patients, epidemiological investigation, as well as monitoring ongoing outbreaks of infections with SARS-CoV-2. In this study, we presented the results of two diagnostic methods: serum total antibody assays against SARS-CoV-2 by CMIA and the RT-PCR for detection of viral RNA. In addition, the combination of the results of the total antibody test and RT-PCR was discussed for detection of SARS-CoV-2 infections. Sensitivity, specificity for detection of SARS-CoV-2 by RT-PCR, and the total antibody test method as well as the combined methods were analysed. cache = ./cache/cord-311801-m2otfdjw.txt txt = ./txt/cord-311801-m2otfdjw.txt === reduce.pl bib === id = cord-311982-wkg56xeq author = Dye, Charlotte title = Genomic RNA sequence of feline coronavirus strain FCoV C1Je date = 2007-06-17 pages = extension = .txt mime = text/plain words = 5240 sentences = 250 flesch = 55 summary = Comparisons of the enteric (jejunum) and non-enteric (liver) derived viral RNA sequences revealed 100% nucleotide identity, a finding that questions the well accepted 'internal mutation theory' of FIPV pathogenicity. Comparisons of the enteric (jejunum) and non-enteric (liver) derived viral RNA sequences revealed 100% nucleotide identity, a finding that questions the well accepted 'internal mutation theory' of FIPV pathogenicity. Furthermore, the structural and accessory gene regions of viral RNA isolated from the liver of the same cat (FCoV C1Li) were sequenced and the data derived from the enteric (jejunum) and non-enteric (liver) sources were compared. Sequence data previously generated for the laboratory strain FCoV, FIPV 79-1146, were used to design primers for conventional reverse transcriptase polymerase chain reaction (RT-PCR) amplification of short lengths (100e500 bases) of the field strain RNA. Analysis of the accessory gene 7 region of the FCoV C1Je genome identifies two ORFs, which have translation products sharing high amino acid identity with proteins 7a and 7b of FIPV 79-1146. cache = ./cache/cord-311982-wkg56xeq.txt txt = ./txt/cord-311982-wkg56xeq.txt === reduce.pl bib === id = cord-312024-qdgqif5j author = Talbot, H. Keipp title = The Diagnosis of Viral Respiratory Disease in Older Adults date = 2010-02-01 pages = extension = .txt mime = text/plain words = 3423 sentences = 175 flesch = 39 summary = The increasing availability of new rapid and sensitive molecular diagnostics such as polymerase chain reaction testing, should provide more accurate and timely diagnoses of viral respiratory infections in older adults in the near future. This article summarizes what is known about the diagnosis of viral respiratory diseases in elderly adults, with the hope of increasing understanding of the utility and limitations of the currently available diagnostic tests for viral respiratory pathogens, such as culture, rapid antigen testing, polymerase chain reaction (PCR) testing, and serologic analysis. Compared with previous studies that have used viral culture for diagnosis, studies using PCR have more accurately detected the presence of viruses (including influenza virus, RSV, hMPV, parainfluenza virus, rhinoviruses, and coronaviruses) in the lower respiratory tract illness in older adults [5, 13, 31, 36, 40, 42] . cache = ./cache/cord-312024-qdgqif5j.txt txt = ./txt/cord-312024-qdgqif5j.txt === reduce.pl bib === id = cord-312139-g1hczx54 author = Liu, Wei title = Non-specific Primers Reveal False-negative Risk in Detection of COVID-19 Infections date = 2020-04-11 pages = extension = .txt mime = text/plain words = 3347 sentences = 212 flesch = 60 summary = Based on the primers provided by research institutes from different countries, especially primers from China, detailed analysis of non-specificity of primer sequences had been conducted, and interference of human mRNA targeted by the primer was discussed deeply for RT-PCR detection of COVID-19 infections. https://doi.org/10.1101/2020.04.07.20056804 doi: medRxiv preprint 8 Although many patients tested one or more negative before receiving positive results for SARS-CoV-2 virus in China, it was difficult to understand the extent to which this abnormal phenomenon occurs. To eliminate the host interference in RT-PCR detection of COVID-19 infections, specific amplification of the intended target of SARS-Cov-2 sequence required that primers matched as little as possible to any human RNA transcript. Hence it was not difficult to draw a conclusion that non-specificity of the primer designed for SARS-CoV-2 virus might be an important factor resulting in so many false-negative diagnoses for COVID-19 infections in China. cache = ./cache/cord-312139-g1hczx54.txt txt = ./txt/cord-312139-g1hczx54.txt === reduce.pl bib === id = cord-312161-egwo19oc author = Aw, Tiong Gim title = Detection of pathogens in water: from phylochips to qPCR to pyrosequencing date = 2011-12-05 pages = extension = .txt mime = text/plain words = 4551 sentences = 209 flesch = 31 summary = Microbial water quality monitoring has undergone tremendous transition in recent years, with novel molecular tools beginning to offer rapid, high-throughput, sensitive and specific detection of a wide spectrum of microbial pathogens that challenge traditional culture-based techniques. High-density microarrays, quantitative real-time PCR (qPCR) and pyrosequencing which are considered to be breakthrough technologies borne out of the 'molecular revolution' are at present emerging rapidly as tools of pathogen detection and discovery. The limitations in detecting and identifying pathogens directly from environmental water samples by culture or microscopy can now be addressed by integrating concentration techniques with molecular tools to provide sensitive, specific and quantitative data on any pathogens of interest. Pyrosequencing technology is revolutionizing the study of microbial ecology as well as direct metagenomic detection Detection of pathogens in water Aw and Rose 425 High levels of several classes of resistance genes in bacterial communities exposed to antibiotic were identified. cache = ./cache/cord-312161-egwo19oc.txt txt = ./txt/cord-312161-egwo19oc.txt === reduce.pl bib === id = cord-312197-d5d8amk7 author = Edmond, Karen title = New Approaches to Preventing, Diagnosing, and Treating Neonatal Sepsis date = 2010-03-09 pages = extension = .txt mime = text/plain words = 5224 sentences = 259 flesch = 38 summary = Health facility infections are also a major problem in lowincome countries, but the more pressing issues are the high proportion of home deliveries in unclean environments predisposing to sepsis and ensuring that all neonates have access to effective interventions from health care providers in the first days of life 2 . Randomised controlled trials (RCTs) of maternal protein-calorie and multiple micronutrient and supplementation have demonstrated significant improvements in rates of prematurity and birth weight and variable impact on mortality; but no studies have examined their impact on rates of neonatal sepsis [20, 21] . New studies from Malawi and Nepal indicate that maternal antisepsis interventions such as vaginal chlorhexidine during labour may have a significant impact on rates of neonatal mortality and sepsis in developing countries [33] . Intrapartum antibiotic prophylaxis has been highly effective in reducing both early-onset neonatal bacterial and maternal sepsis in developed countries [35] . cache = ./cache/cord-312197-d5d8amk7.txt txt = ./txt/cord-312197-d5d8amk7.txt === reduce.pl bib === id = cord-312222-aw5849rc author = Österdahl, Marc F. title = Detecting SARS-CoV-2 at point of care: preliminary data comparing loop-mediated isothermal amplification (LAMP) to polymerase chain reaction (PCR) date = 2020-10-20 pages = extension = .txt mime = text/plain words = 3957 sentences = 201 flesch = 53 summary = METHODS: This prospective service improvement project piloted an RT-LAMP method on nasal and pharyngeal swabs on 21 residents of a high dependency care home, with two index COVID-19 cases, and compared it to multiplex tandem reverse transcription polymerase chain reaction (RT-PCR). We recorded vital signs of patients to correlate clinical and laboratory information and calculated the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of a single swab using RT-LAMP compared with the current standard, RT-PCR, as per Standards for Reporting Diagnostic Accuracy Studies (STARD) guidelines. Since then, a number [13] of other groups have published high-quality studies demonstrating that RT-LAMP has the potential to replace RT-PCR as a means for detecting SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) within RNA extracted from nose -throat swabs and endotracheal secretions/bronchoalveolar lavage fluid [5, 14, 15] . cache = ./cache/cord-312222-aw5849rc.txt txt = ./txt/cord-312222-aw5849rc.txt === reduce.pl bib === id = cord-312240-0k8y86pf author = Schlaberg, Robert title = Viral Pathogen Detection by Metagenomics and Pan-Viral Group Polymerase Chain Reaction in Children With Pneumonia Lacking Identifiable Etiology date = 2017-05-01 pages = extension = .txt mime = text/plain words = 4837 sentences = 239 flesch = 46 summary = Nasopharyngeal/oropharyngeal (NP/OP) swabs from 70 children <5 years with CAP of unknown etiology and 90 asymptomatic controls were tested by next-generation sequencing (RNA-seq) and pan viral group (PVG) PCR for 19 viral families. We first assessed the ability of RNA-seq and PVG PCR to detect known respiratory pathogens using specimens from children with CAP (n = 63) and asymptomatic control (n = 52) subjects in whom viral or atypical bacterial pathogens had been detected using the EPIC study protocol. We validated RNA-seq and PVG PCR methods to detect known respiratory pathogens by testing specimens using both methods from children with CAP (n = 63) and asymptomatic control subjects (n = 52) in whom viral or atypical bacterial pathogens had been detected using the EPIC study protocol. Using RNA-seq and PVG PCR, we identified additional viruses from upper respiratory tract specimens in >30% children hospitalized with clinical and radiographic pneumonia but in whom no pathogen was identified despite extensive testing by culture, molecular, and serologic methods. cache = ./cache/cord-312240-0k8y86pf.txt txt = ./txt/cord-312240-0k8y86pf.txt === reduce.pl bib === id = cord-312996-qzu8pkyt author = Iles, R. K. title = A clinical MALDI-ToF Mass spectrometry assay for SARS-CoV-2: Rational design and multi-disciplinary team work. date = 2020-08-22 pages = extension = .txt mime = text/plain words = 6845 sentences = 375 flesch = 51 summary = Testing limitations, including reagent shortages, remain a bottleneck in the battle to curtail COVID-19 spread in even the wealthiest countries [1, 2] The development of new matrix assisted laser desorption time of flight mass spectrometry (MALDI-ToF MS) diagnostics for SARS-CoV-2 detection is driven by the need for greater diagnostic capacity and alternative applications to complement standard PCR and antibody based diagnostics. Consequently studies where swab samples have been split for simultaneous analysis by RT PCR detection systems of SARS-CoV-2 RNA and by MALDI-ToF mass spectrometry for viral proteins, are compromised [4] . virus grown in vitro and mass spectra of gargle/saliva spiked with culture media from cells infected with SARS-CoV-2: S proteolytic fragments S1 and S2 were seen in all preparations and S2b only in serum free samples. These confirmed PCR-negative gargle samples were analysed by MALDI-ToF mass spectrometry 40 times; the measured peak intensities of which acted as comparative controls to the viral spiked saliva/gargle. cache = ./cache/cord-312996-qzu8pkyt.txt txt = ./txt/cord-312996-qzu8pkyt.txt === reduce.pl bib === id = cord-313107-6cfenpxm author = Singh, Anirudh K. title = Evaluation of pooled sample analysis strategy in expediting case detection in areas with emerging outbreaks of COVID-19: A pilot study date = 2020-09-22 pages = extension = .txt mime = text/plain words = 2889 sentences = 124 flesch = 50 summary = In this context, a pooled sample testing strategy was evaluated in the setting of emerging disease outbreak in 3 central Indian districts to assess if the cost of the test and turn-around time could be reduced without compromising its diagnostic characteristics and thus lead to early containment of the outbreak. At the reported point prevalence of 4.8% in this study, the negative predictive value of qRT-PCR on pooled samples was around 96% suggesting that the adoption of this strategy as an effective screening tool for COVID-19 needs to be carefully evaluated. We hypothesized that testing of pooled respiratory samples, collected from potentially infected individuals, could lead to faster laboratory confirmation and quicker containment of the emerging infection in these districts and, thus, undertook this study to evaluate the diagnostic concordance between the strategies of pooled vs. cache = ./cache/cord-313107-6cfenpxm.txt txt = ./txt/cord-313107-6cfenpxm.txt === reduce.pl bib === id = cord-312456-6lxc2rj2 author = Soltan, Mohamed A. title = Comparison of electron microscopy, ELISA, real time RT-PCR and insulated isothermal RT-PCR for the detection of Rotavirus group A (RVA) in feces of different animal species date = 2016-05-11 pages = extension = .txt mime = text/plain words = 4209 sentences = 218 flesch = 53 summary = title: Comparison of electron microscopy, ELISA, real time RT-PCR and insulated isothermal RT-PCR for the detection of Rotavirus group A (RVA) in feces of different animal species The aim of this investigation was to evaluate a commercially available RT-iiPCR assay for RVA detection in feces from different animal species. Therefore, the aim of our investigation was to evaluate a recently available insulated isothermal RT-PCR (RT-iiPCR) reagent set (POCKIT TM Rotavirus A Reagent Set, GeneReach USA, Lexington, MA, USA) with use of a portable PCR machine, which could potentially be used for point-of-need detection for RVA in the feces of different animal species. Additionally, the sensitivity of the rotavirus RT-iiPCR reagent set was evaluated by comparison with the commercially available rtRT-PCR assay using 10-fold serial dilutions of nucleic acid extracted from a positive bovine clinical sample. There was a significant difference in the number of positive samples detected with the in-house rtRT-PCR assay versus the other two molecular tests. cache = ./cache/cord-312456-6lxc2rj2.txt txt = ./txt/cord-312456-6lxc2rj2.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-312223-qgwzgazd author = Shafagati, Nazly title = The Use of NanoTrap Particles as a Sample Enrichment Method to Enhance the Detection of Rift Valley Fever Virus date = 2013-07-04 pages = extension = .txt mime = text/plain words = 8834 sentences = 495 flesch = 57 summary = RESULTS: Screening of NanoTrap particles indicated that one particle, NT53, was the most efficient at RVFV capture as demonstrated by both qRT-PCR and plaque assays. RVFV that was inactivated through either detergent or heat treatment was still found bound to NT53, indicating the ability to use NanoTrap particles for viral capture prior to transport to a BSL-2 environment. Our study demonstrates that NanoTrap particles are capable of capturing whole virus, and can be assayed with both qRT-PCR and plaque assays. A) Seven different types of NanoTrap particles were incubated with viral supernatants containing RVFV (1E+7 pfu/ml) for 30 minutes at room temperature and washed 4 times with water. In order to determine if the amplification observed in the qRT-PCR assay was due to the NanoTrap particle capturing intact viral particles or association of viral RNA (presumably due to lysed virus) with the particles, plaque assays were performed. cache = ./cache/cord-312223-qgwzgazd.txt txt = ./txt/cord-312223-qgwzgazd.txt === reduce.pl bib === === reduce.pl bib === id = cord-313375-rs3jjiuj author = Panning, Marcus title = Singleplex real-time RT-PCR for detection of influenza A virus and simultaneous differentiation of A/H1N1v and evaluation of the RealStar influenza kit date = 2010-11-13 pages = extension = .txt mime = text/plain words = 2309 sentences = 159 flesch = 57 summary = Study design: A real-time RT-PCR assay targeting the matrix gene of influenza A viruses was developed and validated using in vitro transcribed RNA derived from influenza A/H1N1v, A/H1N1 and A/H3N2 virus as well as plaque-quantified influenza A/H1N1v, A/H1N1 and A/H3N2 virus samples. Study design: A real-time RT-PCR assay targeting the matrix gene of influenza A viruses was developed and validated using in vitro transcribed RNA derived from influenza A/H1N1v, A/H1N1 and A/H3N2 virus as well as plaque-quantified influenza A/H1N1v, A/H1N1 and A/H3N2 virus samples. After validation of the in-house version the commercial RealStar kit was used to assess the clinical performance and specificity on a panel of influenza viruses including A/H1N1v, A/H1N1, swine A/H1N1, A/H3N2, avian A/H5N1 as well as patient specimens. After validation of the in-house version the commercial RealStar kit was used to assess the clinical performance and specificity on a panel of influenza viruses including A/H1N1v, A/H1N1, swine A/H1N1, A/H3N2, avian A/H5N1 as well as patient specimens. cache = ./cache/cord-313375-rs3jjiuj.txt txt = ./txt/cord-313375-rs3jjiuj.txt === reduce.pl bib === === reduce.pl bib === id = cord-313506-6bb4q7nv author = Sano, Akiko title = Physiological Level Production of Antigen-Specific Human Immunoglobulin in Cloned Transchromosomic Cattle date = 2013-10-24 pages = extension = .txt mime = text/plain words = 6695 sentences = 313 flesch = 54 summary = We previously showed that transchromosomic (Tc) cattle carrying a human artificial chromosome (HAC) comprising the entire unrearranged human immunoglobulin heavy-chain (hIGH) and kappa-chain (hIGK) germline loci (named as κHAC) are capable of producing functional hpAbs when both of the bovine immunoglobulin mu heavy-chains, bIGHM and bIGHML1, are homozygously inactivated (double knockouts or DKO). Therefore, in an effort to improve B cell development and hIgG production in Tc cattle, we sought to enhance pre-BCR function by engineering a new HAC into which, in addition to the hIGH, hIGK and hIGL chromosome loci that carry the entire human immunoglobulin gene repertoire, the human VpreB (hVPREB1) and λ5 (hIGLL1) genomic loci from human chromosome 22 (hChr22) was incorporated, and part of CH and TM domains, CH2-TM, of hIGHM gene, was replaced by the corresponding bovine gene sequence (bovinization of the CH2-TM domains of hIGHM). doi: 10.1371/journal.pone.0078119.g002 DT40 colonies were screened with genomic PCR (data not shown) for the correctly modified hChr2, and clone K53 was identified and selected for the final HAC construction ( Figure 5 ). cache = ./cache/cord-313506-6bb4q7nv.txt txt = ./txt/cord-313506-6bb4q7nv.txt === reduce.pl bib === === reduce.pl bib === id = cord-314051-dr27bsvt author = Lother, Sylvain A. title = Preoperative SARS-CoV-2 screening: Can it really rule out COVID-19? date = 2020-06-23 pages = extension = .txt mime = text/plain words = 3121 sentences = 259 flesch = 56 summary = If viral carriage is not detected by testing, patients may proceed with elective surgery whereby signs and symptoms of coronavirus disease (COVID-19) may arise in the postoperative period, leading to adverse outcomes. 3 While screening with RT-PCR may detect some presymptomatic preoperative patients, the window of diagnostic utility is small, and careful interpretation of negative and positive test results must be considered prior to altering the course of therapy. A positive RT-PCR result identifies a group of patients who may be infected with SARS-CoV-2 and should have elective surgeries delayed. Si la présence virale n'est pas dépistée par un test, les patients peuvent aller de l'avant avec leur chirurgie non urgente, à la suite de laquelle les signes et symptômes d'une atteinte au coronavirus (COVID-19) pourraient survenir en période postopératoire, entraînant des devenirs défavorables. cache = ./cache/cord-314051-dr27bsvt.txt txt = ./txt/cord-314051-dr27bsvt.txt === reduce.pl bib === id = cord-313439-cadyykks author = Felten, Sandra title = Diagnosis of Feline Infectious Peritonitis: A Review of the Current Literature date = 2019-11-15 pages = extension = .txt mime = text/plain words = 12466 sentences = 522 flesch = 44 summary = Studies evaluating sensitivity and specificity of the detection of serum antibodies in comparison to either histopathology, a combination of diagnostic tests or clinical suspicion of feline infectious peritonitis (FIP). Recent studies evaluated the use of a quantitative RT-PCR (RT-qPCR) to detect FCoV RNA in FNA samples of the mesenteric lymph nodes and other abnormal tissues of clinical cases [119, 140] and hypothesized that this technique would be a useful tool to diagnose FIP for veterinary practitioners, especially in cats without effusion. Sensitivity and specificity from different studies evaluating the detection of feline coronavirus (FCoV) spike (S) gene mutations in tissue samples. RT-nPCR and subsequent S gene sequencing of serum and plasma samples from cats with FIP (diagnosed by histopathology ± IHC or by positive immunofluorescence in effusion) and control cats (diagnosed with another disease either ante or post mortem) revealed a sensitivity of only 7%, which confirms the very low virus load in blood. cache = ./cache/cord-313439-cadyykks.txt txt = ./txt/cord-313439-cadyykks.txt === reduce.pl bib === === reduce.pl bib === id = cord-314937-jrxu65bl author = Kuwelker, K. title = High attack rates of SARS-CoV-2 infection through household-transmission: a prospective study date = 2020-11-04 pages = extension = .txt mime = text/plain words = 5868 sentences = 391 flesch = 55 summary = The secondary attack rate of SARS-CoV-2 from index cases to household contacts reflects the natural spread of infection in immunologically naive populations with limited preventive measures to control transmission. Here, we estimated the secondary household attack rate of SARS-CoV-2 and identified the determinants of household transmission by measuring SARS-CoV-2-specific antibodies in household members of RT-PCR confirmed cases during the first month of the COVID-19 pandemic in Norway. Our study was specifically designed to assess household attack rates as measured by seropositivity in household members 6-8 weeks after onset of symptoms in the index case, with low prevalence of SARS-CoV-2 virus in the community. We calculated attack rates based on SARS-CoV-2-specific antibodies in household members, whereas the majority of previous studies have ascertained transmission based on RT-PCR, with estimates of 7·6% to 38% (11) (12) (13) (14) (15) (16) (17) (18) (19) (20) . cache = ./cache/cord-314937-jrxu65bl.txt txt = ./txt/cord-314937-jrxu65bl.txt === reduce.pl bib === id = cord-313676-6rebpe57 author = De la Torre, David I. title = Enteric Virus Diversity Examined by Molecular Methods in Brazilian Poultry Flocks date = 2018-03-29 pages = extension = .txt mime = text/plain words = 5867 sentences = 295 flesch = 55 summary = The most common enteric viruses affecting commercial flocks in Brazil include Fowl Adenovirus of group I (FAdV-I), Chicken Parvovirus (ChPV), Chicken Astrovirus (CAstV), Avian Nephritis Virus (ANV), Infectious Bronchitis Virus (IBV), Avian Reovirus (AReo), and Avian Rotavirus (ARtV). The main enteric viruses reported to cause enteric diseases are found in single and multiple infections and include the Fowl Adenovirus of group I (FAdV-I); Chicken Parvovirus (ChPV); two viruses from the Astroviridae family: Chicken Astrovirus (CAstV) and Avian Nephritis Virus (ANV); two viruses from the Reoviridae family: Avian Reovirus (AReo) and Avian Rotavirus (ARtV); and a member of the Coronaviridae family, Infectious Bronchitis Virus (IBV) [4, [6] [7] [8] [9] . The association of enteric virus with the age of broilers, breeders, and layers (Tables 4 and 5) showed that molecular diagnosis of these viruses can be performed at different stages of production, which can be useful in the control of vertical infections. cache = ./cache/cord-313676-6rebpe57.txt txt = ./txt/cord-313676-6rebpe57.txt === reduce.pl bib === id = cord-314069-8dxzf2ip author = Dongliu, Yuan title = Outbreak of acute febrile respiratory illness caused by human adenovirus B P14H11F14 in a military training camp in Shandong China date = 2016-06-28 pages = extension = .txt mime = text/plain words = 4283 sentences = 206 flesch = 51 summary = authors: Dongliu, Yuan; Guoliang, Yang; Haocheng, Xu; Shuaijia, Qing; Li, Bing; Yanglei, Jia This study reports an outbreak of acute febrile respiratory illness caused by human adenovirus B [P14H11F14] in a military training center in China between May and June 2014. A HAdV-B [P14H11F14] virus was confirmed as the etiological pathogen of this acute outbreak of febrile respiratory illness based on clinical manifestations, epidemiological characteristics, specific molecular detection results, phylogenetic analysis, and serological assays. In conclusion, the regional CDC officials concluded that a type-55-like human adenovirus B human/CHN/SD77001/ 2014/[P14H11F14] virus was the etiological pathogen responsible for this acute FRI outbreak based on the clinical manifestations in the patients, the epidemiological characteristics of the outbreak, the HAdV-DNA-specific PCR results, isolation of the virus, sequencing and alignment of the PCR amplicons, homology and phylogenetic analyses based on the complete E1A, penton base, hexon, and fiber gene sequences, and serological assays specific for HAdV IgA/IgG. cache = ./cache/cord-314069-8dxzf2ip.txt txt = ./txt/cord-314069-8dxzf2ip.txt === reduce.pl bib === id = cord-314986-uhpe69k0 author = Cai, Quan title = A model based on CT radiomic features for predicting RT-PCR becoming negative in coronavirus disease 2019 (COVID-19) patients date = 2020-10-20 pages = extension = .txt mime = text/plain words = 3744 sentences = 211 flesch = 48 summary = title: A model based on CT radiomic features for predicting RT-PCR becoming negative in coronavirus disease 2019 (COVID-19) patients Our purpose is to assess a model based on chest computed tomography (CT) radiomic features and clinical characteristics to predict RT-PCR negativity during clinical treatment. METHODS: From February 10 to March 10, 2020, 203 mild COVID-19 patients in Fangcang Shelter Hospital were retrospectively included (training: n = 141; testing: n = 62), and clinical characteristics were collected. We collected the clinical data and chest CT features of mild COVID-19 patients in Fangcang Shelter Hospital in Wuhan, Hubei, aiming to establish a predictive model for RT-PCR becoming negative during the recovery period. We analyzed chest CT images after the abnormal clinical symptoms disappeared, and proposed a combination model of radiomic features and clinical data to predict RT-PCR negativity. cache = ./cache/cord-314986-uhpe69k0.txt txt = ./txt/cord-314986-uhpe69k0.txt === reduce.pl bib === id = cord-314201-6njwigco author = Maher-Sturgess, Sheryl L title = Universal primers that amplify RNA from all three flavivirus subgroups date = 2008-01-24 pages = extension = .txt mime = text/plain words = 4625 sentences = 253 flesch = 54 summary = Tanaka [3] published the first universal primer pair specific for mosquito borne flaviviruses in 1993; the YF1 and YF3 primers targeted the NS5/3'UTR of the genome and were based upon the six flavivirus sequences available at the time. In 2005 Gaunt and Gould designed a universal nested PCR, using six primers targeting the E gene, capable of amplifying cDNA from 60 flavivirus strains. In the present study, we identified conserved sites and developed a universal, non-nested primer pair that amplifies cDNA from each of the major subgroups of flaviviruses, and also TABV, under standard reaction conditions. Since the amplified products represent 8% of the genome, this is sufficient sequence to determine the species of the virus and thus potentially to identify unrecognised flaviviruses. Rapid subgroup identification of the flaviviruses using degenerate primer E-gene RT-PCR and site specific restriction enzyme analysis cache = ./cache/cord-314201-6njwigco.txt txt = ./txt/cord-314201-6njwigco.txt === reduce.pl bib === id = cord-314386-cxq9v218 author = Nitsche, Andreas title = SARS Coronavirus Detection date = 2004-07-17 pages = extension = .txt mime = text/plain words = 1904 sentences = 96 flesch = 55 summary = We developed a set of three real-time reverse transcription–polymerase chain reaction (PCR) assays that amplify three different regions of the SARS-associated coronavirus (SARS-CoV), can be run in parallel or in a single tube, and can detect <10 genome equivalents of SARS-CoV. To improve the ability to detect SARS-CoV safely and reduce the risk of eliciting false-negative results caused by genome sequence variations, we established three individual real-time RT-PCR assays. Target sequences were chosen by using the following criteria: 1) the regions are distributed over the whole genome, including the nonstructural polyprotein 1a and 1ab genes and the spike glycoprotein gene (Table 1) ; 2) the regions are highly conserved among the 89, 90, and 100 respective sequences available in public sequence databases; 3) the regions are suitable for the design of a real-time RT-PCR assay; and 4) the designed primers, 5′-nuclease probes, and amplicons displayed no considerable homology to other viruses, including human CoV OC43 and 229E in BLAST searches (available from http://www.ncbi.nlm.nih.gov/BLAST/). cache = ./cache/cord-314386-cxq9v218.txt txt = ./txt/cord-314386-cxq9v218.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-315476-7rdiesav author = Peret, Teresa C. T. title = Characterization of Human Metapneumoviruses Isolated from Patients in North America date = 2002-06-01 pages = extension = .txt mime = text/plain words = 1959 sentences = 119 flesch = 54 summary = In this study, 11 isolates from 10 patients with respiratory disease from Quebec, Canada, were tested by a reverse-transcriptase polymerase chain reaction based on the fusion protein gene. In this study, 11 isolates from 10 patients with respiratory disease from Quebec, Canada, were tested by a reverse-transcriptase polymerase chain reaction based on the fusion protein gene. In the present article, we describe polymerase chain reaction (PCR) and sequencing studies done on 11 isolates from respiratory specimens from 10 Canadian patients with acute respiratory tract illness. Published nucleocapsid (N) and fusion (F) gene sequences of HMPV and avian pneumovirus were used to develop primers for detection and sequencing of HMPV at the Respiratory Virus Section (Centers for Disease Control and Prevention, Atlanta). We detected virus in isolates from children with acute respiratory tract infection, as described in the first report of HMPV [1] . cache = ./cache/cord-315476-7rdiesav.txt txt = ./txt/cord-315476-7rdiesav.txt === reduce.pl bib === id = cord-315541-tirod4t6 author = Henriques, Ana Margarida title = Development and validation of a real-time PCR for the detection and quantification of porcine circovirus type 2 date = 2018-07-17 pages = extension = .txt mime = text/plain words = 3552 sentences = 167 flesch = 51 summary = This paper reports the development and validation of a real-time PCR targeted to ORF1 and based on a TaqMan probe for the detection of porcine circovirus type 2 DNA in swine samples. The real-time PCR method described in this paper was performed with DNA from this strain, and an amplification curve with Ct 19.9 was obtained, confirming that such mutation in the probe annealing sequence had no effect in the reaction. The test performed with a plasmid containing the fragment to be amplified in the qPCR, with known The DNA samples used for the determination of the intra-and inter-assay variabilities for medium Ct values was not the same due to the lack of available DNA Fig. 2 Amplification curves obtained in the real-time PCR reaction performed for the determination of the limit of detection. cache = ./cache/cord-315541-tirod4t6.txt txt = ./txt/cord-315541-tirod4t6.txt === reduce.pl bib === id = cord-316173-ocdlh310 author = LIU, Dafei title = One-step triplex PCR/RT-PCR to detect canine distemper virus, canine parvovirus and canine kobuvirus date = 2018-01-23 pages = extension = .txt mime = text/plain words = 997 sentences = 48 flesch = 56 summary = title: One-step triplex PCR/RT-PCR to detect canine distemper virus, canine parvovirus and canine kobuvirus To rapidly distinguish Canine distemper virus (CDV), canine parvovirus (CPV), and canine kobuvirus (CaKoV) in practice, a one-step multiplex PCR/RT-PCR assay was developed, with detection limits of 10(2.1) TCID(50) for CDV, 10(1.9) TCID(50) for CPV and 10(3) copies for CaKoV. Therefore, the assay provides a sensitive tool for the rapid clinical detection and epidemiological surveillance of CDV, CPV and CaKoV in dogs. The viral DNA/RNA of fecal samples collected from dogs with clinical symptoms of diarrhea were extracted and tested in parallel with both the one-step multiplex PCR/RT-PCR and the commercial Rapid CDV/CPV Ag Test Kit (Bionote, Gyeonggi, Republic of Korea) for CDV or CPV, according to the manufacturer's instruction, and a traditional simplex RT-PCR for CaKoV, as described previously with minor modification [4] . Detection of canine distemper virus in dogs by real-time RT-PCR cache = ./cache/cord-316173-ocdlh310.txt txt = ./txt/cord-316173-ocdlh310.txt === reduce.pl bib === id = cord-316295-x636ux34 author = Roth, Bernhard title = Isolation of influenza viruses in MDCK 33016PF cells and clearance of contaminating respiratory viruses date = 2012-01-11 pages = extension = .txt mime = text/plain words = 4140 sentences = 190 flesch = 44 summary = Abstract This paper summarizes results obtained by multiplex PCR screening of human clinical samples for respiratory viruses and corresponding data obtained after passaging of virus-positive samples in MDCK 33016PF cells. Using lower inoculum dilutions than those normally applied for preparations containing influenza virus (total dilution of the original sample of ∼104), the positive results for the different viruses turned negative already after 2 or 3 passages in MDCK 33016PF cells. In a similar way, samples with positive and questionable multiplex PCR results only for viruses other than influenza virus were also cultivated for 2 or 3 passages in MDCK 33016PF cells. Considering the selection of specimens, the high percentage of influenza-positive results is not surprising, but a significant number of samples (66/370 or 17.8%) also tested positive for other viruses, such as adenovirus, bocavirus, coronavirus, enterovirus, metapneumovirus (HMPV), parainfluenza virus (PIV), rhinovirus, and respiratory syncytial virus (RSV). cache = ./cache/cord-316295-x636ux34.txt txt = ./txt/cord-316295-x636ux34.txt === reduce.pl bib === id = cord-315780-uhi66unn author = Paton, David title = Detection of transmissible gastroenteritis virus by RT-PCR and differentiation from porcine respiratory coronavirus date = 1997-07-31 pages = extension = .txt mime = text/plain words = 2905 sentences = 149 flesch = 53 summary = Abstract An RT-PCR method was developed that amplified genetic material from the 5′ end of the S protein gene of both transmissible gastroenteritis virus (TGEV) and porcine respiratory coronavirus (PRCV), but discriminated between the two by the size of the product generated. Detection of TGEV in clinical specimens was possible using a spin column method to extract RNA and sensitivity was compared to virus isolation and antigen detection ELISA. There are also reports of the use of DNA probes and of RT-PCR as detectors of TGEV RNA (Bae et al., 1991; Vaughn et al., 1996; Wesley et al., 1991; Jackwood et al., 1995) but the methods were not shown to be suitable for the direct detection of virus in clinical samples. Differentiation of transmissible gastroenteritis virus from porcine respiratory coronavirus and other antigenically related coronaviruses by using cDNA probes specific for the 5' region of the S glycoprotein gene cache = ./cache/cord-315780-uhi66unn.txt txt = ./txt/cord-315780-uhi66unn.txt === reduce.pl bib === id = cord-315949-7id5mitl author = Sentilhes, Anne‐Charlotte title = Respiratory virus infections in hospitalized children and adults in Lao PDR date = 2013-06-25 pages = extension = .txt mime = text/plain words = 4098 sentences = 246 flesch = 49 summary = 8, 9 The purpose of this study was to describe during a limited period of time the viral etiology of acute lower respiratory infections (ALRI) in patients hospitalized in two Lao hospitals by using a set of five multiplex RT-PCR/PCR targeting 18 common respiratory viruses. In this study, we report for the first time in Lao PDR the viral etiologies in patients hospitalized for ALRIs. We identified 186 respiratory viruses in 162 (55%) patients of all ages using 5 multiplex PCR/RT-PCR. Human respiratory syncytial virus is frequently defined as the predominant virus associated with hospitalizations for ALRI in children aged ≤5 years. Respiratory virus coinfections being frequent, 5, 19, 44 it demonstrates the usefulness of the multiplex RT-PCR approach, which allows the detection of the most important viruses in only few reactions while multiple infections are often undetected in viral culture or by direct immunofluorescence. cache = ./cache/cord-315949-7id5mitl.txt txt = ./txt/cord-315949-7id5mitl.txt === reduce.pl bib === id = cord-316309-8xe7cg8q author = Lee, Wah Heng title = LOMA: A fast method to generate efficient tagged-random primers despite amplification bias of random PCR on pathogens date = 2008-09-10 pages = extension = .txt mime = text/plain words = 5895 sentences = 296 flesch = 53 summary = We build on our previous paper [14] describing in further detail the AES algorithm that identifies genomics sequences that can be successfully amplified by random primers, facilitating the design of appropriate microarray probes for detection of the pathogen. In our paper, we reported an observation that experiments using random priming amplification often resulted in incomplete hybridization of the pathogen genome marked by interspersed genomic regions not detected by tiling probes on the microarray (Figure 1. Since our pathogen detection chip contains tiling 40-mer probes of both RSV and HMPV, the number and distribution of the probes with high signal intensities would give a good indication of the amount of PCR products generated across the target genome by a tagged-random primer. We expect that a tagged-random primer with desirable amplification efficiency that generates sufficient PCR products uniformly across the whole target genome would result in high signal intensity probes distributed evenly across the whole genome. cache = ./cache/cord-316309-8xe7cg8q.txt txt = ./txt/cord-316309-8xe7cg8q.txt === reduce.pl bib === id = cord-316250-w0nl88jz author = Yang, Falong title = Selection of reference genes for quantitative real-time PCR analysis in chicken embryo fibroblasts infected with avian leukosis virus subgroup J date = 2013-10-07 pages = extension = .txt mime = text/plain words = 2188 sentences = 112 flesch = 51 summary = title: Selection of reference genes for quantitative real-time PCR analysis in chicken embryo fibroblasts infected with avian leukosis virus subgroup J The objective of our study was to identify suitable reference genes for mRNA expression analysis in chicken embryonic fibroblasts (CEF) after infection with avian leukosis virus subgroup J (ALV-J). CONCLUSIONS: The RPL30 and SDHA were deemed suitable for use as reference genes for real-time PCR analysis of mRNA gene expression during ALV-J infection, whereas commonly used ACTB and GAPDH are unsuitable to be reference genes. This highlights the necessity of reference gene selection during real-time PCR analysis for virus-infected cells. Determination of suitable housekeeping genes for normalisation of quantitative real time PCR analysis of cells infected with human immunodeficiency virus and herpes viruses Selection of reference genes for quantitative real-time PCR analysis in chicken embryo fibroblasts infected with avian leukosis virus subgroup J. cache = ./cache/cord-316250-w0nl88jz.txt txt = ./txt/cord-316250-w0nl88jz.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-316343-u1uup5da author = Luo, Yun title = Longitudinal Surveillance of Betacoronaviruses in Fruit Bats in Yunnan Province, China During 2009–2016 date = 2018-02-01 pages = extension = .txt mime = text/plain words = 3493 sentences = 200 flesch = 58 summary = Total RNA was extracted from the hearts, livers, spleens, lungs, kidneys, brains, and intestines of six bats infected with bat coronaviruses HKU9 or GCCDC1 using the High Pure Viral RNA Kit. Partial RdRp representing HKU9 or GCCDC1 were cloned into the pGEM-T-easy Vector (Promega, Madison, WI, USA) and used as a positive control for quantitative analysis. By RT-PCR detection targeting partial RdRP, 46 (8.29%) samples were positive for HKU9 and 13 (2.34%) were positive for GCCDC1 or closely related viruses (Table 1) . A phylogenetic tree was conducted based on the alignment of partial RdRp sequences along with previously reported HKU9, GCCDC1, and related stains, as well as representative strains of other betacoronaviruses. In this study, we identified all bat species positive for coronavirus by sequencing the Cytb gene and found that HKU9 and GCCDC1 were from two different genera, Rousettus and Eonycteris, respectively. cache = ./cache/cord-316343-u1uup5da.txt txt = ./txt/cord-316343-u1uup5da.txt === reduce.pl bib === id = cord-315598-qwh72inx author = Mendoza, Jose Luis Accini title = ACTUALIZACION DE LA DECLARACIÓN DE CONSENSO EN MEDICINA CRITICA PARA LA ATENCIÓN MULTIDISCIPLINARIA DEL PACIENTE CON SOSPECHA O CONFIRMACIÓN DIAGNÓSTICA DE COVID-19 date = 2020-10-06 pages = extension = .txt mime = text/plain words = 69640 sentences = 6489 flesch = 54 summary = De otorgarse un Consentimiento Informado amplio, éste debería ser única y exclusivamente para los procesos asociados con COVID-19".(71) AMCI ® Se recomienda considerar la transición del cuidado intensivo al cuidado paliativo en todo paciente con sospecha o diagnóstico de COVID-19 sin mejoría a pesar de las intervenciones óptimas, con empeoramiento progresivo de su pronóstico vital y ante un evidente deterioro; aplicando medidas generales en control de síntomas ( Manejo de secreciones -Tratamiento del dolor -Tratamiento de la disnea -Sedación paliativa), así como apoyo espiritual, siempre acompañando al paciente y nunca abandonarlo en el final de la vida. En cuanto hace referencia a la situación actual de pandemia por SARS-CoV-2 y compromiso pulmonar; Wu y cols, en Marzo de 2.020 realizaron un estudio retrospectivo de 201 pacientes con COVID-19 en China; para aquellos pacientes que desarrollaron SDRA, el tratamiento con metilprednisolona estuvo asociado con una disminución del riesgo de muerte (23/50 [46%] con esteroides vs 21/34 [62%] sin esteroides; HR, 0.38 [IC 95%, 0.20-0.72]), con las limitaciones de los estudios retrospectivo, de un solo centro, con un limitado número de pacientes (400). cache = ./cache/cord-315598-qwh72inx.txt txt = ./txt/cord-315598-qwh72inx.txt === reduce.pl bib === id = cord-317129-wa1j2f6b author = Zhang, Jia title = De Novo synthesis of PCR templates for the development of SARS diagnostic assay date = 2003 pages = extension = .txt mime = text/plain words = 2319 sentences = 117 flesch = 58 summary = This highly efficient and safe strategy for obtaining SARS gene fragments is useful for the development of PCR assays, as well as for the preparation of reliable positive controls for PCR testing kits. This single-step sequential primer extension was expected to yield mainly final templates with no intermediate products. As shown in Figure 1 , DNA fragments in lengths of 182 and 204 bp were obtained from primers of set A and set B, respectively, by the single-step sequential primer extension where each reaction contained four partially overlapping a The expected products were extended from reverse primers (AR or BR) to the first forward primers. De novo synthesis of the PCR template complimentary to a viral genome provides a tool for the rapid development of early diagnostic assays for any new pathogen as soon as its sequence is known. cache = ./cache/cord-317129-wa1j2f6b.txt txt = ./txt/cord-317129-wa1j2f6b.txt === reduce.pl bib === === reduce.pl bib === id = cord-316932-fia1w9jt author = Ireland, D. C. title = Improved detection of rhinoviruses in nasal and throat swabs by seminested RT‐PCR date = 2005-12-07 pages = extension = .txt mime = text/plain words = 4099 sentences = 232 flesch = 61 summary = PCR tests in which a primary "touchdown" PCR was followed by secondary reactions using PV or HRV specific primers were able to differentiate HRVs of 48 serotypes from EVs. PVnRT‐PCR and HRVnRT‐PCR were then used to test nasal and throat swabs from adult subjects with naturally acquired respiratory virus infections. 2"PCRs using a primer of sequence A together with primers complementary to either B (HRVnRT-PCR) or C (PVnRT-PCR) are then used to differentiate between HRVs and other PVs. We have applied this test directly to nasal and throat swabs from controls and from individuals with naturally acquired colds and compared the rate of PV detection by PVnRT-PCR and by cell culture. This study has shown that PVnRT-PCR is a t least five times more sensitive than cell culture for the detection of PVs in nasal and throat swabs. cache = ./cache/cord-316932-fia1w9jt.txt txt = ./txt/cord-316932-fia1w9jt.txt === reduce.pl bib === === reduce.pl bib === id = cord-316537-f5rto51t author = Loens, Katherine title = Mycoplasma pneumoniae: Current Knowledge on Nucleic Acid Amplification Techniques and Serological Diagnostics date = 2016-03-31 pages = extension = .txt mime = text/plain words = 4207 sentences = 190 flesch = 34 summary = The clinical significance of a serologic test, both for IgM and IgG, should be defined by studies of patients with a documented infection and for whom detailed information concerning the time lapses between onset of disease and the collection of the serum specimens are known. Comparison of real-time polymerase chain reaction and serological tests for the confirmation of Mycoplasma pneumoniae infection in children with clinical diagnosis of atypical pneumonia Evaluation of five real-time PCR assays for detection of Mycoplasma pneumoniae Sensitive detection of Mycoplasma pneumoniae in human respiratory tract samples by optimized real-time PCR approach Diagnostic sensitivity of a rapid antigen test for the detection of Mycoplasma pneumoniae: comparison with real-time PCR Development of a multiplex real-time PCR assay for detection of Mycoplasma pneumoniae, Chlamydia pneumoniae and mutations associated with macrolide resistance in Mycoplasma pneumoniae from respiratory clinical specimens Real-time PCR detection of Mycoplasma pneumoniae in respiratory specimens Evaluation of a new real-time PCR assay for detection of Mycoplasma pneumoniae in clinical specimens cache = ./cache/cord-316537-f5rto51t.txt txt = ./txt/cord-316537-f5rto51t.txt === reduce.pl bib === === reduce.pl bib === id = cord-318013-5om35tu8 author = Marie, Tré-Hardy title = The role of serology for COVID-19 control: Population, kinetics and test performance do matter date = 2020-05-15 pages = extension = .txt mime = text/plain words = 944 sentences = 59 flesch = 48 summary = (1-4) The authors of these reports or correspondence highlighted the added value of serological testing, which, if captured within the correct timeframe after disease onset, can detect both active and past infections.(1) By providing estimates of who is and is not immune to SARS-CoV-2, serological data can be used to estimate epidemiological variables, such as the attack rate or case-fatality rate, which are necessary to assess how much community transmission has occurred and its burden.(5) They can also be used to strategically deploy immune health-care workers to reduce exposure of the virus to susceptible individuals or to assess the effect of non-pharmaceutical interventions at the population level and inform policy changes to release such measures. After two weeks, all tests demonstrate a sensitivity of 100%, as reported by other groups, (8, 10) except when the cut-off provided by the manufacturer were used for IgG detection (i.e. one of our 15 patients was never considered as positive). cache = ./cache/cord-318013-5om35tu8.txt txt = ./txt/cord-318013-5om35tu8.txt === reduce.pl bib === === reduce.pl bib === id = cord-318341-0827d8to author = Kaushik, Sulochana title = In-vitro and in silico activity of Cyamopsis tetragonoloba (Gaur) L. supercritical extract against the dengue-2 virus date = 2020-08-31 pages = extension = .txt mime = text/plain words = 3838 sentences = 209 flesch = 51 summary = The aim of the present study is to check the in vitro and in silico anti-dengue activity of Cyamopsis tetragonoloba supercritical extract in cell lines. The antiviral assay was performed on C6/36 cell lines with 100 copies of dengue-2 virus and maximum non-toxic dose (31.25 µg/ml) of supercritical extract and their effect was detected by real-time RT-PCR. tetragonoloba extracts) as well as experimental well (cell with 100 copies of the dengue-2 virus treated by MNTD of C. The percentages of cell viability of supercritical plants extract concentrations and anti-dengue data was analyzed by Microsoft Excel 2007 with the help of Tukey's test (each treatment mean value different from each other and compared to control). tetragonoloba show highly significant anti-viral activity against the dengue-2 virus quantitatively with the help of a real-time PCR assay. tetragonoloba extract was found 31.25 lg/ml effective against the DENV-2 virus on C6/36 cells. cache = ./cache/cord-318341-0827d8to.txt txt = ./txt/cord-318341-0827d8to.txt === reduce.pl bib === id = cord-317049-q3bvmkf7 author = Forde, Justin J. title = Yield and Implications of Pre-Procedural COVID-19 PCR Testing on Routine Endoscopic Practice date = 2020-05-25 pages = extension = .txt mime = text/plain words = 1140 sentences = 68 flesch = 47 summary = To fill the knowledge gap in this area, we sought to describe our experience with resuming endoscopy using a two-step approach (patient screening followed by COVID-19 testing) in order to provide needed data for other practices weighing the risks and benefits of resuming endoscopic procedures. On April 13, 2020 our endoscopy unit began mandatory COVID-19 polymerase chain reaction (PCR) testing by nasopharyngeal swab for all patients prior to any endoscopic procedure. On arrival to the endoscopy unit, patients were again screened by nursing staff using the same pre-procedure questionnaire and body temperature checks. Even with a negative result, endoscopy staff used full barrier PPE and ensured compliance with hygiene and social distancing practices in pre-and post-procedure areas to minimize risks to patients and staff. Although preprocedure PCR testing for COVID-19 may help to assuage concerns of the endoscopy unit staff, this needs to be balanced against the substantial false negative rate even with the best available tests. cache = ./cache/cord-317049-q3bvmkf7.txt txt = ./txt/cord-317049-q3bvmkf7.txt === reduce.pl bib === id = cord-318991-tw7wgpsi author = Nair, A. title = A British Society of Thoracic Imaging statement: considerations in designing local imaging diagnostic algorithms for the COVID-19 pandemic date = 2020-05-31 pages = extension = .txt mime = text/plain words = 2949 sentences = 134 flesch = 46 summary = In accordance with guidance from the Chief Medical Officer's office and the Royal College of Radiologists, the British Society of Thoracic Imaging (BSTI) recognises that based on the available evidence computed tomography (CT) currently has no upfront role in the diagnostic work-up of 2019 novel coronavirus (COVID-19) infection (https://www. 2 As such, in the minority of patients with high clinical suspicion but negative initial RT-PCR, the presence of typical CT appearances, such as peripheral ground-glass opacity, could be used to rapidly diagnose COVID-19 infection, until such time as multiple negative testing is sufficient to exclude or change the diagnosis. Therefore, we regard the role of CT in COVID-19 confirmed cases following RT-PCR results to be the same as in any other viral infection, in that it could be used to: (1) find co-existing or underlying diagnoses; (2) help diagnose complications, or investigate a clinically discordant picture (e.g., CRP decline, but increasing hypoxia); and (3) add value in patients with pre-existing lung diseases. cache = ./cache/cord-318991-tw7wgpsi.txt txt = ./txt/cord-318991-tw7wgpsi.txt === reduce.pl bib === === reduce.pl bib === id = cord-318392-r9bbomvk author = Woo, Patrick CY title = Coronavirus HKU15 in respiratory tract of pigs and first discovery of coronavirus quasispecies in 5′-untranslated region date = 2017-06-21 pages = extension = .txt mime = text/plain words = 3771 sentences = 213 flesch = 56 summary = The genomes of two Coronavirus HKU15 strains detected in the nasopharyngeal samples of two different pigs were sequenced following our previous publications 26, 27 with modifications. Divergence times for the Coronavirus HKU15 strains were calculated based on the complete genome sequence data, utilizing the Bayesian Markov chain Monte Carlo method using BEAST 1.8.0 33 with the substitution model GTR (general time-reversible model)+G (gammadistributed rate variation)+I (estimated proportion of invariable sites), a strict molecular clock, and a constant coalescent. In one (S579N) of the two Coronavirus HKU15 genomes that we sequenced in this study, variant sites were observed at four positions; two of them were due to nucleotide substitutions, and the other two were results of indels at mononucleotide polymeric regions (189th and 376th bases). cache = ./cache/cord-318392-r9bbomvk.txt txt = ./txt/cord-318392-r9bbomvk.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-320085-n9i54wzh author = Pfefferle, Susanne title = Evaluation of a quantitative RT-PCR assay for the detection of the emerging coronavirus SARS-CoV-2 using a high throughput system date = 2020-03-05 pages = extension = .txt mime = text/plain words = 2032 sentences = 116 flesch = 52 summary = We evaluated the performance of a molecular assay for the detection of SARS-CoV-2 on a high-throughput platform, the cobas 6800, using the 'open channel' for integration of a laboratory-developed assay. We evaluated the performance of a molecular assay for the detection of SARS-CoV-2 on a high-throughput platform, the cobas 6800, using the 'open channel' for integration of a laboratory-developed assay. The ability to quickly confirm or clear suspected cases is crucial during global outbreak scenarios, especially when clinical manifestations are difficult to distinguish from other respiratory infections such as influenza, molecular diagnostics is key for detection of the emerging virus. In this study, we demonstrated good analytical performance of an adapted SARS-CoV-2 assay on swab samples with an LoD of 689.3 copies/mL (e.g. 275.72 copies/process) at 95% detection probability, which is roughly in line with results published by Corman et al. cache = ./cache/cord-320085-n9i54wzh.txt txt = ./txt/cord-320085-n9i54wzh.txt === reduce.pl bib === id = cord-319845-oob2ktnz author = Proença-Modena, José Luiz title = Detection of Human Bocavirus mRNA in Respiratory Secretions Correlates with High Viral Load and Concurrent Diarrhea date = 2011-06-20 pages = extension = .txt mime = text/plain words = 5857 sentences = 269 flesch = 51 summary = Therefore, in order to test whether active viral replication of human bocavirus is associated with respiratory diseases and to understand the clinical impact of this virus in patients with these diseases, we performed a 3-year retrospective hospital-based study of HBoV in outpatients and inpatients with symptoms of Acute Respiratory Infections (ARI) in Brazil. This article reports a cross-sectional study of HBoV in ARI patients from Ribeirão Preto, Brazil, in which the shedding of VP1 mRNA in respiratory secretions was used as surrogate marker for active HBoV replication, to look for correlations with viral load, and presence of particular clinical manifestations and simultaneous detection of other respiratory viruses. The results of this cross-sectional study of HBoV in ARI patients from Ribeirão Preto, Brazil, indicate that shedding of VP1 mRNA in respiratory secretions, as a marker of HBoV replication, correlates positively with high viral load, presence of diarrhea, and lack of co-infection by other respiratory viruses. cache = ./cache/cord-319845-oob2ktnz.txt txt = ./txt/cord-319845-oob2ktnz.txt === reduce.pl bib === id = cord-319460-n4ezxnjc author = Bertasio, Cristina title = Porcine Epidemic Diarrhea Virus Shedding and Antibody Response in Swine Farms: A Longitudinal Study date = 2016-12-15 pages = extension = .txt mime = text/plain words = 5905 sentences = 262 flesch = 53 summary = During summer 2014, animals on two farms displaying mild clinical signs were detected as positive for PEDV by PCR (Boniotti et al., 2016) , and at the beginning of 2015 a new severe epidemic wave occurred (Efsa Ahaw Panel, 2014) . We conducted a longitudinal study by sampling the feces and blood of piglet groups from each farm at fixed intervals during a 2-5 months period, and then we determined PEDV shedding and the antibody presence. The highest fecal PEDV RNA shedding titer was observed in 3-6 day-old piglets with mean values (among shedding animals) of 5.9, 5.6, 5.6, and 6.2 log 10 copies/mL on F1, F2, F3, and F4, respectively ( Figure 1B; Supplementary Table 3 ). Determining the viral loads and shedding rates of PEDV in real field situations during outbreaks is important in evaluating the virulence of a strain and in predicting the susceptibility of infected animals, at different ages and in the various farm units, within a herd. cache = ./cache/cord-319460-n4ezxnjc.txt txt = ./txt/cord-319460-n4ezxnjc.txt === reduce.pl bib === id = cord-319685-dw0qsl4s author = Porter, Emily title = Amino acid changes in the spike protein of feline coronavirus correlate with systemic spread of virus from the intestine and not with feline infectious peritonitis date = 2014-04-25 pages = extension = .txt mime = text/plain words = 5690 sentences = 272 flesch = 58 summary = Recent evidence suggests that a mutation in the spike protein gene of feline coronavirus (FCoV), which results in an amino acid change from methionine to leucine at position 1058, may be associated with feline infectious peritonitis (FIP). Tissue and faecal samples collected post mortem from cats diagnosed with or without FIP were subjected to RNA extraction and quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR) to detect FCoV RNA. Data evaluating FCoV relative copy numbers in tissue and faecal samples from cats with and without FIP were analysed using a multilevel modelling approach (MLwiN v2.27) [25] , to account for the repeated measures within cats, and a non-parametric Mann-Whitney U test. Moreover, the majority (77%) of FCoV RNA sequences in faecal samples from cats with FIP had a methionine codon at position 1058 in the FCoV S protein gene, suggesting that these animals were shedding an enteric form of the virus. cache = ./cache/cord-319685-dw0qsl4s.txt txt = ./txt/cord-319685-dw0qsl4s.txt === reduce.pl bib === id = cord-319392-zg7gkf0j author = Yi, Li title = Development of a combined canine distemper virus specific RT-PCR protocol for the differentiation of infected and vaccinated animals (DIVA) and genetic characterization of the hemagglutinin gene of seven Chinese strains demonstrated in dogs date = 2011-11-18 pages = extension = .txt mime = text/plain words = 3494 sentences = 200 flesch = 59 summary = title: Development of a combined canine distemper virus specific RT-PCR protocol for the differentiation of infected and vaccinated animals (DIVA) and genetic characterization of the hemagglutinin gene of seven Chinese strains demonstrated in dogs A combined reverse-transcription polymerase chain reaction (RT-PCR) method was developed for the detection and differentiation of wild-type and vaccine strains of the canine distemper virus (CDV). The phylogenetic analysis of the hemagglutinin gene of the local wild-type CDV strains revealed that the seven local isolates all belonged to the Asia-1 lineage, and were clustered closely with one another at the same location. The CDV cDNA products were further simultaneously amplified by a combined two-step RT-PCR assay using two primer sets to distinguish the vaccine and field strains. A multiplex reverse transcriptionnested polymerase chain reaction for detection and differentiation of wild-type and vaccine strains of canine distemper virus cache = ./cache/cord-319392-zg7gkf0j.txt txt = ./txt/cord-319392-zg7gkf0j.txt === reduce.pl bib === id = cord-319970-1gu0a6cb author = Edin, Alicia title = Development and Laboratory Evaluation of a Real-Time PCR Assay for Detecting Viruses and Bacteria of Relevance for Community-Acquired Pneumonia date = 2015-03-13 pages = extension = .txt mime = text/plain words = 5049 sentences = 238 flesch = 39 summary = title: Development and Laboratory Evaluation of a Real-Time PCR Assay for Detecting Viruses and Bacteria of Relevance for Community-Acquired Pneumonia Diagnostic accuracy of the qPCR assay varied between 60% positive agreement with standard tests for Streptococcus pneumoniae and 100% for Mycoplasma pneumoniae, Moraxella catarrhalis, and Staphylococcus aureus. To verify that the method could detect viruses in sputum, sputum specimens each with a volume of 350 mL were spiked with100 mL from a NpA specimen positive for either RSV or influenza A before nucleic acid extraction and qPCR assay analysis were performed as described in the sections DNA and RNA Extraction and Primers Probes and qPCR Conditions, respectively. In the evaluation of the assay performance for detection of virus in sputum, we found that sputum specimens spiked with influenza A-or RSV-containing NpA specimens were positive at 25.9 AE 0.6 (n Z 5) and 27.7 AE 1.1 (n Z 5) cycles, respectively. cache = ./cache/cord-319970-1gu0a6cb.txt txt = ./txt/cord-319970-1gu0a6cb.txt === reduce.pl bib === id = cord-319921-uxtydu60 author = Meli, Marina L. title = Feline Leukemia Virus and Other Pathogens as Important Threats to the Survival of the Critically Endangered Iberian Lynx (Lynx pardinus) date = 2009-03-09 pages = extension = .txt mime = text/plain words = 5506 sentences = 259 flesch = 48 summary = METHODOLOGY/ PRINCIPAL FINDINGS: We systematically analyzed the prevalence and importance of seven viral, one protozoan (Cytauxzoon felis), and several bacterial (e.g., hemotropic mycoplasma) infections in 77 of approximately 200 remaining free-ranging Iberian lynxes of the Doñana and Sierra Morena areas, in Southern Spain, between 2003 and 2007. Furthermore, the presence of feline leukemia virus (FeLV) provirus was recently reported in six samples originating from both the Doñ ana and Sierra Morena areas in southern Spain between 1994 and 2003 [29] . Thus, in the present study, we report on the prevalence of the aforementioned pathogens and we describe a dramatic FeLV epidemic, which most likely led to the death of 6 Iberian lynxes within a 6-months period in 2007, its possible origin, and its relationship to other infectious agents. However, endogenous FeLV sequences related to those of domestic cats are apparently not present in Iberian lynxes: only 5 of the 77 lynxes tested displayed weak signals by quantitative realtime PCR, which is not compatible with presence of enFeLV sequences. cache = ./cache/cord-319921-uxtydu60.txt txt = ./txt/cord-319921-uxtydu60.txt === reduce.pl bib === id = cord-320617-ucm7wx8b author = B’Krong, Nguyen Thi Thuy Chinh title = Enterovirus serotypes in patients with central nervous system and respiratory infections in Viet Nam 1997–2010 date = 2018-04-12 pages = extension = .txt mime = text/plain words = 3958 sentences = 221 flesch = 51 summary = Here, we typed Enterovirus A-D (EV) from central nervous system (CNS) and respiratory infections in Viet Nam. METHODS: Data and specimens from prospective observational clinical studies conducted between 1997 and 2010 were used. In Viet Nam, since 2005, various serotypes of EV A, most commonly enterovirus A71 (EV-A71), coxsackievirus A16 (CV-A16), CV-A10, and CV-A6 have been associated with outbreaks of HFMD [12, 13] and EVs have also been frequently detected in aetiological studies of CNS and respiratory infections [14] [15] [16] [17] [18] . Here we report the clinical associations and serotyping results of EVs that were previously detected in our studies of CNS and respiratory infections in southern and central Viet Nam between 1997 and 2010. Our study illustrates the circulation of diverse enterovirus serotypes belonging to four species (A-D), and their association with respiratory and CNS infections in Viet Nam. These data are important for patient management, laboratory diagnostics and future outbreak response. cache = ./cache/cord-320617-ucm7wx8b.txt txt = ./txt/cord-320617-ucm7wx8b.txt === reduce.pl bib === id = cord-320002-25ivll3q author = Mathew, Joseph L. title = Etiology of community acquired pneumonia among children in India: prospective, cohort study date = 2015-10-21 pages = extension = .txt mime = text/plain words = 4151 sentences = 220 flesch = 44 summary = BACKGROUND: Childhood community acquired pneumonia (CAP) is a significant problem in developing countries, and confirmation of microbial etiology is important for individual, as well as public health. The Pneumonia Research for Child Health (PERCH) project [15] is a 7-site case-control study to identify the cause of pneumonia among children in developing countries. Currently, there is no study from India reporting etiology of CAP in a large cohort of children, using multiple biological samples, and various sensitive as well as specific microbiologic methods. We initiated the Community Acquired Pneumonia Etiology Study (CAPES) to address this knowledge gap by determining the microbiologic etiology of CAP in a cohort of Indian children using multiple biological specimens (blood, nasopharyngeal aspirates, bronchoalveolar lavage) and the relationship between etiology and pneumonia severity. Lower respiratory infections among hospitalized children in New Caledonia: a pilot study for the Pneumonia Etiology Research for Child Health project cache = ./cache/cord-320002-25ivll3q.txt txt = ./txt/cord-320002-25ivll3q.txt === reduce.pl bib === id = cord-320787-dwyyjq6o author = La Rosa, Giuseppina title = First detection of SARS-CoV-2 in untreated wastewaters in Italy date = 2020-05-23 pages = extension = .txt mime = text/plain words = 2747 sentences = 141 flesch = 54 summary = Italy is among the world's worst-affected countries in the COVID-19 pandemic, but so far there are no studies assessing the presence of SARS-CoV-2 in Italian wastewaters. To this aim, twelve influent sewage samples, collected between February and April 2020 from Wastewater Treatment Plants in Milan and Rome, were tested adapting, for concentration, the standard WHO procedure for Poliovirus surveillance. SARS-CoV-2 RNA detection was accomplished in volumes of 250 mL of wastewaters collected in areas of high (Milan) and low (Rome) epidemic circulation, according to clinical data. Herein we report the results of the screening for SARS-CoV-2 presence in sewage samples collected between the end of February and the beginning of April 2020 from WWTPs in Milan (Northern Italy) and Rome (Central Italy). In the absence of a standardized method for SARS-CoV-2 detection in environmental samples, RNAs were tested for the presence of SARS-CoV-2 using three different nested RT-PCR assays and one real-time qPCR assay (Table 1 and Figure 1 b) a newly designed primer set specific for SARS-CoV-2. cache = ./cache/cord-320787-dwyyjq6o.txt txt = ./txt/cord-320787-dwyyjq6o.txt === reduce.pl bib === id = cord-320769-qcpua9ck author = Park, Su-Jin title = Molecular epidemiology of bovine toroviruses circulating in South Korea date = 2008-01-25 pages = extension = .txt mime = text/plain words = 2807 sentences = 147 flesch = 61 summary = These results suggest that the BToV infections are sporadic in diarrheic calves in South Korea, and the Korean BToV strains are more closely related to the Japanese and Dutch BToVs than to the American and Italian BToVs. Toroviruses within the family Coronaviridae are spherical, oval, elongated, or kidney-shaped enveloped viruses that possess a positive-sense single-stranded, polyadenylated RNA genome of approximately 25-30 kb in length (Cornelissen et al., 1997; Horzinek, 1999; Snijder and Horzinek, 1993) . Based on the partial sequence of the BToV M gene, the Korean BToVs were more closely related to the Japanese and Dutch BToVs than to the American and Italian BToVs. To our knowledge, this is the first report of the detection of BToV shedding and its genetic diversity in diarrheic calves in South Korea. cache = ./cache/cord-320769-qcpua9ck.txt txt = ./txt/cord-320769-qcpua9ck.txt === reduce.pl bib === id = cord-320547-law20pmw author = Luchsinger, Vivian title = Comparison of Luminex xTAG® RVP fast assay and real time RT‐PCR for the detection of respiratory viruses in adults with community‐acquired pneumonia date = 2016-02-02 pages = extension = .txt mime = text/plain words = 3944 sentences = 222 flesch = 60 summary = The detection rates of respiratory viruses by Luminex xTAG® RVP fast assay, real time RT‐PCR (rtRT‐PCR) (Sacace®), and immunofluorescence assay (IFA) in adult CAP were performed in nasopharyngeal swabs (NPS) and aspirates (NPA) from 179 hospitalized adults. The aim of this study was to compare the respiratory viruses detection by Luminex xTAG 1 RVP, rtRT-PCR, and IFA in adults presenting with CAP, in secretions obtained by two nasopharyngeal secretion samples, swabs, and aspirates. Although detection rate for each virus by rtRT-PCR and by Luminex 1 were similar in NPS (P > 0.2), 10 viruses were additionally positive by rtRT-PCR (eight RV, one AdV, and one PIV) and 15 by xTAG 1 RVP Fast (eleven RV-EV, two Flu A,one hMPV, and one PIV-4) ( Table SII) , totalizing 24 patients with discordant viral detection. In the adult CAP cases herein studied the overall respiratory viruses detection rate, by both the new Luminex xTAG 1 RVP Fast and the rtRT-PCR technique was similar (51.9% vs. cache = ./cache/cord-320547-law20pmw.txt txt = ./txt/cord-320547-law20pmw.txt === reduce.pl bib === id = cord-321074-7jfy8cn6 author = Caruso, Damiano title = Quantitative Chest CT analysis in discriminating COVID-19 from non-COVID-19 patients date = 2020-10-12 pages = extension = .txt mime = text/plain words = 2918 sentences = 141 flesch = 45 summary = Quantitative Chest CT analysis was performed with a dedicated software that provides total lung volume, healthy parenchyma, GGOs, consolidations and fibrotic alterations, expressed both in liters and percentage. Lung quantification in liters showed significant differences between COVID-19 and non-COVID-19 patients for GGOs (0.55 ± 0.26L vs 0.43 ± 0.23L, p = 0.0005) and fibrotic alterations (0.05 ± 0.03 L vs 0.04 ± 0.03 L, p < 0.0001). A recent consensus statement from the Fleischner Society pointed out as imaging is indicated for medical triage of suspected COVID-19 patients presenting moderate-severe clinical features and a high pre-test probability of disease [13] . According to the hospital internal protocol, at the time of admission suspected COVID-19 patients presenting moderate-severe clinical features and a high pre-test probability of disease (fever defined as > 37.5 °C and respiratory symptoms or direct contact with a confirmed COVID-19 patient) underwent nasopharyngeal and oropharyngeal swabs for SARS-CoV-2. cache = ./cache/cord-321074-7jfy8cn6.txt txt = ./txt/cord-321074-7jfy8cn6.txt === reduce.pl bib === id = cord-320854-ybah03kr author = Kongprajug, Akechai title = Suppression of PmRab11 inhibits YHV infection in Penaeus monodon date = 2017-05-17 pages = extension = .txt mime = text/plain words = 6782 sentences = 396 flesch = 55 summary = Suppression of PmRab11 using dsRNA-PmRab11 either before or after YHV-challenge resulted in significant inhibition of YHV levels in the hemocytes and viral release in the supernatant in both mRNA and protein levels. Protein analysis revealed that an envelope glycoprotein gp64 of YHV cannot be detected in the hemocytes and supernatant of the PmRab11 knockdown group from 24 to 72 h post-YHV challenge. The low signals of PmRab11 protein and YHV glycoprotein 64 (gp64) can be observed inside the hemocytes of PmRab11 knockdown shrimp at 24 h post-infection (Fig. 8B) . In contrast, high signals of PmRab11 and gp64 can be detected in shrimp that was injected with dsRNA-GFP and NaCl followed by YHV challenge at this time point. Similar results of the delay in shrimp mortalities can be demonstrated for the knockdown effects of other Rab proteins including PmRab7 and PmRab5 during YHV infection [11, 12] . cache = ./cache/cord-320854-ybah03kr.txt txt = ./txt/cord-320854-ybah03kr.txt === reduce.pl bib === id = cord-321284-0y69n1ea author = El Kholy, A. A. title = The use of multiplex PCR for the diagnosis of viral severe acute respiratory infection in children: a high rate of co-detection during the winter season date = 2016-06-10 pages = extension = .txt mime = text/plain words = 3345 sentences = 175 flesch = 46 summary = title: The use of multiplex PCR for the diagnosis of viral severe acute respiratory infection in children: a high rate of co-detection during the winter season This study confirms the high rate of detection of viral nucleic acids by multiplex PCR among hospitalized children admitted with SARI, as well as the high rate of co-detection of multiple viruses. Forty healthy age-matched asymptomatic children with no history of a recent respiratory tract infection during the previous 2 weeks, who were not admitted to the hospital, and who do not have any chronic underlying illness were included as a control group. This study confirms the high rate of detection of viral nucleic acids by multiplex PCR) among hospitalized children admitted with severe acute respiratory infection, as well as the high rate of detection of multiple viruses. cache = ./cache/cord-321284-0y69n1ea.txt txt = ./txt/cord-321284-0y69n1ea.txt === reduce.pl bib === id = cord-321076-kont2sff author = Yeo, Wee Song title = Cohort PCR Testing: A Strategic Method for Rapid SARS-CoV-2 Screening date = 2020-05-30 pages = extension = .txt mime = text/plain words = 809 sentences = 47 flesch = 55 summary = title: Cohort PCR Testing: A Strategic Method for Rapid SARS-CoV-2 Screening The world is currently facing an unprecedented outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes viral pneumonias and the coronavirus disease 2019 (COVID-19) in humans. 2, 3 Various diagnostic methods have been utilized in the detection of SARS-CoV-2, among which real time reverse transcription polymerase chain reaction (RT-PCR) assay is the most established and commonly utilized test method. Last, any cohort PCR reaction tubes that are positive for SARS-CoV-2 will be followed up by running RT-PCR on each of the individual RNA samples to identify the infected individual(s). Cohort PCR is applicable for rapid screening of family/living units in the community who are likely to be negative for SARS-CoV-2. If cohort PCR is used to test a family or living unit where one member has confirmed SARS-CoV-2 infection, then there would be a very high likelihood that the pool would be positive (increasing probability with pool size). cache = ./cache/cord-321076-kont2sff.txt txt = ./txt/cord-321076-kont2sff.txt === reduce.pl bib === id = cord-320938-f526k9q1 author = Chen, Hongjun title = Partial and Full PCR-Based Reverse Genetics Strategy for Influenza Viruses date = 2012-09-28 pages = extension = .txt mime = text/plain words = 8614 sentences = 455 flesch = 60 summary = In order to determine whether a Flu PCR amplicon could be transfected into cells and be amplified by the influenza polymerase complex, a PCR product was produced encoding the GFP reporter gene in negative orientation flanked by the influenza segment 7 untranslated regions (UTRs) and further flanked by the human pol1 promoter and the mouse t1 termination signal, pol1EGFPt1 (Fig. 1A, Fig. S1A , Table S1 ). doi:10.1371/journal.pone.0046378.g001 Efficient influenza virus rescue using Flu PCR amplicons in either ''1+7'' or ''2+6'' modes The pol1HA pdm t1 or pol1HA D072 t1 HA PCR amplicons (Table 1) were co-transfected into co-cultured 293T/MDCK cells in a ''1+7'' mode along with 7 RG plasmids encoding the corresponding additional gene segments from the influenza A/Puerto Rico/ 8/1934 (H1N1) strain (PR8). cache = ./cache/cord-320938-f526k9q1.txt txt = ./txt/cord-320938-f526k9q1.txt === reduce.pl bib === id = cord-321181-bqdsfgdc author = Garitano, Ignacio title = Estimando el número de casos de COVID-19 mediante una herramienta web: resultados de la primera semana del proyecto "Covid-19 Trends" en Euskadi date = 2020-05-21 pages = extension = .txt mime = text/plain words = 3190 sentences = 301 flesch = 59 summary = Faltaban datos sobre el numero de casos no testados en España.Para estimar rápidamente el número de casos durante la pandemia de COVID-19, la Fundación Io , lanzó, el 19 de marzo, una herramienta web llamada "Covid-19 Trends", a nivel nacional, a través de las redes sociales. La página web de la Fundación iO muestra el cuestionario (https://covid19.fundacionio.com/epidemiologicalquestionnaire.aspx), así como el enlace a los datos en formatos CVS para ser utilizados por las autoridades de salud u otros grupos como universidades o institutos de investigación, de manera gratuita y a tiempo real. El cuestionario "Covid-19 Trends" estimó más de 6.000 casos compatibles con la definición clínica del Ministerio de Sanidad, Consumo y Bienestar Social en Euskadi durante el mes anterior al primer diagnóstico de COVID-19 mediante RT-PCR; esto indica que este tipo de herramienta podría ser útil como sistema de vigilancia temprana. cache = ./cache/cord-321181-bqdsfgdc.txt txt = ./txt/cord-321181-bqdsfgdc.txt === reduce.pl bib === id = cord-321361-6bkrt49b author = Chang, De title = Reply to Suri et al.: COVID-19 Real-Time RT-PCR: Does Positivity on Follow-up RT-PCR Always Imply Infectivity? date = 2020-07-01 pages = extension = .txt mime = text/plain words = 199 sentences = 23 flesch = 63 summary = key: cord-321361-6bkrt49b title: Reply to Suri et al.: COVID-19 Real-Time RT-PCR: Does Positivity on Follow-up RT-PCR Always Imply Infectivity? cord_uid: 6bkrt49b We read with keen interest the results of the SUMMIT (Study to Understand Mortality and Morbidity in COPD) randomized controlled trial of fluticasone furoate/vilanterol in patients with moderate chronic obstructive pulmonary disease (COPD) with a history of cardiovascular disease or at increased cardiovascular risk (1) . The trial evaluated both the value of aortic pulse wave velocity (aPWV) to predict all-cause mortality (ACM) in this population and Time kinetics of viral clearance and resolution of symptoms in novel coronavirus infection Novel Coronavirus Outbreak Research Team. Epidemiologic features and clinical course of patients infected with SARS-CoV-2 in Singapore Transmission of 2019-nCoV infection from an asymptomatic contact in Germany Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study cache = ./cache/cord-321361-6bkrt49b.txt txt = ./txt/cord-321361-6bkrt49b.txt === reduce.pl bib === id = cord-321432-qi2knswx author = Gardner, Shea N title = A microbial detection array (MDA) for viral and bacterial detection date = 2010-11-25 pages = extension = .txt mime = text/plain words = 8427 sentences = 397 flesch = 50 summary = METHODS: We designed a pan-Microbial Detection Array (MDA) to detect all known viruses (including phages), bacteria and plasmids and developed a novel statistical analysis method to identify mixtures of organisms from complex samples hybridized to the array. We also present a novel statistical algorithm for analysis of detection/discovery arrays, which combines a predictive model of probe hybridization with a greedy likelihood maximization procedure to identify the combination of targets in a complex sample that best explains the observed probe intensity pattern. We developed a novel statistical method for detection array analysis, by modeling the likelihood of the observed probe intensities as a function of the combination of targets present in the sample, and performing greedy maximization to find a locally optimal set of targets; the details of the algorithm are shown in Methods. cache = ./cache/cord-321432-qi2knswx.txt txt = ./txt/cord-321432-qi2knswx.txt === reduce.pl bib === id = cord-321443-89o13sox author = Umazume, Takeshi title = Survey on the use of personal protective equipment and COVID‐19 testing of pregnant women in Japan date = 2020-08-10 pages = extension = .txt mime = text/plain words = 2029 sentences = 116 flesch = 53 summary = AIM: To clarify the status of personal protective equipment (PPE) and coronavirus disease 2019 (COVID‐19) tests for pregnant women, we conducted an urgent survey. Our study also determined that around 65.0% of facilities for doctors and 73.5% of facilities for midwives used PPE beyond the "standard gown or apron, surgical mask, goggles or face shield" during labor of asymptomatic women. 3 In order to clarify the status of PPE usage during labor and delivery and COVID-19 tests for pregnant women, we conducted an urgent survey in Japan. Status of PPE use beyond "standard gown or apron, surgical mask, goggle or face shield" during labor of women without symptoms of COVID-19 Pregnant women were tested for COVID-19 not only in perinatal medical centers and university hospitals, but also other facilities, at a rate of 9-17% (Table S2) . Appropriate guidelines for PPE usage by medical providers and COVID-19 testing for pregnant women before delivery are necessary in Japan. cache = ./cache/cord-321443-89o13sox.txt txt = ./txt/cord-321443-89o13sox.txt === reduce.pl bib === id = cord-321855-7b1c2xdh author = Alshami, Alanoud title = Silent disease and loss of taste and smell are common manifestations of SARS-COV-2 infection in a quarantine facility: Saudi Arabia date = 2020-10-30 pages = extension = .txt mime = text/plain words = 3380 sentences = 190 flesch = 56 summary = title: Silent disease and loss of taste and smell are common manifestations of SARS-COV-2 infection in a quarantine facility: Saudi Arabia PRIMARY AND SECONDARY MEASURES: The clinical presentation, prevalence of asymptomatic carriers among SARS-COV-2 positive quarantined subjects, and the difference between virus clearance among symptomatic and asymptomatic individuals. The persistent positive PCR beyond 14 days observed in the mild symptomatic residents despite being symptoms free, warrant further studies to determine its implications on disease spread and control. have examined 24 asymptomatic infected individuals with a history of close contact with SARS-COV-2 confirmed cases and found that only 20% of them developed symptoms. Our findings are in light with a recent study that reported a 59% prevalence of loss of taste and smell in a cohort of COVID-19 patients [15] . Sudden onset of loss of smell and taste were prevalent in our study and were key symptoms of mild disease. cache = ./cache/cord-321855-7b1c2xdh.txt txt = ./txt/cord-321855-7b1c2xdh.txt === reduce.pl bib === id = cord-321514-knyw023l author = Bénet, Thomas title = Severity of Pneumonia in Under 5-Year-Old Children from Developing Countries: A Multicenter, Prospective, Observational Study date = 2017-07-12 pages = extension = .txt mime = text/plain words = 4441 sentences = 271 flesch = 44 summary = The objectives were to evaluate the microbiological agents linked with hypoxemia in hospitalized children with pneumonia from developing countries, to identify predictors of hypoxemia, and to characterize factors associated with in-hospital mortality. The objectives of the present study are to assess the microbiological agents linked to hypoxemia in hospitalized children with pneumonia in developing countries, to identify clinical and para-clinical predictors of hypoxemia and to pinpoint factors associated with death within 2 weeks after admission. The present study selectively comprised sites with better quality data on oxygen saturation (SO 2 ) at admission, mortality among pneumonia cases, and documented recording of patient follow-up during hospitalization. One of the objectives of this study was to assess microbiological agents and other predictors of hypoxemia and death in under 5-year-old hospitalized children with pneumonia from developing countries. cache = ./cache/cord-321514-knyw023l.txt txt = ./txt/cord-321514-knyw023l.txt === reduce.pl bib === id = cord-322184-kgv9f58a author = Sohn, Yujin title = Assessing Viral Shedding and Infectivity of Asymptomatic or Mildly Symptomatic Patients with COVID-19 in a Later Phase date = 2020-09-10 pages = extension = .txt mime = text/plain words = 3476 sentences = 182 flesch = 55 summary = Conclusions: In conclusion, our study suggests that even if viral shedding is sustained in asymptomatic or mildly symptomatic patients with later phase of COVID-19, it can be expected that the transmission risk of the virus is low. In this study, we attempted to confirm the presence of viable virus by performing RT-PCR assay and culture using salivary and nasopharyngeal swabs of asymptomatic or mildly symptomatic COVID-19 patients who had been diagnosed with the disease and admitted to a CTC at least two weeks previously. Therefore, based on the evidence that the virus is rarely detected in respiratory specimens after 10 days following the onset of symptoms, especially in mild or asymptomatic cases of SARS-CoV-2 infection, even if viral shedding is sustained in the later phase of COVID-19, it can be expected that the transmission risk of the virus is low. cache = ./cache/cord-322184-kgv9f58a.txt txt = ./txt/cord-322184-kgv9f58a.txt === reduce.pl bib === id = cord-322234-1zyy536y author = Lorusso, Alessio title = One-step real-time RT-PCR for pandemic influenza A virus (H1N1) 2009 matrix gene detection in swine samples date = 2009-12-17 pages = extension = .txt mime = text/plain words = 4162 sentences = 195 flesch = 51 summary = To evaluate the applicability of the test as a diagnostic tool in the screening of field specimens from swine, 64 field isolates of North American swine, 5 equine and 48 avian influenza viruses collected during diagnostic investigations were analyzed retrospectively as well as samples collected during an experimental in vivo infection with two novel H1N1 isolates, A/California/04/2009 (H1N1)v virus and A/Mexico/4108/2009 (H1N1)v. Swine and equine influenza virus isolates and the clinical samples from pigs infected experimentally with 2009 (H1N1)v were subjected to the USDA-validated qRT-PCR procedure for the general detection of type A influenza virus RNA (matrix screening assay), following procedures described previously (Spackman and Suarez, 2008) . All endemic North American swine influenza virus isolates were negative for (H1N1) 2009 specific matrix gene RNA using the present qRT-PCR assay, whereas the (H1N1) 2009 strains used as positive control were positive. cache = ./cache/cord-322234-1zyy536y.txt txt = ./txt/cord-322234-1zyy536y.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-322524-bq9ok8h1 author = Belongia, Edward A title = Clinical Features, Severity, and Incidence of RSV Illness During 12 Consecutive Seasons in a Community Cohort of Adults ≥60 Years Old date = 2018-11-27 pages = extension = .txt mime = text/plain words = 5184 sentences = 285 flesch = 45 summary = Studies conducted in the 1980s and 1990s first identified RSV as a cause of acute respiratory illness in a variety of adult populations, including older adults, working-age adults, hospitalized patients, and residents of long-term care facilities [5] [6] [7] [8] [9] . A 6-season study of adults ≥50 years old with predominantly outpatient acute respiratory illness found that RSV was the third most common viral pathogen (after influenza and human rhinovirus) [19] . The objective of this study was to describe the clinical characteristics, severity, clinical outcomes, and long-term incidence of medically attended RSV illness in a community cohort of adults ≥60 years of age from the 2004-2005 through 2015-2016 influenza seasons. Seasonal incidence of medically attended respiratory syncytial virus infection in a community cohort of adults ≥50 years old cache = ./cache/cord-322524-bq9ok8h1.txt txt = ./txt/cord-322524-bq9ok8h1.txt === reduce.pl bib === === reduce.pl bib === id = cord-322566-ye27nqj2 author = Huang, Yuxiang title = Stable Internal Reference Genes for Normalizing Real-Time Quantitative PCR in Baphicacanthus cusia under Hormonal Stimuli and UV Irradiation, and in Different Plant Organs date = 2017-05-03 pages = extension = .txt mime = text/plain words = 5805 sentences = 305 flesch = 49 summary = title: Stable Internal Reference Genes for Normalizing Real-Time Quantitative PCR in Baphicacanthus cusia under Hormonal Stimuli and UV Irradiation, and in Different Plant Organs cusia in this study, and the expression stability was assessed across 60 samples representing different tissues and organs under various conditions, including ultraviolet (UV) irradiation, hormonal stimuli (jasmonic acid methyl ester and abscisic acid), and in different plant organs. However, it is necessary to select suitable reference genes as internal controls under different experimental conditions for accurate RT-qPCR evaluation because of the variability in initial material, RNA integrity, RT-PCR efficiency, and RT-qPCR efficiency (Derveaux et al., 2010) . cusia was evaluated by RNA-Seq (unpublished data) in this study to identify potential reference genes suitable for transcript normalization in experiments under UV irradiation and hormonal stimuli (MeJA and ABA), and also in different plant organs. cache = ./cache/cord-322566-ye27nqj2.txt txt = ./txt/cord-322566-ye27nqj2.txt === reduce.pl bib === id = cord-322657-q4aeood2 author = Jartti, Tuomas title = Respiratory Picornaviruses and Respiratory Syncytial Virus as Causative Agents of Acute Expiratory Wheezing in Children date = 2004-06-17 pages = extension = .txt mime = text/plain words = 3169 sentences = 177 flesch = 45 summary = We studied the viral etiology of acute expiratory wheezing (bronchiolitis, acute asthma) in 293 hospitalized children in a 2-year prospective study in Finland. To prevent and treat acute expiratory wheezing illnesses in children, efforts should be focused on RSV, enterovirus, and rhinovirus infections. The purpose of the study was to investigate the role of 11 respiratory viruses in children hospitalized for acute expiratory wheezing. The supernatants of cell cultures exhibiting a cytopathogenic effect were further studied by antigen detection for adenovirus; influenza A and B viruses; parainfluenza virus types 1, 2, and 3; and RSV or by reverse transcription (RT)-PCR for enterovirus-es and rhinovirus. First, respiratory virus infection was detected in up to 90% of hospitalized children with acute expiratory wheezing. In conclusion, this study showed that acute expiratory wheezing necessitating hospitalization was most often associated with RSV, enterovirus, and rhinovirus infections. cache = ./cache/cord-322657-q4aeood2.txt txt = ./txt/cord-322657-q4aeood2.txt === reduce.pl bib === id = cord-322391-tumpiid5 author = Freymuth, François title = Detection of viral, Chlamydia pneumoniae and Mycoplasma pneumoniae infections in exacerbations of asthma in children date = 1999-08-31 pages = extension = .txt mime = text/plain words = 3813 sentences = 190 flesch = 47 summary = According to the virus, a viral isolation technique, immunofluorescence assays (IFA) or both were used for the detection of rhinovirus, enterovirus, respiratory syncytial (RS) virus, adenovirus, coronavirus 229E, influenza and parainfluenza virus. Results: Using IFA and viral isolation techniques, viruses were detected in 33.3% of cases, and by PCR techniques, nucleic acid sequences of virus, Chlamydia pneumoniae and Mycoplasma pneumoniae were obtained in 71.9% of cases. We also previously reported that molecular techniques were more sensitive than IFA and viral isolation for the detection of RS virus, rhinovirus, adenovirus and parainfluenza virus in nasal specimens collected from infants with bronchiolitis (Freymuth et al., 1997) , and the present study further confirmed that observation. Respiratory viruses, Chlamydia pneumoniae and Mycoplasma pneumoniae alone or associated, were detected in 81.8% of asthmatic exacerbations, with rhinovirus and RS virus being the most frequent isolated agents. cache = ./cache/cord-322391-tumpiid5.txt txt = ./txt/cord-322391-tumpiid5.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-322937-lakdi3x8 author = Kang, Xiao-ping title = A duplex real-time RT-PCR assay for detecting H5N1 avian influenza virus and pandemic H1N1 influenza virus date = 2010-06-02 pages = extension = .txt mime = text/plain words = 2324 sentences = 143 flesch = 61 summary = title: A duplex real-time RT-PCR assay for detecting H5N1 avian influenza virus and pandemic H1N1 influenza virus A duplex real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay was improved for simultaneous detection of highly pathogenic H5N1 avian influenza virus and pandemic H1N1 (2009) influenza virus, which is suitable for early diagnosis of influenza-like patients and for epidemiological surveillance. In this study, a duplex TaqMan real-time RT-PCR assay was improved by adjusting the concentrations of primers and probes in the WHO protocols. The protocol of real-time RT-PCR for influenza A (H1N1) recommended by WHO used a concentration of 1000 nM each of novel SW H1 primers and 250 nM of SW H1 probe [18] . Design of multiplexed detection assays for identification of avian influenza a virus subtypes pathogenic to humans by SmartCycler real-time reverse transcription-PCR A duplex real-time RT-PCR assay for detecting H5N1 avian influenza virus and pandemic H1N1 influenza virus Virology Journal 2010 cache = ./cache/cord-322937-lakdi3x8.txt txt = ./txt/cord-322937-lakdi3x8.txt === reduce.pl bib === id = cord-322987-zv58s79r author = Zali, Alireza title = Correlation between Low-Dose Chest Computed Tomography and RT-PCR Results for the Diagnosis of COVID-19: A Report of 27824 Cases in Tehran, Iran date = 2020-09-21 pages = extension = .txt mime = text/plain words = 3226 sentences = 157 flesch = 48 summary = In addition, our study provides further evidence for considering patients' socioeconomic status as an important risk factor for COVIDKeywords: COVID-19; computed tomography; RT-PCR; polymerase chain reaction; socioeconomic; correlation; diagnosis In this study, we aimed to evaluate the correlation between the number of daily positive chest CT scans and number of daily PCR-confirmed cases and COVID-19-related deaths in Tehran during a three-month period. Figure 2 shows the trend of total patients who underwent chest CT due to high clinical suspicion and also the trend of cases with positive CT scan in each specific hospital during this three-month period. The results of our study, along with the findings of previous reports, provide evidence for policymakers and healthcare leaders to consider low-dose chest CT as a safe, rapid and reliable diagnostic tool to for the detection of COVID-19, particularly in high-prevalent regions with constraint of resources such as insufficient SARS-CoV-2 molecular test kits. cache = ./cache/cord-322987-zv58s79r.txt txt = ./txt/cord-322987-zv58s79r.txt === reduce.pl bib === === reduce.pl bib === id = cord-323029-7hqp8xuq author = Bognár, Zsófia title = Aptamers against Immunoglobulins: Design, Selection and Bioanalytical Applications date = 2020-08-11 pages = extension = .txt mime = text/plain words = 19331 sentences = 873 flesch = 45 summary = For aptamer selection against rIgG [6] and IgE [7] , homogenous processes were used and the separation of bound and unbound nucleic Several different SELEX methods have been used to generate immunoglobulin aptamers including homogeneous, heterogeneous, bead-based SELEX processes, CE-SELEX (capillary electrophoresis-SELEX), µFFE-SELEX (micro-free flow electrophoresis-SELEX) and fully integrated selection processes selection of aptamers with proper binding properties. Molecular Light Switch Complex 100-800 100 [128] Fluorescence enhancement using a DNA aptamer 92-37,000 57 [130] Amplification through allostery-triggered enzymatic recycling amplification NA 5 [131] Fluorescent oligonucleotide probe based on G-quadruplex scaffold for signal-on ultrasensitive protein assay 4.72-7560 0.095 [132] Fluorescence anisotropy 1000-60,000 350 [133] Fluorescence anisotropy assay NA 20 [134] Fluorescence protection assay 100-50,000 100 [136] Aptamer-barcode-based assay based on instantaneous derivatization chemiluminescence coupled to magnetic beads 4.88-20,000 4.6 [137] Competitive fluorescence quenching assay 350-35,000 170 [138] Rapid fluorescence detection of immunoglobulin E using an aptamer switch based on a binding-induced pyrene excimer NA 1600 [139] 6.1. cache = ./cache/cord-323029-7hqp8xuq.txt txt = ./txt/cord-323029-7hqp8xuq.txt === reduce.pl bib === id = cord-323700-5awng7h1 author = Goggin, Rachel K. title = Comparative Viral Sampling in the Sinonasal Passages; Different Viruses at Different Sites date = 2018-09-19 pages = extension = .txt mime = text/plain words = 3528 sentences = 197 flesch = 49 summary = The aim of the study here presented was to establish differences in viral detection and species sampled from different sinonasal sites, in an effort to validate and standardise viral collection techniques, and facilitate further investigation of the sinonasal virome. All DNA extracts first underwent an endogenous retrovirus 3 (ERV3) assay (present as two copies per human diploid cell) in order to confirm respiratory sample collection quality. Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control High rates of detection of respiratory viruses in the nasal washes and mucosae of patients with chronic rhinosinusitis Detection of herpesviruses 1-6 and community-acquired respiratory viruses in patients with chronic rhinosinusitis with nasal polyposis Real-time RT-PCR detection of 12 respiratory viral infections in four triplex reactions Real-time quantitative PCR assays for detection and monitoring of pathogenic human viruses in immunosuppressed pediatric patients cache = ./cache/cord-323700-5awng7h1.txt txt = ./txt/cord-323700-5awng7h1.txt === reduce.pl bib === id = cord-323963-whv88ggl author = Fan, Xiaofeng title = Efficient amplification and cloning of near full-length hepatitis C virus genome from clinical samples date = 2006-08-11 pages = extension = .txt mime = text/plain words = 5713 sentences = 303 flesch = 51 summary = Among RNA templates, hepatitis C virus (HCV) represents an excellent example to challenge the potential of LRP technology due to its extensive secondary structures and its difficulty to be readily cultured in vitro. Thus, our LRP protocol could be applied for the amplification of other difficult RNA templates and may facilitate RNA virus research such as linked viral mutations and reverse genetics. In some experiments, we mixed a RT enzyme with Pfu DNA polymerase (Stratagene), a similar strategy as used in long PCR, to improve full-length cDNA synthesis [8] . A representative neighbor-joining (NJ) tree constructed based on HCV E1 domain of 20 clones derived from 9.1 kb LRP product, which was amplified using mixed serum from samples LIV19 and LIV23. A refined long RT-PCR technique to amplify complete viral RNA genome sequences from clinical samples: Application to a novel hepatitis C virus variant of genotype 6 cache = ./cache/cord-323963-whv88ggl.txt txt = ./txt/cord-323963-whv88ggl.txt === reduce.pl bib === id = cord-324012-q2ilk6gs author = Inui, Ken title = A field‐deployable insulated isothermal RT‐PCR assay for identification of influenza A (H7N9) shows good performance in the laboratory date = 2019-09-05 pages = extension = .txt mime = text/plain words = 1521 sentences = 78 flesch = 55 summary = METHODS: A panel of 59 virus isolates, including H7N9, avian influenza viruses of subtype H1 to H13, swine and human influenza viruses, Newcastle disease virus, and infectious bursal disease virus, were tested by H7 and N9 iiRT‐PCR reagents, using probes and primers specific to H7 or N9, in comparison with laboratory‐based real‐time RT‐PCR assays to determine analytical sensitivity and specificity. Fifty oropharyngeal samples from experimentally infected chicken and ducks with H7N9 and 50 non‐infected control swabs were tested by the H7 iiRT‐PCR to determine diagnostic sensitivity and specificity. The H7 and N9 iiRT-PCR reagents yielded comparable levels of analytical sensitivity and specificity with real-time RT-PCR for the detection of H7N9 virus. Reverse transcription-insulated isothermal PCR (RT-iiRT-PCR) assay for rapid and sensitive detection of foot-and-mouth disease virus A rapid field-deployable reverse transcription-insulated isothermal polymerase chain reaction assay for sensitive and specific detection of bluetongue virus Rapid detection of equine influenza virus H3N8 subtype by insulated isothermal RT-PCR (iiRT-PCR) assay using the POCKIT nucleic acid analyzer cache = ./cache/cord-324012-q2ilk6gs.txt txt = ./txt/cord-324012-q2ilk6gs.txt === reduce.pl bib === id = cord-323987-gh1m05gi author = Dziąbowska, Karolina title = Detection Methods of Human and Animal Influenza Virus—Current Trends date = 2018-10-18 pages = extension = .txt mime = text/plain words = 11112 sentences = 760 flesch = 46 summary = RIDTs with digital readout systems showed many similarities to conventional assays like small sample volume (less than 150 µL) and short analysis time (around 15 min) but exhibited much better sensitivities, even one order of magnitude lower limits of detection (LODs). Among methods mentioned, general diagnostic tests for influenza base on virus culture (conventional and shellvial), detection of viral nucleic acid (PCR) or antigens (by neuraminidase enzymatic activity, fluorescent antibody or enzyme/optical immunoassay) and serologic tests. Main trends for influenza virus detection are: (I) modifications of traditional 'gold star' methods like PCR, RIDTs, ELISA what results in analysis time shortening, costs lowering, LOD and limit of quantification (LOQ) improvement, (II) conjugating of traditional methods and creating new platforms, micro-biochips and others, (III) introducing known solutions to new ones, like smartphone-based analysis control with results data insertion into Google Maps, (IV) reuse of the functions of known devices, like glucometer, smartphone cameras, (V) the most common used detection methods: spectral/optical, electrical, (VI) and entirely new approaches. cache = ./cache/cord-323987-gh1m05gi.txt txt = ./txt/cord-323987-gh1m05gi.txt === reduce.pl bib === === reduce.pl bib === id = cord-324094-23kzr8rq author = Parida, M. M. title = Rapid and real-time detection technologies for emerging viruses of biomedical importance date = 2008-11-01 pages = extension = .txt mime = text/plain words = 5709 sentences = 243 flesch = 46 summary = We have developed two real-time assays ie., SYBR green I based real time reverse transcription polymerase chain reaction (RT-PCR) and RT-loop-mediated isothermal amplification (LAMP) assay for rapid detection as well as typing of some of the emerging viruses of biomedical importance viz. We have developed two real-time assays ie., SYBR green I based real time reverse transcription polymerase chain reaction (RT-PCR) and RT-loop-mediated isothermal amplifi cation (LAMP) assay for rapid detection as well as typing of some of the emerging viruses of biomedical importance viz. A one-step single tube real-time accelerated reverse transcription loop mediated isothermal amplifi cation (RT-LAMP) assays for rapid detection of some of the recently emerged human viral pathogens viz. Rapid detection and differentiation of dengue virus serotypes by a real-time reverse transcription-loop-mediated isothermal amplifi cation assay Development and evaluation of reverse transcription Loop mediated isothermal amplifi cation assay for rapid and Real-time detection of Japanese encephalitis virus cache = ./cache/cord-324094-23kzr8rq.txt txt = ./txt/cord-324094-23kzr8rq.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-324321-y96x8x3h author = Cai, Yingyun title = Down-regulation of transcription of the proapoptotic gene BNip3 in cultured astrocytes by murine coronavirus infection date = 2003-11-10 pages = extension = .txt mime = text/plain words = 8454 sentences = 416 flesch = 49 summary = Furthermore, treatment of cells with chloroquine, which blocks the acidification of endosomes, significantly inhibited the repression of the BNip3 promoter activity induced by the acidic pH-dependent MHV mutant OBLV60, which enters cells via endocytosis, indicating that the down-regulation of BNip3 expression is mediated by fusion between viral envelope and cell membranes during entry. To establish further the specificity of the down-regulation of BNip3 gene expression, we used vesicular stomatitis virus (VSV) in a parallel experiment, because VSV is also an enveloped RNA virus whose infection has a broad host cell range and is mediated by the interaction between the envelope G protein and cell membranes (Riedel et al., 1984) . By extrapolating the data from the mutant virus, we can envision that fusion between viral envelope and plasma/endosomal membranes during wild-type MHV infection is involved in the down-regulation of BNip3 gene expression. cache = ./cache/cord-324321-y96x8x3h.txt txt = ./txt/cord-324321-y96x8x3h.txt === reduce.pl bib === id = cord-324531-lpoelp91 author = Artesi, Maria title = A Recurrent Mutation at Position 26340 of SARS-CoV-2 Is Associated with Failure of the E Gene Quantitative Reverse Transcription-PCR Utilized in a Commercial Dual-Target Diagnostic Assay date = 2020-09-22 pages = extension = .txt mime = text/plain words = 2882 sentences = 185 flesch = 61 summary = title: A Recurrent Mutation at Position 26340 of SARS-CoV-2 Is Associated with Failure of the E Gene Quantitative Reverse Transcription-PCR Utilized in a Commercial Dual-Target Diagnostic Assay At the current time, a number of quantitative real-time PCR (qRT-PCR) assays have been developed to identify SARS-CoV-2, targeting multiple positions in the viral genome. Here, we report the identification of a C-to-U transition at position 26340 of the SARS-CoV-2 genome that is associated with failure of the cobas SARS-CoV-2 E gene qRT-PCR in eight patients. The cobas system (Roche) implements a dual-target assay to detect SARS-CoV-2, with qRT-PCRs targeting both the ORF1ab region and the E gene (see Fig. S1 in the supplemental material). We speculated that these samples carried a common variant that interfered with the E gene qRT-PCR and carried out whole-genome sequencing of the viruses using the Artic Network protocol (17) . cache = ./cache/cord-324531-lpoelp91.txt txt = ./txt/cord-324531-lpoelp91.txt === reduce.pl bib === id = cord-325068-j1lfq60o author = Pene, Frédéric title = Coronavirus 229E-Related Pneumonia in Immunocompromised Patients date = 2003-10-01 pages = extension = .txt mime = text/plain words = 2583 sentences = 134 flesch = 35 summary = The results of inoculation tests performed with HUH7 cells were also positive, revealing corona-like particles that were subsequently identified as coronavirus 229E by RT-PCR performed on both culture supernatant and BAL fluid specimens. However, respiratory symptoms only appeared after completion of antiviral treatment and improvement of skin eruptions, and both viral culture and PCR for VZV performed on BAL fluid specimens were negative. The prevalence of coronavirus pulmonary infections among immunocompromised patients is unknown, and it is probably largely underestimated in the absence of the routine performance of sensitive cell culture, RT-PCR, or electron microscopy on BAL fluid specimens. Thus, only 1 case of coronavirus-associated pneumonia was previously described in an immunocompromised patient following autologous bone marrow transplantation, with the diagnosis based on the presence of viral particles in BAL fluid specimens [22] . cache = ./cache/cord-325068-j1lfq60o.txt txt = ./txt/cord-325068-j1lfq60o.txt === reduce.pl bib === id = cord-324944-ixh3ykrc author = Mitsakakis, Konstantinos title = Diagnostic tools for tackling febrile illness and enhancing patient management date = 2018-12-05 pages = extension = .txt mime = text/plain words = 20805 sentences = 961 flesch = 45 summary = This review gives an overview of diagnostic technologies featuring a platform based approach: (i) assay (nucleic acid amplification technologies are examined); (ii) cartridge (microfluidic technologies are presented); (iii) instrument (various detection technologies are discussed); and at the end proposes a way that such technologies can be interfaced with electronic clinical decision-making algorithms towards a broad and complete diagnostic ecosystem. In studies that have recorded the clinical presentation of patients (and not only their laboratory results), the causes of fever in outpatients could be classified into four main syndromes: 1) acute respiratory infections (ARI, of any type); 2) diarrhea (gastroenteritis); 3) fever with another clear focus (e.g. meningitis or skin infection); and 4) non-specific fevers [13] (each diagnostic platform described in Section 5 focuses on at least one of the aforementioned cases). cache = ./cache/cord-324944-ixh3ykrc.txt txt = ./txt/cord-324944-ixh3ykrc.txt === reduce.pl bib === id = cord-325014-n7mnhk2v author = Gujski, Mariusz title = Prevalence of Current and Past SARS-CoV-2 Infections among Police Employees in Poland, June–July 2020 date = 2020-10-11 pages = extension = .txt mime = text/plain words = 4892 sentences = 254 flesch = 49 summary = As the time window for a positive RT-PCR result is short, serological testing, which provides information about whether a person has been exposed to SARS-CoV-2, may be useful for epidemiological purposes to detect the overall burden of previous infection in a given community. The aim of this study was to determine the prevalence of current and past SARS-CoV-2 infections among police employees, a high-risk population due to their professional duties, during the COVID-19 epidemic. Neither sex (p =0.155) nor other variables listed in Figure 2 were significantly associated with the IgG results ( Figure 2 A logistic regression model predicting a positive anti-SARS-CoV-2 IgM+IgA index was developed (Cox and Snell R Square at 0.015 andNagelkerke R Square at 0.033). After including all variables listed in Figures 1 and 2 along with the number of registered cases and deaths due to COVID-19 (per 10,000 inhabitants), only 4 variables showed a correlation with a positive anti-SARS-CoV-2 IgM+IgA index. cache = ./cache/cord-325014-n7mnhk2v.txt txt = ./txt/cord-325014-n7mnhk2v.txt === reduce.pl bib === id = cord-325124-0hxan9rw author = Li, Chenyu title = Highly sensitive and full-genome interrogation of SARS-CoV-2 using multiplexed PCR enrichment followed by next-generation sequencing date = 2020-05-18 pages = extension = .txt mime = text/plain words = 6119 sentences = 364 flesch = 53 summary = However, it has been reported that only 47-59% of the positive cases were identified by some RT-PCR methods, probably due to low viral load, timing of sampling, degradation of virus RNA in the sampling process, or possible mutations spanning the primer binding sites. With the goal of improving sensitivity and accommodating various application settings, we developed a multiplex-PCR-based method comprised of 343 pairs of specific primers, and demonstrated its efficiency to detect SARS-CoV-2 at low copy numbers. We further amplified the entire SARS-CoV-2 genome from 8 to half a million viral copies purified from 13 COVID-19 positive specimens, and detected mutations through next generation sequencing. Finally, we developed a multiplex-PCR-based metagenomic method in parallel, that required modest sequencing depth for uncovering SARS-CoV-2 mutational diversity and potentially novel or emerging isolates. To overcome this constraint, we developed a multiplex-PCR-based metagenomic method that achieved >96% coverage of the S and N genes of SARS-CoV-2 in the contest of human gDNA, while only required ~0.6M of total reads per library. cache = ./cache/cord-325124-0hxan9rw.txt txt = ./txt/cord-325124-0hxan9rw.txt === reduce.pl bib === id = cord-325137-6c6er06a author = Moser, Lindsey A. title = A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses date = 2016-06-07 pages = extension = .txt mime = text/plain words = 9945 sentences = 514 flesch = 53 summary = Our data demonstrate that this approach provides full-length genomic sequence information not only from high-titer virion preparations but it can also recover specific viral sequence from samples with limited starting material in the background of cellular RNA, and it can be used to identify pathogens from unknown samples. NGS data from this SOP can provide complete genome coverage from viral stocks and can also detect virus-specific reads from limited starting material. Thus, in some instances, large cDNAs, double-stranded DNAs (dsDNAs), or clones containing at least two-thirds of the genome may also be regulated as SAs. Positive-sense RNA viruses span multiple virus families, and the infectious nature of these genomic RNAs coupled with SA/biosafety/biosecurity concerns inhibit rapid removal from BSL-3/4 containment (7) or transport and handling of RNA samples that are known to contain viral genomes from outbreak settings. cache = ./cache/cord-325137-6c6er06a.txt txt = ./txt/cord-325137-6c6er06a.txt === reduce.pl bib === id = cord-325736-gs9d8y55 author = Marin, J title = Persistence of Viruses in Upper Respiratory Tract of Children with Asthma date = 2000-07-31 pages = extension = .txt mime = text/plain words = 1874 sentences = 135 flesch = 61 summary = title: Persistence of Viruses in Upper Respiratory Tract of Children with Asthma Conclusions: The persistent presence of viruses in the upper respiratory tract of asthmatic children shows a possible connection between viral infections and asthma. 4 In this study nasopharyngeal swabs were taken from asthmatic children whose asthma was well controlled, and when they were at least 3 weeks free of any respiratory infections. The samples were examined for the presence of adenovirus DNA and rhinovirus and coronavirus RNA. Five microlitres of c-DNA product were subsequently amplified in 50µl PCR reaction mixture consisting of 10 reaction buffer, 25 mM MgCl 2 , 20 mM dNTP, 5 U/l of DNA Taq polymerase (all reagents provided by Perkin Elmer, New Jersey, USA) and 50 µM of each specific primer for rhinoviruses and coronaviruses (TIB MOLBIOL, Berlin, Germany) (Table I) . found that upper respiratory tract viruses were associated with over 80% of asthma exacerbations in children. cache = ./cache/cord-325736-gs9d8y55.txt txt = ./txt/cord-325736-gs9d8y55.txt === reduce.pl bib === id = cord-325113-sou8xyld author = Kuiper, Johannes W. P. title = Detection of SARS-CoV-2 from raw patient samples by coupled high temperature reverse transcription and amplification date = 2020-11-02 pages = extension = .txt mime = text/plain words = 4973 sentences = 241 flesch = 51 summary = The use of unprocessed swap samples is enabled by employing a heat-stable RNAand DNA-dependent DNA polymerase, which performs the double task of stringent reverse transcription of RNA at elevated temperatures as well as PCR amplification of a SARS-CoV-2 specific target gene. A RNA-and DNA-reading heat-stable polymerase reverse transcribes and amplifies viral RNA Evidence of an acute SARS-CoV-2 infection depends on the detection of viral RNA species in patient samples, which necessitates reverse transcription of RNA followed by PCR amplification of the resulting DNA. To evaluate the potential of the high-temperature RT-PCR protocol using Volvano3G for the detection of viral RNAs in patient material, we assessed the presence of SARS-CoV-2 in RNA isolated from a small cohort of COVID-19 suspected cases. Interestingly, for most positive samples detected by the high-temperature RT-PCR with Volcano3G, the cq-values were lower compared to the standard RT-PCR (Fig 3C and 3D) , indicating that the detection of SARS-CoV-2 from unprocessed patient material is not limited by the sensitivity of this direct approach. cache = ./cache/cord-325113-sou8xyld.txt txt = ./txt/cord-325113-sou8xyld.txt === reduce.pl bib === id = cord-325101-9qslo6qh author = Gizzi, Aline Baumann da Rocha title = Presence of infectious agents and co-infections in diarrheic dogs determined with a real-time polymerase chain reaction-based panel date = 2014-01-16 pages = extension = .txt mime = text/plain words = 5156 sentences = 239 flesch = 50 summary = Although many pathogens have been individually detected with real-time polymerase chain reaction (PCR), a comprehensive panel of agents that cause diarrhea in privately owned dogs has not yet been established. Therefore, the aim of this study was to investigate pathogenic co-infections in populations of diarrheic and control owned dogs using a real-time PCR analysis of a panel of diarrhea-causing agents. The most prevalent agent involved in co-infections was canine parvovirus type 2 (CPV-2), and 21/36 (58.3%) of the diarrheic samples positive for CPV-2 were associated with others agents, most commonly with Clostridium perfringens alpha toxin (CPA), Cryptosporidium spp., and Giardia spp. The detection of individual pathogens in the panel with real-time PCR (Table 3) showed that CPA was the most prevalent pathogen in the fecal samples, infecting 40/104 (38.5%) diarrheic dogs and 6/43 (14.0%) control dogs, and the difference between the groups was highly statistically significant (P = 0.006). cache = ./cache/cord-325101-9qslo6qh.txt txt = ./txt/cord-325101-9qslo6qh.txt === reduce.pl bib === id = cord-326122-5m1727m1 author = Wishaupt, Jérôme O. title = PCR testing for Paediatric Acute Respiratory Tract Infections date = 2014-08-04 pages = extension = .txt mime = text/plain words = 4910 sentences = 259 flesch = 41 summary = The Pediatric Infectious Disease Society (PIDS) and the Infectious Diseases Society of America (IDSA) recommend in their guideline 'Community-Acquired Pneumonia (CAP) in Infants and Children' the use of sensitive and specific tests for the rapid diagnosis of influenza virus and other respiratory viruses in the evaluation of children older than three months of age with CAP [19] . In another recent retrospective study of 177 children with ARI in a general hospital, antibiotic management was not influenced after detecting a viral respiratory pathogen, although the authors state that routine testing of common respiratory pathogens could lead to a better understanding of their role in disease in children with respiratory symptoms [38] . Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children cache = ./cache/cord-326122-5m1727m1.txt txt = ./txt/cord-326122-5m1727m1.txt === reduce.pl bib === id = cord-325969-9zhmmvdg author = To, Kelvin KW title = Additional molecular testing of saliva specimens improves the detection of respiratory viruses date = 2017-06-07 pages = extension = .txt mime = text/plain words = 4543 sentences = 250 flesch = 48 summary = In the first cohort of 159 patients whose nasopharyngeal aspirates (NPAs) tested positive for respiratory viruses during routine testing, the viral load was measured using quantitative reverse transcription PCR. Although NPAs have high viral loads and remain the specimen of choice for most patients with respiratory virus infections, supplementary molecular testing of saliva can improve the clinical management of these patients. The first part of the study consisted of patients whose NPA samples tested positive for respiratory viruses by DFA or the influenza A virus M gene by real-time RT-PCR during routine respiratory virus testing in our clinical microbiology laboratory ( Figure 1 ). In the first part of this study, saliva had a higher viral load than NPA in 17.0% of the patients who tested positive for respiratory viruses by DFA or influenza A virus by RT-PCR in their NPA samples. cache = ./cache/cord-325969-9zhmmvdg.txt txt = ./txt/cord-325969-9zhmmvdg.txt === reduce.pl bib === id = cord-327259-7o7fs4yb author = Correa, I. A. title = Boosting SARS-CoV-2 qRT-PCR detection combining pool sample strategy and mathematical modeling date = 2020-08-19 pages = extension = .txt mime = text/plain words = 4584 sentences = 265 flesch = 56 summary = We aim to evaluate pooling tests in experimental procedures, as well as perform in silico statistical modeling analysis validated with specimen samples obtained from a mass testing program of Industry Federation of the State of Rio de Janeiro (Brazil). This data was validated with the results obtained in our mass testing program: statistical modeling predicted a cost saving of 48.0%, which in practice, was 51.5%, already considering the expenditures with pool sampling that were analyzed individually. To assess the advantages of the pooling approach, we used previous qRT-PCR results obtained in the diagnostic analyses performed with industrial workers of Rio de Janeiro state as a base to calculate the prevalence rates (%) of positive cases and to build the statistical modeling methodology. Our study adopted the statistical modeling approach and validated the data with pooling biological samples for COVID-19 diagnostic, confirming that the pool size must be selected according to the prevalence rate of positive cases in the population (Figure 2) . cache = ./cache/cord-327259-7o7fs4yb.txt txt = ./txt/cord-327259-7o7fs4yb.txt === reduce.pl bib === id = cord-325611-tu1bn4hu author = Pérez-Sautu, Unai title = Target-independent high-throughput sequencing methods provide evidence that already known human viral pathogens play a main role in respiratory infections with unexplained etiology date = 2019-07-23 pages = extension = .txt mime = text/plain words = 5285 sentences = 259 flesch = 41 summary = We systematically collected samples from a prospective cohort of pediatric patients with respiratory infections, that returned negative results by validated molecular RT–PCR assays, and studied them with a target-independent, high-throughput sequencing-based approach. In this report, we performed a systematic study of respiratory specimens collected from a carefully characterized and highly representative, prospective cohort of pediatric cases suffering unexplained ARI, and we compared the rate of detection of pathogens by utilizing validated molecular assays, and a comprehensive sequence-independent, high-throughput sequencing-based analysis. In order to assess for the clinical relevance of the viral identifications made by HTS in the specimens collected from the unexplained cases of respiratory infections, a second cohort of age-matched healthy individuals from the same epidemiologic environment was also studied with the same methodology. Respiratory viral pathogens identified by target-agnostic HTS analysis and confirmed by contig-specific molecular assays in the respiratory specimens from the cases of respiratory infection and from the control group. cache = ./cache/cord-325611-tu1bn4hu.txt txt = ./txt/cord-325611-tu1bn4hu.txt === reduce.pl bib === id = cord-325529-pid58g2r author = Ben-Ami, Roni title = Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection date = 2020-06-23 pages = extension = .txt mime = text/plain words = 2822 sentences = 158 flesch = 50 summary = METHODS: We tested the efficiency and sensitivity of pooling strategies for RNA extraction and RT-PCR detection of SARS-CoV-2. Implementing the 8-sample Dorfman pooling to test 26,576 samples from asymptomatic individuals, we identified 31 (0.12%) SARS-CoV-2 positive samples, achieving a 7.3-fold increase in throughput. Some key constrains are (1) a limit on the number of stages due to the importance of delivering a test result quickly, exemplified by the urgent clinical context of COVID-19 diagnosis; (2) a limit on the ability to dilute samples and still safely identify a single positive sample in a pool; and (3) favorability of simple algorithms which may minimize human error in a laboratory setting. Specifically, we have demonstrated that pooling lysates from 5 or 8 nasopharyngeal swab samples retains sufficient sensitivity of viral RNA detection, allowing identification of SARS-CoV-2-positive individuals, while increasing throughput 5-fold to 7.5-fold. cache = ./cache/cord-325529-pid58g2r.txt txt = ./txt/cord-325529-pid58g2r.txt === reduce.pl bib === id = cord-326130-wm3l1849 author = Van Pelt, Amelia title = Evaluation of COVID-19 Testing Strategies for Repopulating College and University Campuses: A Decision Tree Analysis date = 2020-11-03 pages = extension = .txt mime = text/plain words = 4767 sentences = 246 flesch = 55 summary = To account for individuals presenting with symptoms that mimic COVID-19 disease that would prompt testing or positive diagnosis in the absence of testing, an estimate of .0957 was used based on the prevalence of college students who develop influenza-like illness in November (the earliest month with data available for the first semester) [22] . To the best of our knowledge, this is the first study that used a formal decision tree analysis to evaluate the true positives and negatives and the number of RT-PCR tests needed for a comprehensive range of COVID-19 testing strategies for repopulating a university campus. Based on the analysis of TTP, there is no value of willingness to trade off RT-PCR tests for true positive students detected for which Strategy 3 (universal, single RT-PCR testing) was preferred. In summary, strategies that include RT-PCR testing will identify more COVID-19 cases than symptom-based screening, but all approaches will fail to detect a proportion of infected students. cache = ./cache/cord-326130-wm3l1849.txt txt = ./txt/cord-326130-wm3l1849.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-327069-vjlisnui author = Driscoll, Amanda J. title = Standardization of Laboratory Methods for the PERCH Study date = 2017-06-15 pages = extension = .txt mime = text/plain words = 4725 sentences = 221 flesch = 42 summary = To build capacity at the sites, and in alignment with the priorities of the Bill & Melinda Gates Foundation, all PERCH testing was done locally, with the exception of quality assurance testing and a select subset of specialized assays, which were performed at the study reference laboratory (Canterbury Health Laboratories, Christchurch, New Zealand), which also served as the study specimen and isolate biorepository. Induced sputum, pleural fluid, and lung aspirate specimens were collected in saline in universal containers and either refrigerated at 2°C-8°C for a maximum of 24 hours, or frozen at -80°C prior to nucleic acid extraction. Organism identification was done according to standard microbiological methods that were documented in SOPs and clarified at each site at the outset; antimicrobial susceptibility testing followed the Clinical and Laboratory Standards Institute (CLSI) guidelines [15] . cache = ./cache/cord-327069-vjlisnui.txt txt = ./txt/cord-327069-vjlisnui.txt === reduce.pl bib === id = cord-327105-7dsgs2sd author = Zóka, András title = Distinct changes in the real-time PCR detectability of certain SARS-CoV-2 target sequences date = 2020-05-05 pages = extension = .txt mime = text/plain words = 341 sentences = 24 flesch = 58 summary = title: Distinct changes in the real-time PCR detectability of certain SARS-CoV-2 target sequences [1] highlighted notable aspects of the PCR-based diagnosis of SARS-CoV-2 infection, namely that the PCR-based detectability of certain loci might differ significantly and change over time. In our practice we also observed that the SARS-CoV-2 PCR positivity in the oropharyngeal swabs of patients might persist for weeks [2] , however, the characteristics of positivity (including the target sequences detected) may change in a predictable manner. Our results might indicate that the detectability of the viral Orf1a-related RdRp sequence might fade more rapidly during convalescence, only later followed by the N gene. This phenomenon might affect the interpretation of the results, as detecting a lone N gene might suggest a later presentation within the course of the disease. Dynamic change process of target genes by RT-PCR testing of SARS-Cov-2 during the course of a Coronavirus Disease 2019 patient Profile of RT-PCR for SARS-CoV-2: a preliminary study from 56 COVID-19 patients cache = ./cache/cord-327105-7dsgs2sd.txt txt = ./txt/cord-327105-7dsgs2sd.txt === reduce.pl bib === === reduce.pl bib === id = cord-327675-uo839gvc author = Salamatian, Iman title = In vitro Acquisition and Retention of Low-Pathogenic Avian Influenza H9N2 by Musca domestica (Diptera: Muscidae) date = 2019-10-11 pages = extension = .txt mime = text/plain words = 3648 sentences = 220 flesch = 60 summary = (2011) showed that infective H5N1 virus could be detected at least 72 h PE from house flies while viral RNA was still found by real-time reverse-transcription polymerase chain reaction (RRT-PCR) 96 h PE. The aim of this study was to investigate the acquisition of H9N2 AIV by the house fly under laboratory conditions and to determine virus persistence in external surface and within house fly using quantitative reverse-transcription PCR. The potential of house fly, Musca Domestica (L.) in the mechanical transmission of influenza A subtype H1N1 virus under laboratory conditions Persistence of low-pathogenic avian influenza H5N7 and H7N1 subtypes in house flies (Diptera: Muscidae) Detection and isolation of highly pathogenic H5N1 avian influenza A viruses from blow flies collected in the vicinity of an infected poultry farm in Kyoto Avian influenza virus H5N1 remained exist in gastrointestinal tracts of house flies 24 hours post-infection cache = ./cache/cord-327675-uo839gvc.txt txt = ./txt/cord-327675-uo839gvc.txt === reduce.pl bib === id = cord-327024-1k5jucae author = Zhang, Qingshui title = Isolation and characterization of an astrovirus causing fatal visceral gout in domestic goslings date = 2018-04-19 pages = extension = .txt mime = text/plain words = 4167 sentences = 213 flesch = 47 summary = 18 reported the detection of avian nephritis virus infection in Croatian goose flocks and provided evidence that this AstV was associated with stunting and prehatching mortality of goose embryos. To determine the potential genetic mutation(s) that might occur during the goose embryo passage, the initial virus genome was sequenced using the total RNA extracted from the clinical case tissue homogenate. When the samples were tested by RT-PCR for virus shedding evaluation, the AAstV specific RNA was sequentially detected from the cloacal swabs of infected goslings from 2 to 12 dpi (Fig. 6 ). To evaluate the potential adaptive mutation (s) of the virus that might occur during the process of goose embryo passage, we sequenced the complete genome of initial virus using the total RNA extracted from the clinical case tissue homogenate of kidney, spleen, and liver using the method described above. cache = ./cache/cord-327024-1k5jucae.txt txt = ./txt/cord-327024-1k5jucae.txt === reduce.pl bib === id = cord-327344-8gi1wb76 author = Gambarino, Stefano title = Development of a RT Real-Time PCR for the Detection and Quantification of Human Rhinoviruses date = 2009-03-17 pages = extension = .txt mime = text/plain words = 3506 sentences = 147 flesch = 38 summary = This article describes the development and optimization of a reverse transcription (RT) real-time PCR assay for quantification of HRV RNA in clinical samples. Clinical specimens originated from the Virology Unit of the Fig. 1 Standard curve (from 10 2 to 10 5 copies/reaction) and dynamic range (from 10 7 to 10 1 copies/reaction) of the real-time RT-PCR developed in this study Azienda Ospedaliero-Universitaria San Giovanni Battista, Turin, and included 110 bronchoalveolar lavages (BAL) obtained from 84 patients (M/F, 57/27; mean age, 57.8 years; range, . The performance of the RT real-time PCR developed in this study was examined over different concentrations of HRV RNA and it was found to be very sensitive with a minimum cut-off for detection of 10 0 copy/reaction and was linear up to 10 1 copies. In conclusion, the RT real-time PCR assay developed in this study could represent a useful tool for diagnosing HRV infections, quantifying the viral load and could be applicable for routine diagnostic workup of upper as well as lower respiratory tract diseases. cache = ./cache/cord-327344-8gi1wb76.txt txt = ./txt/cord-327344-8gi1wb76.txt === reduce.pl bib === id = cord-327894-b0bsseui author = Pecellín, Lidia Gestoso title = Recomendaciones y uso de los diferentes tipos de test para detección de infección por SARS-COV-2 date = 2020-10-14 pages = extension = .txt mime = text/plain words = 4897 sentences = 446 flesch = 56 summary = En respuesta a la COVID-19, el gobierno español inicialmente instó a limitar el contacto social como medida general, sin embargo, otros países, además, implementaron pruebas generalizadas para la infección por SARS-COV-2 desde el principio de la pandemia. Son test sencillos de hacer, pero deben ser interpretados con prudencia, en relación con el curso de la infección, sobre todo por la tasa de falsos negativos en la detección de IgM ya que la respuesta de IgM en un enfermo COVID-19 puede tardar en aparecer desde varios días a dos semanas 21 Algunos estudios han mostrado que durante los primeros 7 días desde el inicio de síntomas, menos de un 40% de pacientes presentan anticuerpos IgM detectables. cache = ./cache/cord-327894-b0bsseui.txt txt = ./txt/cord-327894-b0bsseui.txt === reduce.pl bib === id = cord-327682-i3uim0zi author = Santti, Juhana title = Molecular detection and typing of human picornaviruses date = 1999-08-25 pages = extension = .txt mime = text/plain words = 2438 sentences = 131 flesch = 43 summary = It has been shown in a number of studies that virtually all the enterovirus serotypes and most of the HRV isolates can be detected using these primer sequences (Hyypiä et , 1989; Horsnell et al., 1995; Pulli et al., 1995; Arola et al., 1996; Huttunen et al., 1996; Pitkäranta et al., 1997; Hyypiä et al., 1998; Oberste et al., 1998) The authors became convinced of the usefulness of this technique during a recent outbreak of aseptic meningitis in Finland. Partial sequence analysis of virtually all enterovirus serotypes has shown that they belong to these four clusters (Pulli et al., 1995; Huttunen et al., 1996) and that the VP4/VP2 region sequence can be used for molecular typing of clinical isolates (Arola et al., 1996) . In hepatitis A virus infections, the molecular epidemiology has been investigated by many reseach groups and an extensive analysis of partial sequences from different geographic locations has been used to establish a useful database for further studies (Robertson et al., 1992) . cache = ./cache/cord-327682-i3uim0zi.txt txt = ./txt/cord-327682-i3uim0zi.txt === reduce.pl bib === id = cord-328409-px92ff89 author = Hornuss, Daniel title = COVID-19-assoziierte Pneumonie trotz persistierend negativen PCR-Tests aus oropharyngealen Abstrichen date = 2020-05-13 pages = extension = .txt mime = text/plain words = 1575 sentences = 172 flesch = 42 summary = After the first PCR turned in negative another PCR-analysis for SARS-CoV-2 of a deep oral swab-sample was performed since the clinical, laboratory and radiological findings were typical for COVID-19. After the first PCR turned in negative another PCR-analysis for SARS-CoV-2 of a deep oral swab-sample was performed since the clinical, laboratory and radiological findings were typical for COVID-19. After a third attempt for a PCR-analysis of a deep oral swab-sample was negative, analysis of a sputum was performed which finally confirmed the diagnosis of COVID-19 associated pneumonia. After a third attempt for a PCR-analysis of a deep oral swab-sample was negative, analysis of a sputum was performed which finally confirmed the diagnosis of COVID-19 associated pneumonia. Als Diagnostik der Wahl zur schnellen Identifikation von COVID-19-Fällen hat sich dabei die PCR-Analyse auf SARS-CoV-2 aus tiefen nasopharyngealen oder oropharyngealen Abstrichen etabliert [3] . cache = ./cache/cord-328409-px92ff89.txt txt = ./txt/cord-328409-px92ff89.txt === reduce.pl bib === id = cord-328206-iylw1bvw author = Yu, Daojun title = Simultaneous Detection and Differentiation of Human Papillomavirus Genotypes 6, 11, 16 and 18 by AllGlo Quadruplex Quantitative PCR date = 2012-11-09 pages = extension = .txt mime = text/plain words = 4070 sentences = 209 flesch = 48 summary = In this study, applying novel AllGlo fluorescent probes, we established a quadruplex quantitative PCR method to simultaneously detect and differentiate HPV 6, 11, 16 and 18 in a single tube. So AllGlo quadruplex quantitative PCR has the advantages of relatively high throughput, good reproducibility, high sensitivity, high specificity, it is easy for designing the probes and primers of multiplex qPCR and can increase the detection throughput. Two aliquots were used for the detection of HPV6-11 and HPV16-18 mixed types by TaqMan uniplex probe fluorescence quantitative PCR (Guangzhou Da'an Diagnostic Co., Ltd., China). Single-tube AllGlo probe quadruplex fluorescence qPCR could simultaneously type HPV 6, 11, 16, and 18 and quantitatively detect the viral load of each HPV at the same time. Single-tube AllGlo probe quadruplex fluorescence qPCR could simultaneously type HPV 6, 11, 16, and 18 and quantitatively detect the viral load of each HPV at the same time. cache = ./cache/cord-328206-iylw1bvw.txt txt = ./txt/cord-328206-iylw1bvw.txt === reduce.pl bib === id = cord-328373-cubp1cc1 author = Jiang, Yanfang title = Digital PCR is a sensitive new technique for SARS-CoV-2 detection in clinical applications date = 2020-11-04 pages = extension = .txt mime = text/plain words = 3564 sentences = 217 flesch = 50 summary = In the current study the use of a novel digital PCR assay to detect SARS-CoV-2 in both clinical patient-derived samples and environmentally derived samples was investigated, with the ultimate aim of reducing the rate of false negative results. Thirty-two patient samples including nasopharyngeal swabs, throat swabs, oropharyngeal swabs, phlegm, plasma/blood, and eye conjunctiva were collected at multiple timepoints during the disease course, and tested for the presence of SARS-CoV-2 via RT-PCR. SARS-CoV-2 nucleic acid sequences were detected in all clinical patient samples (respiratory tract samples including nasopharyngeal and oropharyngeal swabs). To prevent false-negative SARS-CoV-2 nucleic acid-based test results, and develop a new sensitive detection assay, we evaluated the performance of real-time RT-PCR and digital PCR for detecting SARS-CoV-2 nucleic acid in clinical patient-derived samples and environmentally derived samples. Strikingly, digital PCR detected SARS-CoV-2 nucleic acids in several samples that had previously tested negative via real-time RT-PCR, including 3 patient-derived samples and 5 environmentally derived samples. cache = ./cache/cord-328373-cubp1cc1.txt txt = ./txt/cord-328373-cubp1cc1.txt === reduce.pl bib === id = cord-328526-es8t6t0j author = Hoppes, Sharman title = The Isolation, Pathogenesis, Diagnosis, Transmission, and Control of Avian Bornavirus and Proventricular Dilatation Disease date = 2010-08-02 pages = extension = .txt mime = text/plain words = 5502 sentences = 326 flesch = 54 summary = Since its discovery, avian bornavirus (ABV) has been successfully cultured from the brains of psittacines diagnosed with PDD, providing a source of antigen for serologic assays and nucleic acid for molecular assays. Subsequently the authors have isolated ABV by culture in duck embryo fibroblasts using material from the brains of 5 additional birds with necropsy-confirmed PDD (Fig. 2) . Lierz and colleagues 34 have also shown that apparently healthy birds within an aviary where clinical cases were occurring were also shedding ABV as detected by fecal swabs. Diagnostic tests such as Western blots or fecal PCR can identify many, but not all ABV-infected birds, and should be employed to control the spread of this disease. Advances in understanding of proventricular dilation disease (PDD): detection of virus and viral nucleic acid in infected birds Unususal and severe lesions of proventricular dilatation disease in Cockatiels (Nymphicus hollandicus) as healthy carriers of avian bornavirus and subsequently infected with a virulent strain of the same ABV genotype. cache = ./cache/cord-328526-es8t6t0j.txt txt = ./txt/cord-328526-es8t6t0j.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-329052-jan20ljs author = Gombar, Saurabh title = Persistent detection of SARS-CoV-2 RNA in patients and healthcare workers with COVID-19 date = 2020-05-30 pages = extension = .txt mime = text/plain words = 864 sentences = 59 flesch = 59 summary = BACKGROUND: Current guidelines for returning health care workers (HCW) to service after a positive SARS-CoV-2 RT-PCR test and ceasing of transmission precautions for patients is based on two general strategies. Alternatively, due to the limited availability of testing, many sites employ a symptom-based strategy that recommends excluding HCW from the workforce and keeping patients on contact precautions until a fixed period of time has elapsed from symptom recovery. The underlying assumption of the symptom-based strategy is that waiting for a fixed period of time is a surrogate for negative RT-PCR testing, which itself is a surrogate for the absence of shedding infectious virus. STUDY DESIGN: We performed an observational analysis of 150 patients and HCW that transitioned from RT-PCR SARS-CoV-2 positive to negative over the course of 2 months at a US academic medical center. We performed an observational analysis of 150 patients and HCW that transitioned from RT-PCR SARS-CoV-2 positive to negative over the course of 2 months at a US academic medical center. cache = ./cache/cord-329052-jan20ljs.txt txt = ./txt/cord-329052-jan20ljs.txt === reduce.pl bib === === reduce.pl bib === id = cord-329395-4k8js9v2 author = Ratcliff, Jeremy title = Evaluation of Different PCR Assay Formats for Sensitive and Specific Detection of SARS-CoV-2 RNA date = 2020-07-01 pages = extension = .txt mime = text/plain words = 1662 sentences = 124 flesch = 55 summary = Polymerase chain reaction (PCR)-based assays are the gold standard for detecting viral RNA in patient samples and are used extensively in clinical settings. To enable the application of PCR in resource-poor or non-specialist laboratories, we have developed and evaluated a nested PCR method for SARS-CoV-2 RNA using simple agarose gel electrophoresis for product detection. Using clinical samples tested by conventional qPCR methods and RNA transcripts of defined RNA copy number, the nested PCR based on the RdRP gene demonstrated high sensitivity and specificity for SARS-CoV-2 RNA detection in clinical samples, but showed variable and transcript length-dependent sensitivity for RNA transcripts. The sensitivity of the nested PCR and two RT-qPCR methods was compared by measuring the 118 50% endpoints (50EP) of detection for serial dilutions of the four transcripts described above 119 (Table 1, Figure 2 ). Protocol: Real-time RT-PCR assays for the detection of SARS-CoV-2 cache = ./cache/cord-329395-4k8js9v2.txt txt = ./txt/cord-329395-4k8js9v2.txt === reduce.pl bib === id = cord-328795-rs1sd42z author = Falsey, Ann R. title = Rhinoviruses date = 2016-10-24 pages = extension = .txt mime = text/plain words = 4511 sentences = 222 flesch = 45 summary = The incidence of HRV infection in children during the first 2 years of life was noted to be 0.7-2 infections per year in older studies using cell culture for viral detection (Brownlee and Turner, 2008) . Although symptoms associated with 'the common cold' syndrome are often attributed to HRV disease, the clinical findings of rhinovirus infections are indistinguishable from those of other viral pathogens. Currently, there are no antiviral drugs approved for clinical use in HRV infections although a few agents have been advanced to clinical trials and shown modest results in decreasing either symptom severity or viral activity. Conversely, monoclonal antibody blockade of the ICAM-1 receptor, the site of cellular attachment for the majority of HRV-A and HRV-B serotypes, has also been studied and demonstrated a reduction in the severity of symptoms and viral shedding but failed to prevent infection in the rhinovirus challenge model (Greenberg, 2003) . cache = ./cache/cord-328795-rs1sd42z.txt txt = ./txt/cord-328795-rs1sd42z.txt === reduce.pl bib === id = cord-328961-waxtb759 author = Pratelli, Annamaria title = PCR assay for the detection and the identification of atypical canine coronavirus in dogs date = 2002-10-01 pages = extension = .txt mime = text/plain words = 1889 sentences = 95 flesch = 57 summary = Comparative sequence analysis of the PCR products of the M gene and fragments of the pol1a and pol1b genes of canine coronavirus (CCoV) have demonstrated that two separate clusters of CCoV are present in dogs. The sequence analysis of the PCR products of the M and S genes carried out on the faecal samples from the two pups confirmed that the FCoV-like CCoV had caused the disease (personal observations). On the basis of these preliminary results, a PCR assay was developed to detect and identify the FCoV-like CCoV strains from faecal samples of infected dogs. In a previous study, similar nucleotide substitutions in the binding site of the internal primer CCoV3 used for the n-PCR were demonstrated in the sequence analysis of the PCR products from five faecal samples of pups with diarrhoea. cache = ./cache/cord-328961-waxtb759.txt txt = ./txt/cord-328961-waxtb759.txt === reduce.pl bib === id = cord-329517-3yn80r9h author = Yang, Jin-Long title = Development of a fluorescent quantitative real-time polymerase chain reaction assay for the detection of Goose parvovirus in vivo date = 2009-09-15 pages = extension = .txt mime = text/plain words = 3564 sentences = 192 flesch = 55 summary = title: Development of a fluorescent quantitative real-time polymerase chain reaction assay for the detection of Goose parvovirus in vivo The objective of this study was to develop a fluorescent quantitative real-time polymerase chain reaction (PCR) (FQ-PCR) assay for fast and accurate quantification of GPV DNA in infected goslings, which can aid in the understanding of the regular distribution pattern and the nosogenesis of GPV in vivo. Ten-fold dilutions of the pVP3 plasmid DNA were tested by the established FQ-PCR assay to evaluate the sensitivity of the system, and the detection limit was found to be 2.8 × 10 1 copies/reaction. Viral load quantification using the established FQ-PCR demonstrated that the GPV DNA copy number of each sample could be calculated using the cycle threshold (Ct) value determined from the standard curve. In conclusion, the established real-time PCR assay was rapid, sensitive, and specific for the detection and quantification of GPV DNA. cache = ./cache/cord-329517-3yn80r9h.txt txt = ./txt/cord-329517-3yn80r9h.txt === reduce.pl bib === id = cord-329162-6w8qcv1c author = Ayginin, Andrey A. title = The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels date = 2018-08-12 pages = extension = .txt mime = text/plain words = 4838 sentences = 222 flesch = 49 summary = The existing approaches for the design of oligonucleotides for targeted enrichment are usually involved in the development of primers for the PCR-based detection of particular viral species or genera, but not for families or higher taxonomic orders. We have subsequently designed a genus-specific oligonucleotide panel for targeted enrichment of viral nucleic acids in biological material and demonstrated the possibility of its application for virus detection in bird samples. We have applied this approach to design genus-specific primer pairs for targeted enrichment of cDNA from zoonotic RNA viruses and have evaluated it using several samples from birds. The control samples cDNA was obtained by reverse transcription reaction performed on 5 L of the extracted RNA using the Reverta-L RT kit (AmpliSens; total volume of the reaction mixture is 20 L); after that 5 L of the reaction mixture containing cDNAs was further used for evaluation of the ability of the primer pair to amplify the targeted region of viruses, both in single and in multiplex PCR format. cache = ./cache/cord-329162-6w8qcv1c.txt txt = ./txt/cord-329162-6w8qcv1c.txt === reduce.pl bib === id = cord-329643-hhk900c1 author = Skalina, K. A. title = Extended Storage of SARS-CoV2 Nasopharyngeal Swabs Does Not Negatively Impact Results of Molecular-Based Testing date = 2020-05-20 pages = extension = .txt mime = text/plain words = 1869 sentences = 114 flesch = 49 summary = Here we demonstrate the long-term stability of nasopharyngeal swab specimens for SARS-CoV-2 molecular testing across three assays recently approved by the U.S. FDA under Emergency Use Authorization. This study demonstrates that nasopharyngeal swab specimens can be stored under refrigeration or even ambient conditions for 21 days without clinically impacting the results of the real-time RT-PCR testing. determined that short delays (up to 4 days) in processing influenza nasal and throat swabs did not significantly affect the ability to detect viral particles by real-time RT-PCR.(5) More recently the stability of SARS-CoV-2 detection in different types of storage media over a 14-day period was evaluated. This study utilized three different automated real-time reverse-transcriptase polymerase chain reaction (RT-PCR) in vitro diagnostic platforms (Luminex ARIES, Panther Fusion, and Abbott m2000) currently in use for clinical testing of SARS-CoV-2 at the Department of Pathology, Division of Virology, Montefiore Medical Center, Bronx, NY. cache = ./cache/cord-329643-hhk900c1.txt txt = ./txt/cord-329643-hhk900c1.txt === reduce.pl bib === id = cord-329564-tmi1u224 author = Arashiro, Takeshi title = COVID-19 in 2 Persons with Mild Upper Respiratory Tract Symptoms on a Cruise Ship, Japan date = 2020-06-17 pages = extension = .txt mime = text/plain words = 1991 sentences = 128 flesch = 56 summary = title: COVID-19 in 2 Persons with Mild Upper Respiratory Tract Symptoms on a Cruise Ship, Japan We created an illustration showing the floors where the eventual COVID-19 case-patients worked or shopped, along with dates of symptom onset, potential incubation periods, symptom durations, confirmed times of positive diagnosis, and times of discharge ( Figure 1, panel A) . By February 28, a total of 705 COVID-19 cases were confirmed among 4,061 passengers and crew tested; 392 cases were asymptomatic, 36 persons were admitted to intensive care units, and 6 patients died (2) . Because of the lower threshold for testing persons on board, the cruise ship created an opportunity to observe mild COVID-19 cases and monitor patient symptoms. We describe 2 cases of coronavirus disease in patients with mild upper respiratory symptoms. We describe 2 cases of coronavirus disease in patients with mild upper respiratory symptoms. Clinical courses of 2 case-patients with coronavirus disease (COVID-19) admitted from a cruise ship docked in Japan, 2020. cache = ./cache/cord-329564-tmi1u224.txt txt = ./txt/cord-329564-tmi1u224.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-330602-g0xaonxv author = Sugiura, Hiroaki title = Prescription Surveillance and Polymerase Chain Reaction Testing to Identify Pathogens during Outbreaks of Infection date = 2013-02-07 pages = extension = .txt mime = text/plain words = 3231 sentences = 150 flesch = 34 summary = Japanese traditional surveillance is based on definitive diagnosis and is enforced by the infection control laws in Japan for the early detection of agents of bioterrorism and outbreaks of emerging infectious diseases. The purpose of the present study was to evaluate whether the PCR method triggered by the results of the prescription surveillance system can rapidly and accurately identify causative pathogens of local outbreaks of infection. Between October 4 and 28, 2011, 50 patients were included in the present study who either presented at a single clinic with a chief complaint of respiratory symptoms or fever or were suspected of having respiratory tract infections after being identified through the syndromic prescription surveillance system. Here, we examined a combination of syndromic surveillance and PCR testing and showed the potential to identify pathogens during the early stage of an outbreak of respiratory infections. cache = ./cache/cord-330602-g0xaonxv.txt txt = ./txt/cord-330602-g0xaonxv.txt === reduce.pl bib === id = cord-331455-dfnn9mrf author = Shah, Aditya S. title = The utility of chest computed tomography (CT) and RT-PCR screening of asymptomatic patients for SARS-CoV-2 prior to semiurgent or urgent hospital procedures date = 2020-07-16 pages = extension = .txt mime = text/plain words = 2376 sentences = 130 flesch = 48 summary = title: The utility of chest computed tomography (CT) and RT-PCR screening of asymptomatic patients for SARS-CoV-2 prior to semiurgent or urgent hospital procedures Here, we describe our experience and the results of implementing this safety project of screening and testing patients for SARS-CoV-2 (COVID-19) prior to semiurgent or urgent hospital procedures using both CT chest imaging and RT-PCR testing. If the phone-screening questionnaire was entirely negative, the patient would undergo a SARS-CoV-2 nasopharyngeal swab PCR 48 hours prior to the elective hospital procedure as well as CT imaging of the chest the day before the procedure. 17 Among asymptomatic patients on the Diamond Princess cruise ship who tested positive for SARS-CoV-2 by RT-PCR, CTs scan were negative for pulmonary opacities in 46% of cases, 18 although the prevalence of disease was relatively high in this cohort (~26%). cache = ./cache/cord-331455-dfnn9mrf.txt txt = ./txt/cord-331455-dfnn9mrf.txt === reduce.pl bib === id = cord-331413-fejho1of author = Nakayama, Eiichi title = Rapid optimization of antimicrobial chemotherapy given to pediatric patients with community-acquired pneumonia using PCR techniques with serology and standard culture date = 2007-12-31 pages = extension = .txt mime = text/plain words = 3955 sentences = 198 flesch = 44 summary = title: Rapid optimization of antimicrobial chemotherapy given to pediatric patients with community-acquired pneumonia using PCR techniques with serology and standard culture Abstract Children (n =117; mean age 2.4 ± 2.9 years) were diagnosed as having community-acquired pneumonia (CAP) using clinical symptoms, chest X-rays, and hematological data. The causative pathogen was determined using real-time polymerase chain reaction (PCR) (6 bacteria), multiple reverse transcription-PCR (MPCR; 11 viruses), bacterial culture, and serology. [7] [8] [9] In Japan, antimicrobial chemotherapy for patients with CAP is begun empirically based on (1) chest X-rays, (2) clinical fi ndings including respiratory status, (3) age, and (4) laboratory tests such as white blood cell count (WBC) and C-reactive protein concentration (CRP). The bacteria suspected to be the causative pathogens was determined by standard culture and real-time PCR for six pathogens: Streptococcus pneumoniae, Haemophilus infl uenzae, Mycoplasma pneumoniae, Chlamydophila pneumoniae, Streptococcus pyogenes, and Legionella pneumophila (Table 3) In the patients suspected of having an infection caused by S. cache = ./cache/cord-331413-fejho1of.txt txt = ./txt/cord-331413-fejho1of.txt === reduce.pl bib === id = cord-331475-mmcu18c8 author = Sahu, Amit Ranjan title = Selection and validation of suitable reference genes for qPCR gene expression analysis in goats and sheep under Peste des petits ruminants virus (PPRV), lineage IV infection date = 2018-10-29 pages = extension = .txt mime = text/plain words = 4735 sentences = 257 flesch = 49 summary = title: Selection and validation of suitable reference genes for qPCR gene expression analysis in goats and sheep under Peste des petits ruminants virus (PPRV), lineage IV infection In this study, we evaluated the expression stability of ten most commonly used reference genes (GAPDH, ACTB, HSP90, HMBS, 18S rRNA, B2M, POLR2A, HPRT1, ACAC, YWHAZ) in fourteen different Peste des petits ruminants virus (PPRV) infected tissues of goats and sheep. GAPDH (Glyceraldehyde-3-phosphate dehydrogenase), 18S rRNA (18S ribosomal RNA), B2M (β 2 microglobulin), HSP 90 (heat shock protein 90), ACAC-alpha (Acetyl coenzyme carboxylase alpha), HMBS (Hydroxymethylbilane synthase), YWHAZ (Tyrosine 3-monooxygenase activation protein zeta polypeptide), POLR2A (Polymerase 32 II (DNA directed) polypeptide A), ACTB (beta actin) and HPRT1 (Hypoxanthin Phosphoribosyl transferase 1) in fourteen different tissues obtained from healthy and PPRV infected goats and sheep to identify the best possible reference gene(s) for qRT-PCR normalization. cache = ./cache/cord-331475-mmcu18c8.txt txt = ./txt/cord-331475-mmcu18c8.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-331496-5xak7z6b author = Garnett, Emily title = Clinical Validation and Performance Evaluation of the Automated Vitros Total Anti–SARS-CoV-2 Antibodies Assay for Screening of Serostatus in COVID-19 date = 2020-08-31 pages = extension = .txt mime = text/plain words = 3450 sentences = 187 flesch = 43 summary = We anticipate it will be a useful tool in screening for exposure to SARS-CoV-2; however, the use of the CoV2T and other serologic assays in the clinical management of patients with COVID-19 is unknown and must be evaluated in future studies. In this study, we describe validation of one of the first assays to receive EUA on an automated platform, the Vitros Anti-SARS-CoV-2 Total (CoV2T; Ortho Clinical Diagnostics) antibody assay, for screening of previous exposure to SARS-CoV-2 in our patient population. Seroconversion in our patient population was assessed by correlation of chart review of 55 patients known to be positive for SARS-CoV-2 by RT-PCR and known date of symptom onset with sample reactivity by the CoV2T assay. Specimens from 14 patients with acute infections, previously tested to be negative for SARS-CoV-2 by RT-PCR but positive for another respiratory viral infection by molecular analysis, were nonreactive by the CoV2T assay. cache = ./cache/cord-331496-5xak7z6b.txt txt = ./txt/cord-331496-5xak7z6b.txt === reduce.pl bib === id = cord-331558-6rqd3fmj author = Sun, Chuan-bin title = Role of the Eye in Transmitting Human Coronavirus: What We Know and What We Do Not Know date = 2020-04-24 pages = extension = .txt mime = text/plain words = 5459 sentences = 234 flesch = 48 summary = Although the conjunctiva is directly exposed to extraocular pathogens, and the mucosa of the ocular surface and upper respiratory tract are connected by the nasolacrimal duct and share the same entry receptors for some respiratory viruses, the eye is rarely involved in human CoV infection, conjunctivitis is quite rare in patients with 2019-nCoV infection, and the CoV RNA positive rate by RT-PCR test in tears and conjunctival secretions from patients with 2019-nCoV and SARS-CoV infection is also extremely low. Considering that close doctor-patient contact is quite common in ophthalmic practice and is apt to transmit human CoVs via droplets and fomites, strict hand hygiene and proper personal protection are highly recommended for health care workers to avoid hospital-related viral transmission during ophthalmic practice. Considering that close doctor-patient contact is quite common in ophthalmic practice and is apt to transmit human CoVs via droplets and fomites, strict hand hygiene and proper personal protection are highly recommended for health care workers to avoid hospital-related viral transmission during ophthalmic practice. cache = ./cache/cord-331558-6rqd3fmj.txt txt = ./txt/cord-331558-6rqd3fmj.txt === reduce.pl bib === id = cord-332042-bqtflk7r author = LeBlanc, J. J. title = Validation of the Seegene RV15 multiplex PCR for the detection of influenza A subtypes and influenza B lineages during national influenza surveillance in hospitalized adults date = 2019-07-02 pages = extension = .txt mime = text/plain words = 4562 sentences = 227 flesch = 44 summary = Influenza A and B viruses are identified and characterized using real-time reverse-transcriptase polymerase chain reaction (RT-PCR), and multiplex testing has been performed on a subset of patients to identify other respiratory virus aetiologies. The CIRN SOS Network comprises 15 to 45 acute care (depending on the year) hospitals across Canada, and influenza testing is performed using real-time reverse-transcriptase polymerase chain reaction (RT-PCR) methods derived from the World Health Organization (WHO) [12] [13] [14] . While WHO-based real-time RT-PCRs methods are often viewed as the reference standard for influenza virus detection, diagnostic laboratories and surveillance studies often test for other viral aetiologies of respiratory illness [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] . This study's strengths include prospectively collected specimens from a defined patient population (adults hospitalized with acute respiratory illness), comparison of results against reference methods for influenza A and B detection, and analyses performed on influenza viruses characterized by subtyping or lineage determination. cache = ./cache/cord-332042-bqtflk7r.txt txt = ./txt/cord-332042-bqtflk7r.txt === reduce.pl bib === id = cord-332024-jk983q4p author = Briese, Thomas title = Diagnostic System for Rapid and Sensitive Differential Detection of Pathogens date = 2005-02-17 pages = extension = .txt mime = text/plain words = 1738 sentences = 84 flesch = 36 summary = We describe a diagnostic system for rapid, sensitive, multiplex discrimination of microbial gene sequences and report its application for detecting 22 respiratory pathogens in clinical samples. We describe a diagnostic system for rapid, sensitive, multiplex discrimination of microbial gene sequences and report its application for detecting 22 respiratory pathogens in clinical samples. To address the need for sensitive multiplex assays in diagnostic molecular microbiology, we created a polymerase chain reaction (PCR) platform in which microbial gene targets are coded by a library of 64 distinct Masscode tags (Qiagen Masscode technology, Qiagen, Hilden, Germany). Multiplex primer sets were designed to identify up to 22 respiratory pathogens in a single Mass Tag PCR reaction; sensitivity was established by using synthetic DNA and RNA standards as well as titered viral stocks; the utility of Mass Tag PCR was determined in blinded analysis of previously diagnosed clinical specimens. cache = ./cache/cord-332024-jk983q4p.txt txt = ./txt/cord-332024-jk983q4p.txt === reduce.pl bib === id = cord-331932-oujdl459 author = Lung, O. title = Multiplex PCR and Microarray for Detection of Swine Respiratory Pathogens date = 2015-12-12 pages = extension = .txt mime = text/plain words = 6362 sentences = 293 flesch = 44 summary = The user‐friendly assay detected and differentiated between four viruses [porcine reproductive and respiratory syndrome virus (PRRSV), influenza A virus, porcine circovirus type 2, porcine respiratory corona virus], four bacteria (Mycoplasma hyopneumoniae, Pasteurella multocida, Salmonella enterica serovar Choleraesuis, Streptococcus suis), and further differentiated between type 1 and type 2 PRRSV as well as toxigenic and non‐toxigenic P. Here, a microarray assay with associated multiplex RT-PCRs for detection and differentiation of four viruses and four bacteria involved in PRDC using a novel user-friendly electronic microarray in which capture probe printing, hybridization, washing and reporting are fully integrated and automated is described. Similarly, representative whole-genome sequences, as well as full and partial sequences of homologous genes from related and unrelated non-targets such as TGEV, porcine circovirus type 1 (PCV1), as well as other Salmonella enterica serovars, and Mycoplasma species were downloaded for in silico analysis of probe specificity. The analytical specificity of the viral and bacterial multiplex PCR assays was assessed by amplifying panels of 14 non-target viruses and 21 bacteria, respectively (Table 3) . cache = ./cache/cord-331932-oujdl459.txt txt = ./txt/cord-331932-oujdl459.txt === reduce.pl bib === id = cord-331616-arnuoufn author = Blank, Walter A. title = Virus PCR Assay Panels: An Alternative to the Mouse Antibody Production Test date = 2004 pages = extension = .txt mime = text/plain words = 3515 sentences = 159 flesch = 37 summary = The authors compare MAP testing with PCR-based detection methods, focusing on differences in animal use, laboratory requirements, sample size, and limits of detection. Until recently, the mouse antibody production (MAP) test was the primary method of screening for viruses of murine origin 6 ( Table 1) , but the application of modern molecular biology methods to this purpose presents certain advantages. Because PCR amplifies only DNA molecules, one detects viruses with RNA samples from the animals and test them for virus-specific antibodies using the enzymelinked immunosorbent (ELISA), indirect fluorescent antibody (IFA), or hemagglutination inhibition (HAI) assays. To prevent false-positive results due to contamination with PCR templates, reagent preparation, sample processing, and PCR amplification/product detection should all take place in separate laboratories. Comparison of the sensitivity of in vivo antibody production tests with in vitro PCR-based methods to detect infectious contamination of biological materials cache = ./cache/cord-331616-arnuoufn.txt txt = ./txt/cord-331616-arnuoufn.txt === reduce.pl bib === id = cord-331740-yjt3q9ph author = Jones, R. M. title = Development and Validation of RT‐PCR Tests for the Detection and S1 Genotyping of Infectious Bronchitis Virus and Other Closely Related Gammacoronaviruses Within Clinical Samples date = 2011-04-07 pages = extension = .txt mime = text/plain words = 5863 sentences = 257 flesch = 49 summary = This real-time RT-PCR test was used to examine a panel of field samples and its performance compared to virus isolation in embryonated fowls' eggs. Design and calibration of IBV real-time RT-PCR To confirm that the modified test was suitable for detecting contemporary UK field strains of IBV, a panel of laboratory isolates of IBV representing the major genotypes currently circulating in the UK was tested . The validity of the result obtained for 38 of the 173 real-time RT-PCR positive, virus isolation negative samples could be confirmed by sequencing of the amplicon generated by the diagnostic RT-PCR. Infectious bronchitis virus RNA has been detected in tracheal swab samples by other real-time RT-PCRs for at least 21 days post-vaccination (Callison et al., 2006) and has been isolated from faecal samples in some infected birds as long as 227 days post-infection Gough, 1977, 1978) , making it essential to be able to differentiate between vaccine and field strains for diagnostic purposes. cache = ./cache/cord-331740-yjt3q9ph.txt txt = ./txt/cord-331740-yjt3q9ph.txt === reduce.pl bib === === reduce.pl bib === id = cord-333216-fdwmsnz9 author = Gonzalez, J. E. title = ESTIMATING PREVALENCE AND TIME COURSE OF SARS-CoV-2 BASED ON NEW HOSPITAL ADMISSIONS AND PCR TESTS date = 2020-08-17 pages = extension = .txt mime = text/plain words = 3670 sentences = 202 flesch = 54 summary = Data posted in the COVID 19 tracking website for RT-PCR (PCR) results and hospital admissions are used to estimate the prevalence of the SARS-CoV-2 pandemic in the United States (1). A higher recovered population mitigates the current positive value attainable by limiting the infectivity rate Re. This approach provides an alternate source of information on the pandemic's full time course since the serological testing only views a narrow time slice of its history due to the transient nature of the antibody response and its graduated expression dependency on the severity of the disease. This paper relies on the integration of % PCR positive test results over time, cycle-corrected for the length of disease, and coupled with hospital admissions to control for PCR testing sample bias, to estimate the kinetics and prevalence over the time course of the pandemic in the United States. Figure 4A shows the time course comparison of the SARS-CoV-2 United States infected population obtained from PCR tests and NHA. cache = ./cache/cord-333216-fdwmsnz9.txt txt = ./txt/cord-333216-fdwmsnz9.txt === reduce.pl bib === === reduce.pl bib === id = cord-333413-8buawes0 author = Liebing, J. title = Health status of free-ranging ring-necked pheasant chicks (Phasianus colchicus) in North-Western Germany date = 2020-06-16 pages = extension = .txt mime = text/plain words = 5556 sentences = 306 flesch = 51 summary = Being a typical ground-breeding bird of the agricultural landscape in Germany, the pheasant has experienced a strong and persistent population decline with a hitherto unexplained cause. In the present study, 62 free-ranging pheasant chicks were caught within a two-year period in three federal states of Germany; Lower Saxony, North Rhine-Westphalia and Schleswig-Holstein. Pheasant chick deaths may often have been triggered by poor nutritional status, probably in association with inflammatory changes in various tissues and organs as well as bacterial and parasitic pathogens. In 2014 and 2015, the Institute for Terrestrial and Aquatic Wildlife Research (ITAW), University of Veterinary Medicine Hannover, Foundation, Hannover and the Wildlife Research Institute, State Office for Nature, Environment and Consumer Protection of North Rhine-Westphalia caught free-living Ring-necked Pheasant chicks from Lower Saxony (Cuxhaven, Grafschaft Bentheim, Emsland, Osnabrück, Vechta), North Rhine-Westphalia (Coesfeld, Warendorf) and Schleswig-Holstein (Dithmarschen) to assess the health state by means of pathological, microbiological, virological, parasitological and toxicological investigations. cache = ./cache/cord-333413-8buawes0.txt txt = ./txt/cord-333413-8buawes0.txt === reduce.pl bib === id = cord-333453-v3gap8kj author = Dima, Mirabela title = First neonates with severe acute respiratory syndrome coronavirus 2 infection in Romania: Three case reports date = 2020-08-14 pages = extension = .txt mime = text/plain words = 3020 sentences = 173 flesch = 52 summary = The novel coronavirus officially named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Virus generated a pandemic, which erupted in Hubei, Wuhan, China and quickly spread throughout the world, [1, 2] has been putting medical workers all over the world in difficulty because of the high number of cases combined with the lack of information about the disease. The clinic where the patient was born discharged her and the mother on April 6, 2020 both being negative for SARS-CoV-2 (RT-PCR test). On April 15, after 3 days of observing cough, lethargy, loss of appetite, jaundice, and constant fever, the mother presented in emergency room with the newborn, both being tested positive for SARS-CoV-2. [10] We believe it is important in the current epidemiologic context to mention that all 3 patients were discharged from the clinic where they were born with SARS-CoV-2 negative tests (RT-PCR), which were taken in conformity with our national protocol regarding COVID-19. cache = ./cache/cord-333453-v3gap8kj.txt txt = ./txt/cord-333453-v3gap8kj.txt === reduce.pl bib === id = cord-332053-df44guu7 author = Malka, Jonathan title = The Effect of Viral Infection on Exhaled Nitric Oxide in Children with Acute Asthma Exacerbations date = 2015-07-26 pages = extension = .txt mime = text/plain words = 4754 sentences = 257 flesch = 54 summary = The Effect of Viral Infection on Exhaled Nitric Oxide in Children with Acute Asthma Exacerbations Jonathan Malka, MD a,b , Ronina Covar, MD c,d , Anna Faino, MS e , Jennifer Fish, CPNP f , Paige Pickering, BS g , Preveen Ramamoorthy, MD g , Melanie Gleason, PAC b,h , and Joseph D. All patients who presented to the Urgent Care Clinic at National Jewish Health for an acute asthma exacerbation and who had undergone spirometry and FENO measurements within the last 6 months when clinically stable (visit 1) were approached to participate in the study (Figure 1 ). We found FENO levels to be the highest in children with acute asthma exacerbations that were not associated with viral infections [PCR(À)]. B, Change in exhaled nitric oxide levels from baseline, during an exacerbation, and following a course of prednisone in adjusted models. cache = ./cache/cord-332053-df44guu7.txt txt = ./txt/cord-332053-df44guu7.txt === reduce.pl bib === === reduce.pl bib === id = cord-333261-knj2rrut author = Albright, Catherine J. title = An exercise in molecular epidemiology: Human rhinovirus prevalence and genetics date = 2011-11-11 pages = extension = .txt mime = text/plain words = 3408 sentences = 205 flesch = 59 summary = To facilitate the collections of HRV sequences over a number of years, a virology experiment was designed in which students test nasal lavage samples to look for HRV infection. The extensive data available on HRV genomes enables many bioinformatics opportunities for students, including alignment of genome sequences to look for mutations at the RNA level and differences among protein sequences. Students can examine differences in the HRV serotypes over several years of data regarding a university population to identify HRV mutations that have occurred and their severity in causing symptoms in the host. In this inquiry-based laboratory project, students use a variety of techniques, including RNA isolation, cDNA synthesis, qPCR, and agarose gel electrophoresis to look for the presence of HRV in nasal lavage samples from human subjects. By analyzing surveys in which subjects indicate severity of their symptoms, stress factors, and average hours of rest per night, students can identify possible contributors to HRV infection. cache = ./cache/cord-333261-knj2rrut.txt txt = ./txt/cord-333261-knj2rrut.txt === reduce.pl bib === id = cord-332522-adul9nzf author = Wu, Qingfa title = Development of Taqman RT-nested PCR system for clinical SARS-CoV detection date = 2004-04-02 pages = extension = .txt mime = text/plain words = 2810 sentences = 143 flesch = 62 summary = In this study, 12 sets of nested primers covering the SARS-CoV genome have been screened and showed sufficient sensitivity to detect SARS-CoV in RNA isolated from virus cultured in Vero 6 cells. To optimize further the reaction condition of those nested primers sets, seven sets of nested primers have been chosen to compare their reverse transcribed efficiency with specific and random primers, which is useful to combine RT with the first round of PCR into a one-step RT-PCR. Through investigations on a test panel of whole blood obtained from 30 SARS patients and 9 control persons, the specificity and sensitivity of the Taqman RT-nested PCR system was found to be 100 and 83%, respectively, which suggests that the method is a promising one to diagnose SARS in early stages. To compare the sensitivities of these 12 sets of nested primers, serial 10-fold di-lution genome cDNA of BJ01 that reverse transcribed with random primer was used as the template to carry out the nested PCR. cache = ./cache/cord-332522-adul9nzf.txt txt = ./txt/cord-332522-adul9nzf.txt === reduce.pl bib === id = cord-334090-66d8c75g author = Seger, Waleed title = Genotyping of infectious bronchitis viruses from broiler farms in Iraq during 2014-2015 date = 2016-02-18 pages = extension = .txt mime = text/plain words = 3613 sentences = 178 flesch = 54 summary = Thus, the spread of viral respiratory diseases has become the most commonly reported condition in commercial broiler flocks in Iraq; however, there have been no studies on the detection and genotyping of these viruses using molecular techniques and sequencing. Phylogenetic analysis of the 32 strains (Fig. 2) revealed that Iraqi IBV strains could be classified into four genetic groups or genotypes: group I, variant 2 IS/1494-like viruses, including 15 field isolates (46.87 %); group II, 793/Blike viruses, including 13 field strains (40.62 %); group III, QX-like viruses, including three field strains (9.37); and caused by bacteria and mycoplasmas have already been detected on broiler farms located in the central and southern parts of Iraq. Our result were in line with those of Mahmood et al., who conducted the first study of identification and genotyping of IBV isolates and indicated that the 4/91-like virus is circulating on vaccinated broiler farms of the Kurdistan region of Iraq [21] . cache = ./cache/cord-334090-66d8c75g.txt txt = ./txt/cord-334090-66d8c75g.txt === reduce.pl bib === id = cord-333524-a6p6ma8r author = Khan, Pavana title = Isothermal SARS-CoV-2 Diagnostics: Tools for Enabling Distributed Pandemic Testing as a Means of Supporting Safe Reopenings date = 2020-09-23 pages = extension = .txt mime = text/plain words = 8841 sentences = 603 flesch = 50 summary = 19 The current most common diagnostic method used to identify SARS-CoV-2 infection is a molecular technique for detecting viral RNA through nucleic acid amplification, RT-PCR. Nucleic acid amplification tests (NAATs) are the most common diagnostic tests used to detect pathogens, and many of the current SARS-CoV-2 detection techniques are primarily based on NAATs. 21 NAATs involve nucleic acid amplification, a process that initiates with a small quantity of starting nucleic acids and uses primers that target specific, short nucleic acid sequences in conjunction with enzymes to amplify or increase the quantity of starting nucleic acids. 34 This test incorporates a nested nucleic acid amplification technique showing higher sensitivity of detection than LAMP alone and conventional RT-PCR for minimally processed SARS-CoV-2 samples. 55 The technique first uses RT-LAMP for reverse transcription and isothermal amplification of viral RNA, and then employs the Cas12a enzyme to identify sequences of SARS-CoV-2, allowing cleavage of a reporter molecule ( Figure 5 ). cache = ./cache/cord-333524-a6p6ma8r.txt txt = ./txt/cord-333524-a6p6ma8r.txt === reduce.pl bib === id = cord-335459-tq4fwigw author = Chen, Hui Juan title = Early chest CT features of patients with 2019 novel coronavirus (COVID-19) pneumonia: relationship to diagnosis and prognosis date = 2020-06-09 pages = extension = .txt mime = text/plain words = 2796 sentences = 208 flesch = 63 summary = title: Early chest CT features of patients with 2019 novel coronavirus (COVID-19) pneumonia: relationship to diagnosis and prognosis METHODS: The clinical manifestations, laboratory parameters, and CT imaging findings were analyzed in 34 COVID-19 patients, confirmed by RT-PCR from January 20 to February 4 in Hainan Province. a-c Axial unenhanced chest CT revealed multiple confluent and patchy ground-glass and consolidative pulmonary opacities in the subpleural area bilaterally upon hospital admission on January 29, 2020. The CT images on admission showed bilateral, multiple lobular and subsegmental areas of GGO with subsegmental areas of consolidation, indicating the disease was severe Fig. 3 A 50-year-old woman with a history of exposure presented with cough and white phlegm for 4 days, accompanied by headache, muscle aches, and no fever. cache = ./cache/cord-335459-tq4fwigw.txt txt = ./txt/cord-335459-tq4fwigw.txt === reduce.pl bib === id = cord-335323-p7cv79ig author = DeSerres, Joshua J. title = Best Practice Guidelines for the Management of Acute Craniomaxillofacial Trauma During the COVID-19 Pandemic date = 2020-05-11 pages = extension = .txt mime = text/plain words = 4205 sentences = 217 flesch = 44 summary = The authors have proposed an algorithm for management of CMF trauma during the COVID-19 pandemic to ensure that urgent and emergent CMF injuries are addressed appropriately while optimizing the safety of surgeons and other healthcare providers. So far there has been a significant mortality of otolaryngologists and ophthalmologists in the Wuhan region, thought to be related to exposure to aerosolized virus from the nasal and oral airway mucosa from high risk procedures such as CMF trauma and sinus operations and in some patients despite the use of N95 masks. 19, 20 Given that the majority of CMF trauma procedures involve violation of the mucosa of the oral cavity and sinuses, these patients place the surgeons and the remainder of the operating room staff at high risk of exposure during the COVID-19 pandemic. cache = ./cache/cord-335323-p7cv79ig.txt txt = ./txt/cord-335323-p7cv79ig.txt === reduce.pl bib === id = cord-333805-xmqs2ax7 author = Romoli, Michele title = A systematic review of neurological manifestations of SARS‐CoV‐2 infection: the devil is hidden in the details date = 2020-06-05 pages = extension = .txt mime = text/plain words = 4025 sentences = 257 flesch = 44 summary = BACKGROUND: We systematically reviewed available evidence for reports of neurological signs and symptoms in Coronavirus disease (COVID)‐19 patients to identify cases with severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) infection or immune‐mediated reaction in the nervous system. This study therefore aimed to identify clinical cases of confirmed nervous system invasion or postinfectious neurological disease in the available COVID-19 literature on the basis of a systematic review. A systematic review was carried out to study all cases reporting nervous system involvement in patients with proven SARS-CoV2 infection. There were just 2 cases with positive SARS-CoV-2 PCR in CSF among 27 patients with potential neurologic symptoms and proven COVID-19. In this regard, we see a clear need for the use of precise case definitions and focused diagnostic work-up to distinguish nonspecific complications of severe disease and focused reporting of neurological involvement in association with SARS-CoV-2 infection. cache = ./cache/cord-333805-xmqs2ax7.txt txt = ./txt/cord-333805-xmqs2ax7.txt === reduce.pl bib === id = cord-335359-4rcj75tc author = Jia, Bei title = Evaluation of a PCR-electrospray ionization mass spectrometry platform for detection and identification of fungal pathogens directly from prospectively collected bronchoalveolar lavage specimens date = 2020-01-15 pages = extension = .txt mime = text/plain words = 5126 sentences = 238 flesch = 40 summary = We report here the use of a diagnostic assay that utilizes a universal extraction method, broad spectrum PCR amplification and analysis via electrospray ionization mass spectrometry (PCR/ESI-MS) to detect and identify more than 200 pathogenic fungi directly from bronchoalveolar lavage (BAL) specimens in less than 8 hours. For the clinical performance, the PCR/ESI-MS method was applied to prospectively collected BAL specimens obtained from patients suspected of, or at high risk for, pulmonary fungal infections. All BAL samples were processed at the Johns Hopkins Hospital Microbiology Laboratory for the detection and identification of fungal pathogens using all standard of care reference tests including direct microscopic examination by calcofluor white staining, fungal culture, galactomannan (positive cutoff value: GMI 0.5), and direct fluorescent antibody (DFA) microscopic examination that is the only method used for the detection of Pneumocystis jirovecii. cache = ./cache/cord-335359-4rcj75tc.txt txt = ./txt/cord-335359-4rcj75tc.txt === reduce.pl bib === id = cord-334688-0i1pu8wc author = Martos Pérez, F. title = Comorbidity and prognostic factors on admission in a COVID-19 cohort of a general hospital date = 2020-08-19 pages = extension = .txt mime = text/plain words = 3445 sentences = 208 flesch = 57 summary = Material and methods Retrospective cohort study of patients with COVID-19 admitted from 26th February 2020, who had been discharged or died up to 29th April 2020. Conclusions The presence of cardiopathy, levels of LDH ≥ 345 IU/L and age ≥ 65 years, are associated with a higher risk of death during hospital stay for COVID-19. In this study, we describe the first cases of COVID-19 in patients hospitalized in a general hospital and analyze the characteristics upon admission associated with in-hospital death. Our model shows that a medical history of cardiopathy, LDH levels ≥345 IU/L upon admission, and age ≥65 years are associated with greater in-hospital mortality due to COVID-19. Predictors of Mortality for Patients with COVID-19 Pneumonia Caused by SARS-CoV-2: A Prospective Cohort Study Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study. cache = ./cache/cord-334688-0i1pu8wc.txt txt = ./txt/cord-334688-0i1pu8wc.txt === reduce.pl bib === id = cord-335085-7pxkhgbq author = Dessau, R. B. title = Coronaviruses in spinal fluid of patients with acute monosymptomatic optic neuritis date = 2009-01-29 pages = extension = .txt mime = text/plain words = 2145 sentences = 130 flesch = 64 summary = Material and methods ‐ Spinal fluids from 37 patients with AMON and 15 surgical control patients with protrusion of the intervertebral disk were assayed with a nested multiplex polymerase chain reaction with primers specific for human coronaviruses strain (HCV) 229E and OC43. To investigate the possibility of an infection with human coronaviruses (HCV) in early MS and as a possible cause of AMON we have analyzed cerebrospinal fluid (CSF) from patients with AMON using reverse transcriptase reaction and the polymerase chain reaction (RT-PCR) applying primers specific for HCV. CSF from 4 patients and 1 control ( Table 2) were positive on nested RT-PCR using the HCV-229E primers and all samples were negative with the HCV-OC43 primers. HCV-229E RNA was found in the CSF by RT-PCR in 4 of 37 patients with AMON and in 1 of 15 controls. cache = ./cache/cord-335085-7pxkhgbq.txt txt = ./txt/cord-335085-7pxkhgbq.txt === reduce.pl bib === id = cord-336453-cbq0ui4p author = Machitori, Akihiro title = Computed tomography surveillance helps tracking COVID-19 outbreak date = 2020-08-07 pages = extension = .txt mime = text/plain words = 3802 sentences = 186 flesch = 49 summary = PURPOSE: To reveal that a computed tomography surveillance program (CT-surveillance) could demonstrate the epidemiologic features of COVID-19 infection and simultaneously investigate the type and frequency of CT findings using clinical CT data. Using an online questionnaire, we asked Japanese board-certified radiologists to register their patients' information including patient age and sex, the CT examination date, the results of PCR test for COVID-19 infection, CT findings, and the postal code of the medical institution that performed the CT. We conducted the present study to reveal that CT-surveillance could demonstrate the epidemiologic features of COVID-19 infection as well as simultaneously investigate the type and frequency of characteristic imaging findings on CT by using clinical CT data. CT findings in CT surveillance might distinguish the group that is considered Fig. 2 The epidemic curve of the diurnal patient number in the CT surveillance (a) shows a distribution similar to that of the PCR surveillance (b). cache = ./cache/cord-336453-cbq0ui4p.txt txt = ./txt/cord-336453-cbq0ui4p.txt === reduce.pl bib === id = cord-336671-vfq5ft08 author = Ai, Jing-Wen title = Era of molecular diagnosis for pathogen identification of unexplained pneumonia, lessons to be learned date = 2020-03-16 pages = extension = .txt mime = text/plain words = 1883 sentences = 108 flesch = 50 summary = Unexplained pneumonia (UP) caused by a novel coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) emerged in China in late December 2019 and has infected more than 9000 cases by 31 January 2020. A combinative approach of real-time RT–PCR, CRISPR-based assay and metagenomic next-generation sequencing (mNGS) were used to diagnose this unexplained pneumonia patient. The reasons behind this outbreak are numerous, the highly infectious nature of SARS-CoV-2, limited pathogen detection method for unexplained pneumonia, the high population density of the Hubei Province and across China, etc. On 20 January, Shanghai reported the first imported case of SARS-CoV-2 infection, and through this case, we seek a combinative approach of selected techniques to improve pathogen identification of unexplained pneumonia in the future. We then performed real-time RT-PCR, CRISPR-based assay and metagenomic next-generation sequencing (mNGS) on her respiratory sample and finally diagnosed her with COVID-19. cache = ./cache/cord-336671-vfq5ft08.txt txt = ./txt/cord-336671-vfq5ft08.txt === reduce.pl bib === === reduce.pl bib === id = cord-335393-4buooi2d author = Xiang, Yangxi title = Comparative transcriptome analysis reveals the role of p53 signalling pathway during red‐spotted grouper nervous necrosis virus infection in Lateolabrax japonicus brain cells date = 2019-01-18 pages = extension = .txt mime = text/plain words = 3887 sentences = 221 flesch = 46 summary = title: Comparative transcriptome analysis reveals the role of p53 signalling pathway during red‐spotted grouper nervous necrosis virus infection in Lateolabrax japonicus brain cells To better comprehend the molecular immune mechanism of sea perch (Lateolabrax japonicus) against NNV infection, the comparative transcriptome analysis of red‐spotted grouper nervous necrosis virus (RGNNV)‐infected or mock‐infected L. Based on the analysis of differentially expressed genes (DEGs), we found that p53 signalling pathway might be involved in the immune response against RGNNV, and experimentally revealed the role of L. Of these genes, many well-known immune-related genes were strongly inhibited after RGNNV infecComparative transcriptome analysis showed that 79 DEGs involved in p53 signalling pathway were regulated in RGNNV-infected LJB cells compared to control cells (Supporting Information Figure S1 ). Several studies indicated that p53 functioned as a key player in innate antiviral immunity by both enforcing the type I IFN response and inducing apoptosis in virus-infected cells (Rivas, Aaronson, & Munoz-Fontela, 2010) . cache = ./cache/cord-335393-4buooi2d.txt txt = ./txt/cord-335393-4buooi2d.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-336975-28mtmw2z author = Sadeghi, Christine D title = Twelve years' detection of respiratory viruses by immunofluorescence in hospitalised children: impact of the introduction of a new respiratory picornavirus assay date = 2011-02-07 pages = extension = .txt mime = text/plain words = 3032 sentences = 161 flesch = 41 summary = PCR-based studies have suggested the important role of respiratory picornaviruses (rhinovirus and enterovirus) as a leading cause of lower respiratory tract infections in children [5] , in particular wheezing illnesses such as bronchiolitis [6, 7] , wheezy bronchitis [8] and asthma exacerbations [9] , but also pneumonia [2] . In addition, PCR has allowed for the detection of new respiratory viruses, such as hMPV [10] , which has been implicated in upper and lower respiratory tract infections in children [11] [12] [13] . A significant proportion of asymptomatic children test positive by PCR to respiratory viruses [14] [15] [16] , and picornavirus RNA can be detected by PCR up to 5 weeks after an acute infection [17] . In order to determine the value of DFA in conducting epidemiological studies on respiratory viruses now that assays for respiratory picornaviruses and hMPV are available, we retrospectively analysed the results of 12 years of DFA screening of viral pathogens in hospitalized children with respiratory disease. cache = ./cache/cord-336975-28mtmw2z.txt txt = ./txt/cord-336975-28mtmw2z.txt === reduce.pl bib === === reduce.pl bib === id = cord-337003-7ygcfzii author = Mehrbod, Parvaneh title = Association of IFITM3 rs12252 polymorphisms, BMI, diabetes, and hypercholesterolemia with mild flu in an Iranian population date = 2017-11-09 pages = extension = .txt mime = text/plain words = 4411 sentences = 250 flesch = 49 summary = METHODS: We conducted a case-control study, including 79 mild flu and 125 flu-negative individuals attending primary care centers of three provinces of Iran (i.e, Markazi, Semnan, and Zanjan). Lack of significant association between C allele homozygous and mild flu, observed in this study, might be the result of small sample size in this group. Therefore, we performed this study to identify the association between mild flu and IFITM3 rs12252-C polymorphism, BMI, diabetes and hypercholesterolemia. In this study, we investigated the association between mild flu and IFITM3 rs12252 variant, BMI, diabetes, and hypercholesterolemia in an Iranian population. To control for the effect of residual population admixture on our results, we adjusted genetic association between IFITM3-SNP rs12252 and susceptibility to mild flu for participants' residence area. To the best of our knowledge, this is the first study evaluating the association between IFITM3 rs12252 polymorphism, diabetes, hypercholesterolemia and BMI with susceptibility to mild flu in an Iranian sample. cache = ./cache/cord-337003-7ygcfzii.txt txt = ./txt/cord-337003-7ygcfzii.txt === reduce.pl bib === === reduce.pl bib === id = cord-335784-v7nbck0n author = Barak, N. title = Lessons from applied large-scale pooling of 133,816 SARS-CoV-2 RT-PCR tests date = 2020-10-20 pages = extension = .txt mime = text/plain words = 3136 sentences = 202 flesch = 57 summary = Pooling multiple swab samples prior to RNA extraction and RT-PCR analysis was proposed as a strategy to reduce costs and increase throughput of SARS-CoV-2 tests. Key open questions concern reduced sensitivity due to sample dilution; the rate of false positives; the actual efficiency (number of tests saved by pooling) and the impact of infection rate in the population on assay performance. Major diagnostic challenges have emerged, mainly, the need for high throughput SARS-CoV-2 RT-PCR tests, aimed to detect not only symptomatic but also asymptomatic infectious viral carriers and to screen special or at-risk populations (such as health care personnel or nursing home tenants), in order to contain viral spread and guide control measures. To our knowledge, this is the most extensive analysis, addressing key considerations of efficiency, sensitivity and feasibility in the actual reality of routine, large-scale implementation of sample pooling for SARS-CoV-2 detection. cache = ./cache/cord-335784-v7nbck0n.txt txt = ./txt/cord-335784-v7nbck0n.txt === reduce.pl bib === id = cord-337701-56tmg38b author = Xiao, Yan title = Comparison of three TaqMan Real-Time Reverse Transcription-PCR assays in detecting SARS-CoV-2 date = 2020-07-06 pages = extension = .txt mime = text/plain words = 2122 sentences = 120 flesch = 57 summary = In the present study, we evaluated the sensitivity, specificity, amplification efficiency, and linear detection ranges of three qRT-PCR assays, including the assays developed by our group (IPBCAMS), and the assays recommended by WHO and China CDC (CCDC). No effect of the 152 co-existed other viral nucleic acids on the LOD and the linear detection range was 153 observed, although higher Ct values were generated than those of RNA transcript 154 alone as template in all of the three qRT-PCR assays. Although most of the evaluated 232 assays exhibited good sensitivity, specificity, reproducibility and wide linear detection 233 range, performance test with clinical specimens from suspected COVID-19 patients 234 suggested that the N gene assay in IPBCAMS assays and CCDC assays, and the ORF 235 1b gene assays in IPBCAMS assays were the preferred qRT-PCR assays for accurate 236 detection of SARS-CoV-2. cache = ./cache/cord-337701-56tmg38b.txt txt = ./txt/cord-337701-56tmg38b.txt === reduce.pl bib === === reduce.pl bib === id = cord-339278-9luefzyo author = Zayet, Souheil title = Contribution of anosmia and dysgeusia for diagnostic of COVID-19 in outpatients date = 2020-05-14 pages = extension = .txt mime = text/plain words = 2071 sentences = 112 flesch = 58 summary = Between March, 30th and April, 3rd 2020 we retrospectively collected the following data from the medical files of patients: demographic characteristics (age, sex), interval between illness onset and consultation, functional symptoms (measured fever > 38 °C, myalgia and/ or arthralgia, headache, cough, dyspnea, dysgeusia, anosmia, rhinorrhea, nausea, vomiting, diarrhea, and abdominal pain), clinical signs (crackling sounds heard on pulmonary auscultation) and result of RT-PCR SARS-CoV-2 nasopharyngeal sample. During the study period, 217 samples (nasopharyngeal swabs) were collected in our consultation: 95 patients (44%) had a positive SARS-CoV-2 RT-PCR confirming the infection by COVID-19 and 122 patients (56%) had a negative SARS-CoV-2 RT-PCR. Outpatients presenting with dysgeusia and/or anosmia may be considered as patients infected with COVID-19, until microbiological confirmation has been obtained (as they have a high pre-test probability to be positive for SARS CoV-2 RT-PCR). cache = ./cache/cord-339278-9luefzyo.txt txt = ./txt/cord-339278-9luefzyo.txt === reduce.pl bib === id = cord-339419-b6tr2zyx author = Lee, Thomas Ming-Hung title = DNA-based bioanalytical microsystems for handheld device applications date = 2006-01-18 pages = extension = .txt mime = text/plain words = 5425 sentences = 331 flesch = 49 summary = Recent progresses in the miniaturization of various biological processing steps for the sample preparation, DNA amplification (polymerase chain reaction), and product detection are delineated in detail. The organization of the following contents is based upon the three basic DNA processing modules of sample preparation, target amplification, and product detection. Thermal lysis can be easily adapted to microfabricated amplification systems as the initial high-temperature step (∼95 • C) employed to denature the double-stranded (ds) DNA template is powerful enough to open up the cell membranes [10, 12, 19] . The sensing protocol basically involves the immobilization of an oligonucleotide onto a transducer surface, and upon the hybridization of complementary target sequence, the binding event is detected by optical, microgravimetric (mass-sensitive), or electrochemical methods. To further increase the sensitivity of the gold nanoparticle-based assay, a signal amplification step Pictorial representation of the working principle of the molecular beacon-type capture probe labeled with ferrocene group for the reagentless sequence-specific DNA detection. cache = ./cache/cord-339419-b6tr2zyx.txt txt = ./txt/cord-339419-b6tr2zyx.txt === reduce.pl bib === id = cord-338607-22f04uqe author = Verbeek, A. title = Genomic relationship between turkey and bovine enteric coronaviruses identified by hybridization with BCV or TCV specific cDNA probes date = 1991 pages = extension = .txt mime = text/plain words = 4120 sentences = 192 flesch = 47 summary = title: Genomic relationship between turkey and bovine enteric coronaviruses identified by hybridization with BCV or TCV specific cDNA probes Genomic relationships between turkey and bovine coronavirus (TCV and BCV), which are currently placed in distinct antigenic groups, were demonstrated by hybridization using specific cDNA probes. BCV-specific recombinant plasmids p 52, p 27, and p 247, which served previously for the optimization of hybridization conditions for BCV-RNA detection [33] , and probes pN 17 and pN 9, holding respectively the BCV N and M gene ( Fig. 1) , were used in the detection of several coronaviruses in order to establish the presence of potential genomic homologies. Clinical diagnosis of TCV was assayed with a pool of six 32p-labelled BCV specific recombinant plasmids (pBCV-pool), holding non-overlapping eDNA sequences, in order to amplify the detection signal. Detection signals were absent when testing spotted supernatant fluids of non-infected HRT-18 cells (Fig. 2) and when probing identical blots with 32p-labelled pUC-DNA (not shown), confirming the specificity of the hybridization signals obtained. cache = ./cache/cord-338607-22f04uqe.txt txt = ./txt/cord-338607-22f04uqe.txt === reduce.pl bib === id = cord-338942-q4neat3x author = Zhang, Haoqing title = LAMP-on-a-chip: Revising microfluidic platforms for loop-mediated DNA amplification date = 2019-01-31 pages = extension = .txt mime = text/plain words = 5757 sentences = 314 flesch = 41 summary = Isothermal deoxyribonucleic acid amplification methods, such as loop-mediated isothermal amplification (LAMP), exhibit characteristics ideal for point-of-care (POC) applications, since their instrumentation is simpler in comparison with the standard method of polymerase chain reaction. Nucleic acids amplification methods are primarily required to be performed, as the original number of either DNA or ribonucleic acid (RNA) copies in the clinical sample is insufficient for their direct detection. A microfluidic disk-based LAMP chip, integrating sample preparation and detection, was developed [44] (Fig. 2B ). Loop-mediated isothermal amplification integrated on microfluidic chips for point-of-care quantitative detection of pathogens An integrated rotary microfluidic system with DNA extraction, loop-mediated isothermal amplification, and lateral flow strip based detection for point-ofcare pathogen diagnostics An integrated microfluidic loop-mediated-isothermal-amplification system for rapid sample pre-treatment and detection of viruses Development and application of a loop-mediated isothermal amplification method on rapid detection Escherichia coli O157 strains from food samples cache = ./cache/cord-338942-q4neat3x.txt txt = ./txt/cord-338942-q4neat3x.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-338899-qt17jhg0 author = Lakshmi, Vemu title = Clinical Features and Molecular Diagnosis of Chikungunya Fever from South India date = 2008-05-01 pages = extension = .txt mime = text/plain words = 3623 sentences = 178 flesch = 48 summary = Emergence or reemergence of severe arboviral hemorrhagic fevers caused by mosquitoborne viruses, such as dengue virus and Chikungunya (CHIK) virus, have been frequently reported in the Indian subcontinent in the past few years. We report clinical observations and laboratory investigations involving virus isolation methods and molecular assays performed for 296 clinically suspected cases of CHIK fever. Of particular interest was the applicability of a novel method of gene amplificatio called real-time loop-mediated isothermal amplifica tion (RT-LAMP) as a rapid, sensitive, and specifi real-time method to detect and quantify CHIK virus in the acute phase of the infection. All 132 patients who had clinically suspected CHIK virus but whose RT-PCR and RT-LAMP results were negative presented 17 days after the onset of fever; this may be the reason for the negative test results. The RT-LAMP allows rapid, realtime detection of CHIK virus in acute-phase serum samples, without requiring sophisticated equipment, and has potential usefulness for clinical diagnosis and surveillance of CHIK virus in developing countries. cache = ./cache/cord-338899-qt17jhg0.txt txt = ./txt/cord-338899-qt17jhg0.txt === reduce.pl bib === id = cord-338205-sy91rnse author = Li, Chenxi title = Laboratory Diagnosis of Coronavirus Disease-2019 (COVID-19) date = 2020-07-02 pages = extension = .txt mime = text/plain words = 7515 sentences = 436 flesch = 51 summary = With limited understanding of COVID-19, it is difficult to exclude SARS-CoV-2 infection based on a single negative PCR result, especially when testing was used for upper respiratory tract specimens. The study found that SARS-CoV-2 could be detected in all primer-probe sets applied in the qRT-PCR tests, but significant discrepancy was observed in the detection limit and the ability to identify negatives and positives with a lower viral load. Compared with the qRT-PCR kit, nested RT-PCR analysis showed higher sensitivity and specificity, indicating that it is more suitable for clinical application to detect SARS-CoV-2 in cases with low viral load. In cases where RT-PCR assays are negative and there is a strong epidemiological link to SARS-CoV-2 infection, paired serum samples (in the acute and convalescent-phase) could support diagnosis once validated serology tests are available with the initial samples collected in the first week of COVID-19 and the second collected after 2-4 weeks [28] . cache = ./cache/cord-338205-sy91rnse.txt txt = ./txt/cord-338205-sy91rnse.txt === reduce.pl bib === id = cord-337198-4sors3bg author = Clementi, Nicola title = Combined Prophylactic and Therapeutic Use Maximizes Hydroxychloroquine Anti-SARS-CoV-2 Effects in vitro date = 2020-07-10 pages = extension = .txt mime = text/plain words = 4259 sentences = 224 flesch = 54 summary = In this study, we evidence that the anti-SARS-CoV2 activity of a clinically achievable hydroxychloroquine concentration is maximized only when administered before and after the infection of Vero E6 and Caco-2 cells. In this study, we tested HCQ against a SARS-CoV-2 Italian clinical isolate, by using different protocols of drug administration corresponding to its possible prophylactic, therapeutic, and prophylactic/therapeutic use in patients. A clinical isolate hCoV-19/Italy/UniSR1/2020 (GISAID accession ID: EPI_ISL_413489) was isolated and propagated in Vero E6 cells, and viral titer was determined by 50% tissue culture infective dose (TCID 50 ) and plaque assay for confirming the obtained titer. HCQ EC 50 against SARS-CoV-2 was obtained by both CPE and RT-PCR analysis on results from full-time experimental setting on Vero E6 cells. Different concentrations of HCQ were tested on Vero E6 to determine the effective concentration of the drug against SARS-CoV-2 in vitro infection (Figure 1) . cache = ./cache/cord-337198-4sors3bg.txt txt = ./txt/cord-337198-4sors3bg.txt === reduce.pl bib === === reduce.pl bib === id = cord-340046-kgbvld0y author = Houspie, Lieselot title = Exhaled breath condensate sampling is not a new method for detection of respiratory viruses date = 2011-03-04 pages = extension = .txt mime = text/plain words = 4081 sentences = 219 flesch = 53 summary = BACKGROUND: Exhaled breath condensate (EBC) sampling has been considered an inventive and novel method for the isolation of respiratory viruses. RESULTS: Viral screening resulted in the detection of 4 different viruses in EBC and/or nasal swabs: Rhinovirus, Human Respiratory Syncytial Virus B, Influenza A and Influenza B. This observation has created a growing interest in the use of EBC as a new sampling method for the screening of respiratory viruses infecting the upper airways. The aim of this study was to investigate whether the EBC collection method was suited for the efficient condensation of aerosolised virus particles during normal breathing and to explore the isolation of respiratory viruses in the condensate. In this study, 102 EBCs were collected from otherwise healthy volunteers showing respiratory or flu-like symptoms (defined in Table 1 ), using a commercially available condenser (RTube™, Respiratory Research Inc., Charlottesville, Virginia, USA). Collection of exhaled breath condensates is a novel and non-invasive method for obtaining samples of the upper respiratory tract. cache = ./cache/cord-340046-kgbvld0y.txt txt = ./txt/cord-340046-kgbvld0y.txt === reduce.pl bib === id = cord-339456-82iks0xf author = Mikel, P. title = Methods for Preparation of MS2 Phage-Like Particles and Their Utilization as Process Control Viruses in RT-PCR and qRT-PCR Detection of RNA Viruses From Food Matrices and Clinical Specimens date = 2015-02-25 pages = extension = .txt mime = text/plain words = 10033 sentences = 499 flesch = 53 summary = title: Methods for Preparation of MS2 Phage-Like Particles and Their Utilization as Process Control Viruses in RT-PCR and qRT-PCR Detection of RNA Viruses From Food Matrices and Clinical Specimens The technology for production of MS2 phage-like particles is theoretically well established, uses the knowledge gained from the study of the familiar bacteriophage MS2 and utilizes many different approaches for the construction of the various process control viruses. Also MS2 phage-like particles have been used as the process control virus for the detection of pathogenic RNA viruses in clinical samples. prepared MS2 phage-like particles, also called armored RNA (aRNA), that carried the consensus RNA sequence from human immunodeficiency virus type 1 (HIV-1) packaged in the capsid which can serve as quantitative standard in detection of HIV-1 (Pasloske et al. MS2 phage-like particles carrying the plant-specific ribulose-1,5-bisphosphate carboxyl small subunit (rbcs) gene fragment were used as the process control virus in qRT-PCR detection of severe acute respiratory syndrome coronavirus (SARS-CoV) . cache = ./cache/cord-339456-82iks0xf.txt txt = ./txt/cord-339456-82iks0xf.txt === reduce.pl bib === === reduce.pl bib === id = cord-338582-o976nab9 author = Dahlhausen, Bob title = Future Veterinary Diagnostics date = 2010-09-19 pages = extension = .txt mime = text/plain words = 9199 sentences = 511 flesch = 35 summary = Genome sequencing has allowed efficient, sensitive, and specific diagnostic assays to be developed based on the detection of nucleic acids. PCR uses the highly specific molecular recognition ability of Watson-Crick base pairing to provide the selectivity needed for a nucleic acid probe to bind to a targeted DNA sequence and allow for its exponential amplification. It has been used to develop rapid diagnostic tests for several pathogenic viruses with singlestranded RNA genomes, including influenza A, 13 footand-mouth disease virus, 14 and severe acute respiratory syndrome (SARS)-associated coronavirus. DNA microarrays also permit relatively rapid interrogation of a clinical sample against thousands of genetic targets, allowing for simultaneous detection and discrimination among hundreds of pathogenic agents of veterinary interest. Unlike PCR technology where the target agent must be known to use specific test primers, microarrays can allow for the rapid diagnosis of multiple pathogenic agents in disease outbreaks and epidemics of unknown etiology. cache = ./cache/cord-338582-o976nab9.txt txt = ./txt/cord-338582-o976nab9.txt === reduce.pl bib === id = cord-339995-0pbknb32 author = Feng, Hao title = A case report of COVID-19 with false negative RT-PCR test: necessity of chest CT date = 2020-04-07 pages = extension = .txt mime = text/plain words = 969 sentences = 62 flesch = 63 summary = We report a case of 34-year-old man who was diagnosed as negative for COVID-19 based on the four sequential RT-PCR tests of his pharyngeal swab. It is difficult to distinguish COVID-19 pneumonia from other viral pneumonia on CT findings alone; however, we emphasize the utility of chest CT to detect early change of COVID-19 in cases which RT-PCR tests show negative results. d Follow-up CT 7 days after admission (d1, axial image; d2, ray-summation image; d3, pseudo color MIP; d4, coronal image) shows multifocal bilateral ground-glass opacities and improvement of mixed groundglass opacities and consolidation in left upper lobe. Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: a report of 1014 cases cache = ./cache/cord-339995-0pbknb32.txt txt = ./txt/cord-339995-0pbknb32.txt === reduce.pl bib === id = cord-339656-u0cpklsv author = de Groot-Mijnes, Jolanda D.F. title = Identification of New Pathogens in the Intraocular Fluid of Patients With Uveitis date = 2010-11-30 pages = extension = .txt mime = text/plain words = 4012 sentences = 243 flesch = 44 summary = Methods Ocular fluids from 139 patients suspected of infectious uveitis, but negative for herpes simplex virus, varicella-zoster virus, cytomegalovirus, and Toxoplasma gondii by polymerase chain reaction and/or antibody analysis in intraocular fluids, were assessed for the presence of 18 viruses and 3 bacteria by real-time polymerase chain reaction (PCR). The remainders of ocular fluid samples from patients with PCR-and/or GWC-confirmed infectious uveitis (ocular toxoplasmosis, n ϭ 13; HSV anterior uveitis, n ϭ 10; rubella virus-associated Fuchs heterochromic uveitis syndrome (FHUS), n ϭ 14) and from patients with cataract in the absence of intraocular inflammation (n ϭ 11) served as controls. • NUCLEIC ACID ISOLATION AND REAL-TIME PCR: The ocular fluid samples were analyzed for the presence of adenovirus, EBV, HHV6, Mycoplasma pneumoniae, Chlamydia pneumoniae, and Chlamydia trachomatis DNA and of coronaviruses 229E, OC43, and NL63, enteroviruses, human metapneumovirus, influenza A and B virus, parainfluenza virus 1 to 4, HPeV, respiratory syncytial virus A and B, and rubella virus RNA. cache = ./cache/cord-339656-u0cpklsv.txt txt = ./txt/cord-339656-u0cpklsv.txt === reduce.pl bib === id = cord-340627-xyvzgkxl author = Ornaghi, Sara title = Performance of an extended triage questionnaire to detect suspected cases of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection in obstetric patients: Experience from two large teaching hospitals in Lombardy, Northern Italy date = 2020-09-15 pages = extension = .txt mime = text/plain words = 3804 sentences = 228 flesch = 51 summary = title: Performance of an extended triage questionnaire to detect suspected cases of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection in obstetric patients: Experience from two large teaching hospitals in Lombardy, Northern Italy Initially, a targeted SARS-CoV-2 screening approach triggered by a positive questionnaire and based on RT-PCR testing of nasopharyngeal swabs was used in women with hospital admission after accessing the Emergency Department. On April 8 th , we changed our policy and started testing all women for SARS-CoV-2 infection independent of the type of hospital admission and the questionnaire result, in agreement with a disposition of the Lombardy Region Health Care Authority. Our study investigated the accuracy of a comprehensive questionnaire thoroughly assessing obstetric patients upon hospital admission to identify cases suspected for SARS-CoV-2 infection. Our data show that thorough assessment of obstetric patients upon hospital admission by means of an exhaustive questionnaire is feasible and effective in discriminating women at low risk of SARS-CoV-2 infection in the context of both a targeted and a universal screening cache = ./cache/cord-340627-xyvzgkxl.txt txt = ./txt/cord-340627-xyvzgkxl.txt === reduce.pl bib === id = cord-339973-kj56zi59 author = Coleman, Kristen K. title = Bioaerosol Sampling for Respiratory Viruses in Singapore’s Mass Rapid Transit Network date = 2018-11-30 pages = extension = .txt mime = text/plain words = 4775 sentences = 228 flesch = 46 summary = Although baseline metagenomic maps created from these studies are said to be useful for mitigating bioterrorism and infectious disease outbreaks, most of them focus largely on mapping surface-borne bacterial DNA 17 and neglect to address the threat of weaponized or global catastrophic biological risk-level (GCBR-level) agents, both of which would likely be aerosolized or respiratory-borne RNA viruses 19 . Bioaerosol sampling in the field provides a noninvasive way to monitor and characterize the community of aerosolized respiratory viruses that regularly infect the public, as well as potentially detect or discover novel pathogens with pandemic potential, such as the influenza A(H7N9) virus. Although the air pump flow rate and sample collection times used in our study have been demonstrated to efficiently capture aerosolized influenza virus and RSV RNA [33] [34] [35] , it is possible that these parameters are not optimal for capturing the other respiratory virus DNA/RNA targeted in our study. cache = ./cache/cord-339973-kj56zi59.txt txt = ./txt/cord-339973-kj56zi59.txt === reduce.pl bib === id = cord-340788-p02v46xu author = Zitek, Tony title = The Appropriate Use of Testing for COVID-19 date = 2020-04-13 pages = extension = .txt mime = text/plain words = 1599 sentences = 101 flesch = 61 summary = With regard to the accuracy of the test, the most commonly used test for detecting SARS-CoV-2 is a nasopharyngeal swab that uses a reverse transcriptase-polymerase chain reaction (RT-PCR) to identify viral RNA. One non-peer reviewed publication reports that, based on 87 Chinese patients who were ultimately diagnosed with COVID-19, pharyngeal RT-PCR tests have a sensitivity and specificity of 78.2% and 98.8%, respectively. Along the same lines, Winichakoon et al published a letter to the editor in which they described a case of a COVID-19 patient who had a nasopharygeal/oropharyngeal RT-PCR swab that was negative for COVID-19, but RT-PCR of BAL fluid was positive. 12 Next, in a case series described by Xie et al, five patients from the Hunan province of China had ground-glass opacities on chest computed tomography (CT) that were suggestive of COVID-19, but initial pharyngeal RT-PCR tests were negative. cache = ./cache/cord-340788-p02v46xu.txt txt = ./txt/cord-340788-p02v46xu.txt === reduce.pl bib === === reduce.pl bib === id = cord-340336-u59l0taa author = Perchetti, Garrett A. title = Multiplexing primer/probe sets for detection of SARS-CoV-2 by qRT-PCR date = 2020-06-08 pages = extension = .txt mime = text/plain words = 1390 sentences = 99 flesch = 50 summary =  -Of all 356 samples tested, triplexing demonstrated 99.2% (n=353/356) assay agreement Abstract: Background -The novel respiratory virus SARS-CoV-2, responsible for over 380,000 COVID-19 related deaths, has caused significant strain on healthcare infrastructure and clinical laboratories globally. Methods -Nasopharyngeal swabs submitted to UW Virology for SARS-CoV-2 clinical testing were extracted, amplified by our laboratory developed test (LDT) -a CDC-based quantitative reverse transcriptase PCR reaction -and analyzed for agreement between the multiplexed assay. Methods -Nasopharyngeal swabs submitted to UW Virology for SARS-CoV-2 clinical testing were extracted, amplified by our laboratory developed test (LDT) -a CDC-based quantitative reverse transcriptase PCR reaction -and analyzed for agreement between the multiplexed assay. To increase throughput of SARS-CoV-2 testing in clinical laboratories, we designed a multiplexed real-time quantitative reverse transcription PCR (qRT-PCR) assay utilizing primers and probe sets from the CDC combined with an internal extraction control. cache = ./cache/cord-340336-u59l0taa.txt txt = ./txt/cord-340336-u59l0taa.txt === reduce.pl bib === id = cord-339976-tg2jkss7 author = Wang, Haibin title = Detection and Monitoring of SARS Coronavirus in the Plasma and Peripheral Blood Lymphocytes of Patients with Severe Acute Respiratory Syndrome date = 2004-07-01 pages = extension = .txt mime = text/plain words = 2579 sentences = 120 flesch = 50 summary = title: Detection and Monitoring of SARS Coronavirus in the Plasma and Peripheral Blood Lymphocytes of Patients with Severe Acute Respiratory Syndrome Reliable and sensitive determination of the SARS CoV load would aid in the early identification of infected individuals, provide guidance for treatment (especially the use of steroid hormones and antiviral agents), and aid in monitoring of a patient's clinical course and outcome. The method could detect the CoV load during the SARS course, as demonstrated in Fig. 1B , representative data from the 44 patients tested. High frequency of point mutations clustered within the adenosine triphosphatebinding region of BCR/ABL in patients with chronic myeloid leukemia or Ph-positive acute lymphoblastic leukemia who develop imatinib (STI571) resistance Serial analysis of the plasma concentration of SARS coronavirus RNA in pediatric patients with severe acute respiratory syndrome Quantitative analysis and prognostic implication of SARS coronavirus RNA in the plasma and serum of patients with severe acute respiratory syndrome cache = ./cache/cord-339976-tg2jkss7.txt txt = ./txt/cord-339976-tg2jkss7.txt === reduce.pl bib === === reduce.pl bib === id = cord-340883-zf8jbhdl author = He, Zhongping title = Using patient-collected clinical samples and sera to detect and quantify the severe acute respiratory syndrome coronavirus (SARS-CoV) date = 2007-03-27 pages = extension = .txt mime = text/plain words = 2892 sentences = 119 flesch = 56 summary = title: Using patient-collected clinical samples and sera to detect and quantify the severe acute respiratory syndrome coronavirus (SARS-CoV) Reverse transcriptase polymerase chain reaction (RT-PCR) was used to detect and quantify SARS-CoV in 934 sera and self-collected throat washes and fecal samples from 271 patients with laboratory-confirmed SARS managed at a single institution. The highest SARS-CoV RT-PCR rates (70.4–86.3%) and viral loads (log(10 )4.5–6.1) were seen in fecal samples collected 2–4 weeks after the onset of clinical illness. The aim of this study was to detect and quantify SARS-CoV using RT-PCR in sera and throat washes and stools self-collected by 271 patients with laboratory confirmed SARS managed at a single institution. The use of patient self-collected throat washings may reduce risks to healthcare workers, although lower respiratory tract samples such as sputum, NPAs or bronchoalveolar lavage fluid are likely to have higher viral loads and offer increased likelihood of SARS-CoV detection by RT-PCR. cache = ./cache/cord-340883-zf8jbhdl.txt txt = ./txt/cord-340883-zf8jbhdl.txt === reduce.pl bib === === reduce.pl bib === id = cord-342383-ckswlo9o author = Pawlowski, C. title = Exploratory analysis of immunization records highlights decreased SARS-CoV-2 rates in individuals with recent non-COVID-19 vaccinations date = 2020-07-28 pages = extension = .txt mime = text/plain words = 5479 sentences = 273 flesch = 51 summary = Furthermore, age, race/ethnicity, and blood group stratified analyses reveal significantly lower SARS-CoV-2 rate among black individuals who have taken the PCV13 vaccine, with relative risk of 0.45 at the 5 year time horizon (n: 653, 95% CI: (0.32, 0.64), p-value: 6.9e-05). Given this study population, we assess the rates of SARS-CoV-2 infection among individuals who did and did not receive one of 18 vaccines in the past 1, 2, and 5 years relative to the date of PCR testing. In Figure 6 , we present the results from the tipping point analysis on the statistically significant associations between vaccination and reduced rates of SARS-CoV-2 infection in the overall study population. For example, for the polio vaccine at the 1 year time horizon, an unobserved confounder with a relative risk of 2.78 which is prevalent in 17.8% of the vaccinated cohort and 0% of the unvaccinated cohort could explain the differences in SARS-CoV-2 infection rates that we observe in the data. cache = ./cache/cord-342383-ckswlo9o.txt txt = ./txt/cord-342383-ckswlo9o.txt === reduce.pl bib === id = cord-340481-i3qrxnpr author = Pozo, Francisco title = Aplicación de los métodos moleculares al diagnóstico y el estudio epidemiológico de las infecciones respiratorias causadas por virus date = 2008-07-31 pages = extension = .txt mime = text/plain words = 9085 sentences = 740 flesch = 48 summary = En comparación con las técnicas de diagnóstico clásicas, como son el cultivo de virus en líneas celulares (CC) o la detección de antígenos mediante ensayos de inmunofluorescencia (IF) u otros métodos, la reacción en cadena de la polimerasa (PCR), en sus múltiples variantes, ha permitido incre-mentar de manera considerable el número de muestras respiratorias en las que se detecta la presencia de alguno de los virus asociados con IRA. La elevada sensibilidad de los ensayos de PCR también comporta algunos inconvenientes para el diagnóstico etiológico de la IRA, como son la detección de virus que se encuentran colonizando la mucosa respiratoria de personas asintomáticas o la detección, a consecuencia de excreción prolongada, del virus en secreciones de pacientes que ya se han recuperado de una infección. cache = ./cache/cord-340481-i3qrxnpr.txt txt = ./txt/cord-340481-i3qrxnpr.txt === reduce.pl bib === id = cord-341141-bgrgzfoo author = Hou, Peili title = Rapid detection of infectious bovine Rhinotracheitis virus using recombinase polymerase amplification assays date = 2017-12-13 pages = extension = .txt mime = text/plain words = 4693 sentences = 234 flesch = 51 summary = In this study, we described the development of a lateral flow dipstrip (LFD) of isothermal recombinase polymerase amplification (RPA) method for rapid detection of IBRV. The assay performance on acute-phase high fever clinical samples collected from cattle with no vaccine against IBRV, which were suspected to be infected with IBRV, was validated by detecting 24 fecal, 36 blood, 38 nasal swab and 8 tissue specimens, and compared with SYBR Green I based real-time PCR. The initial agarose gel result showed that Primer set 4-2F/4-2R/ 4-2LF yielded specific amplification efficiency for the RPA assay, and produced the expected size of the product was 250 base-pairs (Fig. 1a) , while the primers/probe targeting glycoprotein gB of the IBRV genome in this study could not be used to amplify effectively in the initial screen (data not show). cache = ./cache/cord-341141-bgrgzfoo.txt txt = ./txt/cord-341141-bgrgzfoo.txt === reduce.pl bib === id = cord-341434-2xrdv92m author = Nowland, Megan H. title = Biology and Diseases of Rabbits date = 2015-07-10 pages = extension = .txt mime = text/plain words = 31591 sentences = 1921 flesch = 47 summary = Etiology Pasteurella multocida is a Gram-negative nonmotile coccobacillus that causes pasteurellosis, also known as 'snuffles', the primary respiratory disease affecting domestic rabbits (Deeb and DiGiacomo, 2000; Guo et al., 2012) . Research Complications Pasteurellosis can cause considerable economic losses (El Tayeb et al., 2004; Ferreira et al., 2012; Stahel et al., 2009 ) and has the potential to affect different types of research studies using rabbits due to the multisystemic nature of the disease, and the possibility of high morbidity and mortality. piliforme is a pleomorphic, Gramnegative, spore-forming, motile, obligate intracellular rod-shaped bacterium that causes Tyzzer's disease and infects various animals including mice, nonhuman primates, gerbils, rats, rabbits, and others (Allen et al., 1965; Ganaway et al., 1971; Pritt et al., 2010) . Research Complications EPEC infection can cause high morbidity and mortality in laboratory rabbit colonies and can affect studies involving intestinal physiology in rabbits. cache = ./cache/cord-341434-2xrdv92m.txt txt = ./txt/cord-341434-2xrdv92m.txt === reduce.pl bib === id = cord-342344-jjnf4yje author = Mello, C. J. title = Absolute quantification and degradation evaluation of SARS-CoV-2 RNA by droplet digital PCR date = 2020-06-26 pages = extension = .txt mime = text/plain words = 3122 sentences = 190 flesch = 55 summary = Diagnostic assays for the presence of SARS-CoV-2 currently use real-time reverse transcriptase PCR (RT-qPCR) to yield a binary (positive or negative) result based on an amplification cycle threshold (Ct) value 9-12 . Current PCR-based assays can detect the presence of very short SARS-CoV-2 RNA sequences but do not distinguish whether these sequences are derived from longer molecules present in the sample at the time of collection. To address these issues, we explored using droplet digital PCR (ddPCR) 19, 20 to more precisely quantify SARS-CoV-2 RNA in biological samples and evaluate the extent to which positive results reflect larger, intact viral nucleic acids. The results yielded definitive evidence of linkage: although only 822 of the 12,220 droplets (6.7%) were positive for either N1 or N2, 75% of the droplets that were positive for N2 (HEX) were also positive for N1 (FAM) (Fig. 2a, Table 1 ); we estimate (using a formula we previously described 21 , which accounts for chance co-encapsulation) that 71% of the detected RNA sequences were physically linked. cache = ./cache/cord-342344-jjnf4yje.txt txt = ./txt/cord-342344-jjnf4yje.txt === reduce.pl bib === === reduce.pl bib === id = cord-342568-3sj235rm author = Bald-Blume, Niklas title = Development of a molecular assay for the general detection of tospoviruses and the distinction between tospoviral species date = 2017-02-11 pages = extension = .txt mime = text/plain words = 5364 sentences = 277 flesch = 54 summary = In this study a new method for plant virus diagnosis is described using the Luminex xTAG technology to test for tospoviruses in general and for the four species TSWV, WSMoV, INSV and CaCV. Infected, dried plant material of 12 tospoviral isolates from eight different species was obtained from the DSMZ including single isolates of alstroemeria necrotic streak virus (ANSV), CaCV, GRSV, IYSV, TCSV and WSMoV as well as three isolates each of INSV and TSWV. The generic tospovirus primers Tospo_GENs/as (without tags) allowed the detection of all eight tospoviruses and of all three isolates of INSV and TSWV tested in RT-PCR experiments. A molecular assay for the detection of tospoviruses in general and for viruses from the four species belonging to this genus (TSWV, INSV, CaCV and WSMoV), using the Luminex xTAG technology, was successfully developed. cache = ./cache/cord-342568-3sj235rm.txt txt = ./txt/cord-342568-3sj235rm.txt === reduce.pl bib === id = cord-342380-lihz7h1k author = Meguid Kassem, Abdel title = SARS-CoV-2 infection among healthcare workers of a gastroenterological service in a tertiary care facility date = 2020-07-21 pages = extension = .txt mime = text/plain words = 3044 sentences = 164 flesch = 51 summary = BACKGROUND AND STUDY AIMS: Frontlines healthcare workers (HCWs) during the coronavirus disease 2019 (COVID-19) pandemic are at increased risk of infection by SARS-CoV-2, but there are limited data on the prevalence of COVID-19 among HCWs in Egypt. SUBJECTS AND METHODS: Seventy-four HCWs at the gastroenterological service of Al-Manial University Hospital, the main hospital of the largest tertiary university hospitals complex in Egypt (Kasr Al-Ainy Faculty of Medicine, Cairo University) were tested using real-time reverse transcription–polymerase chain reaction (RT-PCR) on nasopharyngeal samples, and rapid serological IgM/IgG tests (RST). This work has been conducted to determine the extent of infection by realtime reverse transcription polymerase chain reaction (RT-PCR) and rapid serological test (RST) for SARS-CoV-2 among frontline HCWs providing gastrointestinal services. Previous studies in developed countries reported variable infection rates in HCWs. In a study on 957 employees in a German university hospital, 52 of them (5.4%) tested positive for SARS-CoV-2 by PCR [13] . cache = ./cache/cord-342380-lihz7h1k.txt txt = ./txt/cord-342380-lihz7h1k.txt === reduce.pl bib === === reduce.pl bib === id = cord-343377-6muareue author = Kidszun, André title = Viral Infections in Neonates with Suspected Late-Onset Bacterial Sepsis—A Prospective Cohort Study date = 2016-05-16 pages = extension = .txt mime = text/plain words = 2356 sentences = 163 flesch = 47 summary = Objective The aim of our study was to evaluate the occurrence of viral infections in infants with suspected late-onset bacterial sepsis in a neonatal intensive care unit. Methods In a prospective study, infants with suspected late-onset bacterial sepsis underwent viral testing alongside routine blood culture sampling. Bennett et al performed a surveillance study of viral respiratory infections in two NICUs. All infants of a gestational age < 33 weeks were tested twice a week using multiplex RT-PCR ELISA. Detection of respiratory viral infections in neonates treated for suspicion of nosocomial bacterial sepsis: a feasibility study Viral respiratory tract infections in the neonatal intensive care unit: the VIRIoN-I study Unrecognized viral respiratory tract infections in premature infants during their birth hospitalization: a prospective surveillance study in two neonatal intensive care units Viral respiratory tract infections in the Neonatal Intensive Care Unit cache = ./cache/cord-343377-6muareue.txt txt = ./txt/cord-343377-6muareue.txt === reduce.pl bib === id = cord-342476-0rupk21u author = van Rijn, Anneloes L. title = The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease date = 2019-10-24 pages = extension = .txt mime = text/plain words = 4036 sentences = 220 flesch = 44 summary = The sensitivity, specificity and predictive values of mNGS were calculated based on 24 PCR positive and 1120 PCR negative target results of 88 samples and the normalized read counts (Table 5 ). The following markers were tested for potential associations with clinical severity of exacerbation (exacerbation severity, self-reported exacerbation severity), length of exacerbation and a decrease/increase in FEV 1 (control visit compared to baseline): mNGS pathogen positive versus negative exacerbation (qPCR targets), the number of normalized reads (log, cutoff of �5normalized reads) for the different target viruses (species level). The Shannon diversity scores for bacteriophages (normalized reads, cut-off of �5normalized reads) were comparable for COPD exacerbations of viral aetiology in PCR positive versus negative patients (Fig 5) . In this study, the respiratory virome in patients with COPD exacerbations was analysed with both mNGS and qPCR, and combined with clinical data. cache = ./cache/cord-342476-0rupk21u.txt txt = ./txt/cord-342476-0rupk21u.txt === reduce.pl bib === id = cord-344745-sgkq1l93 author = Selim, Karim title = Molecular characterization of infectious bronchitis viruses isolated from broiler and layer chicken farms in Egypt during 2012 date = 2013-11-18 pages = extension = .txt mime = text/plain words = 2757 sentences = 172 flesch = 56 summary = title: Molecular characterization of infectious bronchitis viruses isolated from broiler and layer chicken farms in Egypt during 2012 The aim of this study aimed to survey the Egyptian chicken field for infectious bronchitis virus and study the genomic differentiation between isolated field samples seeking the new variant strain emerged in the Egyptian field. For virus isolation, the supernatants of IBV-positive selected 13 samples determined by RT-PCR were inoculated into five specific pathogen free embryonated chicken eggs (KoumOshiem SPF chicken farm, Fayoum, Egypt) 10-day-old for each sample. The genetic analysis of 100 amino acids sequence from position 263-362 of SP1 gene for the selected 13 Egyptian viruses was done and the hypervariable region of SP1 gene showed multiple mutations as shown in Table 4 in comparison with variant-2 strain. S1 gene sequence analysis of a nephro-pathogenic strain of avian infectious bronchitis virus in Egypt cache = ./cache/cord-344745-sgkq1l93.txt txt = ./txt/cord-344745-sgkq1l93.txt === reduce.pl bib === id = cord-344782-ond1ziu5 author = Zhang, Jing title = Identification of a novel nidovirus as a potential cause of large scale mortalities in the endangered Bellinger River snapping turtle (Myuchelys georgesi) date = 2018-10-24 pages = extension = .txt mime = text/plain words = 6003 sentences = 280 flesch = 49 summary = Nucleic acid sequencing of the virus isolate has identified the entire genome and indicates that this is a novel nidovirus that has a low level of nucleotide similarity to recognised nidoviruses. Following the detection of the novel virus, in November 2015 (about 6 months after the cessation of the outbreak) an intensive survey of the parts of the river where affected turtles had been detected [2] was undertaken by groups of biologists and ecologists and samples collected from a wide range of aquatic species and some terrestrial animals (n = 360) to establish the size of the remaining population and whether any other animals were carrying this virus. BRV, as a novel nidovirus, was isolated from tissues of diseased animals, very high levels of viral RNA were detected in tissues with marked pathological changes and in situ hybridisation assays demonstrated the presence of specific viral RNA in lesions in kidneys and eye tissue-two of the main affected organs. cache = ./cache/cord-344782-ond1ziu5.txt txt = ./txt/cord-344782-ond1ziu5.txt === reduce.pl bib === id = cord-344751-i4qnrtjq author = Van Praet, Jens T. title = Comparison of four commercial SARS-CoV-2 IgG immuno-assays in RT-PCR negative patients with suspect CT findings date = 2020-09-10 pages = extension = .txt mime = text/plain words = 2399 sentences = 119 flesch = 49 summary = Clinical specificity for Covid-19 of some N protein-based immuno-assays was suboptimal, as positive results were observed in control patients with recent common human coronavirus, influenza B and adenovirus infections. To evaluate the specificity of the immuno-assays, we used a set of serum samples from control patients with recent respiratory viral or atypical bacterial infections. To this end, we tested for cross-reactivity with sera of patients with other respiratory viral or atypical bacterial infections, including common coronavirus infections, since these may present with clinical and radiological findings similar to Covid-19. Our study focused on the clinical sensitivity and specificity of four commercial immuno-assays for anti-SARS-COV-2 IgG in the subset of patients presenting with negative RT-PCR and suspect CT findings. In summary, we found good clinical sensitivity of anti-SARS-Cov-2 IgG immunoassays for Covid-19 in the subset of patients with negative RT-PCR 14 days after onset of symptoms. cache = ./cache/cord-344751-i4qnrtjq.txt txt = ./txt/cord-344751-i4qnrtjq.txt === reduce.pl bib === id = cord-343441-z849jvq5 author = Li, Yan title = Simultaneous detection of hemagglutinin and neuraminidase genes of novel influenza A (H7N9) by duplex real-time reverse transcription polymerase chain reaction date = 2013-09-01 pages = extension = .txt mime = text/plain words = 2236 sentences = 112 flesch = 54 summary = In this study, a duplex real-time reverse transcription polymerase chain reaction (rRT-PCR) assay was developed for the simultaneous detection of hemagglutinin (HA) and neuraminidase (NA) genes of H7N9 influenza viruses. In this study, a duplex real-time reverse transcription polymerase chain reaction (rRT-PCR) assay was developed for the simultaneous detection of hemagglutinin (HA) and neuraminidase (NA) genes of H7N9 influenza viruses. The analytic sensitivity of the duplex TaqMan rRT-PCR assay was compared with the WHO TaqMan assay and a commercial single H7N9 rRT-PCR kit (bioPerfectus technologies, Taizhou, China) with a 10-fold dilution series of a nasopharyngeal aspirate (NPA) from a patient infected with the H7N9 virus (approximately 4.8 × 10 6 copies of the viral genome/mL). To determine the actual detection limit (number of copies per reaction) of the duplex TaqMan rRT-PCR assay, in vitro RNA transcripts of HA and NA genes from the H7N9 virus were prepared with T7 RNA polymerase (TaKaRa Biotechnology Co. Ltd., Dalian, China) according to the manufacturer's instructions using influenza A/Nanjing/1/2013 (H7N9) RNA as a template. cache = ./cache/cord-343441-z849jvq5.txt txt = ./txt/cord-343441-z849jvq5.txt === reduce.pl bib === id = cord-344889-1y4ieamp author = Cameron, Robert J. title = Virus infection in exacerbations of chronic obstructive pulmonary disease requiring ventilation date = 2006-05-24 pages = extension = .txt mime = text/plain words = 4309 sentences = 242 flesch = 46 summary = OBJECTIVES: We aimed to characterise and quantify the incidence of common infectious agents in acute exacerbations of chronic obstructive pulmonary disease (COPD) requiring ventilation, with a focus on respiratory viruses. Abstract Objectives: We aimed to characterise and quantify the incidence of common infectious agents in acute exacerbations of chronic obstructive pulmonary disease (COPD) requiring ventilation, with a focus on respiratory viruses. Of these, influenza types A and B (Inf A, B), parainfluenza types 1, 2 and 3 (Para 1, 2, 3), rhinovirus (RV), adenovirus (AV), respiratory syncytial virus (RSV), coronavirus (CoV) [11, 12] and, less commonly, human metapneumovirus (hMPV) [13] , and enterovirus (EV) [14, 15] have been shown to play significant roles in airway infections. A probable virus pathogen was found in 46 cases (43%) and a probable bacterial aetiology was found in 25 cases (23%) in this study of ventilated COPD exacerbation patients. cache = ./cache/cord-344889-1y4ieamp.txt txt = ./txt/cord-344889-1y4ieamp.txt === reduce.pl bib === id = cord-345211-4ivqlsgt author = Murdoch, David R. title = How recent advances in molecular tests could impact the diagnosis of pneumonia date = 2016-03-07 pages = extension = .txt mime = text/plain words = 5994 sentences = 295 flesch = 35 summary = Guidelines for the management of community-acquired pneumonia in children are even more restrictive, again recommending that tests should mainly be used on patients with severe disease, with a focus on blood cultures and detection of respiratory viruses [11, 12] . While not exactly new (polymerase chain reaction (PCR) assays for respiratory pathogens have been around for over 20 years), the widespread adoption of nucleic acid detection tests (NATs) by diagnostic laboratories has been relatively slow. The NATs that are most widely used in diagnostic laboratories are those that detect potential pneumonia pathogens that are not part of the normal flora, namely respiratory viruses and selected non-colonizing bacteria. Quantitative multiplex PCR has been used to determine the etiology of community-acquired pneumonia in adults using cutoffs developed for interpretation of culture results from lower respiratory tract specimens [85, 86] . cache = ./cache/cord-345211-4ivqlsgt.txt txt = ./txt/cord-345211-4ivqlsgt.txt === reduce.pl bib === id = cord-343860-2j7nbryv author = Thiberville, S.D. title = The viral etiology of an influenza‐like illness during the 2009 pandemic date = 2012-05-14 pages = extension = .txt mime = text/plain words = 3729 sentences = 191 flesch = 54 summary = The identification of the respiratory viruses that are responsible for influenza-like illness has been reported in many countries, and the percentage of positive swabs for at least one virus ranges from 32% to 65% [Bellei et al., 2008; Laguna-Torres et al., 2009; Ren et al., 2009; Buecher et al., 2010; Renois et al., 2010; Razanajatovo et al., 2011] . Although it is possible that some EVs remained undetected, five samples were tested positive for EVs (1.7% of tested patients), which is consistent with previous studies in patients with acute respiratory infection or influenza-like illness [Bellei et al., 2008; Laguna-Torres et al., 2009; Ren et al., 2009] . Several studies have reported the results from respiratory virus testing using respiratory samples that were obtained from patients with influenza-like illness or acute respiratory infection throughout the world and during different times. cache = ./cache/cord-343860-2j7nbryv.txt txt = ./txt/cord-343860-2j7nbryv.txt === reduce.pl bib === id = cord-345312-i7soyabu author = Wabe, Nasir title = The impact of rapid molecular diagnostic testing for respiratory viruses on outcomes for emergency department patients date = 2019-03-05 pages = extension = .txt mime = text/plain words = 2882 sentences = 147 flesch = 46 summary = OBJECTIVE: To determine whether rapid polymerase chain reaction (PCR) testing for influenza and respiratory syncytial viruses (RSV) in emergency departments (EDs) is associated with better patient and laboratory outcomes than standard multiplex PCR testing. Rapid PCR tests were expected to facilitate timely and appropriate initiation of treatment, improve outbreak prevention and infection control measures, and expedite the assessment of patients in EDs. In this study, we analysed routinely collected data to determine whether rapid PCR testing for influenza and RSV infections in EDs is associated with improved patient and laboratory outcomes. Other studies have also reported that hospital admission numbers were significantly lower when rapid influenza virus testing was used in EDs. An analysis of outcomes for more than 300 adults at a tertiary care centre in New York found that early diagnosis of respiratory infections was associated with significantly fewer hospitalisations of influenza-positive patients. cache = ./cache/cord-345312-i7soyabu.txt txt = ./txt/cord-345312-i7soyabu.txt === reduce.pl bib === id = cord-343784-zgvxl4h3 author = Cho, Chi Hyun title = Evaluation of the AdvanSure™ real-time RT-PCR compared with culture and Seeplex RV15 for simultaneous detection of respiratory viruses date = 2014-05-31 pages = extension = .txt mime = text/plain words = 3707 sentences = 204 flesch = 51 summary = Several studies have demonstrated the advantages of multiplex PCR assays such as xTAG RVP, RVP fast (Luminex Molecular Diagnostics, Toronto, ON, Canada), Resplex II (Qiagen, Mississauga, ON, Canada), FilmArray® Respiratory panel (Idaho Technology Inc., Salt Lake City, UT, USA), and Seeplex RV assays (Seegene, Seoul, Korea), which are used routinely for the detection of respiratory viral infection (Bibby et al., 2011; Couturier et al., 2013; Gharabaghi et al., 2011; Kim et al., 2013; Zhang et al., 2012) . In the previous study evaluating Seeplex RV12 detection kit (Seegene, Rockville, MD, USA), viral culture, RV12, and real-time PCR detected 8, 6, and 11 of 11 influenza B-positive specimens, respectively (Bruijnesteijn van Coppenraet et al., 2010) . Simultaneous detection of influenza A, B, and C viruses, respiratory syncytial virus, and adenoviruses in clinical samples by multiplex reverse transcription nested-PCR assay Evaluation of a multiplex real-time PCR assay for the detection of respiratory viruses in clinical specimens cache = ./cache/cord-343784-zgvxl4h3.txt txt = ./txt/cord-343784-zgvxl4h3.txt === reduce.pl bib === === reduce.pl bib === id = cord-344749-omzhhr0k author = Kaya, Sariye Irem title = Electrochemical virus detections with nanobiosensors date = 2020-02-14 pages = extension = .txt mime = text/plain words = 8402 sentences = 508 flesch = 37 summary = Cell culture-based virus isolation has been accepted as a "gold standard" in the detection and identification of viruses and is the technique by which all other test methods have been compared [35] . A novel method for dengue virus detection and antibody screening using a graphene-polymer based electrochemical biosensor Chitosan-carbon nanofiber modified single-use graphite electrodes developed for electrochemical detection of DNA hybridization related to hepatitis B virus A sensitive electrochemical biosensor for specific DNA sequence detection based on flower-like VS2, graphene and Au nanoparticles signal amplification Electrochemical DNA biosensor based on a tetrahedral nanostructure probe for the detection of avian influenza A (H7N9) virus Electrochemical DNA biosensor based on gold nanorods for detecting hepatitis B virus Electrochemical-DNA biosensor development based on a modified carbon electrode with gold nanoparticles for influenza a (H1N1) detection: effect of spacer Magnetic nanoparticle-based immunosensor for electrochemical detection of hepatitis B surface antigen cache = ./cache/cord-344749-omzhhr0k.txt txt = ./txt/cord-344749-omzhhr0k.txt === reduce.pl bib === id = cord-345475-ttrcmtu4 author = de Oliveira, Luisa Abruzzi title = Reference Genes for the Normalization of Gene Expression in Eucalyptus Species date = 2011-12-24 pages = extension = .txt mime = text/plain words = 9744 sentences = 595 flesch = 54 summary = Given the increasing interest in the functional genomics of Eucalyptus and the need for validated reference genes for a broader set of species and experimental conditions, we sought to identify the most stably expressed genes in a set of 21,432 genes assayed by microarray developed to compare stem vascular (xylem) and leaf tissues of E. According to the NormFinder analysis of gene expression in leaves, xylem tissues and among species, the stability values of the 15 genes studied were <0.138, with error bars no greater than 0.044 ( Fig. 3C ; Table 3 ). When we analyzed the gene expression in all tissues/organs and species, the stability value was in the range between 0.017 and 0.106, proving again that all genes elected are good references for RT-qPCR studies in Eucalyptus. By RT-qPCR, the expression stability of eight of the 50 best candidate genes selected by SAM and SDMA was addressed in different organs (leaves and flowers) and vascular tissues (xylem) derived from six species of Eucalyptus. cache = ./cache/cord-345475-ttrcmtu4.txt txt = ./txt/cord-345475-ttrcmtu4.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-346054-k84rcpav author = Niespodziana, Katarzyna title = PreDicta chip-based high resolution diagnosis of rhinovirus-induced wheeze date = 2018-06-18 pages = extension = .txt mime = text/plain words = 7405 sentences = 349 flesch = 47 summary = Here, we develop a chip containing 130 different micro-arrayed RV proteins and peptides and demonstrate in a cohort of 120 pre-school children, most of whom had been hospitalized due to acute wheeze, that it is possible to determine the culprit RV species with a minute blood sample by serology. The analysis of IgG reactivity to structural and non-structural proteins and to recombinant fragments and synthetic peptides spanning VP1, VP2, and VP3 from RV89 is shown in Supplementary Fig. 2a for all 120 children and in Supplementary Fig. 2b for those children (n = 41) who had shown increases of RV89-specific antibody responses in follow-up serum samples taken after recovery. Based on our previous observations that antibody increases specific for the N-terminal portion of VP1 can be detected in serum samples obtained from subjects after RV infection 36 , the PreDicta chip was equipped with a VP1 peptide set which should allow detecting species-specific immune responses at high resolution ( Fig. 1 ). cache = ./cache/cord-346054-k84rcpav.txt txt = ./txt/cord-346054-k84rcpav.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-346467-a0r4xh1c author = Cornelissen, Jan B. W. J. title = Mycoplasma detection by triplex real-time PCR in bronchoalveolar lavage fluid from bovine respiratory disease complex cases date = 2017-04-08 pages = extension = .txt mime = text/plain words = 4082 sentences = 188 flesch = 50 summary = title: Mycoplasma detection by triplex real-time PCR in bronchoalveolar lavage fluid from bovine respiratory disease complex cases BACKGROUND: In this study we evaluated the RespoCheck Mycoplasma triplex real-time PCR for the detection in bronchoalveolar lavage fluid (BALF) of Mycoplasma (M.) dispar, M. RESULTS: The analytical sensitivity of the RespoCheck triplex real-time PCR was, as determined by spiking experiments of the Mycoplasma strains in Phosphate Buffered Saline, 300 colony forming units (cfu)/mL for M. To enable testing of testing for BRD associated pathogens in a routine setting, real-time PCRs for detection of viral, bacterial and mycoplasma pathogens in bronchoalveolar lavage fluid (BALF) of calves have been set up by the Central Veterinary Institute (Lelystad, The Netherlands) under the name RespoCheck. In this study we used the highly conserved 16S rRNA sequence to set up the RespoCheck Mycoplasma triplex real-time PCR assay for the specific detection of M. cache = ./cache/cord-346467-a0r4xh1c.txt txt = ./txt/cord-346467-a0r4xh1c.txt === reduce.pl bib === === reduce.pl bib === id = cord-346436-p61mpc6t author = Onodera, Kenji title = Selection for 3′-End Triplets for Polymerase Chain Reaction Primers date = 2007 pages = extension = .txt mime = text/plain words = 3709 sentences = 225 flesch = 72 summary = Over 2000 primer sequences from successful PCR experiments used with varieties of templates and conditions were analyzed for finding frequencies of the 3′-end triplets. This chapter discusses a trend in 3′-end triplet frequencies in primers used in successful PCR experiments and proposes requirements for the 3′-end of a primer. From the VirOligo database, 2137 PCR primer sequences were retrieved for detailed analysis of the 3 -end triplets of successful PCR primers (8; see Note 1). The analysis of the 3 -end triplets of primers (8; see Fig. 5 and Table 1) showed all 64 types were used in successful PCR experiments from the VirOligo database. 3. When primers are obtained by a primer design program, the user needs to note that some primer search settings such as 3 -end "GC clamp" interfere with the 3 -end triplet selection. cache = ./cache/cord-346436-p61mpc6t.txt txt = ./txt/cord-346436-p61mpc6t.txt === reduce.pl bib === id = cord-346308-9h2fk9qt author = Kaur, Rajwinder title = Microbiology of hospital wastewater date = 2020-05-01 pages = extension = .txt mime = text/plain words = 14673 sentences = 648 flesch = 34 summary = The study of hospital wastewater (HWW) microbiology is important to understand the pollution load, growth of particular pathogenic microbes, shift and drift in microbial community, development and spread of antibiotic resistance in microbes, and subsequent change in treatment efficiencies. Within past years, pieces of evidence have shown mobilization of these resistance genes from the environment into pathogenic bacteria causing health risks to humans and animals and also, demonstrating a link between environmental and clinical resistance [123] . The HWW has been reported to have two overexpressed β-lactam-resistance genes (bla GES and bla OXA ) as compared with the water collected from other aquatic bodies, which could be correlated with antibiotic usage over the time in hospitals and discharge of the residues of antibiotics in the wastewater [176] . Urban wastewater treatment plants as hotspots for antibiotic resistant bacteria and genes spread into the environment: a review cache = ./cache/cord-346308-9h2fk9qt.txt txt = ./txt/cord-346308-9h2fk9qt.txt === reduce.pl bib === id = cord-346574-u28y1ttw author = Chen, Keyan title = Development and evaluation of an immunochromatographic strip for rapid detection of porcine hemagglutinating encephalomyelitis virus date = 2012-08-24 pages = extension = .txt mime = text/plain words = 5509 sentences = 277 flesch = 50 summary = At present, various laboratory methods are available for the detection and surveillance of PHE-CoV, including virus isolation [1] , hemagglutination/hemagglutination inhibition (HA/HI) tests [13] , immunohistochemistry (IHC) assays [10] , and molecular tools such as nestedpolymerase chain reaction (nested PCR) and reverse transcriptase-polymerase chain reaction (RT-PCR) that enable detection of specific CoV RNA sequences from infected tissues [14, 15] . (1) (2) (3) In this study, an immunochromatographic strip with high sensitivity and specificity was developed for the detection of PHE-CoV, combining monoclonal antibody (MAb) and colloidal gold immunochromatography (GICA), and the resulting product is suitable for the surveillance of PHE-CoV. Thus, a lot of brain tissue samples were collected from deceased piglets with suspected PHE-CoV infection, and using RT-PCR and ELISA as reference test, the relative specificity and sensitivity of the immunochromatographic strip were determined to be 100% and 97.78%, respectively. cache = ./cache/cord-346574-u28y1ttw.txt txt = ./txt/cord-346574-u28y1ttw.txt === reduce.pl bib === id = cord-346859-r1v6ir8u author = Mallett, Sue title = At what times during infection is SARS-CoV-2 detectable and no longer detectable using RT-PCR-based tests? A systematic review of individual participant data date = 2020-11-04 pages = extension = .txt mime = text/plain words = 5020 sentences = 277 flesch = 52 summary = BACKGROUND: Tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral ribonucleic acid (RNA) using reverse transcription polymerase chain reaction (RT-PCR) are pivotal to detecting current coronavirus disease (COVID-19) and duration of detectable virus indicating potential for infectivity. METHODS: We conducted an individual participant data (IPD) systematic review of longitudinal studies of RT-PCR test results in symptomatic SARS-CoV-2. Because testing is pivotal to management and containment of COVID-19, we performed an individual participant data (IPD) systematic review of emerging evidence about test accuracy by anatomical sampling site to inform optimal sampling strategies for SARS-CoV-2. Previous studies have established that in COVID-19 infection, viral loads typically peak just before symptoms and at symptom onset [4] and estimated false negative test results over time since exposure from upper respiratory tract samples [2] . • Participants included will be biased to over-represent people with detectable virus in respiratory tract sampling sites and at times frequently used for testing (post symptom onset or at admission to hospital). cache = ./cache/cord-346859-r1v6ir8u.txt txt = ./txt/cord-346859-r1v6ir8u.txt === reduce.pl bib === id = cord-346325-grt67p73 author = Reilev, M. title = Characteristics and predictors of hospitalization and death in the first 9,519 cases with a positive RT-PCR test for SARS-CoV-2 in Denmark: A nationwide cohort date = 2020-05-26 pages = extension = .txt mime = text/plain words = 4655 sentences = 258 flesch = 48 summary = Design, Setting, and Participants Nationwide population-based cohort of all 228.677 consecutive Danish individuals tested (positive or negative) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA from the identification of the first COVID-19 case on February 27th, 2020 until April 30th, 2020. In this population-based study of a Danish COVID-19 cohort capturing all individuals with a positive PCR test for SARS-CoV-2 in Denmark, we provide nationwide data on clinical characteristics and predictors of hospitalization and death for all SARS-CoV-2 PCR-positive cases identified from February 27 th , 2020 to April 30 th , 2020. In this nationwide cohort of SARS-CoV-2 PCR positive cases and test-negative individuals from the general population in Denmark, we found that older age (e.g., >70 years), male sex, and number of comorbidities were risk factors for hospitalization and death. In this first nationwide population-based study, increasing age, sex, and number and type of comorbidities were closely associated with hospitalization requirement and death in SARS-CoV-2 PCR positive cases. cache = ./cache/cord-346325-grt67p73.txt txt = ./txt/cord-346325-grt67p73.txt === reduce.pl bib === id = cord-346989-604gho1u author = Chen-Harris, Haiyin title = Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs date = 2013-02-12 pages = extension = .txt mime = text/plain words = 7125 sentences = 334 flesch = 49 summary = RESULTS: We demonstrate that overlapping read pairs (ORP) -generated by combining short fragment sequencing libraries and longer sequencing reads -significantly reduce sequencing error rates and improve rare variant detection accuracy. We demonstrate the novel use of mismatch rates in the overlapping read pairs (ORP) to provide an unbiased assessment of the sequencer-derived quality scores when selecting a read filtering threshold, as well as to estimate position-dependent sequencing errors without relying on a clonal control. ORPs reduce error rates and provide benchmarks for quality scores For all five samples, 3 natural viral and 2 plasmid controls, Illumina paired-end sequencing was carried out using relatively short sequencing fragment libraries combined with relatively long reads (112 bp) to generate overlapping read pairs (ORP). cache = ./cache/cord-346989-604gho1u.txt txt = ./txt/cord-346989-604gho1u.txt === reduce.pl bib === id = cord-346958-9eeqlkoq author = Caruso, Damiano title = Chest CT Features of COVID-19 in Rome, Italy date = 2020-04-03 pages = extension = .txt mime = text/plain words = 1818 sentences = 123 flesch = 51 summary = In the subgroup of RT-PCR-positive and CT-positive patients, ground-glass opacities (GGO) were present in 58/58 (100%), multilobe and posterior involvement were both present in 54/58 (93%), bilateral pneumonia in 53/58 (91%), and subsegmental vessel enlargement (> 3 mm) in 52/58 (89%) of study participants. As reported by Ai (5) , in a cohort of 1014 patients in Wuhan China, the sensitivity, specificity and accuracy of chest CT in the detection of COVID-19 pneumonia were 97%, 25% and 68% respectively using RT-PCR results as reference standard. The aim of this study was to investigate chest CT features of patients with COVID-19 in Rome, Italy, and to compare the diagnostic performance of chest CT with RT-PCR. To understand the CT features of patients with COVID-19 pneumonia, a sub-analysis was performed considering only study participants with positive RT-PCR testing and chest CT findings. cache = ./cache/cord-346958-9eeqlkoq.txt txt = ./txt/cord-346958-9eeqlkoq.txt === reduce.pl bib === id = cord-347443-0evqo01m author = Litwin, Christine M. title = Seasonality and prevalence of respiratory pathogens detected by multiplex PCR at a tertiary care medical center date = 2013-07-24 pages = extension = .txt mime = text/plain words = 3991 sentences = 218 flesch = 50 summary = Seasonality has been reported for many viruses, including influenza virus, respiratory syncytial virus (RSV), and the recently described human metapneumovirus (hMPV). Major causes of bronchiolitis and lower respiratory tract illnesses in children include respiratory syncytial virus (RSV), parainfluenza viruses, influenza virus, and human metapneumovirus (hMPV). The organism/viruses detected by the FilmArray included adenovirus, influenza A virus (FluA), influenza B virus (FluB), parainfluenza virus 1 (Para 1), parainfluenza virus 2 (Para 2), parainfluenza virus 3 (Para 3), parainfluenza virus 4 (Para 4), respiratory syncytial virus (RSV), coronavirus 229E (CoronaV 229E), CoronaV NL63, CoronaV HKU1, CoronaV OC43, human metapneumovirus (hMPV), Bordetella pertussis, Chlamydophila pneumoniae and Mycoplasma pneumoniae. In our study, 939 specimens were analyzed over the course of a year using a respiratory pathogen multiplex PCR that yielded a positivity rate of 65 % with multiple analytes detected in 12 % of specimens, especially in children. RSV and hMPV PCR-positive cases were statistically much more likely than Rhino/Entero PCR-positive infections to initially present with pneumonia or bronchiolitis in our study. cache = ./cache/cord-347443-0evqo01m.txt txt = ./txt/cord-347443-0evqo01m.txt === reduce.pl bib === id = cord-347462-yz67t10x author = Chan, Tak Yeung title = A Comparative Study of Clinical Features and Outcomes in Young and Older Adults with Severe Acute Respiratory Syndrome date = 2004-07-19 pages = extension = .txt mime = text/plain words = 3590 sentences = 214 flesch = 54 summary = title: A Comparative Study of Clinical Features and Outcomes in Young and Older Adults with Severe Acute Respiratory Syndrome Objectives: To determine the clinical presentation, findings, and outcomes of older adults (> 60) with severe acute respiratory syndrome (SARS) and compare these with a control group of younger patients (≤60). A retrospective study was undertaken in the department of medicine and geriatrics of the hospital to evaluate the clinical course of young and elderly SARS patients. Single or paired serum samples were tested for SARS-CoV antibody in 96% (50/52) of young and 76% (19/25) of older patients. Because the proportion of patients with positive RT-PCR in stool samples was similar in two groups, fewer older patients with diarrhea probably represents a generalized paucity of symptoms rather than a different site of involvement by SARS-CoV. In the current study, similar proportions of young and older patients with SARS had RT-PCR performed, and comparable positivity rates were achieved. cache = ./cache/cord-347462-yz67t10x.txt txt = ./txt/cord-347462-yz67t10x.txt === reduce.pl bib === id = cord-348914-6wzqitun author = Ahouach, B. title = Cutaneous lesions in a patient with COVID‐19: are they related? date = 2020-04-30 pages = extension = .txt mime = text/plain words = 315 sentences = 33 flesch = 62 summary = key: cord-348914-6wzqitun authors: Ahouach, B.; Harant, S.; Ullmer, A.; Martres, P.; Bégon, E.; Blum, L.; Tess, O.; Bachmeyer, C. cord_uid: 6wzqitun A previously healthy 57‐year‐old woman presented with fever (39 °C) lasting for 4 days, and dry cough and rash appeared 2 days before. Diffuse fixed erythematous blanching maculopapular lesions were present, asymptomatic over the limbs and trunk, with burning sensation over the palms (a, b). Thorax computed tomography scan was typical of COVID‐19; nasopharyngeal swab polymerase chain reaction (PCR) confirmed SARS‐CoV‐2. maculopapular lesions were present, asymptomatic over the limbs and trunk, with burning sensation over the palms (a, b). Thorax computed tomography scan was typical of COVID-19; nasopharyngeal swab polymerase chain reaction (PCR) confirmed SARS-CoV-2. PCR on whole-skin biopsy specimen was negative for SARS-CoV-2. Fever and rash resolved within 9 days, dry cough within 2 weeks. Urticarial and chilblain-like lesions have been reported in patients with COVID-19, but other phenotypes could be observed. cache = ./cache/cord-348914-6wzqitun.txt txt = ./txt/cord-348914-6wzqitun.txt === reduce.pl bib === id = cord-348209-rkkhv4mw author = Noerz, Dominik title = Clinical evaluation of a SARS-CoV-2 RT-PCR assay on a fully automated system for rapid on-demand testing in the hospital setting date = 2020-04-11 pages = extension = .txt mime = text/plain words = 1643 sentences = 125 flesch = 61 summary = title: Clinical evaluation of a SARS-CoV-2 RT-PCR assay on a fully automated system for rapid on-demand testing in the hospital setting In this study we evaluated a SARS-CoV-2 LDT for the NeuMoDx 96 system, a fully automated (sample to result) RT-PCR platform offering random-access capabilities and good clinical performance for SARS-CoV-2 testing. In this study we evaluated a SARS-CoV-2 LDT for the NeuMoDx 96 30 system, a fully automated device performing extraction and real-time PCR. Due to its random-access workflow concept and rapid time-to-39 result of about 80 minutes, the device is very well suited for providing fast-tracked SARS-CoV-2 40 diagnostics for urgent clinical samples in the hospital setting. For the assay presented in this study, we used a fully automated random-access platform for molecular 56 diagnostics, handling everything from extraction, amplification, signal detection to reporting of results 57 (10). Evaluation of a quantitative RT-PCR assay for 180 the detection of the emerging coronavirus SARS-CoV-2 using a high throughput system cache = ./cache/cord-348209-rkkhv4mw.txt txt = ./txt/cord-348209-rkkhv4mw.txt === reduce.pl bib === id = cord-349775-zwslhjju author = Brittain-Long, Robin title = Access to a polymerase chain reaction assay method targeting 13 respiratory viruses can reduce antibiotics: a randomised, controlled trial date = 2011-04-26 pages = extension = .txt mime = text/plain words = 4612 sentences = 218 flesch = 45 summary = The objective of this study was to evaluate whether access to a multiplex polymerase chain reaction (PCR) assay panel for etiologic diagnosis of acute respiratory tract infections (ARTIs) would have an impact on antibiotic prescription rate in primary care clinical settings. Acute respiratory tract infections (ARTIs) represent a major global health burden [1] , and viruses cause a large proportion of ARTIs. Distinguishing bacterial ARTIs that require antibiotic treatment from viral ARTIs not needing an antibiotic prescription can be difficult on clinical grounds alone and causes unnecessary use of antibiotics, with the highest rates occurring in the primary care setting [2, 3] . The present study was designed to evaluate whether access to a multiplex RT-PCR method targeting thirteen viruses would have an impact on antibiotic prescription rates for ARTI in a primary care setting. cache = ./cache/cord-349775-zwslhjju.txt txt = ./txt/cord-349775-zwslhjju.txt === reduce.pl bib === === reduce.pl bib === id = cord-349562-ivu632j2 author = Hernes, S. S. title = Swabbing for respiratory viral infections in older patients: a comparison of rayon and nylon flocked swabs date = 2010-09-18 pages = extension = .txt mime = text/plain words = 3364 sentences = 185 flesch = 55 summary = The purpose of this study was to compare the sampling efficacy of rayon swabs and nylon flocked swabs, and of oropharyngeal and nasopharyngeal specimens for the detection of respiratory viruses in elderly patients. Regardless of the sampling site, a calculated 4.8 times higher viral load (95% confidence interval [CI] 1.3–17, p = 0.017) was obtained using the nylon flocked swabs as compared to the rayon swabs. Samples for the diagnosis of a respiratory viral infection can be obtained by swabbing the oropharynx, the nasal cavity, the nasopharynx or alternatively, by nasopharyngeal aspiration (NPA) or nasopharyngeal washings (NPW). The aim of this study was to compare the respective efficacies of rayon swabs and nylon flocked swabs in providing material for direct respiratory virus detection by real-time PCR in adults above 60 years of age. Using monoplex (RSV and human metapneumovirus) or multiplex (influenza A/B, adenovirus/internal control and parainfluenza virus 1-4) PCR methods, the specimens were examined for, in total, nine different respiratory viruses (Table 2) . cache = ./cache/cord-349562-ivu632j2.txt txt = ./txt/cord-349562-ivu632j2.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-349070-bqv03u2e author = Jiang, Shih Sheng title = Sensitive and Quantitative Detection of Severe Acute Respiratory Syndrome Coronavirus Infection by Real-Time Nested Polymerase Chain Reaction date = 2004-01-15 pages = extension = .txt mime = text/plain words = 2465 sentences = 110 flesch = 51 summary = title: Sensitive and Quantitative Detection of Severe Acute Respiratory Syndrome Coronavirus Infection by Real-Time Nested Polymerase Chain Reaction In most of the cases, we and others have found that the single-step real time RT-PCR methods (as suggested by the World Health Organization [WHO] ; available at http://www.who.int/csr/sars/diagnostic tests/en/) could specifically detect SARS-CoV but were unable to proficiently detect !10 copies of virus per test, suggesting that the conventional RT-PCR assay may actually yield falsenegative results. In contrast, the second-round amplification by nested real-time PCR proficiently generated a signal of SARS-CoV DNA without apparent background, compared with no detectable signal for the negative control samples ( figure 1A ). After 25 cycles of first-round amplification and 25 cycles of nested PCR amplification, our assay could detect a theoretical single copy of extracted viral RNA (figure 1A), suggesting its superior sensitivity for detection of SARS-CoV. cache = ./cache/cord-349070-bqv03u2e.txt txt = ./txt/cord-349070-bqv03u2e.txt === reduce.pl bib === id = cord-349745-zlhu1jit author = Konrad, Regina title = Rapid establishment of laboratory diagnostics for the novel coronavirus SARS-CoV-2 in Bavaria, Germany, February 2020 date = 2020-03-05 pages = extension = .txt mime = text/plain words = 2417 sentences = 137 flesch = 55 summary = The need for timely establishment of diagnostic assays arose when Germany was confronted with the first travel-associated outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Europe. We found that the SARS-CoV E gene screening assay with the QuantiTect Virus +Rox Vial kit showed moderate to high amounts of unspecific signals in late cycles in 61% (451/743) of the tested patient samples and also of negative extraction and non-template controls (Table, Figure 2 ), which complicated the evaluation of the qPCR result. The Public Health Microbiology Laboratory in Bavaria was confronted with SARS-CoV-2-related events very early: once the assays and control materials arrived and the PCR assays were performed for the first time, a large contact investigation around the first German COVID-19 patient (data not shown) was immediately started, with so far more than 700 samples. cache = ./cache/cord-349745-zlhu1jit.txt txt = ./txt/cord-349745-zlhu1jit.txt === reduce.pl bib === === reduce.pl bib === id = cord-349838-p6vfzbla author = Algwaiz, Ghada title = Real-world issues and potential solutions in HCT during the COVID-19 pandemic: Perspectives from the WBMT and the CIBMTR's Health Services and International Studies Committee date = 2020-07-24 pages = extension = .txt mime = text/plain words = 4060 sentences = 229 flesch = 44 summary = Realizing the challenges as a result of this pandemic affecting the daily practice of the HCT centers, and the recognition of the variability in practice worldwide, the Worldwide Network for Blood & Marrow Transplantation (WBMT) and the Center for International Blood and Marrow Transplant Research (CIBMTR) Health Services and International Studies Committee have jointly produced an expert opinion statement as a general guide to deal with certain aspects of HCT including diagnostics for SARS-CoV-2 in HCT patients, pre-and-post-HCT management, donor issues, medical tourism and facilities management. While acknowledging all aforementioned challenges and taking into account current recommendations or guidelines issued by the American Society for Transplantation and Cellular Therapy (ASTCT) and the European Society for Blood and Marrow Transplantation (EBMT) (which are WBMT members), herein, we aim at providing a consensus among the authors from WBMT and CIBMTR's HSIS committee and other HCT experts who represent multiple continents and allude to the current worldwide threat to HCT patient from the COVID-19 pandemic (7, 8) . cache = ./cache/cord-349838-p6vfzbla.txt txt = ./txt/cord-349838-p6vfzbla.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-350398-w75flrwv author = Sampath, Rangarajan title = Comprehensive Biothreat Cluster Identification by PCR/Electrospray-Ionization Mass Spectrometry date = 2012-06-29 pages = extension = .txt mime = text/plain words = 11138 sentences = 581 flesch = 50 summary = Coupling biothreat cluster-specific PCR to electrospray ionization mass spectrometry simultaneously provides the breadth of coverage, discrimination of near neighbors, and an extremely low false positive rate due to the requirement that an amplicon with a precise base composition of a biothreat agent be detected by mass spectrometry. In addition to detecting the threat organisms, the biothreat assay described here also detects virulence factors associated with three of the agents: Bacillus anthracis (pXO1 and pXO2), Yersinia pestis (pla and caf), and Vibrio cholera (ctx1). PCR primers were designed to conserved regions within the selected target genes such that the targeted threat agent was clearly identified and differentiated from its near-neighbor species ( Table 1) . In the biothreat assay, the Francisella biocluster is identified by two genus-specific primer pairs targeting the asd (BCT2328) and galE (BCT2332) genes ( Table 1) . cache = ./cache/cord-350398-w75flrwv.txt txt = ./txt/cord-350398-w75flrwv.txt === reduce.pl bib === id = cord-350593-bvmg7f15 author = McDonald, R.S. title = Proportional mouse model for aerosol infection by influenza date = 2012-08-21 pages = extension = .txt mime = text/plain words = 6550 sentences = 324 flesch = 49 summary = CONCLUSIONS: MID (50) for inspired H1N1 aerosols in CD‐1 mice is between 12 and 40 TCID (50); proportionality to dose of weight loss and viral populations makes the CD‐1 mouse a useful model for measuring infectivity by inhalation. Although a few publications have documented the transmissibility of influenza A through inhalation routes (Tellier 2006 (Tellier , 2009 , few studies to date have utilized a mouse model to investigate susceptibility to and pathogenicity of measured aerosol exposures. Table 2 Results of three assays [PCR, direct fluorescent antibody assay (DFA) and CPE] from the homogenates of CD-1 murine lung tissue exposed to an aerosol generated from 1Á58 9 10 6 TCID 50 ml À1 At the 3-min exposure time, no mice were positive for influenza virus as determined by Ct value. cache = ./cache/cord-350593-bvmg7f15.txt txt = ./txt/cord-350593-bvmg7f15.txt === reduce.pl bib === id = cord-350890-ajxvjkmq author = Hsieh, Yi-Fan title = A real-time convective PCR machine in a capillary tube instrumented with a CCD-based fluorometer date = 2013-07-05 pages = extension = .txt mime = text/plain words = 4214 sentences = 207 flesch = 47 summary = This research reports the design, analysis, integration, and test of a prototype of a real-time convective polymerase chain reaction (RT-cPCR) machine that uses a color charged coupled device (CCD) for detecting the emission of fluorescence intensity from an RT-cPCR mix in a microliter volume glass capillary. The measured results from the image-processing scheme indicate that the RT-cPCR prototype with a CCD-based fluorometer can achieve similar DNA quantification reproducibility compared to commercial machines, even when the initial DNA concentration in the test PCR mix is reduced to 10 copies/μL To assess the performance of the prototype, a single DNA template, HBV 122 base pairs, with known concentrations and a single labeling dye, SYBR Green I, was used in the PCR mixes undergoing the same thermal cycling in both the prototype and commercial RT-PCR machines for comparing their measured and predicted fluorescence intensities emitted from the glass capillaries. cache = ./cache/cord-350890-ajxvjkmq.txt txt = ./txt/cord-350890-ajxvjkmq.txt === reduce.pl bib === id = cord-350807-qdq96723 author = Reckziegel, Maria title = Viruses and atypical bacteria in the respiratory tract of immunocompromised and immunocompetent patients with airway infection date = 2020-05-27 pages = extension = .txt mime = text/plain words = 4655 sentences = 283 flesch = 44 summary = Samples were tested by PCR for the presence of herpesviruses (HSV-1/-2; VZV; CMV; HHV6; EBV), adenoviruses, bocaviruses, entero-/rhinoviruses (HRV), parechoviruses, coronaviruses, influenza viruses (IV), parainfluenza viruses as well as for pneumoviruses (HMPV and RSV), and atypical bacteria (Mycoplasma pneumoniae, M.p.; Chlamydia pneumoniae, C.p.). Furthermore, particularly transplant patients are at risk for reactivation of diverse herpesviruses (herpes simplex virus-1/-2, HSV-1/-2; varicella zoster virus, VZV; cytomegalovirus, CMV; human herpesvirus 6, HHV-6; Epstein-Barr virus, EBV) [12, 15, [17] [18] [19] [20] . In this monocentric study, genome equivalents of viruses and M.p. were frequently detected in immunocompromised (66.7%) and immunocompetent (69.2%) patients with respiratory symptoms (Table 1) . Same authors indicated a mean age of 1.8 years Table 2 Detection of multiple pathogens in the respiratory tract of the overall study population (a) as well as of immunocompromised (b) and immunocompetent (c) patients. cache = ./cache/cord-350807-qdq96723.txt txt = ./txt/cord-350807-qdq96723.txt === reduce.pl bib === id = cord-351038-k2m6woow author = Arun Krishnan, R. title = COVID-19: Current Trends in Invitro Diagnostics date = 2020-06-27 pages = extension = .txt mime = text/plain words = 2895 sentences = 172 flesch = 50 summary = Currently the nucleic acid based polymerase chain reaction is used as the reliable diagnostic platform and antigen/antibody detection immunoassays are playing the role of screening tests for early detection and prognosis in COVID-19 treatment. The limitation of rRT-PCR to detect COVID-19 past infection and the progress of the disease, increases the importance of serological assays. Currently COVID-19 antigen LFIA test is under development which will offer more sensitive and specific result for COVID-19 diagnosis and will detect the viral antigen in 3 days of infection [22] . have developed an enzyme linked immunosorbent assay for the detection of COVID-19 IgM and IgG antibody from serum sample. The complexity, cost effectiveness and limitations of nucleic acid based diagnostic tools, impetus the innovative development of well standardized, high sensitive, specific and low cost serological assays for COVID-19 diagnosis. Evaluation of enzyme-linked immunoassay and colloidal gold-immunochromatographic assay kit for detection of novel coronavirus (SARS-Cov-2) causing an outbreak of pneumonia (COVID-19). cache = ./cache/cord-351038-k2m6woow.txt txt = ./txt/cord-351038-k2m6woow.txt === reduce.pl bib === id = cord-351643-8ce807ub author = Poon, LLM title = Rapid detection of reassortment of pandemic H1N1/2009 influenza virus date = 2010-08-01 pages = extension = .txt mime = text/plain words = 2085 sentences = 111 flesch = 52 summary = It should be noted that all of the PCR-positive viral segments fall into the sister group of pandemic H1N1 (see online Supplemental Fig. 2) , which demonstrates the feasibility of using these real-time RT-PCR assays to detect genes from contemporary TR (PB2, PB1, PA, HA, NP, and NS) and EA (NA and M) swine viruses (2 ) . In contrast, melting-curve signals of the HA gene derived from the TR-H1 swine viruses were found to be different from that of the pandemic H1N1/ 2009 virus (Fig. 1B The sequence similarity and diversity of influenza viruses were the major hurdles for the primer design of this study. By use of the 8 established real-time PCR assays we tested RNA from 2 randomly selected samples of the original swine swab specimens that contained the pandemic H1N1/2009 virus. It should be noted that none of these assays can detect viral genes derived from seasonal human influenza viruses. cache = ./cache/cord-351643-8ce807ub.txt txt = ./txt/cord-351643-8ce807ub.txt === reduce.pl bib === id = cord-351100-llyl97ry author = Cariani, Lisa title = Time Length of Negativization and Cycle Threshold Values in 182 Healthcare Workers with Covid-19 in Milan, Italy: An Observational Cohort Study date = 2020-07-23 pages = extension = .txt mime = text/plain words = 3248 sentences = 171 flesch = 53 summary = We aimed to evaluate the time length of negativization from the onset of symptoms in healthcare workers (HCWs) with COVID-19, and to evaluate significant variations in cycle threshold (CT) values and gene positivity (E, RdRP, and N genes) among positive individuals who returned to work. We collected cycle threshold values of the first SARS-CoV-2-positive nasopharyngeal swabs (T0) for all 182 HCWs and CT values at one week before the two negative RT-PCR tests (T1) for the 58 subjects who healed by 30 April 2020 (Figure 2 ). In the present study, we analyzed 2443 nasopharyngeal swabs from 1683 HCWs by molecular laboratory testing for suspected SARS-CoV-2 infection in a large university hospital in Milan, showing 10.8% positive HCWs. Overall, the majority of HCWs with COVID-19 were physicians, and the main reported symptoms were fever, cough, and headache. cache = ./cache/cord-351100-llyl97ry.txt txt = ./txt/cord-351100-llyl97ry.txt === reduce.pl bib === id = cord-351492-8jv7ip67 author = Urwin, S. G. title = FebriDx point-of-care test in patients with suspected COVID-19: a pooled diagnostic accuracy study date = 2020-10-20 pages = extension = .txt mime = text/plain words = 7241 sentences = 397 flesch = 53 summary = Methods: A literature search was performed on the 1st of October 2020 to identify studies reporting diagnostic accuracy statistics of the FebriDx POC test versus real time reverse transcriptase polymerase chain reaction (RT-PCR) testing for SARS-CoV-2. Conclusions: Based on a large sample of patients from two studies during the first wave of the SARS-CoV-2 pandemic, the FebriDx POC test had reasonable diagnostic accuracy in a hospital setting with high COVID-19 prevalence, out of influenza season. In this systematic review and pooled analysis of IPD, we found that the FebriDx LFD had a pooled sensitivity of 0.920 (95% CI: 0.875-0.950) and specificity of 0.862 (0.819-0.896) for COVID-19 across two studies performed within acute hospitals in the UK when compared to RT-PCR on nose and throat swabs during the first wave of the SARS-CoV-2 pandemic. cache = ./cache/cord-351492-8jv7ip67.txt txt = ./txt/cord-351492-8jv7ip67.txt === reduce.pl bib === id = cord-351125-asrezu1f author = Lee, Sangmin title = Identification of Cystoisospora ohioensis in a Diarrheal Dog in Korea date = 2018-08-31 pages = extension = .txt mime = text/plain words = 1718 sentences = 115 flesch = 50 summary = Although multiplex real-time PCR was positive for Cyclospora cayetanensis, the final diagnosis was Cystoisospora ohioensis infection, confirmed by phylogenetic analysis of 18S rRNA. ohioensis was identified in a Korean dog, using microscopy of diarrheal stools and confirmed using phylogenetic analysis of 18S ribosomal RNA (rRNA). Blood chemistry and hematology profile were analyzed using the Fuji DRI-CHEM NX500 automated clinical chemistry analyzer (Fuji, Tokyo, Japan) and veterinary hematology analyzer PE-Identification of Cystoisospora ohioensis in a Diarrheal Dog in Korea 6800 VET (Prokan, Shenzhen, China), respectively. Immunochromatographic assay, multiplex real-time polymerase chain reaction (PCR), and reverse transcription PCR (RT-PCR) were performed at POBANILAB using POBGEN canine enteric pathogen detection kits ( In order to confirm coccidian organisms in fecal samples, sequence analysis was performed as described previously [7] . Based on multiplex real-time PCR and fecal smear analyses, trimethoprim-sulfamethoxazole and metronidazole were initially administered to the puppy for treatment of the condition tentatively diagnosed as canine cyclosporiasis. cache = ./cache/cord-351125-asrezu1f.txt txt = ./txt/cord-351125-asrezu1f.txt === reduce.pl bib === id = cord-352554-hsbyznex author = Lee, Yeon Joo title = Quality of Ribonucleic Acid Extraction for Real-Time Reverse Transcription-PCR (rRT-PCR) of SARS-CoV-2: Importance of Internal Control Monitoring date = 2020-11-01 pages = extension = .txt mime = text/plain words = 1122 sentences = 64 flesch = 56 summary = On 6th February 2020, Emergency Use Authorization (EUA) for COVID-19 testing was implemented in Korea, permitting rapid expansion of capacity in clinical and public health laboratories [5] . To evaluate the performance of the RNA extraction step, 31 and 35 samples were prepared using the Real-Prep-in-use and the new Real-Prep system, respectively, and all 66 eluates were submitted to the same run of rRT-PCR. As the experience of the Middle East Respiratory Syndrome outbreak of 2015 in Korea, an epidemic of emerging infectious diseases necessitates clinical laboratories to conduct new tests at a large scale in a short period of time with kits and equipment that have not been thoroughly validated [10] . Analytical and clinical validation of six commercial Middle East Respiratory Syndrome coronavirus RNA detection kits based on real-time reverse-transcription PCR Comparative evaluation of three homogenization methods for isolating Middle East Respiratory Syndrome coronavirus nucleic acids from sputum samples for real-time reverse transcription PCR cache = ./cache/cord-352554-hsbyznex.txt txt = ./txt/cord-352554-hsbyznex.txt === reduce.pl bib === id = cord-352720-z1cvjc2y author = Díaz-Corvillón, Pilar title = Routine screening for SARS CoV-2 in unselected pregnant women at delivery date = 2020-09-29 pages = extension = .txt mime = text/plain words = 4061 sentences = 244 flesch = 49 summary = While initial evidence suggests that pregnant women were not at increased risk for COVID-19, neither developed a more severe disease compared to non-pregnant adults [3, 4] , recent reports suggest increased rates of preterm birth [5] , pneumonia and intensive care unit admission [6] , and maternal mortality [6, 7] . The main objective of this study was to assess point-prevalence of SARS CoV-2 infection in unselected obstetrical population at the time of delivery and to describe the presentation and clinical evolution of confirmed cases. women were screened for COVID-19 clinical symptoms including fever, cough and shortness of breath by trained personnel, and RT-PCR for SARS CoV-2 (Allplex TM 2019-nCoV Assay [17] ) was performed by nasopharyngeal swab, unless a prior test with no more than 48 hours to admission was reported. cache = ./cache/cord-352720-z1cvjc2y.txt txt = ./txt/cord-352720-z1cvjc2y.txt === reduce.pl bib === id = cord-352640-fycwhyfv author = Goel, Ashish title = Profile of Patients Suspected to be COVID-19: A Retrospective Analysis of Early Pandemic Data date = 2020-08-29 pages = extension = .txt mime = text/plain words = 2756 sentences = 149 flesch = 59 summary = Our study is a short retrospective analysis of the demographic and clinical profiles of subjects presenting with a mild flu-like illness to our hospital who were tested for COVID-19. We present a short retrospective analysis of the demographic and clinical profiles of subjects presenting with a mild flu-like illness to our hospital who were tested for COVID-19. A retrospective analysis of data from subjects who presented to our hospital with mild flu-like illness between the months of March and May 2020 was conducted to understand the disease profile. Data were available for 3,026 subjects who presented to our hospital with either mild flu-like symptoms or with suspected exposure to a confirmed case of COVID-19 during the early phases of the pandemic. In this retrospective analysis, we report that among subjects presenting to the hospital with a mild flu-like illness, those who tested positive for COVID-19 were significantly older and more likely to be men. cache = ./cache/cord-352640-fycwhyfv.txt txt = ./txt/cord-352640-fycwhyfv.txt === reduce.pl bib === id = cord-351854-5s03f0pp author = Ben-Ami, Roni title = Pooled RNA extraction and PCR assay for efficient SARS-CoV-2 detection date = 2020-04-22 pages = extension = .txt mime = text/plain words = 3316 sentences = 197 flesch = 54 summary = title: Pooled RNA extraction and PCR assay for efficient SARS-CoV-2 detection We have implemented the method in a routine clinical diagnosis setting, and already tested 2,168 individuals for SARS-CoV-2 using 311 RNA extraction and RT-PCR kits. Three such limitations might be: (1) a limit on the number of stages due to the importance of delivering a test result quickly, exemplified by the urgent clinical context of COVID-19 diagnosis; (2) a limit on the ability to dilute samples and still safely identify a single positive sample in a pool; (3) favorability of simple algorithms which may minimize human error in a laboratory setting. . https://doi.org/10.1101/2020.04.17.20069062 doi: medRxiv preprint probability of a sample to be positive by p (prevalence of detectable COVID-19 patients in the relevant population) and the pool size by n. This allows for reliable and efficient screening of large asymptomatic populations for the presence of SARS-CoV-2 infection, even when RNA extraction and RT-PCR reagents are in short supply. cache = ./cache/cord-351854-5s03f0pp.txt txt = ./txt/cord-351854-5s03f0pp.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-352894-88c46evj author = Yoon, Soon‐Seek title = Comparison of the diagnostic methods on the canine adenovirus type 2 infection date = 2010-06-02 pages = extension = .txt mime = text/plain words = 2573 sentences = 152 flesch = 46 summary = Methods: Stray dog samples were evaluated by histopathology, polymerase chain reaction (PCR), and immunohistochemistry (IHC) to investigate the status of the CAV‐2 infection on the stray dogs in Korea. Common infectious causes of respiratory disease in dogs include canine distemper virus (CDV) and canine adenovirus type 2 (CAV-2). 3 Pulmonary CAV-2 lesions are consistent with those of bronchointerstitial pneumonia, including the presence of necrosis and large basophilic intranuclear inclusion bodies (IN/IBs) in bronchiolar and alveolar epithelial cells as well as pulmonary macrophages. 5,6 Therefore, pneumonic lung tissues were examined for CAV-2 antigen by immunochemistry and CAV-2 genes by polymerase chain reaction (PCR) in the present study. 5 CAV-2 specific IC/IBs were identified in only three cases in the present study; however, seven cases were IHC positive for CAV-2 antigen detection. These results suggested that CAV-2 particles may fail to create detectable inclusions in some cases although viral antigens were present in the lung tissues. cache = ./cache/cord-352894-88c46evj.txt txt = ./txt/cord-352894-88c46evj.txt === reduce.pl bib === id = cord-353241-ityhcak7 author = Zhu, Hanliang title = IoT PCR for pandemic disease detection and its spread monitoring date = 2020-01-15 pages = extension = .txt mime = text/plain words = 4300 sentences = 208 flesch = 54 summary = Considerable effort has been invested in the development of portable, user-friendly, and cost-effective systems for point-of-care (POC) diagnostics, which could also create an Internet of Things (IoT) for healthcare via a global network. Connecting the easy to use and cost-effective POC devices providing the DENV diagnoses via a mobile network would create an Internet of Things (IoT) [15] for healthcare [16, 17] , an essential tool to tackle any infectious disease outbreak. Prior to testing on an IoT PCR device, we verified the master mix performance and its values of critical threshold (C T ) and the melting temperature (T M ) using a commercial real-time PCR system (Supplementary Section A) beginning with a hot start at 95°C for 30 s followed by 40 cycles of PCR amplification consisting of DNA denaturation at 95°C for 8 s, primer annealing at 60°C for 30 s, and DNA sequence elongation at 72°C for 10 s, then followed by melting curve analysis (MCA) from 72°C to 95°C. cache = ./cache/cord-353241-ityhcak7.txt txt = ./txt/cord-353241-ityhcak7.txt === reduce.pl bib === id = cord-353246-q9qpec7t author = Nijhuis, R. H. T. title = Comparison of ePlex Respiratory Pathogen Panel with Laboratory-Developed Real-Time PCR Assays for Detection of Respiratory Pathogens date = 2017-05-23 pages = extension = .txt mime = text/plain words = 3431 sentences = 147 flesch = 47 summary = The objective of this study was to compare the performance of the RP panel with those of laboratory-developed real-time PCR assays, using a variety of previously collected clinical respiratory specimens. In the current study, the performance of the syndromic RP panel was compared to those of laboratory-developed real-time PCR assays, using clinical specimens previously submitted for diagnosis of respiratory pathogens. The 323 positive clinical specimens contained a total of 464 respiratory pathogens as detected by laboratory-developed real-time PCR assays (Table 1) . Owing to the lack of clinical specimens containing MERS-CoV, dilutions of two different culture isolates were tested in this study, of which dilutions with C T values of Ͻ30 as shown by the laboratory-developed real-time PCR assay could be detected consistently. In conclusion, this study shows excellent performance of the GenMark ePlex RP panel in comparison to laboratory-developed real-time PCR assays for the detection of respiratory pathogens from multiple types of clinical specimens and EQA samples. cache = ./cache/cord-353246-q9qpec7t.txt txt = ./txt/cord-353246-q9qpec7t.txt === reduce.pl bib === id = cord-353499-os328w9o author = Yang, H. S. title = Routine laboratory blood tests predict SARS-CoV-2 infection using machine learning date = 2020-06-19 pages = extension = .txt mime = text/plain words = 2851 sentences = 173 flesch = 55 summary = Here we present a machine learning model incorporating patient demographic features (age, sex, race) with 27 routine laboratory tests to predict an individual's SARS-CoV-2 infection status. Overall, this model employing routine laboratory test results offers opportunities for early and rapid identification of high-risk SARS-COV-2 infected patients before their RT-PCR results are available. In this study, we hypothesized that the results of routine laboratory tests performed within a short time frame as the RT-PCR testing, in conjunction with a limited number of previously identified predictive demographic factors (age, gender, race) (16), can predict SARS-CoV-2 infection status. selected to construct the input feature vectors of the prediction model based on the following criteria: 1) a result available for at least 30% of the patients two days before a specific SARS-CoV-2 RT-PCR test, and 2) showing a significant difference (p-value, pvalue after Bonferroni correction, p-value after demographics adjustment all less than 0.05) between patients with positive and negative RT-PCR results. cache = ./cache/cord-353499-os328w9o.txt txt = ./txt/cord-353499-os328w9o.txt === reduce.pl bib === id = cord-353190-7qcoxl81 author = Nicklas, Werner title = Viral Infections of Laboratory Mice date = 2012-05-17 pages = extension = .txt mime = text/plain words = 27775 sentences = 1482 flesch = 39 summary = This chapter covers infections of mice with the following viruses: herpesviruses, mousepox virus, murine adenoviruses, polyomaviruses, parvoviruses, lactate dehydrogenase-elevating virus, lymphocytic choriomeningitis virus, mammalian orthoreovirus serotype 3, murine hepatitis virus, murine norovirus, murine pneumonia virus, murine rotavirus, Sendai virus, and Theiler's murine encephalomyelitis virus. These results are very difficult to summarize because the outcome of experimental infection in laboratory mice depends on various factors such as mouse strain and age, virus strain and passage history [26] , virus dose and route of inoculation [24] . Experimental infection of laboratory mice with MHV-68 is a frequently used model system for the study of human gammaherpesvirus pathogenesis, e.g. of Kaposi's sarcoma-associated herpesvirus or Epstein-Barr virus (EBV) [62, 63] which are members of the same subfamily. Early descriptions of naturally occurring disease may have been complicated by concurrent infections such as MHV (murine hepatitis virus) or murine rotavirus A (MuRV-A)/epizootic diarrhoea of infant mice (EDIM) virus that contributed to the severity of the lesions especially in liver, pancreas, CNS and intestine. cache = ./cache/cord-353190-7qcoxl81.txt txt = ./txt/cord-353190-7qcoxl81.txt === reduce.pl bib === id = cord-353810-mf753ae9 author = Tan, Cedric Chih Shen title = A novel method for the capture-based purification of whole viral native RNA genomes date = 2019-04-08 pages = extension = .txt mime = text/plain words = 5929 sentences = 352 flesch = 54 summary = This report also describes a successful application of capture-based purification as a direct RNA sequencing strategy that addresses certain limitations of current strategies in sequencing RNA viral genomes. Based on the mapping rates to human and DENV1 reference genomes for pre and post-capture groups, shown in Table 2 , purification factor was calculated to be 272-fold. The minimum coverage required for variant calling was, as described above, benchmarked to that of Illumina reads so that the effectiveness of our capture-based purification method could be more accurately evaluated based on the higher error read rates of direct RNA sequencing technology. Indeed, after comparison of the postcapture and concentrated post-capture sequencing runs (Table 2) , the 2.5-fold increase in the percentage of reads mapping to DENV1 suggests that scaling our method greatly improved the signal-to-noise ratio of this particular downstream RNA assay. cache = ./cache/cord-353810-mf753ae9.txt txt = ./txt/cord-353810-mf753ae9.txt === reduce.pl bib === id = cord-353253-kk2q71vg author = Itokawa, Kentaro title = Disentangling primer interactions improves SARS-CoV-2 genome sequencing by multiplex tiling PCR date = 2020-09-18 pages = extension = .txt mime = text/plain words = 3327 sentences = 179 flesch = 52 summary = Soon after the pandemic was recognized by epidemiologists, a group of biologists comprising the ARTIC Network, has devised a multiplexed polymerase chain reaction (PCR) protocol and primer set for targeted whole-genome amplification of SARS-CoV-2. In our experience, the low to zero depth for those two amplicons was the most frequent bottleneck for using the ARTIC primer set V1 to sequence all targeted genomic regions from samples with middle to low viral load (Ct > 27). The results indicated that preventing primer dimerformation is an effective measure to improve coverage bias in the ARTIC Network's SARS-CoV-2 genome sequencing protocol, and may be applicable to other PrimalSeq methods in general. The formation of primer-dimers is a major cause of coverage bias in the ARTIC Network's multiplex PCR protocol for SARS-CoV-2 genome sequencing. A proposal of an alternative primer for the ARTIC Network's multiplex PCR to improve coverage of SARS-CoV-2 genome sequencing (manuscript version 1) cache = ./cache/cord-353253-kk2q71vg.txt txt = ./txt/cord-353253-kk2q71vg.txt === reduce.pl bib === id = cord-353573-y9jro9gt author = You, Huey-Ling title = Simultaneous detection of respiratory syncytial virus and human metapneumovirus by one-step multiplex real-time RT-PCR in patients with respiratory symptoms date = 2017-03-27 pages = extension = .txt mime = text/plain words = 3452 sentences = 203 flesch = 52 summary = BACKGROUND: Both respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) are important viral pathogens causing respiratory tract infection (RTI) in the pediatric population. RESULTS: Our one-step triplex qRT-PCR assay showed 100% sensitivity and specificity in testing RSV and hMPV in 86 known virus culture supernatants, with excellent linearity (R(2) > 0.99) and reliable reproducibility (CV lower than 1.04%). The aim of this study is to design and assess the diagnostic performance of clinical specimens for the simultaneous identification of RSV and hMPV by using one-step triplex qRT-PCR assay with TaqMan probes. Our one-step triplex qRT-PCR results showed that the viral load of the RSV or hMPV-positive samples from clinical specimens varied over a wide range, presenting threshold between Ct 21 and 44 (21 and 44 cycles). In this study, we established a rapid and internally controlled triplex qRT-PCR assay that can identify RSV and hMPV virus in one reaction mixtures. cache = ./cache/cord-353573-y9jro9gt.txt txt = ./txt/cord-353573-y9jro9gt.txt === reduce.pl bib === id = cord-352562-qfb478sf author = Yamamoto, Lidia title = SARS-CoV-2 infections with emphasis on pediatric patients: a narrative review date = 2020-09-04 pages = extension = .txt mime = text/plain words = 7315 sentences = 341 flesch = 45 summary = In the section devoted to the specific laboratory diagnosis of COVID-19, the most used RT-PCR protocols were described and some studies on the serological diagnosis with IgA, IgM and IgG detection were detailed, including the use of rapid immunochromatographic assays and discussing the ideal period after the onset of symptoms to perform each type of test. They identified 191 cases in hospitalized patients younger than 21 years of age, reported by hospitals in the New York State with the diagnosis of Kawasaki disease, toxic shock syndrome, myocarditis, and suspected multisystem inflammatory syndrome associated with COVID-19 in children (MIS-C). The laboratory diagnosis of COVID-19 are based on the detection of viral RNA by real time amplifications (RT-PCR) 40 or the detection of antibodies (immunoglobulins) anti-SARS-CoV-2 from the classes IgM, IgA and IgG, produced by the host's immune system. Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) infection in children and adolescents: a systematic review cache = ./cache/cord-352562-qfb478sf.txt txt = ./txt/cord-352562-qfb478sf.txt === reduce.pl bib === id = cord-352872-y1qh5nig author = Herpe, Guillaume title = Efficacy of Chest CT for COVID-19 Pneumonia in France date = 2020-09-01 pages = extension = .txt mime = text/plain words = 3832 sentences = 205 flesch = 50 summary = In France, chest CT in combination with reverse transcriptase-polymerase chain reaction (RT-PCR) testing was effective as a diagnostic tool to assess coronavirus disease 2019 (COVID19) pneumonia in symptomatic patients. The final discharge diagnosis based on a multiparametric item including clinical findings, RT-PCR testing, chest CT imaging, risk level of exposure, local estimated prevalence and biological data, was used as reference standard. The survey included the following parameters: clinical patient data (age, sex), results of initial chest CT and initial and/or repeat RT-PCR tests, time intervals between chest CT and RT-PCR, and final discharge summary according to the hospital discharge report. The final discharge diagnosis was based on multiparametric items, risk level of exposure, local estimated prevalence, symptoms (fever, cough, fatigue, dyspnea, anosmia), evolution during hospitalization for inpatient, Diagnostic accuracy, including sensitivity, specificity, PPV, negative predictive value, and accuracy of chest CT imaging, were calculated using final report as the reference standard. cache = ./cache/cord-352872-y1qh5nig.txt txt = ./txt/cord-352872-y1qh5nig.txt === reduce.pl bib === id = cord-353353-njvalb44 author = Lau, Susanna K. P. title = Identification of Novel Rosavirus Species That Infects Diverse Rodent Species and Causes Multisystemic Dissemination in Mouse Model date = 2016-10-13 pages = extension = .txt mime = text/plain words = 6982 sentences = 314 flesch = 44 summary = Analysis of 13 complete genome sequences showed that "Rosavirus B" and "Rosavirus C" represent two potentially novel picornavirus species infecting different rodents. Rosavirus C isolated from 3T3 cells causes multisystemic diseases in a mouse model, with high viral loads and positive viral antigen expression in organs of infected mice after oral or intracerebral inoculation. Rosavirus C isolated from cell culture causes multisystemic diseases in a mouse model, with histopathological changes and positive viral antigen expression in lungs and liver of infected mice. A total of 13 complete genomes from samples of four different wild rodent species (chestnut spiny rat, Coxing's white-bellied rat, roof rat and Indochinese forest rat) positive for "Rosavirus C" and one street rodent species (Norway rat) positive for "Rosavirus B" were sequenced directly from the positive respiratory or alimentary samples and characterized. Infected cell lines and tissues from challenged mice that were tested positive for rosavirus C RASM14A by RT-PCR were subject to viral load studies and immunohistochemical staining for viral VP1 protein as described previously [28, 69] . cache = ./cache/cord-353353-njvalb44.txt txt = ./txt/cord-353353-njvalb44.txt === reduce.pl bib === id = cord-354103-4dldgqzf author = Grubic, Andrew D title = COVID-19 outbreak and surgical practice: The rationale for suspending non-urgent surgeries and role of testing modalities date = 2020-06-27 pages = extension = .txt mime = text/plain words = 4869 sentences = 266 flesch = 47 summary = While epidemiologists and infectious disease physicians are at the forefront in the fight against COVID-19, this pandemic is also a "stress test" to evaluate the capacity and resilience of our surgical community in dealing with the challenges imposed to our health system and society. On the same day, the United States Surgeon General echoed the recommendation from the American College of Surgeons and urged hospitals and healthcare systems to consider suspending elective surgical procedures during the outbreak of COVID-19. This pandemic started with identification of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the causative agent from a cluster of pneumonias in the Hubei providence of China in December 2019. On March 25, 2000, American College of Surgeons released the guidelines for emergency general surgery in COVID-19 positive patients or those at high clinical suspicion for COVID infection. Correlation of Chest CT and RT-PCR Testing in Coronavirus Disease 2019 (COVID-19) in China: A Report of 1014 Cases cache = ./cache/cord-354103-4dldgqzf.txt txt = ./txt/cord-354103-4dldgqzf.txt === reduce.pl bib === === reduce.pl bib === id = cord-354035-i3sl2r0k author = Wylie, Kristine M. title = The Virome of the Human Respiratory Tract date = 2016-12-10 pages = extension = .txt mime = text/plain words = 3901 sentences = 215 flesch = 46 summary = Sensitive, culture-independent molecular assays (polymerase chain reaction and high-throughput sequencing) reveal that in addition to common viruses that cause acute, symptomatic infections the virome also includes viruses that do not cause clinical symptoms, have unknown pathogenic effect, or cause symptoms but are not among the most common viral respiratory tract pathogens. However, as characterization of the respiratory tract virome using molecular methods is a relatively new area of exploration, these studies can be useful in order to determine if viruses beyond the common, known respiratory pathogens are detected. In a study of 71 patients, viruses were assessed in nasal swabs using a panel of targeted PCR assays for common respiratory pathogens. Another study tested 89 nasopharyngeal swabs from adults with upper respiratory tract infections using reverse transcription (RT)-PCR assays for a series of common viruses, including human rhinoviruses, coronaviruses, influenza viruses and others, and by RNA sequencing. cache = ./cache/cord-354035-i3sl2r0k.txt txt = ./txt/cord-354035-i3sl2r0k.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-354733-qxivrhj8 author = Gniazdowski, V. title = Repeat COVID-19 Molecular Testing: Correlation with Recovery of Infectious Virus, Molecular Assay Cycle Thresholds, and Analytical Sensitivity date = 2020-08-06 pages = extension = .txt mime = text/plain words = 3924 sentences = 251 flesch = 56 summary = Whole genome sequencing confirmed the virus genotype in patients with prolonged 28 viral RNA shedding and droplet digital PCR (ddPCR) was used to assess the rate of false 29 negative standard of care PCR results. Whole genome sequencing confirmed the virus genotype in patients with prolonged 28 viral RNA shedding and droplet digital PCR (ddPCR) was used to assess the rate of false 29 negative standard of care PCR results. Prolonged viral RNA shedding was associated with recovery of infectious 31 virus in specimens collected up to 20 days after the first positive result in patients who were 32 symptomatic at the time of specimen collection. Infection control personnel and physicians managing COVID-19 patients and patients under 43 investigation (PUI) continue to face several diagnostic dilemmas related to a lack of 44 understanding of the clinical sensitivities of SARS-CoV-2 molecular diagnostics and the 45 correlation between viral RNA detection and shedding of infectious virus. cache = ./cache/cord-354733-qxivrhj8.txt txt = ./txt/cord-354733-qxivrhj8.txt === reduce.pl bib === id = cord-355102-jcyq8qve author = Avila, Eduardo title = Hemogram data as a tool for decision-making in COVID-19 management: applications to resource scarcity scenarios date = 2020-06-29 pages = extension = .txt mime = text/plain words = 4768 sentences = 242 flesch = 39 summary = PURPOSE: This work describes a machine learning model derived from hemogram exam data performed in symptomatic patients and how they can be used to predict qRT-PCR test results. METHODS: Hemogram exams data from 510 symptomatic patients (73 positives and 437 negatives) were used to model and predict qRT-PCR results through Naïve-Bayes algorithms. In order to evaluate the adequacy and generalization power of the proposed model, as well as its tolerance to handle samples containing missing data (i.e., at least one variable with no informed values), an additional set of 92 samples (10 positives for COVID-19 and 82 negatives) was obtained from the patient database. When no clinical or medical data is available, or when decisions regarding resource management involving multiple symptomatic patients are necessary, the model can be used in multiple individuals simultaneously, aiming to identify those with higher probabilities of presenting positive qRT-PCR results. cache = ./cache/cord-355102-jcyq8qve.txt txt = ./txt/cord-355102-jcyq8qve.txt === reduce.pl bib === id = cord-354773-u86bdmvf author = Suo, Tao title = ddPCR: a more accurate tool for SARS-CoV-2 detection in low viral load specimens date = 2020-06-07 pages = extension = .txt mime = text/plain words = 4490 sentences = 242 flesch = 57 summary = To improve the diagnostic accuracy of nucleic acid detection of SARS-Cov-2 in low viral load samples using droplet digital PCR, we compared the dynamic range and the limit of detection (LoD) with a 95% repeatable probability between ddPCR and RT-PCR in laboratory, and tested the clinical samples from 77 patients by both ddPCR and RT-PCR for head to head comparison. Throat swab samples of each patient were firstly collected for official approved RT-PCR diagnosis in hospitals and blinding laboratory RT-PCR and ddPCR tests simultaneously with the same primers/probe sets approved by Chinese CDC. As shown in Figure 3 , throat swab samples of each suspected outpatient were firstly collected for laboratory RT-PCR, ddPCR tests and official approved RT-PCR diagnosis in hospitals simultaneously with the same primers/probe sets approved by Chinese CDC (Table 1) . In this study, two throat swab samples of each supposed convalescent were collected for laboratory RT-PCR, ddPCR and official approved RT-PCR tests simultaneously with the same primers/probe sets (Table 2) . cache = ./cache/cord-354773-u86bdmvf.txt txt = ./txt/cord-354773-u86bdmvf.txt === reduce.pl bib === id = cord-355874-nz6eqcdb author = Wang, Le title = A GeXP-Based Assay for Simultaneous Detection of Multiple Viruses in Hospitalized Children with Community Acquired Pneumonia date = 2016-09-14 pages = extension = .txt mime = text/plain words = 3067 sentences = 160 flesch = 54 summary = title: A GeXP-Based Assay for Simultaneous Detection of Multiple Viruses in Hospitalized Children with Community Acquired Pneumonia In this study, we used the GeXP-based assay for simultaneous detection of 20 types/subtypes of viruses in 1699 nasopharyngeal specimens collected from hospitalized children with CAP. To evaluate the sensitivity of the GeXP assay, nucleic acid from all 20 target viruses and the internal control pcDNA3.1 (+) DNA were mixed to make the template pool. In the present study, we applied multiplex RT-PCR together with automated capillary electrophoresis, namely the GeXP-based assay, to detect virus in 1699 nasopharyngeal specimens from hospitalized children with CAP. We showed that the GeXP-based assay had high sensitivity and specificity for simultaneous detection of multiple viruses, and about 65% of cases tested were positive for virus. The development of a GeXP-based multiplex reverse transcription-PCR assay for simultaneous detection of sixteen human respiratory virus types/ subtypes cache = ./cache/cord-355874-nz6eqcdb.txt txt = ./txt/cord-355874-nz6eqcdb.txt === reduce.pl bib === id = cord-355014-los6q1k4 author = Ai, J. title = Analysis of factors associated early diagnosis in coronavirus disease 2019 (COVID-19) date = 2020-04-14 pages = extension = .txt mime = text/plain words = 3928 sentences = 232 flesch = 57 summary = Although the real-time RT-PCR detection of the virus nucleic acid is the current golden diagnostic standard, it has high false negative rate when only apply single test. Although the real-time RT-PCR detection of the virus nucleic acid is the current golden diagnostic standard, it has high false negative rate when only apply single test. Nucleic acid RT-PCR test is the diagnosis basis of confirming COVID-19, but the first-time test has relatively high false negative rate. When first RT-PCR test show negative result, the chest CT scan, contact history, age and lymphocyte count of the suspected patient should be used combinedly to assess the possibility of SARS-CoV-2 infection. When first RT-PCR test show negative result, the chest CT scan, contact history, age and lymphocyte count of the suspected patient should be used combinedly to assess the possibility of SARS-CoV-2 infection. cache = ./cache/cord-355014-los6q1k4.txt txt = ./txt/cord-355014-los6q1k4.txt === reduce.pl bib === id = cord-355988-4eldkteb author = SAMPATH, RANGARAJAN title = Rapid Identification of Emerging Infectious Agents Using PCR and Electrospray Ionization Mass Spectrometry date = 2007-04-23 pages = extension = .txt mime = text/plain words = 3430 sentences = 168 flesch = 41 summary = Here we describe a powerful new approach for infectious disease surveillance that is based on polymerase chain reaction (PCR) to amplify nucleic acid targets from large groupings of organisms, electrospray ionization mass spectrometry (ESI‐MS) for accurate mass measurements of the PCR products, and base composition signature analysis to identify organisms in a sample. Most of the new technologies being developed for detection of infectious agents incorporate a version of quantitative polymerase chain reaction (PCR), based upon the use of highly specific primers and probes and designed to selectively identify specific pathogenic organisms. The process uses electrospray ionization mass spectrometry (ESI-MS) and base composition analysis of PCR amplification products from highly conserved genomic regions to identify and determine the relative quantity of pathogenic bacteria, FIGURE 1. Importantly, the base composition data for some of the isolates represented new measurements from regions that have not been sequenced, showing the potential of this strategy to identify previously unknown or newly emerging viruses. cache = ./cache/cord-355988-4eldkteb.txt txt = ./txt/cord-355988-4eldkteb.txt === reduce.pl bib === === reduce.pl bib === id = cord-356370-jjl1hbeb author = Sahajpal, Nikhil Shri title = Role of clinical laboratories in response to the COVID-19 pandemic date = 2020-06-19 pages = extension = .txt mime = text/plain words = 1602 sentences = 77 flesch = 41 summary = In response to the outbreak, several state authorities and commercial companies have developed diagnostic assays to test individuals for the SARS-CoV-2 infection. In the US, clinical laboratories are required to perform 'bridging studies' on FDA approved SARS-CoV-2 diagnostic assays to implement testing under the EUA regulation. Although, the reverse transcription-polymerase chain reaction (RT-PCR) based assays for the detection of SARS-CoV-2 nucleic acid regions might be the most practical approach at present, qualitative assays are far from providing insights into the evolution of the virus and the varied immune response in different populations. In addition, the RT-PCR based assays provide a unique opportunity to implement pooling sample strategy for wide-scale population screening for SARS-CoV-2. Several studies, including from our laboratory (under review) have demonstrated that pooling sample strategy is a practical and feasible method for screening populations for SARS-CoV-2 [2] . Laboratories should therefore prime for serologic testing by validating assays using RT-PCR confirmed COVID-19 samples. cache = ./cache/cord-356370-jjl1hbeb.txt txt = ./txt/cord-356370-jjl1hbeb.txt === reduce.pl bib === id = cord-356007-6b0w36l9 author = Alanazi, Khalid H. title = Scope and extent of healthcare-associated Middle East respiratory syndrome coronavirus transmission during two contemporaneous outbreaks in Riyadh, Saudi Arabia, 2017 date = 2018-12-31 pages = extension = .txt mime = text/plain words = 4028 sentences = 212 flesch = 48 summary = OBJECTIVE: To investigate a Middle East respiratory syndrome coronavirus (MERS-CoV) outbreak event involving multiple healthcare facilities in Riyadh, Saudi Arabia; to characterize transmission; and to explore infection control implications. Of these 10 available HCP, 9 reported prolonged, close contact with an unrecognized patient case before implementation of MERS-CoV IPC measures and with limited PPE use ( Table 3 ). Among the 10 interviewed HCP cases, the time from first positive MERS-CoV result to serum collection was 55-61 days, and 1 was seropositive: a 32-year-old female who had reported headache, muscle aches, and productive cough. Among them, 9 HCP (33%) tested rRT-PCR positive for MERS-CoV; 5 reported contact with index patient B before At hospital B, 34 of 50 MERS-CoV rRT-PCR-negative HCP contacts of cases (68%) were interviewed and provided serum. One was seropositive, a physician who had close, prolonged contact with index B after isolation and while wearing recommended PPE; however, he had previously tested rRT-PCR positive for MERS-CoV in 2013. cache = ./cache/cord-356007-6b0w36l9.txt txt = ./txt/cord-356007-6b0w36l9.txt === reduce.pl bib === id = cord-355489-tkvfneje author = Mendez, Jairo A title = Phylogenetic history demonstrates two different lineages of dengue type 1 virus in Colombia date = 2010-09-14 pages = extension = .txt mime = text/plain words = 4615 sentences = 235 flesch = 48 summary = Yet, the phylogenetic relationships between strains isolated along the covered period of time suggests that viral strains detected in some years, although belonging to the same genotype V, have different recent origins corresponding to multiple re-introduction events of viral strains that were circulating in neighbor countries. Due to the importance of DENV in public health, the particular goals of this research were to reconstruct the phylogenetic history of DENV-1 and to date the phylogenetic tree using isolation time as calibration points to establish date of introduction of virus and rate evolution patterns of virus in Colombia. Previously reported genotypes were represented in the tree and placed most of the Colombian isolates nesting in the genotype V clade (America, Africa) and were closely related to Argentina, Brazil and Paraguay virus strains. cache = ./cache/cord-355489-tkvfneje.txt txt = ./txt/cord-355489-tkvfneje.txt ===== Reducing email addresses cord-000664-085v7n6k cord-006960-9pho3hk6 cord-000830-jiy4cp4n cord-000080-7s5b3lpn cord-005687-gj6q0ft0 cord-017948-fqhl1qb4 cord-015147-h0o0yqv8 cord-008777-i2reanan cord-014794-yppi30a0 cord-048359-lz37rh82 cord-102511-7zgd45fl cord-253502-v2hh3w3r cord-261329-k1p7fo0e cord-263570-6notzm6s cord-275787-5s442sy2 cord-275519-98qxf6xo cord-280442-jtvez46y cord-282278-q7jp224a cord-289676-tjy7f9rk cord-294155-94skyx5f cord-296109-kco85lqn cord-297160-tqw9vx2b cord-304457-8g36h1bz cord-309763-8eywr57j cord-313749-f2ct57em cord-321514-knyw023l cord-322937-lakdi3x8 cord-329162-6w8qcv1c cord-337636-3yc0ribg cord-331496-5xak7z6b cord-337396-g69bb60d Creating transaction Updating adr table ===== Reducing keywords cord-000322-8ctsa9sd cord-000235-782iew86 cord-000113-d0eur1hq cord-000664-085v7n6k cord-000180-howix091 cord-000010-prsvv6l9 cord-000483-zgapjjjw cord-002852-m4l2l2r1 cord-001455-n7quwr4s cord-006960-9pho3hk6 cord-000750-l9ozvlae cord-003047-3ejfxj6r cord-001134-8ljgxnhf cord-005309-147erliy cord-002376-970934vm cord-000830-jiy4cp4n cord-000715-zl1s82yi cord-003505-qr6ukfti cord-001843-ceatyj3o cord-007427-iqwojhq2 cord-000736-6f8vyziv cord-001787-lj1nd922 cord-000979-cav9n18w cord-001858-nmi39n6h cord-001655-uqw74ra0 cord-007066-zn10rnrm cord-004003-rlgzgyzn cord-004810-g0y7ied0 cord-003850-in7he5o4 cord-011436-ud35mf5l cord-011966-7k2cxy8a cord-004717-41ui4lqc cord-000080-7s5b3lpn cord-001932-sklwt76a cord-001371-wf0vonkn cord-004808-6w9n03fy cord-000265-llilwq1u cord-001891-5op0yss9 cord-011322-olvqgs85 cord-010608-eaa2znom cord-000014-e0ou9zjb cord-011073-uiabpbxd cord-007068-vcfs41eb cord-005752-tur57xd9 cord-005687-gj6q0ft0 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cord-351864-zozrj7w5 cord-352831-ydlix2o7 cord-352562-qfb478sf cord-352894-88c46evj cord-352872-y1qh5nig cord-353246-q9qpec7t cord-353241-ityhcak7 cord-353499-os328w9o cord-353810-mf753ae9 cord-353573-y9jro9gt cord-353253-kk2q71vg cord-353353-njvalb44 cord-354103-4dldgqzf cord-353957-0pjg25kn cord-354035-i3sl2r0k cord-354725-lqio7l8k cord-354308-ol8twpay cord-354683-l07w3lc7 cord-354733-qxivrhj8 cord-355874-nz6eqcdb cord-356370-jjl1hbeb cord-355102-jcyq8qve cord-354773-u86bdmvf cord-355988-4eldkteb cord-355014-los6q1k4 cord-354943-wxhbwcfr cord-356007-6b0w36l9 cord-355489-tkvfneje cord-353190-7qcoxl81 Creating transaction Updating pos table Building ./etc/reader.txt cord-005453-4057qib7 cord-023211-kt5gt26t cord-015324-y44sfr0c cord-004133-32w6g7qk cord-000830-jiy4cp4n cord-324944-ixh3ykrc number of items: 972 sum of words: 8,006,474 average size in words: 11,553 average readability score: 49 nouns: patients; cells; virus; results; study; cell; samples; blood; detection; infection; time; disease; analysis; cases; methods; expression; treatment; viruses; group; data; assay; gene; protein; diagnosis; infections; days; test; dna; studies; method; control; years; levels; influenza; age; number; children; patient; system; use; risk; type; sample; mice; testing; reaction; amplification; assays; genes; response verbs: used; showed; detect; including; based; performed; increased; comparing; associated; found; identifying; follows; reported; determine; test; develop; observed; suggests; obtained; cause; evaluated; provides; induced; reduce; confirms; contains; described; require; collected; treated; receive; indicate; isolated; infect; demonstrated; considered; occurs; relates; present; resulting; investigating; reveal; assess; analyzed; known; remaining; measure; expressing; led; produced adjectives: clinical; positive; respiratory; viral; high; human; different; specific; negative; significant; real; non; acute; low; higher; first; molecular; severe; anti; new; diagnostic; present; single; important; lower; available; common; several; rapid; normal; similar; infectious; novel; multiple; immune; bacterial; total; chronic; many; median; large; small; early; possible; primary; nucleic; genetic; potential; inflammatory; healthy adverbs: also; however; well; respectively; significantly; therefore; previously; highly; recently; even; still; often; especially; currently; furthermore; prior; clinically; approximately; moreover; frequently; less; commonly; mainly; directly; usually; first; now; particularly; together; statistically; relatively; finally; potentially; least; later; additionally; generally; widely; subsequently; alone; rapidly; specifically; successfully; fully; rather; yet; interestingly; already; far; almost pronouns: we; it; our; their; its; they; i; them; he; his; she; her; us; one; itself; themselves; your; you; him; my; mcr-9; me; ourselves; mg; himself; ours; clustalx; iga1; mrnas; imagej; p210bcr; ya; itma; herself; em; s; igg4; igfbp2; hmsh2; esat-6; thier; pcv2; p24ag; mutationtaster3; iigp1; igm/; igg1; https://doi.org/10.1101/2020.08; hent1; fusb proper nouns: PCR; RT; RNA; SARS; CoV-2; C; COVID-19; mg; T; A; University; DNA; CT; Fig; B; HSCT; China; C.; S.; el; Table; M; HCV; USA; ⁄; II; ELISA; E.; M.; L; Hospital; RSV; S; CF; HIV; Health; van; CoV; los; HBV; H1N1; B.; GVHD; CMV; D; P.; HLA; RBC; Germany; G keywords: pcr; sars; rna; dna; covid-19; patient; virus; cell; respiratory; study; result; detection; infection; university; method; disease; sample; hiv; hcv; rsv; lamp; ibv; hospital; elisa; group; protein; hrv; expression; china; assay; increase; gene; cov-2; test; ifn; conclusion; pedv; il-6; human; hbv; case; blood; system; dog; cat; mouse; level; influenza; hla; csf one topic; one dimension: patients file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3036576/ titles(s): RNA and DNA Bacteriophages as Molecular Diagnosis Controls in Clinical Virology: A Comprehensive Study of More than 45,000 Routine PCR Tests three topics; one dimension: patients; pcr; patients file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7091844/, https://www.sciencedirect.com/science/article/pii/S0122726220300859?v=s5, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122197/ titles(s): Physicians – Poster Session | ACTUALIZACION DE LA DECLARACIÓN DE CONSENSO EN MEDICINA CRITICA PARA LA ATENCIÓN MULTIDISCIPLINARIA DEL PACIENTE CON SOSPECHA O CONFIRMACIÓN DIAGNÓSTICA DE COVID-19 | Infektionen five topics; three dimensions: patients blood results; pcr virus detection; cells cell protein; covid patients sars; en el expression file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7091844/, https://www.ncbi.nlm.nih.gov/pubmed/20716157/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7163523/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122197/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121700/ titles(s): Physicians – Poster Session | Original Article: Real time reverse transcription (RRT)‐polymerase chain reaction (PCR) methods for detection of pandemic (H1N1) 2009 influenza virus and European swine influenza A virus infections in pigs | Literature review of baseline information on non‐coding RNA (ncRNA) to support the risk assessment of ncRNA‐based genetically modified plants for food and feed | Infektionen | 21 Infecties, ziekte en zwangerschap Type: cord title: keyword-pcr-cord date: 2021-05-25 time: 15:47 username: emorgan patron: Eric Morgan email: emorgan@nd.edu input: keywords:pcr ==== make-pages.sh htm files ==== make-pages.sh complex files ==== make-pages.sh named enities ==== making bibliographics id: cord-282449-7mxp3sdy author: A, Amouroux title: Evidence for and against vertical transmission for SARS-CoV-2 (COVID-19) date: 2020-05-04 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract COVID-19 can severely affect pregnant women and the issue of vertical transmission of sars-cov-2 has also emerged. Sars-cov-2 could be recovered by real-time (RT) PCR from nasal and throat swabs, sputum and feces of symptomatic patients including neonates but not from vaginal swabs, amniotic fluid, placenta, cord blood, neonatal blood or breast milk. Viremia was present in 1% of symptomatic adults. We identified 12 articles published between February 10th and April 4th 2020 reporting on 68 deliveries and 71 neonates with maternal infection in the third trimester of pregnancy. Perinatal exposure, including mode of delivery and time interval from delivery to the diagnosis of neonatal infection are crucial in differentiating congenital from perinatal infection. Neonatal infection is usually asymptomatic. Neonatal infection was diagnosed within 48 hours of life in 4 cases. Detection rates of real-time PCR and the interpretation of IgM and IgG antibodies levels in cord and neonatal blood are discussed in relation with the immaturity of the fetal and neonatal immune system. url: https://www.sciencedirect.com/science/article/pii/S000293782030524X?v=s5 doi: 10.1016/j.ajog.2020.04.039 id: cord-022084-hap7flng author: ARRUDA, EURICO title: Respiratory Tract Viral Infections date: 2009-05-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152450/ doi: 10.1016/b978-0-443-06668-9.50064-8 id: cord-303588-bwllypvq author: Ababneh, Mustafa title: High-resolution melting curve analysis for infectious bronchitis virus strain differentiation date: 2020-03-03 words: 3137.0 sentences: 159.0 pages: flesch: 58.0 cache: ./cache/cord-303588-bwllypvq.txt txt: ./txt/cord-303588-bwllypvq.txt summary: MATERIALS AND METHODS: In this study, qRT-PCR was conducted on a partial fragment S1 gene followed by a high resolution melting curve analysis (qRT-PCR/HRM) on 23 IBV-positive samples in Jordan. Although the third cluster contained the highest number of samples, it displayed no similarity to any of the reference vaccine strains, and, after comparing them with the sequencing results, we found that the samples in the third cluster were similar to the variant II-like (IS-1494-06) IBV field strain. CONCLUSION: Our developed qRT-PCR/HRM curve analysis was able to detect and rapidly identify novel and vaccine-related IBV strains as confirmed by S1 gene nucleotide sequences, making it a rapid and cost-effective tool. High-resolution melting (HRM) curve analysis is a newly established PCR-based technique that has been used to differentiate related strains of the same animal or avian virus [16] [17] [18] [19] . Those 22 samples, along with the five IBV vaccine reference strains, were subjected to qRT-PCR targeting the S1 gene followed with HRM curve analysis. abstract: BACKGROUND AND AIM: Belonging to the Coronaviridae family, avian infectious bronchitis virus (IBV) causes respiratory, reproductive, and renal diseases in poultry. Preventative measures lie mainly in vaccination, while the gold standard for IBV classification and differentiation is based on the sequence analysis of the spike 1 (S1) gene. In this study, we tested a new assay for IBV strain classification that is less expensive and requires reduced time and effort to perform. We carried out a quantitative real-time polymerase chain reaction followed by high-resolution melting (qRT-PCR/HRM) curve analysis. MATERIALS AND METHODS: In this study, qRT-PCR was conducted on a partial fragment S1 gene followed by a high resolution melting curve analysis (qRT-PCR/HRM) on 23 IBV-positive samples in Jordan. For this assay, we utilized the most common IBV vaccine strains (Mass and 4/91) as a reference in the HRM assay. To evaluate the discrimination power of the qRT-PCR/HRM, we did the sequencing of the partial S1 gene. RESULTS: It was shown that HRM was able to classify IBV samples into four clusters based on the degree of similarity between their melting points: The first cluster exhibited the highest similarity to the 4/91 strain, while the second was similar to the Mass-related IBV strain. Although the third cluster contained the highest number of samples, it displayed no similarity to any of the reference vaccine strains, and, after comparing them with the sequencing results, we found that the samples in the third cluster were similar to the variant II-like (IS-1494-06) IBV field strain. Finally, the fourth cluster comprised one unique sample that was found to belong to the Q1 IBV strain. CONCLUSION: Our developed qRT-PCR/HRM curve analysis was able to detect and rapidly identify novel and vaccine-related IBV strains as confirmed by S1 gene nucleotide sequences, making it a rapid and cost-effective tool. url: https://doi.org/10.14202/vetworld.2020.400-406 doi: 10.14202/vetworld.2020.400-406 id: cord-279644-g9cr9m96 author: Abedi Kiasari, Bahman title: Merkel cell polyomavirus DNA in immunocompetent and immunocompromised patients with respiratory disease date: 2011-10-19 words: 2469.0 sentences: 147.0 pages: flesch: 55.0 cache: ./cache/cord-279644-g9cr9m96.txt txt: ./txt/cord-279644-g9cr9m96.txt summary: To determine the prevalence of MCPyV in 305 respiratory samples from immunocompetent and immunocompromised patients and evaluate their contribution to respiratory diseases, specimens were screened for MCPyV using single, multiplex, or real‐time PCR; co‐infection with other viruses was examined. The aim of this study was to determine the prevalence of MCPyV in respiratory specimens collected from immunocompetent and immunocompromised patients and evaluate the possible of contribution of the virus in respiratory disease alone, or in combination with other respiratory viruses. MCPyV DNA was found in 3.27% of nasopharyngeal aspirate samples obtained from patients with respiratory tract disease as determined by both PCR assays (LT and VP1). Although samples tested in this study were only collected during the autumn and winter months, there was no Sequence data from positive specimens showed that the MCPyV found in respiratory specimens was similar to the sequence of viruses identified within Merkel cell carcinomas by Feng et al. abstract: Merkel cell polyomavirus (MCPyV) was identified originally in association with a rare but aggressive skin cancer, Merkel cell carcinoma. The virus has since been found in the respiratory tract of some patients with respiratory disease. However, the role of MCPyV in the causation of respiratory disease has not been established. To determine the prevalence of MCPyV in 305 respiratory samples from immunocompetent and immunocompromised patients and evaluate their contribution to respiratory diseases, specimens were screened for MCPyV using single, multiplex, or real‐time PCR; co‐infection with other viruses was examined. Of the 305 samples tested, 10 (3.27%) were positive for MCPyV. The virus was found in two groups of patients: in 6 (2%) nasopharyngeal aspirate samples from children aged 26 days to 7 months who were immunocompetent; and in 4 (1.3%) of nasopharyngeal aspirate samples taken from patients aged 41 to 69 years who were severely immunosuppressed from leukemia or transplant therapy. Both groups had upper or lower respiratory tract infection. Co‐infections with other viruses were found in 30% of the MCPyV positive samples. The data present a pattern of infection similar to that seen with the polyomaviruses JC and BK in which the virus is acquired during childhood, probably by the respiratory route. The viruses then establish latency and become reactivated in the event of immunosuppression. J. Med. Virol. 83:2220–2224, 2011. © 2011 Wiley Periodicals, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/22012732/ doi: 10.1002/jmv.22222 id: cord-271915-nvilxnzl author: Adachi, D. title: Comprehensive detection and identification of human coronaviruses, including the SARS-associated coronavirus, with a single RT-PCR assay date: 2004-12-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The SARS-associated human coronavirus (SARS-HCoV) is a newly described, emerging virus conclusively established as the etiologic agent of the severe acute respiratory syndrome (SARS). This study presents a single-tube RT-PCR assay that can detect with high analytical sensitivity the SARS-HCoV, as well as several other coronaviruses including other known human respiratory coronaviruses (HCoV-OC43 and HCoV-229E). Species identification is provided by sequencing the amplicon, although a rapid screening test by restriction enzyme analysis has proved to be very useful for the analysis of samples obtained during the SARS outbreak in Toronto, Canada. url: https://www.sciencedirect.com/science/article/pii/S0166093404002162 doi: 10.1016/j.jviromet.2004.07.008 id: cord-327620-fwhhsnmq author: Agut, H title: Détection, quantification et analyse des génomes viraux dans les infections à herpèsvirus humains 6 et 7 (HHV-6, HHV-7) date: 2003-09-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Résumé La détection, la quantification et l’analyse génétique des génomes viraux ont été progressivement introduites dans la pratique quotidienne de la virologie médicale. Dans le cas des infections à herpèsvirus humains 6 et 7 (HHV-6, HHV-7), la détection de l’ADN viral a permis d’impliquer ces infections dans des maladies au-delà de ce qui avait été mis en évidence par les méthodes conventionnelles (culture, sérologie) notamment chez les sujets immunodéprimés. La quantification, en particulier grâce à l’apport récent de la PCR en temps réel, est susceptible d’établir la distinction entre latence et réactivation virales, de prédire la survenue d’évènements cliniques, de suivre les effets d’une thérapeutique spécifique. L’analyse génétique a conduit à l’identification de variants et contribué à caractériser les mutations associées à la résistance aux antiviraux. Comme le montre l’étude des herpèsvirus, ces techniques moléculaires ont aussi des limites qu’il faut connaître mais constituent indiscutablement un progrès décisif en virologie clinique. Abstract The detection, quantification and genetic analysis of viral genomes have become a common practice in clinical virology. This is exemplified by the study of human herpesviruses 6 and 7. The detection of viral DNA has led to implicate theses viruses in human diseases far beyond the evidence obtained by conventional approaches such as virus culture and serology. This is specially the case for immunocompromised subjects. The quantitation of DNA, in particular by means of real-time PCR, is now susceptible to differenciate reactivation from latency, predict the occurrence of clinical events, and monitor the efficacy of antiviral therapy. Genetic analyses have permitted the characterization of variant-specific polymorphisms and mutations responsible for resistance to antivirals. Despite some limitations that users have to be aware of, the study of viral genomes is an outstanding progress in medical virology. url: https://api.elsevier.com/content/article/pii/S0923253203000656 doi: 10.1016/s0923-2532(03)00065-6 id: cord-265268-5xu9hj2n author: Ahmed, W. title: Evaluation of Glass Wool Filters and Hollow-Fiber Ultrafiltration Concentration Methods for qPCR Detection of Human Adenoviruses and Polyomaviruses in River Water date: 2016-08-13 words: 4942.0 sentences: 271.0 pages: flesch: 51.0 cache: ./cache/cord-265268-5xu9hj2n.txt txt: ./txt/cord-265268-5xu9hj2n.txt summary: title: Evaluation of Glass Wool Filters and Hollow-Fiber Ultrafiltration Concentration Methods for qPCR Detection of Human Adenoviruses and Polyomaviruses in River Water Here, we compared the recovery efficiencies of human adenoviruses (HAdVs) and human polyomaviruses (HPyVs) from 10-L river water samples seeded with raw human wastewater (100 and 10 mL) using hollow-fiber ultrafiltration (HFUF) and glass wool filter (GWF) methods. Little has been documented on the recovery efficiencies of HFUF and GWF methods for concentrating HAdVs and HPyVs markers from environmental water samples seeded with raw human wastewater. HFUF method recovered significantly higher concentration of HAdVs (P = 0.004; P = 0.003) and HPyVs (P = 0.01; P = 0.009) compared to GWF method for river water samples seeded with 100 and 10 mL of human wastewater, respectively. abstract: Pathogenic human viruses cause over half of gastroenteritis cases associated with recreational water use worldwide. They are difficult to concentrate from environmental waters due to low numbers and small sizes. Rapid enumeration of viruses by quantitative polymerase chain reaction (qPCR) has the potential to improve water quality analysis and risk assessment. However, capturing and recovering these viruses from environmental water remain formidable barriers to routine use. Here, we compared the recovery efficiencies of human adenoviruses (HAdVs) and human polyomaviruses (HPyVs) from 10-L river water samples seeded with raw human wastewater (100 and 10 mL) using hollow-fiber ultrafiltration (HFUF) and glass wool filter (GWF) methods. The mean recovery efficiencies of HAdVs in river water samples through HFUF were 36 and 86 % for 100 and 10 mL of seeded human wastewater, respectively. In contrast, the estimated mean recovery efficiencies of HAdVs in river water samples through GWF were 1.3 and 3 % for 100 and 10 mL seeded raw human wastewater, respectively. Similar trends were also observed for HPyVs. Recovery efficiencies of HFUF method were significantly higher (P < 0.05) than GWF for both HAdVs and HPyVs. Our results clearly suggest that HFUF would be a preferred method for concentrating HAdVs and HPyVs from river water followed by subsequent detection and quantification with PCR/qPCR assays. url: https://www.ncbi.nlm.nih.gov/pubmed/32214527/ doi: 10.1007/s11270-016-3026-5 id: cord-348914-6wzqitun author: Ahouach, B. title: Cutaneous lesions in a patient with COVID‐19: are they related? date: 2020-04-30 words: 315.0 sentences: 33.0 pages: flesch: 62.0 cache: ./cache/cord-348914-6wzqitun.txt txt: ./txt/cord-348914-6wzqitun.txt summary: key: cord-348914-6wzqitun authors: Ahouach, B.; Harant, S.; Ullmer, A.; Martres, P.; Bégon, E.; Blum, L.; Tess, O.; Bachmeyer, C. cord_uid: 6wzqitun A previously healthy 57‐year‐old woman presented with fever (39 °C) lasting for 4 days, and dry cough and rash appeared 2 days before. Diffuse fixed erythematous blanching maculopapular lesions were present, asymptomatic over the limbs and trunk, with burning sensation over the palms (a, b). Thorax computed tomography scan was typical of COVID‐19; nasopharyngeal swab polymerase chain reaction (PCR) confirmed SARS‐CoV‐2. maculopapular lesions were present, asymptomatic over the limbs and trunk, with burning sensation over the palms (a, b). Thorax computed tomography scan was typical of COVID-19; nasopharyngeal swab polymerase chain reaction (PCR) confirmed SARS-CoV-2. PCR on whole-skin biopsy specimen was negative for SARS-CoV-2. Fever and rash resolved within 9 days, dry cough within 2 weeks. Urticarial and chilblain-like lesions have been reported in patients with COVID-19, but other phenotypes could be observed. abstract: A previously healthy 57‐year‐old woman presented with fever (39 °C) lasting for 4 days, and dry cough and rash appeared 2 days before. Diffuse fixed erythematous blanching maculopapular lesions were present, asymptomatic over the limbs and trunk, with burning sensation over the palms (a, b). She denied any drug intake, excepting paracetamol for fever. Thorax computed tomography scan was typical of COVID‐19; nasopharyngeal swab polymerase chain reaction (PCR) confirmed SARS‐CoV‐2. Infectious enquiry was otherwise negative. Skin biopsy specimen showed slight spongiosis, basal cell vacuolation and mild perivascular lymphocytic infiltrate (c). url: https://www.ncbi.nlm.nih.gov/pubmed/32353170/ doi: 10.1111/bjd.19168 id: cord-355014-los6q1k4 author: Ai, J. title: Analysis of factors associated early diagnosis in coronavirus disease 2019 (COVID-19) date: 2020-04-14 words: 3928.0 sentences: 232.0 pages: flesch: 57.0 cache: ./cache/cord-355014-los6q1k4.txt txt: ./txt/cord-355014-los6q1k4.txt summary: Although the real-time RT-PCR detection of the virus nucleic acid is the current golden diagnostic standard, it has high false negative rate when only apply single test. Although the real-time RT-PCR detection of the virus nucleic acid is the current golden diagnostic standard, it has high false negative rate when only apply single test. Nucleic acid RT-PCR test is the diagnosis basis of confirming COVID-19, but the first-time test has relatively high false negative rate. When first RT-PCR test show negative result, the chest CT scan, contact history, age and lymphocyte count of the suspected patient should be used combinedly to assess the possibility of SARS-CoV-2 infection. When first RT-PCR test show negative result, the chest CT scan, contact history, age and lymphocyte count of the suspected patient should be used combinedly to assess the possibility of SARS-CoV-2 infection. abstract: Background The pandemic of coronavirus disease 2019 (COVID-19) has become the first concern in international affairs as the novel coronavirus (SARS-CoV-2) is spreading all over the world at a terrific speed. The accuracy of early diagnosis is critical in the control of the spread of the virus. Although the real-time RT-PCR detection of the virus nucleic acid is the current golden diagnostic standard, it has high false negative rate when only apply single test. Objective Summarize the baseline characteristics and laboratory examination results of hospitalized COVID-19 patients. Analyze the factors that could interfere with the early diagnosis quantitatively to support the timely confirmation of the disease. Methods All suspected patients with COVID-19 were included in our study until Feb 9th, 2020. The last day of follow-up was Mar 20th, 2020. Throat swab real-time RT-PCR test was used to confirm SARS-CoV-2 infection. The difference between the epidemiological profile and first laboratory examination results of COVID-19 patients and non-COVID-19 patients were compared and analyzed by multiple logistic regression. Receiver operating characteristic (ROC) curve and area under curve (AUC) were used to assess the potential diagnostic value in factors, which had statistical differences in regression analysis. Results In total, 315 hospitalized patients were included. Among them, 108 were confirmed as COVID-19 patients and 207 were non-COVID-19 patients. Two groups of patients have significance in comparing age, contact history, leukocyte count, lymphocyte count, C-reactive protein, erythrocyte sedimentation rate (p<0.10). Multiple logistic regression analysis showed age, contact history and decreasing lymphocyte count could be used as individual factor that has diagnostic value (p<0.05). The AUC of first RT-PCR test was 0.84 (95% CI 0.73-0.89), AUC of cumulative two times of RT-PCR tests was 0.92 (95% CI 0.88-0.96) and 0.96 (95% CI 0.93-0.99) for cumulative three times of RT-PCR tests. Ninety-six patients showed typical pneumonia radiological features in first CT scan, AUC was 0.74 (95% CI 0.60-0.73). The AUC of patients age, contact history with confirmed people and the decreased lymphocytes were 0.66 (95% CI 0.60-0.73), 0.67 (95% CI 0.61-0.73), 0.62 (95% CI 0.56-0.69), respectively. Taking chest CT scan diagnosis together with patients age and decreasing lymphocytes, AUC would be 0.86 (95% CI 0.82-0.90). The age threshold to predict COVID-19 was 41.5 years, with a diagnostic sensitivity of 0.70 (95% CI 0.61-0.79) and a specificity of 0.59 (95% CI 0.52-0.66). Positive and negative likelihood ratios were 1.71 and 0.50, respectively. Threshold of lymphocyte count to diagnose COVID-19 was 1.53x109/L, with a diagnostic sensitivity of 0.82 (95% CI 0.73-0.88) and a specificity of 0.50 (95% CI 0.43-0.57). Positive and negative likelihood ratios were 1.64 and 0.37, respectively. Conclusion Single RT-PCR test has relatively high false negative rate. When first RT-PCR test show negative result in suspected patients, the chest CT scan, contact history, age and lymphocyte count should be used combinedly to assess the possibility of SARS-CoV-2 infection. url: http://medrxiv.org/cgi/content/short/2020.04.09.20059352v1?rss=1 doi: 10.1101/2020.04.09.20059352 id: cord-336671-vfq5ft08 author: Ai, Jing-Wen title: Era of molecular diagnosis for pathogen identification of unexplained pneumonia, lessons to be learned date: 2020-03-16 words: 1883.0 sentences: 108.0 pages: flesch: 50.0 cache: ./cache/cord-336671-vfq5ft08.txt txt: ./txt/cord-336671-vfq5ft08.txt summary: Unexplained pneumonia (UP) caused by a novel coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) emerged in China in late December 2019 and has infected more than 9000 cases by 31 January 2020. A combinative approach of real-time RT–PCR, CRISPR-based assay and metagenomic next-generation sequencing (mNGS) were used to diagnose this unexplained pneumonia patient. The reasons behind this outbreak are numerous, the highly infectious nature of SARS-CoV-2, limited pathogen detection method for unexplained pneumonia, the high population density of the Hubei Province and across China, etc. On 20 January, Shanghai reported the first imported case of SARS-CoV-2 infection, and through this case, we seek a combinative approach of selected techniques to improve pathogen identification of unexplained pneumonia in the future. We then performed real-time RT-PCR, CRISPR-based assay and metagenomic next-generation sequencing (mNGS) on her respiratory sample and finally diagnosed her with COVID-19. abstract: Unexplained pneumonia (UP) caused by a novel coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) emerged in China in late December 2019 and has infected more than 9000 cases by 31 January 2020. Shanghai reported the first imported case of COVID-19 (Coronavirus Disease 2019) in 20 January 2020. A combinative approach of real-time RT–PCR, CRISPR-based assay and metagenomic next-generation sequencing (mNGS) were used to diagnose this unexplained pneumonia patient. Real-time RT–PCR and CRISPR-based assay both reported positive. This sample belonged to Betacoronavirus and shared a more than 99% nucleotide (nt) identity with the Wuhan SARS-CoV-2 isolates. We further compared pros and cons of common molecular diagnostics in UP. In this study, we illustrated the importance of combining molecular diagnostics to rule out common pathogens and performed mNGS to obtain unbiased potential pathogen result for the diagnosis of UP. url: https://doi.org/10.1080/22221751.2020.1738905 doi: 10.1080/22221751.2020.1738905 id: cord-298991-5qae0ege author: Aiello, Francesco title: Coronavirus disease 2019 (SARS-CoV-2) and colonization of ocular tissues and secretions: a systematic review date: 2020-05-18 words: 3143.0 sentences: 183.0 pages: flesch: 50.0 cache: ./cache/cord-298991-5qae0ege.txt txt: ./txt/cord-298991-5qae0ege.txt summary: SARS-CoV-2 may use ocular structure as an additional transmission route, as demonstrated by the COVID-19 patients'' conjunctival secretion and tears positivity to reverse transcriptase-PCR SARS-CoV-2-RNA assay. This systematic review will firstly attempt to analyse the current knowledge on SARS-CoV-2 colonization of ocular and periocular tissues and secretions (i.e., cornea, conjunctiva, lacrimal sac, and tears), in order elucidate if conjunctival transmission occurs, and secondarily aims to propose a potential diagnostic tool in the evaluation of suspected, infected patients. Due to the scant evidence, both original articles, editorials, letters, and reviews providing evidence (i.e., prevalence, anecdotal report) about SARS-CoV-2 colonization of ocular and periocular tissues and secretions were all included in the study. This systematic review analysed 252 SARS-CoV-2infected patients globally who underwent conjunctival swab, and demonstrates the prevalence of ocular conjunctivitis complicating the course of COVID-19 to be as high as 32% (12 patients out 38) , differently as what Lu et al. abstract: Coronavirus disease 19 (COVID-19) has been described to potentially be complicated by ocular involvement. However, scant information is available regarding severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) and ocular structures tropism. We conducted a systematic review of articles referenced in PubMed, Cochrane Library, Web of Science and Chinese Clinical Trial Register (ChiCTR) from December 20, 2019 to April 6, 2020, providing information on the presence of SARS-CoV-2 in cornea, conjunctiva, lacrimal sac, and tears. We excluded ongoing clinical studies as for unobtainable conclusive results. Of 2422 articles, 11 met the inclusion criteria for analysis and were included in the study. None of the studies were multinational. Among the 11 selected papers there were three original articles, one review, four letters, two editorials, and one correspondence letter. Globally, 252 SARS-CoV-2 infected patients were included in our review. The prevalence of ocular conjunctivitis complicating the course of COVID-19 was demonstrated to be as high as 32% in one study only. Globally, three patients had conjunctivitis with a positive tear-PCR, 8 patients had positive tear-PCR in the absence of conjunctivitis, and 14 had conjunctivitis with negative tear-PCR. The majority of the available data regarding SARS-CoV-2 colonization of ocular and periocular tissues and secretions have to be considered controversial. However, it cannot be excluded that SARS-CoV-2 could both infect the eye and the surrounding structures. SARS-CoV-2 may use ocular structure as an additional transmission route, as demonstrated by the COVID-19 patients’ conjunctival secretion and tears positivity to reverse transcriptase-PCR SARS-CoV-2-RNA assay. url: https://doi.org/10.1038/s41433-020-0926-9 doi: 10.1038/s41433-020-0926-9 id: cord-292172-aqsc9fbl author: Al Amin, Md. title: Screening of commercial meat products from supermarket chains for feline derivatives using SP-PCR-RLFP and lab-on-a-chip date: 2020-06-09 words: 4852.0 sentences: 308.0 pages: flesch: 63.0 cache: ./cache/cord-292172-aqsc9fbl.txt txt: ./txt/cord-292172-aqsc9fbl.txt summary: Hence this paper documented the application of species specific polymerase chain reaction-restriction fragment length polymorphism (SP-PCR-RFLP) assay targeting a short-fragments (69 bp) of mitochondrial cytochrome b (cytb) gene to screen feline meat in commercial meat products using lab-on-a-chip. Thus, total 378 samples of two types (chicken and beef) with three commercial meat products (frankfurter, nuggets and meatball) of total six (6) different brands purchased from total six (6) supermarket located at Kedah, Penang and Kuala Lumpur of Malaysia (Fig. 4) were negative for feline meat detection using feline SP-PCR based on lab-on-a-chip (Table 4 ). Henceforward, the amazing stability and established sensitivity of this assay initiates its J o u r n a l P r e -p r o o f application for the screening of larger quantity of samples of three major commercial meat products (frankfurters, nuggets and meatballs) of total six brands from different supermarket chains across Malaysia (three-states) for feline species detection. abstract: Determination of feline meat in food products is an important issue for social, health, economic and religious concern. Hence this paper documented the application of species specific polymerase chain reaction-restriction fragment length polymorphism (SP-PCR-RFLP) assay targeting a short-fragments (69 bp) of mitochondrial cytochrome b (cytb) gene to screen feline meat in commercial meat products using lab-on-a-chip. The SP-PCR assay proved its specificity theoretically and experimentally while testing with different common animal, aquatic and plant species of DNA. The feline specific (69 bp, 43- and 26-bp) characteristic molecular DNA pattern was observed by SP-PCR and RFLP analysis. For assay performance, it was tested in three different types of commercial dummy meat products such as frankfurters, nuggets and meatballs and digested with AluI-restriction enzyme. The highest sensitivity of the assay using lab-on-a-chip was as low as 0.1 pg or 0.01% (w/w) in commercial dummy meat products. We have also applied this assay to screen three important commercial meat products of six different brand from six supermarket chains located at three different states of Malaysia. Thus total 378 samples were tested to validate the specificity, sensitivity, stability of the assay and utilization of it for commercial meat product screening. url: https://api.elsevier.com/content/article/pii/S0889157519302510 doi: 10.1016/j.jfca.2020.103565 id: cord-277276-j2qzhvzi author: Al-Ayed, Mohamed S. title: Viral etiology of respiratory infections in children in southwestern Saudi Arabia using multiplex reverse-transcriptase polymerase chain reaction date: 2014 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: To investigate 15 respiratory viruses in children with acute respiratory tract infections (ARTIs) using multiplex reverse-transcriptase polymerase chain reaction (RT-PCR), and to analyze the clinical and epidemiological features of these viruses. METHODS: In a cross-sectional study, 135 children, ≤5 years of age who presented with ARTIs in Najran Maternity and Children Hospital, Najran, Saudi Arabia between October 2012 and July 2013 were included. The clinical and sociodemographic data, and the laboratory results were recorded using a standardized questionnaire. Two nasopharyngeal swabs were collected from each child: one for bacteriological examination, and the second for viral detection using multiplex RT-PCR. RESULTS: A single viral pathogen was detected in 76 patients, viral coinfections in 9, and mixed viral and bacterial pathogens in 15. Respiratory syncytial virus was isolated in 33 patients, human rhinovirus (hRV) in 22, adenovirus (AdV) in 19, human metapneumovirus in 13, influenza virus in 10, parainfluenza virus in 7, human corona virus (hCoV) in 4, and human bocavirus in one. CONCLUSION: Respiratory syncytial virus, hRV, and AdV were the most frequent viruses, accounting for more than two-thirds of the cases. Other viruses, such as MPV, hCoV NL63, and hCoV OC43, may play a role in pediatric ARTIs. Of significance is the potential use of multiplex RT-PCR to provide epidemiological and virological data for early detection of the emergence of novel respiratory viruses in the era of the Middle East respiratory syndrome coronavirus. url: https://www.ncbi.nlm.nih.gov/pubmed/25399211/ doi: nan id: cord-000988-79fp75u3 author: Al-Siyabi, Turkiya title: A cost effective real-time PCR for the detection of adenovirus from viral swabs date: 2013-06-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Compared to traditional testing strategies, nucleic acid amplification tests such as real-time PCR offer many advantages for the detection of human adenoviruses. However, commercial assays are expensive and cost prohibitive for many clinical laboratories. To overcome fiscal challenges, a cost effective strategy was developed using a combination of homogenization and heat treatment with an “in-house” real-time PCR. In 196 swabs submitted for adenovirus detection, this crude extraction method showed performance characteristics equivalent to viral DNA obtained from a commercial nucleic acid extraction. In addition, the in-house real-time PCR outperformed traditional testing strategies using virus culture, with sensitivities of 100% and 69.2%, respectively. Overall, the combination of homogenization and heat treatment with a sensitive in-house real-time PCR provides accurate results at a cost comparable to viral culture. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3679997/ doi: 10.1186/1743-422x-10-184 id: cord-263389-m6x9gxwe author: AlGhounaim, M. title: Diagnostic yield and clinical impact of routine cell culture for respiratory viruses among children with a negative multiplex RT-PCR result date: 2017-07-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Polymerase chain reaction (PCR) is the reference standard for respiratory virus testing. However, cell culture may still have added value in identifying viruses not detected by PCR. OBJECTIVES: We aimed to estimate the yield and clinical impact of routine respiratory virus culture among children with a negative PCR result. STUDY DESIGN: A retrospective cohort study was performed from Jan. 2013 to Sept. 2015. Respiratory samples from hospitalized or immunocompromised patients <18 years old were routinely inoculated on traditional tube cell culture monolayers if they tested negative by a PCR assay for 12 respiratory viruses. We studied patients with a respiratory specimen negative by PCR and positive by culture. Duplicates and samples of sold services were excluded. Data on demographics, clinical history, laboratory findings, and patient management were collected from patients’ charts. Descriptive and multivariate statistics were performed. RESULTS: Overall, 4638 PCR-negative samples were inoculated in cell culture. Of those, 196 (4.2%) were cell culture positive, and 144 met study inclusion criteria. Most subjects (81.9%) were hospitalized. Mean age was 2.4 ± 3.4 years. The viruses most frequently isolated were cytomegalovirus (33.3%) and enteroviruses (19.4%). Cell culture results prompted a change in management in 5 patients (3.5%), all of whom had acyclovir initiated for localized HSV-1 infection. Four of these had skin or mucosal lesions that could be sampled to establish a diagnosis. CONCLUSION: In children, routine viral culture on respiratory specimens that were negative by PCR has low yield and minimal clinical impact. url: https://api.elsevier.com/content/article/pii/S1386653217302135 doi: 10.1016/j.jcv.2017.07.015 id: cord-356007-6b0w36l9 author: Alanazi, Khalid H. title: Scope and extent of healthcare-associated Middle East respiratory syndrome coronavirus transmission during two contemporaneous outbreaks in Riyadh, Saudi Arabia, 2017 date: 2018-12-31 words: 4028.0 sentences: 212.0 pages: flesch: 48.0 cache: ./cache/cord-356007-6b0w36l9.txt txt: ./txt/cord-356007-6b0w36l9.txt summary: OBJECTIVE: To investigate a Middle East respiratory syndrome coronavirus (MERS-CoV) outbreak event involving multiple healthcare facilities in Riyadh, Saudi Arabia; to characterize transmission; and to explore infection control implications. Of these 10 available HCP, 9 reported prolonged, close contact with an unrecognized patient case before implementation of MERS-CoV IPC measures and with limited PPE use ( Table 3 ). Among the 10 interviewed HCP cases, the time from first positive MERS-CoV result to serum collection was 55-61 days, and 1 was seropositive: a 32-year-old female who had reported headache, muscle aches, and productive cough. Among them, 9 HCP (33%) tested rRT-PCR positive for MERS-CoV; 5 reported contact with index patient B before At hospital B, 34 of 50 MERS-CoV rRT-PCR-negative HCP contacts of cases (68%) were interviewed and provided serum. One was seropositive, a physician who had close, prolonged contact with index B after isolation and while wearing recommended PPE; however, he had previously tested rRT-PCR positive for MERS-CoV in 2013. abstract: OBJECTIVE: To investigate a Middle East respiratory syndrome coronavirus (MERS-CoV) outbreak event involving multiple healthcare facilities in Riyadh, Saudi Arabia; to characterize transmission; and to explore infection control implications. DESIGN: Outbreak investigation. SETTING: Cases presented in 4 healthcare facilities in Riyadh, Saudi Arabia: a tertiary-care hospital, a specialty pulmonary hospital, an outpatient clinic, and an outpatient dialysis unit. METHODS: Contact tracing and testing were performed following reports of cases at 2 hospitals. Laboratory results were confirmed by real-time reverse transcription polymerase chain reaction (rRT-PCR) and/or genome sequencing. We assessed exposures and determined seropositivity among available healthcare personnel (HCP) cases and HCP contacts of cases. RESULTS: In total, 48 cases were identified, involving patients, HCP, and family members across 2 hospitals, an outpatient clinic, and a dialysis clinic. At each hospital, transmission was linked to a unique index case. Moreover, 4 cases were associated with superspreading events (any interaction where a case patient transmitted to ≥5 subsequent case patients). All 4 of these patients were severely ill, were initially not recognized as MERS-CoV cases, and subsequently died. Genomic sequences clustered separately, suggesting 2 distinct outbreaks. Overall, 4 (24%) of 17 HCP cases and 3 (3%) of 114 HCP contacts of cases were seropositive. CONCLUSIONS: We describe 2 distinct healthcare-associated outbreaks, each initiated by a unique index case and characterized by multiple superspreading events. Delays in recognition and in subsequent implementation of control measures contributed to secondary transmission. Prompt contact tracing, repeated testing, HCP furloughing, and implementation of recommended transmission-based precautions for suspected cases ultimately halted transmission. url: https://doi.org/10.1017/ice.2018.290 doi: 10.1017/ice.2018.290 id: cord-323397-5yop6clu author: Albalate, M. title: Alta prevalencia de covid19 asintomático en hemodiálisis. Aprendiendo dia a dia el primer mes de pandemia de covid19 date: 2020-04-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Resumen Los pacientes en diálisis son un grupo de riesgo de sufrir la infección por el SARS-CoV2 y posiblemente de tener más complicaciones, pero la información con la que contamos es escasa. El objetivo de este trabajo es describir la experiencia del primer mes de pandemia por SARS-Cov2 en una unidad hospitalaria de hemodiálisis (HD) que atiende al 2º distrito madrileño con más en incidencia de COVID19 (casi 1000 pacientes en 100000 h). Se presenta mediante un diario las acciones llevadas a cabo, la incidencia de COVID19 en pacientes y en el personal sanitario, algunas características clínicas y el resultado de un cribado entre todos los pacientes de la unidad. Al inicio, teníamos 90 pacientes en HD: 37(41,1%) han tenido COVID19, de los que 17 (45,9%) fueron diagnosticados por síntomas detectados en el triaje o durante la sesión y 15 (40,5%) en un cribado realizado a posteriori en los que no se había hecho test diagnóstico por PCR-SARS-Cov2 hasta ese momento. El síntoma más frecuente fue la fiebre, el 50% presentó linfopenia y el 18,4% saturación de O2 <95%. Precisaron ingreso hospitalario 16(43,2%) y 6 fallecieron (16,2%). Encontramos un agrupamiento de contagio por turnos y también en aquellos que usaban transporte colectivo. En cuanto al personal, de las 44 personas involucradas, 15 (34%) presentaron sintomatología compatible y 4 (9%) tuvieron PCR SARS-Cov-2 positiva determinada por Salud Laboral y 9 (20%) precisaron algún periodo de Incapacidad Laboral Transitoria (ILT), y 5 fueron considerados casos probables. Conclusiones: Detectamos una elevada prevalencia de COVID19 con un elevado porcentaje detectado por cribado y por tanto la necesidad de ser proactivos en el diagnóstico para detener la pandemia. La mayoría están siendo manejados de forma ambulatoria, aunque también aparecen cuadros graves y la mortalidad hasta ahora es del 16,2%. En cuanto al personal un 20% ha precisado ILT en relación con COVID19. Abstract Dialysis patients are a risk group for SARS-CoV2 infection and possibly further complications, but we have little information. The aim of this paper is to describe the experience of the first month of the SARS-Cov2 pandemic in a hospital haemodialysis (HD) unit serving the district of Madrid with the second highest incidence of COVID19 (almost 1000 patients in 100000 h). In the form of a diary, we present the actions undertaken, the incidence of COVID19 in patients and health staff, some clinical characteristics and the results of screening all the patients in the unit. We started with 90 patients on HD: 37 (41.1%) had COVID19, of whom 17 (45.9%) were diagnosed through symptoms detected in triage or during the session, and 15 (40.5%) through subsequent screening of those who, until that time, had not undergone SARS-CoV2 PCR testing. Fever was the most frequent symptom, 50% had lymphopenia and 18.4% <95% O2 saturation. Sixteen (43.2%) patients required hospital admission and 6 (16.2%) died. We found a cluster of infection per shift and also among those using public transport. In terms of staff, of the 44 people involved, 15 (34%) had compatible symptoms, 4 (9%) were confirmed as SARS-Cov2 PCR cases by occupational health, 9 (20%) required some period of sick leave, temporary disability to work (ILT), and 5 were considered likely cases. Conclusions: We detected a high prevalence of COVID19 with a high percentage detected by screening; hence the need for proactive diagnosis to stop the pandemic. Most cases are managed as outpatients, however severe symptoms are also appearing and mortality to date is 16.2%. In terms of staff, 20% have required sick leave in relation to COVID19. url: https://api.elsevier.com/content/article/pii/S0211699520300436 doi: 10.1016/j.nefro.2020.04.005 id: cord-333261-knj2rrut author: Albright, Catherine J. title: An exercise in molecular epidemiology: Human rhinovirus prevalence and genetics date: 2011-11-11 words: 3408.0 sentences: 205.0 pages: flesch: 59.0 cache: ./cache/cord-333261-knj2rrut.txt txt: ./txt/cord-333261-knj2rrut.txt summary: To facilitate the collections of HRV sequences over a number of years, a virology experiment was designed in which students test nasal lavage samples to look for HRV infection. The extensive data available on HRV genomes enables many bioinformatics opportunities for students, including alignment of genome sequences to look for mutations at the RNA level and differences among protein sequences. Students can examine differences in the HRV serotypes over several years of data regarding a university population to identify HRV mutations that have occurred and their severity in causing symptoms in the host. In this inquiry-based laboratory project, students use a variety of techniques, including RNA isolation, cDNA synthesis, qPCR, and agarose gel electrophoresis to look for the presence of HRV in nasal lavage samples from human subjects. By analyzing surveys in which subjects indicate severity of their symptoms, stress factors, and average hours of rest per night, students can identify possible contributors to HRV infection. abstract: Human rhinovirus (HRV) is one of the most common human respiratory pathogens and is responsible for the majority of upper respiratory illnesses. Recently, a phylogeny was constructed from all known American Type Culture Collection (ATCC) HRV sequences. From this study, three HRV classifications (HRVA, HRVB, and HRVC) were determined and techniques for classifying new isolates of HRV were reported. The genetic change of this virus in specific populations over time is of great interest to understand the evolution and epidemiology of viruses. To facilitate the collections of HRV sequences over a number of years, a virology experiment was designed in which students test nasal lavage samples to look for HRV infection. Students will learn a variety of techniques including RNA isolation, cDNA synthesis, qPCR, and agarose gel electrophoresis as well as bioinformatic skills though examination of sequences from the HRV‐field isolates. Furthermore, students can look at symptom data from subjects to investigate correlations between symptom severity and factors such as stress and sleep patterns. Such information can be used to examine hypotheses regarding HRV mutation, symptom severity and epidemiology. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION Vol. 39, No. 6, pp. 457–458, 2011 url: https://doi.org/10.1002/bmb.20530 doi: 10.1002/bmb.20530 id: cord-103735-nil1vv6h author: Alfano, Niccolo title: Non-invasive surveys of mammalian viruses using environmental DNA date: 2020-03-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Environmental DNA (eDNA) and its subdiscipline, invertebrate-derived DNA (iDNA) have been used to survey biodiversity non-invasively [1,2]. Water is ubiquitous in most ecosystems, and, among invertebrates, terrestrial haematophagous leeches are abundant and can be easily collected in many tropical rainforests [3,4]. Such non-invasive nucleic acid sources can mitigate difficulties of obtaining wildlife samples, particularly in remote areas or for rare species. Recently, eDNA/iDNA sources have been applied to monitoring specific wildlife pathogens [5,6]. However, previous studies have focused on known pathogens, whereas most wildlife pathogens are uncharacterized and unknown. Non-invasive approaches to monitoring known and novel pathogens may be of particular benefit in ecosystems prone to viral emergence, many of which occur in areas where invasive sampling is challenging, such as tropical rainforests. Here, we show that both eDNA from natural waterholes, and iDNA from terrestrial haematophagous leeches, can be used to detect unknown viruses circulating in mammalian hosts (Figure 1). Using a curated set of RNA oligonucleotides based on the ViroChip microarray assay [7] as baits in a hybridization capture system, multiple mammalian RNA and DNA viruses were detected from both eDNA and iDNA samples. Congruence was found between host DNA assignment and viruses identified in leeches, and between animals observed visiting the waterholes and the viruses detected. Our results demonstrate that eDNA/iDNA samples may represent an effective non-invasive resource for studying wildlife viral diversity. Several of the detected viruses were novel, highlighting the potential of eDNA/iDNA for epidemiological analysis of emerging viruses prior to their emergence. Highlights Environmental DNA (water and blood-sucking leeches) provided a non-invasive method of screening wildlife for viruses A comprehensive viral RNA oligonucleotide bait set was developed to capture known and unknown mammalian virus diversity Leech blood meal host determination and viruses identified were congruent Viruses determined from water correlated with known and observed species visiting the water sources In brief Alfano, Dayaram, et al. demonstrate that environmental DNA from southeast Asian leech bloodmeals and waterholes from Africa and Mongolia can be used as to detect viruses circulating in wildlife. These nucleic acid sources may represent an effective non-invasive resource for studying wildlife viral diversity and emerging viruses pre-emergence. url: https://doi.org/10.1101/2020.03.26.009993 doi: 10.1101/2020.03.26.009993 id: cord-349838-p6vfzbla author: Algwaiz, Ghada title: Real-world issues and potential solutions in HCT during the COVID-19 pandemic: Perspectives from the WBMT and the CIBMTR''s Health Services and International Studies Committee date: 2020-07-24 words: 4060.0 sentences: 229.0 pages: flesch: 44.0 cache: ./cache/cord-349838-p6vfzbla.txt txt: ./txt/cord-349838-p6vfzbla.txt summary: Realizing the challenges as a result of this pandemic affecting the daily practice of the HCT centers, and the recognition of the variability in practice worldwide, the Worldwide Network for Blood & Marrow Transplantation (WBMT) and the Center for International Blood and Marrow Transplant Research (CIBMTR) Health Services and International Studies Committee have jointly produced an expert opinion statement as a general guide to deal with certain aspects of HCT including diagnostics for SARS-CoV-2 in HCT patients, pre-and-post-HCT management, donor issues, medical tourism and facilities management. While acknowledging all aforementioned challenges and taking into account current recommendations or guidelines issued by the American Society for Transplantation and Cellular Therapy (ASTCT) and the European Society for Blood and Marrow Transplantation (EBMT) (which are WBMT members), herein, we aim at providing a consensus among the authors from WBMT and CIBMTR''s HSIS committee and other HCT experts who represent multiple continents and allude to the current worldwide threat to HCT patient from the COVID-19 pandemic (7, 8) . abstract: The current COVID-19 pandemic, caused by SARS-CoV-2, has impacted many facets of hematopoietic cell transplantation (HCT) in both developed and developing countries. Realizing the challenges as a result of this pandemic affecting the daily practice of the HCT centers, and the recognition of the variability in practice worldwide, the Worldwide Network for Blood & Marrow Transplantation (WBMT) and the Center for International Blood and Marrow Transplant Research (CIBMTR) Health Services and International Studies Committee have jointly produced an expert opinion statement as a general guide to deal with certain aspects of HCT including diagnostics for SARS-CoV-2 in HCT patients, pre-and-post-HCT management, donor issues, medical tourism and facilities management. During these crucial times, which may last for months or years, the HCT community must reorganize to proceed with transplant activity in those patients who urgently require it, albeit with extreme caution.This shared knowledge may be of value to the HCT community in the absence of highquality evidence-based medicine. url: https://api.elsevier.com/content/article/pii/S1083879120304547 doi: 10.1016/j.bbmt.2020.07.021 id: cord-260457-m1jbpo5l author: Allander, Tobias title: Human Bocavirus and Acute Wheezing in Children date: 2007-04-01 words: 3713.0 sentences: 209.0 pages: flesch: 49.0 cache: ./cache/cord-260457-m1jbpo5l.txt txt: ./txt/cord-260457-m1jbpo5l.txt summary: We investigated the presence of human bocavirus by quantitative polymerase chain reaction of nasopharyngeal aspirate specimens and selected serum samples obtained from 259 children (median age, 1.6 years) who had been hospitalized for acute expiratory wheezing. Human bocavirus DNA was frequently detected in serum specimens obtained from patients with acute wheezing, suggesting systemic infection. Results suggest a model for bocavirus infection in which high viral loads are potentially associated with respiratory symptoms and low viral loads indicate asymptomatic shedding. Of the 293 children who were randomized, 259 children (median age, 1.6 years; range, 3 months to 15 years) who had sufficient sample material available for complete virus diagnostic evaluation (nasopharyngeal aspirate specimens were used for PCR [for 16 viruses], virus culture [for 9 viruses], and antigen detection [for 7 viruses]; acute-and convalescent-phase serum samples were used for serologic testing [for 7 viruses]) were included in the present study. abstract: Background. Human bocavirus is a newly discovered parvovirus. It has been detected primarily in children with acute lower respiratory tract infection, but its occurrence, clinical profile, and role as a causative agent of respiratory tract disease are not clear. Methods. We investigated the presence of human bocavirus by quantitative polymerase chain reaction of nasopharyngeal aspirate specimens and selected serum samples obtained from 259 children (median age, 1.6 years) who had been hospitalized for acute expiratory wheezing. The samples were analyzed for 16 respiratory viruses by polymerase chain reaction, virus culture, antigen detection, and serological assays. Results. At least 1 potential etiologic agent was detected in 95% of children, and >1 agent was detected in 34% of children. Human bocavirus was detected in 49 children (19%). A large proportion of the cases were mixed infections with other viruses, but human bocavirus was the only virus detected in 12 children (5%). High viral loads of human bocavirus were noted mainly in the absence of other viral agents, suggesting a causative role for acute wheezing. In addition, infections that had uncertain clinical relevance and low viral loads were prevalent. Human bocavirus DNA was frequently detected in serum specimens obtained from patients with acute wheezing, suggesting systemic infection. Conclusions. Human bocavirus is prevalent among children with acute wheezing and can cause systemic infection. Results suggest a model for bocavirus infection in which high viral loads are potentially associated with respiratory symptoms and low viral loads indicate asymptomatic shedding. Therefore, quantitative polymerase chain reaction analysis may be important for additional studies of human bocavirus. url: https://www.ncbi.nlm.nih.gov/pubmed/17342639/ doi: 10.1086/512196 id: cord-292828-29jbf9ik author: Alsaleh, Asma N title: Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control date: 2014-01-09 words: 3915.0 sentences: 185.0 pages: flesch: 45.0 cache: ./cache/cord-292828-29jbf9ik.txt txt: ./txt/cord-292828-29jbf9ik.txt summary: title: Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control We therefore investigated the impact of sample collection quality and the presence of visible mould in samples upon respiratory virus detection by real-time polymerase chain reaction (PCR) assays. Quality control measures, including monitoring human DNA loads using ERV3 as a marker for epithelial cell components in samples should be undertaken to optimize the validity of real-time PCR results for respiratory virus investigations in community-based studies. Importantly, when using highly sensitive polymerase chain reaction (PCR) assays the detection rates for respiratory viruses are similar in both anterior nasal swab specimens and samples collected by the more traditional method of nasopharyngeal aspiration [18, 19] . The ORChID project is an ongoing comprehensive community-based study using PCR assays to detect respiratory viruses in anterior nasal swab specimens taken weekly by parents from their infants throughout the first 2-years of life. abstract: BACKGROUND: Carefully conducted, community-based, longitudinal studies are required to gain further understanding of the nature and timing of respiratory viruses causing infections in the population. However, such studies pose unique challenges for field specimen collection, including as we have observed the appearance of mould in some nasal swab specimens. We therefore investigated the impact of sample collection quality and the presence of visible mould in samples upon respiratory virus detection by real-time polymerase chain reaction (PCR) assays. METHODS: Anterior nasal swab samples were collected from infants participating in an ongoing community-based, longitudinal, dynamic birth cohort study. The samples were first collected from each infant shortly after birth and weekly thereafter. They were then mailed to the laboratory where they were catalogued, stored at -80°C and later screened by PCR for 17 respiratory viruses. The quality of specimen collection was assessed by screening for human deoxyribonucleic acid (DNA) using endogenous retrovirus 3 (ERV3). The impact of ERV3 load upon respiratory virus detection and the impact of visible mould observed in a subset of swabs reaching the laboratory upon both ERV3 loads and respiratory virus detection was determined. RESULTS: In total, 4933 nasal swabs were received in the laboratory. ERV3 load in nasal swabs was associated with respiratory virus detection. Reduced respiratory virus detection (odds ratio 0.35; 95% confidence interval 0.27-0.44) was observed in samples where the ERV3 could not be identified. Mould was associated with increased time of samples reaching the laboratory and reduced ERV3 loads and respiratory virus detection. CONCLUSION: Suboptimal sample collection and high levels of visible mould can impact negatively upon sample quality. Quality control measures, including monitoring human DNA loads using ERV3 as a marker for epithelial cell components in samples should be undertaken to optimize the validity of real-time PCR results for respiratory virus investigations in community-based studies. url: https://doi.org/10.1186/1471-2334-14-15 doi: 10.1186/1471-2334-14-15 id: cord-321855-7b1c2xdh author: Alshami, Alanoud title: Silent disease and loss of taste and smell are common manifestations of SARS-COV-2 infection in a quarantine facility: Saudi Arabia date: 2020-10-30 words: 3380.0 sentences: 190.0 pages: flesch: 56.0 cache: ./cache/cord-321855-7b1c2xdh.txt txt: ./txt/cord-321855-7b1c2xdh.txt summary: title: Silent disease and loss of taste and smell are common manifestations of SARS-COV-2 infection in a quarantine facility: Saudi Arabia PRIMARY AND SECONDARY MEASURES: The clinical presentation, prevalence of asymptomatic carriers among SARS-COV-2 positive quarantined subjects, and the difference between virus clearance among symptomatic and asymptomatic individuals. The persistent positive PCR beyond 14 days observed in the mild symptomatic residents despite being symptoms free, warrant further studies to determine its implications on disease spread and control. have examined 24 asymptomatic infected individuals with a history of close contact with SARS-COV-2 confirmed cases and found that only 20% of them developed symptoms. Our findings are in light with a recent study that reported a 59% prevalence of loss of taste and smell in a cohort of COVID-19 patients [15] . Sudden onset of loss of smell and taste were prevalent in our study and were key symptoms of mild disease. abstract: OBJECTIVES: In this study, we aimed to study the clinical presentations, and viral clearance of SARS-COV-2 positive quarantined individuals. DESIGN: Cross-sectional study. SETTING: Governmental- designated facility in the eastern province, Saudi Arabia. PARTICIPANTS: 128 laboratory-confirmed COVID-19 quarantined individuals who had a history of travel abroad in the last 14 days before the quarantine or were in direct contact with laboratory-confirmed cases. The study was from March 18th-till April 16th. PRIMARY AND SECONDARY MEASURES: The clinical presentation, prevalence of asymptomatic carriers among SARS-COV-2 positive quarantined subjects, and the difference between virus clearance among symptomatic and asymptomatic individuals. RESULTS: Sixty-nine of the 128 residents (54%) were completely asymptomatic until the end of the study. The remaining 59 residents (46%) had only mild symptoms. The most common symptom was a sudden loss of smell and taste, accounting for 47.5%. The median time to virus clearance was significantly different between the two groups. Symptomatic residents cleared the virus at a median of 17 days (95% CI, 12.4–21.6) from the first positive PCR vs. 11days (95% CI, 8.7–13.3) in the asymptomatic group (P = 0.011). False-negative test results occurred in 18.8% of the total residents and false-positive results in 3%. CONCLUSION: The prevalence of asymptomatic carriers among quarantined travelers and those identified by contact tracing is high in our study. Therefore, testing, tracing, and isolating travelers and contacts of laboratory-confirmed cases, regardless of symptoms, were very effective measures for early disease identification and containment. Loss of taste and smell were the most common presentations in our mild symptomatic residents and should be used as a screening tool for COVID-19. The persistent positive PCR beyond 14 days observed in the mild symptomatic residents despite being symptoms free, warrant further studies to determine its implications on disease spread and control. url: https://doi.org/10.1371/journal.pone.0241258 doi: 10.1371/journal.pone.0241258 id: cord-289612-4x5t4c5u author: Alsuliman, Tamim title: COVID-19 paraclinical diagnostic tools: Updates and future trends date: 2020-06-20 words: 7353.0 sentences: 387.0 pages: flesch: 48.0 cache: ./cache/cord-289612-4x5t4c5u.txt txt: ./txt/cord-289612-4x5t4c5u.txt summary: Laboratory-confirmed SARS-CoV-2 infection requires the detection of viral nucleic acid in respiratory tract samples by the use of real-time reverse-transcription polymerase chain reaction (rRT-PCR) assay. In the course of this phase, upper respiratory specimens were tested by RT-PCR for viral RNA and the majority of the patients showed positive results for SARS-CoV-2. These results contrast with another German smaller study by Wolfel et al., conducted on 9 COVID-19 patients, with no discernible difference in viral loads or detection rates when comparing nasal and throat swabs [38] . found that 66.67% of laboratory-confirmed COVID-19 patients were tested positive for SARS-CoV-2 RNA in stool specimens. enrolled a total of 173 confirmed cases of COVID-19 by the use of rRT-PCR on samples from the respiratory track reported that the seroconversion sequentially appeared for the total antibody (Ab), IgM and then IgG, with a median time of 11, 12 and 14 days, respectively. Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: a report of 1014 cases abstract: MOTIVATION: COVID-19 is one of the most widely affecting pandemics. As for many respiratory viruses-caused diseases, diagnosis of COVID-19 relies on two main compartments: clinical and paraclinical diagnostic criteria. Rapid and accurate diagnosis is vital in such a pandemic. On one side, rapidity may enhance management effectiveness, while on the other, coupling efficiency and less costly procedures may permit more effective community-scale management. METHODOLOGY AND MAIN STRUCTURE: In this review, we shed light on the most used and the most validated diagnostic tools. Furthermore, we intend to include few under-development techniques that may be potentially useful in this context. The practical intent of our work is to provide clinicians with a realistic summarized review of the essential elements in the applied paraclinical diagnosis of COVID-19. url: https://doi.org/10.1016/j.retram.2020.06.001 doi: 10.1016/j.retram.2020.06.001 id: cord-265978-i0fu8e0p author: Amer, Haitham M. title: Development of a SYBR Green I based real-time RT-PCR assay for detection and quantification of bovine coronavirus date: 2011-06-30 words: 4797.0 sentences: 227.0 pages: flesch: 49.0 cache: ./cache/cord-265978-i0fu8e0p.txt txt: ./txt/cord-265978-i0fu8e0p.txt summary: In this report, a real-time RT-PCR system using SYBR Green I and melt curve analysis was developed for detection and quantification of BCoV in clinical samples. The reaction conditions were first optimized by testing variable concentrations of BCoV and internal control QPCR primer sets; MgCl 2 concentrations; template volumes and primer annealing Following amplification, a melt curve analysis was performed to verify the specificity of the amplified products by their specific melting temperatures (Tm). In order to determine the optimal conditions for developing a robust SYBR Green I based real-time qPCR assay that detects BCoV and internal control RNA simultaneously, different variables of the reaction were assessed. The competence of the developed real-time RT-PCR assay, for accurate detection of BCoV in clinical samples, was evaluated by analysis of 103 swab samples (68 fecal and 35 nasal) in comparison to the gel-based RT-PCR assay ( Table 4 ). abstract: Abstract A novel two-step, SYBR Green I based real-time RT-PCR assay was developed for detection and quantification of BCoV using ABI PRISM 7500 sequence detection system. The assay was carried out using two sets of primers designed to amplify highly conserved sequences of the nucleocapsid gene of BCoV and the internal control, bovine glyceraldehyde-3-phosphate dehydrogenase, RNA. Specific identification of both targets was elucidated by melt curve analysis, in which the BCoV amplified product generated a melt peak at 78.35 ± 0.26 °C and the internal control RNA at 82.54 ± 0.32 °C. The assay was highly specific since all negative controls and other viruses of clinical and structural relevance failed to develop any positive results. The detection limit of the reaction was 103 plasmid copies and 1.17 × 10−3 TCID50 of the tissue culture propagated virus. Standard deviation and coefficient of variation was low for both intra-assay and inter-assay variability. The assay performance on field samples was evaluated on 103 (68 fecal and 35 nasal) swab specimens and compared with the conventional RT-PCR assay. The results of both assays matched for the diagnosis of 65 fecal and 33 nasal samples. However, three fecal and two nasal samples tested negative in gel-based assay were positive for the real-time RT-PCR. The robustness and a high-throughput performance of the developed assay make it a powerful tool in diagnostic applications and in BCoV research. url: https://doi.org/10.1016/j.mcp.2011.03.001 doi: 10.1016/j.mcp.2011.03.001 id: cord-270526-o4hsr4pm author: An, Dong-Jun title: An immunochromatography assay for rapid antemortem diagnosis of dogs suspected to have canine distemper date: 2007-10-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A new assay was developed for rapid and antemortem diagnosis of canine distemper (CD). This immunochromatography (IC)-based assay, which employs two monoclonal anti-CDV antibodies, was compared with nested PCR. When serial dilutions of purified CDV were tested, the CDV detection limits of the nested PCR and IC assays were 2 × 10(2) TCID(50)/ml and 5 × 10(2) TCID(50)/ml, respectively. Nasal irrigation fluid, conjunctival swabs, and blood lymphocytes from 66 dogs suspected to have CD were tested. Preliminary IC experiments revealed that the optimal sample volume and reaction time were 100 μl and 5 min, respectively. Relative to nested PCR, the sensitivity and specificity of the IC assay was maximal (100% and 100%, respectively) when conjunctival swabs were tested. This is significant because conjunctival swab specimens are easy to obtain in the early phase of CD infection. However, with blood lymphocytes and nasal samples, the IC assay was slightly less sensitive (89.7% and 85.7%, respectively) and specific (94.6% and 100%, respectively) than nested PCR. Since this novel IC assay does not require special instruments, it is a simple enough for dog owners to use. Since early detection of CD would allow appropriate treatment and quarantine to be instituted quickly, such a test would help reduce the morbidity and mortality associated with CD help to prevent its spread to other animals. url: https://api.elsevier.com/content/article/pii/S0166093407003618 doi: 10.1016/j.jviromet.2007.09.006 id: cord-288962-jgtoehcr author: Andréoletti, Laurent title: Differential detection of rhinoviruses and enteroviruses RNA sequences associated with classical immunofluorescence assay detection of respiratory virus antigens in nasopharyngeal swabs from infants with bronchiolitis date: 2000-06-06 words: 3704.0 sentences: 186.0 pages: flesch: 36.0 cache: ./cache/cord-288962-jgtoehcr.txt txt: ./txt/cord-288962-jgtoehcr.txt summary: To define the role of enteroviruses and human rhinoviruses as etiological agents in childhood bronchiolitis, clinical aspirates from 84 infants admitted to hospital with symptoms of obstructive bronchiolitis were tested by picornavirus RT‐PCR assay, adenovirus PCR assay and classical immunofluorescence antigen detection of common respiratory viral agents. In summary, combination of molecular and classical detection assays of common viruses can be used to demonstrate enterovirus and human rhinovirus respiratory infection in childhood bronchiolitis, and provides an improved approach to obtain new insights into concomitant viral respiratory tract infection in infants. To investigate the role of enteroviruses and human rhinoviruses as etiological agent in bronchiolitis, 84 nasopharyngeal aspirates were tested by picornavirus RT-PCR assay, classical immunofluorescence antigens detection of respiratory syncytial viruses, influenza viruses, parainfluenza viruses, coronaviruses, and adenovirus PCR assay. abstract: To define the role of enteroviruses and human rhinoviruses as etiological agents in childhood bronchiolitis, clinical aspirates from 84 infants admitted to hospital with symptoms of obstructive bronchiolitis were tested by picornavirus RT‐PCR assay, adenovirus PCR assay and classical immunofluorescence antigen detection of common respiratory viral agents. Respiratory syncytial viruses (A&B) were detectable in 45 of 84 (53.6%) nasopharyngeal aspirates from infants with bronchiolitis, whereas coronaviruses, influenza viruses, and parainfluenza viruses were not detectable in the same samples. Adenoviruses were detectable by PCR in 11 of 84 (13.1%) nasopharyngeal swabs. By using a picornavirus RT‐PCR assay followed by a differential molecular hybridisation, rhinovirus and enterovirus RNA sequences were detected in 16 of 84 (19%) and in 10 of 84 (11.9%) of the nasopharyngeal swabs tested. Positive human rhinovirus or enterovirus RT‐PCR assay, however, was the only evidence of respiratory infection in 8 of 84 (9.5%) and in 7 of 84 (8.33%) of the studied patients. Respiratory syncytial viruses, human rhinoviruses, adenoviruses, and enteroviruses occur in dual infections detected in 18 of 84 (21.4%) respiratory samples tested. The median duration of stay in hospital was not significantly different between the patients demonstrating a single viral infection and those with a dual viral infection (6.22 ± 2.07 vs. 5.04 ± 0.95 days; P > 0.05). In summary, combination of molecular and classical detection assays of common viruses can be used to demonstrate enterovirus and human rhinovirus respiratory infection in childhood bronchiolitis, and provides an improved approach to obtain new insights into concomitant viral respiratory tract infection in infants. J. Med. Virol. 61:341–346, 2000. © 2000 Wiley‐Liss, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/10861643/ doi: 10.1002/1096-9071(200007)61:3<341::aid-jmv10>3.0.co;2-0 id: cord-305694-qzf425lw author: Andrés-Lasheras, Sara title: Preliminary studies on isolates of Clostridium difficile from dogs and exotic pets date: 2018-03-09 words: 4542.0 sentences: 253.0 pages: flesch: 48.0 cache: ./cache/cord-305694-qzf425lw.txt txt: ./txt/cord-305694-qzf425lw.txt summary: CONCLUSIONS: The results obtained in this study suggest the implementation of antimicrobial susceptibility surveillance programs to assess the prevalence of metronidazole resistance in dogs; molecular studies to elucidate C. difficile in canine enteric disease is still unclear due to the presence of toxigenic strains or their toxins in asymptomatic animals and the failure to reproduce CDI in healthy dogs with and without antibiotic treatment [9, 10] . difficile, molecular characterisation of the strains obtained (i.e. tpi housekeeping and toxin genes detection by PCR, identification of non-toxigenic strains, and PCR-ribotyping) and antimicrobial susceptibility testing was performed as described elsewhere [21] . Since the ribotypes found in dogs are also commonly found in humans, it is possible Fig. 2 Metronidazole susceptibility test of Clostridium difficile D24 strain after 48 h of incubation. Antibiotic resistance patterns and PCR-ribotyping of Clostridium difficile strains isolated from swine and dogs in Italy abstract: BACKGROUND: Clostridium difficile infection (CDI) is recognised as an emerging disease in both humans and some animal species. During the past few years, insights into human CDI epidemiology changed and C. difficile is also considered as an emerging community-acquired pathogen. Certain ribotypes (RT) are possibly associated with zoonotic transmission. The objective of this study was to assess the presence of C. difficile in a population of pets and to characterise the isolates. RESULTS: Faecal samples from a total of 90 diarrhoeic dogs and 24 from exotic animal species (both diarrhoeic and non-diarrhoeic) were analysed. Clostridium difficile was isolated from 6 (6.7%) dogs and one reptile sample (4.2%). Four (66.7%) of the six dog strains were capable of producing toxins. Four known different RTs were detected in dogs (010, 014, 123 and 358) and a new one was found in a faecal sample of an exotic animal. This new RT isolate was negative for all toxin genes tested and belonged to sequence type 347 which has been proposed as a Clade-III member. Importantly, two dog strains showed a stable resistance to metronidazole (initial MIC values: 128 and 48 μg/ml). CONCLUSIONS: The results obtained in this study suggest the implementation of antimicrobial susceptibility surveillance programs to assess the prevalence of metronidazole resistance in dogs; molecular studies to elucidate C. difficile metronidazole resistance mechanisms are warranted. Based on the similarity between the ribotypes observed in dogs and those described in humans, the zoonotic transmission should be further explored. Furthermore, exotic animals have shown to harbor uncommon C. difficile strains which require further genomic studies. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12917-018-1402-7) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/29523201/ doi: 10.1186/s12917-018-1402-7 id: cord-329564-tmi1u224 author: Arashiro, Takeshi title: COVID-19 in 2 Persons with Mild Upper Respiratory Tract Symptoms on a Cruise Ship, Japan date: 2020-06-17 words: 1991.0 sentences: 128.0 pages: flesch: 56.0 cache: ./cache/cord-329564-tmi1u224.txt txt: ./txt/cord-329564-tmi1u224.txt summary: title: COVID-19 in 2 Persons with Mild Upper Respiratory Tract Symptoms on a Cruise Ship, Japan We created an illustration showing the floors where the eventual COVID-19 case-patients worked or shopped, along with dates of symptom onset, potential incubation periods, symptom durations, confirmed times of positive diagnosis, and times of discharge ( Figure 1, panel A) . By February 28, a total of 705 COVID-19 cases were confirmed among 4,061 passengers and crew tested; 392 cases were asymptomatic, 36 persons were admitted to intensive care units, and 6 patients died (2) . Because of the lower threshold for testing persons on board, the cruise ship created an opportunity to observe mild COVID-19 cases and monitor patient symptoms. We describe 2 cases of coronavirus disease in patients with mild upper respiratory symptoms. We describe 2 cases of coronavirus disease in patients with mild upper respiratory symptoms. Clinical courses of 2 case-patients with coronavirus disease (COVID-19) admitted from a cruise ship docked in Japan, 2020. abstract: We describe 2 cases of coronavirus disease in patients with mild upper respiratory symptoms. Both patients worked on a cruise ship quarantined off the coast of Japan. One patient had persistent, low-grade upper respiratory tract symptoms without fever. The other patient had rapid symptom cessation but persistent viral RNA detection. url: https://doi.org/10.3201/eid2606.200452 doi: 10.3201/eid2606.200452 id: cord-324531-lpoelp91 author: Artesi, Maria title: A Recurrent Mutation at Position 26340 of SARS-CoV-2 Is Associated with Failure of the E Gene Quantitative Reverse Transcription-PCR Utilized in a Commercial Dual-Target Diagnostic Assay date: 2020-09-22 words: 2882.0 sentences: 185.0 pages: flesch: 61.0 cache: ./cache/cord-324531-lpoelp91.txt txt: ./txt/cord-324531-lpoelp91.txt summary: title: A Recurrent Mutation at Position 26340 of SARS-CoV-2 Is Associated with Failure of the E Gene Quantitative Reverse Transcription-PCR Utilized in a Commercial Dual-Target Diagnostic Assay At the current time, a number of quantitative real-time PCR (qRT-PCR) assays have been developed to identify SARS-CoV-2, targeting multiple positions in the viral genome. Here, we report the identification of a C-to-U transition at position 26340 of the SARS-CoV-2 genome that is associated with failure of the cobas SARS-CoV-2 E gene qRT-PCR in eight patients. The cobas system (Roche) implements a dual-target assay to detect SARS-CoV-2, with qRT-PCRs targeting both the ORF1ab region and the E gene (see Fig. S1 in the supplemental material). We speculated that these samples carried a common variant that interfered with the E gene qRT-PCR and carried out whole-genome sequencing of the viruses using the Artic Network protocol (17) . abstract: Control of the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic requires accurate laboratory testing to identify infected individuals while also clearing essential staff to continue to work. At the current time, a number of quantitative real-time PCR (qRT-PCR) assays have been developed to identify SARS-CoV-2, targeting multiple positions in the viral genome. While the mutation rate of SARS-CoV-2 is moderate, given the large number of transmission chains, it is prudent to monitor circulating viruses for variants that might compromise these assays. Here, we report the identification of a C-to-U transition at position 26340 of the SARS-CoV-2 genome that is associated with failure of the cobas SARS-CoV-2 E gene qRT-PCR in eight patients. As the cobas SARS-CoV-2 assay targets two positions in the genome, the individuals carrying this variant were still called SARS-CoV-2 positive. Whole-genome sequencing of SARS-CoV-2 showed all to carry closely related viruses. Examination of viral genomes deposited on GISAID showed this mutation has arisen independently at least four times. This work highlights the necessity of monitoring SARS-CoV-2 for the emergence of single-nucleotide polymorphisms that might adversely affect RT-PCRs used in diagnostics. Additionally, it argues that two regions in SARS-CoV-2 should be targeted to avoid false negatives. url: https://www.ncbi.nlm.nih.gov/pubmed/32690547/ doi: 10.1128/jcm.01598-20 id: cord-257456-15bm9psj author: Arumugam, Arunkumar title: A Rapid SARS-CoV-2 RT-PCR Assay for Low Resource Settings date: 2020-09-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay is the gold standard recommended to test for acute SARS-CoV-2 infection. However, it generally requires expensive equipment such as RNA isolation instruments and real-time PCR thermal cyclers. As a pandemic, COVID-19 has spread indiscriminately, and many low resource settings and developing countries do not have the means for fast and accurate COVID-19 detection to control the outbreak. Additionally, long assay times, in part caused by slow sample preparation steps, have created a large backlog when testing patient samples suspected of COVID-19. With many PCR-based molecular assays including an extraction step, this can take a significant amount of time and labor, especially if the extraction is performed manually. Using COVID-19 clinical specimens, we have collected evidence that the RT-qPCR assay can feasibly be performed directly on patient sample material in virus transport medium (VTM) without an RNA extraction step, while still producing sensitive test results. If RNA extraction steps can be omitted without significantly affecting clinical sensitivity, the turn-around time of COVID-19 tests, and the backlog we currently experience can be reduced drastically. Furthermore, our data suggest that rapid RT-PCR can be implemented for sensitive and specific molecular diagnosis of COVID-19 in locations where sophisticated laboratory instruments are not available. Our USD 300 set up achieved rapid RT-PCR using thin-walled PCR tubes and a water bath setup using sous vide immersion heaters, a Raspberry Pi computer, and a single servo motor that can process up to 96 samples at a time. Using COVID-19 positive clinical specimens, we demonstrated that RT-PCR assays can be performed in as little as 12 min using untreated samples, heat-inactivated samples, or extracted RNA templates with our low-cost water bath setup. These findings can help rapid COVID-19 testing to become more accessible and attainable across the globe. url: https://www.ncbi.nlm.nih.gov/pubmed/32987722/ doi: 10.3390/diagnostics10100739 id: cord-354725-lqio7l8k author: Arumugam, Arunkumar title: A Rapid COVID-19 RT-PCR Detection Assay for Low Resource Settings date: 2020-04-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay is the gold standard recommended to test for acute SARS-CoV-2 infection. It has been used by the Centers for Disease Control and Prevention (CDC) and several other companies in their Emergency Use Authorization (EUA) assays. RT-qPCR requires expensive equipment such as RNA isolation instruments and real-time PCR thermal cyclers, which are not available in many low resource settings and developing countries. As a pandemic, COVID-19 has quickly spread to the rest of the world. Many underdeveloped and developing counties do not have the means for fast and accurate COVID-19 detection to control this outbreak. Using COVID-19 positive clinical specimens, we demonstrated that RT-PCR assays can be performed in as little as 12 minutes using untreated samples, heat-inactivated samples, or extracted RNA templates. Rapid RT-PCR was achieved using thin-walled PCR tubes and a setup including sous vide immersion heaters/circulators. Our data suggest that rapid RT-PCR can be implemented for sensitive and specific molecular diagnosis of COVID-19 in situations where sophisticated laboratory instruments are not available. url: https://doi.org/10.1101/2020.04.29.069591 doi: 10.1101/2020.04.29.069591 id: cord-351038-k2m6woow author: Arun Krishnan, R. title: COVID-19: Current Trends in Invitro Diagnostics date: 2020-06-27 words: 2895.0 sentences: 172.0 pages: flesch: 50.0 cache: ./cache/cord-351038-k2m6woow.txt txt: ./txt/cord-351038-k2m6woow.txt summary: Currently the nucleic acid based polymerase chain reaction is used as the reliable diagnostic platform and antigen/antibody detection immunoassays are playing the role of screening tests for early detection and prognosis in COVID-19 treatment. The limitation of rRT-PCR to detect COVID-19 past infection and the progress of the disease, increases the importance of serological assays. Currently COVID-19 antigen LFIA test is under development which will offer more sensitive and specific result for COVID-19 diagnosis and will detect the viral antigen in 3 days of infection [22] . have developed an enzyme linked immunosorbent assay for the detection of COVID-19 IgM and IgG antibody from serum sample. The complexity, cost effectiveness and limitations of nucleic acid based diagnostic tools, impetus the innovative development of well standardized, high sensitive, specific and low cost serological assays for COVID-19 diagnosis. Evaluation of enzyme-linked immunoassay and colloidal gold-immunochromatographic assay kit for detection of novel coronavirus (SARS-Cov-2) causing an outbreak of pneumonia (COVID-19). abstract: The novel coronavirus SARS-CoV-2 is the seventh known species of coronavirus, infectious to human beings. The pandemic COVID-19 spread all over the world with an unprecedented spreading rate after its first appearance in Wuhan, China. As a novel viral disease there in no antiviral treatment or vaccine for the COVID-19. At present, the early detection and the quarantine of infected patients are the ways to stop the spreading of the disease. This review will discuss about the current invitro diagnostic methods used worldwide for the early and accurate diagnosis of COVID-19. Currently the nucleic acid based polymerase chain reaction is used as the reliable diagnostic platform and antigen/antibody detection immunoassays are playing the role of screening tests for early detection and prognosis in COVID-19 treatment. url: https://doi.org/10.1007/s12291-020-00906-5 doi: 10.1007/s12291-020-00906-5 id: cord-314404-tkhupnko author: Ashokka, Balakrishnan title: Care of the Pregnant Woman with COVID-19 in Labor and Delivery: Anesthesia, Emergency cesarean delivery, Differential diagnosis in the acutely ill parturient, Care of the newborn, and Protection of the healthcare personnel date: 2020-04-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: COVID-19 in pregnancy can cause severe maternal morbidity in up to 9% of affected gravidae. Chest imaging is helpful in pregnant women who have a high pretest probability of COVID-19, but are RT-PCR negative. Vertical transmission is unlikely, but active measures are needed to prevent neonatal infection. We present an algorithm of care for the acutely ill parturient. We present a protocol for intrapartum care of the pregnant woman in labor. url: https://www.sciencedirect.com/science/article/pii/S0002937820304300?v=s5 doi: 10.1016/j.ajog.2020.04.005 id: cord-268468-036i1082 author: Asif, Muhammad title: The role of biosensors in COVID-19 outbreak date: 2020-09-18 words: 3204.0 sentences: 189.0 pages: flesch: 43.0 cache: ./cache/cord-268468-036i1082.txt txt: ./txt/cord-268468-036i1082.txt summary: In this review, the importance of biosensors including electrochemical, surface enhanced Raman scattering, field-effect transistor and surface plasmon resonance biosensors in the detection of SARS-CoV-2 has been underscored. In this outbreak, three different types of diagnosis tests are being used including (i) chest CT scan along with clinical indications, (ii) RNA detection using RT-PCR assay and (iii) lateral flow assays, full automatic chemiluminescence method, enzyme-linked immunosorbent assay (ELISA) for the determination of antibodies [5] . In this review, we have summarized the biosensor based technologies which are able to detect SARS-CoV-2 effectively. The peptide monolayer was successfully coated on SPR biosensor and further functionalized with virus nucleocapsid protein which was finally able to detect SARS-CoV-2 antibodies at nanomolar level. The sensing aptitude of the biosensor was evaluated employing antigen protein, self-cultured virus, and nasopharyngeal swab samples taken from people infected with COVID-19 pneumonia. abstract: Herein, we have summarized and argued about biomarkers and indicators used for the detection of SARS-CoV-2. Antibody detection methods are not considered suitable to screen individuals at early stages and asymptomatic cases. The diagnosis of COVID-19 using biomarkers and indicators at point of care level is much crucial. Therefore, it is urgently needed to develop rapid and sensitive detection methods which can target antigens. We have critically elaborated key role of biosensors to cope the outbreak situation. In this review, the importance of biosensors including electrochemical, surface enhanced Raman scattering, field-effect transistor and surface plasmon resonance biosensors in the detection of SARS-CoV-2 has been underscored. Finally, we have outlined pros and cons of diagnostic approaches as-well-as future directions. url: https://www.ncbi.nlm.nih.gov/pubmed/32984642/ doi: 10.1016/j.coelec.2020.08.011 id: cord-010235-hu6o1ggc author: Atmar, Robert L. title: Nonculturable agents of viral gastroenteritis date: 1997-12-01 words: 3989.0 sentences: 190.0 pages: flesch: 43.0 cache: ./cache/cord-010235-hu6o1ggc.txt txt: ./txt/cord-010235-hu6o1ggc.txt summary: (3) provided the first clear demonstration of the causal relationship between a virus (Norwalk virus [NV] ) and gastroenteritis by using immune electron microscopy (IEM) to detect the presence of viral particles in the stools of individuals from an epidemic outbreak of gastroenteritis. This article describes the structure and genome organization of the human caliciviruses that cause gastroenteritis, the clinical and epidemiologic features of these viruses, and new methods for the laboratory diagnosis of infection with these viruses. The inability to cultivate the HuCVs and establish neutralization assays has prevented the definition of specific serotypes; however, at least five different serotypes are thought to exist based on early human cross-challenge studies and comparisons of the IEM and enzyme-linked immunosorbent assay (ELISA) reactivities of several prototype virus strains. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172954/ doi: 10.1016/s0196-4399(00)89189-8 id: cord-355102-jcyq8qve author: Avila, Eduardo title: Hemogram data as a tool for decision-making in COVID-19 management: applications to resource scarcity scenarios date: 2020-06-29 words: 4768.0 sentences: 242.0 pages: flesch: 39.0 cache: ./cache/cord-355102-jcyq8qve.txt txt: ./txt/cord-355102-jcyq8qve.txt summary: PURPOSE: This work describes a machine learning model derived from hemogram exam data performed in symptomatic patients and how they can be used to predict qRT-PCR test results. METHODS: Hemogram exams data from 510 symptomatic patients (73 positives and 437 negatives) were used to model and predict qRT-PCR results through Naïve-Bayes algorithms. In order to evaluate the adequacy and generalization power of the proposed model, as well as its tolerance to handle samples containing missing data (i.e., at least one variable with no informed values), an additional set of 92 samples (10 positives for COVID-19 and 82 negatives) was obtained from the patient database. When no clinical or medical data is available, or when decisions regarding resource management involving multiple symptomatic patients are necessary, the model can be used in multiple individuals simultaneously, aiming to identify those with higher probabilities of presenting positive qRT-PCR results. abstract: BACKGROUND: COVID-19 pandemics has challenged emergency response systems worldwide, with widespread reports of essential services breakdown and collapse of health care structure. A critical element involves essential workforce management since current protocols recommend release from duty for symptomatic individuals, including essential personnel. Testing capacity is also problematic in several countries, where diagnosis demand outnumbers available local testing capacity. PURPOSE: This work describes a machine learning model derived from hemogram exam data performed in symptomatic patients and how they can be used to predict qRT-PCR test results. METHODS: Hemogram exams data from 510 symptomatic patients (73 positives and 437 negatives) were used to model and predict qRT-PCR results through Naïve-Bayes algorithms. Different scarcity scenarios were simulated, including symptomatic essential workforce management and absence of diagnostic tests. Adjusts in assumed prior probabilities allow fine-tuning of the model, according to actual prediction context. RESULTS: Proposed models can predict COVID-19 qRT-PCR results in symptomatic individuals with high accuracy, sensitivity and specificity, yielding a 100% sensitivity and 22.6% specificity with a prior of 0.9999; 76.7% for both sensitivity and specificity with a prior of 0.2933; and 0% sensitivity and 100% specificity with a prior of 0.001. Regarding background scarcity context, resources allocation can be significantly improved when model-based patient selection is observed, compared to random choice. CONCLUSIONS: Machine learning models can be derived from widely available, quick, and inexpensive exam data in order to predict qRT-PCR results used in COVID-19 diagnosis. These models can be used to assist strategic decision-making in resource scarcity scenarios, including personnel shortage, lack of medical resources, and testing insufficiency. url: https://doi.org/10.7717/peerj.9482 doi: 10.7717/peerj.9482 id: cord-312161-egwo19oc author: Aw, Tiong Gim title: Detection of pathogens in water: from phylochips to qPCR to pyrosequencing date: 2011-12-05 words: 4551.0 sentences: 209.0 pages: flesch: 31.0 cache: ./cache/cord-312161-egwo19oc.txt txt: ./txt/cord-312161-egwo19oc.txt summary: Microbial water quality monitoring has undergone tremendous transition in recent years, with novel molecular tools beginning to offer rapid, high-throughput, sensitive and specific detection of a wide spectrum of microbial pathogens that challenge traditional culture-based techniques. High-density microarrays, quantitative real-time PCR (qPCR) and pyrosequencing which are considered to be breakthrough technologies borne out of the ''molecular revolution'' are at present emerging rapidly as tools of pathogen detection and discovery. The limitations in detecting and identifying pathogens directly from environmental water samples by culture or microscopy can now be addressed by integrating concentration techniques with molecular tools to provide sensitive, specific and quantitative data on any pathogens of interest. Pyrosequencing technology is revolutionizing the study of microbial ecology as well as direct metagenomic detection Detection of pathogens in water Aw and Rose 425 High levels of several classes of resistance genes in bacterial communities exposed to antibiotic were identified. abstract: Waterborne pathogens pose a significant threat to human health and a proper assessment of microbial water quality is important for decision making regarding water infrastructure and treatment investments and eventually to provide early warning of disease, particularly given increasing global disasters associated with severe public health risks. Microbial water quality monitoring has undergone tremendous transition in recent years, with novel molecular tools beginning to offer rapid, high-throughput, sensitive and specific detection of a wide spectrum of microbial pathogens that challenge traditional culture-based techniques. High-density microarrays, quantitative real-time PCR (qPCR) and pyrosequencing which are considered to be breakthrough technologies borne out of the ‘molecular revolution’ are at present emerging rapidly as tools of pathogen detection and discovery. Future challenges lie in integrating these molecular tools with concentration techniques and bioinformatics platforms for unbiased guide of pathogen surveillance in water and developing standardized protocols. url: https://doi.org/10.1016/j.copbio.2011.11.016 doi: 10.1016/j.copbio.2011.11.016 id: cord-266036-qhlo99l7 author: Axell-House, Dierdre B. title: The Estimation of Diagnostic Accuracy of Tests for COVID-19: A Scoping Review date: 2020-08-31 words: 5760.0 sentences: 318.0 pages: flesch: 47.0 cache: ./cache/cord-266036-qhlo99l7.txt txt: ./txt/cord-266036-qhlo99l7.txt summary: OBJECTIVES: To assess the methodologies used in the estimation of diagnostic accuracy of SARS-CoV-2 real-time reverse transcription polymerase chain reaction (rRT-PCR) and other nucleic acid amplification tests (NAATs) and to evaluate the quality and reliability of the studies employing those methods. After its emergence in December 2019, the virus now known as SARS-CoV-2 was identified and sequenced in early January 2020, 1 allowing for the rapid development of diagnostic testing based on the detection of viral nucleic acid (i.e., real-time reverse transcription polymerase chain reaction [rRT-PCR]). Articles were included if they met the following criteria on screening: 1) Peer-reviewed publication, 2) Study evaluated diagnostic test accuracy of NAAT, 3) Diagnostic test performed on ≥10 patients, 4) Diagnostic/Clinical sensitivity, specificity, other correlative statistics, or test positive rate were either identified by name or were included in the publication as a numerical value and we could reproduce the calculations. abstract: OBJECTIVES: To assess the methodologies used in the estimation of diagnostic accuracy of SARS-CoV-2 real-time reverse transcription polymerase chain reaction (rRT-PCR) and other nucleic acid amplification tests (NAATs) and to evaluate the quality and reliability of the studies employing those methods. METHODS: We conducted a systematic search of English-language articles published December 31, 2019-June 19, 2020. Studies of any design that performed tests on ≥10 patients and reported or inferred correlative statistics were included. Studies were evaluated using elements of the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) guidelines. RESULTS: We conducted a narrative and tabular synthesis of studies organized by their reference standard strategy or comparative agreement method, resulting in six categorizations. Critical study details were frequently unreported, including the mechanism for patient/sample selection and researcher blinding to results, which lead to concern for bias. CONCLUSIONS: Current studies estimating test performance characteristics have imperfect study design and statistical methods for the estimation of test performance characteristics of SARS-CoV-2 tests. The included studies employ heterogeneous methods and overall have an increased risk of bias. Employing standardized guidelines for study designs and statistical methods will improve the process for developing and validating rRT-PCR and NAAT for the diagnosis of COVID-19. url: https://doi.org/10.1016/j.jinf.2020.08.043 doi: 10.1016/j.jinf.2020.08.043 id: cord-311410-lgqup9ug author: Ayers, M. title: A single tube RT-PCR assay for the detection of mosquito-borne flaviviruses date: 2006-05-02 words: 3106.0 sentences: 157.0 pages: flesch: 52.0 cache: ./cache/cord-311410-lgqup9ug.txt txt: ./txt/cord-311410-lgqup9ug.txt summary: In this study we present the design and validation of a single tube RT-PCR assay using a pair of consensus primers for the detection of mosquito-borne flaviviruses. For specificity studies, several viral samples were used, including clinical samples found to contain CMV and EBV DNA by PCR testing, as described (Johnson et al., 2000) ; a clinical isolate of influenza virus from the 2004-2005 season, typed as H3 by sequencing of the hemagglutinin gene; echovirus 11 from the laboratory collection at the Hospital for Sick Children; hepatitis C virus RNA was obtained by in vitro transcription of the infectious clone pCV-H77C (Yanagi et al., 1997) (the clone was kindly provided by Dr. J. Coupled with sequencing, it could detect with great sensitivity and identify several mosquito-borne flaviviruses including WNV, Kunjin, SLE, YFV and dengue fever viruses. abstract: Mosquito-borne flaviviruses include several important agents of human disease and have provided striking examples of emerging infections. In this study we present the design and validation of a single tube RT-PCR assay using a pair of consensus primers for the detection of mosquito-borne flaviviruses. Sequencing of the amplicons permits the species identification. The assay was validated using RNA from the yellow fever virus vaccine strain and from representative strains of dengue viruses 1, 2, 3 and 4, West Nile virus, Kunjin virus (a clade of West Nile virus), and St. Louis encephalitis virus. url: https://www.ncbi.nlm.nih.gov/pubmed/16650488/ doi: 10.1016/j.jviromet.2006.03.009 id: cord-329162-6w8qcv1c author: Ayginin, Andrey A. title: The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels date: 2018-08-12 words: 4838.0 sentences: 222.0 pages: flesch: 49.0 cache: ./cache/cord-329162-6w8qcv1c.txt txt: ./txt/cord-329162-6w8qcv1c.txt summary: The existing approaches for the design of oligonucleotides for targeted enrichment are usually involved in the development of primers for the PCR-based detection of particular viral species or genera, but not for families or higher taxonomic orders. We have subsequently designed a genus-specific oligonucleotide panel for targeted enrichment of viral nucleic acids in biological material and demonstrated the possibility of its application for virus detection in bird samples. We have applied this approach to design genus-specific primer pairs for targeted enrichment of cDNA from zoonotic RNA viruses and have evaluated it using several samples from birds. The control samples cDNA was obtained by reverse transcription reaction performed on 5 L of the extracted RNA using the Reverta-L RT kit (AmpliSens; total volume of the reaction mixture is 20 L); after that 5 L of the reaction mixture containing cDNAs was further used for evaluation of the ability of the primer pair to amplify the targeted region of viruses, both in single and in multiplex PCR format. abstract: Advances in the next generation sequencing (NGS) technologies have significantly increased our ability to detect new viral pathogens and systematically determine the spectrum of viruses prevalent in various biological samples. In addition, this approach has also helped in establishing the associations of viromes with many diseases. However, unlike the metagenomic studies using 16S rRNA for the detection of bacteria, it is impossible to create universal oligonucleotides to target all known and novel viruses, owing to their genomic diversity and variability. On the other hand, sequencing the entire genome is still expensive and has relatively low sensitivity for such applications. The existing approaches for the design of oligonucleotides for targeted enrichment are usually involved in the development of primers for the PCR-based detection of particular viral species or genera, but not for families or higher taxonomic orders. In this study, we have developed a computational pipeline for designing the oligonucleotides capable of covering a significant number of known viruses within various taxonomic orders, as well as their novel variants. We have subsequently designed a genus-specific oligonucleotide panel for targeted enrichment of viral nucleic acids in biological material and demonstrated the possibility of its application for virus detection in bird samples. We have tested our panel using a number of collected samples and have observed superior efficiency in the detection and identification of viral pathogens. Since a reliable, bioinformatics-based analytical method for the rapid identification of the sequences was crucial, an NGS-based data analysis module was developed in this study, and its functionality in the detection of novel viruses and analysis of virome diversity was demonstrated. url: https://doi.org/10.1155/2018/3248285 doi: 10.1155/2018/3248285 id: cord-000080-7s5b3lpn author: Ayodeji, Mobolanle title: A Microarray Based Approach for the Identification of Common Foodborne Viruses date: 2009-03-19 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: An oligonucleotide array (microarray) incorporating 13,000 elements representing selected strains of hepatitis A virus (HAV), human coxsackieviruses A and B (CVA and CVB), genogroups I and II of Norovirus (NV), and human rotavirus (RV) gene segments 3,4,10, and 11 was designed based on the principle of tiling. Each oligonucleotide was 29 bases long, starting at every 5th base of every sequence, resulting in an overlap of 24 bases in two consecutive oligonucleotides. The applicability of the array for virus identification was examined using PCR amplified products from multiple HAV and CV strains. PCR products labeled with biotin were hybridized to the array, and the biotin was detected using a brief reaction with Cy3-labeled streptavidin, the array subjected to laser scanning, and the hybridization data plotted as fluorescence intensity against each oligonucleotide in the array. The combined signal intensities of all probes representing a particular strain of virus were calculated and plotted against all virus strains identified on a linear representation of the array. The profile of the total signal intensity identified the strain that is most likely represented in the amplified cDNA target. The results obtained with HAV and CV indicated that the hybridization profile thus generated can be used to identify closely related viral strains. This represents a significant improvement over current methods for virus identification using PCR amplification and amplicon sequencing. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2707758/ doi: 10.2174/1874357900903010007 id: cord-283409-ynwgdz52 author: Baggett, Travis P. title: Clinical Outcomes, Costs, and Cost-effectiveness of Strategies for People Experiencing Sheltered Homelessness During the COVID-19 Pandemic date: 2020-10-20 words: 1741.0 sentences: 111.0 pages: flesch: 44.0 cache: ./cache/cord-283409-ynwgdz52.txt txt: ./txt/cord-283409-ynwgdz52.txt summary: INTERVENTIONS: We assessed daily symptom screening with polymerase chain reaction (PCR) testing of screen-positives, universal PCR testing every 2 weeks, hospital-based COVID-19 care, alternate care sites [ACSs] for mild/moderate COVID-19, and temporary housing, each compared to no intervention. CONCLUSIONS & RELEVANCE: In this modeling study of simulated adults living in homeless shelters, daily symptom screening and ACSs were associated with fewer COVID-19 infections and decreased costs compared with no intervention. In addition, we provide details on the Clinical and Economic Analysis of COVID-19 interventions (CEACOV) model and management strategies for people experiencing sheltered homelessness. The effective magnitude of the transmission rate, however, changes over time as social interventions alter the daily average number of contacts between susceptible and infected individuals as well as the infectivity per contact. PCR-positive individuals with mild/moderate illness remain in temporary housing and are transferred to the hospital if they progress to severe or critical disease abstract: IMPORTANCE: Approximately 356,000 people stay in homeless shelters nightly in the US. They are at high risk for COVID-19. OBJECTIVE: To assess clinical outcomes, costs, and cost-effectiveness of strategies for COVID-19 management among sheltered homeless adults. DESIGN: We developed a dynamic microsimulation model of COVID-19 in sheltered homeless adults in Boston, Massachusetts. We used cohort characteristics and costs from Boston Health Care for the Homeless Program. Disease progression, transmission, and outcomes data were from published literature and national databases. We examined surging, growing, and slowing epidemics (effective reproduction numbers [R(e)] 2.6, 1.3, and 0.9). Costs were from a health care sector perspective; time horizon was 4 months, from April to August 2020. SETTING & PARTICIPANTS: Simulated cohort of 2,258 adults residing in homeless shelters in Boston. INTERVENTIONS: We assessed daily symptom screening with polymerase chain reaction (PCR) testing of screen-positives, universal PCR testing every 2 weeks, hospital-based COVID-19 care, alternate care sites [ACSs] for mild/moderate COVID-19, and temporary housing, each compared to no intervention. MAIN OUTCOMES AND MEASURES: Cumulative infections and hospital-days, costs to the health care sector (US dollars), and cost-effectiveness, as incremental cost per case prevented of COVID-19. RESULTS: We simulated a population of 2,258 sheltered homeless adults with mean age of 42.6 years. Compared to no intervention, daily symptom screening with ACSs for pending tests or confirmed COVID-19 and mild/moderate disease led to 37% fewer infections and 46% lower costs (R(e)=2.6), 75% fewer infections and 72% lower costs (R(e)=1.3), and 51% fewer infections and 51% lower costs (R(e)=0.9). Adding PCR testing every 2 weeks further decreased infections; incremental cost per case prevented was $1,000 (R(e)=2.6), $27,000 (R(e)=1.3), and $71,000 (R(e)=0.9). Temporary housing with PCR every 2 weeks was most effective but substantially more costly than other options. Results were sensitive to cost and sensitivity of PCR and ACS efficacy in preventing transmission. CONCLUSIONS & RELEVANCE: In this modeling study of simulated adults living in homeless shelters, daily symptom screening and ACSs were associated with fewer COVID-19 infections and decreased costs compared with no intervention. In a modeled surging epidemic, adding universal PCR testing every 2 weeks was associated with further decrease in COVID-19 infections at modest incremental cost and should be considered during future surges. url: https://www.ncbi.nlm.nih.gov/pubmed/32817967/ doi: 10.1101/2020.08.07.20170498 id: cord-265221-qtkwciym author: Bahadur, Gulam title: SARS-CoV-2: diagnostic and design conundrums, and the male factor infertility date: 2020-06-03 words: 3261.0 sentences: 182.0 pages: flesch: 49.0 cache: ./cache/cord-265221-qtkwciym.txt txt: ./txt/cord-265221-qtkwciym.txt summary: It is essential to understand the limitations of both antibody and real time polymerase chain reaction (RT-PCR) tests in interpreting SARS-CoV-2 data in relation to semen and testicular tissues analyses without appropriate controls. raising equal concerns for embryo and fetal development (Colaco et al., 2020) .In males, ACE2 receptor sites have been reported in testicular tissue which then have the capability to harbour SARS-CoV-2 virus and eventual shedding into the semen and hence its implication in sexual transmission, early pregnancy or early in utero embryonic development. Studies analysing SARS-CoV-2 in seminal fluid or testicular biopsies have so far lacked appropriate controls and patients suffered from predominantly mild infections and tested several weeks after the infection, thereby increasing the complexity of result interpretation. Also no SARS-CoV-2 was detected in expressed prostatic secretion (EPS) of 18 confirmed Covid-19 infected patients and 5 strongly suspected cases but absent semen analyses. abstract: The question on whether SARS-CoV-2 (Severe acute respiratory syndrome-related coronavirus (SARS-CoV or SARS-CoV-2, Covid-19) can be harboured in testes and/or the semen is currently unanswered. It is essential to understand the limitations of both antibody and real time polymerase chain reaction (RT-PCR) tests in interpreting SARS-CoV-2 data in relation to semen and testicular tissues analyses without appropriate controls. Here we critically analyse the evidence so far and the possible implications. The diagnostic test limitations posed in both sampling and testing methodologies, their validation, and relevancy in interpreting data are also highlighted. url: https://doi.org/10.1016/j.rbmo.2020.05.014 doi: 10.1016/j.rbmo.2020.05.014 id: cord-003047-3ejfxj6r author: Bai, Jianfa title: Comparison data of a two-target real-time PCR assay with and without an internal control in detecting Salmonella enterica from cattle lymph nodes date: 2018-04-22 words: 1095.0 sentences: 66.0 pages: flesch: 60.0 cache: ./cache/cord-003047-3ejfxj6r.txt txt: ./txt/cord-003047-3ejfxj6r.txt summary: title: Comparison data of a two-target real-time PCR assay with and without an internal control in detecting Salmonella enterica from cattle lymph nodes Data was generated by the duplex qPCR assay on 138 enriched cattle lymph node samples without the internal control, and compared with data on the same samples tested by the triplex qPCR assay that has Similar threshold cycle (Ct) data were generated with and without the use of the 18S rRNA gene as internal control. Real-time PCR (qPCR) test data on 138 culture-enriched cattle lymph node samples for Salmonella enterica detections is shown in Table 1 . One Table 1 Real-time PCR threshold cycle (Ct) data on 138 Salmonella-positive cattle lymph node samples with and without the 18S rRNA internal control. A multiplex real-time PCR assay, based on invA and pagC genes, for the detection and quantification of Salmonella enterica from cattle lymph nodes abstract: A real-time PCR (qPCR) assay targeting on invA and pagC genes was developed and validated for the detection and quantification of Salmonella enterica strains (Bai et al., 2018) [1]. A host gene, normally an endogenous housekeeping gene (Beer-Davidson et al., 2018; Poon et al., 2004) [2,3], or an irrelevant exogenous gene (Cheng et al., 2015; Sedlak et al., 2014) [4,5] has been widely used as an internal control to monitor nucleic acid extraction efficiencies and potential PCR inhibitions in PCR-based detection assays. An endogenous internal control designed based on the 18S rRNA gene was used in the above-mentioned qPCR assay. This 18S rRNA internal control amplifies the target gene in multiple species including bovine, swine, ovine, caprine and cervine. Data was generated by the duplex qPCR assay on 138 enriched cattle lymph node samples without the internal control, and compared with data on the same samples tested by the triplex qPCR assay that has the 18S rRNA gene as internal control. Threshold cycle (Ct) data for the duplex and the triplex qPCR on the 138 samples were similar, and are presented in this brief report. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5998743/ doi: 10.1016/j.dib.2018.04.051 id: cord-346096-aml84iv1 author: Bailey, Emily S. title: Molecular surveillance of respiratory viruses with bioaerosol sampling in an airport date: 2018-09-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Recognizing that crowded, high-traffic airports and airplanes have been implicated in respiratory disease transmission, we partnered with administrators of Raleigh Durham International Airport (RDU) in conducting a pilot study of aerosol surveillance for respiratory viruses at RDU. From January to March 2018 we used NIOSH 2-stage samplers to collect 150 min aerosol samples in crowded areas at RDU. Four (17%) of the 24 samples were positive for known respiratory pathogens including influenza D virus and adenovirus. These results suggest the feasibility of employing bioaerosol surveillance techniques in public transportation areas, such as airports, as a noninvasive way to detect and characterize novel respiratory viruses. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s40794-018-0071-7) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s40794-018-0071-7 doi: 10.1186/s40794-018-0071-7 id: cord-304656-v0fyb161 author: Balayla, J. title: Prevalence Threshold and Temporal Interpretation of Screening Tests: The Example of the SARS-CoV-2 (COVID-19) Pandemic date: 2020-05-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The curvilinear relationship between a screening test's positive predictive value (PPV) and its target disease prevalence is proportional. In consequence, there is an inflection point of maximum curvature in the screening curve defined as a function of the sensitivity and specificity beyond which the rate of change of a test's PPV declines sharply relative to disease prevalence. Herein, we demonstrate a mathematical model exploring this phenomenon and define the prevalence threshold point where this change occurs. Understanding where this prevalence point lies in the curve has important implications for the interpretation of test results, the administration of healthcare systems, the implementation of public health measures, and in cases of pandemics like SARS-CoV-2, the functioning of society at large. To illustrate the methods herein described, we provide the example of the screening strategies used in the SARS-CoV-2 (COVID-19) pandemic, and calculate the prevalence threshold statistic of different tests available today. This concept can help contextualize the validity of a screening test in real time, thereby enhancing our understanding of the dynamics of the current pandemic. url: https://doi.org/10.1101/2020.05.17.20104927 doi: 10.1101/2020.05.17.20104927 id: cord-352814-fcl2g5wr author: Balboni, Andrea title: A Real-Time PCR Assay for Bat SARS-Like Coronavirus Detection and Its Application to Italian Greater Horseshoe Bat Faecal Sample Surveys date: 2011-11-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Bats are source of coronaviruses closely related to the severe acute respiratory syndrome (SARS) virus. Numerous studies have been carried out to identify new bat viruses related to SARS-coronavirus (bat-SARS-like CoVs) using a reverse-transcribed-polymerase chain reaction assay. However, a qualitative PCR could underestimate the prevalence of infection, affecting the epidemiological evaluation of bats in viral ecology. In this work an SYBR Green-real time PCR assay was developed for diagnosing infection with SARS-related coronaviruses from bat guano and was applied as screening tool in a survey carried out on 45 greater horseshoe bats (Rhinolophus ferrumequinum) sampled in Italy in 2009. The assay showed high sensitivity and reproducibility. Its application on bats screening resulted in a prevalence of 42%. This method could be suitable as screening tool in epidemiological surveys about the presence of bat-SARS-like CoVs, consequently to obtain a more realistic scenario of the viral prevalence in the population. url: https://www.ncbi.nlm.nih.gov/pubmed/22654650/ doi: 10.1100/2012/989514 id: cord-342568-3sj235rm author: Bald-Blume, Niklas title: Development of a molecular assay for the general detection of tospoviruses and the distinction between tospoviral species date: 2017-02-11 words: 5364.0 sentences: 277.0 pages: flesch: 54.0 cache: ./cache/cord-342568-3sj235rm.txt txt: ./txt/cord-342568-3sj235rm.txt summary: In this study a new method for plant virus diagnosis is described using the Luminex xTAG technology to test for tospoviruses in general and for the four species TSWV, WSMoV, INSV and CaCV. Infected, dried plant material of 12 tospoviral isolates from eight different species was obtained from the DSMZ including single isolates of alstroemeria necrotic streak virus (ANSV), CaCV, GRSV, IYSV, TCSV and WSMoV as well as three isolates each of INSV and TSWV. The generic tospovirus primers Tospo_GENs/as (without tags) allowed the detection of all eight tospoviruses and of all three isolates of INSV and TSWV tested in RT-PCR experiments. A molecular assay for the detection of tospoviruses in general and for viruses from the four species belonging to this genus (TSWV, INSV, CaCV and WSMoV), using the Luminex xTAG technology, was successfully developed. abstract: A Luminex xTAG-based assay for plant-infecting tospoviruses was developed. The test enables the detection of tospoviruses in general and the differentiation of the four important member species of this genus: Tomato spotted wilt virus, Impatiens necrotic spot virus, the proposed ‘Capsicum chlorosis virus’ and Watermelon silver mottle virus. The generic tospovirus primers used in this method are also applicable for detection of tospoviruses by basic RT-PCR. We also describe an economic alternative method for the distinction of the four tospoviruses mentioned and of additional member viruses, based on a restriction fragment length polymorphism (RFLP). The sophisticated Luminex xTAG technology allows the simultaneous detection of various targets. This study is part of a project that aims to develop a method for the simultaneous detection of various plant pathogens (viral, bacterial and fungal) in plant material. url: https://www.ncbi.nlm.nih.gov/pubmed/28190200/ doi: 10.1007/s00705-017-3256-x id: cord-032134-mvj7i1er author: Ballauff, Antje title: Funktions- und Laboruntersuchungen date: 2013 words: 9299.0 sentences: 1365.0 pages: flesch: 49.0 cache: ./cache/cord-032134-mvj7i1er.txt txt: ./txt/cord-032134-mvj7i1er.txt summary: Bei Durchführung des Tests wird nach Verzicht auf ballaststoffreiche Kost für 3 Tage sowie nach einer Nüchternperiode von je nach Alter 8-12 Stunden und nach Mundspülung mit Wasser oder desinfizierender Lösung (morgens nicht Zähneputzen wegen Kohlenhydraten in der Zahnpasta) der Basalwert durch Gewinn von 1-2 Atemproben vor der Gabe der Testsubstanz ermittelt. Andererseits hat der EHEC-Ausbruch im Mai / Juni 2011 in Norddeutschland in eigenen vergleichenden Studien gezeigt, dass die Amplifikation von Zielsequenzen der Shiga-Toxin kodierenden Gene mittels PCR direkt im Stuhl das mit Abstand sensitivste und schnellste Verfahren zum frühen Nachweis oder Ausschluss einer EHEC-Infektion ist (Bialek et al., unveröffentlichtes Manuskript; Robert Koch Institut 2011b) . Nur bei der Amöbenruhr, verursacht durch Entamoeba histolytica, finden sich temperatursensible Trophozoiten im blutig-schleimigen Stuhl, die nur bei noch "warmer" Stuhlprobe mikroskopisch nachweisbar und identifizierbar sind, so dass eine Probe entweder direkt im Labor entnommen werden sollte oder diese warm zu transportieren ist. abstract: Zur Analyse abgeatmeter Gase muss endexspiratorische Luft gewonnen werden, ohne Vermischung mit frühexspiratorischer Luft (sonst Korrektur mit Messung des CO2-Partialdrucks, s. unten). Ältere Kinder blasen nach Anhalten der Atmung über 15 s durch tiefe Ausatmung über einen Strohhalm endexspiratorische Luft in ein Glasröhrchen, das dann luftdicht verschlossen wird (Vacutainer), oder über ein Mundstück oder eine Maske direkt in ein H2-Messgerät oder in Beutel. Bei Säuglingen und Kleinkindern kann mit einer Maske oder einer Sonde, die bis zum nasopharyngealen Übergang vorgeschoben wird, mit einer Spritze atemsynchron exspiratorische Luft abgesaugt und in Vacutainer oder direkt in das Messgerät eingegeben werden. In Vacutainern sind Proben über mehr als 30 Tage stabil und können auch zur Analyse verschickt werden. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7498812/ doi: 10.1007/978-3-642-24710-1_3 id: cord-271421-4dk7mkut author: Balsalobre-Arenas, Luz title: Rapid diagnosis of gastrointestinal tract infections due to parasites, viruses, and bacteria date: 2017-07-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract Rapid diagnostic techniques are valuable tools in the diagnosis of gastrointestinal infections, especially for the detection of some microorganisms and in certain groups of patients. While antigen detection techniques are widely used in Clinical Microbiology laboratories, for the diagnosis of viruses, some parasites and some bacteria, molecular techniques are routinely used only for some pathogens (such as Clostridium difficile). However, molecular techniques are constantly evolving, and they allow a rapid diagnosis for an increasing number of pathogens, with high sensitivity and specificity. In addition, they are also able to detect virulence factors or resistance mechanisms. Syndromic surveillance systems, which detect different pathogens simultaneously, are very promising because they enable the most frequent pathogens to be diagnosed in a few hours and they can be very useful in certain patients. For the diagnosis of Helicobacter pylori infection, molecular techniques are able to detect bacteria and its resistance to clarithromycin and levofloxacin, allowing the most appropriate treatment to be selected for each patient when bacterial culture is not possible. url: https://www.sciencedirect.com/science/article/pii/S2529993X17301491 doi: 10.1016/j.eimce.2017.01.033 id: cord-275787-5s442sy2 author: Banerjee, Arinjay title: Generation and Characterization of Eptesicus fuscus (Big brown bat) kidney cell lines immortalized using the Myotis polyomavirus large T-antigen date: 2016-09-14 words: 5817.0 sentences: 347.0 pages: flesch: 57.0 cache: ./cache/cord-275787-5s442sy2.txt txt: ./txt/cord-275787-5s442sy2.txt summary: title: Generation and Characterization of Eptesicus fuscus (Big brown bat) kidney cell lines immortalized using the Myotis polyomavirus large T-antigen Here we describe a method to establish and immortalize big brown bat (Eptesicus fuscus) kidney (Efk3) cells using the Myotis polyomavirus T-antigen. Cell clones expressed interferon beta in response to poly(I:C) stimulation and supported the replication of four different viruses, namely, vesicular stomatitis virus (VSV), porcine epidemic diarrhea coronavirus (PED-CoV), Middle-East respiratory syndrome coronavirus (MERS-CoV) and herpes simplex virus (HSV). The parental cell line and clones were capable of expressing IFN beta and supported the replication of viruses such as vesicular stomatitis virus (VSV; family Rhabdoviridae, genus Vesiculovirus), herpes simplex virus (HSV; family Herpesviridae, subfamily Alphaherpesvirinae, genus Herpesvirus), PED-CoV and MERS-CoV. Bat kidney cells were immortalized by using ViaFect (Promega, USA) to transfect cells with either 2.5 g of pcDNA3 (Invitrogen, USA) empty vector or plasmids expressing either SV40 large T-antigen (SV40Tag) or Myotis polyomavirus large T-antigen (MyPVTag). abstract: It is speculated that bats are important reservoir hosts for numerous viruses, with 27 viral families reportedly detected in bats. Majority of these viruses have not been isolated and there is little information regarding their biology in bats. Establishing a well-characterized bat cell line supporting the replication of bat-borne viruses would facilitate the analysis of virus-host interactions in an in vitro model. Currently, few bat cell lines have been developed and only Tb1-Lu, derived from Tadarida brasiliensis is commercially available. Here we describe a method to establish and immortalize big brown bat (Eptesicus fuscus) kidney (Efk3) cells using the Myotis polyomavirus T-antigen. Subclones of this cell line expressed both epithelial and fibroblast markers to varying extents. Cell clones expressed interferon beta in response to poly(I:C) stimulation and supported the replication of four different viruses, namely, vesicular stomatitis virus (VSV), porcine epidemic diarrhea coronavirus (PED-CoV), Middle-East respiratory syndrome coronavirus (MERS-CoV) and herpes simplex virus (HSV). To our knowledge, this is the first bat cell line from a northern latitude insectivorous bat developed using a novel technology. The cell line has the potential to be used for isolation of bat viruses and for studying virus-bat interactions in culture. url: https://www.sciencedirect.com/science/article/pii/S0166093416302440 doi: 10.1016/j.jviromet.2016.09.008 id: cord-310748-ao29zx1u author: Banner, Lisa R. title: Random nature of coronavirus RNA recombination in the absence of selection pressure date: 1991-11-30 words: 2839.0 sentences: 155.0 pages: flesch: 52.0 cache: ./cache/cord-310748-ao29zx1u.txt txt: ./txt/cord-310748-ao29zx1u.txt summary: Our results showed that within a 1-kb region of the peplomer gene, RNA recombination occurred at almost every potential crossover site. To study RNA recombination in the absence of selection pressure, we developed a polymer-ase chain reaction (PCR) assay using two primers specific for the potential recombinant viruses which have a crossover site between the two primers. Only recombinant RNAs which had a crossover between the two primers and contained A59-specific sequences on the 5''-side and JHM-DL-specific sequences on the 3''-side could be detected by this PCR approach. DNA sequence analysis of 35 cloned PCR products showed that the crossover sites were almost randomly distributed throughout the nearly 1-kb region of the peplomer gene studied ( Fig. 2A) . Analysis of 53 recombinant clones revealed that, similar to the intracellular recombinants, the crossover sites in the viral recombinant RNAs were almost randomly distributed over the 1 -kb region of the peplomer gene (Fig. 2B) . abstract: Abstract RNA-RNA recombination is thought to occur preferentially at certain selected sites and in only a few RNA viruses; the mechanism for these restrictions is unknown. In this paper we report the development of a recombination assay for coronavirus, using polymerase chain reaction, in the absence of selection pressure. Our results showed that within a 1-kb region of the peplomer gene, RNA recombination occurred at almost every potential crossover site. Thus, coronavirus RNA recombination appears to be more random than previously realized. However, after serial passages of the recombinant viruses in tissue culture, the recombination sites among the progeny viruses became clustered in the region which contains the previously reported “hot spot” for coronavirus recombination. These results suggest that RNA recombination is common and random in nature, but only certain recombinants can be selected. Thus, the presence of recombinational “hot spots” for coronavirus or other RNA viruses most likely resulted from selection of certain recombinant viruses and not restriction on the occurrence of RNA recombination. The failure to detect recombinants in other RNA viruses may therefore be due to unfavorable properties of recombinant viruses. This approach can be used to detect recombinants in these viruses. url: https://www.sciencedirect.com/science/article/pii/004268229190795D doi: 10.1016/0042-6822(91)90795-d id: cord-311439-y9jwu38r author: Bao, Changjun title: Possible Spread of adenovirus type 3 from poultry to humans: indirect evidence from an outbreak in China date: 2007-09-30 words: 4299.0 sentences: 219.0 pages: flesch: 50.0 cache: ./cache/cord-311439-y9jwu38r.txt txt: ./txt/cord-311439-y9jwu38r.txt summary: We describe an outbreak of acute respiratory infection due to adenovirus type 3 that occurred in one county of Jiangsu Province, China, during the period from April 18 th to July 4 th 2004. Pharyngeal swab specimens from children and adolescent patients who were diagnosed with acute upper respiratory tract infections at Township A health care hospital during the outbreak from April through July 2005 were cultured for adenovirus. An infection caused by adenovirus type 3 was verified by entire gene sequence testing to 10 Nested PCR amplification products of positive specimens (from nine patients) in the laboratory of the National CDC of China. Eighteen paired patient serums(acute and convalescent) were used to test neutralization titer with the isolate adenovirus type 3 viral strain simultaneously. This investigation demonstrated that acute respiratory infection caused by adenovirus type 3 caused the outbreak that occurred in over seventy schools in ten townships in 2004. abstract: Abstract Objective To explore the epidemiology and etiology for an outbreak of acute respiratory tract infection that occurred in one county of Jiangsu Province, China 2004. Methods Only cases meeting the case definition were included in the study. We reviewed the medical records of the cases who were admitted to the local hospitals, interviewed cases by a standard questionnaire, and then described the epidemiologic features and analyzed risk factors by means of a case-control study. We collected pharyngeal swab specimens and sent them to different laboratories for isolation and culture. The laboratory used different detection methods such as DIF, PCR, electron microscope examination and microneutralization assay, to identify and then type the positive specimens. Results A total of 871 cases were reported during the period from April 18 to July 4, 2004. The distribution of onset times presented two peaks, one in late May and another in middle June. The epidemic occurred mainly in the elementary and junior high schools in ten townships of one county, and the mean age of the cases was 12 years (range 7 months to 18 years). The course of the disease was acute, and was characterized by fever accompanied with sore throat and tonsillitis. The WBC count of cases was normal or elevated. The mean duration of illness was 5 days (range 2 to 12 days). No fatalities from illness were reported. A case-control study indicated that the possible risk factors were close contact with a case and/or poultry before onset and sharing of towels among members of the family. The typical CPE was observed through inoculating pharyngeal swab specimens into the HEP-2 cell cultures in different laboratories. An infection of adenovirus type 3 was verified by detecting positive specimens in different methods. Conclusion This investigation demonstrated that the acute respiratory infection in cases was caused by adenovirus type 3. Cases occurred in over 70 schools in ten townships in 2004, and the route of transmission was possibly close contact with cases or droplet transmission. url: https://www.sciencedirect.com/science/article/pii/S1007437607600719 doi: 10.1016/s1007-4376(07)60071-9 id: cord-007874-oq8gpl91 author: Bao, Jian R. title: Reverse-transcription polymerase chain reaction/pyrosequencing to characterize neuraminidase H275 residue of influenza A 2009 H1N1 virus for rapid and specific detection of the viral oseltamivir resistance marker in a clinical laboratory date: 2011-10-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Pandemic 2009 H1N1 is normally susceptible to oseltamivir, but variants harboring the H275Y (CAC → TAC) mutation exhibit resistance. We describe the use of a combined reverse-transcription polymerase chain reaction (RT-PCR)/pyrosequencing approach to identify the H275 residue. A total of 223 specimens were tested with this method: 216 randomly selected clinical specimens positive for 2009 H1N1 and 7 cell-culture supernatants from the Centers for Disease Control and Prevention (CDC; 4 resistant, 3 susceptible 2009 H1N1 strains). The assay detected H275Y in 1 clinical respiratory sample (0.5%) and all 4 oseltamivir-resistant strains from the CDC; the remaining 215 clinical and 3 susceptible CDC specimens were wild-type. Sanger sequencing confirmed the results for 50 of 50 selected isolates. The RT-PCR/pyrosequencing method was highly specific, producing no amplicons or valid sequences from samples containing non-H1N1 viruses or bacteria. Our findings suggest that this method provides a rapid tool for H275Y detection, with high sensitivity and potential benefit for patient care. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7125974/ doi: 10.1016/j.diagmicrobio.2011.09.003 id: cord-335784-v7nbck0n author: Barak, N. title: Lessons from applied large-scale pooling of 133,816 SARS-CoV-2 RT-PCR tests date: 2020-10-20 words: 3136.0 sentences: 202.0 pages: flesch: 57.0 cache: ./cache/cord-335784-v7nbck0n.txt txt: ./txt/cord-335784-v7nbck0n.txt summary: Pooling multiple swab samples prior to RNA extraction and RT-PCR analysis was proposed as a strategy to reduce costs and increase throughput of SARS-CoV-2 tests. Key open questions concern reduced sensitivity due to sample dilution; the rate of false positives; the actual efficiency (number of tests saved by pooling) and the impact of infection rate in the population on assay performance. Major diagnostic challenges have emerged, mainly, the need for high throughput SARS-CoV-2 RT-PCR tests, aimed to detect not only symptomatic but also asymptomatic infectious viral carriers and to screen special or at-risk populations (such as health care personnel or nursing home tenants), in order to contain viral spread and guide control measures. To our knowledge, this is the most extensive analysis, addressing key considerations of efficiency, sensitivity and feasibility in the actual reality of routine, large-scale implementation of sample pooling for SARS-CoV-2 detection. abstract: Pooling multiple swab samples prior to RNA extraction and RT-PCR analysis was proposed as a strategy to reduce costs and increase throughput of SARS-CoV-2 tests. However, reports on practical large-scale group testing for SARS-CoV-2 have been scant. Key open questions concern reduced sensitivity due to sample dilution; the rate of false positives; the actual efficiency (number of tests saved by pooling) and the impact of infection rate in the population on assay performance. Here we report analysis of 133,816 samples collected at April-September 2020, tested by pooling for the presence of SARS-CoV-2. We spared 76% of RNA extraction and RT-PCR tests, despite the reality of frequently changing prevalence rate (0.5%-6%). Surprisingly, we observed pooling efficiency and sensitivity that exceed theoretical predictions, which resulted from non-random distribution of positive samples in pools. Overall, the findings strongly support the use of pooling for efficient large high throughput SARS-CoV-2 testing. url: http://medrxiv.org/cgi/content/short/2020.10.16.20213405v1?rss=1 doi: 10.1101/2020.10.16.20213405 id: cord-260866-bzdd4f5h author: Barceló, Damià title: Wastewater-Based Epidemiology to Monitor COVID-19 Outbreak: Present and Future Diagnostic Methods to be in Your Radar date: 2020-09-14 words: 4676.0 sentences: 249.0 pages: flesch: 50.0 cache: ./cache/cord-260866-bzdd4f5h.txt txt: ./txt/cord-260866-bzdd4f5h.txt summary: Paper-based devices would be certainly one of the best measurement solutions for the rapid and onsite detection of COVID-19 in sewage waters and humans as well [2, 16] and also the use of other biomarkers of exposure [1] . Detection of SARS-CoV-2 in sewage has been employed as a complementary method to clinical test .It is an early warning indicator of virus spreading in communities, covering both symptomatic and asymptomatic cases. Hopefully at certain moment applications to detect SARS-CoV-2 and other viruses in wastewater will be developed based on these LOC/POCT systems that will enable simple, fast and sensitive virus detection. PCR platforms like RT-qPCR are still the most widely used methods for SARS-Cov-2 detection in waste waters. Sewage sensors, such as paper-based and smartphones for SARS-CoV2 detection at the population level have as well a clear potential for early warning of COVID-19 pandemic. abstract: The WHO has declared the COVID-19 epidemic on January 31, 2020. This virus has infected millions of people worldwide in just a few months. Shortly afterwards, the National Medical Products Administration (NMPA) announced nucleic acid testing as the gold standard for virus detection. Antibody testing is used as well as a supplementary test for suspected cases where nucleic acid detection was negative. In short, nucleic acid–based polymerase chain reaction (PCR) is the mainstream detection method for clinical samples as well as for the detection of SARS-CoV-2 in wastewaters. First data collected around the globe were reported in the last few months being part of the so-called Wastewater-Based Epidemiology (WBE) approach. Selection of concentration methods and primers, laboratory inter-comparison and various modalities of PCR detection of the virus in complex wastewater matrices were flagged up as main bullets that require urgent improvement. Novel approaches to enhance sensitivity, speed and automate streamlined virus detection will be discussed here as well. This list comprises devices mainly used for clinical purposes like Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), Digital PCR, Lab-on-a-chip (LOC) and related platforms as well as Biosensors. The last part will be devoted to the identification of biomolecules to target Covid-19 outbreak based on inflammatory response biomarkers among others. To this end this opinion paper brings for discussion the issue of PCR detection and its limitations as well as new diagnostic methods in WBE. url: https://api.elsevier.com/content/article/pii/S2666016420300402 doi: 10.1016/j.cscee.2020.100042 id: cord-016640-pvlg3nkp author: Baron, Ellen Jo title: Technical and Clinical Niches for Point of Care Molecular Devices date: 2012-04-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A point of care (POC) device is one that is used outside of a central laboratory environment; generally near , or at the site of the patient/client. Point of care testing (POCT) varies from tests performed in physician’s office labs, or “satellite” or “stat” labs, to tests performed on tabletop instruments in a clinic area, to testing performed with hand-held instruments at the bedside. In peripheral lab settings, POCT may be performed by trained laboratory staff, but clinic and bedside POCT is frequently performed by staff who lack specialized laboratory training and whose primary job is something other than doing lab tests. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120995/ doi: 10.1007/978-1-4614-3970-7_33 id: cord-262730-1dxeg8ci author: Barón-Sánchez, J. title: Smell and taste disorders in Spanish patients with mild COVID-19 date: 2020-10-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Introduction Coronavirus disease 2019 (COVID-19) has spread rapidly throughout the world. Smell and/or taste disorders have emerged as a very frequent symptom as the disease has spread in Europe. Spain is one of the European countries with the highest number of infections. Objective This study aimed to investigate the clinical progression of smell and taste disorders in Spanish patients with mild COVID-19. Methods An online survey was used to conduct a cross-sectional study of patients who presented sudden smell and/or taste disorders during the 2 months of total lockdown due to COVID-19 in Spain. Results In our sample, 91.18% of respondents with impaired smell and/or taste and who were able to undergo PCR testing were positive for SARS-CoV-2 infection. Anosmia and ageusia presented in isolation in 6.5% of participants. The remaining 93.5% presented other mild symptoms: headache (51.6%), cough (51.6%), myalgia (45.2%), asthaenia (38.7%), nasal congestion or rhinorrhoea (35.5%), fever (41.9%), low-grade fever (29.0%), odynophagia (25.8%), or diarrhoea (6.5%). The mean duration of anosmia was 8.33 days, with patients subsequently manifesting hyposmia; complete resolution occurred after a mean of 17.79 days. In 22.6% of respondents, olfactory deficits persisted. All participants recovered their sense of taste. Conclusions Olfactory and gustatory disorders are prevalent symptoms in mild COVID-19. Most patients do not present associated nasal congestion or rhinorrhoea and a small group of patients present these alterations in isolation. url: https://api.elsevier.com/content/article/pii/S2173580820302169 doi: 10.1016/j.nrleng.2020.07.007 id: cord-305462-2wz1f6k6 author: Beckham, J. David title: Respiratory viral infections in patients with chronic, obstructive pulmonary disease date: 2004-09-22 words: 3215.0 sentences: 191.0 pages: flesch: 43.0 cache: ./cache/cord-305462-2wz1f6k6.txt txt: ./txt/cord-305462-2wz1f6k6.txt summary: OBJECTIVES: The purpose of the present study was to apply reverse transcription-PCR (RT-PCR) assays to clinical specimens collected from patients with acute respiratory illness and chronic obstructive pulmonary disease (COPD). METHODS: One hundred and ninety-four samples from two different study cohorts were analysed using RT-PCR assays for picornaviruses, coronaviruses 229E and OC43, influenza A and B viruses, respiratory syncytial virus, parainfluenza types 1–3 viruses, and human metapneumovirus and a PCR assay for adenoviruses. 11 The number of respiratory viral infections identified in asthmatic patients with acute exacerbations of disease increase significantly when RT-PCR assays are used in addition to other diagnostic methods. 3 In order to extend our understanding of the prevalence of respiratory viral infection in acute respiratory illnesses in patients with COPD, we used RT-PCR assays to evaluate samples from the previous two prospective studies for evidence of respiratory virus infection. abstract: OBJECTIVES: The purpose of the present study was to apply reverse transcription-PCR (RT-PCR) assays to clinical specimens collected from patients with acute respiratory illness and chronic obstructive pulmonary disease (COPD). METHODS: One hundred and ninety-four samples from two different study cohorts were analysed using RT-PCR assays for picornaviruses, coronaviruses 229E and OC43, influenza A and B viruses, respiratory syncytial virus, parainfluenza types 1–3 viruses, and human metapneumovirus and a PCR assay for adenoviruses. The results were added to results obtained previously using cell culture and serologic methods. RESULTS: RT-PCR assays identified an additional 35 respiratory virus-associated illnesses not identified previously by cell culture or serology (n=46). Picornaviruses and coronaviruses were the most common viral infections identified only by RT-PCR. Overall, 41.8% of the acute respiratory illnesses evaluated were associated with a respiratory virus infection, with picornaviruses, coronaviruses and influenza viruses being the most common infections recognized. No human metapneumovirus infections were identified by RT-PCR assay. CONCLUSIONS: Respiratory viral infections are commonly associated with acute respiratory illness in COPD patients, and the use of RT-PCR assays significantly increases the ability to diagnose these infections. url: https://www.ncbi.nlm.nih.gov/pubmed/15845430/ doi: 10.1016/j.jinf.2004.07.011 id: cord-301430-gzou8b9k author: Beier, D. title: Establishment of a new bovine leukosis virus producing cell line date: 2004-08-17 words: 4086.0 sentences: 248.0 pages: flesch: 58.0 cache: ./cache/cord-301430-gzou8b9k.txt txt: ./txt/cord-301430-gzou8b9k.txt summary: In addition, earlier investigations demonstrated that contamination of the BLV antigen-producing cell culture systems by bovine viral diarrhea virus (BVDV) may give rise to misinterpretation of serological test results after BVDV vaccination of cattle. Investigations of a panel of well-characterised sera by agar gel immunodiffusion (AGID) and capture ELISA (cELISA) tests using antigen prepared from this new cell line in comparison with antigen of the well-known cell line FLK/BLV yielded comparable results. Standard and field sera were investigated in parallel with a commercially available test kit (Riemser Rinderleukose Test Kit, RTAM/Germany) in order to compare sensitivity and specificity of the antigens from the cell lines PO714 and FLK/BLV. Comparative investigations of sera from cattle infected with BLV of different provirus subtypes with antigen from both cell lines using the gp51 cELISA. abstract: Due to the prevalence of different bovine leukosis virus (BLV) species in the cattle population in Europe, problems may arise in the serological diagnosis of BLV infections. In addition, earlier investigations demonstrated that contamination of the BLV antigen-producing cell culture systems by bovine viral diarrhea virus (BVDV) may give rise to misinterpretation of serological test results after BVDV vaccination of cattle. By co-cultivation of peripheral leukocytes of a BLV-infected cow with a permanent sheep kidney cell line, a new BLV-producing cell line named PO714 was established. This line carries a BLV provirus of the Belgian species and has been tested to be free of a variety of possibly contaminating viruses and mycoplasms. Investigations of a panel of well-characterised sera by agar gel immunodiffusion (AGID) and capture ELISA (cELISA) tests using antigen prepared from this new cell line in comparison with antigen of the well-known cell line FLK/BLV yielded comparable results. False positive results caused by BVDV cross-reactions could be eliminated when tests were carried out with antigen derived from the new cell line. url: https://www.sciencedirect.com/science/article/pii/S016609340400196X doi: 10.1016/j.jviromet.2004.06.017 id: cord-294454-uzfsv2df author: Bellau-Pujol, S. title: Development of three multiplex RT-PCR assays for the detection of 12 respiratory RNA viruses date: 2005-02-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Three multiplex hemi-nested RT-PCR assays were developed to detect simultaneously 12 RNA respiratory viruses: influenza viruses A, B and C, human respiratory syncytial virus (hRSV), human metapneumovirus (hMPV), parainfluenza virus types 1–4 (PIV-1, -2, -3 and -4), human coronavirus OC43 and 229E (HCoV) and rhinovirus (hRV). An internal amplification control was included in one of the RT-PCR assays. The RT-PCR multiplex 1 and the hemi-nested multiplex 1 detected 1 and 0.1 TCID50 of RSV A, respectively, and 0.01 and 0.001 TCID50 of influenza virus A/H3N2, respectively. Two hundred and three nasal aspirates from hospitalised children were retrospectively tested in comparison with two conventional methods: direct immunofluorescence assay and viral isolation technique. Almost all samples (89/91) that were positive by immunofluorescence assay and/or viral isolation technique were detected by the multiplex assay. This method also detected an additional 85 viruses and 33 co-infections. The overall sensitivity (98%), rapidity and enhanced efficiency of these multiplex hemi-nested RT-PCR assays suggest that they would be a significant improvement over conventional methods for the detection of a broad spectrum of respiratory viruses. url: https://www.sciencedirect.com/science/article/pii/S0166093405000352 doi: 10.1016/j.jviromet.2005.01.020 id: cord-322524-bq9ok8h1 author: Belongia, Edward A title: Clinical Features, Severity, and Incidence of RSV Illness During 12 Consecutive Seasons in a Community Cohort of Adults ≥60 Years Old date: 2018-11-27 words: 5184.0 sentences: 285.0 pages: flesch: 45.0 cache: ./cache/cord-322524-bq9ok8h1.txt txt: ./txt/cord-322524-bq9ok8h1.txt summary: Studies conducted in the 1980s and 1990s first identified RSV as a cause of acute respiratory illness in a variety of adult populations, including older adults, working-age adults, hospitalized patients, and residents of long-term care facilities [5] [6] [7] [8] [9] . A 6-season study of adults ≥50 years old with predominantly outpatient acute respiratory illness found that RSV was the third most common viral pathogen (after influenza and human rhinovirus) [19] . The objective of this study was to describe the clinical characteristics, severity, clinical outcomes, and long-term incidence of medically attended RSV illness in a community cohort of adults ≥60 years of age from the 2004-2005 through 2015-2016 influenza seasons. Seasonal incidence of medically attended respiratory syncytial virus infection in a community cohort of adults ≥50 years old abstract: BACKGROUND: The epidemiology and burden of respiratory syncytial virus (RSV) illness are not well defined in older adults. METHODS: Adults ≥60 years old seeking outpatient care for acute respiratory illness were recruited from 2004–2005 through 2015–2016 during the winter seasons. RSV was identified from respiratory swabs by multiplex polymerase chain reaction. Clinical characteristics and outcomes were ascertained by interview and medical record abstraction. The incidence of medically attended RSV was estimated for each seasonal cohort. RESULTS: RSV was identified in 243 (11%) of 2257 enrollments (241 of 1832 individuals), including 121 RSV type A and 122 RSV type B. The RSV clinical outcome was serious in 47 (19%), moderate in 155 (64%), and mild in 41 (17%). Serious outcomes included hospital admission (n = 29), emergency department visit (n = 13), and pneumonia (n = 23) and were associated with lower respiratory tract symptoms during the enrollment visit. Moderate outcomes included receipt of a new antibiotic prescription (n = 144; 59%), bronchodilator/nebulizer (n = 45; 19%), or systemic corticosteroids (n = 28; 12%). The relative risk of a serious outcome was significantly increased in persons aged ≥75 years (vs 60–64 years) and in those with chronic obstructive pulmonary disease or congestive heart failure. The average seasonal incidence was 139 cases/10 000, and it was significantly higher in persons with cardiopulmonary disease compared with others (rate ratio, 1.89; 95% confidence interval, 1.44–2.48). CONCLUSIONS: RSV causes substantial outpatient illness with lower respiratory tract involvement. Serious outcomes are common in older patients and those with cardiopulmonary disease. url: https://www.ncbi.nlm.nih.gov/pubmed/30619907/ doi: 10.1093/ofid/ofy316 id: cord-272955-kkkrkgg1 author: Belsy, Acosta title: Molecular characterization of adenoviral infections in Cuba: report of an unusual association of species D adenoviruses with different clinical syndromes date: 2009-03-12 words: 4219.0 sentences: 233.0 pages: flesch: 39.0 cache: ./cache/cord-272955-kkkrkgg1.txt txt: ./txt/cord-272955-kkkrkgg1.txt summary: title: Molecular characterization of adenoviral infections in Cuba: report of an unusual association of species D adenoviruses with different clinical syndromes The objectives of this study were to identify and characterize members of different adenovirus species at the molecular level and to describe the correlation between viruses and clinical syndromes during a period of 4 years. Four isolates from clinical materials obtained from patients with encephalitis, acute flaccid paralysis and meningoencephalitis were identified as belonging to the species Human adenovirus D. In the present report, the nested PCR method used was able to detect different HAdVs in clinical samples and supernatant culture with a sensitive internal control system to assure the quality of reaction conditions in each individual tube. Human adenovirus DNA was detected in the supernatant of a cell culture infected with viruses obtained from fecal specimens taken from a patient with acute flaccid paralysis (AFP), as well as in two cases of meningoencephalitis. abstract: Adenoviruses are common pathogens that are responsible for a wide variety of infectious syndromes. The objectives of this study were to identify and characterize members of different adenovirus species at the molecular level and to describe the correlation between viruses and clinical syndromes during a period of 4 years. Between 2002 and 2006, 45 of 512 respiratory specimens (8%) from patients with acute respiratory tract infection tested positive for adenovirus. Four adenovirus isolates from samples sent for enterovirus isolation were also analyzed. This research identified 49 confirmed cases of human adenovirus infection by PCR and/or viral culture. The most common diagnosis was upper respiratory infection (44%). Human adenovirus D was the major species found (59%), followed by Human adenovirus C (36%) and Human adenovirus B (4%). Human adenovirus 5 was the major serotype found producing bronchiolitis, followed by human adenovirus 6. In patients with upper respiratory infection, the major serotype found was human adenovirus 17. Viruses of the species Human adenovirus D were identified in seven (77%) cases of acute febrile syndrome. Four isolates from clinical materials obtained from patients with encephalitis, acute flaccid paralysis and meningoencephalitis were identified as belonging to the species Human adenovirus D. Our data demonstrate a surprising result about the identification of an unusual association of viruses of the species Human adenovirus D with different clinical syndromes. This observation could be evaluated as a possible indicator of the emergence of a novel strain but further studies are required. url: https://www.ncbi.nlm.nih.gov/pubmed/19280320/ doi: 10.1007/s00705-009-0338-4 id: cord-016073-uhei3bvr author: Belák, Sándor title: Recent Advances in Veterinary Diagnostic Virology: Report from a Collaborating Centre of the World Organization for Animal Health (OIE) date: 2012-04-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Infectious diseases have a very high impact on animal and human health and welfare today, despite of strong efforts and good results in diagnostics, vaccine developments and control measures, including the early warning systems. There are many reasons, which have to be considered as supporting factors for the spread of infectious diseases, such as the open borders of the European Union, allowing rather free movement of animals over a whole continent, the globalization, the released and accelerated international and national trade and animal transfer. Simultaneously, the emergence and re-emergence of new or already known pathogens is a various serious issue in veterinary and in human medicine. This scenario is clearly illustrated by the regular occurrence of transboundary animal diseases (TADs), such as foot-and-mouth disease (FMD), classical swine fever (CSF), African swine fever (ASF), among others. The recent occurrence of African swine fever in the Caucasus region and the spread afterwards to large territories of Russia clearly illustrates that our health authorities require a very strong preparedness, including prompt and powerful diagnosis, for the successful fight against the novel scenarios. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120236/ doi: 10.1007/978-1-4614-3970-7_36 id: cord-255026-fdp6mies author: Belák, Sándor title: Molecular diagnosis of viral diseases, present trends and future aspects: A view from the OIE Collaborating Centre for the Application of Polymerase Chain Reaction Methods for Diagnosis of Viral Diseases in Veterinary Medicine date: 2007-07-26 words: 5342.0 sentences: 225.0 pages: flesch: 40.0 cache: ./cache/cord-255026-fdp6mies.txt txt: ./txt/cord-255026-fdp6mies.txt summary: The experiences of an OIE-Collaborating Centre and of two EU project consortia are summarised on the diagnostic application of gel-based PCR, general PCR systems, phylogeny, molecular epidemiology, real-time PCR (TaqMan, Molecular Beacons, Primer-Probe Energy Transfer), amplification without thermocycling (Invader), multiplex PCR, nucleic acid extraction and pipetting robotics, automation and quality control, including internal controls. abstract: The emergence and re-emergence of transboundary animal diseases (TADs), e.g., foot-and-mouth disease, classical swine fever and the highly pathogenic avian influenza strongly indicate the need for the development of powerful and robust new diagnostic methods. The experiences of an OIE-Collaborating Centre and of two EU project consortia are summarised on the diagnostic application of gel-based PCR, general PCR systems, phylogeny, molecular epidemiology, real-time PCR (TaqMan, Molecular Beacons, Primer-Probe Energy Transfer), amplification without thermocycling (Invader), multiplex PCR, nucleic acid extraction and pipetting robotics, automation and quality control, including internal controls. By following the steps of OIE validation, the diagnostic assays are nationally and internationally standardised. The development of padlock probes and microarrays, as well as ultra rapid PCR and sequencing methods is further improving the arsenal of nucleic acid based molecular diagnosis. Further trends of diagnostic development are also mentioned, in order to combat TADs and other viral infections more effectively in the future. url: https://www.sciencedirect.com/science/article/pii/S0264410X06012989 doi: 10.1016/j.vaccine.2006.11.068 id: cord-325529-pid58g2r author: Ben-Ami, Roni title: Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection date: 2020-06-23 words: 2822.0 sentences: 158.0 pages: flesch: 50.0 cache: ./cache/cord-325529-pid58g2r.txt txt: ./txt/cord-325529-pid58g2r.txt summary: METHODS: We tested the efficiency and sensitivity of pooling strategies for RNA extraction and RT-PCR detection of SARS-CoV-2. Implementing the 8-sample Dorfman pooling to test 26,576 samples from asymptomatic individuals, we identified 31 (0.12%) SARS-CoV-2 positive samples, achieving a 7.3-fold increase in throughput. Some key constrains are (1) a limit on the number of stages due to the importance of delivering a test result quickly, exemplified by the urgent clinical context of COVID-19 diagnosis; (2) a limit on the ability to dilute samples and still safely identify a single positive sample in a pool; and (3) favorability of simple algorithms which may minimize human error in a laboratory setting. Specifically, we have demonstrated that pooling lysates from 5 or 8 nasopharyngeal swab samples retains sufficient sensitivity of viral RNA detection, allowing identification of SARS-CoV-2-positive individuals, while increasing throughput 5-fold to 7.5-fold. abstract: OBJECTIVES: Testing for active SARS-CoV-2 infection is a fundamental tool in the public health measures taken to control the COVID-19 pandemic. Due to the overwhelming use of SARS-CoV-2 RT-PCR tests worldwide, availability of test kits has become a major bottleneck, while the need to increase testing throughput only rises. We aim to overcome these challenges by pooling samples together, performing RNA extraction and RT-PCR in pools. METHODS: We tested the efficiency and sensitivity of pooling strategies for RNA extraction and RT-PCR detection of SARS-CoV-2. We tested 184 samples both individually and in pools to estimate the effects of pooling. We further implemented Dorfman pooling with a pool size of 8 samples in large-scale clinical tests. RESULTS: We demonstrated pooling strategies that increase testing throughput while maintaining high sensitivity. A comparison of 184 samples tested individually and in pools of 8 samples, showed that test results were not significantly affected. Implementing the 8-sample Dorfman pooling to test 26,576 samples from asymptomatic individuals, we identified 31 (0.12%) SARS-CoV-2 positive samples, achieving a 7.3-fold increase in throughput. CONCLUSIONS: Pooling approaches for SARS-CoV-2 testing allow a drastic increase in throughput while maintaining clinical sensitivity. We report the successful large-scale pooled screening of asymptomatic populations. url: https://www.sciencedirect.com/science/article/pii/S1198743X20303499?v=s5 doi: 10.1016/j.cmi.2020.06.009 id: cord-351854-5s03f0pp author: Ben-Ami, Roni title: Pooled RNA extraction and PCR assay for efficient SARS-CoV-2 detection date: 2020-04-22 words: 3316.0 sentences: 197.0 pages: flesch: 54.0 cache: ./cache/cord-351854-5s03f0pp.txt txt: ./txt/cord-351854-5s03f0pp.txt summary: title: Pooled RNA extraction and PCR assay for efficient SARS-CoV-2 detection We have implemented the method in a routine clinical diagnosis setting, and already tested 2,168 individuals for SARS-CoV-2 using 311 RNA extraction and RT-PCR kits. Three such limitations might be: (1) a limit on the number of stages due to the importance of delivering a test result quickly, exemplified by the urgent clinical context of COVID-19 diagnosis; (2) a limit on the ability to dilute samples and still safely identify a single positive sample in a pool; (3) favorability of simple algorithms which may minimize human error in a laboratory setting. . https://doi.org/10.1101/2020.04.17.20069062 doi: medRxiv preprint probability of a sample to be positive by p (prevalence of detectable COVID-19 patients in the relevant population) and the pool size by n. This allows for reliable and efficient screening of large asymptomatic populations for the presence of SARS-CoV-2 infection, even when RNA extraction and RT-PCR reagents are in short supply. abstract: Testing for active SARS-CoV-2 infection is a fundamental tool in public health measures taken to control the COVID-19 pandemic. Due to the overwhelming use of SARS-CoV-2 RT-PCR tests worldwide, availability of test kits has become a major bottleneck. Here we demonstrate the reliability and efficiency of two simple pooling strategies that can increase testing capacity about 5-fold to 7.5-fold, in populations with a low infection rate. We have implemented the method in a routine clinical diagnosis setting, and already tested 2,168 individuals for SARS-CoV-2 using 311 RNA extraction and RT-PCR kits. url: https://doi.org/10.1101/2020.04.17.20069062 doi: 10.1101/2020.04.17.20069062 id: cord-315094-pzixgqcy author: Benetka, Viviane title: Prevalence of feline coronavirus types I and II in cats with histopathologically verified feline infectious peritonitis date: 2004-03-26 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Feline coronaviruses (FCoV) vary widely in virulence causing a spectrum of clinical manifestations reaching from subclinical course to fatal feline infectious peritonitis (FIP). Independent of virulence variations they are separated into two different types, type I, the original FCoV, and type II, which is closely related to canine coronavirus (CCV). The prevalence of FCoV types in Austrian cat populations without FIP has been surveyed recently indicating that type I infections predominate. The distribution of FCoV types in cats, which had succumbed to FIP, however, was fairly unknown. PCR assays have been developed amplifying parts of the spike protein gene. Type-specific primer pairs were designed, generating PCR products of different sizes. A total of 94 organ pools of cats with histopathologically verified FIP was tested. A clear differentiation was achieved in 74 cats, 86% of them were type I positive, 7% type II positive, and 7% were positive for both types. These findings demonstrate that in FIP cases FCoV type I predominates, too, nonetheless, in 14% of the cases FCoV type II was detected, suggesting its causative involvement in cases of FIP. url: https://api.elsevier.com/content/article/pii/S0378113503003821 doi: 10.1016/j.vetmic.2003.07.010 id: cord-286451-ujo72w06 author: Bennett, Susan title: The development of a multiplex real-time PCR for the detection of herpes simplex virus 1 and 2, varizella zoster virus, adenovirus and Chlamydia trachomatis from eye swabs date: 2012-09-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Infectious conjunctivitis can be difficult to distinguish clinically due to the considerable overlap in clinical presentation so clinical diagnosis of conjunctivitis is often insufficient. It is therefore necessary to have a rapid diagnostic test that differentiates between the different causes of infectious conjunctivitis. Screening clinical samples by sample type/syndrome based multiplex real time PCR would allow for rapid detection of a variety of pathogens simultaneously, which will in turn aid in the treatment and clinical management of the patient. A multiplex real-time PCR assay for rapid and simultaneous detection of HSV 1 and 2, VZV, adenovirus and Chlamydia trachomatis (C. trachomatis) from eye swabs was developed and evaluated. The multiplex assay was shown to be sensitive, specific and robust. Reductions in sample turn around times have been achieved by reducing the amount of separate tests needed to be carried out. url: https://www.sciencedirect.com/science/article/pii/S0166093412002996 doi: 10.1016/j.jviromet.2012.08.020 id: cord-319460-n4ezxnjc author: Bertasio, Cristina title: Porcine Epidemic Diarrhea Virus Shedding and Antibody Response in Swine Farms: A Longitudinal Study date: 2016-12-15 words: 5905.0 sentences: 262.0 pages: flesch: 53.0 cache: ./cache/cord-319460-n4ezxnjc.txt txt: ./txt/cord-319460-n4ezxnjc.txt summary: During summer 2014, animals on two farms displaying mild clinical signs were detected as positive for PEDV by PCR (Boniotti et al., 2016) , and at the beginning of 2015 a new severe epidemic wave occurred (Efsa Ahaw Panel, 2014) . We conducted a longitudinal study by sampling the feces and blood of piglet groups from each farm at fixed intervals during a 2-5 months period, and then we determined PEDV shedding and the antibody presence. The highest fecal PEDV RNA shedding titer was observed in 3-6 day-old piglets with mean values (among shedding animals) of 5.9, 5.6, 5.6, and 6.2 log 10 copies/mL on F1, F2, F3, and F4, respectively ( Figure 1B; Supplementary Table 3 ). Determining the viral loads and shedding rates of PEDV in real field situations during outbreaks is important in evaluating the virulence of a strain and in predicting the susceptibility of infected animals, at different ages and in the various farm units, within a herd. abstract: The porcine epidemic diarrhea virus (PEDV) causes an acute and highly contagious enteric disease characterized by severe enteritis, vomiting, watery diarrhea, and a high mortality rate in seronegative neonatal piglets. In the last few years, PED had a large economic impact on the swine industries in Asia and the US, and in 2014, the PEDV also re-emerged in Europe. Two main PEDV variants circulate worldwide but only the S INDEL variant, considered a mild strain, is spreading in Europe. To gain insights into the pathogenicity of this variant, its viral load and temporal shedding pattern were evaluated in piglets from infected farms. Quantitative real-time PCR (qPCR) targeting the spike gene, was validated according to the minimum information for quantitative real-time PCR experiments guidelines. The qPCR was applied to longitudinal studies conducted in four swine farms naturally infected with the PEDV S INDEL variant. Clinical data, fecal swabs, and blood samples were collected from 103 piglets at 15–30-day intervals for 2–5 months. On all four farms, diarrhea was observed in sows during gestation and in farrowing units, and the mortality rates of piglets were 18, 25, 30, and 35%. Different clinical pictures (0-50% of diarrhea positivity), viral titer levels (mean 5.3-7.2 log(10) genome copies/mL), and antibody conditions (30-80% of positivity) were registered among sows on the four farms. The percentage of qPCR positive piglets varied greatly from the beginning (63–100%) to the end (0%) of the infection course. Clinical signs were present in 96% of the qPCR positive animals. Viral loads ranged from 8.5 log(10) to 4 log(10) genome copies/mL in suckling pigs at 3–6 days of age and were not statistically different among farms, despite the different patterns observed in sows. After 2–3 weeks, only a few piglets still showed detectable viral levels and clinical signs, and they developed antibody responses. Moreover, co-infections with other pathogens and biosecurity procedures limiting the circulation of the virus could have influenced the severity of PED infection. QPCR and clinical data were useful in understanding the dynamics of PEDV infections and, therefore, in implementing appropriate control measures. url: https://www.ncbi.nlm.nih.gov/pubmed/28018330/ doi: 10.3389/fmicb.2016.02009 id: cord-000750-l9ozvlae author: Betts, Corinne title: Pip6-PMO, A New Generation of Peptide-oligonucleotide Conjugates With Improved Cardiac Exon Skipping Activity for DMD Treatment date: 2012-08-14 words: 6521.0 sentences: 337.0 pages: flesch: 46.0 cache: ./cache/cord-000750-l9ozvlae.txt txt: ./txt/cord-000750-l9ozvlae.txt summary: We have previously reported impressive heart activity including high-splicing efficiency and dystrophin restoration following a single administration of an arginine-rich cell-penetrating peptide (CPPs) conjugated to a phosphorodiamidate morpholino oligonucleotide (PMO): Pip5e-PMO. We have previously reported impressive heart activity including high-splicing efficiency and dystrophin restoration following a single administration of an arginine-rich cell-penetrating peptide (CPPs) conjugated to a phosphorodiamidate morpholino oligonucleotide (PMO): Pip5e-PMO. These changes affect the levels of exon skipping and dystrophin restoration in multiple muscle groups, including the heart, following a single, low dose intravenous injection of the corresponding Pip6-PMO conjugates. Therefore, considering the results overall, mdx mice treated with each of the four 5-aa core Pip6-PMOs (Pip6a-, Pip6b-, Pip6e-, and Pip6f-PMO) appear to demonstrate improved dystrophin production and exon skipping in TA, quadriceps, and heart muscles compared with the previous lead candidate, Pip5e-PMO. abstract: Antisense oligonucleotides (AOs) are currently the most promising therapeutic intervention for Duchenne muscular dystrophy (DMD). AOs modulate dystrophin pre-mRNA splicing, thereby specifically restoring the dystrophin reading frame and generating a truncated but semifunctional dystrophin protein. Challenges in the development of this approach are the relatively poor systemic AO delivery and inefficient dystrophin correction in affected non-skeletal muscle tissues, including the heart. We have previously reported impressive heart activity including high-splicing efficiency and dystrophin restoration following a single administration of an arginine-rich cell-penetrating peptide (CPPs) conjugated to a phosphorodiamidate morpholino oligonucleotide (PMO): Pip5e-PMO. However, the mechanisms underlying this activity are poorly understood. Here, we report studies involving single dose administration (12.5 mg/kg) of derivatives of Pip5e-PMO, consecutively assigned as Pip6-PMOs. These peptide-PMOs comprise alterations to the central hydrophobic core of the Pip5e peptide and illustrate that certain changes to the peptide sequence improves its activity; however, partial deletions within the hydrophobic core abolish its efficiency. Our data indicate that the hydrophobic core of the Pip sequences is critical for PMO delivery to the heart and that specific modifications to this region can enhance activity further. The results have implications for therapeutic PMO development for DMD. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3438601/ doi: 10.1038/mtna.2012.30 id: cord-344770-aoi42xq4 author: Bialasiewicz, Seweryn title: Detection of a divergent Parainfluenza 4 virus in an adult patient with influenza like illness using next-generation sequencing date: 2014-05-19 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Human Parainfluenza viruses are a common cause of both upper and lower respiratory tract infections, particularly in children. Of the four Parainfluenza virus serotypes, Parainfluenza 4 is least well characterised from both the clinical, epidemiological and genetic perspectives. METHODS: Flocked nose or throat swabs from a previous study investigating viral prevalence in community-based adults suffering from influenza like illness were used as the basis for this study. Samples in which no virus was detected using a 16 viral respiratory pathogen real-time PCR panel were barcoded and pyrosequenced using the Roche 454 GS FLX Titanium chemistry. The sequences were analysed using the VirusHunter bioinformatic pipeline. Sanger sequencing was used to complete the detected Parainfluenza 4 coding region. RESULTS: A variant Parainfluenza 4 subtype b strain (QLD-01) was discovered in an otherwise healthy adult who presented with influenza like illness. Strain QLD-01 shared genomic similarities with both a and b subtypes. The extent of divergence of this genome from the 5 available whole Parainfluenza 4 genomes impacted the predicted binding efficiencies of the majority of published Parainfluenza 4 PCR assays. CONCLUSIONS: These findings further support a possible role for Parainfluenza 4 in the aetiology of adult respiratory disease within the community setting, and highlight the caution needed to be used in designing PCR assays from limited sequence information or in using proprietary commercial PCR assays. url: https://www.ncbi.nlm.nih.gov/pubmed/24885416/ doi: 10.1186/1471-2334-14-275 id: cord-269839-jxqs51o5 author: Bitome-Essono, Paul-Yannick title: Tracking zoonotic pathogens using blood-sucking flies as 'flying syringes' date: 2017-03-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: About 60% of emerging infectious diseases in humans are of zoonotic origin. Their increasing number requires the development of new methods for early detection and monitoring of infectious agents in wildlife. Here, we investigated whether blood meals from hematophagous flies could be used to identify the infectious agents circulating in wild vertebrates. To this aim, 1230 blood-engorged flies were caught in the forests of Gabon. Identified blood meals (30%) were from 20 vertebrate species including mammals, birds and reptiles. Among them, 9% were infected by different extant malaria parasites among which some belonged to known parasite species, others to new parasite species or to parasite lineages for which only the vector was known. This study demonstrates that using hematophagous flies as ‘flying syringes’ constitutes an interesting approach to investigate blood-borne pathogen diversity in wild vertebrates and could be used as an early detection tool of zoonotic pathogens. DOI: http://dx.doi.org/10.7554/eLife.22069.001 url: https://www.ncbi.nlm.nih.gov/pubmed/28347401/ doi: 10.7554/elife.22069 id: cord-256355-muskjaw3 author: Black, Elizabeth M title: A rapid RT-PCR method to differentiate six established genotypes of rabies and rabies-related viruses using TaqMan™ technology date: 2002-05-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A rapid and sensitive reverse transcriptase-polymerase chain reaction (RT-PCR) assay incorporating TaqMan™ probes has been developed that can distinguish among the six established rabies and rabies-related virus genotypes. TaqMan™ probes were designed and validated against 106 rabies and rabies-related virus isolates, one isolate of the Australian bat Lyssaviruses (genotype 7), and 18 other non-rabies viruses important in the veterinary field. The N gene was used as the target for the probes as it is well conserved and has been intensively used to genotype rabies isolates. Additionally, it was found to contain regions specific to each genotype conducive to probe design. The RT-PCR assay described amplifies a portion of the nucleoprotein gene of all 107 rabies and rabies-related viruses, but none of the other viruses tested. Inclusion of TaqMan™-genotype-specific probes in the RT-PCR assay permits rapid identification of the virus present. By combining RT-PCR with TaqMan™ genotyping probes suspect rabies virus isolates can be identified in a single closed tube system that prevents potential PCR-product carry over contamination. url: https://www.sciencedirect.com/science/article/pii/S0166093402000629 doi: 10.1016/s0166-0934(02)00062-9 id: cord-338641-s006a7m0 author: Black, W. D. title: Reverse transcriptase-polymerase chain reaction for the detection equine rhinitis B viruses and cell culture isolation of the virus date: 2006-08-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Equine rhinitis B virus (ERBV), genus Erbovirus, family Picornaviridae occurs as two serotypes, ERBV1 and ERBV2. An ERBV-specific nested reverse transcriptase-polymerase chain reaction (RT-PCR) that amplified a product within the 3D(pol) and 3′ non-translated region of the viral genome was developed. The RT-PCR detected all 24 available ERBV1 isolates and one available ERBV2 isolate. The limit of detection for the prototype strain ERBV1.1436/71 was 0.1 50% tissue culture infectious doses. The RT-PCR was used to detect viral RNA in six of 17 nasopharyngeal swab samples from horses that had clinical signs of acute febrile respiratory disease but from which ERBV was not initially isolated in cell culture. The sequences of these six ERBV RT-PCR positive samples had 93–96% nucleotide identity with six other partially sequenced ERBV1 isolates and one ERBV2. ERBV was isolated from one of the six samples at fourth cell culture passage when it was shown that the addition of 20 mg/mL MgCl(2) to the cell culture medium enhanced the growth of the virus. This isolated virus was antigenically similar to ERBV2.313/75. Determination of the nucleotide sequence of the P1 region of the genome also indicated that the isolate was ERBV2, and it was therefore designated ERBV2.1576/99. This is the first reported isolation of ERBV in Australia. The study highlights the utility of PCR for the identification of viruses in clinical samples that may initially be considered negative by conventional cell culture isolation. url: https://www.ncbi.nlm.nih.gov/pubmed/16932985/ doi: 10.1007/s00705-006-0810-3 id: cord-346104-18x8u2oe author: Black, Wendy title: Identification of gammaherpesvirus infection in free-ranging black bears (Ursus americanus) date: 2019-01-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Herpesvirus infection was investigated in black bears (Ursus americanus) with neurological signs and brain lesions of nonsuppurative encephalitis of unknown cause. Visible cytopathic effects (CPE) could only be observed on days 3–5 post-infection in HrT-18G cell line inoculated with bear tissue extracts. The observed CPE in HrT-18G cells included syncytia, intranuclear inclusions, and cell detachments seen in herpesvirus infection in vitro. Herpesvirus-like particles were observed in viral culture supernatant under the electron microscope, however, capsids ranging from 60 nm to 100 nm in size were often observed in viral cultures within the first two passages of propagation. Herpesvirus infection in the bear tissues and tissue cultures were detected by PCR using degenerate primers specific to the DNA polymerase gene (DPOL) and glycoprotein B gene (gB). DNA sequencing of the amplicon revealed that the detected herpesvirus has 94–95% identity to Ursid gammaherpesvirus 1 (UrHV-1) DNA sequences of DPOL. Phylogenetic analysis of DPOL sequences indicates that black bear herpesviruses and UrHV-1 are closely related and have small distances to members of Rhadinovirus. Interestingly, black bear herpesvirus infections were also found in bears without neurological signs. The DPOL DNA sequence of black bear herpesviruses detected in neurological bears were similar to the those detected in the non-neurological bears. However, the gB DNA sequence detected from the neurological bear is different from non-neurological bear and has only 64.5%–70% identity to each other. It is possible that at least two different types of gammaherpesviruses are present in the U. americanus population or several gammaherpesviruses exist in ursine species. url: https://www.sciencedirect.com/science/article/pii/S0168170218303678 doi: 10.1016/j.virusres.2018.10.016 id: cord-331616-arnuoufn author: Blank, Walter A. title: Virus PCR Assay Panels: An Alternative to the Mouse Antibody Production Test date: 2004 words: 3515.0 sentences: 159.0 pages: flesch: 37.0 cache: ./cache/cord-331616-arnuoufn.txt txt: ./txt/cord-331616-arnuoufn.txt summary: The authors compare MAP testing with PCR-based detection methods, focusing on differences in animal use, laboratory requirements, sample size, and limits of detection. Until recently, the mouse antibody production (MAP) test was the primary method of screening for viruses of murine origin 6 ( Table 1) , but the application of modern molecular biology methods to this purpose presents certain advantages. Because PCR amplifies only DNA molecules, one detects viruses with RNA samples from the animals and test them for virus-specific antibodies using the enzymelinked immunosorbent (ELISA), indirect fluorescent antibody (IFA), or hemagglutination inhibition (HAI) assays. To prevent false-positive results due to contamination with PCR templates, reagent preparation, sample processing, and PCR amplification/product detection should all take place in separate laboratories. Comparison of the sensitivity of in vivo antibody production tests with in vitro PCR-based methods to detect infectious contamination of biological materials abstract: Antibody production tests have traditionally been used to test biological materials for viral contamination. Now molecular biology techniques have emerged as an alternative. The authors compare MAP testing with PCR-based detection methods, focusing on differences in animal use, laboratory requirements, sample size, and limits of detection. url: https://www.ncbi.nlm.nih.gov/pubmed/15235643/ doi: 10.1038/laban0204-26 id: cord-020568-c5425959 author: Blatny, Janet Martha title: Detecting and Responding to Bioterrorism date: 2007 words: 3480.0 sentences: 204.0 pages: flesch: 42.0 cache: ./cache/cord-020568-c5425959.txt txt: ./txt/cord-020568-c5425959.txt summary: The avian flu outbreak in several Asian countries killing approximately 50 million chickens has revealed the need for establishing rapid molecular diagnostics for mass screening of the Biological threat agents may be difficult to detect and identify quickly and reliable both from a civilian (public health) and a military point of view. Real-time PCR is the most commonly used nucleic acid-based method for specific and sensitive identification of biological threat agents. Internal controls may consist of either a plasmid or a DNA fragment in which the amplified DNA sequence is Several real-time PCR assays have been outlined for a number of biological threat agents, and commercial kits containing the specific reagents are available. An essential part of bioterrorism preparedness and response includes the design of efficient and reliable systems for detection and identification of biological threat agents. Classical microbiology, immunoassays, and nucleic acid-based methods, including molecular forensics, are laboratory approaches for detecting, identifying, and verifying various biological threat agents. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7139443/ doi: 10.1007/978-1-4020-5808-0_7 id: cord-323029-7hqp8xuq author: Bognár, Zsófia title: Aptamers against Immunoglobulins: Design, Selection and Bioanalytical Applications date: 2020-08-11 words: 19331.0 sentences: 873.0 pages: flesch: 45.0 cache: ./cache/cord-323029-7hqp8xuq.txt txt: ./txt/cord-323029-7hqp8xuq.txt summary: For aptamer selection against rIgG [6] and IgE [7] , homogenous processes were used and the separation of bound and unbound nucleic Several different SELEX methods have been used to generate immunoglobulin aptamers including homogeneous, heterogeneous, bead-based SELEX processes, CE-SELEX (capillary electrophoresis-SELEX), µFFE-SELEX (micro-free flow electrophoresis-SELEX) and fully integrated selection processes selection of aptamers with proper binding properties. Molecular Light Switch Complex 100-800 100 [128] Fluorescence enhancement using a DNA aptamer 92-37,000 57 [130] Amplification through allostery-triggered enzymatic recycling amplification NA 5 [131] Fluorescent oligonucleotide probe based on G-quadruplex scaffold for signal-on ultrasensitive protein assay 4.72-7560 0.095 [132] Fluorescence anisotropy 1000-60,000 350 [133] Fluorescence anisotropy assay NA 20 [134] Fluorescence protection assay 100-50,000 100 [136] Aptamer-barcode-based assay based on instantaneous derivatization chemiluminescence coupled to magnetic beads 4.88-20,000 4.6 [137] Competitive fluorescence quenching assay 350-35,000 170 [138] Rapid fluorescence detection of immunoglobulin E using an aptamer switch based on a binding-induced pyrene excimer NA 1600 [139] 6.1. abstract: Nucleic acid aptamers show clear promise as diagnostic reagents, as highly specific strands were reported against a large variety of biomarkers. They have appealing benefits in terms of reproducible generation by chemical synthesis, controlled modification with labels and functionalities providing versatile means for detection and oriented immobilization, as along with high biochemical and temperature resistance. Aptamers against immunoglobulin targets—IgA, IgM, IgG and IgE—have a clear niche for diagnostic applications, therefore numerous aptamers have been selected and used in combination with a variety of detection techniques. The aim of this review is to overview and evaluate aptamers selected for the recognition of antibodies, in terms of their design, analytical properties and diagnostic applications. Aptamer candidates showed convincing performance among others to identify stress and upper respiratory tract infection through SIgA detection, for cancer cell recognition using membrane bound IgM, to detect and treat hemolytic transfusion reactions, autoimmune diseases with IgG and detection of IgE for allergy diseases. However, in general, their use still lags significantly behind what their claimed benefits and the plethora of application opportunities would forecast. url: https://www.ncbi.nlm.nih.gov/pubmed/32796581/ doi: 10.3390/ijms21165748 id: cord-324213-3uqlimov author: Bolotin, S. title: Development of a novel real-time reverse-transcriptase PCR method for the detection of H275Y positive influenza A H1N1 isolates date: 2009-01-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: During the 2007–2008 influenza season global strain surveillance for antiviral resistance revealed the sudden emergence of oseltamivir resistance in influenza A H1N1 isolates. Although oseltamivir resistance rates vary from region to region, 16% of isolates tested globally were found to be oseltamivir resistant by a histidine to tyrosine mutation of residue 275 of the neuraminidase gene of influenza A. In order to implement effective resistance testing locally a novel real-time reverse-transcriptase PCR (RT-PCR) assay was developed for the detection of the H275Y mutation. To evaluate this method, 40 oseltamivir resistant and 61 oseltamivir sensitive H1N1 influenza isolates were tested using Sanger sequencing, which is the reference method for detection of resistance, pyrosequencing and the novel H275Y RT-PCR assay. In comparison to Sanger sequencing, the sensitivity and specificity of the H275Y RT-PCR assay were 100% (40/40) and 100% (61/61) respectively, while the sensitivity and specificity of pyrosequencing were 100% (40/40) and 97.5% (60/61) respectively. Although all three methods were effective in detecting the H275Y mutation associated with oseltamivir resistance, the H275Y RT-PCR assay was the most rapid and could easily be incorporated into an influenza subtyping protocol. url: https://api.elsevier.com/content/article/pii/S0166093409000251 doi: 10.1016/j.jviromet.2009.01.016 id: cord-014942-4hk0veck author: Boone, Stephanie A. title: The Prevalence of Human Parainfluenza Virus 1 on Indoor Office Fomites date: 2010-02-09 words: 3437.0 sentences: 199.0 pages: flesch: 54.0 cache: ./cache/cord-014942-4hk0veck.txt txt: ./txt/cord-014942-4hk0veck.txt summary: The objective of this study was to evaluate the potential role of fomites in human parainfluenza virus 1 (HPIV1) transmission by assessing the occurrence of HPIV1 on surfaces in an adult setting (office). Data revealed a statistically significant difference between the percentage of HPIV1 positive fomites in office cubicles and conference rooms (Chi-square P < 0.011, Fisher''s Exact P = 0.054). A study conducted at the San Francisco University Medical Center during the 2002 influenza season found HPIV1 in healthy adults with respiratory infections after using polymerase chain reaction (PCR) for diagnosis (Louie et al. The offices sampled in Arizona indicated a greater variation in the total percentage of HPIV1 positive surfaces per building (Fig. 3) . Potential role of hands in the spread of respiratory viral infections: Studies with human Parainfluenza virus 3 and Rhinovirus 14 abstract: The objective of this study was to evaluate the potential role of fomites in human parainfluenza virus 1 (HPIV1) transmission by assessing the occurrence of HPIV1 on surfaces in an adult setting (office). In 2004, a total of 328 fomites from 12 different office buildings in five different cities were evaluated for HPIV1 viral RNA. HPIV1 was isolated using reverse transcriptase–polymerase chain reaction (RT–PCR) and detected on 37% of all office fomites. HPIV1 RNA was frequently isolated on desk tops (47%), and infrequently isolated on light switches (19%). Data revealed a statistically significant difference between the percentage of HPIV1 positive fomites in office cubicles and conference rooms (Chi-square P < 0.011, Fisher’s Exact P = 0.054). A statistically significant difference was also found among positive fomites in different buildings (Chi-square P < 0.011). HPIV1 was consistently isolated on various indoor fomites in the 12 office buildings assessed during 2004, a low HPIV incident year. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7091332/ doi: 10.1007/s12560-010-9026-5 id: cord-321739-dnuu6jok author: Bowman, Andrew S title: Investigating the introduction of porcine epidemic diarrhea virus into an Ohio swine operation date: 2015-02-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Porcine Epidemic Diarrhea virus (PEDV) is a highly transmissible coronavirus that causes a severe enteric disease that is particularly deadly for neonatal piglets. Since its introduction to the United States in 2013, PEDV has spread quickly across the country and has caused significant financial losses to pork producers. With no fully licensed vaccines currently available in the United States, prevention and control of PEDV disease is heavily reliant on biosecurity measures. Despite proven, effective biosecurity practices, multiple sites and production stages, within and across designated production flows in an Ohio swine operation broke with confirmed PEDV in January 2014, leading the producer and attending veterinarian to investigate the route of introduction. CASE PRESENTATION: On January 12, 2014, several sows within a production flow were noted with signs of enteric illness. Within a few days, illness had spread to most of the sows in the facility and was confirmed by RT-PCR to be PEDV. Within a short time period, confirmed disease was present on multiple sites within and across breeding and post weaning production flows of the operation and mortality approached 100% in neonatal piglets. After an epidemiologic investigation, an outsourced, pelleted piglet diet was identified for assessment, and a bioassay, where naïve piglets were fed the suspected feed pellets, was initiated to test the pellets for infectious PEDV. CONCLUSIONS: The epidemiological investigation provided strong evidence for contaminated feed as the source of the outbreak. In addition, feed pellets collected from unopened bags at the affected sites tested positive for PEDV using RT-PCR. However, the bioassay study was not able to show infectivity when feeding the suspected feed pellets to a small number of naïve piglets. The results highlight the critical need for surveillance of feed and feed components to further define transmission avenues in an effort to limit the spread of PEDV throughout the U.S. swine industry. url: https://doi.org/10.1186/s12917-015-0348-2 doi: 10.1186/s12917-015-0348-2 id: cord-016796-g4kqqpy1 author: Bramhachari, Pallaval Veera title: Advanced Immunotechnological Methods for Detection and Diagnosis of Viral Infections: Current Applications and Future Challenges date: 2019-11-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Diagnosis and identification of viruses is an important component of diagnostic virology laboratory. Although various modes of diagnostic methods are now available at disposal, a vast majority of the diseases across the globe remain undiagnosed. This is largely due to the overlapping undifferentiated set of symptoms across myriad set of RNA and DNA viral diseases. As such, it becomes critical to take into consideration several factors for viral diagnosis ranging from the type and quality of specimen collected, time of specimen collection, mode of transport, accuracy, specificity, sensitivity, and the type of diagnostic method used. This chapter broadly emphasizes various methods on diagnostic virology ranging from the classical methods of diagnosis to the most recently developed molecular methods of detection of virus. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121190/ doi: 10.1007/978-981-15-1045-8_17 id: cord-309540-4pk5tq5w author: Brandsma, E. title: Rapid, sensitive and specific SARS coronavirus-2 detection: a multi-center comparison between standard qRT-PCR and CRISPR based DETECTR. date: 2020-07-29 words: 4283.0 sentences: 268.0 pages: flesch: 54.0 cache: ./cache/cord-309540-4pk5tq5w.txt txt: ./txt/cord-309540-4pk5tq5w.txt summary: Recent advances in CRISPR-based diagnostics suggest that DETECTR, a combination of isothermal reverse transcriptase loop mediated amplification (RT-LAMP) and subsequent Cas12 bystander nuclease activation by amplicon targeting ribonucleoprotein complexes, could be a faster and cheaper alternative to qRT-PCR without sacrificing sensitivity/specificity. Isothermal reverse transcriptase loop mediated isothermal amplification (RT-LAMP) in combination with Cas12 detection does not need expensive specialised equipment, is highly sensitive and specific, has a short TAT and is easy to implement and therefore could be used as an alternative for qRT-PCR (5, 6) . Since DETECTR depends on both signal amplification by RT-LAMP and reporter degradation after Cas12-dependent amplicon recognition, the assay produces a binary readout and is potentially more sensitive and specific compared to qRT-PCR (5, 6) . In this manuscript we describe the development of an in-house SARS-CoV-2 DETECTR assay, compare its performance with routine diagnostic qRT-PCR on almost 400 patient samples of three Dutch hospitals, thereby providing a first field test of this novel Cas12-mediated SARS-CoV-2 detection tool. abstract: Recent advances in CRISPR-based diagnostics suggest that DETECTR, a combination of isothermal reverse transcriptase loop mediated amplification (RT-LAMP) and subsequent Cas12 bystander nuclease activation by amplicon targeting ribonucleoprotein complexes, could be a faster and cheaper alternative to qRT-PCR without sacrificing sensitivity/specificity. Here we compare qRT-PCR with DETECTR to diagnose COVID-19 on 378 patient samples and report a 95% reproducibility. Patient sample dilution assays suggest a higher analytical sensitivity of DETECTR compared to qRT-PCR, however, this was not confirmed in a large patient cohort. The data showed that both techniques are equally sensitive in detecting SARS-CoV-2 providing an added value of DETECTR to the currently used qRT-PCR platforms. For DETECTR, different gRNAs can be used simultaneously to obviate negative results due to mutations in N-gene. Lateral flow strips, suitable as a point of care test (POCT), showed a 100% correlation to the high-throughput DETECTR assay. Importantly, DETECTR was 100% specific for SARS-CoV-2 and did not detect other human coronaviruses. As there is no need for specialized equipment, DETECTR could be rapidly implemented as a complementary technically independent approach to qRT-PCR thereby increasing the testing capacity of medical microbiological laboratories and relieving the existent PCR-platforms for routine non- SARS-CoV-2 diagnostic testing. url: http://medrxiv.org/cgi/content/short/2020.07.27.20147249v1?rss=1 doi: 10.1101/2020.07.27.20147249 id: cord-266175-4jyltfus author: Brendish, Nathan J title: Clinical impact of molecular point-of-care testing for suspected COVID-19 in hospital (COV-19POC): a prospective, interventional, non-randomised, controlled study date: 2020-10-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: The management of the COVID-19 pandemic is hampered by long delays associated with centralised laboratory PCR testing. In hospitals, these delays lead to poor patient flow and nosocomial transmission. Rapid, accurate tests are therefore urgently needed in preparation for the next wave of the pandemic. METHODS: We did a prospective, interventional, non-randomised, controlled study of molecular point-of-care testing in patients aged 18 years or older presenting with suspected COVID-19 to the emergency department or other acute areas of Southampton General Hospital during the first wave of the pandemic in the UK. Nose and throat swab samples taken at admission from patients in the point-of-care testing group were tested with the QIAstat-Dx Respiratory SARS-CoV-2 Panel. Samples taken from patients in a contemporaneous control group were tested by laboratory PCR. The primary outcome was time to results in the full cohort. This study is registered with ISRCTN (ISRCTN14966673) and is completed. FINDINGS: Between March 20 and April 29, 2020, 517 patients were assessed for eligibility, of whom 499 were recruited to the point-of-care testing group and tested by the QIAstat-Dx Respiratory SARS-CoV-2 Panel. 555 contemporaneously identified patients were included in the control group and tested by laboratory PCR. The two groups were similar with regard to the distribution of sex, age, and ethnicity. 197 (39%) patients in the point-of-care testing group and 155 (28%) in the control group tested positive for COVID-19 (difference 11·5% [95% CI 5·8–17·2], p=0·0001). Median time to results was 1·7 h (IQR 1·6–1·9) in the point-of-care testing group and 21·3 h (16·0–27·9) in the control group (difference 19·6 h [19·0–20·3], p<0·0001). A Cox proportional hazards regression model controlling for age, sex, time of presentation, and severity of illness also showed that time to results was significantly shorter in the point-of-care testing group than in the control group (hazard ratio 4023 [95% CI 545–29 696], p<0·0001). INTERPRETATION: Point-of-care testing is associated with large reductions in time to results and could lead to improvements in infection control measures and patient flow compared with centralised laboratory PCR testing. FUNDING: University Hospitals Southampton NHS Foundation Trust. url: https://www.ncbi.nlm.nih.gov/pubmed/33038974/ doi: 10.1016/s2213-2600(20)30454-9 id: cord-332024-jk983q4p author: Briese, Thomas title: Diagnostic System for Rapid and Sensitive Differential Detection of Pathogens date: 2005-02-17 words: 1738.0 sentences: 84.0 pages: flesch: 36.0 cache: ./cache/cord-332024-jk983q4p.txt txt: ./txt/cord-332024-jk983q4p.txt summary: We describe a diagnostic system for rapid, sensitive, multiplex discrimination of microbial gene sequences and report its application for detecting 22 respiratory pathogens in clinical samples. We describe a diagnostic system for rapid, sensitive, multiplex discrimination of microbial gene sequences and report its application for detecting 22 respiratory pathogens in clinical samples. To address the need for sensitive multiplex assays in diagnostic molecular microbiology, we created a polymerase chain reaction (PCR) platform in which microbial gene targets are coded by a library of 64 distinct Masscode tags (Qiagen Masscode technology, Qiagen, Hilden, Germany). Multiplex primer sets were designed to identify up to 22 respiratory pathogens in a single Mass Tag PCR reaction; sensitivity was established by using synthetic DNA and RNA standards as well as titered viral stocks; the utility of Mass Tag PCR was determined in blinded analysis of previously diagnosed clinical specimens. abstract: Naturally emerging and deliberately released pathogens demand new detection strategies to allow early recognition and containment. We describe a diagnostic system for rapid, sensitive, multiplex discrimination of microbial gene sequences and report its application for detecting 22 respiratory pathogens in clinical samples. url: https://www.ncbi.nlm.nih.gov/pubmed/15752453/ doi: 10.3201/eid1102.040492 id: cord-301254-093yih5n author: Brittain-Long, Robin title: Prospective evaluation of a novel multiplex real-time PCR assay for detection of fifteen respiratory pathogens—Duration of symptoms significantly affects detection rate date: 2010-01-18 words: 2860.0 sentences: 160.0 pages: flesch: 48.0 cache: ./cache/cord-301254-093yih5n.txt txt: ./txt/cord-301254-093yih5n.txt summary: OBJECTIVES: The aim of the present study was to evaluate the diagnostic performance and clinical use of a novel multiplex PCR method in adults with community-acquired respiratory viral infection, and the impact of duration of symptoms on detection rates. CONCLUSIONS: Duration of symptoms significantly affects the detection rate of respiratory pathogens by multiplex real-time PCR in nasopharyngeal swab samples from adult patients with respiratory infections. The aim of the present study was to evaluate the diagnostic performance and clinical use of a novel multiplex PCR method in adults with community-acquired respiratory viral infection, and the impact of duration of symptoms on detection rates. All patients still positive for the same agent on follow-up had a higher Ct-value (corresponding to a lower Table 2 Follow-up (10 ± 2 days after initial visit) test result from analysis with real-time PCR of nasopharyngeal/throat swab specimens. abstract: BACKGROUND: Nucleic acid amplification techniques have improved the diagnostic possibilities in respiratory tract infections, although their clinical applicability is not yet fully defined. We have evaluated a multiplex real-time PCR method for the detection of 13 respiratory viruses and 2 bacteria (Mycoplasma and Chlamydophila) in a clinical setting. OBJECTIVES: The aim of the present study was to evaluate the diagnostic performance and clinical use of a novel multiplex PCR method in adults with community-acquired respiratory viral infection, and the impact of duration of symptoms on detection rates. STUDY DESIGN: Nasopharyngeal swab samples were prospectively collected from 209 adult outpatients with respiratory infections and 100 asymptomatic controls. RESULTS: An infectious agent was identified in 43% of samples from patients and 2% of asymptomatic controls. The detection rate was significantly higher in samples from patients with a duration of symptoms of 6 days or less (51%) than in samples from patients with a duration of symptoms of 7 days or more (30%, p < 0.01). For human corona viruses, and influenza virus A and B there was a correlation between the amount of virus in each patient sample as measured Ct values and duration of symptoms. CONCLUSIONS: Duration of symptoms significantly affects the detection rate of respiratory pathogens by multiplex real-time PCR in nasopharyngeal swab samples from adult patients with respiratory infections. Our finding should be taken into account when using these tests in clinical practise. url: https://www.ncbi.nlm.nih.gov/pubmed/20080440/ doi: 10.1016/j.jcv.2009.12.010 id: cord-313749-f2ct57em author: Brittain-Long, Robin title: Multiplex real-time PCR for detection of respiratory tract infections date: 2007-12-26 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Broad diagnostics of respiratory infection by molecular assays has not yet won acceptance due to technical difficulties and high costs. OBJECTIVES: To evaluate clinical applicability of multiplex real-time PCR. STUDY DESIGN: An assay targeting influenza virus A (IfA) and B (IfB), parainfluenza 1-3 (PIV), human metapneumovirus (MPV), respiratory syncytial virus (RSV), rhinovirus (RV), enterovirus (EV), adenovirus (AdV), human coronaviruses (229E, OC43, NL63), M. pneumoniae and Ch. pneumoniae was developed and run daily on consecutive clinical nasopharyngeal swab samples. RESULTS: An etiology was identified in 48% of the 954 samples, with IfA in 25%, RV in 20%, MPV in 10% and M. pneumoniae in 10% of the positive. By a rational procedure costs could be reduced and the customer price set relatively low (€33 per sample). CONCLUSION: Streamlined testing and cost limitation is achievable and probably critical for implementation of a broad molecular diagnostics of respiratory infections. url: https://api.elsevier.com/content/article/pii/S1386653207003940 doi: 10.1016/j.jcv.2007.10.029 id: cord-349775-zwslhjju author: Brittain-Long, Robin title: Access to a polymerase chain reaction assay method targeting 13 respiratory viruses can reduce antibiotics: a randomised, controlled trial date: 2011-04-26 words: 4612.0 sentences: 218.0 pages: flesch: 45.0 cache: ./cache/cord-349775-zwslhjju.txt txt: ./txt/cord-349775-zwslhjju.txt summary: The objective of this study was to evaluate whether access to a multiplex polymerase chain reaction (PCR) assay panel for etiologic diagnosis of acute respiratory tract infections (ARTIs) would have an impact on antibiotic prescription rate in primary care clinical settings. Acute respiratory tract infections (ARTIs) represent a major global health burden [1] , and viruses cause a large proportion of ARTIs. Distinguishing bacterial ARTIs that require antibiotic treatment from viral ARTIs not needing an antibiotic prescription can be difficult on clinical grounds alone and causes unnecessary use of antibiotics, with the highest rates occurring in the primary care setting [2, 3] . The present study was designed to evaluate whether access to a multiplex RT-PCR method targeting thirteen viruses would have an impact on antibiotic prescription rates for ARTI in a primary care setting. abstract: BACKGROUND: Viral respiratory infections are common worldwide and range from completely benign disease to life-threatening illness. Symptoms can be unspecific, and an etiologic diagnosis is rarely established because of a lack of suitable diagnostic tools. Improper use of antibiotics is common in this setting, which is detrimental in light of the development of bacterial resistance. It has been suggested that the use of diagnostic tests could reduce antibiotic prescription rates. The objective of this study was to evaluate whether access to a multiplex polymerase chain reaction (PCR) assay panel for etiologic diagnosis of acute respiratory tract infections (ARTIs) would have an impact on antibiotic prescription rate in primary care clinical settings. METHODS: Adult patients with symptoms of ARTI were prospectively included. Nasopharyngeal and throat swabs were analysed by using a multiplex real-time PCR method targeting thirteen viruses and two bacteria. Patients were recruited at 12 outpatient units from October 2006 through April 2009, and samples were collected on the day of inclusion (initial visit) and after 10 days (follow-up visit). Patients were randomised in an open-label treatment protocol to receive a rapid or delayed result (on the following day or after eight to twelve days). The primary outcome measure was the antibiotic prescription rate at the initial visit, and the secondary outcome was the total antibiotic prescription rate during the study period. RESULTS: A total sample of 447 patients was randomised. Forty-one were excluded, leaving 406 patients for analysis. In the group of patients randomised for a rapid result, 4.5% (9 of 202) of patients received antibiotics at the initial visit, compared to 12.3% (25 of 204) (P = 0.005) of patients in the delayed result group. At follow-up, there was no significant difference between the groups: 13.9% (28 of 202) in the rapid result group and 17.2% (35 of 204) in the delayed result group (P = 0.359), respectively. CONCLUSIONS: Access to a rapid method for etiologic diagnosis of ARTIs may reduce antibiotic prescription rates at the initial visit in an outpatient setting. To sustain this effect, however, it seems necessary to better define how to follow and manage the patient according to the result of the test, which warrants further investigation. TRIAL REGISTRATION: ClinicalTrials.gov identifier: NCT01133782. url: https://www.ncbi.nlm.nih.gov/pubmed/21521505/ doi: 10.1186/1741-7015-9-44 id: cord-258008-t78svobg author: Bruijnesteijn van Coppenraet, L.E.S. title: Comparison of two commercial molecular assays for simultaneous detection of respiratory viruses in clinical samples using two automatic electrophoresis detection systems date: 2010-08-05 words: 3519.0 sentences: 181.0 pages: flesch: 49.0 cache: ./cache/cord-258008-t78svobg.txt txt: ./txt/cord-258008-t78svobg.txt summary: Two molecular assays were compared with real-time RT-PCR and viral culture for simultaneous detection of common viruses from respiratory samples: a multiplex ligation-dependant probe amplification (MLPA) and a dual priming oligonucleotide system (DPO). A panel of 168 culture-positive and negative samples was tested by the molecular assays for the presence of influenza A and B virus, respiratory syncytial virus, human metapneumovirus, rhinovirus, coronaviruses, parainfluenza viruses and adenovirus. Both molecular assays are comparable with real-time RT-PCR, more sensitive than viral culture and can detect dual infections easily. In this study, two commercial molecular assays, both designed for simultaneous detection of the most common viruses from a variety of respiratory samples, were compared with real-time RT-PCR and viral culture: a multiplex ligation-dependant probe amplification (MLPA) and a dual priming oligonucleotide system (DPO). Defined as true positives were samples that yielded positive viral detections by more than one method (culture, DPO, MLPA or real-time RT-PCR). abstract: Two molecular assays were compared with real-time RT-PCR and viral culture for simultaneous detection of common viruses from respiratory samples: a multiplex ligation-dependant probe amplification (MLPA) and a dual priming oligonucleotide system (DPO). In addition, the positive detections of MLPA and DPO were identified using two different automatic electrophoresis systems. A panel of 168 culture-positive and negative samples was tested by the molecular assays for the presence of influenza A and B virus, respiratory syncytial virus, human metapneumovirus, rhinovirus, coronaviruses, parainfluenza viruses and adenovirus. One hundred and twenty-nine (77%) samples were positive as detected by at least one method. Sixty-nine (41%) samples were positive by cell culture (excluding human metapneumovirus and coronaviruses), 116 (69%) by RT-PCR, 127 (76%) by MLPA and 100 (60%) by DPO. The MLPA yielded results in one attempt for all samples included while 12 (7.2%) samples had to be repeated by the DPO assay due to inconclusive results. The MLPA assay performed well in combination with either electrophoresis system, while the performance of the DPO assay was influenced by the electrophoresis systems. Both molecular assays are comparable with real-time RT-PCR, more sensitive than viral culture and can detect dual infections easily. Results can be obtained within 1 day. url: https://www.ncbi.nlm.nih.gov/pubmed/20691735/ doi: 10.1016/j.jviromet.2010.07.032 id: cord-255043-uxdsjr39 author: Bustin, Stephen A. title: RT-qPCR Testing of SARS-CoV-2: A Primer date: 2020-04-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Testing for the presence of coronavirus is an essential diagnostic tool for monitoring and managing the current COVID-19 pandemic. The only reliable test in current use for testing acute infection targets the genome of SARS-CoV-2, and the most widely used method is quantitative fluorescence-based reverse transcription polymerase chain reaction (RT-qPCR). Despite its ubiquity, there is a significant amount of uncertainty about how this test works, potential throughput and reliability. This has resulted in widespread misrepresentation of the problems faced using this test during the current COVID-19 epidemic. This primer provides simple, straightforward and impartial information about RT-qPCR. url: https://www.ncbi.nlm.nih.gov/pubmed/32344568/ doi: 10.3390/ijms21083004 id: cord-010608-eaa2znom author: Butt, Salman L. title: Real-time, MinION-based, amplicon sequencing for lineage typing of infectious bronchitis virus from upper respiratory samples date: 2020-03-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Infectious bronchitis (IB) causes significant economic losses in the global poultry industry. Control of IB is hindered by the genetic diversity of the causative agent, infectious bronchitis virus (IBV), which has led to the emergence of several serotypes that lack complete serologic cross-protection. Although serotyping requires immunologic characterization, genotyping is an efficient means to identify IBVs detected in samples. Sanger sequencing of the S1 subunit of the spike gene is currently used to genotype IBV; however, the universal S1 PCR was created to work from cultured IBV, and it is inefficient at detecting multiple viruses in a single sample. We describe herein a MinION-based, amplicon-based sequencing (AmpSeq) method that genetically categorized IBV from clinical samples, including samples with multiple IBVs. Total RNA was extracted from 15 tracheal scrapings and choanal cleft swab samples, randomly reverse transcribed, and PCR amplified using modified S1-targeted primers. Amplicons were barcoded to allow for pooling of samples, processed per manufacturer’s instructions into a 1D MinION sequencing library, and then sequenced on the MinION. The AmpSeq method detected IBV in 13 of 14 IBV-positive samples. AmpSeq accurately detected and genotyped both IBV lineages in 3 of 5 samples containing 2 IBV lineages. Additionally, 1 sample contained 3 IBV lineages, and AmpSeq accurately detected 2 of the 3 lineages. Strain identification, including detection of different IBVs from the same lineage, was also possible with this AmpSeq method. Our results demonstrate the feasibility of using MinION-based AmpSeq for rapid and accurate identification and lineage typing of IBV from oral swab samples. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7201198/ doi: 10.1177/1040638720910107 id: cord-321514-knyw023l author: Bénet, Thomas title: Severity of Pneumonia in Under 5-Year-Old Children from Developing Countries: A Multicenter, Prospective, Observational Study date: 2017-07-12 words: 4441.0 sentences: 271.0 pages: flesch: 44.0 cache: ./cache/cord-321514-knyw023l.txt txt: ./txt/cord-321514-knyw023l.txt summary: The objectives were to evaluate the microbiological agents linked with hypoxemia in hospitalized children with pneumonia from developing countries, to identify predictors of hypoxemia, and to characterize factors associated with in-hospital mortality. The objectives of the present study are to assess the microbiological agents linked to hypoxemia in hospitalized children with pneumonia in developing countries, to identify clinical and para-clinical predictors of hypoxemia and to pinpoint factors associated with death within 2 weeks after admission. The present study selectively comprised sites with better quality data on oxygen saturation (SO 2 ) at admission, mortality among pneumonia cases, and documented recording of patient follow-up during hospitalization. One of the objectives of this study was to assess microbiological agents and other predictors of hypoxemia and death in under 5-year-old hospitalized children with pneumonia from developing countries. abstract: Pneumonia is the leading cause of death in children. The objectives were to evaluate the microbiological agents linked with hypoxemia in hospitalized children with pneumonia from developing countries, to identify predictors of hypoxemia, and to characterize factors associated with in-hospital mortality. A multicenter, observational study was conducted in five hospitals, from India (Lucknow, Vadu), Madagascar (Antananarivo), Mali (Bamako), and Paraguay (San Lorenzo). Children aged 2–60 months with radiologically confirmed pneumonia were enrolled prospectively. Respiratory and whole blood specimens were collected, identifying viruses and bacteria by real-time multiplex polymerase chain reaction (PCR). Microbiological agents linked with hypoxemia at admission (oxygen saturation < 90%) were analyzed by multivariate logistic regression, and factors associated with 14-day in-hospital mortality were assessed by bivariate Cox regression. Overall, 405 pneumonia cases (3,338 hospitalization days) were analyzed; 13 patients died within 14 days of hospitalization. Hypoxemia prevalence was 17.3%. Detection of human metapneumovirus (hMPV) and respiratory syncytial virus (RSV) in respiratory samples was independently associated with increased risk of hypoxemia (adjusted odds ratio [aOR] = 2.4, 95% confidence interval [95% CI] = 1.0–5.8 and aOR = 2.5, 95% CI = 1.1–5.3, respectively). Lower chest indrawing and cyanosis were predictive of hypoxemia (positive likelihood ratios = 2.3 and 2.4, respectively). Predictors of death were Streptococcus pneumoniae detection by blood PCR (crude hazard ratio [cHR] = 4.6, 95% CI = 1.5–14.0), procalcitonin ≥ 50 ng/mL (cHR = 22.4, 95% CI = 7.3–68.5) and hypoxemia (cHR = 4.8, 95% CI = 1.6–14.4). These findings were consistent on bivariate analysis. hMPV and RSV in respiratory samples were linked with hypoxemia, and S. pneumoniae in blood was associated with increased risk of death among hospitalized children with pneumonia in developing countries. url: https://www.ncbi.nlm.nih.gov/pubmed/28719310/ doi: 10.4269/ajtmh.16-0733 id: cord-320617-ucm7wx8b author: B’Krong, Nguyen Thi Thuy Chinh title: Enterovirus serotypes in patients with central nervous system and respiratory infections in Viet Nam 1997–2010 date: 2018-04-12 words: 3958.0 sentences: 221.0 pages: flesch: 51.0 cache: ./cache/cord-320617-ucm7wx8b.txt txt: ./txt/cord-320617-ucm7wx8b.txt summary: Here, we typed Enterovirus A-D (EV) from central nervous system (CNS) and respiratory infections in Viet Nam. METHODS: Data and specimens from prospective observational clinical studies conducted between 1997 and 2010 were used. In Viet Nam, since 2005, various serotypes of EV A, most commonly enterovirus A71 (EV-A71), coxsackievirus A16 (CV-A16), CV-A10, and CV-A6 have been associated with outbreaks of HFMD [12, 13] and EVs have also been frequently detected in aetiological studies of CNS and respiratory infections [14] [15] [16] [17] [18] . Here we report the clinical associations and serotyping results of EVs that were previously detected in our studies of CNS and respiratory infections in southern and central Viet Nam between 1997 and 2010. Our study illustrates the circulation of diverse enterovirus serotypes belonging to four species (A-D), and their association with respiratory and CNS infections in Viet Nam. These data are important for patient management, laboratory diagnostics and future outbreak response. abstract: BACKGROUND: Enteroviruses are the most common causative agents of human illness. Enteroviruses have been associated with regional and global epidemics, recently, including with severe disease (Enterovirus A71 and D68), and are of interest as emerging viruses. Here, we typed Enterovirus A-D (EV) from central nervous system (CNS) and respiratory infections in Viet Nam. METHODS: Data and specimens from prospective observational clinical studies conducted between 1997 and 2010 were used. Species and serotypes were determined using type-specific RT-PCR and viral protein 1 or 4 (VP1, VP4) sequencing. RESULTS: Samples from patients with CNS infection (51 children – 10 CSF and 41 respiratory/rectal swabs) and 28 adults (28 CSF) and respiratory infection (124 children – 124 respiratory swabs) were analysed. Twenty-six different serotypes of the four Enterovirus species (A-D) were identified, including EV-A71 and EV-D68. Enterovirus B was associated with viral meningitis in children and adults. Hand, foot and mouth disease associated Enteroviruses A (EV-A71 and Coxsackievirus [CV] A10) were detected in children with encephalitis. Diverse serotypes of all four Enterovirus species were found in respiratory samples, including 2 polio-vaccine viruses, but also 8 CV-A24 and 8 EV-D68. With the exception of EV-D68, the relevance of these viruses in respiratory infection remains unknown. CONCLUSION: We describe the diverse spectrum of enteroviruses from patients with CNS and respiratory infections in Viet Nam between 1997 and 2010. These data confirm the global circulation of Enterovirus genera and their associations and are important for clinical diagnostics, patient management, and outbreak response. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12985-018-0980-0) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/29650033/ doi: 10.1186/s12985-018-0980-0 id: cord-305872-66vij492 author: Caasi, Donna Ria J. title: A multi-target, non-infectious and clonable artificial positive control for routine PCR-based assays date: 2013-09-05 words: 4830.0 sentences: 228.0 pages: flesch: 47.0 cache: ./cache/cord-305872-66vij492.txt txt: ./txt/cord-305872-66vij492.txt summary: To test this concept, artificial positive controls (APCs) for use in PCR were synthesized to contain primer sequences targeting four viruses (Barley yellow dwarf virus, Soilborne wheat mosaic virus, Triticum mosaic virus and Wheat streak mosaic virus) pathogenic to wheat and, as internal control, the plant mitochondrial nad5 gene. Plasmid construct-based synthetic controls harboring a custom and de novo designed insert can enhance technologies such as polymerase chain reaction (PCR) to improve biosafety, speed of processing and overall detection without compromising sensitivity and specificity. The Plot ΔG or energy dot plot contains the Table 1 Primers used for designing the APC synthetic inserts, performing PCR of the targets within APCs, and RT-PCR of in vivo reference positive controls a . PCR products from APCs may differ in size from those generated by traditionally-used positive controls (Fig. 2) due to the discrepancy in the lengths between the annealing sites of the target sequences in vivo and the arrangement of primer sequences in the APC template (Table 1) . abstract: Positive controls are essential for PCR reliability and are challenging to obtain for rare, exotic and/or emerging pathogens and pose biosafety risks if manufactured using infectious pathogens. Custom synthetic DNA inserts can be designed de novo in tandems of forward and reverse complement priming sequences to be inserted in circular plasmid vectors. To test this concept, artificial positive controls (APCs) for use in PCR were synthesized to contain primer sequences targeting four viruses (Barley yellow dwarf virus, Soilborne wheat mosaic virus, Triticum mosaic virus and Wheat streak mosaic virus) pathogenic to wheat and, as internal control, the plant mitochondrial nad5 gene. Thermodynamics and folding parameters of twenty-four APC inserts were assessed in silico. Two thermodynamically different APCs, designated optimal and sub-optimal, were cloned and tested using end point PCR. The optimal APC had a 100% amplification rate, while only 92% of virus-infected plant tissues, commonly used as reference positive controls, amplified. An array of APC priming sequences from different organisms and/or previously tested primers can be accommodated in a large and flexible number of positive control targets. APCs will streamline and standardize routine PCR, improve reliability and biosafety, and create opportunities for development and commercialization of new synthetic positive control sequences. url: https://www.sciencedirect.com/science/article/pii/S0167701213002832 doi: 10.1016/j.mimet.2013.08.017 id: cord-314986-uhpe69k0 author: Cai, Quan title: A model based on CT radiomic features for predicting RT-PCR becoming negative in coronavirus disease 2019 (COVID-19) patients date: 2020-10-20 words: 3744.0 sentences: 211.0 pages: flesch: 48.0 cache: ./cache/cord-314986-uhpe69k0.txt txt: ./txt/cord-314986-uhpe69k0.txt summary: title: A model based on CT radiomic features for predicting RT-PCR becoming negative in coronavirus disease 2019 (COVID-19) patients Our purpose is to assess a model based on chest computed tomography (CT) radiomic features and clinical characteristics to predict RT-PCR negativity during clinical treatment. METHODS: From February 10 to March 10, 2020, 203 mild COVID-19 patients in Fangcang Shelter Hospital were retrospectively included (training: n = 141; testing: n = 62), and clinical characteristics were collected. We collected the clinical data and chest CT features of mild COVID-19 patients in Fangcang Shelter Hospital in Wuhan, Hubei, aiming to establish a predictive model for RT-PCR becoming negative during the recovery period. We analyzed chest CT images after the abnormal clinical symptoms disappeared, and proposed a combination model of radiomic features and clinical data to predict RT-PCR negativity. abstract: BACKGROUND: Coronavirus disease 2019 (COVID-19) has emerged as a global pandemic. According to the diagnosis and treatment guidelines of China, negative reverse transcription-polymerase chain reaction (RT-PCR) is the key criterion for discharging COVID-19 patients. However, repeated RT-PCR tests lead to medical waste and prolonged hospital stays for COVID-19 patients during the recovery period. Our purpose is to assess a model based on chest computed tomography (CT) radiomic features and clinical characteristics to predict RT-PCR negativity during clinical treatment. METHODS: From February 10 to March 10, 2020, 203 mild COVID-19 patients in Fangcang Shelter Hospital were retrospectively included (training: n = 141; testing: n = 62), and clinical characteristics were collected. Lung abnormalities on chest CT images were segmented with a deep learning algorithm. CT quantitative features and radiomic features were automatically extracted. Clinical characteristics and CT quantitative features were compared between RT-PCR-negative and RT-PCR-positive groups. Univariate logistic regression and Spearman correlation analyses identified the strongest features associated with RT-PCR negativity, and a multivariate logistic regression model was established. The diagnostic performance was evaluated for both cohorts. RESULTS: The RT-PCR-negative group had a longer time interval from symptom onset to CT exams than the RT-PCR-positive group (median 23 vs. 16 days, p < 0.001). There was no significant difference in the other clinical characteristics or CT quantitative features. In addition to the time interval from symptom onset to CT exams, nine CT radiomic features were selected for the model. ROC curve analysis revealed AUCs of 0.811 and 0.812 for differentiating the RT-PCR-negative group, with sensitivity/specificity of 0.765/0.625 and 0.784/0.600 in the training and testing datasets, respectively. CONCLUSION: The model combining CT radiomic features and clinical data helped predict RT-PCR negativity during clinical treatment, indicating the proper time for RT-PCR retesting. url: https://www.ncbi.nlm.nih.gov/pubmed/33081700/ doi: 10.1186/s12880-020-00521-z id: cord-324321-y96x8x3h author: Cai, Yingyun title: Down-regulation of transcription of the proapoptotic gene BNip3 in cultured astrocytes by murine coronavirus infection date: 2003-11-10 words: 8454.0 sentences: 416.0 pages: flesch: 49.0 cache: ./cache/cord-324321-y96x8x3h.txt txt: ./txt/cord-324321-y96x8x3h.txt summary: Furthermore, treatment of cells with chloroquine, which blocks the acidification of endosomes, significantly inhibited the repression of the BNip3 promoter activity induced by the acidic pH-dependent MHV mutant OBLV60, which enters cells via endocytosis, indicating that the down-regulation of BNip3 expression is mediated by fusion between viral envelope and cell membranes during entry. To establish further the specificity of the down-regulation of BNip3 gene expression, we used vesicular stomatitis virus (VSV) in a parallel experiment, because VSV is also an enveloped RNA virus whose infection has a broad host cell range and is mediated by the interaction between the envelope G protein and cell membranes (Riedel et al., 1984) . By extrapolating the data from the mutant virus, we can envision that fusion between viral envelope and plasma/endosomal membranes during wild-type MHV infection is involved in the down-regulation of BNip3 gene expression. abstract: Murine coronavirus mouse hepatitis virus (MHV) causes encephalitis and demyelination in the central nervous system of susceptible rodents. Astrocytes are the major target for MHV persistence. However, the mechanisms by which astrocytes survive MHV infection and permit viral persistence are not known. Here we performed DNA microarray analysis on differential gene expression in astrocyte DBT cells by MHV infection and found that the mRNA of the proapoptotic gene BNip3 was significantly decreased following MHV infection. This finding was further confirmed by quantitative reverse transcription–polymerase chain reaction, Western blot analysis, and BNip3-promoter-luciferase reporter system. Interestingly, infection with live and ultraviolet light-inactivated viruses equally repressed BNip3 expression, indicating that the down-regulation of BNip3 expression does not require virus replication and is mediated during cell entry. Furthermore, treatment of cells with chloroquine, which blocks the acidification of endosomes, significantly inhibited the repression of the BNip3 promoter activity induced by the acidic pH-dependent MHV mutant OBLV60, which enters cells via endocytosis, indicating that the down-regulation of BNip3 expression is mediated by fusion between viral envelope and cell membranes during entry. Deletion analysis showed that the sequence between nucleotides 262 and 550 of the 588-base-pair BNip3 promoter is necessary and sufficient for driving the BNip3 expression and that it contains signals that are responsible for MHV-induced down-regulation of BNip3 expression in DBT cells. These results may provide insights into the mechanisms by which MHV evades host antiviral defense and promotes cell survival, thereby allowing its persistence in the host astrocytes. url: https://www.ncbi.nlm.nih.gov/pubmed/14599795/ doi: 10.1016/j.virol.2003.07.007 id: cord-257600-0plhquk9 author: Calles, Antonio title: Outcomes of COVID-19 in Patients With Lung Cancer Treated in a Tertiary Hospital in Madrid date: 2020-09-16 words: 6981.0 sentences: 353.0 pages: flesch: 47.0 cache: ./cache/cord-257600-0plhquk9.txt txt: ./txt/cord-257600-0plhquk9.txt summary: Differences in health-care systems, in the incidence and prevalence of SARS-CoV-2 infection by geographic regions, and patient access to intensive support care -including MVand treatment with antivirals or anti-IL6/IL1 agents may ultimately influence outcomes in patients with lung cancer affected by COVID-19. We aimed to describe the clinical characteristics of lung cancer patients with COVID-19 attended in a tertiary hospital in Madrid, one of the most hit regions by coronavirus in the world so far, and analyze factors associated with worse outcome, including type of treatment receiving at the time of COVID-19 diagnosis. We performed SARS-CoV-2 RT-PCR to every suspicious case and included all lung cancer patients attended at our hospital (emergency room, hospitalization, ambulatory office, day care area). Data from Wuhan, in China, showed that active cancer treatment received in the 14 days before SARS-CoV-2 infection had an increase on the risk of severe outcomes of COVID-19 (HR 4.079, 95%CI, 1.086-15.322; p = 0.037) (9) . abstract: Background: Cancer patients represent a vulnerable population for COVID-19 illness. We aimed to analyze outcomes of lung cancer patients affected by COVID-19 in a tertiary hospital of a high-incidence region during the pandemic. Methods: We annotated 23 lung cancer patients consecutively diagnosed with COVID-19 at our institution (HGUGM; Madrid, Spain) between March 4th, 2020 and May 12th, 2020. Only patients with a confirmatory SARS-CoV-2 RT-PCR were included in the study. Results: All patients had at least 1 COVID-19 related symptom; cough (48%), shortness of breath (48%), fever (39%), and low-grade fever (30%) were the most common. Time from symptoms onset to first positive SARS-CoV-2 PCR was 5.5 days (range 1–17), with 13% of cases needed from a 2nd PCR to confirm diagnosis. There was a high variability on thoracic imaging findings, with multilobar pneumonia as the most commonly found pattern (74%). Main lab test abnormalities were low lymphocytes count (87%), high neutrophil to lymphocyte ratio -NLR- (78%), and elevated inflammatory markers: fibrinogen (91%), c-reactive protein -CRP- (87%), and D-dimer (70%). In our series, hospitalization rate was 74%, 39% of patients developed acute respiratory distress syndrome (ARDS), and the case-fatality rate was 35% (8/23). 87% of patients received anti-viral treatment (87% hydroxychloroquine, 74% lopinavir/ritonavir, 13% azithromycin), 43% corticosteroids, 26% interferon-β, 4% tocilizumab, and 82% of hospitalized patients received anticoagulation. High-oxygen requirements were needed in 39% of patients, but only 1 pt was admitted for invasive MV and was discharged 42 days after admission. Multiple variables related to tumor status, clinical baseline conditions, and inflammation markers were associated with mortality but did not remain statistically significant in a multivariate model. In patients with lung cancer receiving systemic therapy (n = 242) incidence and mortality from COVID-19 were 4.5, and 2.1%, respectively, with no differences found by type of treatment. Conclusions: Lung cancer patients represent a vulnerable population for COVID-19, according to the high rate of hospitalization, onset of ARDS, and high mortality rate. Although larger series are needed, no differences in mortality were found by type of cancer treatment. Measures to minimize the risk of SARS-CoV-2 infection remain key to protect lung cancer patients. url: https://www.ncbi.nlm.nih.gov/pubmed/33042826/ doi: 10.3389/fonc.2020.01777 id: cord-264071-hg0qslyx author: Camelo-Castillo, Anny title: Nasopharyngeal Microbiota in Children With Invasive Pneumococcal Disease: Identification of Bacteria With Potential Disease-Promoting and Protective Effects date: 2019-01-28 words: 7151.0 sentences: 335.0 pages: flesch: 39.0 cache: ./cache/cord-264071-hg0qslyx.txt txt: ./txt/cord-264071-hg0qslyx.txt summary: Principal coordinate analysis revealed three different microbiota profiles: microbiota A, dominated by the genus Dolosigranulum (44.3%); Microbiota B, mostly represented by Streptococcus (36.9%) and Staphylococcus (21.3%) and a high diversity of anaerobic genera including Veillonella, Prevotella and Porphyromonas; and Microbiota C, mainly containing Haemophilus (52.1%) and Moraxella (31.4%). To test this hypothesis, the objective of the present study was to characterize the nasopharyngeal microbiota profiles in two groups of children: (i) children with invasive pneumococcal disease (IPD), considered as a case group whose nasopharyngeal microbiota was suffering an important disturbance; and (ii) a matched control group of healthy children representative of a healthy nasopharyngeal niche. Sequence files and metadata for all samples used in this study are stored in the MG-RAST server to be publicly available by accessing the project Invasive Pneumococcal Disease (IPD) in children is associated with a highly diverse nasopharyngeal microbiota: a case-control study, ID mgp80930. abstract: Background and Aims: The risk of suffering from some infectious diseases can be related to specific microbiota profiles. Specifically, the nasopharyngeal microbiota could play a role as a risk or protective factor in the development of invasive disease caused by S. pneumoniae. Methodology: We analyzed the nasopharyngeal microbiota of children with invasive pneumococcal disease (IPD) and that of healthy controls matched by age, sex, and seasonality from Catalonia, Spain. Epidemiological, microbiological and clinical variables were considered to compare microbiota profiles, analyzed by sequencing the V1–V4 region of the 16S rRNA gene. Results: Twenty-eight children with IPD (median age 43 months) and 28 controls (42.6 months) were included in the study. IPD children presented a significantly higher bacterial diversity and richness (p < 0.001). Principal coordinate analysis revealed three different microbiota profiles: microbiota A, dominated by the genus Dolosigranulum (44.3%); Microbiota B, mostly represented by Streptococcus (36.9%) and Staphylococcus (21.3%) and a high diversity of anaerobic genera including Veillonella, Prevotella and Porphyromonas; and Microbiota C, mainly containing Haemophilus (52.1%) and Moraxella (31.4%). The only explanatory factor for the three microbiotas was the classification of children into disease or healthy controls (p = 0.006). A significant negative correlation was found between Dolosigranulum vs. Streptococcus (p = 0.029), suggesting a potential antagonistic effect against pneumococcal pathogens. Conclusions: The higher bacterial diversity and richness in children with IPD could suggest an impaired immune response. This lack of immune competence could be aggravated by breastfeeding <6 months and by the presence of keystone pathogens such as Porphyromonas, a bacterium which has been shown to be able to manipulate the immune response, and that could favor the overgrowth of many proteolytic anaerobic organisms giving rise to a dramatic dysbiosis. From an applied viewpoint, we found suggestive microbiota profiles associated to IPD or asymptomatic colonization that could be used as disease biomarkers or to pave the way for characterizing health-associated inhabitants of the respiratory tract. The identification of beneficial bacteria could be useful to prevent pneumococcal infections by integrating those microorganisms in a probiotic formula. The present study suggests not only respiratory tract samples, but also breast milk, as a potential source of those beneficial bacteria. url: https://doi.org/10.3389/fmicb.2019.00011 doi: 10.3389/fmicb.2019.00011 id: cord-344889-1y4ieamp author: Cameron, Robert J. title: Virus infection in exacerbations of chronic obstructive pulmonary disease requiring ventilation date: 2006-05-24 words: 4309.0 sentences: 242.0 pages: flesch: 46.0 cache: ./cache/cord-344889-1y4ieamp.txt txt: ./txt/cord-344889-1y4ieamp.txt summary: OBJECTIVES: We aimed to characterise and quantify the incidence of common infectious agents in acute exacerbations of chronic obstructive pulmonary disease (COPD) requiring ventilation, with a focus on respiratory viruses. Abstract Objectives: We aimed to characterise and quantify the incidence of common infectious agents in acute exacerbations of chronic obstructive pulmonary disease (COPD) requiring ventilation, with a focus on respiratory viruses. Of these, influenza types A and B (Inf A, B), parainfluenza types 1, 2 and 3 (Para 1, 2, 3), rhinovirus (RV), adenovirus (AV), respiratory syncytial virus (RSV), coronavirus (CoV) [11, 12] and, less commonly, human metapneumovirus (hMPV) [13] , and enterovirus (EV) [14, 15] have been shown to play significant roles in airway infections. A probable virus pathogen was found in 46 cases (43%) and a probable bacterial aetiology was found in 25 cases (23%) in this study of ventilated COPD exacerbation patients. abstract: OBJECTIVES: We aimed to characterise and quantify the incidence of common infectious agents in acute exacerbations of chronic obstructive pulmonary disease (COPD) requiring ventilation, with a focus on respiratory viruses. DESIGN: An epidemiological study conducted over 3 years. SETTING: A 12-bed intensive care unit (ICU). PARTICIPANTS: ICU patients over 45 years of age with a primary diagnosis of COPD exacerbation requiring non-invasive ventilation (NIV) or ventilation via endotracheal tube (ETT). MATERIALS AND METHODS: Nasopharyngeal aspirates (NPA) and posterior pharyngeal swabs (PS) were tested for viruses with immunofluorescence assay (IFA), virus culture (VC) and polymerase chain reaction (PCR). Paired virus and atypical pneumonia serology assays were taken. Blood, sputum and endotracheal aspirates were cultured for bacteria. RESULTS: 107 episodes in 105 patients were recorded. Twenty-three (21%) died within 28 days. A probable infectious aetiology was found in 69 patient episodes (64%). A virus was identified in 46 cases (43%), being the sole organism in 35 cases (33%) and part of a mixed infection in 11 cases (10%). A probable bacterial aetiology was found in 25 cases (23%). There was no statistically significant difference in clinical characteristics or outcomes between the group with virus infections and that without. CONCLUSION: Forty-six (43%) of the patients with COPD exacerbation requiring mechanical ventilation had a probable viral pathogen. Prodromal, clinical and outcome parameters did not distinguish virus from non-virus illness. PCR was the most sensitive whilst virus culture was the least of virus assays. ELECTRONIC SUPPLEMENTARY MATERIAL: The electronic reference of this article is http://dx.doi.org/10.1007/s00134-006-0202-x. The online full-text version of this article includes electronic supplementary material. This material is available to authorised users and can be accessed by means of the ESM button beneath the abstract or in the structured full-text article. To cite or link to this article you can use the above reference. url: https://www.ncbi.nlm.nih.gov/pubmed/16791664/ doi: 10.1007/s00134-006-0202-x id: cord-254265-8i86c8kt author: Camps, Marta title: Prevalence of human metapneumovirus among hospitalized children younger than 1 year in Catalonia, Spain date: 2008-06-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Human metapneumovirus was discovered recently respiratory virus implicated in both upper and lower respiratory tract infection. In children, the clinical symptoms of human metapneumovirus are similar to those produced by respiratory syncytial virus, ranging from mild to severe diseases such as bronchiolitis and pneumonia. The aim of the present study was to describe the prevalence of human metapneumovirus and other common respiratory viruses among admitted to hospital infants. From January 2006 to June 2006, 99 nasopharyngeal aspirates were collected from hospitalized children younger than 12 months in order to study respiratory viruses. Human metapneumovirus detection was performed by cell culture and two RT‐PCR targeting on polymerase and fusion genes. The latter gene was used for phylogenetic analysis. In 67/99 children (67%) at least one viral pathogen was identified, the viruses detected most frequently were respiratory syncytial virus (35%), human metapneumovirus (25%) and rhinovirus (19%). The results obtained in this study, show that: (1) human metapneumovirus is one of the most important viruses among children less than 12 months; (2) children infected with human metapneumovirus were significantly older than those infected by respiratory syncytial virus; (3) human metapneumovirus was associated more frequently with pneumonia whereas respiratory syncytial virus was only detected in patients with bronchiolitis; (4) there was a clear epidemiological succession pattern with only a small overlap among the viruses detected most frequently; (5) all human metapneumovirus samples were clustered within sublineage A2. J. Med. Virol. 80:1452–1460, 2008. © 2008 Wiley‐Liss, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/18551601/ doi: 10.1002/jmv.21209 id: cord-316500-vik30moa author: Cardillo, Lorena title: Lifestyle as Risk Factor for Infectious Causes of Death in Young Dogs: A Retrospective Study in Southern Italy (2015–2017) date: 2020-06-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Infectious diseases are a common cause of death in young dogs. Several factors are thought to predispose young dogs to microbiological infections. Identifying the cause of death is often a challenge, and broad diagnostic analysis is often needed. Here, we aimed to determine the infectious causes of death in young dogs aged up to 1 year, examining how it relates to age (under and over 6 months), lifestyle (owned versus ownerless), breed (purebred and crossbreed), and gender. A retrospective study was conducted in a 3-year period (2015–2017) on 138 dead dogs that had undergone necropsy and microbiological diagnostics. Enteritis and pneumonia were the most commonly observed lesions. Polymicrobism was more prevalent (62.3%) than single-agent infections and associated with a higher rate of generalised lesions. Ownerless dogs showed over a three-fold higher predisposition to viral coinfections than owned dogs. Above all, canine parvovirus was the most prevalent agent (77.5%), followed by canine coronavirus (31.1%) and canine adenovirus (23.9%); ownerless pups had a higher predisposition to these viruses. Escherichia coli (23.9%), Clostridium perfringens type A (18.1%), and Enterococcus spp. (8.7%) were the most commonly identified bacteria, which mostly involved in coinfections. A lower prevalence of CDV and Clostridium perfringens type A was observed in puppies under 6 months of age. In conclusion, this study is the first comprehensive survey on a wide panel of microbiological agents related to necropsy lesions. It lays the groundwork for future studies attempting to understand the circulation of infectious agents in a determined area. url: https://www.ncbi.nlm.nih.gov/pubmed/32566119/ doi: 10.1155/2020/6207297 id: cord-342277-v6310fjh author: Carducci, A. title: Environmental survey to assess viral contamination of air and surfaces in hospital settings date: 2011-01-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The presence of pathogenic viruses in healthcare settings represents a serious risk for both staff and patients. Direct viral detection in the environment poses significant technical problems and the indirect indicators currently in use suffer from serious limitations. The aim of this study was to monitor surfaces and air in hospital settings to reveal the presence of hepatitis C virus, human adenovirus, norovirus, human rotavirus and torque teno virus by nucleic acid assays, in parallel with measurements of total bacterial count and haemoglobin presence. In total, 114 surface and 62 air samples were collected. Bacterial contamination was very low (<1 cfu/cm(2)) on surfaces, whereas the ‘medium’ detected value in air was 282 cfu/m(3). Overall, 19 (16.7%) surface samples tested positive for viral nucleic acids: one for norovirus, one for human adenovirus and 17 (14.9%) for torque teno virus (TTV). Only this latter virus was directly detected in 10 air samples (16.1%). Haemoglobin was found on two surfaces. No relationship was found between viral, biochemical or bacterial indicators. The data obtained confirm the difficulty of assessing viral contamination using bacterial indicators. The frequent detection of TTV suggests its possible use as an indicator for general viral contamination of the environment. url: https://doi.org/10.1016/j.jhin.2010.10.010 doi: 10.1016/j.jhin.2010.10.010 id: cord-351100-llyl97ry author: Cariani, Lisa title: Time Length of Negativization and Cycle Threshold Values in 182 Healthcare Workers with Covid-19 in Milan, Italy: An Observational Cohort Study date: 2020-07-23 words: 3248.0 sentences: 171.0 pages: flesch: 53.0 cache: ./cache/cord-351100-llyl97ry.txt txt: ./txt/cord-351100-llyl97ry.txt summary: We aimed to evaluate the time length of negativization from the onset of symptoms in healthcare workers (HCWs) with COVID-19, and to evaluate significant variations in cycle threshold (CT) values and gene positivity (E, RdRP, and N genes) among positive individuals who returned to work. We collected cycle threshold values of the first SARS-CoV-2-positive nasopharyngeal swabs (T0) for all 182 HCWs and CT values at one week before the two negative RT-PCR tests (T1) for the 58 subjects who healed by 30 April 2020 (Figure 2 ). In the present study, we analyzed 2443 nasopharyngeal swabs from 1683 HCWs by molecular laboratory testing for suspected SARS-CoV-2 infection in a large university hospital in Milan, showing 10.8% positive HCWs. Overall, the majority of HCWs with COVID-19 were physicians, and the main reported symptoms were fever, cough, and headache. abstract: Background: Coronavirus Disease 2019 (COVID-19) has rapidly spread worldwide, becoming an unprecedented public health emergency. Rapid detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) suspected cases is crucial to control the spread of infection. We aimed to evaluate the time length of negativization from the onset of symptoms in healthcare workers (HCWs) with COVID-19, and to evaluate significant variations in cycle threshold (CT) values and gene positivity (E, RdRP, and N genes) among positive individuals who returned to work. Methods: We retrospectively analyzed a consecutive cohort of 182 SARS-CoV-2-positive HCWs in Milan, from 16 March to 30 April 2020. Nasopharyngeal swabs were tested by RT-PCR. Results: Asymptomatic HCWs were 17.6% (32/182), and 58 healed at 30 April 2020. The median time length of negativization was 4 weeks (35% of symptomatic versus 40% of asymptomatic HCWs). Four HCWs, healed at 30 April, turned positive within three weeks during controls set up in the work unit. Three-gene positivity had the greatest variability, and increasing CT values from single- to three-gene positivity among all age groups were observed. Conclusions: Self-isolation longer than two weeks and prolonged follow-up periods for the staff returning to work after COVID-19 could be the most suitable choices to counter the SARS-CoV-2 spread. Further studies are needed to investigate infectiousness profiles among positive individuals. url: https://doi.org/10.3390/ijerph17155313 doi: 10.3390/ijerph17155313 id: cord-252268-o63ep08b author: Carolan, Louise A. title: TaqMan real time RT-PCR assays for detecting ferret innate and adaptive immune responses date: 2014-09-01 words: 6643.0 sentences: 358.0 pages: flesch: 52.0 cache: ./cache/cord-252268-o63ep08b.txt txt: ./txt/cord-252268-o63ep08b.txt summary: As this equation relies on consistency between samples in the RNA quantity assayed, and the optimum reaction efficiency, as well as minimal fluctuation in the expression of housekeeping genes (endogenous controls) (Peters et al., 2007; Mane et al., 2008; Bruder et al., 2010) , these parameters were optimized using RNA extracted from cultured ferret lymph node cells stimulated with mitogens or with influenza virus. To test the ability of ferret leukocytes to produce mRNA cytokines and chemokines, lymph node cells from naïve ferrets were cultured with various mitogens known to activate T and B lymphocyte and macrophage/monocyte responses (Fig. 5) and with live or heat inactivated influenza virus (Fig. 6 ) and the cytokine and chemokine expression profiles were determined (summarized in (ConA) or Phytohaemagglutinin (PHA), which act by cross linking T cell receptors via sugars on the surface of human T lymphocytes (Chilson and Kelly-Chilson, 1989) , induced similar cytokine profiles, increasing expression of IL2, IL4, IL6, IL10, IL17, Granzyme A, TNF␣ and IFN␥, most with high fold changes, consistent with effective stimulation of T lymphocytes (Fig. 5) . abstract: The ferret is an excellent model for many human infectious diseases including influenza, SARS-CoV, henipavirus and pneumococcal infections. The ferret is also used to study cystic fibrosis and various cancers, as well as reproductive biology and physiology. However, the range of reagents available to measure the ferret immune response is very limited. To address this deficiency, high-throughput real time RT-PCR TaqMan assays were developed to measure the expression of fifteen immune mediators associated with the innate and adaptive immune responses (IFNα, IFNβ, IFNγ, IL1α, IL1β, IL2, IL4, IL6, IL8, IL10, IL12p40, IL17, Granzyme A, MCP1, TNFα), as well as four endogenous housekeeping genes (ATF4, HPRT, GAPDH, L32). These assays have been optimized to maximize reaction efficiency, reduce the amount of sample required (down to 1 ng RNA per real time RT-PCR reaction) and to select the most appropriate housekeeping genes. Using these assays, the expression of each of the tested genes could be detected in ferret lymph node cells stimulated with mitogens or infected with influenza virus in vitro. These new tools will allow a more comprehensive analysis of the ferret immune responses following infection or in other disease states. url: https://doi.org/10.1016/j.jviromet.2014.04.014 doi: 10.1016/j.jviromet.2014.04.014 id: cord-271920-1dzkgt6w author: Carpenter, Christopher R. title: Diagnosing COVID‐19 in the Emergency Department: A Scoping Review of Clinical Exam, Labs, Imaging Accuracy and Biases date: 2020-06-16 words: 7248.0 sentences: 523.0 pages: flesch: 48.0 cache: ./cache/cord-271920-1dzkgt6w.txt txt: ./txt/cord-271920-1dzkgt6w.txt summary: 3 As waves of COVID-19 patients present to ED''s in coming months with symptoms or potential exposures, understanding the diagnostic accuracy and reliability of history, physical exam, routine labs, advanced imaging, and an evolving array of COVID-19 diagnostics will be essential knowledge to inform the timing of testing, optimal specimen and test selection, shared decision-making, and ultimately derivation of clinical instruments to guide disposition, follow-up, and shared The search strategy used a combination of standardized terms and key words, including but not limited to (Covid-19 OR Novel Coronavirus OR SARS-COV-2) AND (diagnosis OR polymerase chain reaction OR serology OR CRISPR-CAS OR sensitivity/specificity) (Appendix). 40,42 It is known, however, that false negatives are frequent, so current recommendations advise incorporating patient''s exposure risk, clinical signs and symptoms, routine lab and imaging findings, serology, and (when available) CT results into real-time determination of COVID-19 status. abstract: In December 2019 a novel viral respiratory pathogen emerged in China, ultimately named severe acute respiratory syndrome coronavirus 2 (SARS‐Co‐V‐2) with the clinical illness dubbed coronavirus disease (COVID‐19). COVID‐19 became a global pandemic in early 2020 forcing governments worldwide to enact social isolation policies with dire economic ramifications. Emergency departments (ED) encountered decreased patient volumes before some in Seattle, New York City, New Orleans, and Detroit experienced waves of COVID‐19 patients mixed with asymptomatic patients or those concerned about potential exposures. Diagnosing COVID‐19 was hampered by inadequate supplies of reagents and kits, which was compounded by clinical and radiographic features that overlap with numerous seasonal viral respiratory infections. url: https://doi.org/10.1111/acem.14048 doi: 10.1111/acem.14048 id: cord-292347-d7xq7x5g author: Carter, Linda J. title: Assay Techniques and Test Development for COVID-19 Diagnosis date: 2020-04-30 words: 3426.0 sentences: 227.0 pages: flesch: 51.0 cache: ./cache/cord-292347-d7xq7x5g.txt txt: ./txt/cord-292347-d7xq7x5g.txt summary: 375 While RT-PCR-based viral RNA detection has been widely 376 used in diagnosis of COVID-19, it cannot be used to monitor 377 the progress of the disease stages and cannot be applied to 378 broad identification of past infection and immunity. 46,47 410 The determination of SARS-CoV-2 exposure relies largely 411 on the detection of either IgM or IgG antibodies that are 412 specific for various viral antigens including, but not exclusively, 413 the spike glycoprotein (S1 and S2 subunits, receptor-binding 414 domain) and nucleocapsid protein. While RT-PCR has been 571 the dominant technique for detection of viral RNA, other 572 nucleic acid assays including isothermal amplification assays, 573 hybridization microarray assays, amplicon-based metagenomics 574 sequencing, and the cutting-edge CRISPR-related technologies 575 are also under development or have resulted in approved 576 tests. abstract: nan url: https://doi.org/10.1021/acscentsci.0c00501 doi: 10.1021/acscentsci.0c00501 id: cord-264261-98h1bmb2 author: Caruana, Giorgia title: Diagnostic strategies for SARS-CoV-2 infection and interpretation of microbiological results date: 2020-06-25 words: 1417.0 sentences: 99.0 pages: flesch: 48.0 cache: ./cache/cord-264261-98h1bmb2.txt txt: ./txt/cord-264261-98h1bmb2.txt summary: It is recommended to use real-time RT-PCR for RNA viruses in order (i) to perform a rapid and accurate diagnostic, (ii) to guide patient care and management and (iii) to guide epidemiological strategies. IMPLICATIONS: Real-time RT-PCR remains the reference method for diagnosis of SARS-CoV-2 infection. On the other hand, notwithstanding its varying sensitivity according to the time of infection, serology represents a valid asset (i) to try to solve possible discrepancies between a highly suggestive clinical and radiological presentation and negative RT-PCR, (ii) to solve discrepancies between different PCR assays, and (iii) for epidemiological purposes. Improved molecular diagnosis of COVID-19 by the novel, highly sensitive 316 and specific COVID-19-RdRp/Hel real-time reverse transcription-polymerase chain 317 reaction assay validated in vitro and with clinical specimens Antibody responses to SARS-CoV-2 in patients of 373 novel coronavirus disease 2019 SARS-CoV-2 viral load in 413 upper respiratory specimens of infected patients abstract: BACKGROUND: To face the current COVID-19 pandemic, diagnostic tools are essential. It is recommended to use real-time RT-PCR for RNA viruses in order (i) to perform a rapid and accurate diagnostic, (ii) to guide patient care and management and (iii) to guide epidemiological strategies. Further studies are warranted to define the role of serological diagnosis and a possible correlation between serological response and prognosis. OBJECTIVES: To guide clinical microbiologists in the use of these diagnostic tests and clinicians in the interpretation of their results. SOURCES: A research of literature was performed through PubMed and Google Scholar using the keywords SARS-CoV-2, SARS-CoV-2 molecular diagnosis, SARS-CoV-2 immune response, SARS-CoV-2 serology/antibody testing, coronavirus diagnosis. CONTENT: The present review discusses performances, limitations and use of current and future diagnostic tests for SARS-CoV-2. IMPLICATIONS: Real-time RT-PCR remains the reference method for diagnosis of SARS-CoV-2 infection. On the other hand, notwithstanding its varying sensitivity according to the time of infection, serology represents a valid asset (i) to try to solve possible discrepancies between a highly suggestive clinical and radiological presentation and negative RT-PCR, (ii) to solve discrepancies between different PCR assays, and (iii) for epidemiological purposes. url: https://www.ncbi.nlm.nih.gov/pubmed/32593741/ doi: 10.1016/j.cmi.2020.06.019 id: cord-321074-7jfy8cn6 author: Caruso, Damiano title: Quantitative Chest CT analysis in discriminating COVID-19 from non-COVID-19 patients date: 2020-10-12 words: 2918.0 sentences: 141.0 pages: flesch: 45.0 cache: ./cache/cord-321074-7jfy8cn6.txt txt: ./txt/cord-321074-7jfy8cn6.txt summary: Quantitative Chest CT analysis was performed with a dedicated software that provides total lung volume, healthy parenchyma, GGOs, consolidations and fibrotic alterations, expressed both in liters and percentage. Lung quantification in liters showed significant differences between COVID-19 and non-COVID-19 patients for GGOs (0.55 ± 0.26L vs 0.43 ± 0.23L, p = 0.0005) and fibrotic alterations (0.05 ± 0.03 L vs 0.04 ± 0.03 L, p < 0.0001). A recent consensus statement from the Fleischner Society pointed out as imaging is indicated for medical triage of suspected COVID-19 patients presenting moderate-severe clinical features and a high pre-test probability of disease [13] . According to the hospital internal protocol, at the time of admission suspected COVID-19 patients presenting moderate-severe clinical features and a high pre-test probability of disease (fever defined as > 37.5 °C and respiratory symptoms or direct contact with a confirmed COVID-19 patient) underwent nasopharyngeal and oropharyngeal swabs for SARS-CoV-2. abstract: INTRODUCTION: COVID-19 pneumonia is characterized by ground-glass opacities (GGOs) and consolidations on Chest CT, although these CT features cannot be considered specific, at least on a qualitative analysis. The aim is to evaluate if Quantitative Chest CT could provide reliable information in discriminating COVID-19 from non-COVID-19 patients. MATERIALS AND METHODS: From March 31, 2020 until April 18, 2020, patients with Chest CT suggestive for interstitial pneumonia were retrospectively enrolled and divided into two groups based on positive/negative COVID-19 RT-PCR results. Patients with pulmonary resection and/or CT motion artifacts were excluded. Quantitative Chest CT analysis was performed with a dedicated software that provides total lung volume, healthy parenchyma, GGOs, consolidations and fibrotic alterations, expressed both in liters and percentage. Two radiologists in consensus revised software analysis and adjusted areas of lung impairment in case of non-adequate segmentation. Data obtained were compared between COVID-19 and non-COVID-19 patients and p < 0.05 were considered statistically significant. Performance of statistically significant parameters was tested by ROC curve analysis. RESULTS: Final population enrolled included 190 patients: 136 COVID-19 patients (87 male, 49 female, mean age 66 ± 16) and 54 non-COVID-19 patients (25 male, 29 female, mean age 63 ± 15). Lung quantification in liters showed significant differences between COVID-19 and non-COVID-19 patients for GGOs (0.55 ± 0.26L vs 0.43 ± 0.23L, p = 0.0005) and fibrotic alterations (0.05 ± 0.03 L vs 0.04 ± 0.03 L, p < 0.0001). ROC analysis of GGOs and fibrotic alterations showed an area under the curve of 0.661 (cutoff 0.39 L, 68% sensitivity and 59% specificity, p < 0.001) and 0.698 (cutoff 0.02 L, 86% sensitivity and 44% specificity, p < 0.001), respectively. CONCLUSIONS: Quantification of GGOs and fibrotic alterations on Chest CT could be able to identify patients with COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/33044733/ doi: 10.1007/s11547-020-01291-y id: cord-346958-9eeqlkoq author: Caruso, Damiano title: Chest CT Features of COVID-19 in Rome, Italy date: 2020-04-03 words: 1818.0 sentences: 123.0 pages: flesch: 51.0 cache: ./cache/cord-346958-9eeqlkoq.txt txt: ./txt/cord-346958-9eeqlkoq.txt summary: In the subgroup of RT-PCR-positive and CT-positive patients, ground-glass opacities (GGO) were present in 58/58 (100%), multilobe and posterior involvement were both present in 54/58 (93%), bilateral pneumonia in 53/58 (91%), and subsegmental vessel enlargement (> 3 mm) in 52/58 (89%) of study participants. As reported by Ai (5) , in a cohort of 1014 patients in Wuhan China, the sensitivity, specificity and accuracy of chest CT in the detection of COVID-19 pneumonia were 97%, 25% and 68% respectively using RT-PCR results as reference standard. The aim of this study was to investigate chest CT features of patients with COVID-19 in Rome, Italy, and to compare the diagnostic performance of chest CT with RT-PCR. To understand the CT features of patients with COVID-19 pneumonia, a sub-analysis was performed considering only study participants with positive RT-PCR testing and chest CT findings. abstract: BACKGROUND: The standard for diagnosis of SARS-CoV-2 virus is reverse transcription polymerase chain reaction (RT-PCR) test, but chest CT may play a complimentary role in the early detection of COVID-19 pneumonia. PURPOSE: To investigate CT features of patients with COVID-19 in Rome, Italy, and to compare the accuracy of CT with RT-PCR. METHODS: In this prospective study from March 4, 2020, until March 19, 2020, consecutive patients with suspected COVID-19 infection and respiratory symptoms were enrolled. Exclusion criteria were: chest CT with contrast medium performed for vascular indications, patients who refused chest CT or hospitalization, and severe CT motion artifact. All patients underwent RT-PCR and chest CT. Diagnostic performance of CT was calculated using RT-PCR as reference. Chest CT features were calculated in a subgroup of RT-PCR-positive and CT-positive patients. CT features of hospitalized patients and patient in home isolation were compared by using Pearson chi squared test. RESULTS: Our study population comprised 158 consecutive study participants (83 male and 75 female, mean age 57 y ±17). Fever was observed in 97/158 (61%), cough in 88/158 (56%), dyspnea in 52/158 (33%), lymphocytopenia in 95/158 (60%), increased C-reactive protein level in 139/158 (88%), and elevated lactate dehydrogenase in 128/158 (81%) study participants. Sensitivity, specificity, and accuracy of CT were 97% (60/62)[95% IC, 88-99%], 56% (54/96)[95% IC,45-66%] and 72% (114/158)[95% IC 64-78%], respectively. In the subgroup of RT-PCR-positive and CT-positive patients, ground-glass opacities (GGO) were present in 58/58 (100%), multilobe and posterior involvement were both present in 54/58 (93%), bilateral pneumonia in 53/58 (91%), and subsegmental vessel enlargement (> 3 mm) in 52/58 (89%) of study participants. CONCLUSION: The typical pattern of COVID-19 pneumonia in Rome, Italy, was peripherally ground-glass opacities with multilobe and posterior involvement, bilateral distribution, and subsegmental vessel enlargement (> 3 mm). Chest CT sensitivity was high (97%) but with lower specificity (56%). url: https://www.ncbi.nlm.nih.gov/pubmed/32243238/ doi: 10.1148/radiol.2020201237 id: cord-245161-xbw72k4m author: Castano, Nicolas title: Fomite transmission and disinfection strategies for SARS-CoV-2 and related viruses date: 2020-05-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Contaminated objects or surfaces, referred to as fomites, play a critical role in the spread of viruses, including SARS-CoV-2, the virus responsible for the COVID-19 pandemic. The long persistence of viruses (hours to days) on surfaces calls for an urgent need for surface disinfection strategies to intercept virus transmission and the spread of the disease. Elucidating the physicochemical processes and surface science underlying the adsorption and transfer of virus between surfaces, as well as their inactivation, are important in understanding how the disease is transmitted, and in developing effective interception strategies. This review aims to summarize the current knowledge and underlying physicochemical processes of virus transmission, in particular via fomites, and common disinfection approaches. Gaps in knowledge and needs for further research are also identified. The review focuses on SARS-CoV-2, but will supplement the discussions with related viruses. url: https://arxiv.org/pdf/2005.11443v1.pdf doi: nan id: cord-254506-cxdklz4u author: Castellvi, J. title: Impact On Clinical Practice Of The Preoperative Screening Of Covid-19 Infection In Surgical Oncological Patients. Prospective Cohort Study date: 2020-08-11 words: 1850.0 sentences: 131.0 pages: flesch: 52.0 cache: ./cache/cord-254506-cxdklz4u.txt txt: ./txt/cord-254506-cxdklz4u.txt summary: The aim of this study was to describe the impact on clinical practice of sequential preoperative screening for COVID-19-infection in deciding whether to proceed or postpone surgery. Sequential preoperative screening for COVID-19-infection: two-time medical history (telematic and face-to-face), PCR and chest CT, 48 hours before of surgical intervention. Conclusion preoperative screening for COVID-19-infection using medical history and PCR helped the surgeon to decide whether to go ahead or postpone surgery in oncological patients. Three preoperative screening tests have been proposed: a detailed history, a COVID-19 PCR determination and a chest radiological imaging (CT or Xray), despite not having any control studies available [6] [7] [8] [9] [10] [11] [12] . Therefore, our working hypothesis is that sequential preoperative screening: clinical (detailed history), PCR and radiology (chest CT) of COVID-19 infection and pneumonia will identify symptomatic and asymptomatic infected patients. abstract: Abstract Background in the oncological patient, an COVID-19-Infection, whether symptomatic or asymptomatic, a surgical procedure may carry a higher postoperative morbidity and mortality. The aim of this study was to describe the impact on clinical practice of sequential preoperative screening for COVID-19-infection in deciding whether to proceed or postpone surgery. Methods prospective, cohort study, based on consecutive patients’ candidates for an oncological surgical intervention. Sequential preoperative screening for COVID-19-infection: two-time medical history (telematic and face-to-face), PCR and chest CT, 48 hours before of surgical intervention. COVID-19-infection was considered positive if the patient had a suggestive medical history and/or PCR-positive and/or CT of pneumonia. Results Between April 15th and May 4th, 2020, 179 patients were studied, 97 were male (54%), mean (sd) age 66.7(13,6). Sequential preoperative screening was performed within 48 hours before to surgical intervention. The prevalence of preoperative COVID-19-infection was 4.5%, 95%CI:2.3-8.6% (8 patients). Of the operated patients (171), all had a negative medical history, PCR and chest CT.. The complications was 14.8% (I-II) and 2.5% (III-IV). There was no mortality. The hospital stay was 3.1 (sd 2.7) days. In the 8 patients with COVID-19-infection, the medical history was suggestive in all of them, 7 presented PCR-positive and 5 had a chest CT suggestive of pneumonia. The surgical intervention was postponed between 15 and 21 days. Conclusion preoperative screening for COVID-19-infection using medical history and PCR helped the surgeon to decide whether to go ahead or postpone surgery in oncological patients. The chest CT may be useful in unclear cases. url: https://www.sciencedirect.com/science/article/pii/S2405857220300589?v=s5 doi: 10.1016/j.ijso.2020.08.003 id: cord-263142-o8qbqxhx author: Cavalcante, Liliane T. F. title: Clinical and Molecular Features of Feline Foamy Virus and Feline Leukemia Virus Co-Infection in Naturally-Infected Cats date: 2018-12-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Feline foamy virus (FFV) and feline leukemia virus (FeLV) belong to the Retroviridae family. While disease has not been reported for FFV infection, FeLV infection can cause anemia and immunosuppression (progressive infection). Co-infection with FFV/FeLV allows evaluation of the pathogenic potential and epidemiology of FFV infection in cats with FeLV pathology. Blood and buccal swab samples from 81 cats were collected in Rio de Janeiro. Plasma was serologically tested for FeLV. DNA extracted from peripheral blood mononuclear cells and buccal swabs was used to PCR detect FFV and FeLV. A qPCR was developed to detect and measure FFV proviral loads (pVLs) in cats. FeLV qPCR was performed using previous methods. The median log10 pVL of FFV mono-infected individuals was lower than found in FFV/FeLV co-infected cats in buccal swabs (p = 0.003). We found 78% of cats had detectable buccal FFV DNA in FFV mono-infected and FFV co-infected FeLV-progressive cats, while in FeLV-regressive cats (those without signs of disease) 22% of cats had detectable buccal FFV DNA (p = 0.004). Our results suggest that regressive FeLV infection may reduce FFV saliva transmission, the main mode of FV transmission. We did not find evidence of differences in pathogenicity in FFV mono- and -dually infected cats. In summary, we show that FVs may interact with FeLV within the same host. Our study supports the utility of cats naturally co-infected with retroviruses as a model to investigate the impact of FV on immunocompromised mammalian hosts. url: https://www.ncbi.nlm.nih.gov/pubmed/30544924/ doi: 10.3390/v10120702 id: cord-323473-e2pgjynr author: Cevey-Macherel, Manon title: Etiology of community-acquired pneumonia in hospitalized children based on WHO clinical guidelines date: 2009-02-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Community-acquired pneumonia (CAP) is a major cause of death in developing countries and of morbidity in developed countries. The objective of the study was to define the causative agents among children hospitalized for CAP defined by WHO guidelines and to correlate etiology with clinical severity and surrogate markers. Investigations included an extensive etiological workup. A potential causative agent was detected in 86% of the 99 enrolled patients, with evidence of bacterial (53%), viral (67%), and mixed (33%) infections. Streptococcus pneumoniae was accounted for in 46% of CAP. Dehydration was the only clinical sign associated with bacterial pneumonia. CRP and PCT were significantly higher in bacterial infections. Increasing the number of diagnostic tests identifies potential causes of CAP in up to 86% of children, indicating a high prevalence of viruses and frequent co-infections. The high proportion of pneumococcal infections re-emphasizes the importance of pneumococcal immunization. url: https://www.ncbi.nlm.nih.gov/pubmed/19238436/ doi: 10.1007/s00431-009-0943-y id: cord-254064-qxgpehuy author: Chacko, J. title: Hydroxychloroquine in COVID-19: A systematic review and meta-analysis date: 2020-05-19 words: 4034.0 sentences: 289.0 pages: flesch: 57.0 cache: ./cache/cord-254064-qxgpehuy.txt txt: ./txt/cord-254064-qxgpehuy.txt summary: In spite of several observational studies and a few randomized controlled trials, the effect of hydroxychloroquine on patients with COVID 19 infection remains unclear. Conclusions Our meta-analysis does not suggest improvement in clinical progression, mortality, or viral clearance by RT PCR among patients with COVID 19 infection who are treated with hydroxychloroquine. Hence, we performed a systematic review and meta-analysis of available controlled studies to evaluate the safety and efficacy of hydroxychloroquine in the treatment of COVID-19 infection. Studies were considered eligible if they included patients who received hydroxychloroquine alone or in combination with other specific treatment modalities for COVID-19 infection and were compared with a control group. Data on at least one of the following outcomes had to be available for inclusion in the meta-analysis: (i) mortality, (ii) clinical progress, (iii) results of the reverse transcription-polymerase chain reaction (RT-PCR) test after the commencement of treatment, (iv) changes on computed tomography (CT) imaging of the chest, and (iv) adverse clinical events. abstract: Abstract Background Hydroxychloroquine is being administered among patients with COVID19 infection in many healthcare systems across the world considering its in vitro effect against the SARS CoV 2 virus. In spite of several observational studies and a few randomized controlled trials, the effect of hydroxychloroquine on patients with COVID 19 infection remains unclear. We undertook this systematic review with meta-analysis to evaluate the efficacy and safety of hydroxychloroquine among patients with COVID 19 infection. Methods We searched PubMed, Embase, the Cochrane Library, Web of Science, medRxiv, and other relevant resources until May 13, 2020. We included randomized controlled trials and observational studies in which hydroxychloroquine was adminstered and compared to a control group. Data were extracted, and quality assessment of the studies was carried out. We evaluated symptomatic progression, mortality, viral clearance, the evolution of changes on chest CT imaging, and adverse events. A fixed or random-effects model was used depending on outcome heterogeneity. Results We included eleven studies including, three randomized controlled trials and eight observational studies. Among these, 2354 patients received hydroxychloroquine alone or in combination, while 1952 did not. Mortality was reported at different points of time. The overall mortality was not significantly different among patients who received hydroxychloroquine compared to the control group (OR: 1.41, 95% CI: 0.76 to 2.62; p = 0.28). Clinical worsening or lack of symptomatic improvement did not differ between patients who received hydroxychloroquine compared to those who did not (OR 1.1, 95% CI: 0.6 to 2.02; p = 0.76). Viral clearance, assessed by RT-PCR, did not differ significantly between the hydroxychloroquine and the control groups (OR: 1.13, CI: 0.26 to 5.01; p = 0.87). The evolution of changes on chest CT imaging was reported only in two studies; a more pronounced improvement was observed with the use of hydroxychloroquine compared to standard care (OR: 2.68, CI: 1.1 to 6.6; P = 0.03). The incidence of adverse events was significantly higher with hydroxychloroquine (OR: 4.1, CI: 1.42 to 11.88; p = 0.009). Conclusions Our meta-analysis does not suggest improvement in clinical progression, mortality, or viral clearance by RT PCR among patients with COVID 19 infection who are treated with hydroxychloroquine. There was a significantly higher incidence of adverse events with hydroxychloroquine use. url: https://doi.org/10.1101/2020.05.14.20101774 doi: 10.1101/2020.05.14.20101774 id: cord-277359-za2hh71g author: Chae, Kum Ju title: Positive conversion of COVID-19 after two consecutive negative RT-PCR results: A role of low-dose CT date: 2020-06-09 words: 600.0 sentences: 39.0 pages: flesch: 61.0 cache: ./cache/cord-277359-za2hh71g.txt txt: ./txt/cord-277359-za2hh71g.txt summary: , and we would like to discuss a role of low-dose CT in discharge decision based on our recent experience regarding the positive conversion of COVID-19 after two consecutive negative RT-PCR results. In order to discharge patients from the hospital, most guidelines include no fever for more than 3 days, improvement of symptoms, and two consecutive negative real-time polymerase chain reaction (RT-PCR) test results [2] . The patient therefore met the criteria for hospital discharge (absence of fever or symptoms and two negative RT-PCR results) established by the Korea Centers for Disease J o u r n a l P r e -p r o o f Control and Prevention [5] ; however, follow-up LDCT prior to discharge revealed newly developed multifocal GGOs in the lower lobes, which led to cancelation of discharge. With continued treatment, the patient was discharged after two consecutive negative RT-PCR results and near complete resolution of her previous pneumonia without new lesions on LDCT (Figure 1) . abstract: nan url: https://api.elsevier.com/content/article/pii/S0720048X20303119 doi: 10.1016/j.ejrad.2020.109122 id: cord-306135-pt4jsr6d author: Chan, Kamfai title: A Rapid and Low-Cost PCR Thermal Cycler for Infectious Disease Diagnostics date: 2016-02-12 words: 6292.0 sentences: 284.0 pages: flesch: 56.0 cache: ./cache/cord-306135-pt4jsr6d.txt txt: ./txt/cord-306135-pt4jsr6d.txt summary: Many molecular diagnostic assays are developed based on using thermal cyclers to carry out polymerase chain reaction (PCR) and reverse-transcription PCR for DNA and RNA amplification and detection, respectively. This thermos thermal cycler (TTC) uses a very simple design that performs PCR amplification based on the "archaic" method of hand-transferring reaction tubes through a series of water baths, minimizing the temperature ramping time needed for PCR tubes to reach thermal equilibrium (Fig 1) . The TTC RT-PCR was performed using protocols similar to the HIV test, with PCR tubes transferred between three thermoses (reverse transcription, denaturation, and annealing/extension) and an optional room-temperature water bath. The gel photo in Fig 3 shows that the TTC can produce multiplexed amplicons with the correct sizes and that the yield is similar to a three-step reaction performed in the commercial cycler with same number of PCR cycles. abstract: The ability to make rapid diagnosis of infectious diseases broadly available in a portable, low-cost format would mark a great step forward in global health. Many molecular diagnostic assays are developed based on using thermal cyclers to carry out polymerase chain reaction (PCR) and reverse-transcription PCR for DNA and RNA amplification and detection, respectively. Unfortunately, most commercial thermal cyclers are expensive and need continuous electrical power supply, so they are not suitable for uses in low-resource settings. We have previously reported a low-cost and simple approach to amplify DNA using vacuum insulated stainless steel thermoses food cans, which we have named it thermos thermal cycler or TTC. Here, we describe the use of an improved set up to enable the detection of viral RNA targets by reverse-transcription PCR (RT-PCR), thus expanding the TTC’s ability to identify highly infectious, RNA virus-based diseases in low resource settings. The TTC was successful in demonstrating high-speed and sensitive detection of DNA or RNA targets of sexually transmitted diseases, HIV/AIDS, Ebola hemorrhagic fever, and dengue fever. Our innovative TTC costs less than $200 to build and has a capacity of at least eight tubes. In terms of speed, the TTC’s performance exceeded that of commercial thermal cyclers tested. When coupled with low-cost endpoint detection technologies such as nucleic acid lateral-flow assay or a cell-phone-based fluorescence detector, the TTC will increase the availability of on-site molecular diagnostics in low-resource settings. url: https://doi.org/10.1371/journal.pone.0149150 doi: 10.1371/journal.pone.0149150 id: cord-347462-yz67t10x author: Chan, Tak Yeung title: A Comparative Study of Clinical Features and Outcomes in Young and Older Adults with Severe Acute Respiratory Syndrome date: 2004-07-19 words: 3590.0 sentences: 214.0 pages: flesch: 54.0 cache: ./cache/cord-347462-yz67t10x.txt txt: ./txt/cord-347462-yz67t10x.txt summary: title: A Comparative Study of Clinical Features and Outcomes in Young and Older Adults with Severe Acute Respiratory Syndrome Objectives: To determine the clinical presentation, findings, and outcomes of older adults (> 60) with severe acute respiratory syndrome (SARS) and compare these with a control group of younger patients (≤60). A retrospective study was undertaken in the department of medicine and geriatrics of the hospital to evaluate the clinical course of young and elderly SARS patients. Single or paired serum samples were tested for SARS-CoV antibody in 96% (50/52) of young and 76% (19/25) of older patients. Because the proportion of patients with positive RT-PCR in stool samples was similar in two groups, fewer older patients with diarrhea probably represents a generalized paucity of symptoms rather than a different site of involvement by SARS-CoV. In the current study, similar proportions of young and older patients with SARS had RT-PCR performed, and comparable positivity rates were achieved. abstract: Objectives: To determine the clinical presentation, findings, and outcomes of older adults (> 60) with severe acute respiratory syndrome (SARS) and compare these with a control group of younger patients (≤60). Design: Retrospective cohort study. Setting: A community‐based, acute hospital in Hong Kong. Participants: All adult inpatients with a clinical diagnosis of SARS. Measurements: Clinical presentations, investigations, treatment, and 30‐ and 150‐day mortality. Results: There were 52 young and 25 older patients with a mean age±standard deviation of 39.5±11.7 and 72.1±7.2, respectively. Fever, chills, and diarrhea were more common in younger patients, whereas decrease in appetite and general condition occurred only in older patients. The prevalence of positive reverse‐transcriptase polymerase chain reaction for SARS‐associated coronavirus (SARS‐CoV) in nasopharyngeal secretions and stool samples was similar in the two groups. The prevalence of positive serological tests for SARS‐CoV was significantly lower in older patients (42% vs 92%, P<.001). This was largely due to incomplete testing in elderly patients. Older patients were more likely to develop secondary nosocomial infection, be admitted to an intensive care unit, and require mechanical ventilation. The cumulative 30‐ and 150‐day mortality rates were 3.8% and 7.6%, respectively, in young patients with SARS and 56% and 60%, respectively, in older patients (P<.001). Conclusion: Older patients with SARS more often presented with nonspecific symptoms, and the prognosis was poor. Reverse‐transcriptase polymerase chain reaction was useful in diagnosing SARS in older patients, but the role of serological tests in individual elderly is limited. url: https://www.ncbi.nlm.nih.gov/pubmed/15271120/ doi: 10.1111/j.1532-5415.2004.52362.x id: cord-321361-6bkrt49b author: Chang, De title: Reply to Suri et al.: COVID-19 Real-Time RT-PCR: Does Positivity on Follow-up RT-PCR Always Imply Infectivity? date: 2020-07-01 words: 199.0 sentences: 23.0 pages: flesch: 63.0 cache: ./cache/cord-321361-6bkrt49b.txt txt: ./txt/cord-321361-6bkrt49b.txt summary: key: cord-321361-6bkrt49b title: Reply to Suri et al.: COVID-19 Real-Time RT-PCR: Does Positivity on Follow-up RT-PCR Always Imply Infectivity? cord_uid: 6bkrt49b We read with keen interest the results of the SUMMIT (Study to Understand Mortality and Morbidity in COPD) randomized controlled trial of fluticasone furoate/vilanterol in patients with moderate chronic obstructive pulmonary disease (COPD) with a history of cardiovascular disease or at increased cardiovascular risk (1) . The trial evaluated both the value of aortic pulse wave velocity (aPWV) to predict all-cause mortality (ACM) in this population and Time kinetics of viral clearance and resolution of symptoms in novel coronavirus infection Novel Coronavirus Outbreak Research Team. Epidemiologic features and clinical course of patients infected with SARS-CoV-2 in Singapore Transmission of 2019-nCoV infection from an asymptomatic contact in Germany Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32401535/ doi: 10.1164/rccm.202004-1458le id: cord-298697-v1qdizwx author: Chang, Jia Jin Marc title: Takeaways from Mobile DNA Barcoding with BentoLab and MinION date: 2020-09-24 words: 7206.0 sentences: 395.0 pages: flesch: 56.0 cache: ./cache/cord-298697-v1qdizwx.txt txt: ./txt/cord-298697-v1qdizwx.txt summary: One of the most common applications of MinION is for nanopore-based DNA barcoding in situ for species identification and discovery, yet the existing sample capability is limited (n ≤ 10). We also tested the performance of the newly released R10.3 nanopore flow cell for DNA barcoding, and showed that the barcodes generated were ~99.9% accurate when compared to Illumina references. For the field sequencing phase, an additional 31 samples were collected and subjected to QE-based DNA extraction on the BentoLab. While we did not run the gel check in situ to save time, a postliminary amplification check on agarose back at the laboratory revealed 20 observable gel bands. For the field sequencing phase, an additional 31 samples were collected and subjected to QE-based DNA extraction on the BentoLab. While we did not run the gel check in situ to save time, a postliminary amplification check on agarose back at the laboratory revealed 20 observable gel bands. abstract: Since the release of the MinION sequencer in 2014, it has been applied to great effect in the remotest and harshest of environments, and even in space. One of the most common applications of MinION is for nanopore-based DNA barcoding in situ for species identification and discovery, yet the existing sample capability is limited (n ≤ 10). Here, we assembled a portable sequencing setup comprising the BentoLab and MinION and developed a workflow capable of processing 32 samples simultaneously. We demonstrated this enhanced capability out at sea, where we collected samples and barcoded them onboard a dive vessel moored off Sisters’ Islands Marine Park, Singapore. In under 9 h, we generated 105 MinION barcodes, of which 19 belonged to fresh metazoans processed immediately after collection. Our setup is thus viable and would greatly fortify existing portable DNA barcoding capabilities. We also tested the performance of the newly released R10.3 nanopore flow cell for DNA barcoding, and showed that the barcodes generated were ~99.9% accurate when compared to Illumina references. A total of 80% of the R10.3 nanopore barcodes also had zero base ambiguities, compared to 50–60% for R9.4.1, suggesting an improved homopolymer resolution and making the use of R10.3 highly recommended. url: https://www.ncbi.nlm.nih.gov/pubmed/32987804/ doi: 10.3390/genes11101121 id: cord-351864-zozrj7w5 author: Chappleboim, A. title: ApharSeq: An Extraction-free Early-Pooling Protocol for Massively Multiplexed SARS-CoV-2 Detection date: 2020-08-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The global SARS-CoV-2 pandemic led to a steep increase in the need for viral detection tests worldwide. Most current tests for SARS-CoV-2 are based on RNA extraction followed by quantitative reverse-transcription PCR assays that involve a separate RNA extraction and qPCR reaction for each sample with a fixed cost and reaction time. While automation and improved logistics can increase the capacity of these tests, they cannot exceed this lower bound dictated by one extraction and reaction per sample. Multiplexed next generation sequencing (NGS) assays provide a dramatic increase in throughput, and hold the promise of richer information on viral strains and host immune response. Here, we establish a significant improvement of existing RNA-seq detection protocols. Our workflow, ApharSeq, includes a fast and cheap RNA capture step, that is coupled to barcoding of individual samples, followed by sample-pooling prior to the reverse transcription, PCR and massively parallel sequencing. Thus, only one step is performed before pooling hundreds of barcoded samples for subsequent steps and further analysis. We characterize the quantitative aspects of the assay, and test ApharSeq on dozens of clinical samples in a robotic workflow. Our proposed workflow is estimated to reduce costs by 10-50 fold, labor by 5-100 fold, automated liquid handling by 5-10 fold, and reagent requirements by 100-1000 fold compared to existing testing methods. url: http://medrxiv.org/cgi/content/short/2020.08.08.20170746v1?rss=1 doi: 10.1101/2020.08.08.20170746 id: cord-271339-wt5o9sgm author: Chen, Chao-Ju title: Optimization of the CDC Protocol of Molecular Diagnosis of COVID-19 for Timely Diagnosis date: 2020-05-21 words: 2084.0 sentences: 122.0 pages: flesch: 57.0 cache: ./cache/cord-271339-wt5o9sgm.txt txt: ./txt/cord-271339-wt5o9sgm.txt summary: The real-time reverse transcriptase polymerase chain was one of the most quickly established methods in the novel viral pandemic and was considered as the gold standard for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To ensure the whole process of the COVID-19 diagnostic testing took place without a problem, we simultaneously added primers and a probe of human RNase P gene (RP gene) as an internal control in the same well with the RdRp gene assay according to the protocol from the U.S. CDC [6] (Figure 3 ). In the present report, we demonstrated our experience of relying on a protocol template from the Taiwan CDC to establish an optimized COVID-19 molecular diagnostic test within our routine services in a public health emergency. abstract: Coronavirus disease 2019 (COVID-19), the current uncontrolled outbreak of infectious disease, has caused significant challenges throughout the world. A reliable rapid diagnostic test for COVID-19 is demanded worldwide. The real-time reverse transcriptase polymerase chain was one of the most quickly established methods in the novel viral pandemic and was considered as the gold standard for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this report, we illustrate our experience of applying a protocol from the Taiwan CDC and achieving assay optimization in the immediate circumstances to meet the urgent medical and public health needs. url: https://doi.org/10.3390/diagnostics10050333 doi: 10.3390/diagnostics10050333 id: cord-302829-1o1jo8uk author: Chen, Hao-tai title: Rapid detection of porcine circovirus type 2 by loop-mediated isothermal amplification date: 2008-03-19 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A method of loop-mediated isothermal amplification (LAMP) was employed to develop a rapid and simple detection system for porcine circovirus type 2 (PCV2). The amplification could be finished in 60 min under isothermal condition at 64 °C by employing a set of four primers targeting the cap gene of PCV2. The LAMP assay showed higher sensitivity than the conventional PCR, with a detection limit of five copies per tube of purified PCV2 genomic DNA. No cross-reactivity was observed from the samples of other related viruses including porcine circovirus type 1 (PCV1), porcine parvovirus (PPV), porcine pseudorabies virus (PRV) and porcine reproductive and respiratory syndrome virus (PRRSV). The detection rate of PCV2 LAMP for 86 clinical samples was 96.5% and appeared greater than that of the PCR method. The LAMP assay reported can provide a rapid yet simple test of PCV2 suitable for laboratory diagnosis and pen-side detection due to ease of operation and the requirement of only a regular water bath or heat block for the reaction. url: https://www.ncbi.nlm.nih.gov/pubmed/18355932/ doi: 10.1016/j.jviromet.2008.01.023 id: cord-320938-f526k9q1 author: Chen, Hongjun title: Partial and Full PCR-Based Reverse Genetics Strategy for Influenza Viruses date: 2012-09-28 words: 8614.0 sentences: 455.0 pages: flesch: 60.0 cache: ./cache/cord-320938-f526k9q1.txt txt: ./txt/cord-320938-f526k9q1.txt summary: In order to determine whether a Flu PCR amplicon could be transfected into cells and be amplified by the influenza polymerase complex, a PCR product was produced encoding the GFP reporter gene in negative orientation flanked by the influenza segment 7 untranslated regions (UTRs) and further flanked by the human pol1 promoter and the mouse t1 termination signal, pol1EGFPt1 (Fig. 1A, Fig. S1A , Table S1 ). doi:10.1371/journal.pone.0046378.g001 Efficient influenza virus rescue using Flu PCR amplicons in either ''''1+7'''' or ''''2+6'''' modes The pol1HA pdm t1 or pol1HA D072 t1 HA PCR amplicons (Table 1) were co-transfected into co-cultured 293T/MDCK cells in a ''''1+7'''' mode along with 7 RG plasmids encoding the corresponding additional gene segments from the influenza A/Puerto Rico/ 8/1934 (H1N1) strain (PR8). abstract: Since 1999, plasmid-based reverse genetics (RG) systems have revolutionized the way influenza viruses are studied. However, it is not unusual to encounter cloning difficulties for one or more influenza genes while attempting to recover virus de novo. To overcome some of these shortcomings we sought to develop partial or full plasmid-free RG systems. The influenza gene of choice is assembled into a RG competent unit by virtue of overlapping PCR reactions containing a cDNA copy of the viral gene segment under the control of RNA polymerase I promoter (pol1) and termination (t1) signals – herein referred to as Flu PCR amplicons. Transfection of tissue culture cells with either HA or NA Flu PCR amplicons and 7 plasmids encoding the remaining influenza RG units, resulted in efficient virus rescue. Likewise, transfections including both HA and NA Flu PCR amplicons and 6 RG plasmids also resulted in efficient virus rescue. In addition, influenza viruses were recovered from a full set of Flu PCR amplicons without the use of plasmids. url: https://doi.org/10.1371/journal.pone.0046378 doi: 10.1371/journal.pone.0046378 id: cord-335459-tq4fwigw author: Chen, Hui Juan title: Early chest CT features of patients with 2019 novel coronavirus (COVID-19) pneumonia: relationship to diagnosis and prognosis date: 2020-06-09 words: 2796.0 sentences: 208.0 pages: flesch: 63.0 cache: ./cache/cord-335459-tq4fwigw.txt txt: ./txt/cord-335459-tq4fwigw.txt summary: title: Early chest CT features of patients with 2019 novel coronavirus (COVID-19) pneumonia: relationship to diagnosis and prognosis METHODS: The clinical manifestations, laboratory parameters, and CT imaging findings were analyzed in 34 COVID-19 patients, confirmed by RT-PCR from January 20 to February 4 in Hainan Province. a-c Axial unenhanced chest CT revealed multiple confluent and patchy ground-glass and consolidative pulmonary opacities in the subpleural area bilaterally upon hospital admission on January 29, 2020. The CT images on admission showed bilateral, multiple lobular and subsegmental areas of GGO with subsegmental areas of consolidation, indicating the disease was severe Fig. 3 A 50-year-old woman with a history of exposure presented with cough and white phlegm for 4 days, accompanied by headache, muscle aches, and no fever. abstract: OBJECTIVE: To determine the consistency between CT findings and real-time reverse transcription–polymerase chain reaction (RT-PCR) and to investigate the relationship between CT features and clinical prognosis in COVID-19. METHODS: The clinical manifestations, laboratory parameters, and CT imaging findings were analyzed in 34 COVID-19 patients, confirmed by RT-PCR from January 20 to February 4 in Hainan Province. CT scores were compared between the discharged patients and the ICU patients. RESULTS: Fever (85%) and cough (79%) were most commonly seen. Ten (29%) patients demonstrated negative results on their first RT-PCR. Of the 34 (65%) patients, 22 showed pure ground-glass opacity. Of the 34 (50%) patients, 17 had five lobes of lung involvement, while the 23 (68%) patients had lower lobe involvement. The lesions of 24 (71%) patients were distributed mainly in the subpleural area. The initial CT lesions of ICU patients were distributed in both the subpleural area and centro-parenchyma (80%), and the lesions were scattered. Sixty percent of ICU patients had five lobes involved, while this was seen in only 25% of the discharged patients. The lesions of discharged patients were mainly in the subpleural area (75%). Of the discharged patients, 62.5% showed pure ground-glass opacities; 80% of the ICU patients were in the progressive stage, and 75% of the discharged patients were at an early stage. CT scores of the ICU patients were significantly higher than those of the discharged patients. CONCLUSION: Chest CT plays a crucial role in the early diagnosis of COVID-19, particularly for those patients with a negative RT-PCR. The initial features in CT may be associated with prognosis. KEY POINTS: • Chest CT is valuable for the early diagnosis of COVID-19, particularly for those patients with a negative RT-PCR. • The early CT findings of COVID-19 in ICU patients differed from those of discharged patients. url: https://doi.org/10.1007/s00330-020-06978-4 doi: 10.1007/s00330-020-06978-4 id: cord-303818-z3js3mr4 author: Chen, Huixin title: Development and Evaluation of a SYBR Green–Based Real-Time Multiplex RT-PCR Assay for Simultaneous Detection and Serotyping of Dengue and Chikungunya Viruses date: 2015-10-11 words: 3836.0 sentences: 196.0 pages: flesch: 51.0 cache: ./cache/cord-303818-z3js3mr4.txt txt: ./txt/cord-303818-z3js3mr4.txt summary: title: Development and Evaluation of a SYBR Green–Based Real-Time Multiplex RT-PCR Assay for Simultaneous Detection and Serotyping of Dengue and Chikungunya Viruses In the present study, we aimed to develop and evaluate a SYBR Green Iebased multiplex real-time RT-PCR assay to detect, differentiate, and quantify DENV and CHIKV and simultaneously to serotype DENV based on Tm analysis of the PCR amplicon. A set of 22 serum samples from CHIKV-infected patients and 30 from uninfected individuals were collected at the National University Hospital, Singapore, with informed consent, to evaluate the clinical sensitivity and specificity of the real-time RT-PCR assay. To our knowledge, this is the first SYBR Green Iebased real-time RT-PCR assay reported that is able to detect, quantify, differentiate, and serotype DENV and CHIKV simultaneously. Establishment of one-step SYBR green-based real time-PCR assay for rapid detection and quantification of chikungunya virus infection Development of group-and serotype-specific one-step SYBR green I-based real-time reverse transcription-PCR assay for dengue virus abstract: Chikungunya virus (CHIKV) and dengue virus (DENV) have emerged as the two most important arbovirus diseases of global health significance. Similar clinical manifestations, transmission vectors, geographical distribution, and seasonal correlation often result in misdiagnosis of chikungunya infections as dengue cases and vice versa. In this study, we developed a rapid and accurate laboratory confirmative method to simultaneously detect, quantify, and differentiate DENV serotypes 1, 2, 3, and 4 and CHIKV. This SYBR Green I–based one-step multiplex real-time RT-PCR assay is highly sensitive and specific for CHIKV and DENV. Melting temperature analysis of PCR amplicons was used to serotype DENV and to differentiate from CHIKV. The detection limit of the assay was 20, 10, 50, 5, and 10 RNA copies/reaction for DENV-1, DENV-2, DENV-3, DENV-4, and CHIKV, respectively. Our assay did not cross-react with a panel of viruses that included other flaviviruses, alphaviruses, influenza viruses, human enteroviruses, and human coronaviruses. The feasibility of using this assay for clinical diagnosis was evaluated in DENV- and CHIKV-positive patient sera. Accordingly, the assay sensitivity for DENV-1, DENV-2, DENV-3, DENV-4, and CHIKV was 89.66%, 96.67%, 96.67%, 94.12%, and 95.74%, respectively, with 100% specificity. These findings confirmed the potential of our assay to be used as a rapid test for simultaneous detection and serotyping of DENV and CHIKV in clinical samples. url: https://www.sciencedirect.com/science/article/pii/S1525157815001567 doi: 10.1016/j.jmoldx.2015.06.008 id: cord-262467-epqqd8n8 author: Chen, Jun title: COVID-19 infection: the China and Italy perspectives date: 2020-06-08 words: 7596.0 sentences: 384.0 pages: flesch: 47.0 cache: ./cache/cord-262467-epqqd8n8.txt txt: ./txt/cord-262467-epqqd8n8.txt summary: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the COVID-19 disease as originally shown in Wuhan, China, as early as documented from 1 December 2019 (ref. A recent prospective study failed to find antiviral activity or clinical benefit of this combination for the treatment of our hospitalized patients with severe COVID-19 (ref. More recently, a randomized, controlled study conducted in Wuhan, China also failed to identify beneficial effect of LPV/r beyond standard therapy in hospitalized patients with severe Covid-19 (ref. Clinical trials also showed that in patients with severe H1N1 influenza A, in the 2009 pandemic, therapy with convalescent plasma from patients who recovered, especially within 5 days of symptom onset, resulted in a lower viral load and lower mortality 66, 67 . The duration from onset of symptoms to viral clearance is significantly longer in severe and critical ill SARS-CoV-2infected patients compared with that in the mild cases 48 . abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the COVID-19 pandemic. Since its first report in December 2019, despite great efforts made in almost every country worldwide, this disease continues to spread globally, especially in most parts of Europe, Iran, and the United States. Here, we update the recent understanding in clinical characteristics, diagnosis strategies, as well as clinical management of COVID-19 in China as compared to Italy, with the purpose to integrate the China experience with the global efforts to outline references for prevention, basic research, treatment as well as final control of the disease. Being the first two countries we feel appropriate to evaluate the evolution of the disease as well as the early result of the treatment, in order to offer a different baseline to other countries. It is also interesting to compare two countries, with a very significant difference in population, where the morbidity and mortality has been so different, and unrelated to the size of the country. url: https://www.ncbi.nlm.nih.gov/pubmed/32513951/ doi: 10.1038/s41419-020-2603-0 id: cord-346574-u28y1ttw author: Chen, Keyan title: Development and evaluation of an immunochromatographic strip for rapid detection of porcine hemagglutinating encephalomyelitis virus date: 2012-08-24 words: 5509.0 sentences: 277.0 pages: flesch: 50.0 cache: ./cache/cord-346574-u28y1ttw.txt txt: ./txt/cord-346574-u28y1ttw.txt summary: At present, various laboratory methods are available for the detection and surveillance of PHE-CoV, including virus isolation [1] , hemagglutination/hemagglutination inhibition (HA/HI) tests [13] , immunohistochemistry (IHC) assays [10] , and molecular tools such as nestedpolymerase chain reaction (nested PCR) and reverse transcriptase-polymerase chain reaction (RT-PCR) that enable detection of specific CoV RNA sequences from infected tissues [14, 15] . (1) (2) (3) In this study, an immunochromatographic strip with high sensitivity and specificity was developed for the detection of PHE-CoV, combining monoclonal antibody (MAb) and colloidal gold immunochromatography (GICA), and the resulting product is suitable for the surveillance of PHE-CoV. Thus, a lot of brain tissue samples were collected from deceased piglets with suspected PHE-CoV infection, and using RT-PCR and ELISA as reference test, the relative specificity and sensitivity of the immunochromatographic strip were determined to be 100% and 97.78%, respectively. abstract: BACKGROUND: The incidence of PHE among pigs in many countries is on the rise, and it has caused great economic losses to the pig industry. Therefore, the development of a sensitive, specific, and easily-performed assay is crucial for the rapid detection and surveillance of PHE-CoV infection and transmission. RESULTS: An immunochromatographic strip was developed for the detection of PHE-CoV. The colloidal gold-labeled MAb 4D4 was used as the detection reagent, and the MAb 1E2 and goat anti-mouse IgG coated the strip's test and control lines, respectively. The immunochromatographic strip was capable of specifically detecting PHE-CoV with a HA unit of 2 within 10 min. Storage of the strips at room temperature for 6 months or at 4°C for 12 months did not change their sensitivity or specificity. Using RT-PCR as a reference test, the relative specificity and sensitivity of the immunochromatographic strip were determined to be 100% and 97.78%, respectively. There was an excellent agreement between the results obtained by RT-PCR and the immunochromatographic strips (kappa = 0.976). Additionally, there was a strong agreement between the sandwich enzyme-linked immunosorbent assay (ELISA) and immunochromatographic strips (Kappa = 0.976). When the immunochromatographic strips were used for diagnosing PHE-CoV infection in the Jilin Province, the PHE-CoV-positive rate ranged from 61.54% in the Jilin district to 17.95% in the Songyuan district. CONCLUSIONS: Based on its high specificity, sensitivity, and stability, the immunochromatographic strip would be suitable for on-site detection of PHE-CoV for surveillance and epidemiological purposes. url: https://doi.org/10.1186/1743-422x-9-172 doi: 10.1186/1743-422x-9-172 id: cord-353957-0pjg25kn author: Chen, Shilong title: Avian Interferon-Inducible Transmembrane Protein Family Effectively Restricts Avian Tembusu Virus Infection date: 2017-04-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Avian Tembusu virus (ATMUV) is a highly pathogenic flavivirus that causes significant economic losses to the Chinese poultry industry. Our previous experiments demonstrated that ATMUV infection effectively triggered host innate immune response through MDA5 and TLR3-dependent signaling pathways. However, little information is available on the role of interferon-stimulated genes (ISGs) in defending against ATMUV infection. In this study, we found that ATMUV infection induced robust expression of type I and type III interferon (IFNs) in duck tissues. Furthermore, we observed that expression of interferon-inducible transmembrane proteins (IFITMs) was significantly upregulated in DEF and DF-1 cells after infection with ATMUV. Similar results were obtained from in vivo studies using ATMUV-infected ducklings. Importantly, we showed that knockdown of endogenous IFITM1 or IFITM3 by specific shRNA markedly enhanced ATMUV replication in DF-1 cells. However, disruption of IFITM2 expression had no obvious effect on the ATMUV replication. In addition, overexpression of chicken or duck IFITM1 and IFITM3 in DF-1 cells impaired the replication of ATMUV. Taken together, these results reveal that induced expression of avian IFITM1 and IFITM3 in response to ATMUV infection can effectively restrict the virus replication, and suggest that increasing IFITM proteins in host may be a useful strategy for control of ATMUV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/28473814/ doi: 10.3389/fmicb.2017.00672 id: cord-255019-iie8wxb4 author: Chen, Xin title: Acute lower respiratory tract infections by human metapneumovirus in children in Southwest China: A 2‐year study date: 2010-06-25 words: 4005.0 sentences: 234.0 pages: flesch: 50.0 cache: ./cache/cord-255019-iie8wxb4.txt txt: ./txt/cord-255019-iie8wxb4.txt summary: title: Acute lower respiratory tract infections by human metapneumovirus in children in Southwest China: A 2‐year study Specimens were collected over a 2‐year period from children hospitalized with acute lower respiratory tract infections (ALRTI) and analyzed for the presence of hMPV using real‐time RT‐PCR assays. 2, 3 Human metapneumovirus (hMPV) was first isolated in 2001 from nasopharyngeal aspirates (NPAs) obtained from children with acute lower respiratory tract infections (ALRTI) in the Netherlands. The validated assay was then used to detect the presence of hMPV in NPAs from pediatric patients presenting at a large teaching children''s hospital located in southwest China over a period of 2 years. NPAs from pediatric patients presenting with ALRTI in the daytime were collected at the Respiratory Ward, Children''s Hospital of Chongqing Medical University, on three fixed days each week over a 2-year period from April 2006 to March 2008. abstract: Human metapneumovirus (hMPV) has been reported to cause both upper and lower respiratory tract diseases in susceptible populations, particularly in children and the elderly. In this study, we describe a hospital‐based epidemiological study of hMPV in patients presenting to a children's hospital and show the demographic and clinical characteristics associated with hMPV infection in China, retrospectively. Specimens were collected over a 2‐year period from children hospitalized with acute lower respiratory tract infections (ALRTI) and analyzed for the presence of hMPV using real‐time RT‐PCR assays. The presence of hMPV was detected in 227 (25.9%) of the 878 children studied and may circulate year‐round in the area, peaking during the winter–spring season. Younger children (aged less than 6 months) had the highest positive rate. Infections by hMPV showed similar epidemiology and clinical manifestations as for respiratory syncytial virus (RSV) and were found in high co‐infections with RSV. Subgroup A2 hMPV was the most predominant genotype identified during the study period. This study indicates that hMPV is one of the major respiratory pathogens found in children in southwest China and vaccine development should be under consideration. Pediatr. Pulmonol. 2010; 45:824–831. © 2010 Wiley‐Liss, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/20583291/ doi: 10.1002/ppul.21264 id: cord-272104-i79b79un author: Chen, Yan title: Re-evaluation of retested nucleic acid-positive cases in recovered COVID-19 patients: Report from a designated transfer hospital in Chongqing, China date: 2020-06-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Since the outbreak of coronavirus disease 2019 (COVID-19) in Wuhan, Hubei Province, China [1], a large number of confirmed cases met the discharge criteria (one of which is two consecutive negative nucleic acid tests with an interval of at least 24 h) [2]. Previous studies have paid more attention to the epidemic situation of COVID-19 and patient diagnosis and treatment. Close attention also should be paid to the discharged patients. Surprisingly, a previous follow-up reported that some patients’ nucleic acid retest results were positive again after discharge [3]. Factors impacting these follow-up test results should be further investigated. Since the first confirmed case was diagnosed in our hospital (Chongqing Emergency Medical Center, the designated transfer hospital) on February 4th, we confirmed a total of 17 cases. All patients infected with the novel coronavirus were transferred to a designated hospital in Southwest China’s Chongqing by ambulance with an inbuilt negative-pressure chamber [4]. In the follow-up examination of these patients, RT-PCR tests were conducted again 3 days after discharged from the designated hospital. Four patients showed recurrence of positive results after a few days of discharge. Thus, we examined these cases herein, aiming to provide information for policy formulation and modification of discharge plans. url: https://doi.org/10.1016/j.jiph.2020.06.008 doi: 10.1016/j.jiph.2020.06.008 id: cord-326596-8ux1q9xw author: Chen, Yanyu title: Biological and phylogenetic characterization of a novel hemagglutination‐negative avian avulavirus 6 isolated from wild waterfowl in China date: 2018-09-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Up to now only nine whole genome sequences of avian avulavirus 6 (AAvV‐6) had been documented in the world since the first discovery of AAvV‐6 (AAvV‐6/duck/HongKong/18/199/77) at a domestic duck in 1977 from Hong Kong of China. Very limited information is known about the regularities of transmission, genetic and biological characteristics of AAvV‐6 because of the lower isolation rate and mild losses for poultry industry. To better further explore the relationships among above factors, an AAvV‐6 epidemiological surveillance of domestic poultry and wild birds in six provinces of China suspected of sites of inter‐species transmission and being intercontinental flyways during the year 2013–2017 was conducted. Therefore, 9,872 faecal samples from wild birds and 1,642 cloacal and tracheal swab samples from clinically healthy poultry of live bird market (LBM) were collected respectively. However, only one novel hemagglutination‐negative AAvV‐6 isolate (AAvV‐6/mallard/Hubei/2015) was isolated from a fresh faecal sample obtained from mallard at a wetland of Hubei province. Sequencing and phylogenetic analyses of this AAvV‐6 isolate (AAvV‐6/mallard/Hubei/2015) indicated that this isolate grouping to genotype I were epidemiological intercontinentally linked with viruses from the wild birds in Europe and America. Meanwhile, at least two genotypes (I and II) are existed within serotype AAvV‐6. In additional, this novel hemagglutination‐negative AAvV‐6 isolate in chicken embryos restored its hemagglutination when pre‐treated with trypsin. These findings, together with data from other AAvV‐6, suggest potential epidemiological intercontinental spreads among AAvV‐6 transmission by wild migratory birds, and reveal potential threats to wild birds and domestic poultry worldwide. url: https://doi.org/10.1111/tbed.13005 doi: 10.1111/tbed.13005 id: cord-016179-4i1n9j4x author: Chen, Yi-Ning title: Real-Time Reverse Transcription-Polymerase Chain Reaction for Detection and Quantitation of Turkey Coronavirus RNA in Feces and Intestine Tissues date: 2015-09-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Turkey coronavirus (TCoV) infection causes acute atrophic enteritis in turkey poults, leading to significant economic loss in the turkey industry. Rapid detection, differentiation, and quantitation of TCoV are critical to the diagnosis and control of the disease. A specific one-step real-time reverse transcription-polymerase chain reaction (RT-PCR) assay using TCoV-specific primers and dual-labeled fluorescent probe for detection and quantitation of TCoV in feces and intestine tissues is described in this chapter. The fluorogenic probe labeled with a reporter dye (FAM, 6-carboxytetramethylrhodamine) and a quencher dye (Absolute Quencher™) was designed to bind to a 186 base-pair fragment flanked by the two PCR primers targeting the 3′ end of spike gene (S2) of TCoV. The assay is highly specific and sensitive and can quantitate between 10(2) and 10(10) copies/mL of viral genome. It is useful in monitoring the progression of TCoV-induced atrophic enteritis in the turkey flocks. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120390/ doi: 10.1007/978-1-4939-3414-0_13 id: cord-017984-w19kd6yp author: Chen, Yi-Ning title: PCR Amplification and Sequencing Analysis of Full-Length Turkey Coronavirus Spike Gene date: 2015-09-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Turkey coronaviral enteritis caused by turkey coronavirus (TCoV) continues to infect turkey flocks, resulting in significant economic loss. Determining and understanding genetic relationships among different TCoV isolates or strains is important for controlling the disease. Using two-step RT-PCR assays that amplify the full length of TCoV spike (S) gene, TCoV isolates can be sequenced, analyzed, and genotyped. Described in this chapter is the protocol on PCR amplification and sequencing analysis of full-length TCoV S gene. Such protocol is useful in molecular epidemiology for establishing an effective strategy to control the transmission of TCoV among turkey flocks. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122697/ doi: 10.1007/978-1-4939-3414-0_14 id: cord-274644-gr1eaj6k author: Chen, Zhao-Chi title: Thermally stable and uniform DNA amplification with picosecond laser ablated graphene rapid thermal cycling device date: 2019-12-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Rapid thermal cycling (RTC) in an on-chip device can perform DNA amplification in vitro through precise thermal control at each step of the polymerase chain reaction (PCR). This study reports a straightforward fabrication technique for patterning an on-chip graphene-based device with hole arrays, in which the mechanism of surface structures can achieve stable and uniform thermal control for the amplification of DNA fragments. A thin-film based PCR device was fabricated using picosecond laser (PS-laser) ablation of the multilayer graphene (MLG). Under the optimal fluence of 4.72 J/cm(2) with a pulse overlap of 66%, the MLG can be patterned with arrays of 250 μm(2) hole surface structures. A 354-bp DNA fragment of VP1, an effective marker for diagnosing the BK virus, was amplified on an on-chip device in less than 60 min. A thin-film electrode with the aforementioned MLG as the heater was demonstrated to significantly enhance temperature stability for each stage of the thermal cycle. The temperature control of the heater was performed by means of a developed programmable PCR apparatus. Our results demonstrated that the proposed integration of a graphene-based device and a laser-pulse ablation process to form a thin-film PCR device has cost benefits in a small-volume reagent and holds great promise for practical medical use of DNA amplification. url: https://api.elsevier.com/content/article/pii/S0956566319306608 doi: 10.1016/j.bios.2019.111581 id: cord-298076-rujylmib author: Chen, Zhiyong title: Comparison of reverse transcription loop-mediated isothermal amplification, conventional PCR and real-time PCR assays for Japanese encephalitis virus date: 2010-11-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: We developed and evaluated a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for detecting Japanese encephalitis virus (JEV). The sensitivity of the JEV RT-LAMP assay was in concordance with that of real-time RT-PCR and 10-fold more sensitive than that of conventional RT-PCR, which the detection limit was 24 copies/μl. The JEV RT-LAMP was highly specific, which no cross-reactivity was found with dengue-2 virus, rabies virus, norovirus, astrovirus and human enterovirus 71. The JEV RT-LAMP assay was more simple and less time-consuming compared to the conventional RT-PCR and real-time RT-PCR, which the amplification could be completed in a single tube within 1 h under isothermal conditions at temperature of 63°C. The results suggest that the RT-LAMP assay can be applied as a practical molecular diagnostic tool for JEV infection and surveillance. url: https://doi.org/10.1007/s11033-010-0525-0 doi: 10.1007/s11033-010-0525-0 id: cord-346989-604gho1u author: Chen-Harris, Haiyin title: Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs date: 2013-02-12 words: 7125.0 sentences: 334.0 pages: flesch: 49.0 cache: ./cache/cord-346989-604gho1u.txt txt: ./txt/cord-346989-604gho1u.txt summary: RESULTS: We demonstrate that overlapping read pairs (ORP) -generated by combining short fragment sequencing libraries and longer sequencing reads -significantly reduce sequencing error rates and improve rare variant detection accuracy. We demonstrate the novel use of mismatch rates in the overlapping read pairs (ORP) to provide an unbiased assessment of the sequencer-derived quality scores when selecting a read filtering threshold, as well as to estimate position-dependent sequencing errors without relying on a clonal control. ORPs reduce error rates and provide benchmarks for quality scores For all five samples, 3 natural viral and 2 plasmid controls, Illumina paired-end sequencing was carried out using relatively short sequencing fragment libraries combined with relatively long reads (112 bp) to generate overlapping read pairs (ORP). abstract: BACKGOUND: High throughput sequencing is beginning to make a transformative impact in the area of viral evolution. Deep sequencing has the potential to reveal the mutant spectrum within a viral sample at high resolution, thus enabling the close examination of viral mutational dynamics both within- and between-hosts. The challenge however, is to accurately model the errors in the sequencing data and differentiate real viral mutations, particularly those that exist at low frequencies, from sequencing errors. RESULTS: We demonstrate that overlapping read pairs (ORP) -- generated by combining short fragment sequencing libraries and longer sequencing reads -- significantly reduce sequencing error rates and improve rare variant detection accuracy. Using this sequencing protocol and an error model optimized for variant detection, we are able to capture a large number of genetic mutations present within a viral population at ultra-low frequency levels (<0.05%). CONCLUSIONS: Our rare variant detection strategies have important implications beyond viral evolution and can be applied to any basic and clinical research area that requires the identification of rare mutations. url: https://doi.org/10.1186/1471-2164-14-96 doi: 10.1186/1471-2164-14-96 id: cord-296736-jsm6o5pq author: Chidlow, Glenys R. title: An Economical Tandem Multiplex Real-Time PCR Technique for the Detection of a Comprehensive Range of Respiratory Pathogens date: 2009-06-08 words: 4131.0 sentences: 183.0 pages: flesch: 43.0 cache: ./cache/cord-296736-jsm6o5pq.txt txt: ./txt/cord-296736-jsm6o5pq.txt summary: title: An Economical Tandem Multiplex Real-Time PCR Technique for the Detection of a Comprehensive Range of Respiratory Pathogens The aim of this study was to modify real-time PCR assays to facilitate the rapid screening of respiratory samples for a comprehensive range of viral and bacterial pathogens. This tandem multiplex real-time PCR assay, in combination with the semi-nested picornavirus and human metapneumovirus PCR assays, tests for 35 respiratory agents from a sample volume of 180µL compared to 720 µL required for the individual assays. Further work is planned to incorporate the picornavirus and human metapneumovirus assays into the tandem multiplex real-time PCR assay, but so far we have been unable to design or use published real-time PCR primers and probes that detect all types of these viruses with the same sensitivity as our nested assays. A tandem multiplex real-time assay is presented which detects a comprehensive range of respiratory pathogens from a specimen sample of 180µL. Multiplex real-time PCR assay for detection of Influenza and human respiratory syncytial viruses abstract: This study used real-time PCR assays to screen small sample volumes for a comprehensive range of 35 respiratory pathogens. Initial thermocycling was limited to 20 cycles to avoid competition for reagents, followed by a secondary real-time multiplex PCR. Supplementary semi-nested human metapneumovirus and picornavirus PCR assays were required to complete the acute respiratory pathogen profile. Potential pathogens were detected in 85 (70%) of pernasal aspirates collected from 121 children with acute respiratory symptoms. Multiple pathogens were detected in 29 (24%) of those samples. The tandem multiplex real-time PCR was an efficient method for the rapid detection of multiple pathogens. url: https://www.ncbi.nlm.nih.gov/pubmed/21994537/ doi: 10.3390/v1010042 id: cord-301066-62qe4fb0 author: Chiu, Susan S. title: Human Coronavirus NL63 Infection and Other Coronavirus Infections in Children Hospitalized with Acute Respiratory Disease in Hong Kong, China date: 2005-06-15 words: 3944.0 sentences: 220.0 pages: flesch: 56.0 cache: ./cache/cord-301066-62qe4fb0.txt txt: ./txt/cord-301066-62qe4fb0.txt summary: In 2001 and 2002, we performed prospective clinical and virological studies of children (age, р18 years) with acute respiratory tract infection who were admitted to Queen Mary Hospital (Hong Kong, China). We studied a systematic sample of children (age, р18 years) with acute respiratory infection admitted to Queen Mary Hospital during the period from August 2001 to March 2002. One child with HCoV-NL63 upper respiratory tract infection had positive results of only the consensus primer PCR, so no viral load could be measured. We documented that human coronavirus infection was a significant cause of hospitalization for children aged р18 years, accounting for 4.4% of all admissions for acute respiratory infections. A previous study showed that 8.2% of children aged !18 months who were admitted to a Chicago, Illinois, hospital with lower respiratory tract diseases had serological evidence of HCoV-229E or HCoV-OC43 infection [13] . abstract: Background. Human coronavirus NL63 (HCoV-NL63) is a recently discovered human coronavirus found to cause respiratory illness in children and adults that is distinct from the severe acute respiratory syndrome (SARS) coronavirus and human coronaviruses 229E (HCoV-229E) and OC43 (HCoV-OC43). Methods. We investigated the role that HCoV-NL63, HCoV-OC43, and HCoV-229E played in children hospitalized with fever and acute respiratory symptoms in Hong Kong during the period from August 2001 through August 2002. Results. Coronavirus infections were detected in 26 (4.4%) of 587 children studied; 15 (2.6%) were positive for HCoV-NL63, 9 (1.5%) were positive for HCoV-OC43, and 2 (0.3%) were positive for HCoV-229E. In addition to causing upper respiratory disease, we found that HCoV-NL63 can present as croup, asthma exacerbation, febrile seizures, and high fever. The mean age (± standard deviation [SD]) of the infected children was 30.7 ± 19.8 months (range, 6–57 months). The mean maximum temperature (±SD) for the 12 children who were febrile was 39.3°C ± 0.9°C, and the mean total duration of fever (±SD) for all children was 2.6 ± 1.2 days (range, 1–5 days). HCoV-NL63 infections were noted in the spring and summer months of 2002, whereas HCoV-OC43 infection mainly occurred in the fall and winter months of 2001. HCoV-NL63 viruses appeared to cluster into 2 evolutionary lineages, and viruses from both lineages cocirculated in the same season. Conclusions. HCoV-NL63 is a significant pathogen that contributes to the hospitalization of children, and it was estimated to have caused 224 hospital admissions per 100,000 population aged ⩽6 years each year in Hong Kong. url: https://www.ncbi.nlm.nih.gov/pubmed/15909257/ doi: 10.1086/430301 id: cord-343784-zgvxl4h3 author: Cho, Chi Hyun title: Evaluation of the AdvanSure™ real-time RT-PCR compared with culture and Seeplex RV15 for simultaneous detection of respiratory viruses date: 2014-05-31 words: 3707.0 sentences: 204.0 pages: flesch: 51.0 cache: ./cache/cord-343784-zgvxl4h3.txt txt: ./txt/cord-343784-zgvxl4h3.txt summary: Several studies have demonstrated the advantages of multiplex PCR assays such as xTAG RVP, RVP fast (Luminex Molecular Diagnostics, Toronto, ON, Canada), Resplex II (Qiagen, Mississauga, ON, Canada), FilmArray® Respiratory panel (Idaho Technology Inc., Salt Lake City, UT, USA), and Seeplex RV assays (Seegene, Seoul, Korea), which are used routinely for the detection of respiratory viral infection (Bibby et al., 2011; Couturier et al., 2013; Gharabaghi et al., 2011; Kim et al., 2013; Zhang et al., 2012) . In the previous study evaluating Seeplex RV12 detection kit (Seegene, Rockville, MD, USA), viral culture, RV12, and real-time PCR detected 8, 6, and 11 of 11 influenza B-positive specimens, respectively (Bruijnesteijn van Coppenraet et al., 2010) . Simultaneous detection of influenza A, B, and C viruses, respiratory syncytial virus, and adenoviruses in clinical samples by multiplex reverse transcription nested-PCR assay Evaluation of a multiplex real-time PCR assay for the detection of respiratory viruses in clinical specimens abstract: Abstract Recently, AdvanSure™ kit based on multiplex real-time PCR was developed for simultaneous detection of 14 respiratory viruses (RVs). We compared the performance of AdvanSure with those of Seeplex® RV 15 ACE and culture by determining their sensitivities and specificities against a composite reference standard. Four hundred thirty-seven respiratory samples were tested by modified shell vial culture method, RV 15 ACE, and AdvanSure. One hundred fourteen samples (26.2%) out of 437 samples were positive by culture, while additional 91 (20.8%) were positive by AdvanSure or RV15. One hundred twelve of 114 culture-positive samples were positive by AdvanSure except 2 samples (1 adenovirus, 1 respiratory syncytial virus [RSV]). Overall, the sensitivities of culture, RV15, and AdvanSure were 74.5%, 89.8%, and 95.1%, respectively. Sensitivities of culture, RV15, and AdvanSure for each virus tested were as follows: 91/100/96% for influenza A, 60/0/100% for influenza B, 63/95/97% for RSV, 69/81/89% for adenovirus, and 87/93/93% for parainfluenza virus. For viruses not covered by culture, sensitivities of RV15 and AdvanSure were as follows: 77/88% for rhinovirus, 100/100% for coronavirus OC43, 40/100% for coronavirus 229E/NL63, 13/100% for metapneumovirus, and 44/100% for bocavirus. The overall specificities of culture, RV15, and AdvanSure were 100/98.9/99.5%, respectively. Of 45 coinfected specimens, AdvanSure detected 41 specimens (91.1%) as coinfected, while RV15 detected 27 specimens (60.0%) as coinfected. AdvanSure assay demonstrated exquisite performance for the detection of RVs and will be a valuable tool for the management of RV infection. url: https://api.elsevier.com/content/article/pii/S0732889314000492 doi: 10.1016/j.diagmicrobio.2014.01.016 id: cord-259886-j0bpp7iw author: Cho, Hyejin title: Positive control synthesis method for COVID-19 diagnosis by one-step real-time RT-PCR date: 2020-10-12 words: 2319.0 sentences: 136.0 pages: flesch: 53.0 cache: ./cache/cord-259886-j0bpp7iw.txt txt: ./txt/cord-259886-j0bpp7iw.txt summary: SPT oligonucleotides contain probe binding and virus-irrelevant regions as templates for detecting SARS-CoV-2 genes (RdRP, E, and N SARS-CoV-2) by real-time RT-PCR was performed in a concentration-dependent manner. Therefore, this approach may be integrated into the molecular diagnosis of COVID-19 and provides a general method for preparing positive controls for diagnosing emerging RNA virus infections. Therefore, a new preparation design that provides contamination-free positive controls for COVID-19 real-time RT-PCR testing is urgently needed. Here, we present a new approach for producing synthetic positive controls using synthetic positive template (SPT) oligonucleotides that contain probe binding and virusirrelevant regions as templates for detecting SARS-CoV-2 genes by real-time RT-PCR. We performed multiplex real-time RT-PCR using an SPT (positive control) as a template in a concentration-dependent manner, to determine the limit of detection (LOD) for individual SARS-CoV-2 genes. In previous studies, the Uni-Control method for preparing real-time RT-PCR positive controls has been developed as a generic approach for diagnosing viral infections [22] . abstract: Backgrounds The coronavirus disease 2019 (COVID-19) pandemic is still ongoing. Real-time reverse transcription polymerase chain reaction (real-time RT-PCR) is regarded as a gold-standard method. However, COVID-19 test kits, especially the positive control samples that are synthesized by laboratories or companies, have increased the inconclusiveness of disease interpretation. Therefore, development of new methods for the preparation of reliable positive controls that are not impaired by contamination for diagnosing COVID-19 remains a challenge. Methods A new approach for producing synthetic positive controls using synthetic positive template (SPT) oligonucleotides was designed. SPT oligonucleotides contain probe binding and virus-irrelevant regions as templates for detecting SARS-CoV-2 genes (RdRP, E, and N SARS-CoV-2) by real-time RT-PCR was performed in a concentration-dependent manner. The limit of detection (LOD) for individual SARS-CoV-2 genes by Ct values with concentration ranges was determined with SPT templates and genomic RNAs prepared from SARS-CoV-2. Results LODs with SPT templates were >10-15 (atto) M for RdRP, 10-12 (femto) to 10-13 (100 atto) M for E gene, and 10-12 to 10-14 (10 atto) M for N gene, respectively. Real-time RT-PCR assay using serially diluted genomic RNAs prepared from SARS-CoV-2 showed that picogram quantities of RNAs prepared from COVID-19 virus cultures resulted in the LOD. The sensitivity based on Ct values for RdRP and E genes were less sensitive to this platform than N gene. Conclusion This method significantly decreased the risk of contamination and false-positive reactions that result from contamination of the synthesis procedures that are used to produce positive control materials. Therefore, this approach may be integrated into the molecular diagnosis of COVID-19 and provides a general method for preparing positive controls for diagnosing emerging RNA virus infections. url: https://www.sciencedirect.com/science/article/pii/S0009898120304721?v=s5 doi: 10.1016/j.cca.2020.10.001 id: cord-292831-oihcay6w author: Choudhary, Manohar L. title: Development of a multiplex one step RT-PCR that detects eighteen respiratory viruses in clinical specimens and comparison with real time RT-PCR date: 2013-01-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Rapid and accurate diagnosis of viral respiratory infections is crucial for patient management. Multiplex reverse transcriptase polymerase chain reaction (mRT-PCR) is used increasingly to diagnose respiratory infections and has shown to be more sensitive than viral culture and antigen detection. Objective of the present study was to develop a one-step mRT-PCR that could detect 18 respiratory viruses in three sets. The method was compared with real time RT-PCR (rRT-PCR) for its sensitivity and specificity. Clinical specimens from 843 pediatric patients with respiratory symptoms were used in the study. 503 (59.7%) samples were detected positive by mRT-PCR. Of these 462 (54.8%) exhibited presence of a single pathogen and 41 (4.9%) had multiple pathogens. rRT-PCR detected 439 (52.1%) positive samples, where 419 (49.7%) exhibited one virus and 20 (2.4%) showed co-infections. Concordance between mRT-PCR and rRT-PCR was 91.9% and kappa correlation 0.837. Sensitivity and specificity of mRT-PCR were 99.5% and 83.7% while that of rRT-PCR was 86.9% and 99.4% respectively. Rhinovirus (17.2%) was the most frequently detected virus followed by respiratory syncytial virus B (15.4%), H1N1pdm09 (8.54%), parainfluenza virus-3 (5.8%) and metapneumovirus (5.2%). In conclusion, mRT-PCR is a rapid, cost effective, specific and highly sensitive method for detection of respiratory viruses. url: https://api.elsevier.com/content/article/pii/S0166093413000049 doi: 10.1016/j.jviromet.2012.12.017 id: cord-004840-4rbrzv5o author: Choudhary, Manohar Lal title: Development of real-time RT-PCR for detection of human metapneumovirus and genetic analysis of circulating strains (2009-2011) in Pune, India date: 2013-08-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Human metapneumovirus (HMPV) is an important respiratory virus implicated in respiratory infections. The purpose of this study was to develop a one-step real-time RT-PCR assay that can detect all four lineages of HMPV and to identify the HMPV lineages circulating in Pune, India. Conserved regions of the nucleoprotein gene were used to design real-time primers and a probe. A total of 224 clinical samples that were positive for different respiratory viruses (including 51 samples that were positive for HMPV) were tested using the real time RT-PCR assay, and the specificity of the assay was observed to be 100 %. Using in vitro-synthesized RNA, the sensitivity of the assay was ascertained to be 100 copies of the target gene per reaction. Phylogenetic analysis of the nucleoprotein (N) and attachment glycoprotein (G) genes confirmed that this assay detected all lineages of HMPV. A2, B1 and B2 strains were observed during the study period. Our assay is highly sensitive and specific for all known lineages of HMPV, making it a valuable tool for rapid detection of the virus. A2 and B2 were the predominant subtypes circulating in Pune, Western India. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087245/ doi: 10.1007/s00705-013-1812-6 id: cord-261279-6mef38eo author: Chu, Daniel K W title: Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia date: 2020-01-31 words: 2971.0 sentences: 178.0 pages: flesch: 54.0 cache: ./cache/cord-261279-6mef38eo.txt txt: ./txt/cord-261279-6mef38eo.txt summary: RESULTS: Using RNA extracted from cells infected by SARS coronavirus as a positive control, these assays were shown to have a dynamic range of at least seven orders of magnitude (2x10(−4)-2000 TCID(50)/reaction). In this study, we report the development of RT-PCR assays to detect this novel virus in human clinical specimens. Two monoplex real-time RT-PCR assays targeting the ORF1b and N gene regions of 2019-nCoV were designed based on the first publicly available sequence in Genbank (Accession number: MN908947). Viral RNA from cells infected by SARS coronavirus or DNA plasmids containing the target sequences were positive in the assays as expected. In addition, the N gene RT-PCR assay was found to be more sensitive in detecting 2019-nCoV RNA in the studied clinical samples. abstract: BACKGROUND: A novel coronavirus of zoonotic origin (2019-nCoV) has recently been identified in patients with acute respiratory disease. This virus is genetically similar to SARS coronavirus and bat SARS-like coronaviruses. The outbreak was initially detected in Wuhan, a major city of China, but has subsequently been detected in other provinces of China. Travel-associated cases have also been reported in a few other countries. Outbreaks in health care workers indicate human-to-human transmission. Molecular tests for rapid detection of this virus are urgently needed for early identification of infected patients. METHODS: We developed two 1-step quantitative real-time reverse-transcription PCR assays to detect two different regions (ORF1b and N) of the viral genome. The primer and probe sets were designed to react with this novel coronavirus and its closely related viruses, such as SARS coronavirus. These assays were evaluated using a panel of positive and negative controls. In addition, respiratory specimens from two 2019-nCoV-infected patients were tested. RESULTS: Using RNA extracted from cells infected by SARS coronavirus as a positive control, these assays were shown to have a dynamic range of at least seven orders of magnitude (2x10(−4)-2000 TCID(50)/reaction). Using DNA plasmids as positive standards, the detection limits of these assays were found to be below 10 copies per reaction. All negative control samples were negative in the assays. Samples from two 2019-nCoV-infected patients were positive in the tests. CONCLUSIONS: The established assays can achieve a rapid detection of 2019n-CoV in human samples, thereby allowing early identification of patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32031583/ doi: 10.1093/clinchem/hvaa029 id: cord-275519-98qxf6xo author: Chun, Jong-Yoon title: Dual priming oligonucleotide system for the multiplex detection of respiratory viruses and SNP genotyping of CYP2C19 gene date: 2007-02-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Successful PCR starts with proper priming between an oligonucleotide primer and the template DNA. However, the inevitable risk of mismatched priming cannot be avoided in the currently used primer system, even though considerable time and effort are devoted to primer design and optimization of reaction conditions. Here, we report a novel dual priming oligonucleotide (DPO) which contains two separate priming regions joined by a polydeoxyinosine linker. The linker assumes a bubble-like structure which itself is not involved in priming, but rather delineates the boundary between the two parts of the primer. This structure results in two primer segments with distinct annealing properties: a longer 5′-segment that initiates stable priming, and a short 3′-segment that determines target-specific extension. This DPO-based system is a fundamental tool for blocking extension of non-specifically primed templates, and thereby generates consistently high PCR specificity even under less than optimal PCR conditions. The strength and utility of the DPO system are demonstrated here using multiplex PCR and SNP genotyping PCR. url: https://www.ncbi.nlm.nih.gov/pubmed/17287288/ doi: 10.1093/nar/gkm051 id: cord-337198-4sors3bg author: Clementi, Nicola title: Combined Prophylactic and Therapeutic Use Maximizes Hydroxychloroquine Anti-SARS-CoV-2 Effects in vitro date: 2020-07-10 words: 4259.0 sentences: 224.0 pages: flesch: 54.0 cache: ./cache/cord-337198-4sors3bg.txt txt: ./txt/cord-337198-4sors3bg.txt summary: In this study, we evidence that the anti-SARS-CoV2 activity of a clinically achievable hydroxychloroquine concentration is maximized only when administered before and after the infection of Vero E6 and Caco-2 cells. In this study, we tested HCQ against a SARS-CoV-2 Italian clinical isolate, by using different protocols of drug administration corresponding to its possible prophylactic, therapeutic, and prophylactic/therapeutic use in patients. A clinical isolate hCoV-19/Italy/UniSR1/2020 (GISAID accession ID: EPI_ISL_413489) was isolated and propagated in Vero E6 cells, and viral titer was determined by 50% tissue culture infective dose (TCID 50 ) and plaque assay for confirming the obtained titer. HCQ EC 50 against SARS-CoV-2 was obtained by both CPE and RT-PCR analysis on results from full-time experimental setting on Vero E6 cells. Different concentrations of HCQ were tested on Vero E6 to determine the effective concentration of the drug against SARS-CoV-2 in vitro infection (Figure 1) . abstract: While the SARS-CoV-2 pandemic is heavily hitting the world, it is of extreme importance that significant in vitro observations guide the quick set up of clinical trials. In this study, we evidence that the anti-SARS-CoV2 activity of a clinically achievable hydroxychloroquine concentration is maximized only when administered before and after the infection of Vero E6 and Caco-2 cells. This suggests that only a combined prophylactic and therapeutic use of hydroxychloroquine may be effective in limiting viral replication in patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32754147/ doi: 10.3389/fmicb.2020.01704 id: cord-300313-w8njg569 author: Clifford, S. title: Strategies to reduce the risk of SARS-CoV-2 re-introduction from international travellers date: 2020-07-24 words: 7266.0 sentences: 363.0 pages: flesch: 51.0 cache: ./cache/cord-300313-w8njg569.txt txt: ./txt/cord-300313-w8njg569.txt summary: To mitigate SARS-CoV-2 transmission risks from international travellers, many countries currently use a combination of up to 14 days of self-quarantine on arrival and testing for active infection. Due to differences in COVID-19 prevalence and estimated travel volume in July 2020, the expected numbers of infectious entries per week in a no-intervention scenario (apart from self-reporting of symptoms and syndromic screening at departure) from the USA are approximately double that of the EU (up to 28 and up to 12, respectively). While the acceptable number of infected travellers entering the community will depend on the local context of SARS-CoV-2 transmission we find that for travellers arriving from low prevalence destinations the absolute risk of seeding new outbreaks is likely low and hence either testing and/or quarantine-based strategies may do little to further reduce such risk, particularly when many infectious arrivals are asymptomatic cases. abstract: To mitigate SARS-CoV-2 transmission risks from international travellers, many countries currently use a combination of up to 14 days of self-quarantine on arrival and testing for active infection. We used a simulation model of air travellers arriving to the UK from the EU or the USA and the timing of their stages of infection to evaluate the ability of these strategies to reduce the risk of seeding community transmission. We find that a quarantine period of 8 days on arrival with a PCR test on day 7 (with a 1-day delay for test results) can reduce the number of infectious arrivals released into the community by a median 94% compared to a no quarantine, no test scenario. This reduction is similar to that achieved by a 14-day quarantine period (median 99% reduction). Shorter quarantine periods still can prevent a substantial amount of transmission; all strategies in which travellers spend at least 5 days (the mean incubation period) in quarantine and have at least one negative test before release are highly effective (e.g. a test on day 5 with release on day 6 results in a median 88% reduction in transmission potential). Without intervention, the current high prevalence in the US (40 per 10,000) results in a higher expected number of infectious arrivals per week (up to 23) compared to the EU (up to 12), despite an estimated 8 times lower volume of travel in July 2020. Requiring a 14-day quarantine period likely results in less than 1 infectious traveller each entering the UK per week from the EU and the USA (97.5th percentile). We also find that on arrival the transmission risk is highest from pre-symptomatic travellers; quarantine policies will shift this risk increasingly towards asymptomatic infections if eventually-symptomatic individuals self-isolate after the onset of symptoms. As passenger numbers recover, strategies to reduce the risk of re-introduction should be evaluated in the context of domestic SARS-CoV-2 incidence, preparedness to manage new outbreaks, and the economic and psychological impacts of quarantine. url: http://medrxiv.org/cgi/content/short/2020.07.24.20161281v1?rss=1 doi: 10.1101/2020.07.24.20161281 id: cord-000830-jiy4cp4n author: Cobo, Fernando title: Application of Molecular Diagnostic Techniques for Viral Testing date: 2012-11-30 words: 7969.0 sentences: 385.0 pages: flesch: 39.0 cache: ./cache/cord-000830-jiy4cp4n.txt txt: ./txt/cord-000830-jiy4cp4n.txt summary: The use of amplification techniques such as polymerase chain reaction, real-time polymerase chain reaction or nucleic acid sequence-based amplification for virus detection, genotyping and quantification have some advantages like high sensitivity and reproducibility, as well as a broad dynamic range. The use of amplification techniques such as polymerase chain reaction (PCR), real-time PCR or nucleic acid sequence-based amplification (NASBA) [3] for virus detection, genotyping and quantification have some advantages like high sensitivity and reproducibility, as well as a broad dynamic range [4, 5] . NASBA assays could identify active infection by detecting viral messenger RNA (mRNA) but the most widely used tests in clinical virus diagnosis are quantitative real-time PCR techniques [8] . Some real-time PCR assays such as LightCycler parvovirus B19 quantitative assay (Roche Diagnostics, Indianapolis, IN) and ABI TaqMan (Applied Biosystems) have been developed for detecting B19 nucleic acids in association with infection during pregnancy or assessing the prevalence of the virus DNA in blood products [62, 63] . abstract: Nucleic acid amplification techniques are commonly used currently to diagnose viral diseases and manage patients with this kind of illnesses. These techniques have had a rapid but unconventional route of development during the last 30 years, with the discovery and introduction of several assays in clinical diagnosis. The increase in the number of commercially available methods has facilitated the use of this technology in the majority of laboratories worldwide. This technology has reduced the use of some other techniques such as viral culture based methods and serological assays in the clinical virology laboratory. Moreover, nucleic acid amplification techniques are now the methods of reference and also the most useful assays for the diagnosis in several diseases. The introduction of these techniques and their automation provides new opportunities for the clinical laboratory to affect patient care. The main objectives in performing nucleic acid tests in this field are to provide timely results useful for high-quality patient care at a reasonable cost, because rapid results are associated with improvements in patients care. The use of amplification techniques such as polymerase chain reaction, real-time polymerase chain reaction or nucleic acid sequence-based amplification for virus detection, genotyping and quantification have some advantages like high sensitivity and reproducibility, as well as a broad dynamic range. This review is an up-to-date of the main nucleic acid techniques and their clinical applications, and special challenges and opportunities that these techniques currently provide for the clinical virology laboratory. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522074/ doi: 10.2174/1874357901206010104 id: cord-302486-z36hcvrx author: Cobo, Fernando title: Diagnostic approaches for viruses and prions in stem cell banks date: 2006-03-30 words: 7276.0 sentences: 347.0 pages: flesch: 41.0 cache: ./cache/cord-302486-z36hcvrx.txt txt: ./txt/cord-302486-z36hcvrx.txt summary: Viral and prion contamination of cell cultures and "feeder" cells, which is a common risk in all biotechnological products derived from the cell lines, is the most challenging and potentially serious outcome to address, due to the difficulty involved in virus and prion detection and the potential to cause serious disease in recipients of these cell products. The use of bovine fetal serum in stem cell cultures requires an urgent need for a risk assessment for Transmissible Spongiform Encephalopathies (TSEs) by means of a sensitive and specific test in all products derived from ruminants (U.S. Food and Drugs Administration, 1999; Directive 2004/C 24/ 03). This panel of tests should necessarily include reverse transcriptase detection as a general test for retroviruses, electron microscopy that can detect different kinds of viral particles and characterize many unknown isolates present in cell cultures and molecular techniques like PCR (conventional or real-time) and RT-PCR tests to include all the viruses that we know pose a risk to the product. abstract: Some stem cell lines may contain an endogenous virus or can be contaminated with exogenous viruses (even of animal origin) and may secrete viral particles or express viral antigens on their surface. Moreover, certain biotechnological products (e.g. bovine fetal serum, murine feeder cells) may contain prion particles. Viral and prion contamination of cell cultures and “feeder” cells, which is a common risk in all biotechnological products derived from the cell lines, is the most challenging and potentially serious outcome to address, due to the difficulty involved in virus and prion detection and the potential to cause serious disease in recipients of these cell products. Stem cell banks should introduce adequate quality assurance programs like the microbiological control program and can provide researchers with valuable support in the standardization and safety of procedures and protocols used for the viral and prion testing and in validation programs to assure the quality and safety of the cells. url: https://api.elsevier.com/content/article/pii/S0042682205007725 doi: 10.1016/j.virol.2005.11.026 id: cord-288327-r20zowty author: Coiras, M.T. title: Oligonucleotide array for simultaneous detection of respiratory viruses using a reverse‐line blot hybridization assay date: 2005-04-15 words: 5919.0 sentences: 286.0 pages: flesch: 47.0 cache: ./cache/cord-288327-r20zowty.txt txt: ./txt/cord-288327-r20zowty.txt summary: Biotin‐labeled PCR products obtained with two multiplex reverse transcription (RT)‐polymerase chain reaction (PCR) assays described previously, which allow for the detection of fourteen different groups of respiratory viruses, were hybridized to the oligonucleotide array. Biotin-labeled PCR products obtained with two multiplex reverse transcription (RT)-polymerase chain reaction (PCR) assays described previously, which allow for the detection of fourteen different groups of respiratory viruses, were hybridized to the oligonucleotide array. To evaluate the validity of this method for routine diagnosis was performed a comparative analysis using reference strains from a wide range of respiratory viruses, viral isolates and clinical specimens that have been analyzed by both nested PCR and RLB assays. In conclusion, a RT-PCR-RLB method has been developed for simultaneous detection and typing of a wide range of respiratory viruses, based on the hybridization of biotinylated PCR products, obtained with two multiplex RT-PCR assays described previously, to an array of oligonucleotides that are immobilized and orientated on a nylon membrane. abstract: The interest in developing new diagnostic methods based on arrays of multiple probes to detect and type simultaneously a wide range of different infectious agents is increasing. This becomes a necessity in the case of infectious agents such as respiratory viruses that cause diseases with very similar signs and symptoms. Such tools will permit rapid and accurate diagnosis of different agents causing respiratory infection leading to the most adequate prevention and/or treatment measures. In this article a reverse‐line blot hybridization (RLB) assay for the detection of a wide range of respiratory viruses is presented and evaluated for its usefulness in routine diagnosis. This assay employs an array of 18 oligonucleotide probes immobilized on a nylon membrane. Biotin‐labeled PCR products obtained with two multiplex reverse transcription (RT)‐polymerase chain reaction (PCR) assays described previously, which allow for the detection of fourteen different groups of respiratory viruses, were hybridized to the oligonucleotide array. Detection was performed using a chemiluminescent method. The standardization of the method showed that the RLB assay could be an alternative to the nested PCR assay for enhancing the sensitivity in the detection of the amplified products, avoiding the problem of cross‐over contamination, increasing the specificity, and therefore simplifying the method. This is of main interest in laboratories with few facilities. The feasibility and accuracy of the RT‐PCR‐RLB assay for detecting respiratory viruses proves that such approach could be a first stage to develop a microarray assay for routine diagnosis of infectious diseases. J. Med. Virol. 76:256–264, 2005. © 2005 Wiley‐Liss, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/15834876/ doi: 10.1002/jmv.20350 id: cord-021596-5s8lksxp author: Colegrove, Kathleen M. title: Pinnipediae date: 2018-10-26 words: 10418.0 sentences: 613.0 pages: flesch: 39.0 cache: ./cache/cord-021596-5s8lksxp.txt txt: ./txt/cord-021596-5s8lksxp.txt summary: Hepatic hemosiderosois is seen frequently in several pinniped species including young northern elephant and harbor seals, Hawaiian monk seals, northern fur seals, and CSLs. Mild chronic cholecystitis and portal hepatitis are common findings in wild pinnipeds secondary to trematode infection and trematode-associated pigment accumulation can occur. is most commonly reported in free-ranging pinnipeds including CSLs, harbor, and northern elephant seals along the Pacific coast of North America (Colegrove et al., 2005b; Gulland et al., 1996b) . pinnipedii has not been reported for any phocid species; however, the potential host range is broad and transmission from infected fur seals and sea lions has been described for zoo species, domestic cattle, and humans (Cousins et al., 2003; Kiers et al., 2008; Loeffler et al., 2014; Moser et al., 2008; Thompson et al., 1993; Thorel et al., 1998) . Harbor seals are the most commonly reported species to develop severe fatal disease with infection, and in California subadults and adults are primarily affected (Barbosa et al., 2015; Miller, 2008) . abstract: This chapter reviews common diseases of pinnipeds, including species in the Otariidae (fur seals and sea lions), Phocidae (true seals), and Odobenidae (walrus) families. Much of the knowledge on pathologic conditions of pinnipeds comes from necropsies of stranded animals and those housed in captivity. As such, disease knowledge is biased toward species frequently housed in zoos and aquaria, those that strand more commonly, or those in which free-ranging populations are more easily accessible. Though historically systematic evaluations of wild populations have rarely been accomplished, in the past 10 years, with advances in marine mammal medicine and anesthesia, biologists and veterinarians more frequently completed live animal health field investigations to evaluate health and disease in free-ranging pinniped populations. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7150363/ doi: 10.1016/b978-0-12-805306-5.00023-7 id: cord-339973-kj56zi59 author: Coleman, Kristen K. title: Bioaerosol Sampling for Respiratory Viruses in Singapore’s Mass Rapid Transit Network date: 2018-11-30 words: 4775.0 sentences: 228.0 pages: flesch: 46.0 cache: ./cache/cord-339973-kj56zi59.txt txt: ./txt/cord-339973-kj56zi59.txt summary: Although baseline metagenomic maps created from these studies are said to be useful for mitigating bioterrorism and infectious disease outbreaks, most of them focus largely on mapping surface-borne bacterial DNA 17 and neglect to address the threat of weaponized or global catastrophic biological risk-level (GCBR-level) agents, both of which would likely be aerosolized or respiratory-borne RNA viruses 19 . Bioaerosol sampling in the field provides a noninvasive way to monitor and characterize the community of aerosolized respiratory viruses that regularly infect the public, as well as potentially detect or discover novel pathogens with pandemic potential, such as the influenza A(H7N9) virus. Although the air pump flow rate and sample collection times used in our study have been demonstrated to efficiently capture aerosolized influenza virus and RSV RNA [33] [34] [35] , it is possible that these parameters are not optimal for capturing the other respiratory virus DNA/RNA targeted in our study. abstract: As a leading global city with a high population density, Singapore is at risk for the introduction of novel biological threats. This risk has been recently reinforced by human epidemics in Singapore of SARS coronavirus, 2009 pandemic H1N1 influenza A virus, and enterovirus 71. Other major threats to Singapore include MERS-coronavirus and various avian and swine influenza viruses. The ability to quickly identify and robustly track such threats to initiate an early emergency response remains a significant challenge. In an effort to enhance respiratory virus surveillance in Singapore, our team conducted a pilot study employing a noninvasive bioaerosol sampling method to detect respiratory viruses in Singapore’s Mass Rapid Transit (MRT) network. Over a period of 52 weeks, 89 aerosol samples were collected during peak MRT ridership hours. Nine (10%) tested positive for adenovirus, four (4.5%) tested positive for respiratory syncytial virus type A, and one (1%) tested positive for influenza A virus using real-time RT-PCR/PCR. To our knowledge, this is the first time molecular evidence for any infectious respiratory agent has been collected from Singapore’s MRT. Our pilot study data support the possibility of employing bioaerosol samplers in crowded public spaces to noninvasively monitor for respiratory viruses circulating in communities. url: https://doi.org/10.1038/s41598-018-35896-1 doi: 10.1038/s41598-018-35896-1 id: cord-263567-6uacorpp author: Collignon, C. title: Polyarthrite associée à une leishmaniose chez un jeune chien date: 2009-03-31 words: 3626.0 sentences: 323.0 pages: flesch: 58.0 cache: ./cache/cord-263567-6uacorpp.txt txt: ./txt/cord-263567-6uacorpp.txt summary: Lors du dernier examen, après deux mois de traitement, la PCR sur sang est négative, et seule une légère protéinurie persiste. La période d''incubation peut être extrêmement variable avant l''apparition de la maladie (trois à 12 mois à quatre à 15 ans, selon les auteurs) [1, [5] [6] [7] [8] ; dans une étude portant sur 390 chiens en Espagne, deux pics d''âges sont notés : trois et sept ans, et plus. En effet, une étude montre qu''en dépit d''une thérapeutique combinée (antimoniate de méglumine et allopurinol pendant un mois) en relais longue durée avec de l''allopurinol, les chiens cliniquement améliorés restent PCR positifs dans les tissus (moelle ou noeuds lymphatiques) [26] [27] [28] . Ainsi, il peut être intéressant d''arrêter l''antimoniate de méglumine dès que les signes cliniques ont disparu et que la PCR sur sang est négative, afin de diminuer les effets secondaires (surtout hépatiques et rénaux), liés à l''utilisation de cette molécule [29] , et de réduire le coût du traitement. abstract: Résumé Un chien de race Cane corso, mâle, âgé de deux ans, est examiné en consultation pour abattement et dysorexie. Il présente également une boiterie d’appui persistante du membre postérieur gauche depuis plusieurs semaines. À l’examen clinique, le chien est en hyperthermie (39,3°C) ; il a des saignements spontanés des babines, une polyadénomégalie périphérique, notamment des nœuds lymphatiques poplités, ainsi qu’une splénomégalie. Par ailleurs, l’examen orthopédique montre que les tarses sont gonflés et chauds. Cela laisse suspecter une synovite bilatérale. L’examen cytologique des nœuds lymphatiques et du liquide synovial permet de diagnostiquer avec certitude une leishmaniose. En effet, de très nombreuses formes amastigotes sont visualisées dans les macrophages. Une analyse par PCR sur sang, liquide synovial, suc ganglionnaire et ponction de moelle osseuse écarte l’ehrlichiose et la borréliose. Une PCR leishmaniose sur sang est également effectuée pour suivre la réponse au traitement. Malgré une forte infestation, une anémie non régénérative, une leucopénie, des signes de néphropathie et l’apparition d’une épistaxis, le chien est traité avec succès principalement à l’aide d’antimoniate de méglumine, d’allopurinol, de corticostéroïdes, associés à des antibiotiques. Summary A 2-year-old male Cane Corso dog was presented with lameness anorexia and lethargy since several weeks. At presentation, the animal had fever (39.3°C), generalised lymphadenopathy (in particular popliteal lymph nodes), splenomegaly and bilateral swelling of the tarsal joints. Synovial fluid from tarsal joints and fine-needle aspirations of lymph nodes were submitted to cytological examination: Leishmania amastigotes contained in macrophages were observed. Some other causes of polyarthritis (Borrelia and Ehrlichia) were excluded by PCR. The follow-up of the treatment was done with PRC Leishmania on blood. Although the animal had non-regenerative anaemia, nephropathy, leukopenia and epistaxis, it was successfully treated with meglumine antimoniate, allopurinol, corticoids, and antibiotherapy. url: https://api.elsevier.com/content/article/pii/S075818820900003X doi: 10.1016/j.anicom.2009.01.002 id: cord-017867-8cn4c6cu author: Collántes-Fernández, Esther title: Trichomonas date: 2017-11-08 words: 24060.0 sentences: 1231.0 pages: flesch: 48.0 cache: ./cache/cord-017867-8cn4c6cu.txt txt: ./txt/cord-017867-8cn4c6cu.txt summary: In addition, the OIE Terrestrial Manual also provides recommendations for PCR analyses, which can be applied in combination either with or after culture as an ancillary test or-more often-direct as the primary test to examine bovine samples-i.e., preputial material, uterine or vaginal secretions, or abomasal content of aborted fetuses. In bovine tritrichomonosis cultivation became an important diagnostic tool, because parasite numbers in bovine samples-e.g., preputial smegma or cervico-vaginal mucus-are usually too low to be detected by direct microscopy and a multiplication of parasites after a few days of cultivation increases the chance to find infected bulls. Sensitivity and specificity of culture and PCR of smegma samples of bulls experimentally infected with Tritrichomonas foetus Evaluation of a PCR test for the diagnosis of Tritrichomonas foetus infection in bulls: effects of sample collection method, storage and transport medium on the test Comparison of sampling and culture methods for the diagnosis of Tritrichomonas foetus infection in bulls abstract: The most widely known trichomonad in veterinary medicine is Tritrichomonas foetus. It is the etiologic agent of bovine tritrichomonosis, a sexually transmitted disease in extensively managed herds throughout many geographic regions worldwide. The same trichomonad species is also regarded as the causative agent of chronic diarrhea in the domestic cat, although more recent studies observed molecular differences between bovine- and feline-derived T. foetus. Trichomonosis in cats has a worldwide distribution and is mainly present among cats from high-density housing environments. Other trichomonads are found as inhabitants of the gastrointestinal tract in birds, such as Trichomonas gallinae. Particularly, Columbiformes, Falconiformes, Strigiformes, and wild Passeriformes can be severely affected by avian trichomonads. Diagnosis of trichomonosis is often complicated by the fragility of the parasite. To ensure valid test results, it is essential to collect and handle specimens in the right way prior to analysis. Cultivation tests, the specific amplification of parasites, or a combination of both test methods is the most efficient and most commonly used way to diagnose trichomonosis in animals. Bovine tritrichomonosis is mainly controlled by the identification and withdrawal of infected animals from bovine herds. The control of feline and avian trichomonosis relies mainly on preventive measures. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122547/ doi: 10.1007/978-3-319-70132-5_14 id: cord-289017-vwye3pk9 author: Comach, Guillermo title: Sentinel Surveillance of Influenza-Like Illness in Two Hospitals in Maracay, Venezuela: 2006–2010 date: 2012-09-11 words: 6262.0 sentences: 301.0 pages: flesch: 47.0 cache: ./cache/cord-289017-vwye3pk9.txt txt: ./txt/cord-289017-vwye3pk9.txt summary: CONCLUSIONS/SIGNIFICANCE: Influenza viruses were the most commonly detected viral organisms among patients with acute febrile respiratory illnesses presenting at two hospitals in Maracay, Venezuela. Recent prospective studies, which utilized more sensitive methods for detecting respiratory viruses such as multiplex polymerase chain reaction (PCR), have similarly demonstrated that the highest rates of viral respiratory infection occur among children and the frequency of infection tends to decrease with age due to increasing acquired immunity [8] . On the other hand, the percentage of influenza viruses (not including pH1N1) detected in our study during a similar period of time, but in different years accounted for the significant differences found in both studies: a) the collection, preservation and further processing of respiratory samples, and b) the type of cells and IFA reagents used for virus isolation and identification. In contrast, a prospective study of ILI among Brazilian adults, which utilized viral isolation and RT-PCR testing on respiratory samples, detected rhinoviruses in 19.6% of patients [14] . abstract: BACKGROUND: Limited information exists on the epidemiology of acute febrile respiratory illnesses in tropical South American countries such as Venezuela. The objective of the present study was to examine the epidemiology of influenza-like illness (ILI) in two hospitals in Maracay, Venezuela. METHODOLOGY/PRINCIPAL FINDINGS: We performed a prospective surveillance study of persons with ILI who presented for care at two hospitals in Maracay, Venezuela, from October 2006 to December 2010. A respiratory specimen and clinical information were obtained from each participant. Viral isolation and identification with immunofluorescent antibodies and molecular methods were employed to detect respiratory viruses such as adenovirus, influenza A and B, parainfluenza, and respiratory sincytial virus, among others. There were 916 participants in the study (median age: 17 years; range: 1 month – 86 years). Viruses were identified in 143 (15.6%) subjects, and one participant was found to have a co-infection with more than one virus. Influenza viruses, including pandemic H1N1 2009, were the most frequently detected pathogens, accounting for 67.4% (97/144) of the viruses detected. Adenovirus (15/144), parainfluenza virus (13/144), and respiratory syncytial virus (11/144) were also important causes of ILI in this study. Pandemic H1N1 2009 virus became the most commonly isolated influenza virus during its initial appearance in 2009. Two waves of the pandemic were observed: the first which peaked in August 2009 and the second - higher than the preceding - that peaked in October 2009. In 2010, influenza A/H3N2 re-emerged as the most predominant respiratory virus detected. CONCLUSIONS/SIGNIFICANCE: Influenza viruses were the most commonly detected viral organisms among patients with acute febrile respiratory illnesses presenting at two hospitals in Maracay, Venezuela. Pandemic H1N1 2009 influenza virus did not completely replace other circulating influenza viruses during its initial appearance in 2009. Seasonal influenza A/H3N2 was the most common influenza virus in the post-pandemic phase. url: https://www.ncbi.nlm.nih.gov/pubmed/22984519/ doi: 10.1371/journal.pone.0044511 id: cord-263538-0wozg085 author: Cooch, P. B. title: Supervised self-collected SARS-CoV-2 testing in indoor summer camps to inform school reopening date: 2020-10-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Background and Objectives: Testing strategies for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in school settings are needed to assess the efficacy of infection mitigation strategies and inform school reopening policies. We hypothesized that supervised serial self-collected non-nasopharyngeal testing in summer camp settings would be acceptable and feasible. Methods: We performed a cohort study at two urban day camps for kindergarten-8th graders in June and July 2020. Eligible participants were campers, up to two adult household contacts, and camp staff. We assessed participation rates for providing, at two time points, supervised, self-collected anterior nares samples for reverse transcription polymerase chain reaction (RT-PCR) and saliva samples for antibody testing. We qualitatively assessed testing feasibility and adherence to stated camp infection mitigation strategies. Results: 76% (186/246) of eligible participants consented. The cohort completing both rounds of testing (n=163) comprised 67 campers, 76 household contacts, and 20 staff. Among those present, 100% of campers and staff completed test collection at both time points. Testing was feasible to implement, including staff participation supervising camper test collection. No virus was detected by RT-PCR; seven participants had antibodies. Observed adherence to stated camp mitigation policies for masking, physical distancing, and stable cohorting was generally high. Conclusions: Supervised, self-collected serial anterior nasal and saliva-based SARS-CoV-2 testing was acceptable, with successful repeated participation by children ages 5-14. This strategy for testing and the observed infection mitigation practices comprise potential core components for safe school reopening. url: https://doi.org/10.1101/2020.10.21.20214338 doi: 10.1101/2020.10.21.20214338 id: cord-000664-085v7n6k author: Cordey, Samuel title: Pilot Evaluation of RT-PCR/Electrospray Ionization Mass Spectrometry (PLEX-ID/Flu assay) on Influenza-Positive Specimens date: 2012-05-09 words: 2027.0 sentences: 100.0 pages: flesch: 43.0 cache: ./cache/cord-000664-085v7n6k.txt txt: ./txt/cord-000664-085v7n6k.txt summary: The PLEX-ID/Flu assay has been recently developed to enable the detection and typing of influenza viruses based on the RT-PCR/electrospray ionization mass spectrometry technology. Taken together, and although our results need to be confirmed by further prospective studies, the PLEX-ID/Flu assay detected positively and gave a typing result for 93% of all NPS detected positively by real-time RT-PCR, thus suggesting a potential role for influenza virus surveillance among other techniques. The typing performance of the PLEX-ID/Flu assay versus the Sanger-based sequencing method was then compared for all influenza specimens with low viral loads (C T values 30; 19 influenza A and 18 influenza B-positive NPS; Table 2 ). Based on a selection of positive NPS collected in Switzerland during the 2010-2011 influenza season, this study suggests that the PLEX-ID/Flu assay is a convenient platform for the detection, typing, and subtyping (lineage characterization for influenza B) of circulating influenza viruses. abstract: The PLEX-ID/Flu assay has been recently developed to enable the detection and typing of influenza viruses based on the RT-PCR/electrospray ionization mass spectrometry technology. This novel assay was evaluated for typing performance on 201 positive influenza A or B nasopharyngeal swab specimens (NPS) detected by real-time RT-PCR during the 2010-2011 season. The PLEX-ID/Flu assay detected and characterized 91.3% and 95.3% of all influenza A and B samples, respectively. All non-typeable influenza A and B specimens by the assay showed low viral loads with threshold cycle values ≥ 33. Taken together, and although our results need to be confirmed by further prospective studies, the PLEX-ID/Flu assay detected positively and gave a typing result for 93% of all NPS detected positively by real-time RT-PCR, thus suggesting a potential role for influenza virus surveillance among other techniques. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3355350/ doi: 10.2174/1874357901206010064 id: cord-346467-a0r4xh1c author: Cornelissen, Jan B. W. J. title: Mycoplasma detection by triplex real-time PCR in bronchoalveolar lavage fluid from bovine respiratory disease complex cases date: 2017-04-08 words: 4082.0 sentences: 188.0 pages: flesch: 50.0 cache: ./cache/cord-346467-a0r4xh1c.txt txt: ./txt/cord-346467-a0r4xh1c.txt summary: title: Mycoplasma detection by triplex real-time PCR in bronchoalveolar lavage fluid from bovine respiratory disease complex cases BACKGROUND: In this study we evaluated the RespoCheck Mycoplasma triplex real-time PCR for the detection in bronchoalveolar lavage fluid (BALF) of Mycoplasma (M.) dispar, M. RESULTS: The analytical sensitivity of the RespoCheck triplex real-time PCR was, as determined by spiking experiments of the Mycoplasma strains in Phosphate Buffered Saline, 300 colony forming units (cfu)/mL for M. To enable testing of testing for BRD associated pathogens in a routine setting, real-time PCRs for detection of viral, bacterial and mycoplasma pathogens in bronchoalveolar lavage fluid (BALF) of calves have been set up by the Central Veterinary Institute (Lelystad, The Netherlands) under the name RespoCheck. In this study we used the highly conserved 16S rRNA sequence to set up the RespoCheck Mycoplasma triplex real-time PCR assay for the specific detection of M. abstract: BACKGROUND: In this study we evaluated the RespoCheck Mycoplasma triplex real-time PCR for the detection in bronchoalveolar lavage fluid (BALF) of Mycoplasma (M.) dispar, M. bovis and M. bovirhinis, all three associated with bovine respiratory disease (BRD). Primers and probes of the RespoCheck Mycoplasma triplex real-time PCR are based on the V3/V4 region of the 16S rRNA gene of the three Mycoplasma species. RESULTS: The analytical sensitivity of the RespoCheck triplex real-time PCR was, as determined by spiking experiments of the Mycoplasma strains in Phosphate Buffered Saline, 300 colony forming units (cfu)/mL for M. dispar, and 30 cfu/mL for M. bovis or M. bovirhinis. The analytical sensitivity of the RespoCheck Mycoplasma triplex real-time PCRwas, as determined on purified DNA, 10 fg DNA per assay for M. dispar and 100 fg fo rM. bovis and M. bovirhinis. The analytical specificity of the RespoCheck Mycoplasma triplex real-time PCR was, as determined by testing Mycoplasmas strains (n = 17) and other bacterial strains (n = 107), 100, 98.2 and 99.1% for M. bovis, M. dispar and M. bovirhinis respectively. The RespoCheck Mycoplasma triplex real-time PCR was compared with the PCR/DGGE analysis for M. bovis, M. dispar and M. bovirhinis respectively by testing 44 BALF samples from calves. CONCLUSION: In conclusion, the RespoCheck PCR assay can be a valuable tool for timely and accurate detection of three Mycoplasma species associated with in bovine respiratory disease. url: https://doi.org/10.1186/s12917-017-1023-6 doi: 10.1186/s12917-017-1023-6 id: cord-327259-7o7fs4yb author: Correa, I. A. title: Boosting SARS-CoV-2 qRT-PCR detection combining pool sample strategy and mathematical modeling date: 2020-08-19 words: 4584.0 sentences: 265.0 pages: flesch: 56.0 cache: ./cache/cord-327259-7o7fs4yb.txt txt: ./txt/cord-327259-7o7fs4yb.txt summary: We aim to evaluate pooling tests in experimental procedures, as well as perform in silico statistical modeling analysis validated with specimen samples obtained from a mass testing program of Industry Federation of the State of Rio de Janeiro (Brazil). This data was validated with the results obtained in our mass testing program: statistical modeling predicted a cost saving of 48.0%, which in practice, was 51.5%, already considering the expenditures with pool sampling that were analyzed individually. To assess the advantages of the pooling approach, we used previous qRT-PCR results obtained in the diagnostic analyses performed with industrial workers of Rio de Janeiro state as a base to calculate the prevalence rates (%) of positive cases and to build the statistical modeling methodology. Our study adopted the statistical modeling approach and validated the data with pooling biological samples for COVID-19 diagnostic, confirming that the pool size must be selected according to the prevalence rate of positive cases in the population (Figure 2) . abstract: qRT-PCR is the gold standard technique available for SARS-CoV-2 detection. However, the long test run time and costs associated with this type of molecular testing are a challenge in the actual pandemic scenario. Due to high testing demand, pooling sample strategy is an interesting approach to allow cost savings. We aim to evaluate pooling tests in experimental procedures, as well as perform in silico statistical modeling analysis validated with specimen samples obtained from a mass testing program of Industry Federation of the State of Rio de Janeiro (Brazil). Although the sensitivity reduction in samples pooled with 32 individuals was observed, the high-test sensitivity is maintained even when 16 and 8 samples were pooled. The in silico analysis showed high-cost savings in populations with positive rates lower than 15.0% according to the pool size. This data was validated with the results obtained in our mass testing program: statistical modeling predicted a cost saving of 48.0%, which in practice, was 51.5%, already considering the expenditures with pool sampling that were analyzed individually. Our data confirmed that mathematical modeling is a powerful strategy to improve the pooling approach for SARS-CoV-2 mass testing around the world while maintaining high sensitivity and robustness. url: http://medrxiv.org/cgi/content/short/2020.08.16.20167536v1?rss=1 doi: 10.1101/2020.08.16.20167536 id: cord-281844-c0uhcatg author: Costa, Lusmaia D.C. title: Exacerbation of asthma and airway infection: is the virus the villain? date: 2014-12-31 words: 6547.0 sentences: 351.0 pages: flesch: 45.0 cache: ./cache/cord-281844-c0uhcatg.txt txt: ./txt/cord-281844-c0uhcatg.txt summary: Abstract Objective To review the available literature on the association between acute viral respiratory tract infection and the onset of asthma exacerbations, identifying the most prevalent viruses, detection methods, as well as preventive and therapeutic aspects. Studies using reverse transcriptase polymerase chain reaction (RT-PCR) as the detection technique, isolated or combined with traditional methods, observed positivity for respiratory viruses in up to 92.2% of episodes of acute asthma exacerbation in children. Several authors have performed studies aiming to detect viruses in respiratory secretions of exacerbated asthma patients, showing a prevalence of viral identification that varies with several factors, such as patient age, time of the year, method of sample collection, and method of viral detection. The use of viral detection techniques with high sensitivity and specificity has increased the identification of some respiratory viruses in children with asthma exacerbation. abstract: Abstract Objective To review the available literature on the association between acute viral respiratory tract infection and the onset of asthma exacerbations, identifying the most prevalent viruses, detection methods, as well as preventive and therapeutic aspects. Sources A search was conducted in PubMed, Lilacs, and SciELO databases, between the years 2002 and 2013, using the following descriptors: asthma exacerbation, virus, child, and acute respiratory infection. Summary of the findings A total of 42 original articles addressing the identification of respiratory viruses during episodes of asthma exacerbation were selected, mostly cross-sectional studies. There was a wide variation in the methodology of the assessed studies, particularly in relation to the children's age and methods of collection and viral detection. The results indicate that, in up to 92.2% of exacerbations, a viral agent was potentially the main triggering factor, and human rhinovirus was the most frequently identified factor. The pattern of viral circulation may have been responsible for the seasonality of exacerbations. The association between viral infections and allergic inflammation appears to be crucial for the clinical and functional uncontrolled asthma, but few studies have evaluated other triggering factors in association with viral infection. Conclusions Respiratory viruses are present in the majority of asthmatic children during episodes of exacerbation. The involved physiopathological mechanisms are yet to be fully established, and the synergism between allergic inflammation and viral infection appears to determine uncontrolled disease. The role of other triggering and protective agents is yet to be clearly determined. url: https://doi.org/10.1016/j.jped.2014.07.001 doi: 10.1016/j.jped.2014.07.001 id: cord-260647-7bjhobg7 author: Coudray-Meunier, Coralie title: A Novel High-Throughput Method for Molecular Detection of Human Pathogenic Viruses Using a Nanofluidic Real-Time PCR System date: 2016-01-29 words: 5581.0 sentences: 278.0 pages: flesch: 48.0 cache: ./cache/cord-260647-7bjhobg7.txt txt: ./txt/cord-260647-7bjhobg7.txt summary: A nanofluidic real-time PCR system was used to develop novel high-throughput methods for qualitative molecular detection (RT-qPCR array) and quantification of human pathogenic viruses by digital RT-PCR (RT-dPCR). The aim of this study was to develop real time RT-PCR assays for detection of a total of 19 human enteric viruses (including 3 genogroupes of norovirus and 4 coronaviruses) and two control process viruses (mengovirus and murine norovirus) generally used for monitoring the recovery of viral foodstuff extraction methods. The sensitivity of conventional qPCR assays targeting 21 viral genomes was compared to the quantitative digital RT-PCR array and to the qualitative nanofluidic real-time PCR array performed on Fluidigm''s BioMark System. Similarly, by testing genomes from viruses in stools and RNA from virus production in cells, the limit of detection (LOD) as determined by RT-dPCR was respectively 1.5 to 3.4 log 10 and 1.6 to 2.1 log 10 lower than the expected copy numbers calculated via the standard curve by RT-qPCR. abstract: Human enteric viruses are recognized as the main causes of food- and waterborne diseases worldwide. Sensitive and quantitative detection of human enteric viruses is typically achieved through quantitative RT-PCR (RT-qPCR). A nanofluidic real-time PCR system was used to develop novel high-throughput methods for qualitative molecular detection (RT-qPCR array) and quantification of human pathogenic viruses by digital RT-PCR (RT-dPCR). The performance of high-throughput PCR methods was investigated for detecting 19 human pathogenic viruses and two main process controls used in food virology. The conventional real-time PCR system was compared to the RT-dPCR and RT-qPCR array. Based on the number of genome copies calculated by spectrophotometry, sensitivity was found to be slightly better with RT-qPCR than with RT-dPCR for 14 viruses by a factor range of from 0.3 to 1.6 log(10). Conversely, sensitivity was better with RT-dPCR than with RT-qPCR for seven viruses by a factor range of from 0.10 to 1.40 log(10). Interestingly, the number of genome copies determined by RT-dPCR was always from 1 to 2 log(10) lower than the expected copy number calculated by RT-qPCR standard curve. The sensitivity of the RT-qPCR and RT-qPCR array assays was found to be similar for two viruses, and better with RT-qPCR than with RT-qPCR array for eighteen viruses by a factor range of from 0.7 to 3.0 log(10). Conversely, sensitivity was only 0.30 log(10) better with the RT-qPCR array than with conventional RT-qPCR assays for norovirus GIV detection. Finally, the RT-qPCR array and RT-dPCR assays were successfully used together to screen clinical samples and quantify pathogenic viruses. Additionally, this method made it possible to identify co-infection in clinical samples. In conclusion, given the rapidity and potential for large numbers of viral targets, this nanofluidic RT-qPCR assay should have a major impact on human pathogenic virus surveillance and outbreak investigations and is likely to be of benefit to public health. url: https://www.ncbi.nlm.nih.gov/pubmed/26824897/ doi: 10.1371/journal.pone.0147832 id: cord-287466-ag5y781z author: Cowley, J.A. title: Nidoviruses of Fish and Crustaceans date: 2016-09-09 words: 17715.0 sentences: 760.0 pages: flesch: 47.0 cache: ./cache/cord-287466-ag5y781z.txt txt: ./txt/cord-287466-ag5y781z.txt summary: As evidenced by the presence of genomic-length and sgmRNA-length replicativeintermediate double-stranded (ds)RNAs in shrimp cells infected with gill-associated virus (GAV) (Cowley et al., 2002a) , the type species okavirus (Cowley et al., 2012) , it is speculated that transcription termination of the antisense RNAs might occur at precise positions, resulting in common 3′-termini, and that these then act directly as promoters for transcription initiation of the genomic and sgmRNAs. In all other nidoviruses, however, and for the longest of the sgmRNAs transcribed by toroviruses, the (−) and (+) strand sgmRNAs are transcribed using a far more complex discontinuous process involving the splicing of a common "anti-leader" sequence derived from the genome 5′-terminus to each (−) strand sgmRNA that then acts as a universal promoter for transcribing each (+) strand sgmRNA (Pasternak et al., 2006; Sawicki et al., 2007; Smits et al., 2005; van Vliet et al., 2002) . Nidoviruses of aquatic species include the rod-shaped okaviruses GAV and yellow head virus (YHV) that primarily infect Penaeid shrimp (Longyant et al., 2005; Flegel, 2012; Flegel et al., 1997a; Cowley et al., 2000a Cowley et al., , 2002a Cowley and Walker, 2002; Sittidilokratna et al., 2008) and a morphologically similar virus with a ~22 kb ssRNA genome detected in diseased Chinese mitten crabs (Zhang and Bonami, 2007) . abstract: Viruses with diverse virion architectures demarcated into four families in the order Nidovirales have been discovered in vertebrate mammalian and fish species, as well as in invertebrate crustacean and mosquito species. The order is unified by nidoviruses sharing intermediate (12.7 kb) to very long (31.7 kb) (+) ssRNA genomes, each possessing a long 5′-terminal gene encoding overlapping ORF1a and ORF1b reading frames that contain a diversity of functionally related enzymes and that are translated in toto using a −1 ribosomal frameshift mechanism, as well as by semiconserved strategies for transcribing a nested set of 3′-coterminal subgenomic mRNAs that translate the viral proteins. The nidovirus that is most important to an aquaculture species is yellow head virus (YHV), which causes disease in shrimp farmed throughout the Eastern Hemisphere and is classified in the genus Okavirus, family Roniviridae. Fathead minnow nidovirus, genus Bafinivirus, subfamily Torovirinae, family Coronaviridae, also causes disease in minnows grown for the baitfish industry in the United States. Virions similar in morphology to okaviruses and bafiniviruses have also been detected in several crab species. Of these, however, only Eriocheir sinensis ronivirus, which causes disease in the Chinese mitten crab, an important freshwater aquaculture species in China, has been shown to possess a ~22 kb ssRNA genome that supports its being a nidovirus, but its taxonomic classification awaits genome sequence analysis. This chapter provides an overview of the structure, replication and biology of these viruses with a particular focus on YHV disease characteristics, diagnostic methods and disease prevention strategies. url: https://www.sciencedirect.com/science/article/pii/B9780128015735000322 doi: 10.1016/b978-0-12-801573-5.00032-2 id: cord-284372-v95fzp8n author: Coyle, Peter V title: A touchdown nucleic acid amplification protocol as an alternative to culture backup for immunofluorescence in the routine diagnosis of acute viral respiratory tract infections date: 2004-10-25 words: 4717.0 sentences: 224.0 pages: flesch: 43.0 cache: ./cache/cord-284372-v95fzp8n.txt txt: ./txt/cord-284372-v95fzp8n.txt summary: title: A touchdown nucleic acid amplification protocol as an alternative to culture backup for immunofluorescence in the routine diagnosis of acute viral respiratory tract infections To overcome this problem we developed a diagnostic molecular strip which combined a generic nested touchdown protocol with in-house primer master-mixes that could recognise 12 common respiratory viruses. CONCLUSIONS: The touchdown protocol with pre-dispensed primer master-mixes was suitable for replacing virus culture for the diagnosis of respiratory viruses which were negative by immunofluorescence. To test the feasibility of its routine use we needed to clinically validate its performance in a routine setting on specimens tested in parallel with our standard immunofluorescence protocol for the diagnosis of acute virus respiratory infections. In conclusion the use of the touchdown protocol with pre-dispensed and quality checked primer master-mixes was suitable for replacing virus culture for the diagnosis of respiratory viruses for immunofluorescence negative specimens. abstract: BACKGROUND: Immunofluorescence and virus culture are the main methods used to diagnose acute respiratory virus infections. Diagnosing these infections using nucleic acid amplification presents technical challenges, one of which is facilitating the different optimal annealing temperatures needed for each virus. To overcome this problem we developed a diagnostic molecular strip which combined a generic nested touchdown protocol with in-house primer master-mixes that could recognise 12 common respiratory viruses. RESULTS: Over an 18 month period a total of 222 specimens were tested by both immunofluorescence and the molecular strip. The specimens came from 103 males (median age 3.5 y), 80 females (median age 9 y) and 5 quality assurance scheme specimens. Viruses were recovered from a number of specimen types including broncho-alveolar lavage, nasopharyngeal secretions, sputa, post-mortem lung tissue and combined throat and nasal swabs. Viral detection by IF was poor in sputa and respiratory swabs. A total of 99 viruses were detected in the study from 79 patients and 4 quality control specimens: 31 by immunofluorescence and 99 using the molecular strip. The strip consistently out-performed immunofluorescence with no loss of diagnostic specificity. CONCLUSIONS: The touchdown protocol with pre-dispensed primer master-mixes was suitable for replacing virus culture for the diagnosis of respiratory viruses which were negative by immunofluorescence. Results by immunofluorescence were available after an average of 4–12 hours while molecular strip results were available within 24 hours, considerably faster than viral culture. The combined strip and touchdown protocol proved to be a convenient and reliable method of testing for multiple viruses in a routine setting. url: https://www.ncbi.nlm.nih.gov/pubmed/15504232/ doi: 10.1186/1471-2180-4-41 id: cord-262592-0rdiosxd author: Cuevas, José M. title: Human norovirus hyper-mutation revealed by ultra-deep sequencing date: 2016-04-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Human noroviruses (NoVs) are a major cause of gastroenteritis worldwide. It is thought that, similar to other RNA viruses, high mutation rates allow NoVs to evolve fast and to undergo rapid immune escape at the population level. However, the rate and spectrum of spontaneous mutations of human NoVs have not been quantified previously. Here, we analyzed the intra-patient diversity of the NoV capsid by carrying out RT-PCR and ultra-deep sequencing with 100,000-fold coverage of 16 stool samples from symptomatic patients. This revealed the presence of low-frequency sequences carrying large numbers of U-to-C or A-to-G base transitions, suggesting a role for hyper-mutation in NoV diversity. To more directly test for hyper-mutation, we performed transfection assays in which the production of mutations was restricted to a single cell infection cycle. This confirmed the presence of sequences with multiple U-to-C/A-to-G transitions, and suggested that hyper-mutation contributed a large fraction of the total NoV spontaneous mutation rate. The type of changes produced and their sequence context are compatible with ADAR-mediated editing of the viral RNA. url: https://api.elsevier.com/content/article/pii/S1567134816301435 doi: 10.1016/j.meegid.2016.04.017 id: cord-001932-sklwt76a author: Cunningham, Scott A. title: Rapid PCR Detection of Mycoplasma hominis, Ureaplasma urealyticum, and Ureaplasma parvum date: 2013-03-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Objective. We compared laboratory developed real-time PCR assays for detection of Mycoplasma hominis and for detection and differentiation of Ureaplasma urealyticum and parvum to culture using genitourinary specimens submitted for M. hominis and Ureaplasma culture. Methods. 283 genitourinary specimens received in the clinical bacteriology laboratory for M. hominis and Ureaplasma species culture were evaluated. Nucleic acids were extracted using the Total Nucleic Acid Kit on the MagNA Pure 2.0. 5 μL of the extracts were combined with 15 μL of each of the two master mixes. Assays were performed on the LightCycler 480 II system. Culture was performed using routine methods. Results. M. hominis PCR detected 38/42 M. hominis culture-positive specimens, as well as 2 that were culture negative (sensitivity, 90.5%; specificity, 99.2%). Ureaplasma PCR detected 139/144 Ureaplasma culture-positive specimens, as well as 9 that were culture negative (sensitivity, 96.5%; specificity, 93.6%). Of the specimens that tested positive for Ureaplasma species, U. urealyticum alone was detected in 33, U. parvum alone in 109, and both in 6. Conclusion. The described PCR assays are rapid alternatives to culture for detection of M. hominis and Ureaplasma species, and, unlike culture, the Ureaplasma assay easily distinguishes U. urealyticum from parvum. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4745450/ doi: 10.1155/2013/168742 id: cord-268094-ubz0q7e9 author: Curland, N. title: Investigation into diseases in free-ranging ring-necked pheasants (Phasianus colchicus) in northwestern Germany during population decline with special reference to infectious pathogens date: 2018-02-06 words: 8168.0 sentences: 451.0 pages: flesch: 46.0 cache: ./cache/cord-268094-ubz0q7e9.txt txt: ./txt/cord-268094-ubz0q7e9.txt summary: title: Investigation into diseases in free-ranging ring-necked pheasants (Phasianus colchicus) in northwestern Germany during population decline with special reference to infectious pathogens In the present study, carcasses of 258 deceased free-ranging pheasants of different age groups, predominantly adult pheasants, collected over a period of 4 years in the states of Lower Saxony, North Rhine–Westphalia and Schleswig-Holstein, were examined pathomorphologically, parasitologically, virologically and bacteriologically, with a focus set on infectious pathogens. In China, antibodies against infectious bursal disease virus (IBDV) were detected in 14 out of 40 samples of free-ranging pheasants (Gu et al. The aim of the present study was to elucidate pathogens in free-ranging pheasants during the current population decline in Northwestern Germany using pathomorphological, virological, microbiological and parasitological investigations. Non-purulent mostly perivascularly accentuated inflammations with different cellular compositions and gradual variable infiltrations of lymphocytes, plasma cells and macrophages were detected in 68 birds (68.7% of affected pheasants) (Fig. 2) . abstract: The population of ring-necked pheasants (Phasianus colchicus) is decreasing all over Germany since the years 2008/2009. Besides impacts of habitat changes caused by current rates of land conversion, climatic influences or predators, a contribution of infectious pathogens needs also to be considered. Infectious and non-infectious diseases in free-living populations of ring-necked pheasants have been scarcely investigated so far. In the present study, carcasses of 258 deceased free-ranging pheasants of different age groups, predominantly adult pheasants, collected over a period of 4 years in the states of Lower Saxony, North Rhine–Westphalia and Schleswig-Holstein, were examined pathomorphologically, parasitologically, virologically and bacteriologically, with a focus set on infectious pathogens. A periocular and perinasal dermatitis of unknown origin was present in 62.3% of the pheasants. Additional alterations included protozoal cysts in the skeletal musculature (19.0%), hepatitis (21.7%), enteritis (18.7%), gastritis (12.6%), and pneumonia (11.7%). In single cases, neoplasms (2.6%) and mycobacteriosis (1.7%) occurred. Further findings included identification of coronaviral DNA from trachea or caecal tonsils (16.8%), siadenoviral DNA (7.6%), avian metapneumoviral RNA (6.6%), and infectious bursal disease viral RNA (3.7%). Polymerase chain reaction (PCR) on herpesvirus, avian influenza virus (AIV), paramyxovirus type 1 (PMV-1), avian encephalomyelitis virus (AEV), and chlamydia were negative. Based on the present results, there is no indication of a specific pathogen as a sole cause for population decline in adult pheasants. However, an infectious disease can still not be completely excluded as it may only affect reproduction effectivity or a certain age group of pheasants (e.g., chicks) which were not presented in the study. url: https://www.ncbi.nlm.nih.gov/pubmed/32214944/ doi: 10.1007/s10344-018-1173-2 id: cord-308655-zntwwqod author: Dabisch-Ruthe, Mareike title: Comparison of three multiplex PCR assays for the detection of respiratory viral infections: evaluation of xTAG respiratory virus panel fast assay, RespiFinder 19 assay and RespiFinder SMART 22 assay date: 2012-07-24 words: 5799.0 sentences: 312.0 pages: flesch: 48.0 cache: ./cache/cord-308655-zntwwqod.txt txt: ./txt/cord-308655-zntwwqod.txt summary: title: Comparison of three multiplex PCR assays for the detection of respiratory viral infections: evaluation of xTAG respiratory virus panel fast assay, RespiFinder 19 assay and RespiFinder SMART 22 assay METHODS: The analytical sensitivity of three multiplex PCR assays, RespiFinder-19, RespiFinder-SMART-22 and xTAG-Respiratory-Virus-Panel-Fast-Assay (RVP), were compared to monoplex real-time PCR with quantified standardized control material. RESULTS: To compare the analytical sensitivity of the multiplex assays, samples were inoculated with 13 different quantified viruses in the range of 10(1) to 10(5) copies/ml. This study presents the first comparison of the analytical sensitivity of three novel multiplex PCR methods, the RespiFinder-19 assay, RespiFinder-SMART(Single tube Multiplex Amplification in Real-Time)-22 assay (both PathoFinder, Maastricht, Netherlands) and the xTAG Respiratory Virus Panel Fast Assay (Abbott Molecular, Wiesbaden, Germany), with quantified virus control material. Previous studies with clinical samples showed that the sensitivity and specificity of the RVP assay was 78.8% and 99.6%, respectively, compared to real-time PCR-methods, that are currently declared as the gold standard [21] . abstract: BACKGROUND: A broad spectrum of pathogens is causative for respiratory tract infections, but symptoms are mostly similar. Therefore, the identification of the causative viruses and bacteria is only feasible using multiplex PCR or several monoplex PCR tests in parallel. METHODS: The analytical sensitivity of three multiplex PCR assays, RespiFinder-19, RespiFinder-SMART-22 and xTAG-Respiratory-Virus-Panel-Fast-Assay (RVP), were compared to monoplex real-time PCR with quantified standardized control material. All assays include the most common respiratory pathogens. RESULTS: To compare the analytical sensitivity of the multiplex assays, samples were inoculated with 13 different quantified viruses in the range of 10(1) to 10(5) copies/ml. Concordant results were received for rhinovirus, whereas the RVP detected influenzavirus, RSV and hMPV more frequently in low concentrations. The RespiFinder-19 and the RespiFinder-SMART-22 showed a higher analytical sensitivity for adenoviruses and coronaviruses, whereas the RVP was incapable to detect adenovirus and coronavirus in concentrations of 10(4) copies/ml. The RespiFinder-19 and RespiFinder-SMART-22A did not detect influenzaviruses (10(4) copies/ml) and RSV (10(3) copies/ml). The detection of all 13 viruses in one sample was only achieved using monoplex PCR. To analyze possible competitive amplification reactions between the different viruses, samples were further inoculated with only 4 different viruses in one sample. Compared to the detection of 13 viruses in parallel, only a few differences were found. The incidence of respiratory viruses was compared in tracheal secretion (TS) samples (n = 100) of mechanically ventilated patients in winter (n = 50) and summer (n = 50). In winter, respiratory viruses were detected in 32 TS samples (64%) by RespiFinder-19, whereas the detection rate with RVP was only 22%. The most frequent viruses were adenovirus (32%) and PIV-2 (20%). Multiple infections were detected in 16 TS samples (32%) by RespiFinder-19. Fewer infections were found in summer (RespiFinder-19: 20%; RVP: 6%). All positive results were verified using monoplex PCR. CONCLUSIONS: Multiplex PCR tests have a broad spectrum of pathogens to test at a time. Analysis of multiple inoculated samples revealed a different focus of the detected virus types by the three assays. Analysis of clinical samples showed a high concordance of detected viruses by the RespiFinder-19 compared to monoplex tests. url: https://www.ncbi.nlm.nih.gov/pubmed/22828244/ doi: 10.1186/1471-2334-12-163 id: cord-338582-o976nab9 author: Dahlhausen, Bob title: Future Veterinary Diagnostics date: 2010-09-19 words: 9199.0 sentences: 511.0 pages: flesch: 35.0 cache: ./cache/cord-338582-o976nab9.txt txt: ./txt/cord-338582-o976nab9.txt summary: Genome sequencing has allowed efficient, sensitive, and specific diagnostic assays to be developed based on the detection of nucleic acids. PCR uses the highly specific molecular recognition ability of Watson-Crick base pairing to provide the selectivity needed for a nucleic acid probe to bind to a targeted DNA sequence and allow for its exponential amplification. It has been used to develop rapid diagnostic tests for several pathogenic viruses with singlestranded RNA genomes, including influenza A, 13 footand-mouth disease virus, 14 and severe acute respiratory syndrome (SARS)-associated coronavirus. DNA microarrays also permit relatively rapid interrogation of a clinical sample against thousands of genetic targets, allowing for simultaneous detection and discrimination among hundreds of pathogenic agents of veterinary interest. Unlike PCR technology where the target agent must be known to use specific test primers, microarrays can allow for the rapid diagnosis of multiple pathogenic agents in disease outbreaks and epidemics of unknown etiology. abstract: The development of rapid, accurate, and sensitive diagnostic methods for detecting pathogens is the basis for treating, controlling, and eradicating infectious diseases of veterinary importance. Scientific and technological advancements have revolutionized the field of veterinary diagnostics. Genome sequencing has allowed efficient, sensitive, and specific diagnostic assays to be developed based on the detection of nucleic acids. The integration of advances in biochemistry, proteomics, engineering, and medicine offers enormous potential for the rapid and accurate diagnosis of viral, microbial, genetic, and metabolic disease. In the future, polymerase chain reaction assays, microarray testing, genomic analysis, and metabolic profiling will be accomplished in a rapid, portable, sensitive, and cost-efficient manner. url: https://doi.org/10.1053/j.jepm.2010.05.006 doi: 10.1053/j.jepm.2010.05.006 id: cord-306780-9xelf8oh author: Dale, Timothy D. title: Enhancement of wildlife disease surveillance using multiplex quantitative PCR: development of qPCR assays for major pathogens in UK squirrel populations date: 2016-07-28 words: 6931.0 sentences: 371.0 pages: flesch: 54.0 cache: ./cache/cord-306780-9xelf8oh.txt txt: ./txt/cord-306780-9xelf8oh.txt summary: However, comparatively few wildlife epidemiological studies use quantitative PCR (qPCR) for pathogen detection, even fewer employ an internal control, to ensure confidence in negative results, and PCR''s ability to multiplex and therefore detect several targets in a single reaction is underutilised. Tests on infected squirrel tissue demonstrate that simple swab samples (particularly from distal antebrachial skin) are sufficient to detect and identify the relative quantity of SQPV DNA in both squirrel species, while rectal swabs and blood cell pellets can be used to reliably indicate SADV infection. As grey squirrels appear asymptomatic, lower infection loads are recorded, and thus it is essential to use the more sensitive qPCR assays when screening for SQPV presence as part of a wildlife disease management programme for red squirrels. abstract: Rapid development in polymerase chain reaction (PCR) technology has revolutionised the speed and accuracy of many diagnostic assays. However, comparatively few wildlife epidemiological studies use quantitative PCR (qPCR) for pathogen detection, even fewer employ an internal control, to ensure confidence in negative results, and PCR’s ability to multiplex and therefore detect several targets in a single reaction is underutilised. Here, we describe the development of two multiplex qPCR assays for the red and grey squirrel that detect the pathogens squirrelpox virus (SQPV) and adenovirus in squirrels (SADV), both of which cause mortality in the red squirrel. Both assays use a section of the squirrel phosphoglycerate kinase gene as an endogenous internal control that identifies and compensates for both, inadequate sampling or PCR inhibition. Tests on infected squirrel tissue demonstrate that simple swab samples (particularly from distal antebrachial skin) are sufficient to detect and identify the relative quantity of SQPV DNA in both squirrel species, while rectal swabs and blood cell pellets can be used to reliably indicate SADV infection. These assays are sensitive and specific with an endogenous internal control providing confidence in negative results and allowing comparison across laboratories. Using such assays should prove advantageous in wildlife studies with limited resources while allowing the maximum data yield. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s10344-016-1031-z) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s10344-016-1031-z doi: 10.1007/s10344-016-1031-z id: cord-000014-e0ou9zjb author: Dare, Ryan K. title: Screening Pneumonia Patients for Mimivirus date: 2008-03-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Acanthamoeba polyphaga mimivirus (APM), a virus of free-living amebae, has reportedly caused human respiratory disease. Using 2 newly developed real-time PCR assays, we screened 496 respiratory specimens from 9 pneumonia-patient populations for APM. This virus was not detected in any specimen, which suggests it is not a common respiratory pathogen. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570813/ doi: 10.3201/eid1403.071027 id: cord-313000-as507p4t author: Dare, Ryan K. title: Human Coronavirus Infections in Rural Thailand: A Comprehensive Study Using Real-Time Reverse-Transcription Polymerase Chain Reaction Assays date: 2007-11-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Background. We sought to determine whether infections with human coronaviruses (HCoVs) 229E, OC43, HKU1, and NL63 are associated with pneumonia and to define the epidemiology of HCoV infection in rural Thailand. Methods. We developed a real-time reverse-transcription polymerase chain reaction (RT-PCR) assay panel for the recognized HCoV types and compared HCoV infections in patients hospitalized with pneumonia, outpatients with influenza-like illness, and asymptomatic control patients between September 2003 and August 2005. Results. During study year 1, 43 (5.9%) of 734 patients with pneumonia had HCoV infections; 72.1% of the infections were with OC43. During study year 2, when control patients were available, 21 (1.8%) of 1156 patients with pneumonia, 12 (2.3%) of 513 outpatients, and 6 (2.1%) of 281 control patients had HCoV infections. Compared with infection in control patients, infection with any HCoV type or with all types combined was not associated with pneumonia (adjusted odds ratio for all HCoV types, 0.67 [95% confidence interval, 0.26–1.75]; P= .40 ). HCoV infections were detected throughout both study years; 93.6% of OC43 infections in the first year occurred from January through March. Conclusions. HCoV infections were infrequently detected in rural Thailand by use of sensitive real-time RTPCR assays. We found no association between HCoV infection and illness. However, we noted year-to-year variation in the prevalence of HCoV strains, which likely influenced our results. url: https://www.ncbi.nlm.nih.gov/pubmed/17922396/ doi: 10.1086/521308 id: cord-318120-vfznyyz6 author: Dauner, Allison L. title: Development of a pan-serotype reverse transcription loop-mediated isothermal amplification assay for the detection of dengue virus date: 2015-05-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: During dengue outbreaks, acute diagnosis at the patient's point of need followed by appropriate supportive therapy reduces morbidity and mortality. To facilitate needed diagnosis, we developed and optimized a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay that detects all 4 serotypes of dengue virus (DENV). We used a quencher to reduce nonspecific amplification. The assay does not require expensive thermocyclers, utilizing a simple water bath to maintain the reaction at 63 °C. Results can be visualized using UV fluorescence, handheld readers, or lateral flow immunochromatographic tests. We report a sensitivity of 86.3% (95% confidence interval [CI], 72.7–94.8%) and specificity of 93.0% (95% CI, 83.0–98.1%) using a panel of clinical specimens characterized by DENV quantitative reverse transcription–polymerase chain reaction. This pan-serotype DENV RT-LAMP can be adapted to field-expedient formats where it can provide actionable diagnosis near the patient's point of need. url: https://www.sciencedirect.com/science/article/pii/S0732889315001571 doi: 10.1016/j.diagmicrobio.2015.05.004 id: cord-262485-sx2q5ol4 author: Davda, Jayeshkumar Narsibhai title: An Inexpensive RT-PCR Endpoint Diagnostic Assay for SARS-CoV-2 Using Nested PCR: Direct Assessment of Detection Efficiency of RT-qPCR Tests and Suitability for Surveillance date: 2020-06-08 words: 3255.0 sentences: 193.0 pages: flesch: 59.0 cache: ./cache/cord-262485-sx2q5ol4.txt txt: ./txt/cord-262485-sx2q5ol4.txt summary: The method employs real time quantitative reverse transcription polymerase chain reaction (RT-qPCR) of RNA extracted from nasopharyngeal (NP) swab samples, to measure amplification of a short segment of a viral gene in the course of a PCR reaction following reverse transcription of viral RNA. We developed and tested a RT-nPCR protocol comprising a multiplex primary RT-PCR for amplification of four SARS-CoV-2 amplicons and a control human RPP30 amplicon followed by a secondary nested PCR for individual amplicons 4 and visualization by agarose gel electrophoresis. Based on the experimentally measured false negative rate by RT-nPCR tests from this study we estimated that as many as 50% of positive samples may escape detection in single pass testing by RT-qPCR in an actual testing scenario. To detect the presence of SARS-CoV-2 in RNA isolated from NP swabs we performed a multiplex one-step RT-PCR on RNA from positive and negative samples using pooled primers for the four viral amplicons together with human RPP30 control. abstract: With a view to extending testing capabilities for the ongoing SARS-CoV-2 pandemic we have developed a test that lowers cost and does not require real time quantitative reverse transcription polymerase chain reaction (RT-qPCR). We developed a reverse transcription nested PCR endpoint assay (RT-nPCR) and showed that RT-nPCR has comparable performance to the standard RT-qPCR test. In the course of comparing the results of both tests, we found that the standard RT-qPCR test can have low detection efficiency (less than 50%) in a real testing scenario which may be only partly explained by low viral representation in many samples. This finding points to the importance of directly monitoring detection efficiency in test environments. We also suggest measures that would improve detection efficiency. url: https://doi.org/10.1101/2020.06.08.139477 doi: 10.1101/2020.06.08.139477 id: cord-313676-6rebpe57 author: De la Torre, David I. title: Enteric Virus Diversity Examined by Molecular Methods in Brazilian Poultry Flocks date: 2018-03-29 words: 5867.0 sentences: 295.0 pages: flesch: 55.0 cache: ./cache/cord-313676-6rebpe57.txt txt: ./txt/cord-313676-6rebpe57.txt summary: The most common enteric viruses affecting commercial flocks in Brazil include Fowl Adenovirus of group I (FAdV-I), Chicken Parvovirus (ChPV), Chicken Astrovirus (CAstV), Avian Nephritis Virus (ANV), Infectious Bronchitis Virus (IBV), Avian Reovirus (AReo), and Avian Rotavirus (ARtV). The main enteric viruses reported to cause enteric diseases are found in single and multiple infections and include the Fowl Adenovirus of group I (FAdV-I); Chicken Parvovirus (ChPV); two viruses from the Astroviridae family: Chicken Astrovirus (CAstV) and Avian Nephritis Virus (ANV); two viruses from the Reoviridae family: Avian Reovirus (AReo) and Avian Rotavirus (ARtV); and a member of the Coronaviridae family, Infectious Bronchitis Virus (IBV) [4, [6] [7] [8] [9] . The association of enteric virus with the age of broilers, breeders, and layers (Tables 4 and 5) showed that molecular diagnosis of these viruses can be performed at different stages of production, which can be useful in the control of vertical infections. abstract: Enteric viruses play an important role in the Brazilian poultry industry due to the economic impact of resulting low yields of broilers, layers, and breeders. The most common enteric viruses affecting commercial flocks in Brazil include Fowl Adenovirus of group I (FAdV-I), Chicken Parvovirus (ChPV), Chicken Astrovirus (CAstV), Avian Nephritis Virus (ANV), Infectious Bronchitis Virus (IBV), Avian Reovirus (AReo), and Avian Rotavirus (ARtV). The aim of this study was to identify single and multiple infections using data obtained from 270 samples from eleven Brazilian states, corresponding to the period between 2010 and 2017. This was accompanied by an analysis of the relationship between the age of birds, clinical signs, and geographical distribution, using Polymerase Chain Reaction (PCR) and Reverse Transcription-PCR (RT-PCR) techniques. Twenty-five profiles of virus combinations were detected. Single infections were encountered in 86.3% of samples, and multiple infections were present in the remaining 13.7%. Both single and multiple infections affected all kinds of commercial chickens with digestive problems, stunting syndrome, decreases in egg and meat production, increased mortality, and respiratory signs. FAdV-I, ChPV, CAstV, ANV, and ARtV were mostly detected in young broilers, in contrast with IBV, which was detected in hens from one to greater than 51 weeks of age. These results exhibit the complexity of enteric diseases and the still poorly understood role of each pathogen as a unique etiological agent. url: https://doi.org/10.3390/vetsci5020038 doi: 10.3390/vetsci5020038 id: cord-335323-p7cv79ig author: DeSerres, Joshua J. title: Best Practice Guidelines for the Management of Acute Craniomaxillofacial Trauma During the COVID-19 Pandemic date: 2020-05-11 words: 4205.0 sentences: 217.0 pages: flesch: 44.0 cache: ./cache/cord-335323-p7cv79ig.txt txt: ./txt/cord-335323-p7cv79ig.txt summary: The authors have proposed an algorithm for management of CMF trauma during the COVID-19 pandemic to ensure that urgent and emergent CMF injuries are addressed appropriately while optimizing the safety of surgeons and other healthcare providers. So far there has been a significant mortality of otolaryngologists and ophthalmologists in the Wuhan region, thought to be related to exposure to aerosolized virus from the nasal and oral airway mucosa from high risk procedures such as CMF trauma and sinus operations and in some patients despite the use of N95 masks. 19, 20 Given that the majority of CMF trauma procedures involve violation of the mucosa of the oral cavity and sinuses, these patients place the surgeons and the remainder of the operating room staff at high risk of exposure during the COVID-19 pandemic. abstract: Coronavirus disease 2019 (COVID-19) is an infectious disease that is caused by severe respiratory syndrome coronavirus 2. Although elective surgical procedures are being cancelled in many parts of the world during the COVID-19 pandemic, acute craniomaxillofacial (CMF) trauma will continue to occur and will need to be appropriately managed. Surgical procedures involving the nasal, oral, or pharyngeal mucosa carry a high risk of transmission due to aerosolization of the virus which is known to be in high concentration in these areas. Intraoperative exposure to high viral loads through aerosolization carries a very high risk of transmission, and the severity of the disease contracted in this manner is worse than that transmitted through regular community transmission. This places surgeons operating in the CMF region at particularly high risk during the pandemic. There is currently a paucity of information to delineate the best practice for the management of acute CMF trauma during the COVID-19 pandemic. In particular, a clear protocol describing optimal screening, timing of intervention and choice of personal protective equipment, is needed. The authors have proposed an algorithm for management of CMF trauma during the COVID-19 pandemic to ensure that urgent and emergent CMF injuries are addressed appropriately while optimizing the safety of surgeons and other healthcare providers. The algorithm is based on available evidence at the time of writing. As the COVID-19 pandemic continues to evolve and more evidence and better testing becomes available, the algorithm should be modified accordingly. url: https://www.ncbi.nlm.nih.gov/pubmed/32404623/ doi: 10.1097/scs.0000000000006654 id: cord-276271-3nz3169p author: Deborggraeve, Stijn title: T. cruzi OligoC-TesT: A Simplified and Standardized Polymerase Chain Reaction Format for Diagnosis of Chagas Disease date: 2009-06-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: PCR has evolved into one of the most promising tools for T. cruzi detection in the diagnosis and control of Chagas disease. However, general use of the technique is hampered by its complexity and the lack of standardization. METHODOLOGY: We here present the development and phase I evaluation of the T. cruzi OligoC-TesT, a simple and standardized dipstick format for detection of PCR amplified T. cruzi DNA. The specificity and sensitivity of the assay were evaluated on blood samples from 60 Chagas non-endemic and 48 endemic control persons and on biological samples from 33 patients, 7 reservoir animals, and 14 vectors collected in Chile. PRINCIPAL FINDINGS: The lower detection limits of the T. cruzi OligoC-TesT were 1 pg and 1 to 10 fg of DNA from T. cruzi lineage I and II, respectively. The test showed a specificity of 100% (95% confidence interval [CI]: 96.6%–100%) on the control samples and a sensitivity of 93.9% (95% CI: 80.4%–98.3%), 100% (95% CI: 64.6%–100%), and 100% (95% CI: 78.5%–100%) on the human, rodent, and vector samples, respectively. CONCLUSIONS: The T. cruzi OligoC-TesT showed high sensitivity and specificity on a diverse panel of biological samples. The new tool is an important step towards simplified and standardized molecular diagnosis of Chagas disease. url: https://doi.org/10.1371/journal.pntd.0000450 doi: 10.1371/journal.pntd.0000450 id: cord-296197-ohfhnpma author: Deborggraeve, Stijn title: A Simplified and Standardized Polymerase Chain Reaction Format for the Diagnosis of Leishmaniasis date: 2008-11-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Background. Definite diagnosis of Leishmania infections is based on demonstration of the parasite by microscopic analysis of tissue biopsy specimens or aspirate samples. However, microscopy generally shows low sensitivity and requires invasive sampling. Methods. We describe here the development of a simple and rapid test for the detection of polymerase chain reaction-amplified Leishmania DNA. A phase 1 evaluation of the text was conducted in clinical samples from 60 nonendemic and 45 endemic control subjects and from 44 patients with confirmed cutaneous leishmaniasis (CL), 12 with mucocutaneous leishmaniasis (MCL), and 43 with visceral leishmaniasis (VL) from Peru, Kenya, and Sudan. Results. The lower detection limits of the assay are 10 fg of Leishmania DNA and 1 parasite in 180 µL of blood. The specificity was 98.3% (95% confidence interval [CI], 91.1%–99.7%) and 95.6% (95% CI, 85.2%–98.8%) for nonendemic and endemic control samples, respectively, and the sensitivity was 93.2% (95% CI, 81.8%–97.7%), 91.7% (95% CI, 64.6%–98.5%), and 86% (95% CI, 72.7%–93.4%) for lesions from patients with CL or MCL and blood from patients with VL, respectively. Conclusions. The Leishmania OligoC-TesT showed high specificity and sensitivity in clinical samples and was able to detect the parasite in samples obtained by less invasive means, such as blood, lymph, and lesion scrapings. The assay is a promising new tool for simplified and standardized molecular detection of Leishmania parasites. url: https://www.ncbi.nlm.nih.gov/pubmed/18816188/ doi: 10.1086/592509 id: cord-255384-tljyx6ua author: Decaro, Nicola title: Full-Genome Analysis of a Canine Pneumovirus Causing Acute Respiratory Disease in Dogs, Italy date: 2014-01-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: An outbreak of canine infectious respiratory disease (CIRD) associated to canine pneumovirus (CnPnV) infection is reported. The outbreak occurred in a shelter of the Apulia region and involved 37 out of 350 dogs that displayed cough and/or nasal discharge with no evidence of fever. The full-genomic characterisation showed that the causative agent (strain Bari/100-12) was closely related to CnPnVs that have been recently isolated in the USA, as well as to murine pneumovirus, which is responsible for respiratory disease in mice. The present study represents a useful contribution to the knowledge of the pathogenic potential of CnPnV and its association with CIRD in dogs. Further studies will elucidate the pathogenicity and epidemiology of this novel pneumovirus, thus addressing the eventual need for specific vaccines. url: https://doi.org/10.1371/journal.pone.0085220 doi: 10.1371/journal.pone.0085220 id: cord-257284-dash9udv author: Decaro, Nicola title: Development and validation of a real-time PCR assay for specific and sensitive detection of canid herpesvirus 1 date: 2010-07-30 words: 3138.0 sentences: 149.0 pages: flesch: 52.0 cache: ./cache/cord-257284-dash9udv.txt txt: ./txt/cord-257284-dash9udv.txt summary: The detection limit was 10(1) and 1.20 × 10(1) DNA copies per 10 μl(−1) of template for standard DNA and a CHV-1-positive kidney sample, respectively: about 1-log higher than a gel-based PCR assay targeting the thymidine kinase gene. Unlike other CHV-1-specific diagnostic methods, this quantitative assay permits simultaneous detection and quantitation of CHV-1 DNA in a wide range of canine tissues and body fluids, thus providing a useful tool for confirmation of a clinical diagnosis, for the study of viral pathogenesis and for evaluation of the efficacy of vaccines and antiviral drugs. To evaluate the detection limits of the real-time PCR assay, 10fold dilutions of the plasmid DNA, ranging from 10 9 to 10 0 copies, were made in a CHV-1-negative kidney homogenate and tested subsequently. The development and validation of a real-time PCR assay for detection and absolute quantitation of CHV-1 DNA in tissue samples and body fluids of dogs are described. abstract: A TaqMan-based real-time PCR assay targeting the glycoprotein B-encoding gene was developed for diagnosis of canid herpesvirus 1 (CHV-1) infection. The established assay was highly specific, since no cross-reactions were observed with other canine DNA viruses, including canine parvovirus type 2, canine minute virus, or canine adenovirus types 1 and 2. The detection limit was 10(1) and 1.20 × 10(1) DNA copies per 10 μl(−1) of template for standard DNA and a CHV-1-positive kidney sample, respectively: about 1-log higher than a gel-based PCR assay targeting the thymidine kinase gene. The assay was also reproducible, as shown by satisfactory low intra-assay and inter-assay coefficients of variation. CHV-1 isolates of different geographical origins were recognised by the TaqMan assay. Tissues and clinical samples collected from three pups which died of CHV-1 neonatal infection were also tested, displaying a wide distribution of CHV-l DNA in their organs. Unlike other CHV-1-specific diagnostic methods, this quantitative assay permits simultaneous detection and quantitation of CHV-1 DNA in a wide range of canine tissues and body fluids, thus providing a useful tool for confirmation of a clinical diagnosis, for the study of viral pathogenesis and for evaluation of the efficacy of vaccines and antiviral drugs. url: https://api.elsevier.com/content/article/pii/S0166093410002636 doi: 10.1016/j.jviromet.2010.07.021 id: cord-259988-3s7b5ovi author: Decaro, Nicola title: Virological and molecular characterization of a mammalian orthoreovirus type 3 strain isolated from a dog in Italy date: 2005-08-10 words: 3336.0 sentences: 191.0 pages: flesch: 57.0 cache: ./cache/cord-259988-3s7b5ovi.txt txt: ./txt/cord-259988-3s7b5ovi.txt summary: A mammalian orthoreovirus (MRV) strain was isolated from a pup with fatal diarrhea, which had a concurrent infection by canine parvovirus type 2. Assignment of the isolated virus to MRV-3 was confirmed by type-specific RT-PCR assays, targeting the S1 gene, and by subsequent sequence analysis of the PCR product. A total of 110 fecal samples, 56 nasal and 31 ocular swabs from dogs with diarrhea or nasal/ocular discharge were tested by a nested-PCR assay specific for reoviruses, and no sample was found to contain MRV RNA, a finding that is apparently in contrast with the seroprevalence (25.77%) observed in dogs. In the present study, the isolation and molecular characterization of a MRV-3 strain from a dog with diarrhea are reported. By the type-specific RT-PCR assays the isolate was recognized as MRV-3 (Fig. 5) , and therefore designated T3/ canine/Italy/Decaro/2004 (T3D/04), according to the conventional system used to identify MRV strains. abstract: A mammalian orthoreovirus (MRV) strain was isolated from a pup with fatal diarrhea, which had a concurrent infection by canine parvovirus type 2. The reovirus isolate showed an atypical hemagglutination pattern and a retarded electrophoretic mobility of the S1 segment, which is characteristic of MRV type 3 (MRV-3). Assignment of the isolated virus to MRV-3 was confirmed by type-specific RT-PCR assays, targeting the S1 gene, and by subsequent sequence analysis of the PCR product. By phylogeny based on the S1 gene of several MRVs, the isolate fell into lineage E, along with the murine strain T3C9/61 and the bovine strains T3C18/61 and T3C31/59. Conversely, L1 sequences were found to segregate regardless of the viral type. A total of 110 fecal samples, 56 nasal and 31 ocular swabs from dogs with diarrhea or nasal/ocular discharge were tested by a nested-PCR assay specific for reoviruses, and no sample was found to contain MRV RNA, a finding that is apparently in contrast with the seroprevalence (25.77%) observed in dogs. url: https://www.ncbi.nlm.nih.gov/pubmed/15964158/ doi: 10.1016/j.vetmic.2005.05.014 id: cord-260250-t48y27wg author: Decaro, Nicola title: Quantitation of canine coronavirus RNA in the faeces of dogs by TaqMan RT-PCR date: 2004-05-07 words: 3322.0 sentences: 157.0 pages: flesch: 51.0 cache: ./cache/cord-260250-t48y27wg.txt txt: ./txt/cord-260250-t48y27wg.txt summary: A TaqMan(®) fluorogenic reverse transcriptase-polymerase chain reaction (RT-PCR) assay was developed for the detection and quantitation of canine coronavirus (CCoV) RNA in the faeces of naturally or experimentally infected dogs. The CCoV fluorogenic RT-PCR assay, which targeted the ORF5 (M gene), was more sensitive than a conventional RT-PCR assay targeting the same gene, showing a detection limit of 10 copies of CCoV standard RNA, and was linear from 10 to 10(8) copies, allowing quantitation of samples with a wide range of CCoV RNA loads. As shown in Table 2 , the detec-tion limit of the TaqMan RT-PCR was 1-2 log higher than that of conventional RT-PCR, ranging around 10 1 copies/l and 10 −1.50 TCID 50 /50 l for standard RNA and CCoV strain, respectively, with a detection rate of 100% for each positive dilution. The results of the conventional amplification and real-time analysis carried out on the faecal samples of the CCoV experimentally infected dog are summarized in Fig. 3 . abstract: A TaqMan(®) fluorogenic reverse transcriptase-polymerase chain reaction (RT-PCR) assay was developed for the detection and quantitation of canine coronavirus (CCoV) RNA in the faeces of naturally or experimentally infected dogs. The CCoV fluorogenic RT-PCR assay, which targeted the ORF5 (M gene), was more sensitive than a conventional RT-PCR assay targeting the same gene, showing a detection limit of 10 copies of CCoV standard RNA, and was linear from 10 to 10(8) copies, allowing quantitation of samples with a wide range of CCoV RNA loads. A total of 78 faecal samples of diarrhoeic dogs were tested simultaneously by conventional and fluorogenic RT-PCR: 29 were negative by both techniques, whereas 27 tested positive by conventional RT-PCR and 48 by the established CCoV fluorogenic assay. One sample, which was positive by conventional RT-PCR, gave no signal in the fluorogenic assay. In addition, by the fluorogenic assay CCoV shedding in the faecal samples of an experimentally infected dog was monitored for 28 days. The high sensitivity, simplicity and reproducibility of the CCoV fluorogenic RT-PCR assay, combined with its wide dynamic range and high throughput, make this method especially suitable for efficacy trials on CCoV vaccines. url: https://api.elsevier.com/content/article/pii/S0166093404001028 doi: 10.1016/j.jviromet.2004.03.012 id: cord-308315-g6udfu2a author: Decaro, Nicola title: Characterisation of bubaline coronavirus strains associated with gastroenteritis in water buffalo (Bubalus bubalis) calves date: 2010-10-26 words: 3701.0 sentences: 172.0 pages: flesch: 50.0 cache: ./cache/cord-308315-g6udfu2a.txt txt: ./txt/cord-308315-g6udfu2a.txt summary: Recently, a coronavirus strain (179/07-11) was isolated from water buffalo (Bubalus bubalis) and the virus which displayed a strict genetic and biological relatedness with bovine coronavirus (BCoV) was referred to as bubaline coronavirus (BuCoV). There are multiple genetic and antigenic evidences that several subgroup 2a CoVs, such as HCoV-OC43, HECoV-4408, PHEV and CRCoV, have arisen as consequence of trans-species infections caused by BCoV (Zhang et al., 1994; Vijgen et al., 2005 Vijgen et al., , 2006 Erles et al., Veterinary Microbiology 145 (2010) [245] [246] [247] [248] [249] [250] [251] Recently, a coronavirus strain (179/07-11) was isolated from water buffalo (Bubalus bubalis) and the virus which displayed a strict genetic and biological relatedness with bovine coronavirus (BCoV) was referred to as bubaline coronavirus (BuCoV). Recently, another bovine-like CoV, which was referred to as bubaline coronavirus (BuCoV), was isolated from water buffalo (Bubalus bubalis) calves with fatal gastroenteritis in Italy (Decaro et al., 2008d) . abstract: Recently, a coronavirus strain (179/07-11) was isolated from water buffalo (Bubalus bubalis) and the virus which displayed a strict genetic and biological relatedness with bovine coronavirus (BCoV) was referred to as bubaline coronavirus (BuCoV). Here, we report the characterisation of four BuCoVs strains identified in the faeces or intestinal contents of water buffalo calves with acute gastroenteritis. Single BuCoV infections were detected in all but one cases from which two clostridia species were also isolated. Sequence and phylogenetic analyses of the 5′ end of the spike-protein gene showed that three BuCoVs were closely related to the prototype strain 179/07-11, whereas the fourth isolate (339/08-C) displayed a higher genetic identity to recent BCoV reference strains. Three strains adapted to the in vitro grow on human rectal tumour cells were also evaluated for their ability to replicate in a bovine cell line (Madin Darby bovine kidney) and to cause haemagglutination of chicken erythrocytes and all displayed biological properties similar to those already described for the prototype BuCoV. The present report shows that albeit genetically heterogeneous, the different BuCoV strains possess a common biological pattern which is different from most BCoV and BCoV-like isolates. url: https://www.sciencedirect.com/science/article/pii/S0378113510001914 doi: 10.1016/j.vetmic.2010.04.010 id: cord-007427-iqwojhq2 author: Dedkov, Vladimir G. title: Development and Evaluation of a One-Step Quantitative RT-PCR Assay for Detection of Lassa Virus date: 2019-06-03 words: 4043.0 sentences: 213.0 pages: flesch: 53.0 cache: ./cache/cord-007427-iqwojhq2.txt txt: ./txt/cord-007427-iqwojhq2.txt summary: Based on sequencing data, LASV-specific assay was developed using synthetic MS2-phage-based armored RNA particles, RNA from Lassa virus strain Josiah, and further, evaluated in field conditions using samples from patients and Mastomys natalensis rodents. Viral RNAs were examined for Lassa immediately after extraction by the staff of the Virology Laboratory of Hemorrhagic Fevers Research Project of Gamal Abdel Nasser University of Conakry, Guinea and were then used to assess diagnostic sensitivity and specificity. In addition, LOD was assessed using a series of 10-fold dilutions of ARPs. For this purpose, eight LASV sequences of a maximal number of mismatches in the targeting region of L gene were selected (including a sequence of the strain Josiah, which was also used for the generation of the positive controls) and generated for the production of ARPs as described above (Table 2 ) . abstract: Lassa fever is a severe viral hemorrhagic illness caused by Lassa virus. Based on estimates, the number of LASV infections ranges from 300,000 to 500,000 cases in endemic areas with a fatality rate of 1%. Development of fast and sensitive tools for the control and prevention of Lassa virus infection as well as for clinical diagnostics of Lassa fever are crucial. Here we reported development and evaluation of a one-step quantitative RT-qPCR assay for the Lassa virus detection – LASV-Fl. This assay is suitable for the detection of lineages I-IV of Lassa virus. The limit of detection of the assay ranged from 10(3) copies/ml to 10(5) copies/ml and has 96.4% diagnostic sensitivity, whereas analytical and diagnostic specificities both were 100%. Serum, whole blood and tissue are suitable for use with the assay. The assay contains all the necessary components to perform the analysis, including an armored positive control (ARC+) and an armored internal control (IC). The study was done during the mission of specialized anti-epidemic team of the Russian Federation (SAET) in the Republic of Guinea in 2015-2018. Based on sequencing data, LASV-specific assay was developed using synthetic MS2-phage-based armored RNA particles, RNA from Lassa virus strain Josiah, and further, evaluated in field conditions using samples from patients and Mastomys natalensis rodents. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7113850/ doi: 10.1016/j.jviromet.2019.113674 id: cord-306502-jkqg1qal author: Dee, Scott title: An evaluation of contaminated complete feed as a vehicle for porcine epidemic diarrhea virus infection of naïve pigs following consumption via natural feeding behavior: proof of concept date: 2014-08-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Since its initial detection in May 2013, porcine epidemic diarrhea virus (PEDV) has spread rapidly throughout the US swine industry. Initially, contaminated feed was proposed as a risk factor for PEDV; however, data were not available to support this theory. Here we provide proof of concept of this risk by describing a novel means for recovering PEDV-contaminated complete feed material from commercial swine sites and conducting an in vivo experiment to prove its infectivity. RESULTS: For on-farm detection of PEDV RNA in feed, paint rollers were used to collect material from at-risk feed bins from 3 clinically affected breeding herds. This material was tested by PCR and determined to be positive for PEDV-RNA (Ct = 19.50-22.20 range). To test infectivity, this material was pooled (Ct = 20.65) and a Treatment group of 3-week old PEDV-naïve piglets were allowed to consume it via natural feeding behavior. For the purpose of a Positive control, piglets were allowed to ingest feed spiked with stock PEDV (Ct = 18.23) while the negative control group received PEDV-free feed. Clinical signs of PEDV infection (vomiting and diarrhea) and viral shedding were observed in both the Positive control and Treatment group’ post-consumption with virus and microscopic lesions detected in intestinal samples No evidence of infection was observed in the Negative controls. CONCLUSIONS: These data provide proof of concept that contaminated complete feed can serve as a vehicle for PEDV infection of naïve pigs using natural feeding behavior. url: https://www.ncbi.nlm.nih.gov/pubmed/25091641/ doi: 10.1186/s12917-014-0176-9 id: cord-273608-dxx3p1x5 author: Deng, Jikui title: Respiratory virus multiplex RT-PCR assay sensitivities and influence factors in hospitalized children with lower respiratory tract infections date: 2013-04-11 words: 3461.0 sentences: 187.0 pages: flesch: 51.0 cache: ./cache/cord-273608-dxx3p1x5.txt txt: ./txt/cord-273608-dxx3p1x5.txt summary: Total nucleic acids were extracted using the EZ1 system (Qiagen, Germany) and 17 respiratory viruses and genotypes including influenza A virus (FluA), FluB, parainfluenza virus 1 (PIV1), PIV2, PIV3, PIV4, respiratory syncytial virus (RSV), human metapneumovirus (hMPV), rhinoviruses (RhV), enteroviruses (EnV), human bocaviruses (hBoV), adenoviruses (AdV), four coronaviruses (229E, OC43, NL63 and HKU1), and FluA 2009 pandemic H1N1(H1N1-p) were detected and identified by the ResPlex II kit. In this study, we evaluated the ResPlex II V2.0 kit (Qiagen, Germany), which uses a target enriched multiplexing RT-PCR amplification coupled with a suspension array detection, for detection and identification of a panel of respiratory specimens in pediatric inpatients with LRTIs. Clinical accuracy of the ResPlex II assay was validated on a panel of prospectively collected consecutive nasopharyngeal swab (NPS) specimens in comparison to viral culture and a monoplex real-time TaqMan RT-PCR. abstract: Multiplex RT-PCR assays have been widely used tools for detection and differentiation of a panel of respiratory viral pathogens. In this study, we evaluated the Qiagen ResPlex II V2.0 kit and explored factors influencing its sensitivity. Nasopharyngeal swab (NPS) specimens were prospectively collected from pediatric inpatients with lower respiratory tract infections at the time of admission in the Shenzhen Children’s Hospital from May 2009 to April 2010. Total nucleic acids were extracted using the EZ1 system (Qiagen, Germany) and 17 respiratory viruses and genotypes including influenza A virus (FluA), FluB, parainfluenza virus 1 (PIV1), PIV2, PIV3, PIV4, respiratory syncytial virus (RSV), human metapneumovirus (hMPV), rhinoviruses (RhV), enteroviruses (EnV), human bocaviruses (hBoV), adenoviruses (AdV), four coronaviruses (229E, OC43, NL63 and HKU1), and FluA 2009 pandemic H1N1(H1N1-p) were detected and identified by the ResPlex II kit. In parallel, 16 real-time TaqMan quantitative RT-PCR assays were used to quantitatively detect each virus except for RhV. Influenza and parainfluenza viral cultures were also performed. Among the total 438 NPS specimens collected during the study period, one or more viral pathogens were detected in 274 (62.6%) and 201(45.9%) specimens by monoplex TaqMan RT-PCR and multiplex ResPlex, respectively. When results from monoplex PCR or cell culture were used as the reference standard, the multiplex PCR possessed specificities of 92.9–100.0%. The sensitivity of multiplex PCR for PIV3, hMPV, PIV1 and BoV were 73.1%, 70%, 66.7% and 55.6%, respectively, while low sensitivities (11.1%–40.0%) were observed for FluA, EnV, OC43, RSV and H1N1. Among the seven viruses/genotypes detected with higher frequencies, multiplex PCR sensitivities were correlated significantly with viral loads determined by the TaqMan RT-PCR in FluA, H1N1-p and RSV (p=0.011−0.000). The Qiagen ResPlex II multiplex RT-PCR kit possesses excellent specificity for simultaneous detection of 17 viral pathogens in NPS specimens in pediatric inpatients at the time of admission. The sensitivity of multiplex RT-PCR was influenced by viral loads, specimen process methods, primer and probe design and amplification condition. url: https://doi.org/10.1007/s12250-013-3312-y doi: 10.1007/s12250-013-3312-y id: cord-271919-pbs95hy0 author: Desenclos, Jean-Claude title: Introduction of SARS in France, March–April, 2003 date: 2004-02-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: We describe severe acute respiratory syndrome (SARS) in France. Patients meeting the World Health Organization definition of a suspected case underwent a clinical, radiologic, and biologic assessment at the closest university-affiliated infectious disease ward. Suspected cases were immediately reported to the Institut de Veille Sanitaire. Probable case-patients were isolated, their contacts quarantined at home, and were followed for 10 days after exposure. Five probable cases occurred from March through April 2003; four were confirmed as SARS coronavirus by reverse transcription–polymerase chain reaction, serologic testing, or both. The index case-patient (patient A), who had worked in the French hospital of Hanoi, Vietnam, was the most probable source of transmission for the three other confirmed cases; two had been exposed to patient A while on the Hanoi-Paris flight of March 22–23. Timely detection, isolation of probable cases, and quarantine of their contacts appear to have been effective in preventing the secondary spread of SARS in France. url: https://www.ncbi.nlm.nih.gov/pubmed/15030682/ doi: 10.3201/eid1002.030351 id: cord-335085-7pxkhgbq author: Dessau, R. B. title: Coronaviruses in spinal fluid of patients with acute monosymptomatic optic neuritis date: 2009-01-29 words: 2145.0 sentences: 130.0 pages: flesch: 64.0 cache: ./cache/cord-335085-7pxkhgbq.txt txt: ./txt/cord-335085-7pxkhgbq.txt summary: Material and methods ‐ Spinal fluids from 37 patients with AMON and 15 surgical control patients with protrusion of the intervertebral disk were assayed with a nested multiplex polymerase chain reaction with primers specific for human coronaviruses strain (HCV) 229E and OC43. To investigate the possibility of an infection with human coronaviruses (HCV) in early MS and as a possible cause of AMON we have analyzed cerebrospinal fluid (CSF) from patients with AMON using reverse transcriptase reaction and the polymerase chain reaction (RT-PCR) applying primers specific for HCV. CSF from 4 patients and 1 control ( Table 2) were positive on nested RT-PCR using the HCV-229E primers and all samples were negative with the HCV-OC43 primers. HCV-229E RNA was found in the CSF by RT-PCR in 4 of 37 patients with AMON and in 1 of 15 controls. abstract: Acute monosymptomatic optic neuritis (AMON) may be an initial symptom of multiple sclerosis (MS). Coronaviruses have been implicated in the etiology of MS. The objective of the present study was to look for coronaviral RNA in AMON, which could be present in the initial stages of the development of MS. Material and methods ‐ Spinal fluids from 37 patients with AMON and 15 surgical control patients with protrusion of the intervertebral disk were assayed with a nested multiplex polymerase chain reaction with primers specific for human coronaviruses strain (HCV) 229E and OC43. Results ‐ Four patients and 1 control were positive for HCV‐229E. No evidence of HCV‐OC43 was found. The frequency of positive samples was low and there was no statistical difference between AMON and controls. Conclusion ‐ This study does not provide evidence for an etiological role of human coronaviruses in acute monosymptomatic optic neuritis. url: https://www.ncbi.nlm.nih.gov/pubmed/10442448/ doi: 10.1111/j.1600-0404.1999.tb01043.x id: cord-265634-7n4cvgs4 author: Dhar, Arun K. title: Quantitative assay for measuring the Taura syndrome virus and yellow head virus load in shrimp by real-time RT-PCR using SYBR Green chemistry date: 2002-03-26 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Taura syndrome virus (TSV) and yellow head virus (YHV) are the two RNA viruses infecting penaeid shrimp (Penaeus sp.) that have caused major economic losses to shrimp aquaculture. A rapid and highly sensitive detection and quantification method for TSV and YHV was developed using the GeneAmp(®) 5700 Sequence Detection System and SYBR Green chemistry. The reverse transcriptase polymerase chain reaction (RT-PCR) mixture contained a fluorescent dye, SYBR Green, which exhibits fluorescence enhancement upon binding to double strand cDNA. The enhancement of fluorescence was found to be proportional to the initial concentration of the template cDNA. A linear relationship was observed between input plasmid DNA and cycle threshold (C(T)) values for 10(6) down to a single copy of both viruses. To control for the variation in sample processing and in reverse transcription reaction among samples, shrimp β-actin and elongation factor-1α (EF-1α) genes were amplified in parallel with the viral cDNA. The sensitivity and the efficiency of amplification of EF-1α was greater than β-actin when compared to TSV and YHV amplification efficiency suggesting that EF-1α is a better internal control for the RT-PCR detection of TSV and YHV. In addition, sample to sample variation in EF-1α C(T) value was lower than the variation in β-actin C(T) value of the corresponding samples. The specificity of TSV, YHV, EF-1α and β-actin amplifications was confirmed by analyzing the dissociation curves of the target amplicon. The C(T) values of TSV and YHV samples were normalized against EF-1α C(T) values for determining the absolute copy number from the standard curve of the corresponding virus. The method described here is highly robust and is amenable to high throughput assays making it a useful tool for diagnostic, epidemiological and genetic studies in shrimp aquaculture. url: https://www.ncbi.nlm.nih.gov/pubmed/12020794/ doi: 10.1016/s0166-0934(02)00042-3 id: cord-024080-eh3ztsv5 author: Dheda, Keertan title: Diagnosis of COVID-19: Considerations, Controversies and Challenges in South Africa date: 2020-04-17 words: 3953.0 sentences: 214.0 pages: flesch: 44.0 cache: ./cache/cord-024080-eh3ztsv5.txt txt: ./txt/cord-024080-eh3ztsv5.txt summary: Recent data from infections in special contexts such as cruise liners (9) and in close contacts of COVID-19 patients (10) have demonstrated that SARS-CoV-2-specific RT-PCR may be positive in the early phase of the disease, and that viral shedding in the asymptomatic phase and in the early prodromal phase can be considerable. (19) This false negativity phenomenon may be due to several factors, including a low viral load below the detection limit of the assay, low sample volume or cellular mass during acquisition, sampling location (upper versus lower respiratory tract), sample degradation during transport or storage, sample processing methodology and the timing of sampling in relation to the stage of the disease (RT-PCR positivity may progressively increase during the course of the disease). In patients with more severe diseases, including those with lower respiratory tract infection, but also in individuals with mild disease, high viral loads can be detected often for several days after the resolution of symptoms. abstract: Coronavirus disease 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus 2 is a global pandemic that has resulted in over 1.5 million confirmed cases and close to 100,000 deaths. In the majority of symptomatic cases COVID-19 results in a mild disease predominantly characterised by upper respiratory tract symptoms. Reverse transcription polymerase chain reaction (RT-PCR), using a nasopharyngeal sample, is the mainstay of diagnosis, but there is an ~30% false negative rate early in the disease and in patients with mild disease. RT-PCR positivity can persist for several days after a resolution of symptoms. IgM and IgG antibody responses become positive several days after the onset of symptoms, and robust antibody responses are detectable in the second week of illness. Antibody-based immunoassays have a limited role in the diagnosis of early symptomatic disease. However, their incremental benefit over RT-PCR in the first 2 weeks of illness is currently being clarified in ongoing studies. Such assays may be useful for surveillance purposes. However, their role in potentially selecting individuals that may benefit from vaccination, or as a biomarker identifying persons that could be redeployed into essential employment roles are being investigated. Rapid antibody-based immunoassays that detect viral antigen in nasopharyngeal samples are being developed and evaluated. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7187744/ doi: 10.18772/26180197.2020.v2nsia1 id: cord-308344-ao9z00t7 author: Diep, Nguyen Van title: Novel Porcine Epidemic Diarrhea Virus (PEDV) Variants with Large Deletions in the Spike (S) Gene Coexist with PEDV Strains Possessing an Intact S Gene in Domestic Pigs in Japan: A New Disease Situation date: 2017-01-17 words: 4179.0 sentences: 193.0 pages: flesch: 52.0 cache: ./cache/cord-308344-ao9z00t7.txt txt: ./txt/cord-308344-ao9z00t7.txt summary: title: Novel Porcine Epidemic Diarrhea Virus (PEDV) Variants with Large Deletions in the Spike (S) Gene Coexist with PEDV Strains Possessing an Intact S Gene in Domestic Pigs in Japan: A New Disease Situation Among 17 PEDV samples isolated from individual pigs, all of them contained at least two distinct genotypes with large genomic deletions, and 94.1% of them were found to consist of strains with an intact S gene. In this study, variants with large deletions in the S gene were found in eight primary and nine recurrent outbreaks from 16 pig farms, and they mostly (94.1%) coexisted with PEDV strains with an intact S gene. Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene New porcine epidemic diarrhoea virus variant with a large deletion in the spike gene identified in domestic pigs abstract: Since late 2013, after an absence of seven years, outbreaks of porcine epidemic diarrhea virus (PEDV) infection have reemerged and swept rapidly across Japan, resulting in significant economic losses. In this study, we report the emergence, mixed infection, and genetic characterization of 15 novel field PEDV variants with large genomic deletions. The sizes of deletion varied between 582 nt (194 aa) and 648 nt (216 aa) at positions 28–714 (10–238) on the S gene (protein). Among 17 PEDV samples isolated from individual pigs, all of them contained at least two distinct genotypes with large genomic deletions, and 94.1% of them were found to consist of strains with an intact S gene. These variants were found in eight primary and nine recurrent outbreaks, and they might be associated with persistent PEDV infection in the farms. Full-length S and ORF3 genes of eight variants derived from 2 samples were characterized. This is the first report of mixed infections caused by various genotypes of PEDV and would be important for the studies of viral isolation, pathogenesis, and molecular epidemiology of the disease. url: https://www.ncbi.nlm.nih.gov/pubmed/28095455/ doi: 10.1371/journal.pone.0170126 id: cord-333453-v3gap8kj author: Dima, Mirabela title: First neonates with severe acute respiratory syndrome coronavirus 2 infection in Romania: Three case reports date: 2020-08-14 words: 3020.0 sentences: 173.0 pages: flesch: 52.0 cache: ./cache/cord-333453-v3gap8kj.txt txt: ./txt/cord-333453-v3gap8kj.txt summary: The novel coronavirus officially named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Virus generated a pandemic, which erupted in Hubei, Wuhan, China and quickly spread throughout the world, [1, 2] has been putting medical workers all over the world in difficulty because of the high number of cases combined with the lack of information about the disease. The clinic where the patient was born discharged her and the mother on April 6, 2020 both being negative for SARS-CoV-2 (RT-PCR test). On April 15, after 3 days of observing cough, lethargy, loss of appetite, jaundice, and constant fever, the mother presented in emergency room with the newborn, both being tested positive for SARS-CoV-2. [10] We believe it is important in the current epidemiologic context to mention that all 3 patients were discharged from the clinic where they were born with SARS-CoV-2 negative tests (RT-PCR), which were taken in conformity with our national protocol regarding COVID-19. abstract: RATIONALE: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, which quickly spread throughout the world, has been putting medical workers all over the world in difficulty because of the high number of cases combined with the lack of information about the disease. Although pediatric cases are rare, the group age under 12 months has been in general more susceptible to develop severe forms of the disease compared with the patients in the age interval of 1 to 18 years. PATIENT CONCERNS: Three newborns have been tested positive for SARS-CoV-2 infection. One of them presented bilateral decreased air entry, while the other 2 had no respiratory symptomatology. All 3 developed diaper erythema and oral candidiasis. DIAGNOSIS: For building up the report, newborns that were positive for coronavirus disease 2019 (COVID-19) infection were included in the case series. The chest X-ray of the symptomatic patient revealed a medium degree of hilar parenchymal infiltration and a slight infiltration of the visceral pleura. INTERVENTIONS: The patients were admitted in our isolated neonatology ward. All of them received antifungal treatment for the oral candidiasis and topic cream for diaper erythema. The symptomatic patient also received prophylactic antibiotherapy, human immunoglobulins, aminophylline, and parenteral nutrition. OUTCOMES: All 3 neonates were discharged after 2 consecutive negative tests for SARS-CoV-2. Patients 1 and 2 fully recovered, whereas the condition of patient 3 improved. LESSONS: Even if there are only a few reported cases of neonates infected with COVID-19 and most of them present mild manifestations, newborns need a more careful insight because of the nonspecific symptomatology. url: https://www.ncbi.nlm.nih.gov/pubmed/32871986/ doi: 10.1097/md.0000000000021284 id: cord-307768-xx46w6dc author: Ding, Yun title: From single-molecule detection to next-generation sequencing: microfluidic droplets for high-throughput nucleic acid analysis date: 2017-03-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Droplet-based microfluidic technologies have proved themselves to be of significant utility in the performance of high-throughput chemical and biological experiments. By encapsulating and isolating reagents within femtoliter–nanoliter droplet, millions of (bio) chemical reactions can be processed in a parallel fashion and on ultra-short timescales. Recent applications of such technologies to genetic analysis have suggested significant utility in low-cost, efficient and rapid workflows for DNA amplification, rare mutation detection, antibody screening and next-generation sequencing. To this end, we describe and highlight some of the most interesting recent developments and applications of droplet-based microfluidics in the broad area of nucleic acid analysis. In addition, we also present a cursory description of some of the most essential functional components, which allow the creation of integrated and complex workflows based on flowing streams of droplets. url: https://www.ncbi.nlm.nih.gov/pubmed/32214953/ doi: 10.1007/s10404-017-1889-4 id: cord-255983-3dq99xz9 author: Do, Lien Anh Ha title: A sensitive real-time PCR for detection and subgrouping of human respiratory syncytial virus date: 2012-01-17 words: 4267.0 sentences: 193.0 pages: flesch: 50.0 cache: ./cache/cord-255983-3dq99xz9.txt txt: ./txt/cord-255983-3dq99xz9.txt summary: The quantitative assay was compared to a commercial conventional multiplex PCR method (Seeplex TM RV detection kit, Seegene, Inc., Seoul, Korea) (Kim et al., 2009; Roh et al., 2008) respiratory samples from a study (Do et al., 2011) on acute respiratory infection in children at the Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam. All samples were analyzed in parallel by the commercial multiplex Seeplex TM RV detection kit (Seegene, Inc., Seoul, Korea) according to the manufacturer''s instructions, to determine the presence of 12 respiratory viruses: human RSV subgroups A and B (RSV A, RSV B); influenza virus A (InfV A); influenza virus B (InfV B); human coronaviruses (229E, OC43), human metapneumovirus (hMPV), parainfluenza virus 1, 2 and 3 (PIV1, 2, 3), human rhinovirus (hRV A) and adenovirus (AdV) (Kim et al., 2009; Roh et al., 2008) and by the newly developed RSV LNA real-time RT-PCR. abstract: Improved diagnostic tools for rapid detection, quantitation, and subgrouping of human respiratory syncytial virus (RSV) are needed to aid the development and evaluation of novel intervention strategies. A quantitative real-time RT-PCR using specific locked nucleic acid (LNA) probes was developed to identify RSV and to distinguish RSV subgroups A and B (RSV LNA assay). RSV subgroup diversity and the relationship between viral load and disease severity in confirmed RSV infections were also explored. 264 archived respiratory specimens from pediatric patients were tested in parallel using the commercial multiplex Seeplex™ RV detection kit (Seegene) and the novel RSV LNA assay. The LNA assay demonstrated a significantly higher sensitivity than Seeplex, improving overall detection rates from 24% (64/264) to 32% (84/264). Detection limits of 9.0 × 10(1) and 6.0 × 10(2) copies/mL were observed for RSV A and B, respectively. RSV A was detected in 53/84 (63%) cases, and 31/84 (37%) were positive for RSV B. This novel method offers a rapid, quantitative, highly specific and sensitive approach to laboratory diagnosis of RSV. url: https://doi.org/10.1016/j.jviromet.2011.11.012 doi: 10.1016/j.jviromet.2011.11.012 id: cord-103417-2uinislh author: Doi, Hideyuki title: On-site eDNA detection of species using ultra-rapid mobile PCR date: 2020-10-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Molecular methods, including environmental DNA (eDNA) methods, provide essential information for biological and conservation sciences. Molecular measurements are often performed in the laboratory, which limits their scope, especially for rapid on-site analysis. eDNA methods for species detection provide essential information for the management and conservation of species and communities in various environments. We developed an innovative novel method for on-site eDNA measurements using an ultra-rapid mobile PCR platform. We tested the ability of our method to detect the distribution of silver carp, Hypophthalmichthys molitrix, an invasive fish in Japanese rivers and lakes. Our method reduced the measurement time to 30 min and provided high detectability of aquatic organisms compared to the national observation surveys using multiple fishing nets and laboratory extraction/detection using a benchtop qPCR platform. Our on-site eDNA method can be immediately applied to various taxa and environments. url: https://doi.org/10.1101/2020.09.28.314625 doi: 10.1101/2020.09.28.314625 id: cord-265258-2rmtsyns author: Domanska‐Blicharz, K. title: Specific detection of GII‐1 lineage of infectious bronchitis virus date: 2017-07-03 words: 3393.0 sentences: 170.0 pages: flesch: 53.0 cache: ./cache/cord-265258-2rmtsyns.txt txt: ./txt/cord-265258-2rmtsyns.txt summary: The real-time RT-PCR assays seem to be effective tools for IBV-type identification and although S1 coding region is prone to mutations, methods aimed in this gene detection has been recently developed and used for GI-1 (Mass, Connecticut), GI-9 (Arkansas), GI-11 (SAI), G1-16 (ASAII) and GIV-1 (DE072/GA98) lineages (Acevedo et al. Here, we describe the development of a TaqMan probe-based real-time RT-PCR for the detection of GII-1 (D1466-like) IBV lineage. Moreover, the assay developed in the present study showed to be highly specific as no fluorescent signals were detected with other tested IBV lineages or chicken RNA viral pathogens. In conclusion, the TaqMan probe-based real-time RT-PCR assay described here is a time-saving, specific, sensitive and reliable method of detection of GII-1 lineage (D1466-like) of IBV which could successfully replace standard nested RT-PCR. Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens abstract: Infectious bronchitis virus (IBV) is a worldwide prevalent RNA virus that causes highly contagious and economically devastating disease in chicken. The virus exists in many different genetic forms which made the disease control very difficult. The present study describes the development and validation of TaqMan probe‐based real‐time reverse transcription‐polymerase chain reaction (real‐time RT‐PCR) targeting the S1 coding region of S gene characteristic for the GII‐1 lineage (formerly the D1466‐like variant) of IBV. These strains are quite different from other European IBV belonging to different lineages of the GI genotype. The developed method was 30‐fold more sensitive than used so far for standard nested RT‐PCR with detection limit of 56 RNA copies per reaction. The specificity of the assay was also evaluated with a panel of different poultry pathogens. Repeatability and reproducibility of the method was very high with coefficients of variation lower than 4%. One hundred and twenty‐seven IBV‐positive samples were tested by this method and GII‐1 strains were detected in four of them (3·15%) which indicate a decrease in the GII‐1 IBV prevalence in Poland. The assay was proven to be a valuable tool for rapid diagnosis of GII‐1 lineage of IBV strains and moreover it enabled the monitoring of viral loads which can be used to assess disease progression. SIGNIFICANCE AND IMPACT OF THE STUDY: This study reports a TaqMan probe‐based real‐time reverse transcription‐polymerase chain reaction (real‐time RT‐PCR) for rapid and accurate identification of GII‐1 lineage (formerly D1466‐like variant) of infectious bronchitis virus (IBV). The assay revealed to be more sensitive than standard nested RT‐PCR assay, previously used for this purpose. The developed assay has been tested on numerous field samples and revealed 3·15% prevalence of this lineage of IBV in Polish chicken population. Moreover, this new assay enables the assessment of viral load measurement which might be useful for epidemiology and pathogenesis studies. url: https://www.ncbi.nlm.nih.gov/pubmed/28493279/ doi: 10.1111/lam.12753 id: cord-314069-8dxzf2ip author: Dongliu, Yuan title: Outbreak of acute febrile respiratory illness caused by human adenovirus B P14H11F14 in a military training camp in Shandong China date: 2016-06-28 words: 4283.0 sentences: 206.0 pages: flesch: 51.0 cache: ./cache/cord-314069-8dxzf2ip.txt txt: ./txt/cord-314069-8dxzf2ip.txt summary: authors: Dongliu, Yuan; Guoliang, Yang; Haocheng, Xu; Shuaijia, Qing; Li, Bing; Yanglei, Jia This study reports an outbreak of acute febrile respiratory illness caused by human adenovirus B [P14H11F14] in a military training center in China between May and June 2014. A HAdV-B [P14H11F14] virus was confirmed as the etiological pathogen of this acute outbreak of febrile respiratory illness based on clinical manifestations, epidemiological characteristics, specific molecular detection results, phylogenetic analysis, and serological assays. In conclusion, the regional CDC officials concluded that a type-55-like human adenovirus B human/CHN/SD77001/ 2014/[P14H11F14] virus was the etiological pathogen responsible for this acute FRI outbreak based on the clinical manifestations in the patients, the epidemiological characteristics of the outbreak, the HAdV-DNA-specific PCR results, isolation of the virus, sequencing and alignment of the PCR amplicons, homology and phylogenetic analyses based on the complete E1A, penton base, hexon, and fiber gene sequences, and serological assays specific for HAdV IgA/IgG. abstract: This study reports an outbreak of acute febrile respiratory illness caused by human adenovirus B [P14H11F14] in a military training center in China between May and June 2014. In total, 164 military personnel were affected, and two patients were admitted into the intensive care unit of the military regional central hospital. A HAdV-B [P14H11F14] virus was confirmed as the etiological pathogen of this acute outbreak of febrile respiratory illness based on clinical manifestations, epidemiological characteristics, specific molecular detection results, phylogenetic analysis, and serological assays. The virus was isolated by the rhabdomyosarcoma cell culture method, and the complete sequences of the E1A, penton base, hexon, and fiber genes were determined and deposited in the GenBank database. Phylogenetic and sequence homology analyses indicated that the isolated strain is most closely related to some HAdV-55 strains from mainland China. However, this strain appeared to be less virulent than former HAdV-55 strains. According to the chest X-ray results of 31 affected patients, there was no radiological evidence of pneumonia. The most frequent symptoms in these patients were sore throat (95.12 %, 156/164) and tonsillitis (93.29 %, 153/164). During the course of the outbreak, incorrect response measures and some potential risk factors, such as fire training and marching training, may have exacerbated the spread of the infection. This outbreak illustrates the urgent need to improve the epidemiological and etiological surveillance of HAdV infections and to improve the ability of doctors and health officials in basic units of the Chinese army to respond effectively to febrile respiratory illness. url: https://doi.org/10.1007/s00705-016-2949-x doi: 10.1007/s00705-016-2949-x id: cord-289050-9w7ks01n author: Donoso, Alejandro F. title: Fatal hemorrhagic pneumonia caused by human metapneumovirus in an immunocompetent child date: 2008-08-25 words: 1780.0 sentences: 119.0 pages: flesch: 50.0 cache: ./cache/cord-289050-9w7ks01n.txt txt: ./txt/cord-289050-9w7ks01n.txt summary: 5, 6 The aim of the present study was to report the case of a pediatric, immunocompetent patient who presented with severe acute respiratory distress syndrome (ARDS), for whom there was a fatal outcome, and in whom hMPV was the only etiologic agent found even on post-mortem necropsy. Human metapneumovirus could be more severe in patients with underlying medical conditions such as chronic lung disease caused by prematurity, cardiac disease, and immunodefi ciency. The accumulation of cases, however, and comprehensive microbiological analysis including (RT-) PCR for other respiratory viruses are needed to confi rm that infection with hMPV alone can result in such severe lung disease. We believe that the present case should warn us about the occasional role of hMPV as an agent of severe lung infection in children without a predisposing condition. Human metapneumovirus detection in patients with severe acute respiratory syndrome abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/18937761/ doi: 10.1111/j.1442-200x.2008.02673.x id: cord-340317-gwqy6u9x author: Dora, Amy V title: Using Serologic Testing to Assess the Effectiveness of Outbreak Control Efforts, Serial PCR Testing, and Cohorting of Positive SARS-CoV-2 Patients in a Skilled Nursing Facility date: 2020-08-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: We characterized serology following a nursing home outbreak where residents were serially tested by RT-PCR and positive residents were cohorted. When tested 46-76 days later, 24/26 RT-PCR-positive residents were seropositive; none of the 124 RT-PCR-negative residents had confirmed seropositivity, supporting serial SARS-CoV-2 RT-PCR testing and cohorting in nursing homes. url: https://www.ncbi.nlm.nih.gov/pubmed/32857830/ doi: 10.1093/cid/ciaa1286 id: cord-013589-3l8kar3k author: Doummar, Diane title: Biallelic PDE2A variants: a new cause of syndromic paroxysmal dyskinesia date: 2020-05-28 words: 4136.0 sentences: 249.0 pages: flesch: 47.0 cache: ./cache/cord-013589-3l8kar3k.txt txt: ./txt/cord-013589-3l8kar3k.txt summary: A homozygous missense variant leading to drastic decrease of PDE2A enzymatic activity was reported in one patient with childhood-onset choreodystonia preceded by paroxysmal dyskinesia and associated with cognitive impairment and interictal EEG abnormalities. The phenotype of the two oldest patients, aged 9 and 26, was characterized by childhood-onset refractory paroxysmal dyskinesia initially misdiagnosed as epilepsy due to interictal EEG abnormalities. Together with previously reported case, our three patients confirm that biallelic PDE2A variants are a cause of childhood-onset refractory paroxysmal dyskinesia with cognitive impairment, sometimes associated with choreodystonia and interictal baseline EEG abnormalities or epilepsy. reported a missense homozygous variant in PDE2A in a patient with cognitive impairment, interictal EEG abnormalities, and childhoodonset chorea [8] . indicate that biallelic variants in PDE2A leading to loss of function are involved in heterogeneous phenotypes characterized by early-onset paroxysmal hyperkinetic movement disorders associated with cognitive impairment and possibly epilepsy. abstract: Cause of complex dyskinesia remains elusive in some patients. A homozygous missense variant leading to drastic decrease of PDE2A enzymatic activity was reported in one patient with childhood-onset choreodystonia preceded by paroxysmal dyskinesia and associated with cognitive impairment and interictal EEG abnormalities. Here, we report three new cases with biallelic PDE2A variants identified by trio whole-exome sequencing. Mitochondria network was analyzed after Mitotracker™ Red staining in control and mutated primary fibroblasts. Analysis of retrospective video of patients’ movement disorder and refinement of phenotype was carried out. We identified a homozygous gain of stop codon variant c.1180C>T; p.(Gln394*) in PDE2A in siblings and compound heterozygous variants in young adult: a missense c.446C>T; p.(Pro149Leu) and splice-site variant c.1922+5G>A predicted and shown to produce an out of frame transcript lacking exon 22. All three patients had cognitive impairment or developmental delay. The phenotype of the two oldest patients, aged 9 and 26, was characterized by childhood-onset refractory paroxysmal dyskinesia initially misdiagnosed as epilepsy due to interictal EEG abnormalities. The youngest patient showed a proven epilepsy at the age of 4 months and no paroxysmal dyskinesia at 15 months. Interestingly, analysis of the fibroblasts with the biallelic variants in PDE2A variants revealed mitochondria network morphology changes. Together with previously reported case, our three patients confirm that biallelic PDE2A variants are a cause of childhood-onset refractory paroxysmal dyskinesia with cognitive impairment, sometimes associated with choreodystonia and interictal baseline EEG abnormalities or epilepsy. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7608189/ doi: 10.1038/s41431-020-0641-9 id: cord-327069-vjlisnui author: Driscoll, Amanda J. title: Standardization of Laboratory Methods for the PERCH Study date: 2017-06-15 words: 4725.0 sentences: 221.0 pages: flesch: 42.0 cache: ./cache/cord-327069-vjlisnui.txt txt: ./txt/cord-327069-vjlisnui.txt summary: To build capacity at the sites, and in alignment with the priorities of the Bill & Melinda Gates Foundation, all PERCH testing was done locally, with the exception of quality assurance testing and a select subset of specialized assays, which were performed at the study reference laboratory (Canterbury Health Laboratories, Christchurch, New Zealand), which also served as the study specimen and isolate biorepository. Induced sputum, pleural fluid, and lung aspirate specimens were collected in saline in universal containers and either refrigerated at 2°C-8°C for a maximum of 24 hours, or frozen at -80°C prior to nucleic acid extraction. Organism identification was done according to standard microbiological methods that were documented in SOPs and clarified at each site at the outset; antimicrobial susceptibility testing followed the Clinical and Laboratory Standards Institute (CLSI) guidelines [15] . abstract: The Pneumonia Etiology Research for Child Health study was conducted across 7 diverse research sites and relied on standardized clinical and laboratory methods for the accurate and meaningful interpretation of pneumonia etiology data. Blood, respiratory specimens, and urine were collected from children aged 1–59 months hospitalized with severe or very severe pneumonia and community controls of the same age without severe pneumonia and were tested with an extensive array of laboratory diagnostic tests. A standardized testing algorithm and standard operating procedures were applied across all study sites. Site laboratories received uniform training, equipment, and reagents for core testing methods. Standardization was further assured by routine teleconferences, in-person meetings, site monitoring visits, and internal and external quality assurance testing. Targeted confirmatory testing and testing by specialized assays were done at a central reference laboratory. url: https://www.ncbi.nlm.nih.gov/pubmed/28575358/ doi: 10.1093/cid/cix081 id: cord-260690-h5pjv2dw author: Druce, Julian title: Laboratory diagnosis and surveillance of human respiratory viruses by PCR in Victoria, Australia, 2002–2003 date: 2004-11-12 words: 3803.0 sentences: 201.0 pages: flesch: 45.0 cache: ./cache/cord-260690-h5pjv2dw.txt txt: ./txt/cord-260690-h5pjv2dw.txt summary: A total of 333 additional respiratory specimens, including 20 from asymptomatic laboratory staff was used to validate the PCR assays for influenza A virus (H1 and H3 subtypes), influenza B virus, RSV, parainfluenza viruses (at least one of types 1-3), picornaviruses (a mixture of enteroviruses and rhinoviruses), and adenoviruses (each of different serotype) (Table III) . The process included the design and evaluation of primers; optimization of nucleic acid extraction conditions; establishment of optimum PCR amplification conditions; evaluation of applicable specimen types; determination of assay sensitivity compared to conventional assays; specificity testing using clinical material likely to be negative (including asymptomatic staff volunteers); or material previously shown to be positive for respiratory viruses by conventional assays or by sequencing of an amplified product where no other confirmatory method was available. abstract: Respiratory viruses were identified by the polymerase chain reaction (PCR) in more than 4,200 specimens collected during 2002 and 2003 in Victoria, Australia from patients admitted to hospitals or participating in an influenza surveillance program. Influenza viruses and picornaviruses were important causes of morbidity in both years. Additional testing of picornavirus‐positive samples suggested that rhinoviruses but not enteroviruses were more likely to be associated with respiratory symptoms, irrespective of the season in which they circulated. Detection of influenza viruses was strongly associated with the clinical symptoms of cough, fever, and fatigue; but each of the other respiratory viruses occasionally caused these symptoms or was responsible for symptoms severe enough to require hospitalization. Human coronaviruses HCoV‐OC43 and HCoV‐229E circulated at low levels throughout the study period with peak activity in winter, but overall did not circulate as widely as has often been reported for these agents. Evidence for the human metapneumovirus (hMPV) was only sought in the second year of the study and revealed low‐level circulation of this virus, mainly in the cooler months among the very young and adult populations. The detection rate of all viruses declined with increasing age of the patient, particularly in hospital patients. Infection with more than one respiratory virus occurred in a small number of patients; picornaviruses were most commonly implicated in these dual infections. J. Med. Virol. 75:122–129, 2005. © 2005 Wiley‐Liss, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/15543580/ doi: 10.1002/jmv.20246 id: cord-284625-to6w5hm2 author: Duan, Xiaopei title: A retrospective study of the initial 25 COVID-19 patients in Luoyang, China date: 2020-05-26 words: 3347.0 sentences: 183.0 pages: flesch: 55.0 cache: ./cache/cord-284625-to6w5hm2.txt txt: ./txt/cord-284625-to6w5hm2.txt summary: Given the concept of the early diagnosis and treatment of SARS-CoV-2, this article mainly focused on the 25 initial laboratory-confirmed patients in the Luoyang area, discussing their imaging features and clinical characteristics. From January 10 to February 8, 2020, 25 patients with laboratory-confirmed SARS-CoV-2 infection in the area of Luoyang, Henan Province, China, were enrolled in the study. In addition, COVID-19 patients were not found to have combined a On the admission day, the unenhanced CT scan shows diffuse bilateral multiple patchy GGO (white arrow), and the partial boundary is clear while some have unclear boundaries, which are especially significant in the lower lobes of both lungs; strip consolidative opacities (black arrow) are in the focal area. A woman who is the wife of the patient 3 and mother of patient 22 had two negative PCR results, but the lesions in her lung had the same progression, and the blood test also confirmed the SARS-CoV-2 infection. abstract: PURPOSE: To summarize the chest CT imaging and clinical features of the initial COVID-19 patients and provide a clinical diagnostic method that is more effective and can be performed earlier. METHODS: This retrospective study investigated the clinical, laboratory and imaging information of 25 patients in the Luoyang area. There were 15 (60%) male and 10 (40%) female patients ranging from 24 to 88 years old (52 ± 19.30). Data were analyzed by Microsoft Excel and are expressed as the mean ± standard deviation or percentage. RESULTS: Thirteen (52%) patients had been in Wuhan or were in contact with people who had been in Wuhan, and ten (40%) patients were infected by their families or colleagues. The median time from initial symptoms to diagnosis was 7 days. Ninety-two percent of patients had respiratory symptoms, and 8% of them had digestive symptoms. Fever (92%), cough (60%) and fatigue (56%) were the most common symptoms. Most patients had a normal or reduced WBC (96%), reduced lymphocyte count (60%), increased CRP (48%) and increased ESR (44%). Ground glass opacity (GGO) was the typical radiological finding on chest CT. CONCLUSION: Characteristic chest CT imaging features could appear earlier than the viral nucleic acid assay results. url: https://www.ncbi.nlm.nih.gov/pubmed/32458125/ doi: 10.1007/s11604-020-00988-4 id: cord-307702-n74wvika author: Durant, Thomas J S title: Impact of COVID-19 Pandemic on Laboratory Utilization date: 2020-07-14 words: 2811.0 sentences: 162.0 pages: flesch: 44.0 cache: ./cache/cord-307702-n74wvika.txt txt: ./txt/cord-307702-n74wvika.txt summary: METHODS: We performed a retrospective assessment of laboratory test order and specimen container utilization at a single, urban tertiary care medical center. We performed a retrospective assessment of laboratory test order and specimen container utilization at a single, urban tertiary care medical center. Total testing volumes were calculated during the first and last two-weeks of the observation period and used as reference points to examine the absolute and relative differences in test order volume between the pre-pandemic and COVID-19 surge periods. Total testing volumes were calculated during the first and last two-weeks of the observation period and used as reference points to examine the absolute and relative differences in test order volume between the pre-pandemic and COVID-19 surge periods. While volume increases were seen for laboratory tests related to COVID-19 diagnostics and management, including some with limited evidence to support their use, overall testing volumes decreased substantially. abstract: BACKGROUND: Coronavirus Disease 2019 (COVID-19) was formally characterized as a pandemic on March 11, 2020. Since that time, the COVID-19 pandemic has led to unprecedented demand for healthcare resources. The purpose of this study was to identify changes in laboratory test utilization in the setting of increasing local incidence of COVID-19. METHODS: We performed a retrospective assessment of laboratory test order and specimen container utilization at a single, urban tertiary care medical center. Data were extracted from the laboratory information system database over a 10-week period, spanning the primordial inflection of COVID-19 incidence in our region. Total testing volumes were calculated during the first and last two-weeks of the observation period and used as reference points to examine the absolute and relative differences in test order volume between the pre-pandemic and COVID-19 surge periods. RESULTS: Between February 2, 2020 and April 11, 2020, there were 873,397 tests ordered and final verified. The in-house SARS-CoV-2 PCR positivity rate for admitted patients in the last week of the observation period was 30.8%. Significant increases in workload were observed in the send-out laboratory section and for COVID-19 diagnosis (PCR) and management-related testing. Otherwise, there was a net decrease in overall demand across nearly all laboratory sections. Increases in testing were noted for tests related to COVID-19 management. Viral transport media and citrated blue top containers demonstrated increases in utilization. CONCLUSION: Increasing local incidence of COVID-19 had a profound impact on laboratory operations. While volume increases were seen for laboratory tests related to COVID-19 diagnostics and management, including some with limited evidence to support their use, overall testing volumes decreased substantially. During events such as COVID-19, monitoring of such patterns can help inform laboratory management, staffing, and test stewardship recommendations for managing resource and supply availability. url: https://doi.org/10.1093/jalm/jfaa121 doi: 10.1093/jalm/jfaa121 id: cord-291281-ygrh8ces author: Durner, J. title: Critical Questions when Interpreting Coronavirus PCR Diagnostics date: 2020-06-14 words: 1912.0 sentences: 121.0 pages: flesch: 57.0 cache: ./cache/cord-291281-ygrh8ces.txt txt: ./txt/cord-291281-ygrh8ces.txt summary: In contrast to other PCR examinations, or laboratory medical analyses, currently SARS-CoV-2 diagnostic information about the device or the detection limit / sensitivity is not usually provided by the laboratory. Using a protocol without purification of viral RNA, i.e. the Munich Extraction Protocol (MEP) [2] , we could show that the type of transport medium had little influence on the detection sensitivity of SARS-CoV-2 in the PCR (Table 1) . By using this system, the sensitivity could be increased by at least one more dilution step compared to the use of commercial purification methods in PCR (Table 3) . . https://doi.org/10.1101/2020.06.11.20127241 doi: medRxiv preprint Table 1 Comparison of different types of transport media for their influence on the detectability of SARS-CoV-2. . https://doi.org/10.1101/2020.06.11.20127241 doi: medRxiv preprint Table 2 Comparison of different purification systems for their influence on the detectability of SARS-CoV-2 (Cp = crossing point). abstract: The results of PCR measurements are regarded as unquestionable. This statement must be put into perspective. This relativization is particularly important in connection with the interpretation of SARS-CoV-2 results. Members of the critical infrastructure, such as nurses, may be quarantined although this is not necessary and are therefore missing from patient care. With our small but impressive comparison of methods and transport media for SARS-CoV-2, we not only show the different sensitivity of common routine systems and media in laboratory medicine. Further, we would like to inform clinically working physicians, who are not familiar with the technical weaknesses of the PCR investigation, about gaps and present solutions for their daily work. url: http://medrxiv.org/cgi/content/short/2020.06.11.20127241v1?rss=1 doi: 10.1101/2020.06.11.20127241 id: cord-274828-67yeag50 author: Dybkær, Karen title: Identification of acute myeloid leukemia patients with diminished expression of CD13 myeloid transcripts by competitive reverse transcription polymerase chain reaction (RT-PCR) date: 2000-04-21 words: 6048.0 sentences: 342.0 pages: flesch: 50.0 cache: ./cache/cord-274828-67yeag50.txt txt: ./txt/cord-274828-67yeag50.txt summary: In this study we determine surface expression and transcript levels of CD13 within mononuclear cells originating from 40 AML patients with median blast percent of 90% and four healthy controls. Mononuclear cells of bone marrow aspirations from 40 AML patients and four healthy controls were analysed by competitive RT-PCR, and content of CD13 and GAPDH transcripts were determined. For the 32 AML patients and the four healthy controls having intermediate to high values of normalised CD13 transcripts levels there was a linear correlation between normalised CD13 transcript levels and cell surface expression of CD13 (r = 0.59, P B 0.001, n = 36). Such differences of up to 200-fold variation in normalised transcript levels were found only for AML patients having less than 15% surface expression of CD13 antigen. The diversity of normalised CD13 transcript levels found for patients with less than 15% CD13 antigen on the surface of their mononuclear cells was not caused by limitations of the competitive RT-PCR method. abstract: Normal myeloid cells of monocytic and granulocytic origin express the metallopeptidase cluster of differentiation 13 (CD13) on the surface just as leukemic blasts in most acute myeloid leukemias (AML). A minor percentage of AML patients, however, lack the surface expression of CD13 antigen. To study this difference in CD13 surface expression, specific CD13 mRNA from 44 individuals were quantified by competitive reverse transcription polymerase chain reaction (RT-PCR). Absolute values for CD13 transcripts were normalised against glyceraldehyde-3-phosphate dehydrogenase (GAPDH) transcript levels to control for variations in sample preparation and mRNA degradation. By correlating normalised CD13 transcript levels and CD13 surface expression, a subgroup of AML patients was identified, having simultaneous diminished levels of myeloid CD13 transcripts and surface expression of the corresponding antigen. For this subgroup we suggest CD13/aminopeptidase N (APN) gene expression to be restricted primarily by limited amounts of transcripts. For the majority of AML patients determinants in addition to transcript levels must be involved in regulating CD13/APN gene expression. url: https://www.ncbi.nlm.nih.gov/pubmed/10781684/ doi: 10.1016/s0145-2126(00)00021-7 id: cord-311982-wkg56xeq author: Dye, Charlotte title: Genomic RNA sequence of feline coronavirus strain FCoV C1Je date: 2007-06-17 words: 5240.0 sentences: 250.0 pages: flesch: 55.0 cache: ./cache/cord-311982-wkg56xeq.txt txt: ./txt/cord-311982-wkg56xeq.txt summary: Comparisons of the enteric (jejunum) and non-enteric (liver) derived viral RNA sequences revealed 100% nucleotide identity, a finding that questions the well accepted ''internal mutation theory'' of FIPV pathogenicity. Comparisons of the enteric (jejunum) and non-enteric (liver) derived viral RNA sequences revealed 100% nucleotide identity, a finding that questions the well accepted ''internal mutation theory'' of FIPV pathogenicity. Furthermore, the structural and accessory gene regions of viral RNA isolated from the liver of the same cat (FCoV C1Li) were sequenced and the data derived from the enteric (jejunum) and non-enteric (liver) sources were compared. Sequence data previously generated for the laboratory strain FCoV, FIPV 79-1146, were used to design primers for conventional reverse transcriptase polymerase chain reaction (RT-PCR) amplification of short lengths (100e500 bases) of the field strain RNA. Analysis of the accessory gene 7 region of the FCoV C1Je genome identifies two ORFs, which have translation products sharing high amino acid identity with proteins 7a and 7b of FIPV 79-1146. abstract: This paper reports the first genomic RNA sequence of a field strain feline coronavirus (FCoV). Viral RNA was isolated at post mortem from the jejunum and liver of a cat with feline infectious peritonitis (FIP). A consensus sequence of the jejunum-derived genomic RNA (FCoV C1Je) was determined from overlapping cDNA fragments produced by reverse transcriptase polymerase chain reaction (RT-PCR) amplification. RT-PCR products were sequenced by a reiterative sequencing strategy and the genomic RNA termini were determined using a rapid amplification of cDNA ends PCR strategy. The FCoV C1Je genome was found to be 29,255 nucleotides in length, excluding the poly(A) tail. Comparison of the FCoV C1Je genomic RNA sequence with that of the laboratory strain FCoV FIP virus (FIPV) 79-1146 showed that both viruses have a similar genome organisation and predictions made for the open reading frames and cis-acting elements of the FIPV 79-1146 genome hold true for FCoV C1Je. In addition, the sequence of the 3′-proximal third of the liver derived genomic RNA (FCoV C1Li), which encompasses the structural and accessory protein genes of the virus, was also determined. Comparisons of the enteric (jejunum) and non-enteric (liver) derived viral RNA sequences revealed 100% nucleotide identity, a finding that questions the well accepted ‘internal mutation theory’ of FIPV pathogenicity. url: https://www.ncbi.nlm.nih.gov/pubmed/17363313/ doi: 10.1016/j.jfms.2006.12.002 id: cord-323987-gh1m05gi author: Dziąbowska, Karolina title: Detection Methods of Human and Animal Influenza Virus—Current Trends date: 2018-10-18 words: 11112.0 sentences: 760.0 pages: flesch: 46.0 cache: ./cache/cord-323987-gh1m05gi.txt txt: ./txt/cord-323987-gh1m05gi.txt summary: RIDTs with digital readout systems showed many similarities to conventional assays like small sample volume (less than 150 µL) and short analysis time (around 15 min) but exhibited much better sensitivities, even one order of magnitude lower limits of detection (LODs). Among methods mentioned, general diagnostic tests for influenza base on virus culture (conventional and shellvial), detection of viral nucleic acid (PCR) or antigens (by neuraminidase enzymatic activity, fluorescent antibody or enzyme/optical immunoassay) and serologic tests. Main trends for influenza virus detection are: (I) modifications of traditional ''gold star'' methods like PCR, RIDTs, ELISA what results in analysis time shortening, costs lowering, LOD and limit of quantification (LOQ) improvement, (II) conjugating of traditional methods and creating new platforms, micro-biochips and others, (III) introducing known solutions to new ones, like smartphone-based analysis control with results data insertion into Google Maps, (IV) reuse of the functions of known devices, like glucometer, smartphone cameras, (V) the most common used detection methods: spectral/optical, electrical, (VI) and entirely new approaches. abstract: The basic affairs connected to the influenza virus were reviewed in the article, highlighting the newest trends in its diagnostic methods. Awareness of the threat of influenza arises from its ability to spread and cause a pandemic. The undiagnosed and untreated viral infection can have a fatal effect on humans. Thus, the early detection seems pivotal for an accurate treatment, when vaccines and other contemporary prevention methods are not faultless. Public health is being attacked with influenza containing new genes from a genetic assortment between animals and humankind. Unfortunately, the population does not have immunity for mutant genes and is attacked in every viral outbreak season. For these reasons, fast and accurate devices are in high demand. As currently used methods like Rapid Influenza Diagnostic Tests lack specificity, time and cost-savings, new methods are being developed. In the article, various novel detection methods, such as electrical and optical were compared. Different viral elements used as detection targets and analysis parameters, such as sensitivity and specificity, were presented and discussed. url: https://doi.org/10.3390/bios8040094 doi: 10.3390/bios8040094 id: cord-022889-lv6fy6e6 author: Dávalos, Alberto title: Literature review of baseline information on non‐coding RNA (ncRNA) to support the risk assessment of ncRNA‐based genetically modified plants for food and feed date: 2019-08-07 words: 96011.0 sentences: 5041.0 pages: flesch: 51.0 cache: ./cache/cord-022889-lv6fy6e6.txt txt: ./txt/cord-022889-lv6fy6e6.txt summary: This report suggests that some plant ncRNAs (e.g miRNAs and siRNAs) show higher stability as compared to other ncRNAs due to peculiar chemical characteristics (2''‐O‐methylation at 3'' end).However, ingested or administered ncRNA must overcome many extracellular and cellular barriers to reach the intended target tissue or functional location in sufficient amount to exert any biological effect. Finally, the publications reporting the outcome of two EFSA procurements aiming respectively at investigating and summarising the state of knowledge on the mode-of-action of dsRNA and miRNA pathways, the potential for non-target gene regulation by dsRNA-derived siRNAs or miRNAs, the determination of siRNA pools in plant tissues and the importance of individual siRNAs for silencing 6 ; and reviewing relevant scientific information on RNA interference that could serve as baseline information for the environmental risk assessment of RNAi-based GM plants ) 7 were also used. abstract: This report is the outcome of an EFSA procurement (NP/EFSA/GMO/2016/01) reviewing relevant scientific information on ncRNA and on RNA interference(RNAi) that could support the food and feed risk assessment of ncRNA‐based genetically modified (GM) plants. Information was retrieved through key words and key questions covering the stability and degradation of ncRNAs after oral ingestion, the passage of ncRNAs from food and feed to human and animal organs and tissues via the gastrointestinal tract and other barriers, as well as the potential effects on the gastrointestinal tract, the immune system or the entire organism.Full description of the strategy used for the literature search and for studies selectionis provided and the number of retrieved publications is reported. This report is divided into four partsdiscussing the kinetics of exogenous ncRNAs in humans and animals, with focus on ingested ncRNAs (Part 1); the possible effects of ncRNAs on the gastrointestinal tract (Part 2), systemically(Part 3)and on the immune system (Part 4). This report suggests that some plant ncRNAs (e.g miRNAs and siRNAs) show higher stability as compared to other ncRNAs due to peculiar chemical characteristics (2’‐O‐methylation at 3’ end).However, ingested or administered ncRNA must overcome many extracellular and cellular barriers to reach the intended target tissue or functional location in sufficient amount to exert any biological effect. Literature data indicate that chemically unmodified and unformulated ncRNAs exhibit very low stability in the gastrointestinal tract and in biological fluids and, in general, do not elicit major biological effects.This report also provides an overview of the RNA content in plant‐derived foods and diets and discusses the controversies on the presence of dietary exogenous RNAs in the biological fluids of humans and animals and their effects. Finally, gaps in the scientific literature are highlighted and recommendations provided url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7163523/ doi: 10.2903/sp.efsa.2019.en-1688 id: cord-352720-z1cvjc2y author: Díaz-Corvillón, Pilar title: Routine screening for SARS CoV-2 in unselected pregnant women at delivery date: 2020-09-29 words: 4061.0 sentences: 244.0 pages: flesch: 49.0 cache: ./cache/cord-352720-z1cvjc2y.txt txt: ./txt/cord-352720-z1cvjc2y.txt summary: While initial evidence suggests that pregnant women were not at increased risk for COVID-19, neither developed a more severe disease compared to non-pregnant adults [3, 4] , recent reports suggest increased rates of preterm birth [5] , pneumonia and intensive care unit admission [6] , and maternal mortality [6, 7] . The main objective of this study was to assess point-prevalence of SARS CoV-2 infection in unselected obstetrical population at the time of delivery and to describe the presentation and clinical evolution of confirmed cases. women were screened for COVID-19 clinical symptoms including fever, cough and shortness of breath by trained personnel, and RT-PCR for SARS CoV-2 (Allplex TM 2019-nCoV Assay [17] ) was performed by nasopharyngeal swab, unless a prior test with no more than 48 hours to admission was reported. abstract: BACKGROUND: South America has become the epicenter of coronavirus pandemic. It seems that asymptomatic population may contribute importantly to the spread of the disease. Transmission from asymptomatic pregnant patients’ needs to be characterized in larger population cohorts and symptom assessment needs to be standardized. OBJECTIVE: To assess the prevalence of SARS CoV-2 infection in an unselected obstetrical population and to describe their presentation and clinical evolution. METHODS: A cross-sectional study was designed. Medical records of pregnant women admitted at the Obstetrics & Gynecology department of Clínica Dávila for labor & delivery, between April 27(th) and June 7(th), 2020 were reviewed. All patients were screened with RT-PCR for SARS CoV-2 at admission. After delivery, positive cases were inquired by the researchers for clinical symptoms presented before admission and clinical evolution. All neonates born from mothers with confirmed SARS CoV-2 were isolated and tested for SARS CoV-2 infection. RESULTS: A total of 586 patients were tested for SARS CoV-2 during the study period. Outcomes were obtained from 583 patients which were included in the study. Thirty-seven pregnant women had a positive test for SARS CoV-2 at admission. Cumulative prevalence of confirmed SARS CoV-2 infection was 6.35% (37/583) [CI 95%: 4.63–8.65]. From confirmed cases, 43.2% (16/37) were asymptomatic. From symptomatic patients 85.7% (18/21) had mild symptoms and evolved without complications and 14.3% (3/21) presented severe symptoms requiring admission to intensive care unit. Only 5.4% (2/37) of the neonates born to mothers with a positive test at admission had a positive RT-PCR for SARS CoV-2. CONCLUSION: In our study nearly half of pregnant patients with SARS CoV-2 were asymptomatic at the time of delivery. Universal screening, in endemic areas, is necessary for adequate patient isolation, prompt neonatal testing and targeted follow-up. url: https://www.ncbi.nlm.nih.gov/pubmed/32991621/ doi: 10.1371/journal.pone.0239887 id: cord-282321-svoshzz8 author: Eboigbodin, Kevin title: Reverse transcription strand invasion based amplification (RT-SIBA): a method for rapid detection of influenza A and B date: 2016-04-11 words: 4409.0 sentences: 217.0 pages: flesch: 48.0 cache: ./cache/cord-282321-svoshzz8.txt txt: ./txt/cord-282321-svoshzz8.txt summary: The RT-SIBA method includes a reverse transcriptase enzyme that allows one-step reverse transcription of RNA to complementary DNA (cDNA) and simultaneous amplification and detection of the cDNA by SIBA under isothermal reaction conditions. The RT-SIBA method includes a reverse transcriptase enzyme that allows a one-step reverse transcription of RNA to cDNA and simultaneous amplification and detection of the cDNA with SIBA under isothermal reaction conditions. The use of an Influenza A assay IO with no seeding region resulted in reactions with the longest detection time, suggesting that the seeding region is of vital importance for efficient amplification of the target DNA. The recombinasemediated target duplex separation and polymerase-mediated extension are the basis for exponential amplification conclusion, IOs for both influenza A and B assays used in the following experiments were designed to contain seeding regions consisting of a polyC sequence of 10 and 14 nucleotides in length, respectively. abstract: Rapid and accurate diagnosis of influenza viruses plays an important role in infection control, as well as in preventing the misuse of antibiotics. Isothermal nucleic acid amplification methods offer significant advantages over the polymerase chain reaction (PCR), since they are more rapid and do not require the sophisticated instruments needed for thermal cycling. We previously described a novel isothermal nucleic acid amplification method, ‘Strand Invasion Based Amplification’ (SIBA®), with high analytical sensitivity and specificity, for the detection of DNA. In this study, we describe the development of a variant of the SIBA method, namely, reverse transcription SIBA (RT-SIBA), for the rapid detection of viral RNA targets. The RT-SIBA method includes a reverse transcriptase enzyme that allows one-step reverse transcription of RNA to complementary DNA (cDNA) and simultaneous amplification and detection of the cDNA by SIBA under isothermal reaction conditions. The RT-SIBA method was found to be more sensitive than PCR for the detection of influenza A and B and could detect 100 copies of influenza RNA within 15 min. The development of RT-SIBA will enable rapid and accurate diagnosis of viral RNA targets within point-of-care or central laboratory settings. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00253-016-7491-y) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/27063012/ doi: 10.1007/s00253-016-7491-y id: cord-319970-1gu0a6cb author: Edin, Alicia title: Development and Laboratory Evaluation of a Real-Time PCR Assay for Detecting Viruses and Bacteria of Relevance for Community-Acquired Pneumonia date: 2015-03-13 words: 5049.0 sentences: 238.0 pages: flesch: 39.0 cache: ./cache/cord-319970-1gu0a6cb.txt txt: ./txt/cord-319970-1gu0a6cb.txt summary: title: Development and Laboratory Evaluation of a Real-Time PCR Assay for Detecting Viruses and Bacteria of Relevance for Community-Acquired Pneumonia Diagnostic accuracy of the qPCR assay varied between 60% positive agreement with standard tests for Streptococcus pneumoniae and 100% for Mycoplasma pneumoniae, Moraxella catarrhalis, and Staphylococcus aureus. To verify that the method could detect viruses in sputum, sputum specimens each with a volume of 350 mL were spiked with100 mL from a NpA specimen positive for either RSV or influenza A before nucleic acid extraction and qPCR assay analysis were performed as described in the sections DNA and RNA Extraction and Primers Probes and qPCR Conditions, respectively. In the evaluation of the assay performance for detection of virus in sputum, we found that sputum specimens spiked with influenza A-or RSV-containing NpA specimens were positive at 25.9 AE 0.6 (n Z 5) and 27.7 AE 1.1 (n Z 5) cycles, respectively. abstract: Community-acquired pneumonia may present with similar clinical symptoms, regardless of viral or bacterial cause. Diagnostic assays are needed to rapidly discriminate between causes, because this will guide decisions on appropriate treatment. Therefore, a quantitative real-time PCR (qPCR) assay with duplex reactions targeting eight bacteria and six viruses was developed. Technical performance was examined with linear plasmids. Upper and lower respiratory tract specimens were used to compare the qPCR assay with standard microbiological methods. The limit of detection was 5 to 20 DNA template copies with approximately 1000-fold differences in concentrations of the two competing templates. SDs for positive controls were <5%. The use of the qPCR assay resulted in 113 positive identifications in 94 respiratory specimens compared with 38 by using standard diagnostics. Diagnostic accuracy of the qPCR assay varied between 60% positive agreement with standard tests for Streptococcus pneumoniae and 100% for Mycoplasma pneumoniae, Moraxella catarrhalis, and Staphylococcus aureus. Negative percentage of agreement was >95% for M. pneumoniae, Streptococcus pyogenes, respiratory syncytial virus, and influenza A virus; whereas it was only 56% for Haemophilus influenzae. Multiple microbial agents were identified in 19 of 44 sputum and 19 of 50 nasopharynx specimens. We conclude that in parallel qPCR detection of the targeted respiratory bacteria and viruses is feasible. The results indicate good technical performance of the assay in clinical specimens. url: https://doi.org/10.1016/j.jmoldx.2015.01.005 doi: 10.1016/j.jmoldx.2015.01.005 id: cord-312197-d5d8amk7 author: Edmond, Karen title: New Approaches to Preventing, Diagnosing, and Treating Neonatal Sepsis date: 2010-03-09 words: 5224.0 sentences: 259.0 pages: flesch: 38.0 cache: ./cache/cord-312197-d5d8amk7.txt txt: ./txt/cord-312197-d5d8amk7.txt summary: Health facility infections are also a major problem in lowincome countries, but the more pressing issues are the high proportion of home deliveries in unclean environments predisposing to sepsis and ensuring that all neonates have access to effective interventions from health care providers in the first days of life 2 . Randomised controlled trials (RCTs) of maternal protein-calorie and multiple micronutrient and supplementation have demonstrated significant improvements in rates of prematurity and birth weight and variable impact on mortality; but no studies have examined their impact on rates of neonatal sepsis [20, 21] . New studies from Malawi and Nepal indicate that maternal antisepsis interventions such as vaginal chlorhexidine during labour may have a significant impact on rates of neonatal mortality and sepsis in developing countries [33] . Intrapartum antibiotic prophylaxis has been highly effective in reducing both early-onset neonatal bacterial and maternal sepsis in developed countries [35] . abstract: Karen Edmond and Anita Zaidi highlight new approaches that could reduce the burden of neonatal sepsis worldwide. url: https://www.ncbi.nlm.nih.gov/pubmed/20231868/ doi: 10.1371/journal.pmed.1000213 id: cord-321284-0y69n1ea author: El Kholy, A. A. title: The use of multiplex PCR for the diagnosis of viral severe acute respiratory infection in children: a high rate of co-detection during the winter season date: 2016-06-10 words: 3345.0 sentences: 175.0 pages: flesch: 46.0 cache: ./cache/cord-321284-0y69n1ea.txt txt: ./txt/cord-321284-0y69n1ea.txt summary: title: The use of multiplex PCR for the diagnosis of viral severe acute respiratory infection in children: a high rate of co-detection during the winter season This study confirms the high rate of detection of viral nucleic acids by multiplex PCR among hospitalized children admitted with SARI, as well as the high rate of co-detection of multiple viruses. Forty healthy age-matched asymptomatic children with no history of a recent respiratory tract infection during the previous 2 weeks, who were not admitted to the hospital, and who do not have any chronic underlying illness were included as a control group. This study confirms the high rate of detection of viral nucleic acids by multiplex PCR) among hospitalized children admitted with severe acute respiratory infection, as well as the high rate of detection of multiple viruses. abstract: Respiratory tract infection is a major cause of hospitalization in children. Although most such infections are viral in origin, it is difficult to differentiate bacterial and viral infections, as the clinical symptoms are similar. Multiplex polymerase chain reaction (PCR) methods allow testing for multiple pathogens simultaneously and are, therefore, gaining interest. This prospective case-control study was conducted from October 2013 to February 2014. Nasopharyngeal (NP) and oropharyngeal (throat) swabs were obtained from children admitted with severe acute respiratory infection (SARI) at a tertiary hospital. A control group of 40 asymptomatic children was included. Testing for 16 viruses was done by real-time multiplex PCR. Multiplex PCR detected a viral pathogen in 159/177 (89.9 %) patients admitted with SARI. There was a high rate of co-infection (46.9 %). Dual detections were observed in 64 (36.2 %), triple detections in 17 (9.6 %), and quadruple detections in 2 (1.1 %) of 177 samples. Seventy-eight patients required intensive care unit (ICU) admission, of whom 28 (35.8 %) had co-infection with multiple viruses. AdV, HBoV, HRV, HEV, and HCoV-OC43 were also detected among asymptomatic children. This study confirms the high rate of detection of viral nucleic acids by multiplex PCR among hospitalized children admitted with SARI, as well as the high rate of co-detection of multiple viruses. AdV, HBoV, HRV, HEV, and HCoV-OC43 were also detected in asymptomatic children, resulting in challenges in clinical interpretation. Studies are required to provide quantitative conclusions that will facilitate clinical interpretation and application of the results in the clinical setting. url: https://doi.org/10.1007/s10096-016-2698-5 doi: 10.1007/s10096-016-2698-5 id: cord-011322-olvqgs85 author: El-Senousy, Waled M. title: Clinical and Environmental Surveillance of Rotavirus Common Genotypes Showed High Prevalence of Common P Genotypes in Egypt date: 2020-04-11 words: 9515.0 sentences: 482.0 pages: flesch: 53.0 cache: ./cache/cord-011322-olvqgs85.txt txt: ./txt/cord-011322-olvqgs85.txt summary: The objective of this study was to compare the prevalence of human rotavirus group A common G and P genotypes in human Egyptian stool specimens and raw sewage samples to determine the most common genotypes for future vaccine development. Also, previous studies reported that rotavirus group A was the most frequent RNA enteric viruses in Egyptian clinical specimens and aquatic environment and was the most resistant one to sewage and water treatment processes (El-Senousy et al. The present study was conducted to estimate the burden of rotavirus gastroenteritis as well as to compare the prevalence of rotavirus common G and P genotypes among children ≤ 5 years of age visiting Abo El-Reech hospital (from Oct. 2015 to Sep. 2017 ) and in raw sewage samples collected from WWTPs in Greater Cairo during winter and autumn months in the same period to determine the most common G and P genotypes for future vaccine development. abstract: The objective of this study was to compare the prevalence of human rotavirus group A common G and P genotypes in human Egyptian stool specimens and raw sewage samples to determine the most common genotypes for future vaccine development. From 1026 stool specimens of children with acute diarrhea and using nested RT-PCR, 250 samples (24.37%) were positive for human rotavirus group A. Using multiplex RT-PCR, rotavirus common P and G genotypes were detected as 89.20% and 46.40% of the positive clinical specimens respectively. This low percentage of common G genotypes frequency may affect the efficiency of the available live attenuated oral rotavirus vaccines [Rotarix® (human rotavirus G1P[8]) and RotaTeq® (reassortant bovine–human rotavirus G1-4P[5] and G6P[8])], however the percentage of clinical specimens which were negative for common G genotypes but positive for P[8] genotype was 12.00%. From 24 positive raw sewage samples for rotavirus group A VP6 collected from Zenin and El-Gabal El-Asfar wastewater treatment plants (WWTPs), 21 samples (87.50%) were typeable for common P genotypes while 13 samples (54.17%) were typeable for common G genotypes. Phylogenetic analysis of a VP8 partial gene of 45 P-typeable clinical isolates and 20 P-typeable raw sewage samples showed high similarity to reference strains and the majority of mutations were silent and showed lower to non-significant similarity with the two vaccine strains. This finding is useful for determining the most common antigens required for future vaccine development. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12560-020-09426-0) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7224034/ doi: 10.1007/s12560-020-09426-0 id: cord-013416-ooq1q5gy author: El-Tholoth, Mohamed title: Molecular Characterization and Developing a Point-of-Need Molecular Test for Diagnosis of Bovine Papillomavirus (BPV) Type 1 in Cattle from Egypt date: 2020-10-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: SIMPLE SUMMARY: Bovine papillomatosis is a disease caused by bovine papillomavirus (BPV), which is a diverse group of oncogenic viruses that challenge cattle industry, resulting in significant economic losses. The present study investigated the occurrence of bovine papillomatosis among cattle (n = 308) with cutaneous warts on the head and neck from New valley Province, Egypt through molecular detection of BPV-1, -2, -4, -5, and -10. The work also involved a phylogenetic analysis of the positive samples for detection of the genetic relatedness of the virus. Interestingly, BPV-1 DNA was detected in 84.6% of the collected samples. Furthermore, the study included the development of an isothermal nucleic acid amplification test, which is a field test combining molecular and lateral flow immunoassays for point-of-need testing appropriate for veterinary use in resource-limited settings. Collectively, our study provided interesting data related to the combined use of molecular and immunoassays methods in the detection of the virus besides better understanding the genetic relatedness of the circulating genotypes of BPV-1 in Egypt. Our study suggested further research to explore more about the other genotypes of BPV in the Egyptian environment that could be helpful for the implementation of control strategies for combating this disease. ABSTRACT: Bovine papillomatosis is a viral disease of cattle causing cutaneous warts. A diagnosis of this viral infection is very mandatory for combating the resulting economic losses. Given the limited data available about bovine papillomavirus (BPV) in Egypt, the present study involved the molecular diagnosis of bovine papillomavirus type-1 (BPV-1), -2, -4, -5, and -10 in cattle presenting cutaneous warts on the head and neck from New Valley Province, Egypt. The phylogenetic analysis of the detected types of BPV was also performed, followed by developing a point-of-need molecular assay for the rapid identification of identified BPV types. In this regard, a total of 308 cattle from private farms in Egypt were clinically examined, of which 13 animals presented cutaneous warts due to suspected BPV infection. The symptomatic animals were treated surgically, and biopsies from skin lesions were collected for BPV-1, -2, -4, -5, and -10 molecular identification using polymerase chain reaction (PCR). The presence of BPV-1 DNA was confirmed in 11 collected samples (84.6%), while BPV-2, -4, -5, and -10 were not detected. Sequencing of the PCR products suggested the Egyptian virus is closely related to BPV found in India. An isothermal nucleic acid amplification test (NAAT) with labeled primers specific for the BPV-1 L1 gene sequence, and based on recombinase polymerase amplification (RPA), in combination with a lateral flow strip assay for the detection of RPA products, was developed and tested. The point-of-need molecular assay demonstrated a diagnostic utility comparable to PCR-based testing. Taken together, the present study provides interesting molecular data related to the occurrence of BPV-1 in Egypt and reveals the genetic relatedness of the Egyptian BPV-1 with BPV-1 found in buffalo in India. In addition, a simple, low-cost combined test was also validated for diagnosis of the infection. The present study suggests the necessity of future investigations about the circulating strains of the virus among the cattle in Egypt to assess their genetic relatedness and better understand the epidemiological pattern of the disease. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7588879/ doi: 10.3390/ani10101929 id: cord-263570-6notzm6s author: Elia, Gabriella title: Detection of infectious canine parvovirus type 2 by mRNA real-time RT-PCR date: 2007-08-10 words: 3990.0 sentences: 224.0 pages: flesch: 58.0 cache: ./cache/cord-263570-6notzm6s.txt txt: ./txt/cord-263570-6notzm6s.txt summary: The load and distribution of CPV-2 mRNA in samples from infected dogs were estimated in comparison with the load of virus DNA, as evaluated by real-time PCR. The analytic specificity of spliced CPV-2 mRNA detection by real-time RT-PCR was assessed by testing RNA and DNA preparations of other canine pathogens, including canine coronavirus types I and II (CCoVI, CCoVII) (Decaro et al., 2005d) , canine distemper virus (CDV) (Elia et al., 2006) , canine adenovirus (CAdV) (Decaro et al., 2006a) , reoviruses (Decaro et al., 2005b) and rotaviruses . To compare the amount of viral DNA in the tissue samples and in the infected cell cultures, a real-time PCR assay was used as described previously (Decaro et al., 2005c) . The newly developed real-time RT-PCR assay was applied to determine the viral mRNA loads in different tissues of CPV-2 naturally infected dogs. A real-time PCR assay for rapid detection and quantitation of canine parvovirus type 2 DNA in the feces of dogs abstract: A TaqMan real-time RT-PCR assay was developed for detection of RNA transcripts produced by replicating CPV-2. A pair of primers and a TaqMan probe targeting the spliced NS2 mRNA were designed. A synthetic DNA fragment was constructed to mimic the spliced NS2 mRNA by PCR-based gene assembly and was used for generation of standard RNAs. The detection limit of the assay was 1 × 10(2) RNA copies and standard curve displayed a linear range from 1 × 10(2) to 1 × 10(9) copies and a good reproducibility. The assay was then applied to determine the mRNA loads in the tissues of dogs naturally infected by CPV-2. mRNA was detected in a variety of tissues, including the central nervous system. url: https://www.ncbi.nlm.nih.gov/pubmed/17692932/ doi: 10.1016/j.jviromet.2007.06.017 id: cord-274184-hm516x6p author: Elli, Luca title: Endoscopy during the Covid-19 outbreak: experience and recommendations from a single center in a high-incidence scenario date: 2020-04-27 words: 4843.0 sentences: 280.0 pages: flesch: 50.0 cache: ./cache/cord-274184-hm516x6p.txt txt: ./txt/cord-274184-hm516x6p.txt summary: From the abovementioned reasons we must deduce that: -in high SARS-CoV-2 incidence areas where PCR assays are not extensively performed, Covid-19 cannot be ruled out by simple clinical examination or epidemiological link; -the greatest amount of efforts and precautions are required to minimize the spread of the disease and to preserve medical staff from infection. In our current situation, which is characterized by high incidence of Covid-19 and relative scarcity of surveillance assays in asymptomatic subjects, for the abovementioned reasons we recommend different modalities of individual protection based on a strict clinical and epidemiological stratification of patients with potential SARS-CoV-2 infection undergoing endoscopic examination. In this setting, regardless of the classification of patients (high/low-risk, , in order to prevent the medical staff from becoming infected, we suggest high-performance personal protection equipment, i.e. a N95 or FFP2/FFP3 respirator, a hairnet, a double pair of gloves, a disposable waterproof surgical gown, a face shield (which we prefer because it allows to protect, and then spare, respirators) or goggles, and work safety clogs (Table 1) . abstract: A dramatic SARS-Cov-2 outbreak is hitting Italy hard. To face the new scenario all the hospitals have been re-organised in order to reduce all the outpatient services and to devote almost all their personnel and resources to the management of Covid-19 patients. As a matter of fact, all the services have undergone a deep re-organization guided by: the necessity to reduce exams, to create an environment that helps reduce the virus spread, and to preserve the medical personnel from infection. In these days a re-organization of the endoscopic unit, sited in a high-incidence area, has been adopted, with changes to logistics, work organization and patients selection. With the present manuscript, we want to support gastroenterologists and endoscopists in the organization of a “new” endoscopy unit that responds to the “new” scenario, while remaining fully aware that resources availability and local circumstances may extremely vary from unit to unit. url: https://www.sciencedirect.com/science/article/pii/S1590865820301730?v=s5 doi: 10.1016/j.dld.2020.04.018 id: cord-255495-xnoppq3y author: Elrashdy, Fatma title: On the potential role of exosomes in the COVID-19 reinfection/reactivation opportunity date: 2020-07-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: We propose here that one of the potential mechanisms for the relapse of the COVID-19 infection could be a cellular transport pathway associated with the release of the SARS-CoV-2-loaded exosomes and other extracellular vesicles. It is possible that this “Trojan horse” strategy represents possible explanation for the re-appearance of the viral RNA in the recovered COVID-19 patients 7–14 day post discharge, suggesting that viral material was hidden within such exosomes or extracellular vesicles during this “silence” time period and then started to re-spread again. Communicated by Ramaswamy H. Sarma url: https://www.ncbi.nlm.nih.gov/pubmed/32643586/ doi: 10.1080/07391102.2020.1790426 id: cord-286443-t0asknzu author: Emerson, Julia title: Home Self-Collection of Nasal Swabs for Diagnosis of Acute Respiratory Virus Infections in Children With Cystic Fibrosis date: 2013-07-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Understanding the importance of respiratory viruses in children with cystic fibrosis (CF) has been limited because of challenges using clinic- or hospital-based diagnostic testing. We conducted a pilot study to assess feasibility of home self- (or parent-) collection of nasal swabs (NS). METHODS: Cystic fibrosis patients aged 6–18 years with new respiratory illness participated. In clinic, a deep nasal flocked swab was collected by research staff and compared with an anterior foam NS obtained after instillation of saline spray. At home, up to 2 self-collections of paired foam NS (with and without saline) were collected and mailed for real-time polymerase chain reaction (PCR) testing. RESULTS: Paired swabs were collected from 28 patients: 18 sets in clinic (deep nasal vs saline foam NS) and 43 sets at home (saline vs dry foam NS) with 9 (50%) and 35 (81%) virus detections, respectively. Home-collected NS were obtained closer to illness onset, with a mean difference in symptom days of −2.3 between home and clinic collections (95% confidence interval [CI] −3.5, −1.2; P < .001). Rhinovirus comprised 73% of virus detections; the difference in mean PCR cycle threshold values for rhinovirus between swabs collected at home versus clinic was −3.8 (95% CI −6.8, −0.9; P = .014), indicating significantly higher viral load for home-collected swabs. CONCLUSIONS: Home-collected foam NS had a higher positivity rate compared with clinic-collected swabs, likely because collection was closer to illness onset. Home self-collection is feasible and well tolerated for timely respiratory virus diagnosis and provides a novel approach for clinical diagnostics and surveillance of respiratory virus infections among CF patients. url: http://europepmc.org/articles/pmc3869469?pdf=render doi: 10.1093/jpids/pit039 id: cord-309107-2xzam3x9 author: Emmler, Laura title: Feline coronavirus with and without spike gene mutations detected by real-time RT-PCRs in cats with feline infectious peritonitis date: 2019-11-15 words: 4623.0 sentences: 228.0 pages: flesch: 54.0 cache: ./cache/cord-309107-2xzam3x9.txt txt: ./txt/cord-309107-2xzam3x9.txt summary: title: Feline coronavirus with and without spike gene mutations detected by real-time RT-PCRs in cats with feline infectious peritonitis This study investigated the presence of FCoV with and without S gene mutations in cats with FIP using two different real-time RT-PCRs on different samples obtained under clinical conditions. METHODS: Fine-needle aspirates (FNAs) and incisional biopsies (IBs) of popliteal and mesenteric lymph nodes, liver, spleen, omentum and kidneys (each n = 20), EDTA blood (n = 13), buffy coat smears (n = 13), serum (n = 11), effusion (n = 14), cerebrospinal fluid (n = 16), aqueous humour (n = 20) and peritoneal lavage (n = 6) were obtained from 20 cats with FIP diagnosed by immunohistochemistry. This study investigated the presence of FCoV with and without S gene mutations in different tissue and body fluid samples from cats with IHC-confirmed FIP via realtime RT-PCR. abstract: OBJECTIVES: Feline infectious peritonitis (FIP) emerges when feline coronaviruses (FCoVs) mutate within their host to a highly virulent biotype and the immune response is not able to control the infection. FCoV spike (S) gene mutations are considered to contribute to the change in virulence by enabling FCoV infection of and replication in macrophages. This study investigated the presence of FCoV with and without S gene mutations in cats with FIP using two different real-time RT-PCRs on different samples obtained under clinical conditions. METHODS: Fine-needle aspirates (FNAs) and incisional biopsies (IBs) of popliteal and mesenteric lymph nodes, liver, spleen, omentum and kidneys (each n = 20), EDTA blood (n = 13), buffy coat smears (n = 13), serum (n = 11), effusion (n = 14), cerebrospinal fluid (n = 16), aqueous humour (n = 20) and peritoneal lavage (n = 6) were obtained from 20 cats with FIP diagnosed by immunohistochemistry. Samples were examined by RT-PCR targeting the FCoV 7b gene, detecting all FCoV, and S gene mutation RT-PCR targeting mutations in nucleotides 23531 and 23537. The prevalence of FCoV detected in each sample type was calculated. RESULTS: In 20/20 cats, FCoV with S gene mutations was present in at least one sample, but there was variation in which sample was positive. FCoV with mutations in the S gene were most frequently found in effusion (64%, 95% confidence interval [CI] 39–89), followed by spleen, omentum and kidney IBs (50%, 95% CI 28–72), mesenteric lymph node IBs and FNAs (45%, 95% CI 23–67), and FNAs of spleen and liver and liver IBs (40%, 95% CI 19–62). CONCLUSIONS AND RELEVANCE: In these 20 cats with FIP, FCoVs with S gene mutations were found in every cat in at least one tissue or fluid sample. This highlights the association between mutated S gene and systemic FCoV spread. Examining a combination of different samples increased the probability of finding FCoV with the mutated S gene. url: https://doi.org/10.1177/1098612x19886671 doi: 10.1177/1098612x19886671 id: cord-348522-r7ev9br6 author: Englund, Stina title: The occurrence of Chlamydia spp. in pigs with and without clinical disease date: 2012-01-26 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Within the genera Chlamydia, the development of refined diagnostic techniques has allowed the identification of four species that are capable of infecting pigs. The epidemiology, clinical, and zoonotic impacts of these species are however largely unknown. The study aimed to investigate the presence of Chlamydia spp. in the intestines of growing pigs and in conjunctival swabs from finisher pigs, and relate the findings to clinical signs. RESULTS: By histology, 20 of 48 pigs had intestinal lesions that may be consistent with chlamydial infection. By PCR, forty-six of the pigs were positive whereas two samples were inhibited. Sequencing of 19 DNA extracts identified these as Chlamydia suis. By immunohistochemistry, 32 of 44 samples were positive and a significant relationship was detected between macroscopically visible intestinal lesions and a high degree of infection. By real-time PCR, a significant difference was detected between pigs with and without conjunctivitis when a Ct value of 36 was employed but not when a Ct value of 38 was employed. CONCLUSIONS: Chlamydia suis was demonstrated in most samples and overall, no correlation to clinical signs was detected. However, a correlation was noted between samples with a high degree of infection and the presence of clinical signs. It is possible, that the intensive pig production systems studied might predispose for the transmission and maintenance of the infection thus increasing the infectious load and the risk for disease in the pig. url: https://www.ncbi.nlm.nih.gov/pubmed/22280482/ doi: 10.1186/1746-6148-8-9 id: cord-269194-b1wlr3t7 author: Engstrom-Melnyk, Julia title: Chapter 5 Clinical Applications of Quantitative Real-Time PCR in Virology date: 2015-12-31 words: 12542.0 sentences: 501.0 pages: flesch: 36.0 cache: ./cache/cord-269194-b1wlr3t7.txt txt: ./txt/cord-269194-b1wlr3t7.txt summary: Complementing serologic testing by detecting infections within the pre-seroconversion window period and infections with immunovariant viruses, real-time PCR provides a highly valuable tool for screening, diagnosing, or monitoring diseases, as well as evaluating medical and therapeutic decision points that allows for more timely predictions of therapeutic failures than traditional methods and, lastly, assessing cure rates following targeted therapies. Beyond this, quantitative real-time PCR facilitates advancements in the quality of diagnostics by driving consensus management guidelines following standardisation to improve patient outcomes, pushing for disease eradication with assays offering progressively lower limits of detection, and rapidly meeting medical needs in cases of emerging epidemic crises involving new pathogens that may result in significant health threats. With the development and administration of newer drugs that target specific biological processes of HIV, routine and clinical monitoring of viral loads using a real-time quantitative PCR assay continues to be critical to predict treatment failure and early emergence of drug resistance mutations, within a timeframe that would increase subsequent treatment success. abstract: Abstract Since the invention of the polymerase chain reaction (PCR) and discovery of Taq polymerase, PCR has become a staple in both research and clinical molecular laboratories. As clinical and diagnostic needs have evolved over the last few decades, demanding greater levels of sensitivity and accuracy, so too has PCR performance. Through optimisation, the present-day uses of real-time PCR and quantitative real-time PCR are enumerable. The technique, combined with adoption of automated processes and reduced sample volume requirements, makes it an ideal method in a broad range of clinical applications, especially in virology. Complementing serologic testing by detecting infections within the pre-seroconversion window period and infections with immunovariant viruses, real-time PCR provides a highly valuable tool for screening, diagnosing, or monitoring diseases, as well as evaluating medical and therapeutic decision points that allows for more timely predictions of therapeutic failures than traditional methods and, lastly, assessing cure rates following targeted therapies. All of these serve vital roles in the continuum of care to enhance patient management. Beyond this, quantitative real-time PCR facilitates advancements in the quality of diagnostics by driving consensus management guidelines following standardisation to improve patient outcomes, pushing for disease eradication with assays offering progressively lower limits of detection, and rapidly meeting medical needs in cases of emerging epidemic crises involving new pathogens that may result in significant health threats. url: https://api.elsevier.com/content/article/pii/S0580951715000069 doi: 10.1016/bs.mim.2015.04.005 id: cord-277838-931sco95 author: Erles, Kerstin title: Detection of a group 2 coronavirus in dogs with canine infectious respiratory disease date: 2003-06-05 words: 5077.0 sentences: 270.0 pages: flesch: 60.0 cache: ./cache/cord-277838-931sco95.txt txt: ./txt/cord-277838-931sco95.txt summary: Sequence analysis of four positive samples showed the presence of a coronavirus with high similarity to both bovine and human coronavirus (strain OC43) in their polymerase and spike genes, whereas there was a low similarity to comparable genes in the enteric canine coronavirus. This investigation sought to detect coronaviruses associated with CIRD in a large kenneled dog population with a history of endemic respiratory disease, using virus culture and PCR techniques as well as serology on paired serum samples. Of the group of dogs which developed respiratory disease, 17 were positive for antibodies to CRCV on the day of entry into the kennel and 64 were negative. Furthermore, serological analysis revealed that dogs with antibodies to CRCV on the day of entry into the kennel developed respiratory disease less frequently than dogs RT-PCR results from tracheal and lung samples of 119 dogs with different respiratory signs (none to severe) using a nested PCR directed against the coronavirus spike gene. abstract: An investigation into the causes of canine infectious respiratory disease was carried out in a large rehoming kennel. Tissue samples taken from the respiratory tract of diseased dogs were tested for the presence of coronaviruses using RT–PCR with conserved primers for the polymerase gene. Sequence analysis of four positive samples showed the presence of a coronavirus with high similarity to both bovine and human coronavirus (strain OC43) in their polymerase and spike genes, whereas there was a low similarity to comparable genes in the enteric canine coronavirus. This canine respiratory coronavirus (CRCV) was detected by RT–PCR in 32/119 tracheal and 20/119 lung samples, with the highest prevalence being detected in dogs with mild clinical symptoms. Serological analysis showed that the presence of antibodies against CRCV on the day of entry into the kennel decreased the risk of developing respiratory disease. url: https://api.elsevier.com/content/article/pii/S0042682203001600 doi: 10.1016/s0042-6822(03)00160-0 id: cord-289745-qtorq2qq author: Esper, Frank title: Evidence of a Novel Human Coronavirus That Is Associated with Respiratory Tract Disease in Infants and Young Children date: 2005-02-15 words: 3627.0 sentences: 205.0 pages: flesch: 53.0 cache: ./cache/cord-289745-qtorq2qq.txt txt: ./txt/cord-289745-qtorq2qq.txt summary: We sought to determine whether novel human coronaviruses (HCoVs) are circulating in New Haven, Connecticut, and, if so, whether they are associated with respiratory tract disease in infants and young children. To determine whether novel HCoVs are circulating and, if so, whether they are responsible for respiratory tract disease in children, we developed a strategy to screen for previously unknown HCoVs. Our initial assumption was that all CoVs must have conserved functions and that these conserved functions are reflected in the genome. These specimens, which were obtained from both ambulatory and hospitalized patients, were screened for presence of human metapneumovirus (hMPV) by use of an RT-PCR-based approach described elsewhere [12, 13] and were submitted to the Clinical Virology Laboratory, Yale-New Haven Hospital, for diagnostic testing. The novel HCoV identified in New Haven and The Netherlands was associated with both upper and lower respiratory tract disease in infants and young children. abstract: Background. The etiological agents responsible for a substantial proportion of respiratory tract diseases have not been identified. We sought to determine whether novel human coronaviruses (HCoVs) are circulating in New Haven, Connecticut, and, if so, whether they are associated with respiratory tract disease in infants and young children. Methods. We developed a polymerase chain reaction (PCR)-based approach for screening specimens from the respiratory tracts of symptomatic children. PCR probes that target regions of the replicase 1a gene that are conserved among genetically diverse animal CoVs and HCoVs were designed. Using these probes, we identified genomic sequences of a novel HCoV, designated “New Haven coronavirus” (HCoV-NH). Thereafter, we designed specific probes to screen respiratory specimens from children <5 years old for this novel HCoV. Clinical features associated with HCoV-NH infection were identified. Results. Seventy-nine (8.8%) of 895 children tested positive for HCoV-NH. Cough, rhinorrhea, tachypnea, fever, abnormal breath sounds, and hypoxia were the most common findings associated with HCoV-NH infection. Sequence analysis revealed that HCoV-NH is closely related to a novel HCoV recently reported in The Netherlands. Conclusions. The novel HCoVs identified in New Haven and The Netherlands are similar and likely represent the same species. This newly discovered virus may have worldwide distribution and may account for a significant proportion of respiratory tract disease in infants and young children. url: https://www.ncbi.nlm.nih.gov/pubmed/15655770/ doi: 10.1086/428138 id: cord-306278-c4q4la5c author: Esposito, Susanna title: Epidemiology and Clinical Characteristics of Respiratory Infections Due to Adenovirus in Children Living in Milan, Italy, during 2013 and 2014 date: 2016-04-05 words: 4660.0 sentences: 220.0 pages: flesch: 48.0 cache: ./cache/cord-306278-c4q4la5c.txt txt: ./txt/cord-306278-c4q4la5c.txt summary: To evaluate the predominant human adenovirus (HAdV) species and types associated with pediatric respiratory infections, nasopharyngeal swabs were collected from otherwise healthy children attending an emergency room in Milan, Italy, due to a respiratory tract infection from January 1 to February 28 of two subsequent years, 2013 and 2014. To evaluate the circulation of the different HAdV types and the possible relationship between viral load, viral genetic characteristics, and the severity of infection, nasopharyngeal swabs were collected from otherwise healthy children consecutively attending the Emergency Room of the Fondazione IRCCS Ca'' Granda Ospedale Maggiore Policlinico, University of Milan, Italy, due to a respiratory tract infection. However, further studies are needed to identify the potential pathogenetic role of the different species and types of HAdV and the importance of viral load in the severity of infection. abstract: To evaluate the predominant human adenovirus (HAdV) species and types associated with pediatric respiratory infections, nasopharyngeal swabs were collected from otherwise healthy children attending an emergency room in Milan, Italy, due to a respiratory tract infection from January 1 to February 28 of two subsequent years, 2013 and 2014. The HAdVs were detected using a respiratory virus panel fast assay (xTAG RVP FAST v2) and with a HAdV-specific real-time polymerase chain reaction; their nucleotides were sequenced, and they were tested for positive selection. Among 307 nasopharyngeal samples, 61 (19.9%) tested positive for HAdV. HAdV was the only virus detected in 31/61 (50.8%) cases, whereas it was found in association with one other virus in 25 (41.0%) cases and with two or more viruses in 5 (8.2%) cases. Human Enterovirus/human rhinovirus and respiratory syncytial virus were the most common co-infecting viral agents and were found in 12 (19.7%) and 7 (11.5%) samples, respectively. Overall, the HAdV strain sequences analyzed were highly conserved. In comparison to HAdV-negative children, those infected with HAdV had a reduced frequency of lower respiratory tract involvement (36.1% vs 55.2%; p = 0.007), wheezing (0.0% vs 12.5%; p = 0.004), and hospitalization (27.9% vs 56.1%; p<0.001). Antibiotic therapy and white blood cell counts were more frequently prescribed (91.9% vs 57.1%; p = 0.04) and higher (17,244 ± 7,737 vs 9,565 ± 3,211 cells/μL; p = 0.04), respectively, in children infected by HAdV-C than among those infected by HAdV-B. On the contrary, those infected by HAdV-B had more frequently lower respiratory tract involvement (57.1% vs 29.7%) but difference did not reach statistical significant (p = 0.21). Children with high viral load were absent from child care attendance for a longer period of time (14.5 ± 7.5 vs 5.5 ± 3.2 days; p = 0.002) and had higher C reactive protein levels (41.3 ± 78.5 vs 5.4 ± 9.6 μg/dL; p = 0.03). This study has shown that HAdV infections are diagnosed more commonly than usually thought and that HAdVs are stable infectious agents that do not frequently cause severe diseases. A trend toward more complex disease in cases due to HAdV species C and in those with higher viral load was demonstrated. However, further studies are needed to clarify factors contributing to disease severity to understand how to develop adequate preventive and therapeutic measures. url: https://www.ncbi.nlm.nih.gov/pubmed/27045588/ doi: 10.1371/journal.pone.0152375 id: cord-281162-2pu7x5rj author: Etemadi, Mohammad Reza title: Diversity of respiratory viruses detected among hospitalized children with acute lower respiratory tract infections at Hospital Serdang, Malaysia date: 2019-03-22 words: 4902.0 sentences: 280.0 pages: flesch: 49.0 cache: ./cache/cord-281162-2pu7x5rj.txt txt: ./txt/cord-281162-2pu7x5rj.txt summary: The aim of this study was to use conventional and molecular detection methods to assess the epidemiology of respiratory viral infections in children less than five years of age that were hospitalized with ALRTIs. Methods: The cross-sectional study was designed to investigate the occurrence of respiratory viruses including respiratory syncytisl virus (RSV), human metapneumovirus (HMPV), influenza virus A and B (IFV-A and B), parainfluenzavirus 1, 2, 3 and 4 (PIV 1, 2, 3 and 4), human rhinoviruses (HRV), human enterovirus (HEV), human coronaviruses (HCoV) 229E and OC43, human bocavirus (HBoV) and human adenovirus (HAdV) in hospitalized children with ALRTIs, at Hospital Serdang, Malaysia, from June 16 to December 21, 2009. abstract: BACKGROUND: The role of respiratory viruses as the major cause of acute lower respiratory tract infections (ALRTIs) in children is becoming increasingly evident due to the use of sensitive molecular detection methods. The aim of this study was to use conventional and molecular detection methods to assess the epidemiology of respiratory viral infections in children less than five years of age that were hospitalized with ALRTIs. METHODS: The cross-sectional study was designed to investigate the occurrence of respiratory viruses including respiratory syncytisl virus (RSV), human metapneumovirus (HMPV), influenza virus A and B (IFV-A and B), parainfluenzavirus 1, 2, 3 and 4 (PIV 1, 2, 3 and 4), human rhinoviruses (HRV), human enterovirus (HEV), human coronaviruses (HCoV) 229E and OC43, human bocavirus (HBoV) and human adenovirus (HAdV) in hospitalized children with ALRTIs, at Hospital Serdang, Malaysia, from June 16 to December 21, 2009. The study was also designed in part to assess the performance of the conventional methods against molecular methods. RESULTS: Viral pathogens were detected in 158 (95.8%) of the patients. Single virus infections were detected in 114 (67.9%) patients; 46 (27.9%) were co-infected with different viruses including double-virus infections in 37 (22.4%) and triple-virus infections in 9 (5.5%) cases. Approximately 70% of samples were found to be positive using conventional methods compared with 96% using molecular methods. A wide range of respiratory viruses were detected in the study. There was a high prevalence of RSV (50.3%) infections, particularly group B viruses. Other etiological agents including HAdV, HMPV, IFV-A, PIV 1–3, HBoV, HCoV-OC43 and HEV were detected in 14.5, 9.6, 9.1, 4.8, 3.6, 2.4 and 1.8 percent of the samples, respectively. CONCLUSION: Our results demonstrated the increased sensitivity of molecular detection methods compared with conventional methods for the diagnosis of ARTIs in hospitalized children. This is the first report of HMPV infections in Malaysia. url: https://www.sciencedirect.com/science/article/pii/S0166093418305937 doi: 10.1016/j.jviromet.2019.03.013 id: cord-261867-6n0g3bz5 author: Evermann, James F. title: Canine Reproductive, Respiratory, and Ocular Diseases due to Canine Herpesvirus date: 2011-10-28 words: 8808.0 sentences: 468.0 pages: flesch: 41.0 cache: ./cache/cord-261867-6n0g3bz5.txt txt: ./txt/cord-261867-6n0g3bz5.txt summary: Infection rates, based on serologic studies, are high enough to explain entry of CHV into multidog environments, either as an active infection or as the result of reactivation of latent virus in environments associated with natural, or pharmacologically induced immunosuppression. In fetal and neonatal dogs with primary CHV infection, severe intraocular lesions are frequently present concurrent with systemic viral disease. The results of this study showed that topical ocular prednisolone at the concentration and treatment regimen used did not result in detectable reactivation of CHV latency, based on a combination of recrudescent clinical signs, confocal microscopy findings, ocular infectious virus shedding, real-time PCR findings, and serologic response. Primary and recurrent CHV infection in mature dogs is associated with mucosal viral shedding that it detectable by PCR assay or virus isolation. Experimental recurrent ocular CHV infection induced by systemic corticosteroid administration to dogs recovered from primary ocular infection again resulted in viral shedding. abstract: This review documents how clinical inquiry expands as our knowledge base about canine herpesvirus (CHV) increases. We must understand the various forms of CHV infection that may occur in the dog population. This has prompted the veterinary community to develop more sensitive diagnostic assays. CHV is more common than we considered a decade ago. Up to 70% of some high-risk dog populations have been infected with and are latent carriers of CHV. Recognition of the various forms of CHV-induced disease, availability of diagnostic assays with increased sensitivity, and the formation of reliable biosecurity measures will allow for better control steps. url: https://doi.org/10.1016/j.cvsm.2011.08.007 doi: 10.1016/j.cvsm.2011.08.007 id: cord-002399-z3in6bi2 author: FAZ, Mirna title: Reliability of clinical diagnosis and laboratory testing techniques currently used for identification of canine parvovirus enteritis in clinical settings date: 2016-11-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Canine parvovirus type 2 (CPV-2) is the main etiological agent of viral enteritis in dogs. Actually in literature, CPV-2 has been reported with clinical signs that vary from the classical disease, and immunochromatography test and PCR technique have been introduced to veterinary hospitals to confirm CPV-2 diagnosis and other infections. However, the reliability of these techniques has been poorly analyzed. In this study, we evaluated the sensitivity and specificity of veterinary clinical diagnosis, immunochromatography test and PCR technique. Our data indicate that variations in the clinical signs of CPV-2 complicate the gathering of an appropriate diagnosis; and immunochromatography test and PCR technique do not have adequate sensitivity to diagnose positive cases. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5289263/ doi: 10.1292/jvms.16-0227 id: cord-279576-wt4crton author: Fajardo, Álvaro title: Evaluation Of SYBR Green Real Time PCR For Detecting SARS-CoV-2 From Clinical Samples date: 2020-05-13 words: 4842.0 sentences: 263.0 pages: flesch: 54.0 cache: ./cache/cord-279576-wt4crton.txt txt: ./txt/cord-279576-wt4crton.txt summary: Several methods based on real time reverse transcription polymerase chain reaction (RT-qPCR) for the detection of SARS-CoV-2 genomic RNA have been developed. The aim of the study was to set up an alternative molecular protocol to detect SARS-CoV-2 from clinical samples, without the need of TaqMan probes or post-PCR steps (i.e. gel electrophoresis), which can be implemented in case of difficulties to get specific reagents or kits because of the current pandemic situation. In order to select an appropriate amount of control vector to use in the comparison between the two real time qPCR methods, we prepared plasmids dilutions (107, 106, 105 and 104 copies/μL) and assayed them following both protocols: the probe-based One Step RT-qPCR developed by the University of Hong Kong Poon et al. The amplification data for the SYBR Green-based qPCR protocol showed that the ORF1b-nsp14 region was correctly amplified for all SARS-CoV-2 positive samples (1 to 7) (Fig. 3) . abstract: The pandemic caused by SARS-CoV-2 has triggered an extraordinary collapse of healthcare systems and hundred thousand of deaths worldwide. Following the declaration of the outbreak as a Public Health Emergency of International Concern by the World Health Organization (WHO) on January 30th, 2020, it has become imperative to develop diagnostic tools to reliably detect the virus in infected patients. Several methods based on real time reverse transcription polymerase chain reaction (RT-qPCR) for the detection of SARS-CoV-2 genomic RNA have been developed. In addition, these methods have been recommended by the WHO for laboratory diagnosis. Since all these protocols are based on the use of fluorogenic probes and one-step reagents (cDNA synthesis followed by PCR amplification in the same tube), these techniques can be difficult to perform given the limited supply of reagents in low and middle income countries. In the interest of economy, time and availability of chemicals and consumables, the SYBR Green-based detection was implemented to establish a convenient assay. Therefore, we adapted one of WHO recommended Taqman-based one-step real time PCR protocols (from the University of Hong Kong) to SYBR Green. Our results suggest that SYBR-Green detection represents a reliable cost-effective alternative to increase the testing capacity. url: https://doi.org/10.1101/2020.05.13.093609 doi: 10.1101/2020.05.13.093609 id: cord-328795-rs1sd42z author: Falsey, Ann R. title: Rhinoviruses date: 2016-10-24 words: 4511.0 sentences: 222.0 pages: flesch: 45.0 cache: ./cache/cord-328795-rs1sd42z.txt txt: ./txt/cord-328795-rs1sd42z.txt summary: The incidence of HRV infection in children during the first 2 years of life was noted to be 0.7-2 infections per year in older studies using cell culture for viral detection (Brownlee and Turner, 2008) . Although symptoms associated with ''the common cold'' syndrome are often attributed to HRV disease, the clinical findings of rhinovirus infections are indistinguishable from those of other viral pathogens. Currently, there are no antiviral drugs approved for clinical use in HRV infections although a few agents have been advanced to clinical trials and shown modest results in decreasing either symptom severity or viral activity. Conversely, monoclonal antibody blockade of the ICAM-1 receptor, the site of cellular attachment for the majority of HRV-A and HRV-B serotypes, has also been studied and demonstrated a reduction in the severity of symptoms and viral shedding but failed to prevent infection in the rhinovirus challenge model (Greenberg, 2003) . abstract: Human rhinoviruses (HRV) are ubiquitous pathogens and the leading cause of the common cold syndrome. HRV are very diverse with more than 100 serotypes identified which cause disease in persons of all ages with the highest incidence documented in young children. Although illness is typically mild and self-limited, lost time from work and school creates a considerable economic burden. Infection of the upper airways is the most common site of infection, although lower airways disease is also well documented, as is the link between HRV infection and exacerbations of asthma. Unfortunately, effective specific antiviral treatments and vaccines remain elusive. url: https://www.sciencedirect.com/science/article/pii/B9780128036785003866 doi: 10.1016/b978-0-12-803678-5.00386-6 id: cord-323963-whv88ggl author: Fan, Xiaofeng title: Efficient amplification and cloning of near full-length hepatitis C virus genome from clinical samples date: 2006-08-11 words: 5713.0 sentences: 303.0 pages: flesch: 51.0 cache: ./cache/cord-323963-whv88ggl.txt txt: ./txt/cord-323963-whv88ggl.txt summary: Among RNA templates, hepatitis C virus (HCV) represents an excellent example to challenge the potential of LRP technology due to its extensive secondary structures and its difficulty to be readily cultured in vitro. Thus, our LRP protocol could be applied for the amplification of other difficult RNA templates and may facilitate RNA virus research such as linked viral mutations and reverse genetics. In some experiments, we mixed a RT enzyme with Pfu DNA polymerase (Stratagene), a similar strategy as used in long PCR, to improve full-length cDNA synthesis [8] . A representative neighbor-joining (NJ) tree constructed based on HCV E1 domain of 20 clones derived from 9.1 kb LRP product, which was amplified using mixed serum from samples LIV19 and LIV23. A refined long RT-PCR technique to amplify complete viral RNA genome sequences from clinical samples: Application to a novel hepatitis C virus variant of genotype 6 abstract: Abstract Long RT-PCR (LRP) amplification of RNA templates is sometimes difficult compared to long PCR of DNA templates. Among RNA templates, hepatitis C virus (HCV) represents an excellent example to challenge the potential of LRP technology due to its extensive secondary structures and its difficulty to be readily cultured in vitro. The only source for viral genome amplification is clinical samples in which HCV is usually present at low titers. We have created a comprehensive optimization protocol that allows robust amplification of a 9.1kb fragment of HCV, followed by efficient cloning into a novel vector. Detailed analyses indicate the lack of potential LRP-mediated recombination and the preservation of viral diversity. Thus, our LRP protocol could be applied for the amplification of other difficult RNA templates and may facilitate RNA virus research such as linked viral mutations and reverse genetics. url: https://api.elsevier.com/content/article/pii/S0006291X06012964 doi: 10.1016/j.bbrc.2006.06.039 id: cord-000483-zgapjjjw author: Faux, Cassandra E. title: Usefulness of Published PCR Primers in Detecting Human Rhinovirus Infection date: 2011-02-17 words: 1668.0 sentences: 83.0 pages: flesch: 48.0 cache: ./cache/cord-000483-zgapjjjw.txt txt: ./txt/cord-000483-zgapjjjw.txt summary: We conducted a preliminary comparison of the relative sensitivity of a cross-section of published human rhinovirus (HRV)–specific PCR primer pairs, varying the oligonucleotides and annealing temperature. We conducted a preliminary comparison of the relative sensitivity of a cross-section of published HRV-specifi c PCR primer pairs (most of which were fi rst published before HRV-C was reported), independent of most variables described above, by testing a panel of 57 clinical specimen nucleic acid extracts from combined nose and throat swabs from preschool children with colds and infl uenza-like illnesses in Melbourne, Australia. Five primer pairs, including real-time PCR (rtPCR) pair 5, did not amplify the HEVs, a positive feature for HRV-specifi c studies. We next selected 4 frequently published primer pairs (1, 5, 7, and 8) to examine 44 picornavirus-positive specimens (39 HRVs, 3 HEVs, and 2 untypeable picornaviruses) from nonhospitalized children with acute asthma exacerbation (6) . abstract: We conducted a preliminary comparison of the relative sensitivity of a cross-section of published human rhinovirus (HRV)–specific PCR primer pairs, varying the oligonucleotides and annealing temperature. None of the pairs could detect all HRVs in 2 panels of genotyped clinical specimens; >1 PCR is required for accurate description of HRV epidemiology. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204776/ doi: 10.3201/eid1702.101123 id: cord-293966-5c466xvz author: Fehr, Anthony R. title: Bacterial Artificial Chromosome-Based Lambda Red Recombination with the I-SceI Homing Endonuclease for Genetic Alteration of MERS-CoV date: 2019-09-14 words: 3813.0 sentences: 229.0 pages: flesch: 62.0 cache: ./cache/cord-293966-5c466xvz.txt txt: ./txt/cord-293966-5c466xvz.txt summary: Quickly after the identification of Middle East respiratory syndrome-CoV (MERS-CoV), both in vitro ligation and BAC-based reverse genetic technologies were engineered for MERS-CoV to study its basic biological properties, develop live-attenuated vaccines, and test antiviral drugs. Here, I will describe how lambda red recombination can be used with the MERS-CoV BAC to quickly and efficiently introduce virtually any type of genetic modification (point mutations, insertions, deletions) into the MERS-CoV genome and recover recombinant virus. In the method described here, this recognition site is engineered on a plasmid (pEP-KanS) just outside of the positive selection marker, and its cleavage with the I-SceI enzyme allows for the removal of the positive selection marker by intramolecular Red recombination utilizing sequence duplication introduced in the original PCR primers. Using 1 μL of the BAC DNA, use the external primers located 100-200 bp outside the region of homology you previously designed to test for the insertion of Kan r -I-SceI by PCR. abstract: Over the past two decades, several coronavirus (CoV) infectious clones have been engineered, allowing for the manipulation of their large viral genomes (~30 kb) using unique reverse genetic systems. These reverse genetic systems include targeted recombination, in vitro ligation, vaccinia virus vectors, and bacterial artificial chromosomes (BACs). Quickly after the identification of Middle East respiratory syndrome-CoV (MERS-CoV), both in vitro ligation and BAC-based reverse genetic technologies were engineered for MERS-CoV to study its basic biological properties, develop live-attenuated vaccines, and test antiviral drugs. Here, I will describe how lambda red recombination can be used with the MERS-CoV BAC to quickly and efficiently introduce virtually any type of genetic modification (point mutations, insertions, deletions) into the MERS-CoV genome and recover recombinant virus. url: https://doi.org/10.1007/978-1-0716-0211-9_5 doi: 10.1007/978-1-0716-0211-9_5 id: cord-268977-hcg2rrhl author: Feikin, Daniel R. title: Etiology and Incidence of Viral and Bacterial Acute Respiratory Illness among Older Children and Adults in Rural Western Kenya, 2007–2010 date: 2012-08-24 words: 6440.0 sentences: 402.0 pages: flesch: 53.0 cache: ./cache/cord-268977-hcg2rrhl.txt txt: ./txt/cord-268977-hcg2rrhl.txt summary: METHODOLOGY/PRINCIPAL FINDINGS: From March 1, 2007, to February 28, 2010, among a surveillance population of 21,420 persons >5 years old in rural western Kenya, we collected blood for culture and malaria smears, nasopharyngeal and oropharyngeal swabs for quantitative real-time PCR for ten viruses and three atypical bacteria, and urine for pneumococcal antigen testing on outpatients and inpatients meeting a ARI case definition (cough or difficulty breathing or chest pain and temperature >38.0°C or oxygen saturation <90% or hospitalization). CONCLUSIONS/SIGNFICANCE: Vaccination against influenza and pneumococcus (by potential herd immunity from childhood vaccination or of HIV-infected adults) might prevent much of the substantial ARI incidence among persons >5 years old in similar rural African settings. Compared with other regions, the mortality rate among older children and adults remains several-fold higher in sub-Saharan Africa, where acute respiratory infections (ARI) are a leading cause of this high mortality, as well as associated morbidity [1] . abstract: BACKGROUND: Few comprehensive data exist on disease incidence for specific etiologies of acute respiratory illness (ARI) in older children and adults in Africa. METHODOLOGY/PRINCIPAL FINDINGS: From March 1, 2007, to February 28, 2010, among a surveillance population of 21,420 persons >5 years old in rural western Kenya, we collected blood for culture and malaria smears, nasopharyngeal and oropharyngeal swabs for quantitative real-time PCR for ten viruses and three atypical bacteria, and urine for pneumococcal antigen testing on outpatients and inpatients meeting a ARI case definition (cough or difficulty breathing or chest pain and temperature >38.0°C or oxygen saturation <90% or hospitalization). We also collected swabs from asymptomatic controls, from which we calculated pathogen-attributable fractions, adjusting for age, season, and HIV-status, in logistic regression. We calculated incidence by pathogen, adjusting for health-seeking for ARI and pathogen-attributable fractions. Among 3,406 ARI patients >5 years old (adjusted annual incidence 12.0 per 100 person-years), influenza A virus was the most common virus (22% overall; 11% inpatients, 27% outpatients) and Streptococcus pneumoniae was the most common bacteria (16% overall; 23% inpatients, 14% outpatients), yielding annual incidences of 2.6 and 1.7 episodes per 100 person-years, respectively. Influenza A virus, influenza B virus, respiratory syncytial virus (RSV) and human metapneumovirus were more prevalent in swabs among cases (22%, 6%, 8% and 5%, respectively) than controls. Adenovirus, parainfluenza viruses, rhinovirus/enterovirus, parechovirus, and Mycoplasma pneumoniae were not more prevalent among cases than controls. Pneumococcus and non-typhi Salmonella were more prevalent among HIV-infected adults, but prevalence of viruses was similar among HIV-infected and HIV-negative individuals. ARI incidence was highest during peak malaria season. CONCLUSIONS/SIGNFICANCE: Vaccination against influenza and pneumococcus (by potential herd immunity from childhood vaccination or of HIV-infected adults) might prevent much of the substantial ARI incidence among persons >5 years old in similar rural African settings. url: https://www.ncbi.nlm.nih.gov/pubmed/22937071/ doi: 10.1371/journal.pone.0043656 id: cord-313439-cadyykks author: Felten, Sandra title: Diagnosis of Feline Infectious Peritonitis: A Review of the Current Literature date: 2019-11-15 words: 12466.0 sentences: 522.0 pages: flesch: 44.0 cache: ./cache/cord-313439-cadyykks.txt txt: ./txt/cord-313439-cadyykks.txt summary: Studies evaluating sensitivity and specificity of the detection of serum antibodies in comparison to either histopathology, a combination of diagnostic tests or clinical suspicion of feline infectious peritonitis (FIP). Recent studies evaluated the use of a quantitative RT-PCR (RT-qPCR) to detect FCoV RNA in FNA samples of the mesenteric lymph nodes and other abnormal tissues of clinical cases [119, 140] and hypothesized that this technique would be a useful tool to diagnose FIP for veterinary practitioners, especially in cats without effusion. Sensitivity and specificity from different studies evaluating the detection of feline coronavirus (FCoV) spike (S) gene mutations in tissue samples. RT-nPCR and subsequent S gene sequencing of serum and plasma samples from cats with FIP (diagnosed by histopathology ± IHC or by positive immunofluorescence in effusion) and control cats (diagnosed with another disease either ante or post mortem) revealed a sensitivity of only 7%, which confirms the very low virus load in blood. abstract: Feline infectious peritonitis (FIP) is a fatal disease that poses several challenges for veterinarians: clinical signs and laboratory changes are non-specific, and there are two pathotypes of the etiologic agent feline coronavirus (FCoV), sometimes referred to as feline enteric coronavirus (FECV) and feline infectious peritonitis virus (FIPV) that vary fundamentally in their virulence, but are indistinguishable by a number of diagnostic methods. This review focuses on all important steps every veterinary practitioner has to deal with and new diagnostic tests that can be considered when encountering a cat with suspected FIP with the aim to establish a definitive diagnosis. It gives an overview on all available direct and indirect diagnostic tests and their sensitivity and specificity reported in the literature in different sample material. By providing summarized data for sensitivity and specificity of each diagnostic test and each sample material, which can easily be accessed in tables, this review can help to facilitate the interpretation of different diagnostic tests and raise awareness of their advantages and limitations. Additionally, diagnostic trees depict recommended diagnostic steps that should be performed in cats suspected of having FIP based on their clinical signs or clinicopathologic abnormalities. These steps can easily be followed in clinical practice. url: https://doi.org/10.3390/v11111068 doi: 10.3390/v11111068 id: cord-339995-0pbknb32 author: Feng, Hao title: A case report of COVID-19 with false negative RT-PCR test: necessity of chest CT date: 2020-04-07 words: 969.0 sentences: 62.0 pages: flesch: 63.0 cache: ./cache/cord-339995-0pbknb32.txt txt: ./txt/cord-339995-0pbknb32.txt summary: We report a case of 34-year-old man who was diagnosed as negative for COVID-19 based on the four sequential RT-PCR tests of his pharyngeal swab. It is difficult to distinguish COVID-19 pneumonia from other viral pneumonia on CT findings alone; however, we emphasize the utility of chest CT to detect early change of COVID-19 in cases which RT-PCR tests show negative results. d Follow-up CT 7 days after admission (d1, axial image; d2, ray-summation image; d3, pseudo color MIP; d4, coronal image) shows multifocal bilateral ground-glass opacities and improvement of mixed groundglass opacities and consolidation in left upper lobe. Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: a report of 1014 cases abstract: The definite diagnosis of corona virus disease 2019 (COVID-19) is based on the viral isolation or positive result of polymerase chain reaction (PCR) from sputum, or nasal swab, or throat swab. However, the sensitivity to detect COVID-19 of real time (RT)-PCR is reported to be lower than that of chest CT. We report a case of 34-year-old man who was diagnosed as negative for COVID-19 based on the four sequential RT-PCR tests of his pharyngeal swab. Chest CT showed patchy ground-glass opacity on admission, and it rapidly progressed to segmental mixed consolidation and ground-glass opacity 3 days after admission, and it resolved in left upper lobe, but showed multifocal ground-glass opacities 7 days after admission, and they resolved within 2 weeks. The fifth RT-PCR test finally revealed positive results at the fifth day after admission. It is difficult to distinguish COVID-19 pneumonia from other viral pneumonia on CT findings alone; however, we emphasize the utility of chest CT to detect early change of COVID-19 in cases which RT-PCR tests show negative results. url: https://www.ncbi.nlm.nih.gov/pubmed/32266524/ doi: 10.1007/s11604-020-00967-9 id: cord-021052-qydc404w author: Fernandez-Flores, Angel title: Aportaciones de la anatomía patológica en el diagnóstico de las infecciones cutáneas: una perspectiva histórica date: 2015-11-02 words: 4484.0 sentences: 462.0 pages: flesch: 59.0 cache: ./cache/cord-021052-qydc404w.txt txt: ./txt/cord-021052-qydc404w.txt summary: Las té cnicas de Romanovsky fueron introducidas en 1891 con un uso principal en la identificació n de pará sitos en hematología.El avance en este caso se centró en que los microorganismos podían verse en su contexto tisular. Gracias a ello, en 1950 se realizaron las primeras observaciones de un virus al microscopio electró nico mediante sombreado de los viriones, pero fue en 1960 cuando se difundió el uso del microscopio electró nico en virología 20 para enfermedades que hasta ese momento se diagnosticaban con cultivo, a veces no concluyente. Un magnífico ejemplo lo representaron los anticuerpos contra el herpesvirus humano 8 (HHV8) y contra el virus del carcinoma de cé lulas de Merkel. De otro, el virus tambié n fue detectado en tejido no tumoral de pacientes tanto con carcinoma de cé lulas de Merkel como sin é l 51 . abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7148901/ doi: 10.1016/j.piel.2015.08.007 id: cord-259590-ot933axv author: Fielding, Burtram C title: Human coronavirus NL63: a clinically important virus? date: 2011-03-02 words: 4014.0 sentences: 238.0 pages: flesch: 51.0 cache: ./cache/cord-259590-ot933axv.txt txt: ./txt/cord-259590-ot933axv.txt summary: In this article, the current knowledge of human coronavirus HCoV-NL63, with special reference to the clinical features, prevalence and seasonal incidence, and coinfection with other respiratory viruses, will be discussed. In this article, the current knowledge of human coronavirus HCoV-NL63, with special reference to the clinical features, prevalence and seasonal incidence, and coinfection with other respiratory viruses, will be discussed. A recent comprehen sive 2year populationbased study, using data from different countries, on children under 3 years of age with lower respiratory tract infec tion (LRTI) shows that HCoVNL63 infections peak in winter months. Another study reports that HCoVNL63, when compared with other respiratory viruses, is the virus secondmost com monly associated with young children (median age 13 months) hospitalized with croup [17] . A novel pancoronavirus RTPCR assay: frequent detection of human coronavirus NL63 in children hospitalized with respiratory tract infections in Belgium abstract: Respiratory tract infection is a leading cause of morbidity and mortality worldwide, especially among young children. Human coronaviruses (HCoVs) have only recently been shown to cause both lower and upper respiratory tract infections. To date, five coronaviruses (HCoV-229E, HCoV-OC43, SARS-CoV, HCoV-NL63 and HCoV HKU-1) that infect humans have been identified, four of which (HCoV-229E, HCoV-OC43, HCoV-NL63 and HCoV-HKU-1) circulate continuously in the human population. Human coronavirus NL63 (HCoV-NL63) was first isolated from the aspirate from a 7-month-old baby in early 2004. Infection with HCoV-NL63 has since been shown to be a common worldwide occurrence and has been associated with many clinical symptoms and diagnoses, including severe lower respiratory tract infection, croup and bronchiolitis. HCoV-NL63 causes disease in children, the elderly and the immunocompromised, and has been detected in 1.0–9.3% of respiratory tract infections in children. In this article, the current knowledge of human coronavirus HCoV-NL63, with special reference to the clinical features, prevalence and seasonal incidence, and coinfection with other respiratory viruses, will be discussed. url: https://doi.org/10.2217/fmb.10.166 doi: 10.2217/fmb.10.166 id: cord-271130-6s79q1c1 author: Filoni, Claudia title: Putative progressive and abortive feline leukemia virus infection outcomes in captive jaguarundis (Puma yagouaroundi) date: 2017-11-17 words: 6584.0 sentences: 337.0 pages: flesch: 47.0 cache: ./cache/cord-271130-6s79q1c1.txt txt: ./txt/cord-271130-6s79q1c1.txt summary: title: Putative progressive and abortive feline leukemia virus infection outcomes in captive jaguarundis (Puma yagouaroundi) Thus, the aim of this study was to perform additional serological and molecular tests and monitor the population of jaguarundis at FPZSP for FeLV infection and development of FeLV-related diseases for 5 years (2003) (2004) (2005) (2006) (2007) . Two captive-born male jaguarundis, the geriatric #1 and the mature adult #4, presented serological and molecular FeLV test results similar to the progressive FeLV infection outcome in domestic cats [25] . Moreover, consistent with findings in domestic cats with a progressive FeLV infection, no antibodies to FeLV antigens were detected in jaguarundis #1 and #4. Two captive-born jaguarundis, #2 and #22, presented test results similar to those reported for domestic cats with abortive FeLV infection and seroconversion as the only marker of FeLV exposure [28] . abstract: BACKGROUND: Feline leukemia virus (FeLV) is an exogenous gammaretrovirus of domestic cats (Felis catus) and some wild felids. The outcomes of FeLV infection in domestic cats vary according to host susceptibility, virus strain, and infectious challenge dose. Jaguarundis (Puma yagouaroundi) are small wild felids from South and Central America. We previously reported on FeLV infections in jaguarundis. We hypothesized here that the outcomes of FeLV infection in P. yagouaroundi mimic those observed in domestic cats. The aim of this study was to investigate the population of jaguarundis at Fundação Parque Zoológico de São Paulo for natural FeLV infection and resulting outcomes. METHODS: We investigated the jaguarundis using serological and molecular methods and monitored them for FeLV-related diseases for 5 years. We retrieved relevant biological and clinical information for the entire population of 23 jaguarundis held at zoo. Post-mortem findings from necropsies were recorded and histopathological and immunohistopathological analyses were performed. Sequencing and phylogenetic analyses were performed for FeLV-positive samples. For sample prevalence, 95% confidence intervals (CI) were calculated. Fisher’s exact test was used to compare frequencies between infected and uninfected animals. P-values <0.05 were considered significant. RESULTS: In total, we detected evidence of FeLV exposure in four out of 23 animals (17%; 95% CI 5–39%). No endogenous FeLV (enFeLV) sequences were detected. An intestinal B-cell lymphoma in one jaguarundi was not associated with FeLV. Two jaguarundis presented FeLV test results consistent with an abortive FeLV infection with seroconversion, and two other jaguarundis had results consistent with a progressive infection and potentially FeLV-associated clinical disorders and post-mortem changes. Phylogenetic analysis of env revealed the presence of FeLV-A, a common origin of the virus in both animals (100% identity) and the closest similarity to FeLV-FAIDS and FeLV-3281 (98.4% identity), originally isolated from cats in the USA. CONCLUSIONS: We found evidence of progressive and abortive FeLV infection outcomes in jaguarundis, and domestic cats were probably the source of infection in these jaguarundis. url: https://www.ncbi.nlm.nih.gov/pubmed/29149857/ doi: 10.1186/s12985-017-0889-z id: cord-262599-19aj551d author: Fongaro, Gislaine title: Evaluation and molecular characterization of human adenovirus in drinking water supplies: viral integrity and viability assays date: 2013-05-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Human adenoviruses (HAdVs) are the second-leading cause of childhood gastroenteritis worldwide. This virus is commonly found in environmental waters and is very resistant to water disinfection and environmental stressors, especially UV light inactivation. Molecular techniques, such as PCR-based methods (Polymerase Chain Reaction), are commonly used to detect and identify viral contamination in water, although PCR alone does not allow the discrimination between infectious and non-infectious viral particles. A combination of cell culture and PCR has allowed detection of infectious viruses that grow slowly or fail to produce cytopathic effects (CPE) in cell culture. This study aimed to assess the integrity and viability of human adenovirus (HAdV) in environmental water and evaluate circulating strains by molecular characterization in three sites of the water supply in Florianópolis, Santa Catarina Island, Brazil: Peri Lagoon water, spring source water, and water from the public water supply system. METHODS: Water samples were collected, concentrated and HAdV quantified by real-time PCR. Viral integrity was evaluated by enzymatic assay (DNase I) and infectivity by plaque assay (PA) and integrated cell culture using transcribed mRNA (ICC-RT-qPCR). Samples containing particles of infectious HAdV were selected for sequencing and molecular characterization. RESULTS: The analyzed sites contained 83, 66 and 58% undamaged HAdV particles (defined as those in which the genetic material is protected by the viral capsid) at Peri Lagoon, spring source water and public supply system water, respectively. Of these, 66% of the particles (by PA) and 75% (by ICC-RT-qPCR) HAdV were shown to be infectious, due to being undamaged in Peri Lagoon, 33% (by PA) and 58% (by ICC-RT-qPCR) in spring source water and 8% (by PA) and 25% (by ICC-RT-qPCR) in the public water supply system. ICC-RT-qPCR, a very sensitive and rapid technique, was able to detect as low as 1 × 10(2) HAdV genome copies per milliliter of infectious viral particles in the environmental water samples. The molecular characterization studies indicated that HAdV-2 was the prevalent serotype. CONCLUSIONS: These results indicate a lack of proper public health measures. We suggest that HAdV can be efficiently used as a marker of environmental and drinking water contamination and ICC-RT-qPCR demonstrated greater sensitivity and speed of detection of infectious viral particles compared to PA. url: https://doi.org/10.1186/1743-422x-10-166 doi: 10.1186/1743-422x-10-166 id: cord-000113-d0eur1hq author: Fooks, Anthony R. title: Emerging Technologies for the Detection of Rabies Virus: Challenges and Hopes in the 21st Century date: 2009-09-29 words: 6937.0 sentences: 319.0 pages: flesch: 38.0 cache: ./cache/cord-000113-d0eur1hq.txt txt: ./txt/cord-000113-d0eur1hq.txt summary: The advent of molecular biology and new technological initiatives that combine advances in biology with other disciplines will support the development of techniques capable of high throughput testing with a low turnaround time for rabies diagnosis. The advent of molecular biology and new technological initiatives that combine advances in biology with other disciplines will support the development of techniques capable of high throughput testing with a low turnaround time for rabies diagnosis. Another method for the detection of rabies virus antigen from postmortem samples is a recently developed rapid immunodiagwww.plosntds.org nostic test (RIDT) based on the principles of immunochromatography [13] . Development of RT-LAMP assays for use in diagnosis and surveillance is challenged by the considerable sequence variation observed within the rabies virus genome [44] that can frustrate specific primer design. Currently, high-throughput rabies virus molecular detection methods augment standard diagnostic tests or are in the process of development and refinement for use alone. abstract: The diagnosis of rabies is routinely based on clinical and epidemiological information, especially when exposures are reported in rabies-endemic countries. Diagnostic tests using conventional assays that appear to be negative, even when undertaken late in the disease and despite the clinical diagnosis, have a tendency, at times, to be unreliable. These tests are rarely optimal and entirely dependent on the nature and quality of the sample supplied. In the course of the past three decades, the application of molecular biology has aided in the development of tests that result in a more rapid detection of rabies virus. These tests enable viral strain identification from clinical specimens. Currently, there are a number of molecular tests that can be used to complement conventional tests in rabies diagnosis. Indeed the challenges in the 21st century for the development of rabies diagnostics are not of a technical nature; these tests are available now. The challenges in the 21st century for diagnostic test developers are two-fold: firstly, to achieve internationally accepted validation of a test that will then lead to its acceptance by organisations globally. Secondly, the areas of the world where such tests are needed are mainly in developing regions where financial and logistical barriers prevent their implementation. Although developing countries with a poor healthcare infrastructure recognise that molecular-based diagnostic assays will be unaffordable for routine use, the cost/benefit ratio should still be measured. Adoption of rapid and affordable rabies diagnostic tests for use in developing countries highlights the importance of sharing and transferring technology through laboratory twinning between the developed and the developing countries. Importantly for developing countries, the benefit of molecular methods as tools is the capability for a differential diagnosis of human diseases that present with similar clinical symptoms. Antemortem testing for human rabies is now possible using molecular techniques. These barriers are not insurmountable and it is our expectation that if such tests are accepted and implemented where they are most needed, they will provide substantial improvements for rabies diagnosis and surveillance. The advent of molecular biology and new technological initiatives that combine advances in biology with other disciplines will support the development of techniques capable of high throughput testing with a low turnaround time for rabies diagnosis. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745658/ doi: 10.1371/journal.pntd.0000530 id: cord-317049-q3bvmkf7 author: Forde, Justin J. title: Yield and Implications of Pre-Procedural COVID-19 PCR Testing on Routine Endoscopic Practice date: 2020-05-25 words: 1140.0 sentences: 68.0 pages: flesch: 47.0 cache: ./cache/cord-317049-q3bvmkf7.txt txt: ./txt/cord-317049-q3bvmkf7.txt summary: To fill the knowledge gap in this area, we sought to describe our experience with resuming endoscopy using a two-step approach (patient screening followed by COVID-19 testing) in order to provide needed data for other practices weighing the risks and benefits of resuming endoscopic procedures. On April 13, 2020 our endoscopy unit began mandatory COVID-19 polymerase chain reaction (PCR) testing by nasopharyngeal swab for all patients prior to any endoscopic procedure. On arrival to the endoscopy unit, patients were again screened by nursing staff using the same pre-procedure questionnaire and body temperature checks. Even with a negative result, endoscopy staff used full barrier PPE and ensured compliance with hygiene and social distancing practices in pre-and post-procedure areas to minimize risks to patients and staff. Although preprocedure PCR testing for COVID-19 may help to assuage concerns of the endoscopy unit staff, this needs to be balanced against the substantial false negative rate even with the best available tests. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S001650852034734X?v=s5 doi: 10.1053/j.gastro.2020.05.062 id: cord-016020-awanrm9u author: Fox, Julie D. title: Respiratory Pathogens date: 2007 words: 4603.0 sentences: 220.0 pages: flesch: 30.0 cache: ./cache/cord-016020-awanrm9u.txt txt: ./txt/cord-016020-awanrm9u.txt summary: In addition, despite the well-recognized association of viral infections with upper and lower respiratory tract infections, the current diagnostic virology procedures do not provide an answer rapidly enough to with parainfluenza virus type 4, human coronaviruses, rhinoviruses, and some enteroviruses would not ordinarily be identified without RNA detection methods. Published diagnostic methods for detection of respiratory pathogen DNA or RNA directly from clinical specimens utilize target amplification procedures such as polymerase chain reaction (PCR) or nucleic acid sequence-based amplification (NASBA).Although direct detection methods based on nucleic acid hybridization would be theoretically possible, the amount of target nucleic acid in specimens may be minimal and such methods would lack sensitivity compared to amplification methods, unless the organism was propagated before analysis. Thus, the molecular amplification procedures reported for direct detection of respiratory pathogens in clinical samples include PCR (e.g., Reference 19 and Figure 41 assays have utilized bacterial ribosomal RNA (rRNA; e.g., Reference 22 ). abstract: Respiratory tract infections are among the most common presenting complaints of patients in both hospital and community settings. They are a considerable burden in terms of both patient morbidity and public health interventions. Laboratory diagnosis of respiratory tract infections should provide guidance in therapy and prognosis, as well as useful epidemiological information reflecting trends in the community. Understanding and monitoring such trends facilitates early recognition of new infectious agents in a population. A summary of the common viruses and bacteria causing respiratory tract infections and their clinical relevance is given in Tables 41–1 and 41–2, respectively. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120168/ doi: 10.1007/978-0-387-33227-7_41 id: cord-332510-x3znuwc0 author: Freire-Álvarez, Eric title: COVID-19-associated encephalitis successfully treated with combination therapy date: 2020-11-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Background Acute encephalitis can occur in different viral diseases due to infection of the brain or by an immune mechanism. Severe novel coronavirus disease 2019 (COVID-19) is associated with a major immune inflammatory response with cytokine upregulation including interleukin 6 (IL-6). We report a case presenting with acute encephalitis that was diagnosed as having severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection with hyperinflammatory systemic response and recovered after therapy with immunoglobulins and cytokine blockade. Case Report: A 39-year-old-man was brought to the Emergency Department with drowsiness, mental disorientation, intermittent fever and headache. A brain magnetic resonance imaging showed extensive involvement of the brain including cortical and subcortical right frontal regions, right thalamus, bilateral temporal lobes and cerebral peduncles, with no leptomeningeal enhancement. Cerebrospinal fluid (CSF) showed a leukocyte count of 20/µL (90% lymphocytes), protein level of 198 mg/dL, and glucose of 48 mg/dL. SARS-CoV-2 was detected in nasopharyngeal swabs by reverse-transcriptase-PCR (RT-PCR) but it was negative in the CSF. Remarkable laboratory findings in blood tests included low lymphocyte count and elevated ferritin, IL-6 and D-dimer. He had a complicated clinical course requiring mechanical ventilation. Intravenous immunoglobulins and cytokine blockade with tocilizumab, an IL-6 receptor antagonist, were added considering acute demyelinating encephalomyelitis. The patient made a full recovery, suggesting that it could have been related to host inflammatory response. Conclusion This case report indicates that COVID-19 may present as an encephalitis syndrome mimicking acute demyelinating encephalomyelitis that could be amenable to therapeutic modulation. url: https://doi.org/10.1016/j.clinpr.2020.100053 doi: 10.1016/j.clinpr.2020.100053 id: cord-257661-iwwzli0w author: Freymuth, François title: Comparison of multiplex PCR assays and conventional techniques for the diagnostic of respiratory virus infections in children admitted to hospital with an acute respiratory illness date: 2006-09-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The performances of four multiplex PCR (m‐PCR) were compared to direct immunofluorescence assay (DFA) and HuH7 cell culture for the detection of viruses in 263 children admitted to hospital with an acute respiratory illness. One hundred fifty (57.6%) nasal aspirates were found DFA‐positive; 188 (72.3%) were found positive by both DFA and HuH7 cell culture, and 242 (92%) were PCR‐positive. The m‐PCR detected 124 viruses which were not found by conventional methods: 68 rhinovirus, 17 human metapneumovirus, 15 respiratory syncytial virus (RSV), 8 parainfluenza virus (PIV), 5 coronavirus 229E, 3 OC43 and 3 NL63, 4 enterovirus, 2 influenza virus B and C virus. The m‐PCR were more sensitive, had the advantages of a shorter delay in specific diagnosis, and a lower cost than DFA and culture. Using these m‐PCR, the prevalence of each virus was compared between in‐patient and out‐patient groups of children attending the emergency unit of the hospital. Nasal aspirates from 411 (91.5%) children were found positive by the PCRs. RSV, rhinovirus, and influenza virus were the most frequent viruses detected in this population, representing 43.6%, 31.8%, and 8.8% of the virus found, respectively, followed by human metapneumovirus (4.4%), coronavirus (3.4%), parainfluenza virus (3.2%), adenovirus (2.3%), and enterovirus (2.1%). RSVs were detected more significantly in the in‐patient group than in the out‐patient group, and influenza viruses were detected more frequently in the out‐patient group than in the in‐patient group. Moreover, the use of m‐PCR pointed out the frequency of rhinovirus and mixed viral detections in these patients. In conclusion, according to the requirements of speed and low cost of the methods, and to achieve the highest rate of detection of respiratory viruses, the combined use of DFA and m‐PCR is today likely to be the best way to improve diagnosis of respiratory illnesses in children. J. Med. Virol. 78:1498–1504, 2006. © 2006 Wiley‐Liss, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/16998894/ doi: 10.1002/jmv.20725 id: cord-322391-tumpiid5 author: Freymuth, François title: Detection of viral, Chlamydia pneumoniae and Mycoplasma pneumoniae infections in exacerbations of asthma in children date: 1999-08-31 words: 3813.0 sentences: 190.0 pages: flesch: 47.0 cache: ./cache/cord-322391-tumpiid5.txt txt: ./txt/cord-322391-tumpiid5.txt summary: According to the virus, a viral isolation technique, immunofluorescence assays (IFA) or both were used for the detection of rhinovirus, enterovirus, respiratory syncytial (RS) virus, adenovirus, coronavirus 229E, influenza and parainfluenza virus. Results: Using IFA and viral isolation techniques, viruses were detected in 33.3% of cases, and by PCR techniques, nucleic acid sequences of virus, Chlamydia pneumoniae and Mycoplasma pneumoniae were obtained in 71.9% of cases. We also previously reported that molecular techniques were more sensitive than IFA and viral isolation for the detection of RS virus, rhinovirus, adenovirus and parainfluenza virus in nasal specimens collected from infants with bronchiolitis (Freymuth et al., 1997) , and the present study further confirmed that observation. Respiratory viruses, Chlamydia pneumoniae and Mycoplasma pneumoniae alone or associated, were detected in 81.8% of asthmatic exacerbations, with rhinovirus and RS virus being the most frequent isolated agents. abstract: Abstract Background: A high frequency of virus infections has been recently pointed out in the exacerbations of asthma in children. Objectives: To confirm this, using conventional and molecular detection methods, and expanding the study to younger children. Study design: One hundred and thirty-two nasal aspirates from 75 children hospitalized for a severe attack of asthma were studied (32 infants, mean age 9.1 months; and 43 children, mean age 5.6 years). According to the virus, a viral isolation technique, immunofluorescence assays (IFA) or both were used for the detection of rhinovirus, enterovirus, respiratory syncytial (RS) virus, adenovirus, coronavirus 229E, influenza and parainfluenza virus. Polymerase chain reaction (PCR) assays were used for the detection of rhinovirus, enterovirus, RS virus, adenovirus, coronavirus 229E and OC43, Chlamydia pneumoniae and Mycoplasma pneumoniae. Results: Using IFA and viral isolation techniques, viruses were detected in 33.3% of cases, and by PCR techniques, nucleic acid sequences of virus, Chlamydia pneumoniae and Mycoplasma pneumoniae were obtained in 71.9% of cases. The combination of conventional and molecular techniques detects 81.8% of positive samples. Two organisms were identified in the same nasal sample in 20.4% of the cases. The percentage of detections was higher (85.9%) in the younger group than in the other (77%). The most frequently detected agents were rhinovirus (46.9%) and RS virus (21.2%). Using PCR rather than conventional techniques, the detection rates were increased 5.8- and 1.6-fold in rhinovirus and RS virus infections, respectively. The detection levels of the other organisms are as follows: 9.8, 5.1, 4.5, 4.5, 4.5, 3.7, and 2.2% for enterovirus, influenza virus, Chlamydia pneumoniae, adenovirus, coronavirus, parainfluenza virus, and Mycoplasma pneumoniae, respectively. Conclusion: These results confirm the previously reported high frequency of rhinovirus detection in asthmatic exacerbations in children. They also point out the frequency of RS virus detection, and emphasize the fact that PCR assays may be necessary to diagnose respiratory infections in asthma. url: https://www.ncbi.nlm.nih.gov/pubmed/10443789/ doi: 10.1016/s1386-6532(99)00030-x id: cord-284376-plwyjhl8 author: Fu, Xinmiao title: Simulating and forecasting the cumulative confirmed cases of SARS-CoV-2 in China by Boltzmann function-based regression analyses date: 2020-05-31 words: 14726.0 sentences: 782.0 pages: flesch: 49.0 cache: ./cache/cord-284376-plwyjhl8.txt txt: ./txt/cord-284376-plwyjhl8.txt summary: All specimens tested negative by direct examination for PJ, whereas 27 were positive by real-time PCR (BAL, n = 18; sputa, n = 7, and TA, n = 2); Following stringent clinical, microbiological and imaging criteria ( Table 1 ) , PJP was deemed to be the most probable diagnosis in 12 episodes occurring in unique patients. In contrast, corticosteroid use within the month before sampling was not different between The probability of Pneumocystis jirovecii (PJ) pneumonia (PJP) for each patient was retrospectively evaluated by an expert committee including infectious diseases and microbiology specialists at both centers, on the basis of (i) documented PJ presence in respiratory specimens by microscopy; (ii) compatibility of clinical signs and symptoms (at least 2 of the following: subtle onset of progressive dyspnea, pyrexia, nonproductive cough, hypoxaemia and chest pain), (iii) compatible (suggestive) radiological findings (chest radiograph and/or high-resolution computed tomographic scan detection of interstitial opacities and/or diffuse infiltration infiltrates); (iv) complete resolution of symptoms after a full course of anti-PJP treatment; (v) absence of alternative diagnosis. abstract: • Cumulative confirmed cases in China were well fitted with Boltzmann function. • Potential total numbers of confirmed cases in different regions were estimated. • Key dates indicating minimal daily number of new confirmed cases were estimated. • Cumulative confirmed cases of 2003 SARS-CoV were well fitted to Boltzmann function. • The Boltzmann function was, for the first time, applied to epidemic analysis. url: https://api.elsevier.com/content/article/pii/S0163445320300980 doi: 10.1016/j.jinf.2020.02.019 id: cord-302503-7s9f8wje author: Fu, Yuguang title: Rapid and efficient detection methods of pathogenic swine enteric coronaviruses date: 2020-05-19 words: 6349.0 sentences: 295.0 pages: flesch: 51.0 cache: ./cache/cord-302503-7s9f8wje.txt txt: ./txt/cord-302503-7s9f8wje.txt summary: In October 2010, a severe PED outbreak caused by a highly virulent PEDV variant emerged in southern China with high mortality ranging from 70 to 100%; the result was devastating damage to the pig farm industry and tremendous economic losses, and later, the PEDV variant spreads to other countries, e.g., USA, Canada, and Mexico ( For the early and rapid detection of PEDV, different types of PCR methods have been developed. A TaqMan probe-based real-time PCR to differentiate porcine epidemic diarrhea virus virulent strains from attenuated vaccine strains Development and evaluation of a duplex real-time RT-PCR for detection and differentiation of virulent and variant strains of porcine epidemic diarrhea viruses from the United States Development of a TaqMan-based real-time RT-PCR assay for the detection of SADS-CoV associated with severe diarrhea disease in pigs abstract: ABSTRACT: Porcine enteric coronaviruses (CoVs) cause highly contagious enteric diarrhea in suckling piglets. These COV infections are characterized by clinical signs of vomiting, watery diarrhea, dehydration, and high morbidity and mortality, resulting in significant economic losses and tremendous threats to the pig farming industry worldwide. Because the clinical manifestations of pigs infected by different CoVs are similar, it is difficult to differentiate between the specific pathogens. Effective high-throughput detection methods are powerful tools used in the prevention and control of diseases. The immune system of piglets is not well developed, so serological methods to detect antibodies against these viruses are not suitable for rapid and early detection. This paper reviews various PCR-based methods used for the rapid and efficient detection of these pathogenic CoVs in swine intestines. KEY POINTS: 1. Swine enteric coronaviruses (CoVs) emerged and reemerged in past years. 2. Enteric CoVs infect pigs at all ages with high mortality rate in suckling pigs. 3. Rapid and efficient detection methods are needed and critical for diagnosis. url: https://doi.org/10.1007/s00253-020-10645-5 doi: 10.1007/s00253-020-10645-5 id: cord-256244-f5zsy56p author: Funakoshi, Yu title: Enterovirus D68 respiratory infection in a children''s hospital in Japan in 2015 date: 2019-08-22 words: 3854.0 sentences: 231.0 pages: flesch: 47.0 cache: ./cache/cord-256244-f5zsy56p.txt txt: ./txt/cord-256244-f5zsy56p.txt summary: Mycoplasma pneumonia was tested for using the loop-mediated isothermal amplification method (Eiken Chemical, Tokyo, Japan) 15 when physicians in charge considered it as a potential etiologic pathogen based on patient age and symptoms regardless of the patient''s eligibility for this study. We encountered an outbreak of EV-D68 in the autumn of 2015 (September-October), in which the number of patients with respiratory symptoms who required treatment for wheezing increased dramatically compared with previous years. 19, 29, 30 In the present study, EV-D68 infection with a history of asthma was not associated with either severity (defined as ICU admission, magnesium sulfate use, or ventilation support) nor prolonged hospitalization. In contrast to previous research, asthma history was not associated with the risk of developing severe respiratory infections in the present study. Two cases of acute severe flaccid myelitis associated with enterovirus D68 infection in children abstract: BACKGROUND: Outbreaks of enterovirus D68 (EV‐D68) respiratory infections in children were reported globally in 2014. In Japan, there was an EV‐D68 outbreak in the autumn of 2015 (September–October). The aim of this study was to compare EV‐D68‐specific polymerase chain reaction (PCR)‐positive and EV‐D68‐specific PCR‐negative patients. METHODS: Pediatric patients admitted for any respiratory symptoms between September and October 2015 were enrolled. Nasopharyngeal swabs were tested for multiplex respiratory virus PCR and EV‐D68‐specific reverse transcription‐PCR. EV‐D68‐specific PCR‐positive and ‐negative patients were compared regarding demographic data and clinical information. RESULTS: A nasopharyngeal swab was obtained from 76 of 165 patients admitted with respiratory symptoms during the study period. EV‐D68 was detected in 40 samples (52.6%). Median age in the EV‐D68‐specific PCR‐positive and ‐negative groups was 3.0 years (IQR, 5.5 years) and 3.0 years (IQR, 4.0 years), respectively. The rates of coinfection in the two groups were 32.5% and 47.2%, respectively. There was no significant difference in the history of asthma or recurrent wheezing, length of hospitalization, or pediatric intensive care unit admission rate between the groups. The median days between symptom onset and admission was significantly lower for the EV‐D68‐positive group (3.0 days vs 5.0 days, P = 0.001). EV‐D68 was identified as clade B on phylogenetic analysis. No cases of acute flaccid myelitis were encountered. CONCLUSIONS: More than half of the samples from the children admitted with respiratory symptoms were positive for EV‐D68‐specific PCR during the outbreak. Asthma history was not associated with the risk of developing severe respiratory infection. url: https://www.ncbi.nlm.nih.gov/pubmed/31136073/ doi: 10.1111/ped.13903 id: cord-322448-s04e6po9 author: Gadsby, Naomi J. title: Comprehensive Molecular Testing for Respiratory Pathogens in Community-Acquired Pneumonia date: 2016-04-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Background. The frequent lack of a microbiological diagnosis in community-acquired pneumonia (CAP) impairs pathogen-directed antimicrobial therapy. This study assessed the use of comprehensive multibacterial, multiviral molecular testing, including quantification, in adults hospitalized with CAP. Methods. Clinical and laboratory data were collected for 323 adults with radiologically-confirmed CAP admitted to 2 UK tertiary care hospitals. Sputum (96%) or endotracheal aspirate (4%) specimens were cultured as per routine practice and also tested with fast multiplex real-time polymerase-chain reaction (PCR) assays for 26 respiratory bacteria and viruses. Bacterial loads were also calculated for 8 bacterial pathogens. Appropriate pathogen-directed therapy was retrospectively assessed using national guidelines adapted for local antimicrobial susceptibility patterns. Results. Comprehensive molecular testing of single lower respiratory tract (LRT) specimens achieved pathogen detection in 87% of CAP patients compared with 39% with culture-based methods. Haemophilus influenzae and Streptococcus pneumoniae were the main agents detected, along with a wide variety of typical and atypical pathogens. Viruses were present in 30% of cases; 82% of these were codetections with bacteria. Most (85%) patients had received antimicrobials in the 72 hours before admission. Of these, 78% had a bacterial pathogen detected by PCR but only 32% were culture-positive (P < .0001). Molecular testing had the potential to enable de-escalation in number and/or spectrum of antimicrobials in 77% of patients. Conclusions. Comprehensive molecular testing significantly improves pathogen detection in CAP, particularly in antimicrobial-exposed patients, and requires only a single LRT specimen. It also has the potential to enable early de-escalation from broad-spectrum empirical antimicrobials to pathogen-directed therapy. url: https://www.ncbi.nlm.nih.gov/pubmed/26747825/ doi: 10.1093/cid/civ1214 id: cord-261128-j55v4clu author: Gagliardi, T.B. title: Concurrent detection of other respiratory viruses in children shedding viable human respiratory syncytial virus date: 2013-07-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Human respiratory syncytial virus (HRSV) is an important cause of respiratory disease. The majority of studies addressing the importance of virus co‐infections to the HRSV‐disease have been based on the detection of HRSV by RT‐PCR, which may not distinguish current replication from prolonged shedding of remnant RNA from previous HRSV infections. To assess whether co‐detections of other common respiratory viruses are associated with increased severity of HRSV illnesses from patients who were shedding viable‐HRSV, nasopharyngeal aspirates from children younger than 5 years who sought medical care for respiratory infections in Ribeirão Preto (Brazil) were tested for HRSV by immunofluorescence, RT‐PCR and virus isolation in cell culture. All samples with viable‐HRSV were tested further by PCR for other respiratory viruses. HRSV‐disease severity was assessed by a clinical score scale. A total of 266 samples from 247 children were collected and 111 (42%) were HRSV‐positive. HRSV was isolated from 70 (63%), and 52 (74%) of them were positive for at least one additional virus. HRSV‐positive diseases were more severe than HRSV‐negative ones, but there was no difference in disease severity between patients with viable‐HRSV and those HRSV‐positives by RT‐PCR. Co‐detection of other viruses did not correlate with increased disease severity. HRSV isolation in cell culture does not seem to be superior to RT‐PCR to distinguish infections associated with HRSV replication in studies of clinical impact of HRSV. A high rate of co‐detection of other respiratory viruses was found in samples with viable‐HRSV, but this was not associated with more severe HRSV infection. J Med. Virol. 85:1852–1859, 2013. © 2013 Wiley Periodicals, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/23861138/ doi: 10.1002/jmv.23648 id: cord-300285-su2fueox author: Gajurel, Kiran title: Persistently positive severe acute respiratory syndrome coronavirus 2 (SARS‐COV2) nasopharyngeal PCR in a kidney transplant recipient date: 2020-07-27 words: 384.0 sentences: 27.0 pages: flesch: 54.0 cache: ./cache/cord-300285-su2fueox.txt txt: ./txt/cord-300285-su2fueox.txt summary: title: Persistently positive severe acute respiratory syndrome coronavirus 2 (SARS‐COV2) nasopharyngeal PCR in a kidney transplant recipient Severe acute respiratory syndrome coronavirus 2 (SARS-COV2 ) infection is usually diagnosed by a positive PCR test in respiratory samples. While the respiratory PCR may remain positive for 2-3 weeks in the general population there have been occasional reports of persistent and recurrent positive SARS-COV2 PCR beyond 4 weeks despite clinical resolution 1-6 . This is particularly relevant in transplant recipients who carry a significant mortality and morbidity associated with SARS COV2 infection. 8 Here, we would like to share our experience of a Follow-up NP SARS COV2 PCR, however, remained intermittently positive for 57 days after the first positive test (Table 1) . Quantifying the prevalence of SARS-CoV-2 long-term shedding among non-hospitalized COVID-19 patients Case report: viral shedding for 60 days in a woman with COVID-19 abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-COV2 ) infection is usually diagnosed by a positive PCR test in respiratory samples. While the respiratory PCR may remain positive for 2-3 weeks in the general population there have been occasional reports of persistent and recurrent positive SARS-COV2 PCR beyond 4 weeks despite clinical resolution 1-6 . url: https://www.ncbi.nlm.nih.gov/pubmed/32652872/ doi: 10.1111/tid.13408 id: cord-327344-8gi1wb76 author: Gambarino, Stefano title: Development of a RT Real-Time PCR for the Detection and Quantification of Human Rhinoviruses date: 2009-03-17 words: 3506.0 sentences: 147.0 pages: flesch: 38.0 cache: ./cache/cord-327344-8gi1wb76.txt txt: ./txt/cord-327344-8gi1wb76.txt summary: This article describes the development and optimization of a reverse transcription (RT) real-time PCR assay for quantification of HRV RNA in clinical samples. Clinical specimens originated from the Virology Unit of the Fig. 1 Standard curve (from 10 2 to 10 5 copies/reaction) and dynamic range (from 10 7 to 10 1 copies/reaction) of the real-time RT-PCR developed in this study Azienda Ospedaliero-Universitaria San Giovanni Battista, Turin, and included 110 bronchoalveolar lavages (BAL) obtained from 84 patients (M/F, 57/27; mean age, 57.8 years; range, . The performance of the RT real-time PCR developed in this study was examined over different concentrations of HRV RNA and it was found to be very sensitive with a minimum cut-off for detection of 10 0 copy/reaction and was linear up to 10 1 copies. In conclusion, the RT real-time PCR assay developed in this study could represent a useful tool for diagnosing HRV infections, quantifying the viral load and could be applicable for routine diagnostic workup of upper as well as lower respiratory tract diseases. abstract: Human Rhinoviruses (HRV) are the most common viral agents, being responsible for upper as well as lower respiratory tract infections. Evidence demonstrating that HRV disease is not exclusively limited to the upper airways and may cause lower respiratory complications, together with the frequency of HRV infections and the increasing number of immunocompromised patients underline the need for including HRV in virological diagnostics of acute lower respiratory tract illness. This article describes the development and optimization of a reverse transcription (RT) real-time PCR assay for quantification of HRV RNA in clinical samples. Efficiency, sensitivity, specificity, inter- and intra-assay variability, and dynamic range have been determined. Subsequently, the assay has been validated on bronchoalveolar lavage (BAL) specimens obtained from immunocompetent and immunocompromised patients. url: https://doi.org/10.1007/s12033-009-9164-x doi: 10.1007/s12033-009-9164-x id: cord-273846-l0elcfe8 author: Ganapathy, Kannan title: Effects of cold storage on detection of avian infectious bronchitis virus in chicken carcasses and local antibodies in tracheal washes date: 2005-02-24 words: 2440.0 sentences: 134.0 pages: flesch: 59.0 cache: ./cache/cord-273846-l0elcfe8.txt txt: ./txt/cord-273846-l0elcfe8.txt summary: title: Effects of cold storage on detection of avian infectious bronchitis virus in chicken carcasses and local antibodies in tracheal washes In order to test the survivability of infectious bronchitis virus (IBV) in dead chicken carcasses during 24 h of cold storage, 7 week-old specific-pathogen-free chickens were infected with virulent IBV Massachusetts strain M41, and were killed humanely 10 days later. Trachea, lung, kidney and rectum were collected for virus isolation by tracheal organ culture (TOC) or embryonated chicken eggs (ECE), and detection by nested reverse-transcriptase polymerase chain reaction (RT-PCR). Diagnosis of infectious bronchitis virus (IBV) is confirmed by isolation of the virus using either chicken embryonated eggs (ECE) or tracheal organ culture (TOC) and detection by reverse-transcriptase polymerase chain reaction (RT-PCR) (Cavanagh and Naqi, 2003; Gelb and Jackwood, 1998) . The use of chicken tracheal organ cultures for the isolation and assay of avian infectious bronchitis virus abstract: In order to test the survivability of infectious bronchitis virus (IBV) in dead chicken carcasses during 24 h of cold storage, 7 week-old specific-pathogen-free chickens were infected with virulent IBV Massachusetts strain M41, and were killed humanely 10 days later. Carcasses were stored in a cold room at 4 °C. After 1, 3, 6, 9, 12 or 24 h of storage, necropsies were carried out. Trachea, lung, kidney and rectum were collected for virus isolation by tracheal organ culture (TOC) or embryonated chicken eggs (ECE), and detection by nested reverse-transcriptase polymerase chain reaction (RT-PCR). IBV was detected by RT-PCR at all sampling times, except for 1 and 6 h of storage in kidney and 9 h of storage in kidney and rectum. For ECE, isolation was obtained at all sampling points, except at 1 and 24 h of storage in lungs. Isolation by tracheal organ cultures was less successful, except from rectum. In addition to sampling for virus, tracheal washes were collected from each carcass to measure the ability to detect local antibodies after storage. Levels of IgA in tracheal washes remained high for up to 9 h of storage, suggesting that accurate sampling for research purposes when required must be carried out within this time. url: https://www.ncbi.nlm.nih.gov/pubmed/15847923/ doi: 10.1016/j.jviromet.2005.01.024 id: cord-000265-llilwq1u author: Gao, Rongbao title: A Systematic Molecular Pathology Study of a Laboratory Confirmed H5N1 Human Case date: 2010-10-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Autopsy studies have shown that human highly pathogenic avian influenza virus (H5N1) can infect multiple human organs other than just the lungs, and that possible causes of organ damage are either viral replication and/or dysregulation of cytokines and chemokines. Uncertainty still exists, partly because of the limited number of cases analysed. In this study, a full autopsy including 5 organ systems was conducted on a confirmed H5N1 human fatal case (male, 42 years old) within 18 hours of death. In addition to the respiratory system (lungs, bronchus and trachea), virus was isolated from cerebral cortex, cerebral medullary substance, cerebellum, brain stem, hippocampus ileum, colon, rectum, ureter, aortopulmonary vessel and lymph-node. Real time RT-PCR evidence showed that matrix and hemagglutinin genes were positive in liver and spleen in addition to positive tissues with virus isolation. Immunohistochemistry and in-situ hybridization stains showed accordant evidence of viral infection with real time RT-PCR except bronchus. Quantitative RT-PCR suggested that a high viral load was associated with increased host responses, though the viral load was significantly different in various organs. Cells of the immunologic system could also be a target for virus infection. Overall, the pathogenesis of HPAI H5N1 virus was associated both with virus replication and with immunopathologic lesions. In addition, immune cells cannot be excluded from playing a role in dissemination of the virus in vivo. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2953511/ doi: 10.1371/journal.pone.0013315 id: cord-103787-qhftb6d7 author: Garcia, Elizabeth P. title: Scalable Transcriptional Analysis Routine—Multiplexed Quantitative Real-Time Polymerase Chain Reaction Platform for Gene Expression Analysis and Molecular Diagnostics date: 2005-10-31 words: 7354.0 sentences: 355.0 pages: flesch: 47.0 cache: ./cache/cord-103787-qhftb6d7.txt txt: ./txt/cord-103787-qhftb6d7.txt summary: Scalable transcriptional analysis routine (STAR) represents a novel integration of reverse transcriptase-polymerase chain reaction and capillary electrophoresis that allows detection of dozens of gene transcripts in a multiplexed format using amplicon size as an identifier for each target. Scalable transcriptional analysis routine (STAR) represents a novel integration of reverse transcriptase-polymerase chain reaction and capillary electrophoresis that allows detection of dozens of gene transcripts in a multiplexed format using amplicon size as an identifier for each target. We have developed STAR (scalable transcription analysis routine), a gene expression analysis platform that represents an innovative integration of real-time multiplex PCR and capillary electrophoresis (CE), allowing the simultaneous quantitative measurement of multiple targets in a single sample with high sensitivity. In a typical STAR experiment (diagrammatically shown in Figure 1A ), a PCR reaction is set up in a single tube containing the analyte, common PCR reagents (eg, DNA polymerase, dNTPs), and, for each target to be amplified, gene-specific primers where at least one of each pair is labeled with a fluorophore. abstract: We report the development of a new technology for simultaneous quantitative detection of multiple targets in a single sample. Scalable transcriptional analysis routine (STAR) represents a novel integration of reverse transcriptase-polymerase chain reaction and capillary electrophoresis that allows detection of dozens of gene transcripts in a multiplexed format using amplicon size as an identifier for each target. STAR demonstrated similar or better sensitivity and precision compared to two commonly used methods, SYBR Green-based and TaqMan probe-based real-time reverse transcriptase-polymerase chain reaction. STAR can be used as a flexible platform for building a variety of applications to monitor gene expression, from single gene assays to assays analyzing the expression level of multiple genes. Using severe acute respiratory syndrome (SARS) corona virus as a model system, STAR technology detected single copies of the viral genome in a two-gene multiplex. Blinded studies using RNA extracted from various tissues of a SARS-infected individual showed that STAR correctly identified all samples containing SARS virus and yielded negative results for non-SARS control samples. Using alternate priming strategies, STAR technology can be adapted to transcriptional profiling studies without requiring a priori sequence information. Thus, STAR technology offers a flexible platform for development of highly multiplexed assays in gene expression analysis and molecular diagnostics. url: https://api.elsevier.com/content/article/pii/S1525157810605752 doi: 10.1016/s1525-1578(10)60575-2 id: cord-321432-qi2knswx author: Gardner, Shea N title: A microbial detection array (MDA) for viral and bacterial detection date: 2010-11-25 words: 8427.0 sentences: 397.0 pages: flesch: 50.0 cache: ./cache/cord-321432-qi2knswx.txt txt: ./txt/cord-321432-qi2knswx.txt summary: METHODS: We designed a pan-Microbial Detection Array (MDA) to detect all known viruses (including phages), bacteria and plasmids and developed a novel statistical analysis method to identify mixtures of organisms from complex samples hybridized to the array. We also present a novel statistical algorithm for analysis of detection/discovery arrays, which combines a predictive model of probe hybridization with a greedy likelihood maximization procedure to identify the combination of targets in a complex sample that best explains the observed probe intensity pattern. We developed a novel statistical method for detection array analysis, by modeling the likelihood of the observed probe intensities as a function of the combination of targets present in the sample, and performing greedy maximization to find a locally optimal set of targets; the details of the algorithm are shown in Methods. abstract: BACKGROUND: Identifying the bacteria and viruses present in a complex sample is useful in disease diagnostics, product safety, environmental characterization, and research. Array-based methods have proven utility to detect in a single assay at a reasonable cost any microbe from the thousands that have been sequenced. METHODS: We designed a pan-Microbial Detection Array (MDA) to detect all known viruses (including phages), bacteria and plasmids and developed a novel statistical analysis method to identify mixtures of organisms from complex samples hybridized to the array. The array has broader coverage of bacterial and viral targets and is based on more recent sequence data and more probes per target than other microbial detection/discovery arrays in the literature. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable detection of divergent species with homology to sequenced organisms, and to have no significant matches to the human genome sequence. RESULTS: In blinded testing on spiked samples with single or multiple viruses, the MDA was able to correctly identify species or strains. In clinical fecal, serum, and respiratory samples, the MDA was able to detect and characterize multiple viruses, phage, and bacteria in a sample to the family and species level, as confirmed by PCR. CONCLUSIONS: The MDA can be used to identify the suite of viruses and bacteria present in complex samples. url: https://www.ncbi.nlm.nih.gov/pubmed/21108826/ doi: 10.1186/1471-2164-11-668 id: cord-299944-1e44usl6 author: Gardner, Shea N. title: Multiplex Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes date: 2014-08-03 words: 4147.0 sentences: 175.0 pages: flesch: 52.0 cache: ./cache/cord-299944-1e44usl6.txt txt: ./txt/cord-299944-1e44usl6.txt summary: The major difference is that it begins with a consensus sequence containing degenerate bases and selects primers with fewer than 3 or 4 degenerate bases, so that in the end a majority of strains are amplified, 2 Advances in Bioinformatics Table 1 : Summary of average lengths, number of sequences, and percentage of conserved bases in a multiple sequence alignment (with MUSCLE [5] ), and number of tiled primers required for the short and long amplicon settings. The method here differs in that it takes the full multiple sequence alignment as input rather than a consensus, and it seeks to automatically design a minimal, degenerate set of multiplex compatible primers to amplify all the strains for a given region in a single reaction. The run tiled primers process can be summarized as follows: split a multiple sequence alignment into overlapping regions, and for each region design a degenerate multiplex set of primers that in combination amplify that region in all strains with as few primers as possible. abstract: Background. Targeted enrichment improves coverage of highly mutable viruses at low concentration in complex samples. Degenerate primers that anneal to conserved regions can facilitate amplification of divergent, low concentration variants, even when the strain present is unknown. Results. A tool for designing multiplex sets of degenerate sequencing primers to tile overlapping amplicons across multiple whole genomes is described. The new script, run_tiled_primers, is part of the PriMux software. Primers were designed for each segment of South American hemorrhagic fever viruses, tick-borne encephalitis, Henipaviruses, Arenaviruses, Filoviruses, Crimean-Congo hemorrhagic fever virus, Rift Valley fever virus, and Japanese encephalitis virus. Each group is highly diverse with as little as 5% genome consensus. Primer sets were computationally checked for nontarget cross reactions against the NCBI nucleotide sequence database. Primers for murine hepatitis virus were demonstrated in the lab to specifically amplify selected genes from a laboratory cultured strain that had undergone extensive passage in vitro and in vivo. Conclusions. This software should help researchers design multiplex sets of primers for targeted whole genome enrichment prior to sequencing to obtain better coverage of low titer, divergent viruses. Applications include viral discovery from a complex background and improved sensitivity and coverage of rapidly evolving strains or variants in a gene family. url: https://doi.org/10.1155/2014/101894 doi: 10.1155/2014/101894 id: cord-321181-bqdsfgdc author: Garitano, Ignacio title: Estimando el número de casos de COVID-19 mediante una herramienta web: resultados de la primera semana del proyecto "Covid-19 Trends" en Euskadi date: 2020-05-21 words: 3190.0 sentences: 301.0 pages: flesch: 59.0 cache: ./cache/cord-321181-bqdsfgdc.txt txt: ./txt/cord-321181-bqdsfgdc.txt summary: Faltaban datos sobre el numero de casos no testados en España.Para estimar rápidamente el número de casos durante la pandemia de COVID-19, la Fundación Io , lanzó, el 19 de marzo, una herramienta web llamada "Covid-19 Trends", a nivel nacional, a través de las redes sociales. La página web de la Fundación iO muestra el cuestionario (https://covid19.fundacionio.com/epidemiologicalquestionnaire.aspx), así como el enlace a los datos en formatos CVS para ser utilizados por las autoridades de salud u otros grupos como universidades o institutos de investigación, de manera gratuita y a tiempo real. El cuestionario "Covid-19 Trends" estimó más de 6.000 casos compatibles con la definición clínica del Ministerio de Sanidad, Consumo y Bienestar Social en Euskadi durante el mes anterior al primer diagnóstico de COVID-19 mediante RT-PCR; esto indica que este tipo de herramienta podría ser útil como sistema de vigilancia temprana. abstract: Resumen Objetivo: En Euskadi, dos casos de COVID-19 fueron diagnosticados el 28 de febrero de 2020. El 14 de marzo el Gobierno español estableció el estado de alarma. La única información acerca del número de casos de Covid-19 eran los confirmados por RT-PCR. Lanzamos una herramienta de vigilancia basada en la web para estimar el número mínimo de casos sintomáticos de Covid-19 y generar información útil para la toma de decisiones en salud pública. Material y métodos: Implementamos un cuestionario web anónimo y lo difundimos a través de redes sociales. Recopilamos información epidemiológica sobre variables de “tiempo” (fecha de inicio de los síntomas), “lugar” (código postal) y “persona” (género, edad). Comparamos los casos positivos detectados mediante RT-PCR con los casos estimados según la definición de caso del Ministerio de Sanidad Consumo y Bienestar Social. Calculamos la tasa de respuesta al cuestionario y la incidencia acumulada a 14 días. Resultados: Entre el 19 y 26 de marzo de 2020, el cuestionario fue contestado por 128.182 personas (5,5% de la población vasca).De ellas 27.599 cumplieron la definición de caso. Los casos estimados fueron seis veces más que los RT-PCR positivos para COVID-19. La incidencia acumulada a 14 días fue de 463,3 por 100.000 habitantes comparada con la de los casos positivos por RT-PCR que fue de 139,6 por 100.000 habitantes. Conclusiones: Esta herramienta mostró su utilidad para estimar el mínimo número de casos sintomáticos en Euskadi lo cual podría apoyar aciones de salud pública. Summary Objective: In the Basque Country, two cases of COVID-19 were diagnosed on February 28 2020. On March 14, the Spanish Government established a state of alarm. Only cases confirmed by molecular biology (reverse-transcriptase polymerase chain reaction [RT-PCR]) were known. We launched a web-based surveillance tool to estimate the number of symptomatic cases of COVID-19 to contribute to Public Health decision-making. Material and methods: We implemented an anonymous web questionnaire and disseminated it through online social media social. We collected epidemiological information about "time" (date of onset of symptoms), "place" (zip code), and "person" (gender, age). We compared cases detected by RT-PCR with the estimated cases, according to the case definition of the Ministry of Health. We calculated the questionnaire response rate and the cumulative incidence at 14 days. Results: Between March 19 and 26, 128,009 people answered the questionnaire (5.5% of the Basque population). Of these, 26,375 met the case definition (symptom prevalence of 21.4%). The estimated cases were almost six times more than COVID-19 positive RT-PCR. The estimated 14-day cumulative incidence was 578.3 per 100,000 population compared to RT-PCR positive cases, which was 139.6 per 100,000 population. Conclusions: This tool was useful in estimating the minimum number of symptomatic cases in the Basque Country, which could support Public Health actions. url: https://www.ncbi.nlm.nih.gov/pubmed/32513502/ doi: 10.1016/j.semerg.2020.05.011 id: cord-331496-5xak7z6b author: Garnett, Emily title: Clinical Validation and Performance Evaluation of the Automated Vitros Total Anti–SARS-CoV-2 Antibodies Assay for Screening of Serostatus in COVID-19 date: 2020-08-31 words: 3450.0 sentences: 187.0 pages: flesch: 43.0 cache: ./cache/cord-331496-5xak7z6b.txt txt: ./txt/cord-331496-5xak7z6b.txt summary: We anticipate it will be a useful tool in screening for exposure to SARS-CoV-2; however, the use of the CoV2T and other serologic assays in the clinical management of patients with COVID-19 is unknown and must be evaluated in future studies. In this study, we describe validation of one of the first assays to receive EUA on an automated platform, the Vitros Anti-SARS-CoV-2 Total (CoV2T; Ortho Clinical Diagnostics) antibody assay, for screening of previous exposure to SARS-CoV-2 in our patient population. Seroconversion in our patient population was assessed by correlation of chart review of 55 patients known to be positive for SARS-CoV-2 by RT-PCR and known date of symptom onset with sample reactivity by the CoV2T assay. Specimens from 14 patients with acute infections, previously tested to be negative for SARS-CoV-2 by RT-PCR but positive for another respiratory viral infection by molecular analysis, were nonreactive by the CoV2T assay. abstract: OBJECTIVES: Evaluation of serostatus against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emerged as an important tool in identification of exposure to coronavirus disease 2019 (COVID-19). We report on the validation of the Vitros Anti–SARS-CoV-2 Total (CoV2T) assay for qualitative serologic testing of SARS-CoV-2 antibodies. METHODS: We performed validation studies according to Commission of Office Laboratories Accreditation guidelines, using samples previously tested for SARS-CoV-2 by reverse transcription–polymerase chain reaction (RT-PCR). We evaluated precision, analytical interferences, and cross-reactivity with other viral infections; evaluated concordance with molecular and other serologic testing; and evaluated seroconversion. RESULTS: The Vitros CoV2T assay exhibited acceptable precision and did not exhibit cross-reactivity with other acute respiratory virus infections. The CoV2T assay exhibited 100% negative predictive agreement (56/56) and 71% positive predictive agreement (56/79) with RT-PCR across all patient samples and was concordant with other serologic assays. Concordance with RT-PCR was 97% more than 7 days after symptom onset. The CoV2T assay was robust to icterus and lipemia but had interference from significant hemolysis. CONCLUSIONS: The Vitros CoV2T assay was successfully validated in our laboratory. We anticipate it will be a useful tool in screening for exposure to SARS-CoV-2; however, the use of the CoV2T and other serologic assays in the clinical management of patients with COVID-19 is unknown and must be evaluated in future studies. url: https://doi.org/10.1093/ajcp/aqaa157 doi: 10.1093/ajcp/aqaa157 id: cord-011073-uiabpbxd author: Gebrekidan, Hagos title: An appraisal of oriental theileriosis and the Theileria orientalis complex, with an emphasis on diagnosis and genetic characterisation date: 2019-12-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Oriental theileriosis, a tick-borne disease of bovids caused by members of the Theileria orientalis complex, has a worldwide distribution. Globally, at least 11 distinct genotypes of T. orientalis complex, including type 1 (chitose), type 2 (ikeda), type 3 (buffeli), types 4 to 8, and N1–N3, have been described based on the sequence of the major piroplasm surface protein (MPSP) gene. Of these 11 genotypes, mainly ikeda and chitose are known to be pathogenic and cause considerable morbidity (including high fever, anaemia, jaundice and abortion), production losses and/or mortality in cattle. Mixed infections with two or more genotypes of T. orientalis is common, but do not always lead to a clinical disease, posing challenges in the diagnosis of asymptomatic or subclinical forms of oriental theileriosis. The diagnosis of oriental theileriosis is usually based on clinical signs, the detection of piroplasms of T. orientalis in blood smears, and/or the use of serological or molecular techniques. This paper reviews current methods used for the diagnosis of T. orientalis infections and the genetic characterisation of members of the T. orientalis complex, and proposes that advanced genomic tools should be established for investigations of these and related haemoparasites. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223495/ doi: 10.1007/s00436-019-06557-7 id: cord-297160-tqw9vx2b author: Geerligs, H.J. title: The use of RT-PCR for determination of separate end-points for the strains IB H120 and IB D274 in titration of the combination vaccine Poulvac IB(®) primer date: 2013-07-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Poulvac IB(®) Primer is a lyophilized vaccine containing two attenuated infectious bronchitis strains in one vial, IB H120 and IB D274. For quantification of the viral content of the vaccine, dilution series of the final product are inoculated in embryonated chicken eggs. After the incubation period of seven days standard practice is for the embryos to be taken from each egg and examined visually for IB specific lesions; these readings are used to determine an end-point in viral titrations. The result is a titre value to which both strains contribute. However, it is not clear what the live virus titre is for strain IB H120 and for strain IB D274. In order to determine end-points in the titration for each of the two strains, we collected the allantoic fluids from each egg after the incubation period and tested these for the presence of IB H120 and IB D274 by a strain specific reverse phase PCR. Based on the data obtained by PCR we were able to determine an end-point for each of the two strains. For a given commercial batch of Poulvac IB primer we determined titres of 10(6.31) EID(50) per vial for IB H120 and 10(6.59) EID(50) for IB D274 using PCR for end-point determination. These end-points matched well with the end-point determined for both strains cumulatively after visual examination, i.e. 10(6.67) EID(50) per vial. It is concluded that PCR is a suitable means to determine end-points in titrations of live viruses. url: https://doi.org/10.1016/j.jviromet.2013.06.029 doi: 10.1016/j.jviromet.2013.06.029 id: cord-256931-wj0esjwi author: Gelfer, Gita title: The clinical impact of the detection of potential etiologic pathogens of community-acquired pneumonia date: 2015-08-05 words: 4850.0 sentences: 280.0 pages: flesch: 49.0 cache: ./cache/cord-256931-wj0esjwi.txt txt: ./txt/cord-256931-wj0esjwi.txt summary: The etiology of community-acquired pneumonia (CAP) is determined in less than half of the patients based on cultures of sputum and blood plus testing urine for the antigens of Streptococcus pneumoniae and Legionella pneumophila. A common core diagnostic test bundle was applied to all patients in the study: i.e., 2 blood cultures; sputum culture and sensitivity; serum PCT level; and urine antigen testing for L. If a respiratory virus was detected and the serum PCT was above 0.5 ng/mL and/or a bacterial pathogen was found in the sputum culture, the patient was assumed to have a dual infection with the identified virus and bacteria. If a respiratory virus was detected, an associated bacterial infection was deemed present if a bacterial pathogen was identified by culture or PCR or urine antigens or if the serum PCT concentration was N0.5 ng/mL. abstract: The etiology of community-acquired pneumonia (CAP) is determined in less than half of the patients based on cultures of sputum and blood plus testing urine for the antigens of Streptococcus pneumoniae and Legionella pneumophila. This study added nasal polymerase chain reaction (PCR) probes for S. pneumoniae, Staphylococcus aureus, and respiratory viruses. Serum procalcitonin (PCT) levels were measured. Pathogens were identified in 78% of the patients. For detection of viruses, patients were randomized to either a 5-virus laboratory-generated PCR bundle or the 17-virus FilmArray PCR platform. The FilmArray PCR platform detected more viruses than the laboratory-generated bundle and did so in less than 2 hours. There were fewer days of antibiotic therapy, P = 0.003, in CAP patients with viral infections and a low serum PCT levels. url: https://www.ncbi.nlm.nih.gov/pubmed/26341706/ doi: 10.1016/j.diagmicrobio.2015.08.001 id: cord-329148-zs18ez5q author: Geng, Yunyun title: Development of real-time recombinase polymerase amplification assay for rapid and sensitive detection of canine parvovirus 2 date: 2017-11-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Canine parvovirus 2, a linear single-stranded DNA virus belonging to the genus Parvovirus within the family Parvoviridae, is a highly contagious pathogen of domestic dogs and several wild canidae species. Early detection of canine parvovirus (CPV-2) is crucial to initiating appropriate outbreak control strategies. Recombinase polymerase amplification (RPA), a novel isothermal gene amplification technique, has been developed for the molecular detection of diverse pathogens. In this study, a real-time RPA assay was developed for the detection of CPV-2 using primers and an exo probe targeting the CPV-2 nucleocapsid protein gene. RESULTS: The real-time RPA assay was performed successfully at 38 °C, and the results were obtained within 4–12 min for 10(5)–10(1) molecules of template DNA. The assay only detected CPV-2, and did not show cross-detection of other viral pathogens, demonstrating a high level of specificity. The analytical sensitivity of the real-time RPA was 10(1) copies/reaction of a standard DNA template, which was 10 times more sensitive than the common RPA method. The clinical sensitivity of the real-time RPA assay matched 100% (n = 91) to the real-time PCR results. CONCLUSION: The real-time RPA assay is a simple, rapid, reliable and affordable method that can potentially be applied for the detection of CPV-2 in the research laboratory and point-of-care diagnosis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12917-017-1232-z) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/29110666/ doi: 10.1186/s12917-017-1232-z id: cord-292928-a4bn30ul author: Ghosh, Bipasha title: Review of bioaerosols in indoor environment with special reference to sampling, analysis and control mechanisms date: 2015-10-03 words: 16757.0 sentences: 730.0 pages: flesch: 39.0 cache: ./cache/cord-292928-a4bn30ul.txt txt: ./txt/cord-292928-a4bn30ul.txt summary: This review also provides the information on the concentration levels of various airborne microorganisms in different indoor environments, their associated health effects as well as various bioaerosol control mechanisms worked upon till now. A recently developed electrostatic precipitator had no charging unit in the inlet while the physical collection efficiency strongly depended on the precipitation voltage which eventually depended on the charge present on the airborne microbes naturally due to aerosolization (Kunkel, 1950; Flagan, 2001 ) thereby making collection possible by differentiating between the positively and negatively charged microorganisms by adding a signature to the bioaerosol particle sampled (Lee et al., 2004a; ; Lee et al., 2004b) . Whole genome sequencing has also been applied to study the airborne microbial community in various indoor and outdoor environments of NYC after collecting air samples using a Wet Cyclone Portable Air Sampler at the flow rate of 450 L/min (Yooseph et al., 2013) . abstract: Several tiny organisms of various size ranges present in air are called airborne particles or bioaerosol which mainly includes live or dead fungi and bacteria, their secondary metabolites, viruses, pollens, etc. which have been related to health issues of human beings and other life stocks. Bio-terror attacks in 2001 as well as pandemic outbreak of flue due to influenza A H1N1 virus in 2009 have alarmed us about the importance of bioaerosol research. Hence characterization i.e. identification and quantification of different airborne microorganisms in various indoor environments is necessary to identify the associated risks and to establish exposure threshold. Along with the bioaerosol sampling and their analytical techniques, various literatures revealing the concentration levels of bioaerosol have been mentioned in this review thereby contributing to the knowledge of identification and quantification of bioaerosols and their different constituents in various indoor environments (both occupational and non-occupational sections). Apart from recognition of bioaerosol, developments of their control mechanisms also play an important role. Hence several control methods have also been briefly reviewed. However, several individual levels of efforts such as periodic cleaning operations, maintenance activities and proper ventilation system also serve in their best way to improve indoor air quality. url: https://doi.org/10.1016/j.envint.2015.09.018 doi: 10.1016/j.envint.2015.09.018 id: cord-306605-mnafslqw author: Gibson, CS title: Fetal exposure to herpesviruses may be associated with pregnancy‐induced hypertensive disorders and preterm birth in a Caucasian population date: 2008-02-06 words: 4772.0 sentences: 281.0 pages: flesch: 49.0 cache: ./cache/cord-306605-mnafslqw.txt txt: ./txt/cord-306605-mnafslqw.txt summary: Objective To investigate the role of fetal viral infection in the development of a range of adverse pregnancy outcomes (APOs), including pregnancy‐induced hypertensive disorders (PIHD), antepartum haemorrhage (APH), birthweight <10th percentile (small for gestational age, SGA) and preterm birth (PTB). Main outcome measure Odds ratios and 95% CIs for specific APOs. Results For both term and PTBs, the risk of developing PIHD was increased in the presence of DNA from Herpes PCR group B viruses (OR 3.57, 95% CI 1.10–11.70), CMV (OR 3.89, 95% CI 1.67–9.06), any herpesvirus (OR 5.70, 95% CI 1.85–17.57) and any virus (OR 5.17, 95% CI 1.68–15.94). 2, 3 It has been postulated that fetal viral infection in utero may increase the risk of adverse pregnancy outcomes (APOs), such as pregnancy-induced hypertensive disorders (PIHD), birthweight <10th percentile (small for gestational age, SGA) and preterm birth (PTB). This study investigated the role of fetal exposure to viral infection (detected through the presence of viral nucleic acids in newborn screening cards) in APOs, including SGA, PIHD, antepartum haemorrhage (APH) and PTB. abstract: Objective To investigate the role of fetal viral infection in the development of a range of adverse pregnancy outcomes (APOs), including pregnancy‐induced hypertensive disorders (PIHD), antepartum haemorrhage (APH), birthweight <10th percentile (small for gestational age, SGA) and preterm birth (PTB). Design Population‐based case–control study. Setting Laboratory‐based study. Population The newborn screening cards of 717 adverse pregnancy cases and 609 controls. Methods Newborn screening cards were tested for RNA from enteroviruses and DNA from herpesviruses using polymerase chain reaction (PCR). The herpesviruses were detected using two PCRs, one detecting nucleic acids from herpes simplex virus (HSV)‐1, HSV‐2, Epstein–Barr virus (EBV), cytomegalovirus (CMV) and human herpesvirus (HHV)‐8, hereafter designated Herpes PCR group A viruses, and the other detecting nucleic acids from varicella‐zoster virus (VZV), HHV‐6 and HHV‐7, hereafter designated Herpes PCR group B viruses. Main outcome measure Odds ratios and 95% CIs for specific APOs. Results For both term and PTBs, the risk of developing PIHD was increased in the presence of DNA from Herpes PCR group B viruses (OR 3.57, 95% CI 1.10–11.70), CMV (OR 3.89, 95% CI 1.67–9.06), any herpesvirus (OR 5.70, 95% CI 1.85–17.57) and any virus (OR 5.17, 95% CI 1.68–15.94). The presence of CMV was associated with PTB (OR 1.61, 95% CI 1.14–2.27). No significant association was observed between SGA or APH and exposure to viral infection. Conclusions Fetal exposure to herpesvirus infection was associated with PIHD for both term and PTBs in this exploratory study. Exposure to CMV may also be associated with PTB. These findings need confirmation in future studies. url: https://doi.org/10.1111/j.1471-0528.2007.01653.x doi: 10.1111/j.1471-0528.2007.01653.x id: cord-269726-z0frgm7s author: Gidari, Anna title: Is recurrence possible in coronavirus disease 2019 (COVID-19)? Case series and systematic review of literature date: 2020-10-10 words: 6678.0 sentences: 441.0 pages: flesch: 54.0 cache: ./cache/cord-269726-z0frgm7s.txt txt: ./txt/cord-269726-z0frgm7s.txt summary: Criteria for patients'' selection were diagnosis of SARS-CoV-2 infection [5] ; the subsequent meeting of criteria for hospital discharge (improvement of symptoms and two negative swabs collected at least 24 h apart) [4] ; and a positive respiratory sample collected after discharge. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) Statement protocol [8] , a systematic review has been performed concerning the patients with a diagnosis of COVID-19 that, after clinical and virological recovery, presented a new positive respiratory sample (swab, sputum, saliva, tracheal aspirate, or BAL). The patient was discharged in good clinical conditions with indication to repeat quarantine and swab tests that came negative for SARS-CoV-2 (Allplex™ 2019-nCoV Assay) on April 27 and 28 (Fig. 1b) . abstract: Can a patient diagnosed with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) be infected again? This question is still unsolved. We tried to analyze local and literature cases with a positive respiratory swab after recovery. We collected data from symptomatic patients diagnosed with SARS-CoV-2 infection in the Italian Umbria Region that, after recovery, were again positive for SARS-CoV-2 in respiratory tract specimens. Samples were also assessed for infectivity in vitro. A systematic review of similar cases reported in the literature was performed. The study population was composed of 9 patients during a 4-month study period. Among the new positive samples, six were inoculated in Vero-E6 cells and showed no growth and negative molecular test in culture supernatants. All patients were positive for IgG against SARS-CoV-2 nucleoprotein and/or S protein. Conducting a review of the literature, 1350 similar cases have been found. The presumptive reactivation occurred in 34.5 days on average (standard deviation, SD, 18.7 days) after COVID-19 onset, when the 5.6% of patients presented fever and the 27.6% symptoms. The outcome was favorable in 96.7% of patients, while the 1.1% of them were still hospitalized at the time of data collection and the 2.1% died. Several hypotheses have been formulated to explain new positive respiratory samples after confirmed negativity. According to this study, the phenomenon seems to be due to the prolonged detection of SARS-CoV-2 RNA traces in respiratory samples of recovered patients. The failure of the virus to replicate in vitro suggests its inability to replicate in vivo. url: https://doi.org/10.1007/s10096-020-04057-6 doi: 10.1007/s10096-020-04057-6 id: cord-306656-cbtf2y2f author: Giuliano, A. title: Idiopathic sterile pyogranuloma in three domestic cats date: 2018-05-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Pyogranulomatous inflammation has been extensively described in cats, in particular in cases of feline infectious peritonitis and also associated with Mycobacteria, Actinomyces, Nocardia, Rhodococcus and fungal infections. Idiopathic sterile pyogranulomatous dermatitis has also been described. In this case series we describe the clinical presentation, histopathology and outcome of three cases of feline idiopathic sterile steroid‐responsive pyogranuloma with different presentation and different locations of the lesion, but with the common feature of having a mass with no superficial skin involvement. url: https://doi.org/10.1111/jsap.12853 doi: 10.1111/jsap.12853 id: cord-325101-9qslo6qh author: Gizzi, Aline Baumann da Rocha title: Presence of infectious agents and co-infections in diarrheic dogs determined with a real-time polymerase chain reaction-based panel date: 2014-01-16 words: 5156.0 sentences: 239.0 pages: flesch: 50.0 cache: ./cache/cord-325101-9qslo6qh.txt txt: ./txt/cord-325101-9qslo6qh.txt summary: Although many pathogens have been individually detected with real-time polymerase chain reaction (PCR), a comprehensive panel of agents that cause diarrhea in privately owned dogs has not yet been established. Therefore, the aim of this study was to investigate pathogenic co-infections in populations of diarrheic and control owned dogs using a real-time PCR analysis of a panel of diarrhea-causing agents. The most prevalent agent involved in co-infections was canine parvovirus type 2 (CPV-2), and 21/36 (58.3%) of the diarrheic samples positive for CPV-2 were associated with others agents, most commonly with Clostridium perfringens alpha toxin (CPA), Cryptosporidium spp., and Giardia spp. The detection of individual pathogens in the panel with real-time PCR (Table 3) showed that CPA was the most prevalent pathogen in the fecal samples, infecting 40/104 (38.5%) diarrheic dogs and 6/43 (14.0%) control dogs, and the difference between the groups was highly statistically significant (P = 0.006). abstract: BACKGROUND: Infectious diarrhea can be caused by bacteria, viruses, or protozoan organisms, or a combination of these. The identification of co-infections in dogs is important to determine the prognosis and to plan strategies for their treatment and prophylaxis. Although many pathogens have been individually detected with real-time polymerase chain reaction (PCR), a comprehensive panel of agents that cause diarrhea in privately owned dogs has not yet been established. The objective of this study was to use a real-time PCR diarrhea panel to survey the frequencies of pathogens and co-infections in owned dogs attended in a veterinary hospital with and without diarrhea, as well the frequency in different countries. Feces samples were tested for canine distemper virus, canine coronavirus, canine parvovirus type 2 (CPV-2), Clostridium perfringens alpha toxin (CPA), Cryptosporidium spp., Giardia spp., and Salmonella spp. using molecular techniques. RESULTS: In total, 104 diarrheic and 43 control dogs that were presented consecutively at a major private veterinary hospital were included in the study. Overall, 71/104 (68.3%) dogs with diarrhea were positive for at least one pathogen: a single infection in 39/71 dogs (54.9%) and co-infections in 32/71 dogs (45.1%), including 21/32 dogs (65.6%) with dual, 5/32 (15.6%) with triple, and 6/32 (18.8%) with quadruple infections. In the control group, 13/43 (30.2%) dogs were positive, all with single infections only. The most prevalent pathogens in the diarrheic dogs were CPA (40/104 dogs, 38.5%), CPV-2 (36/104 dogs, 34.6%), and Giardia spp. (14/104 dogs, 13.5%). CPV-2 was the most prevalent pathogen in the dual co-infections, associated with CPA, Cryptosporidium spp., or Giardia spp. No statistical difference (P = 0.8374) was observed in the duration of diarrhea or the number of deaths (P = 0.5722) in the presence or absence of single or co-infections. CONCLUSIONS: Diarrheic dogs showed a higher prevalence of pathogen infections than the controls. Whereas the healthy dogs had only single infections, about half the diarrheic dogs had co-infections. Therefore, multiple pathogens should be investigated in dogs presenting with diarrhea. The effects of multiple pathogens on the disease outcomes remain unclear because the rate of death and the duration of diarrhea did not seem to be affected by these factors. url: https://www.ncbi.nlm.nih.gov/pubmed/24433321/ doi: 10.1186/1746-6148-10-23 id: cord-354733-qxivrhj8 author: Gniazdowski, V. title: Repeat COVID-19 Molecular Testing: Correlation with Recovery of Infectious Virus, Molecular Assay Cycle Thresholds, and Analytical Sensitivity date: 2020-08-06 words: 3924.0 sentences: 251.0 pages: flesch: 56.0 cache: ./cache/cord-354733-qxivrhj8.txt txt: ./txt/cord-354733-qxivrhj8.txt summary: Whole genome sequencing confirmed the virus genotype in patients with prolonged 28 viral RNA shedding and droplet digital PCR (ddPCR) was used to assess the rate of false 29 negative standard of care PCR results. Whole genome sequencing confirmed the virus genotype in patients with prolonged 28 viral RNA shedding and droplet digital PCR (ddPCR) was used to assess the rate of false 29 negative standard of care PCR results. Prolonged viral RNA shedding was associated with recovery of infectious 31 virus in specimens collected up to 20 days after the first positive result in patients who were 32 symptomatic at the time of specimen collection. Infection control personnel and physicians managing COVID-19 patients and patients under 43 investigation (PUI) continue to face several diagnostic dilemmas related to a lack of 44 understanding of the clinical sensitivities of SARS-CoV-2 molecular diagnostics and the 45 correlation between viral RNA detection and shedding of infectious virus. abstract: Repeat molecular testing for SARS-CoV-2 may result in scenarios including multiple positive results, positive test results after negative tests, and repeated false negative results in symptomatic individuals. Consecutively collected specimens from a retrospective cohort of COVID-19 patients at the Johns Hopkins Hospital were assessed for RNA and infectious virus shedding. Whole genome sequencing confirmed the virus genotype in patients with prolonged viral RNA shedding and droplet digital PCR (ddPCR) was used to assess the rate of false negative standard of care PCR results. Recovery of infectious virus was associated with Ct values of 18.8 {+/-} 3.4. Prolonged viral RNA shedding was associated with recovery of infectious virus in specimens collected up to 20 days after the first positive result in patients who were symptomatic at the time of specimen collection. The use of Ct values and clinical symptoms provides a more accurate assessment of the potential for infectious virus shedding. url: https://doi.org/10.1101/2020.08.05.20168963 doi: 10.1101/2020.08.05.20168963 id: cord-352640-fycwhyfv author: Goel, Ashish title: Profile of Patients Suspected to be COVID-19: A Retrospective Analysis of Early Pandemic Data date: 2020-08-29 words: 2756.0 sentences: 149.0 pages: flesch: 59.0 cache: ./cache/cord-352640-fycwhyfv.txt txt: ./txt/cord-352640-fycwhyfv.txt summary: Our study is a short retrospective analysis of the demographic and clinical profiles of subjects presenting with a mild flu-like illness to our hospital who were tested for COVID-19. We present a short retrospective analysis of the demographic and clinical profiles of subjects presenting with a mild flu-like illness to our hospital who were tested for COVID-19. A retrospective analysis of data from subjects who presented to our hospital with mild flu-like illness between the months of March and May 2020 was conducted to understand the disease profile. Data were available for 3,026 subjects who presented to our hospital with either mild flu-like symptoms or with suspected exposure to a confirmed case of COVID-19 during the early phases of the pandemic. In this retrospective analysis, we report that among subjects presenting to the hospital with a mild flu-like illness, those who tested positive for COVID-19 were significantly older and more likely to be men. abstract: Background and Objectives Coronavirus disease 2019 (COVID-19), a global public health emergency of profound magnitude, has brought life to an unprecedented near-standstill. The clinical profile of the disease is still emerging and is marked by considerable geographical variability in terms of transmissibility, clinical profile, virulence, and mortality of the disease. As clinical data is being reported from around the globe, it becomes important to focus on local subjects in a global milieu, lest one misses the trees for the forest. Our study is a short retrospective analysis of the demographic and clinical profiles of subjects presenting with a mild flu-like illness to our hospital who were tested for COVID-19. It compares the differences in age and sex of those who tested positive with those negative. In addition, it reviews the length of time it might take for a case testing positive on reverse transcriptase-polymerase chain reaction (RT-PCR) test to become negative. Methodology A retrospective analysis of data from adults who presented to our hospital with a mild flu-like illness between the months of March and May 2020 was conducted to understand the disease profile. The nasal/oropharyngeal swabs were collected from each patient and were transported to state-approved laboratories chain for RT-PCR analysis. Information was collected from reports received, clinical information forms, and sample collection forms that were being maintained as a part of the clinical management protocol. Data were analysed using Stata software, version 13 (StataCorp LLC, College Station, TX, USA). Observations and Results Three thousand twenty-six subjects presented to our hospital with either mild flu-like symptoms or with suspected exposure to a confirmed case of COVID-19. The subjects had a mean age of 37.3 (± 15.1) years and 1,805 (60.3%) were males. A regression analysis revealed an adjusted odds of 1.6 (95% confidence interval (CI): 1.2, 2.1) for testing positive for males as compared to females. For every one year increase in age, the odds for testing positive increased by 1.02 (95% CI: 1.01, 1.03). Of the 2,592 individuals for whom data was available, 201 (7.6%) were found positive on RT-PCR analysis. Those testing positive were significantly older (41.0 years vs 36.8 years; p = 0.001) and more likely to be male (number: 138; 9.0% vs 6.7%; p = 0.05). Cough, followed by fever, was a common presenting feature. A survival time analysis using data from 54 participants documented 455 days of the total observation period. A median time of eight days was required for the test to convert from positive to negative if the patient remained mildly symptomatic and did not develop a severe complicated illness. The time to conversion did not differ with age or sex. Conclusions Our analysis shows that patients with COVID-19 have presented with milder symptoms and have recovered well. The low test positivity rate is indicative of the early phase of the pandemic in the country and is a reflection of active infection control measures. url: https://doi.org/10.7759/cureus.10125 doi: 10.7759/cureus.10125 id: cord-323700-5awng7h1 author: Goggin, Rachel K. title: Comparative Viral Sampling in the Sinonasal Passages; Different Viruses at Different Sites date: 2018-09-19 words: 3528.0 sentences: 197.0 pages: flesch: 49.0 cache: ./cache/cord-323700-5awng7h1.txt txt: ./txt/cord-323700-5awng7h1.txt summary: The aim of the study here presented was to establish differences in viral detection and species sampled from different sinonasal sites, in an effort to validate and standardise viral collection techniques, and facilitate further investigation of the sinonasal virome. All DNA extracts first underwent an endogenous retrovirus 3 (ERV3) assay (present as two copies per human diploid cell) in order to confirm respiratory sample collection quality. Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control High rates of detection of respiratory viruses in the nasal washes and mucosae of patients with chronic rhinosinusitis Detection of herpesviruses 1-6 and community-acquired respiratory viruses in patients with chronic rhinosinusitis with nasal polyposis Real-time RT-PCR detection of 12 respiratory viral infections in four triplex reactions Real-time quantitative PCR assays for detection and monitoring of pathogenic human viruses in immunosuppressed pediatric patients abstract: Background: With the emergence of the microbiome as an important factor in health and disease in the respiratory tract standardised, validated techniques are required for its accurate characterisation. No standardised technique has been reported specifically for viral sampling in the sinonasal passages. Aim: To optimise viral sampling techniques from the sinonasal cavity. Methods: Sterile cytology brushes were used under endoscopic guidance to sample the sinonasal mucosa at time of endoscopic sinus surgery at both the middle and inferior meatuses (MM and IM). DNA and RNA were extracted from the samples and underwent PCR or RT-PCR testing, respectively, for a panel of 15 common upper respiratory tract viruses. Results: Twenty-four adult patients were recruited for this study. 18/24 (75%) patients were positive for virus in at least one site, while 8/24 (33%) were positive for virus at both sites. The mean number of viruses identified at the two sites were similar (0.875 ± 0.899 at the MM vs. 0.750 ± 1.032 at the IM). 6/24 (25%) of patients showed no virus at either site, while 3/24 (12.5%) demonstrated the same viral species at both sites. Conclusion: Although the number of viruses present at different sites with the nasal cavity are similar, discord exists in the viral species between sites. It is therefore recommended that both sites are sampled in the clinical and research setting better to characterise the viral species within the nasal cavity. url: https://doi.org/10.3389/fcimb.2018.00334 doi: 10.3389/fcimb.2018.00334 id: cord-332539-v1bfm57x author: Gohl, Daryl M. title: A Rapid, Cost-Effective Tailed Amplicon Method for Sequencing SARS-CoV-2 date: 2020-05-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The global COVID-19 pandemic has led to an urgent need for scalable methods for clinical diagnostics and viral tracking. Next generation sequencing technologies have enabled large-scale genomic surveillance of SARS-CoV-2 as thousands of isolates are being sequenced around the world and deposited in public data repositories. A number of methods using both short- and long-read technologies are currently being applied for SARS-CoV-2 sequencing, including amplicon approaches, metagenomic methods, and sequence capture or enrichment methods. Given the small genome size, the ability to sequence SARS-CoV-2 at scale is limited by the cost and labor associated with making sequencing libraries. Here we describe a low-cost, streamlined, all amplicon-based method for sequencing SARS-CoV-2, which bypasses costly and time-consuming library preparation steps. We benchmark this tailed amplicon method against both the ARTIC amplicon protocol and sequence capture approaches and show that an optimized tailed amplicon approach achieves comparable amplicon balance, coverage metrics, and variant calls to the ARTIC v3 approach and represents a cost-effective and highly scalable method for SARS-CoV-2 sequencing. url: https://doi.org/10.1101/2020.05.11.088724 doi: 10.1101/2020.05.11.088724 id: cord-315167-ph15z424 author: Goka, E. A. title: Pan-human coronavirus and human bocavirus SYBR Green and TaqMan PCR assays; use in studying influenza A viruses co-infection and risk of hospitalization date: 2014-12-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: PURPOSE: Influenza A viruses, human coronaviruses (hCoV) and human bocavirus (hBoV) are emerging respiratory viruses. This study investigated the association between influenza A viruses co-infection with hBoV and hCoV and severity and the sensitivity of a real-time polymerase chain reaction (RT-PCR) assay for identification of 15 coronaviruses. METHODOLOGY: Published sequences for the 15 human coronaviruses were used to design a consensus PCR targeting the replicase open reading frame 1b. A previously published PCR targeting the NS1 Gene of all known human bocavirus strains was also utilized. A series of 217 samples from patients aged 37.7 (SD ± 30.4)] with seasonal influenza A viruses (SeasFluA) identified between 06/2011 and 06/2012 in NW England were tested for hCoV and hBoV using RT-PCR. Association between co-infection and disease outcome was assessed using logistic regression. RESULTS: The limit of detection of hCoV RT-PCR assay was 2 copies/µl of human coronavirus RNA template, a sensitivity comparable to a previously published SYBR green assay for human coronaviruses. A total of 12 hCoV and 17 hBoV were identified in the 217 influenza A positive samples. A higher proportion (61.5 %; 8/13) of SeasFluA/hBoV co-infections were identified in patients that were admitted either to a general ward or the intensive care unit compared to 44.3 % (66/149) of single SeasFlu A virus infections (OR 2.5 95 % CI 0.67–9.34, p = 0.17). In a stratified analysis, there was a trend towards higher association between FluA, hCoV and hBoV with increasing age (especially in patients aged 24–45 years and >65 year old). CONCLUSION: Our hCoV RT-PCR protocol appeared to be of adequate analytical sensitivity for diagnosis. More and larger studies are needed to confirm the role of hCoV, hBoV in causing severe disease when they co-infect with influenza A viruses. url: https://doi.org/10.1007/s15010-014-0710-5 doi: 10.1007/s15010-014-0710-5 id: cord-329052-jan20ljs author: Gombar, Saurabh title: Persistent detection of SARS-CoV-2 RNA in patients and healthcare workers with COVID-19 date: 2020-05-30 words: 864.0 sentences: 59.0 pages: flesch: 59.0 cache: ./cache/cord-329052-jan20ljs.txt txt: ./txt/cord-329052-jan20ljs.txt summary: BACKGROUND: Current guidelines for returning health care workers (HCW) to service after a positive SARS-CoV-2 RT-PCR test and ceasing of transmission precautions for patients is based on two general strategies. Alternatively, due to the limited availability of testing, many sites employ a symptom-based strategy that recommends excluding HCW from the workforce and keeping patients on contact precautions until a fixed period of time has elapsed from symptom recovery. The underlying assumption of the symptom-based strategy is that waiting for a fixed period of time is a surrogate for negative RT-PCR testing, which itself is a surrogate for the absence of shedding infectious virus. STUDY DESIGN: We performed an observational analysis of 150 patients and HCW that transitioned from RT-PCR SARS-CoV-2 positive to negative over the course of 2 months at a US academic medical center. We performed an observational analysis of 150 patients and HCW that transitioned from RT-PCR SARS-CoV-2 positive to negative over the course of 2 months at a US academic medical center. abstract: BACKGROUND: Current guidelines for returning health care workers (HCW) to service after a positive SARS-CoV-2 RT-PCR test and ceasing of transmission precautions for patients is based on two general strategies. A test-based strategy that requires negative respiratory RT-PCR tests obtained after the resolution of symptoms. Alternatively, due to the limited availability of testing, many sites employ a symptom-based strategy that recommends excluding HCW from the workforce and keeping patients on contact precautions until a fixed period of time has elapsed from symptom recovery. The underlying assumption of the symptom-based strategy is that waiting for a fixed period of time is a surrogate for negative RT-PCR testing, which itself is a surrogate for the absence of shedding infectious virus. OBJECTIVES: To better understand the appropriate length of symptom based return to work and contact precaution strategies. STUDY DESIGN: We performed an observational analysis of 150 patients and HCW that transitioned from RT-PCR SARS-CoV-2 positive to negative over the course of 2 months at a US academic medical center. RESULTS: We found that the average time to transition from RT-PCR positive to negative was 24 days after symptom onset and 10 % remained positive even 33 days after symptom onset. No difference was seen in HCW and patients. CONCLUSIONS: These findings suggest until definitive evidence of the length of infective viral shedding is obtained that the fixed length of time before returning to work or ceasing contract precautions be revised to over one-month. url: https://www.sciencedirect.com/science/article/pii/S1386653220302195?v=s5 doi: 10.1016/j.jcv.2020.104477 id: cord-298049-gabjdkx9 author: Gomez, D.E. title: Detection of Bovine Coronavirus in Healthy and Diarrheic Dairy Calves date: 2017-09-15 words: 4538.0 sentences: 257.0 pages: flesch: 62.0 cache: ./cache/cord-298049-gabjdkx9.txt txt: ./txt/cord-298049-gabjdkx9.txt summary: OBJECTIVES: To investigate the detection rates of bovine coronavirus (BCoV) in feces of healthy and diarrheic calves and to describe the usefulness of a pancoronavirus reverse transcriptase (RT) PCR (PanCoV‐RT‐PCR) assay to identify BCoV in samples of diarrheic calves. The objectives of this study were to investigate the detection rates of BCoV in feces of healthy and diarrheic dairy calves and to describe the usefulness of a PanCoV-RT-PCR assay to identify BCoV in nasal and fecal samples of a group of calves from a dairy farm suffering an outbreak of diarrhea. The results of this study demonstrated a positive association between BCoV and diarrhea in dairy calves as detection rates of this agent were higher in diarrheic calves than in farm-, season-, aged-matched nondiarrheic calves. abstract: BACKGROUND: BCoV is identified in both healthy and diarrheic calves, complicating its assessment as a primary pathogen. OBJECTIVES: To investigate the detection rates of bovine coronavirus (BCoV) in feces of healthy and diarrheic calves and to describe the usefulness of a pancoronavirus reverse transcriptase (RT) PCR (PanCoV‐RT‐PCR) assay to identify BCoV in samples of diarrheic calves. ANIMALS: Two hundred and eighty‐six calves <21 days. Calves with liquid or semiliquid feces, temperature >39.5°C, and inappetence were considered as cases, and those that had pasty or firm feces and normal physical examination were designated as controls. METHODS: Prospective case–control study. A specific BCoV‐RT‐PCR assay was used to detect BCoV in fecal samples. Association between BCoV and health status was evaluated by exact and random effect logistic regression. Fecal (n = 28) and nasal (n = 8) samples from diarrheic calves were tested for the presence of BCoV by both the PanCoV‐RT‐PCR and a specific BCoV‐RT‐PCR assays. A Kappa coefficient test was used to assess the level of agreement of both assays. RESULTS: BCoV was detected in 55% (157/286) of calves; 46% (66/143), and 64% (91/143) of healthy and diarrheic calves, respectively. Diarrheic calves had higher odds of BCoV presence than healthy calves (OR: 2.16, 95% CI: 1.26 to 3.83, P = 0.004). A good agreement between PanCoV‐RT‐PCR and BCoV‐RT‐PCR to detect BCoV was identified (κ = 0.68, 95% CI: 0.392 to 0.967; P < 0.001). CONCLUSIONS AND CLINICAL IMPORTANCE: BCoV was more likely to be detected in diarrheic than healthy calves. The PanCoV‐RT‐PCR assay can be a useful tool to detect CoV samples from diarrheic calves. url: https://doi.org/10.1111/jvim.14811 doi: 10.1111/jvim.14811 id: cord-333216-fdwmsnz9 author: Gonzalez, J. E. title: ESTIMATING PREVALENCE AND TIME COURSE OF SARS-CoV-2 BASED ON NEW HOSPITAL ADMISSIONS AND PCR TESTS date: 2020-08-17 words: 3670.0 sentences: 202.0 pages: flesch: 54.0 cache: ./cache/cord-333216-fdwmsnz9.txt txt: ./txt/cord-333216-fdwmsnz9.txt summary: Data posted in the COVID 19 tracking website for RT-PCR (PCR) results and hospital admissions are used to estimate the prevalence of the SARS-CoV-2 pandemic in the United States (1). A higher recovered population mitigates the current positive value attainable by limiting the infectivity rate Re. This approach provides an alternate source of information on the pandemic''s full time course since the serological testing only views a narrow time slice of its history due to the transient nature of the antibody response and its graduated expression dependency on the severity of the disease. This paper relies on the integration of % PCR positive test results over time, cycle-corrected for the length of disease, and coupled with hospital admissions to control for PCR testing sample bias, to estimate the kinetics and prevalence over the time course of the pandemic in the United States. Figure 4A shows the time course comparison of the SARS-CoV-2 United States infected population obtained from PCR tests and NHA. abstract: Data posted in the COVID 19 tracking website for RT-PCR (PCR) results and hospital admissions are used to estimate the prevalence of the SARS-CoV-2 pandemic in the United States (1). Hospital admissions mitigate positive sampling bias in PCR tests due to their initially limited test numbers and application as a diagnostic, instead of a surveying tool. As of July 31, the United States' cumulative recovered population is estimated at 47% or 155 million. The remaining susceptible population is 53%, or 47% excepting the 6% infectious population. The estimated mortality rate of the cumulative recovered population is 0.09% death per case. New York and Massachusetts show SARS-CoV-2 prevalence of 87% and 55%, respectively. Likewise, each state exhibits relatively low current positive PCR results at 1 % and 1.7%. Also, these states show about twice the mortality rate of the nation. Florida, California, and Texas showed recovered population percent around 40%, higher current PCR positive test results ranging from 7% to 13%. A higher recovered population mitigates the current positive value attainable by limiting the infectivity rate Re. This approach provides an alternate source of information on the pandemic's full time course since the serological testing only views a narrow time slice of its history due to the transient nature of the antibody response and its graduated expression dependency on the severity of the disease. The deficiency of serological testing to estimate the recovered population is made even more acute due to the large proportion of asymptomatic and sub-clinical cases in the COVID-19 pandemic url: http://medrxiv.org/cgi/content/short/2020.08.15.20175653v1?rss=1 doi: 10.1101/2020.08.15.20175653 id: cord-277357-lpurk7pe author: González-González, Everardo title: Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection date: 2020-08-13 words: 3999.0 sentences: 211.0 pages: flesch: 49.0 cache: ./cache/cord-277357-lpurk7pe.txt txt: ./txt/cord-277357-lpurk7pe.txt summary: title: Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection Here, we demonstrate the use of the miniPCR, a commercial compact and portable PCR device recently available on the market, in combination with a commercial well-plate reader as a diagnostic system for detecting genetic material of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of COVID-19. Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection containing the amplification products of each one of three experiments, where the three different sets of primers (namely N1, N2, and N3) were used to amplify the same range of concentrations of template. Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection others), we observe differences in the performance of each primer pair. abstract: The coronavirus disease 2019 (COVID-19) pandemic has crudely demonstrated the need for massive and rapid diagnostics. By the first week of July, more than 10,000,000 positive cases of COVID-19 have been reported worldwide, although this number could be greatly underestimated. In the case of an epidemic emergency, the first line of response should be based on commercially available and validated resources. Here, we demonstrate the use of the miniPCR, a commercial compact and portable PCR device recently available on the market, in combination with a commercial well-plate reader as a diagnostic system for detecting genetic material of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of COVID-19. We used the miniPCR to detect and amplify SARS-CoV-2 DNA sequences using the sets of initiators recommended by the World Health Organization (WHO) for targeting three different regions that encode for the N protein. Prior to amplification, samples were combined with a DNA intercalating reagent (i.e., EvaGreen Dye). Sample fluorescence after amplification was then read using a commercial 96-well plate reader. This straightforward method allows the detection and amplification of SARS-CoV-2 nucleic acids in the range of ~625 to 2×10(5) DNA copies. The accuracy and simplicity of this diagnostics strategy may provide a cost-efficient and reliable alternative for COVID-19 pandemic testing, particularly in underdeveloped regions where RT-QPCR instrument availability may be limited. The portability, ease of use, and reproducibility of the miniPCR makes it a reliable alternative for deployment in point-of-care SARS-CoV-2 detection efforts during pandemics. url: https://www.ncbi.nlm.nih.gov/pubmed/32790779/ doi: 10.1371/journal.pone.0237418 id: cord-001891-5op0yss9 author: Gordon, Julian title: A simple novel device for air sampling by electrokinetic capture date: 2015-12-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: A variety of different sampling devices are currently available to acquire air samples for the study of the microbiome of the air. All have a degree of technical complexity that limits deployment. Here, we evaluate the use of a novel device, which has no technical complexity and is easily deployable. RESULTS: An air-cleaning device powered by electrokinetic propulsion has been adapted to provide a universal method for collecting samples of the aerobiome. Plasma-induced charge in aerosol particles causes propulsion to and capture on a counter-electrode. The flow of ions creates net bulk airflow, with no moving parts. A device and electrode assembly have been re-designed from air-cleaning technology to provide an average air flow of 120 lpm. This compares favorably with current air sampling devices based on physical air pumping. Capture efficiency was determined by comparison with a 0.4 μm polycarbonate reference filter, using fluorescent latex particles in a controlled environment chamber. Performance was compared with the same reference filter method in field studies in three different environments. For 23 common fungal species by quantitative polymerase chain reaction (qPCR), there was 100 % sensitivity and apparent specificity of 87 %, with the reference filter taken as “gold standard.” Further, bacterial analysis of 16S RNA by amplicon sequencing showed equivalent community structure captured by the electrokinetic device and the reference filter. Unlike other current air sampling methods, capture of particles is determined by charge and so is not controlled by particle mass. We analyzed particle sizes captured from air, without regard to specific analyte by atomic force microscopy: particles at least as low as 100 nM could be captured from ambient air. CONCLUSIONS: This work introduces a very simple plug-and-play device that can sample air at a high-volume flow rate with no moving parts and collect particles down to the sub-micron range. The performance of the device is substantially equivalent to capture by pumping through a filter for microbiome analysis by quantitative PCR and amplicon sequencing. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4696304/ doi: 10.1186/s40168-015-0141-2 id: cord-279563-4lu1n0s7 author: Gorzalski, Andrew J. title: High-Throughput Transcription-mediated amplification on the Hologic Panther is a highly sensitive method of detection for SARS-CoV-2 date: 2020-06-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: As the demand for laboratory testing for SARS-CoV-2 increases, additional varieties of testing methodologies are being considered. While real time polymerase chain reaction (RT-PCR) has performed as the main method for virus detection, other methods are becoming available, including transcription mediated amplification (TMA). The Hologic Aptima SARS-CoV-2 Assay utilizes TMA as a target amplification mechanism, and it has only recently received Emergency Use Authorization (EUA) by the Food and Drug Administration (FDA). OBJECTIVES: We sought to compare the sensitivity and specificity of the Aptima SARS-CoV-2 Assay to RTPCR as a means of SARS-CoV-2 detection in a diagnostic setting. STUDY DESIGN: We performed a limit-of-detection study (LoD) to assess the analytical sensitivity of TMA and RT-PCR. This preceded a comparison of the methods using previously evaluated clinical specimens (nasopharyngeal swabs) using 116 human specimens tested by both methodologies. Specimens included sixty-one (61) specimens found reactive by real-time PCR, fifty-one (51) found non-reactive, and four (4) deemed inconclusive. RESULTS: The Aptima SARS-CoV-2 Assay showed a markedly higher analytical sensitivity than RT-PCR by LoD study. Evaluation of clinical specimens resulted in fewer inconclusive results by the SARS-CoV-2 assay, leading to potentially higher clinical sensitivity. CONCLUSIONS: The higher analytical sensitivity may explain the assay’s ability to ascertain for the presence of SARS-CoV-2 genome in human specimens deemed inconclusive by real-time PCR. TMA provides an effective, highly sensitive means of detection of SARS-CoV-2 in nasopharyngeal specimens. url: https://www.sciencedirect.com/science/article/pii/S1386653220302432?v=s5 doi: 10.1016/j.jcv.2020.104501 id: cord-259823-ia1g5dt4 author: Gowin, Ewelina title: Assessment of the Usefulness of Multiplex Real-Time PCR Tests in the Diagnostic and Therapeutic Process of Pneumonia in Hospitalized Children: A Single-Center Experience date: 2017-01-15 words: 3883.0 sentences: 198.0 pages: flesch: 43.0 cache: ./cache/cord-259823-ia1g5dt4.txt txt: ./txt/cord-259823-ia1g5dt4.txt summary: British, American, and Polish guidelines state that, in children hospitalized due to pneumonia, microbiological examinations should include blood cultures, the detection of the presence of viruses with the use of PCR (Polymerase Chain Reaction) or immunofluorescence in material collected from the nasopharynx (smear or upper respiratory aspirate), the assessment of antibodies against Mycoplasma and Chlamydophila in classes IgM and IgG, and the comparison of antibody levels in the acute phase of the disease and during convalescence [4] [5] [6] . achieved positive results of multiplex real-time PCR tests detecting only viral factors in 76% of cases in a group of children below the age of six with symptoms of respiratory tract infection and the dominant pathogen was RSV [12] . abstract: The aim of the study was assessment of the usefulness of multiplex real-time PCR tests in the diagnostic and therapeutic process in children hospitalized due to pneumonia and burdened with comorbidities. Methods. The study group included 97 children hospitalized due to pneumonia at the Karol Jonscher Teaching Hospital in Poznań, in whom multiplex real-time PCR tests (FTD respiratory pathogens 33; fast-track diagnostics) were used. Results. Positive test results of the test were achieved in 74 patients (76.3%). The average age in the group was 56 months. Viruses were detected in 61 samples (82% of all positive results); bacterial factors were found in 29 samples (39% of all positive results). The presence of comorbidities was established in 90 children (92.78%). On the basis of the obtained results, 5 groups of patients were established: viral etiology of infection, 34 patients; bacterial etiology, 7 patients; mixed etiology, 23 patients; pneumocystis, 9 patients; and no etiology diagnosed, 24 patients. Conclusions. Our analysis demonstrated that the participation of viruses in causing severe lung infections is significant in children with comorbidities. Multiplex real-time PCR tests proved to be more useful in establishing the etiology of pneumonia in hospitalized children than the traditional microbiological examinations. url: https://www.ncbi.nlm.nih.gov/pubmed/28182108/ doi: 10.1155/2017/8037963 id: cord-259422-5ex12eun author: Graat, Judith M title: A prospective, community-based study on virologic assessment among elderly people with and without symptoms of acute respiratory infection date: 2003-12-11 words: 3897.0 sentences: 196.0 pages: flesch: 42.0 cache: ./cache/cord-259422-5ex12eun.txt txt: ./txt/cord-259422-5ex12eun.txt summary: title: A prospective, community-based study on virologic assessment among elderly people with and without symptoms of acute respiratory infection METHODS: In a 1-year community-based study, we prospectively investigated the possible virologic cause of acute respiratory infections in 107 symptomatic case episodes and 91 symptom-free control periods. Therefore, in this prospective, community-based study, we investigated the presence of known respiratory viruses in elderly persons both with and without symptoms of an acute upper respiratory tract infection. Second, we compared the clinical characteristics of the persons suffering from an acute respiratory infection, during episodes with positive and negative virologic laboratory diagnosis. Cases who reported their symptoms after 3 days to the study nurse were excluded for virologic assessment to overcome false negative test results. Preliminary results of a Dutch study being performed in persons consulting their general practitioner for signs and symptoms of an acute respiratory infection, showed a positive virologic assessment in 19% of the controls [16] . abstract: BACKGROUND AND OBJECTIVE: Community-based elderly studies concerning microbiology of acute respiratory infections are scarce. Data on subclinical infections are even totally absent, although asymptomatic persons might act as a source of respiratory infections. METHODS: In a 1-year community-based study, we prospectively investigated the possible virologic cause of acute respiratory infections in 107 symptomatic case episodes and 91 symptom-free control periods. Participants, persons ⩾60 years, reported daily the presence of respiratory symptoms in a diary. Virologic assessment was performed by polymerase chain reaction (PCR) and serology. RESULTS: In 58% of the case episodes a pathogen was demonstrated, the most common being rhinoviruses (32%), coronaviruses (17%), and influenzaviruses (7%). The odds ratio for demonstrating a virus in cases with symptoms vs. controls without symptoms was 30.0 (95% confidence interval 10.2–87.6). In 4% of the symptom-free control periods a virus was detected. CONCLUSION: This study supports the importance of rhinovirus infections in community-dwelling elderly persons, whereas asymptomatic elderly persons can also harbor pathogens as detected by PCR, and thus might be a source of infection for their environment. url: https://www.ncbi.nlm.nih.gov/pubmed/14680673/ doi: 10.1016/s0895-4356(03)00171-9 id: cord-299737-r34d0rx7 author: Grant, Paul R title: Extraction-free COVID-19 (SARS-CoV-2) diagnosis by RT-PCR to increase capacity for national testing programmes during a pandemic date: 2020-04-08 words: 1383.0 sentences: 78.0 pages: flesch: 63.0 cache: ./cache/cord-299737-r34d0rx7.txt txt: ./txt/cord-299737-r34d0rx7.txt summary: The standard molecular diagnostic test is a multistep process involving viral RNA extraction and real-time quantitative reverse transcriptase PCR (qRT-PCR). We have developed a simplified qRT-PCR assay that removes the need for an RNA extraction process and can be run on a real-time thermal cycler. The standard molecular diagnostic test for this virus is a multistep process involving viral RNA extraction and real-time quantitative reverse transcriptase PCR (qRT-PCR). Using the same primers and probes, we have now developed a qRT-PCR that can be run on a real-time thermal cycler without the need for an RNA extraction process. Direct addition of samples to the qRT-PCR without extraction with a diagnostic sensitivity of 98.0%, specificity of 100% and accuracy of 98.8% compared to the method on the Panther Fusion. Many laboratories use real-time thermal cyclers, so this method can be used to increase national screening capacity without the need for other specialized equipment or RNA extraction reagents. abstract: Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) causes Coronavirus disease 2019 (COVID-19), a respiratory tract infection. The standard molecular diagnostic test is a multistep process involving viral RNA extraction and real-time quantitative reverse transcriptase PCR (qRT-PCR). Laboratories across the globe face constraints on equipment and reagents during the COVID-19 pandemic. We have developed a simplified qRT-PCR assay that removes the need for an RNA extraction process and can be run on a real-time thermal cycler. The assay uses custom primers and probes, and maintains diagnostic sensitivity within 98.0% compared to the assay run on a high-throughput, random-access automated platform, the Panther Fusion (Hologic). This assay can be used to increase capacity for COVID-19 testing for national programmes worldwide. url: https://doi.org/10.1101/2020.04.06.028316 doi: 10.1101/2020.04.06.028316 id: cord-281174-3c1vue0y author: Greene, Shermalyn R title: Evaluation of the NucliSens® Basic Kit assay for detection of Norwalk virus RNA in stool specimens date: 2003-01-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Norwalk-like viruses (NLVs) are a genetically diverse group of human caliciviruses that are the most common cause of epidemic gastroenteritis and are detected typically in stool by reverse transcription (RT)-PCR or electron microscopy (EM). The application of a rapid nucleic acid sequence-based amplification (NASBA) assay for the detection of NLV RNA in stool is described using the NucliSens® Basic Kit. Primers and probes for the NLV Basic Kit assay were based on the RNA polymerase region of the prototype NLV, Norwalk virus (NV) genome and could consistently detect 10(4) RT-PCR detectable units of NV RNA in a stool filtrate. When compared directly with RT-PCR on a dilution series of NV stool filtrate, the NucliSens® Basic Kit assay was equally sensitive. Cross-reactivity studies with a representative panel of other enteric pathogens were negative. When applied to 15 stool specimens from NV-challenged volunteers, the NASBA Basic Kit application for NV detection yielded 100% sensitivity, 50% specificity, and 67% concordance, using RT-PCR as the ‘gold standard’. Despite the specificity of the NASBA primer/probe sequences for NV, other representatives from both NLV genogroups I and II could be detected by the Basic Kit assay in outbreak stool specimens, although the results were inconsistent. Our results suggest that the NucliSens® Basic Kit assay provides a rapid and sensitive alternative to RT-PCR for detecting NV RNA in stool specimens. However, improvements in test specificity and primer design will be needed before the assay can be used routinely in the clinical setting. url: https://www.sciencedirect.com/science/article/pii/S0166093402002860 doi: 10.1016/s0166-0934(02)00286-0 id: cord-280846-bbv6f5gf author: Greninger, Alexander L. title: A Metagenomic Analysis of Pandemic Influenza A (2009 H1N1) Infection in Patients from North America date: 2010-10-18 words: 8023.0 sentences: 327.0 pages: flesch: 44.0 cache: ./cache/cord-280846-bbv6f5gf.txt txt: ./txt/cord-280846-bbv6f5gf.txt summary: To determine whether a pan-viral microarray assay was capable of identifying novel 2009 H1N1 in the absence of a priori sequence information, we used the Virochip to comprehensively screen for viruses in 29 nasopharyngeal swab samples from individuals with influenza-like illness. To further characterize the metagenomics of 2009 H1N1 infection in humans, we labeled the 17 influenza samples positive for 2009 H1N1 by Virochip with distinct molecular barcodes and analyzed them by paired-end deep sequencing on three lanes of an Illumina Genome Analyzer IIx. After trimming reads to remove barcodes and exclude low-complexity or primer sequences, 11,427,212 high-quality 60-bp sequence reads were subjected to an iterative BLASTN analysis pipeline (Fig. 1B) . After stratifying by originating location and corresponding method of sample processing (pre-DNase and/or post-DNase treatment), the percentage of total reads aligning to influenza was linearly correlated with calculated viral titers by realtime quantitative RT-PCR for sites in the United States (California) and Canada but not in Mexico (Fig. 5A ). abstract: Although metagenomics has been previously employed for pathogen discovery, its cost and complexity have prevented its use as a practical front-line diagnostic for unknown infectious diseases. Here we demonstrate the utility of two metagenomics-based strategies, a pan-viral microarray (Virochip) and deep sequencing, for the identification and characterization of 2009 pandemic H1N1 influenza A virus. Using nasopharyngeal swabs collected during the earliest stages of the pandemic in Mexico, Canada, and the United States (n = 17), the Virochip was able to detect a novel virus most closely related to swine influenza viruses without a priori information. Deep sequencing yielded reads corresponding to 2009 H1N1 influenza in each sample (percentage of aligned sequences corresponding to 2009 H1N1 ranging from 0.0011% to 10.9%), with up to 97% coverage of the influenza genome in one sample. Detection of 2009 H1N1 by deep sequencing was possible even at titers near the limits of detection for specific RT-PCR, and the percentage of sequence reads was linearly correlated with virus titer. Deep sequencing also provided insights into the upper respiratory microbiota and host gene expression in response to 2009 H1N1 infection. An unbiased analysis combining sequence data from all 17 outbreak samples revealed that 90% of the 2009 H1N1 genome could be assembled de novo without the use of any reference sequence, including assembly of several near full-length genomic segments. These results indicate that a streamlined metagenomics detection strategy can potentially replace the multiple conventional diagnostic tests required to investigate an outbreak of a novel pathogen, and provide a blueprint for comprehensive diagnosis of unexplained acute illnesses or outbreaks in clinical and public health settings. url: https://doi.org/10.1371/journal.pone.0013381 doi: 10.1371/journal.pone.0013381 id: cord-354103-4dldgqzf author: Grubic, Andrew D title: COVID-19 outbreak and surgical practice: The rationale for suspending non-urgent surgeries and role of testing modalities date: 2020-06-27 words: 4869.0 sentences: 266.0 pages: flesch: 47.0 cache: ./cache/cord-354103-4dldgqzf.txt txt: ./txt/cord-354103-4dldgqzf.txt summary: While epidemiologists and infectious disease physicians are at the forefront in the fight against COVID-19, this pandemic is also a "stress test" to evaluate the capacity and resilience of our surgical community in dealing with the challenges imposed to our health system and society. On the same day, the United States Surgeon General echoed the recommendation from the American College of Surgeons and urged hospitals and healthcare systems to consider suspending elective surgical procedures during the outbreak of COVID-19. This pandemic started with identification of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the causative agent from a cluster of pneumonias in the Hubei providence of China in December 2019. On March 25, 2000, American College of Surgeons released the guidelines for emergency general surgery in COVID-19 positive patients or those at high clinical suspicion for COVID infection. Correlation of Chest CT and RT-PCR Testing in Coronavirus Disease 2019 (COVID-19) in China: A Report of 1014 Cases abstract: One-hundred years after the 1918-19 H1N1 flu pandemic and 10 years after the 2009 H1N1 flu pandemic, another respiratory virus has now inserted itself into the human population. Severe acute respiratory syndrome coronavirus has become a critical challenge to global health with immense economic and social disruption. In this article we review salient aspects of the coronavirus disease 2019 (COVID-19) outbreak that are relevant to surgical practice. The emphasis is on considerations during the pre-operative and post-operative periods as well as the utility and limitations of COVID-19 testing. The focus of the media during this pandemic is centered on predictive epidemiologic curves and models. While epidemiologists and infectious disease physicians are at the forefront in the fight against COVID-19, this pandemic is also a “stress test” to evaluate the capacity and resilience of our surgical community in dealing with the challenges imposed to our health system and society. As recently pointed out by Dr. Anthony Fauci, the virus decides the timelines in the models. However, the models can also change based on our decisions and behavior. It is our role as surgeons, to make every effort to bend the curves against the virus’ will. url: https://doi.org/10.4240/wjgs.v12.i6.259 doi: 10.4240/wjgs.v12.i6.259 id: cord-260168-rb7j94dh author: Gu, Jiang title: H5N1 infection of the respiratory tract and beyond: a molecular pathology study date: 2007-09-27 words: 6291.0 sentences: 369.0 pages: flesch: 51.0 cache: ./cache/cord-260168-rb7j94dh.txt txt: ./txt/cord-260168-rb7j94dh.txt summary: Negative controls also included an unrelated antisense probe against the fragment of the polymerase gene (R1AB) of the severe acute respiratory syndrome-associated coronavirus (SARS-CoV), 20 as well as H5N1 in-situ hybridisation probes to tissues (including lung and tracheal) obtained from seven adults who died from infectious lung diseases other than H5N1 infl uenza (four, SARS; one, purulent bronchitis; two, pneumonia), one adult who died from a non-infectious disease (gastric ulcer), one pregnant woman who died from an amniotic embolism, and one aborted fetus. Presence of viral sequences and antigens in the CNS is consistent with the recent isolation of H5N1 virus from cerebrospinal fl uid of a boy who died from encephalitis 6 with neurological symptoms commonly seen in patients with H5N1 infl uenza (Gao Zh, unpublished), including the two cases in this study. abstract: BACKGROUND: Human infection with avian influenza H5N1 is an emerging infectious disease characterised by respiratory symptoms and a high fatality rate. Previous studies have shown that the human infection with avian influenza H5N1 could also target organs apart from the lungs. METHODS: We studied post-mortem tissues of two adults (one man and one pregnant woman) infected with H5N1 influenza virus, and a fetus carried by the woman. In-situ hybridisation (with sense and antisense probes to haemagglutinin and nucleoprotein) and immunohistochemistry (with monoclonal antibodies to haemagglutinin and nucleoprotein) were done on selected tissues. Reverse-transcriptase (RT) PCR, real-time RT-PCR, strand-specific RT-PCR, and nucleic acid sequence-based amplification (NASBA) detection assays were also undertaken to detect viral RNA in organ tissue samples. FINDINGS: We detected viral genomic sequences and antigens in type II epithelial cells of the lungs, ciliated and non-ciliated epithelial cells of the trachea, T cells of the lymph node, neurons of the brain, and Hofbauer cells and cytotrophoblasts of the placenta. Viral genomic sequences (but no viral antigens) were detected in the intestinal mucosa. In the fetus, we found viral sequences and antigens in the lungs, circulating mononuclear cells, and macrophages of the liver. The presence of viral sequences in the organs and the fetus was also confirmed by RT-PCR, strand-specific RT-PCR, real-time RT-PCR, and NASBA. INTERPRETATION: In addition to the lungs, H5N1 influenza virus infects the trachea and disseminates to other organs including the brain. The virus could also be transmitted from mother to fetus across the placenta. url: https://www.sciencedirect.com/science/article/pii/S0140673607615153 doi: 10.1016/s0140-6736(07)61515-3 id: cord-295401-3p6q92x4 author: Gueudin, M title: Quantitation of respiratory syncytial virus RNA in nasal aspirates of children by real-time RT-PCR assay date: 2003-02-18 words: 3975.0 sentences: 206.0 pages: flesch: 60.0 cache: ./cache/cord-295401-3p6q92x4.txt txt: ./txt/cord-295401-3p6q92x4.txt summary: title: Quantitation of respiratory syncytial virus RNA in nasal aspirates of children by real-time RT-PCR assay RSV and GAPDH were quantified in nasal aspirates from 75 children hospitalised for acute respiratory tract disease: 31 (41.3%) were positive according to the immunofluorescence assay (IFA), 34 (45.3%) were culture-positive and 42 (56%) were positive according to our real-time RT-PCR method. RNA and DNA extracted from cell cultures infected with different respiratory viruses were screened by the real-time RT-PCR for RSV to assess the specificity of this assay. Of the 42 samples found to be positive by the real-time RT-PCR assay for RSV, six could not be quantitated as the number of RSV RNA copies contained was below the detection limit of the technique; two of these six samples were also culturepositive. The sensitivity of the real-time RT-PCR assay for RSV on clinical samples was 56%, which is significantly higher than the sensitivity of conventional techniques for the detection of RSV in nasal aspirates. abstract: A method was developed for the quantitation of respiratory syncytial virus (RSV) based on real-time RT-PCR using a LightCycler instrument. A control real-time RT-PCR was undertaken on GAPDH mRNA (a human housekeeping gene) was carried out to standardise the non-homogeneous respiratory samples. The real-time RT-PCR method was one log more sensitive for the detection of RSV according to the endpoint dilution technique than the culture method or a conventional qualitative RT-PCR-hybridization-EIA. No cross-reactivity was observed with any of the viruses that could be found in the respiratory tract. RSV and GAPDH were quantified in nasal aspirates from 75 children hospitalised for acute respiratory tract disease: 31 (41.3%) were positive according to the immunofluorescence assay (IFA), 34 (45.3%) were culture-positive and 42 (56%) were positive according to our real-time RT-PCR method. The sensitivity, specificity, positive and negative predictive values of the real-time RT-PCR were 100, 90, 92, 100%, respectively. The samples found to be positive for RSV were classified according to the severity of the disease. The mean number of RSV RNA copies was higher in the severe disease group than in the non-severe group 4.05×10(7) vs 9.1×10(6) (P=0.055). However, the mean ratio of RSV RNA copies to GAPDH mRNA copies was 42.8 in the severe group, and 22.2 in non-severe group (P=NS). url: https://www.ncbi.nlm.nih.gov/pubmed/12668266/ doi: 10.1016/s0166-0934(03)00042-9 id: cord-325014-n7mnhk2v author: Gujski, Mariusz title: Prevalence of Current and Past SARS-CoV-2 Infections among Police Employees in Poland, June–July 2020 date: 2020-10-11 words: 4892.0 sentences: 254.0 pages: flesch: 49.0 cache: ./cache/cord-325014-n7mnhk2v.txt txt: ./txt/cord-325014-n7mnhk2v.txt summary: As the time window for a positive RT-PCR result is short, serological testing, which provides information about whether a person has been exposed to SARS-CoV-2, may be useful for epidemiological purposes to detect the overall burden of previous infection in a given community. The aim of this study was to determine the prevalence of current and past SARS-CoV-2 infections among police employees, a high-risk population due to their professional duties, during the COVID-19 epidemic. Neither sex (p =0.155) nor other variables listed in Figure 2 were significantly associated with the IgG results ( Figure 2 A logistic regression model predicting a positive anti-SARS-CoV-2 IgM+IgA index was developed (Cox and Snell R Square at 0.015 andNagelkerke R Square at 0.033). After including all variables listed in Figures 1 and 2 along with the number of registered cases and deaths due to COVID-19 (per 10,000 inhabitants), only 4 variables showed a correlation with a positive anti-SARS-CoV-2 IgM+IgA index. abstract: Background: Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We aimed to determine the prevalence of current and past SARS-CoV-2 infections among police employees. Methods: This cross-sectional survey was undertaken among 5082 police employees from Mazowieckie Province, Poland. RT-PCR testing for current SARS-CoV-2 infection and serological tests (ELISA) for the presence of anti-SARS-CoV-2 IgM+IgA and IgG antibodies were performed. Results: All RT-PCR tests were negative. The anti-SARS-CoV-2 IgM+IgA index was positive (>8) in 8.9% of participants, including 11.2% women and 7.7% men (p < 0.001). Equivocal IgM+IgA index (6–8) was found in 9.8% of participants, including 11.9% women and 8.7% men (p < 0.001). The IgG index was positive (>6) in 4.3% and equivocal (4–6) in 13.2% of participants. A higher odds of positive IgM+IgA index was found in women vs. men (OR: 1.742) and police officers vs. civilian employees (OR: 1.411). Participants aged ≥60 years had a higher odds of positive IgG index vs. those aged 20–29 years (OR: 3.309). Daily vaping also increased the odds of positive IgG index (OR: 2.058). Conclusions: The majority of Polish police employees are seronegative for SARS-CoV-2 infection. Vaping and older age (≥60 years) were associated with a higher risk of SARS-CoV-2 infection. url: https://doi.org/10.3390/jcm9103245 doi: 10.3390/jcm9103245 id: cord-277909-rn1dow26 author: Gunson, R.N. title: Practical experience of high throughput real time PCR in the routine diagnostic virology setting date: 2006-02-07 words: 6853.0 sentences: 342.0 pages: flesch: 54.0 cache: ./cache/cord-277909-rn1dow26.txt txt: ./txt/cord-277909-rn1dow26.txt summary: In comparison to traditional gel-based PCR assays, real time PCR offers increased sensitivity and specificity in a rapid format (turn around time from sample receipt to result <5 h). Most of the published real time probe based PCR assays for viral diagnosis utilise either molecular beacons or dual labelled probes although more recent publications tend to favour the use of dual labelled probes. In real time PCR, the signal is detected early in the amplification process, and therefore the end-point variation seen in gel-based assays does not affect the result. Despite this we still perform an initial optimisation of both primer and probe concentrations to ensure we are running our real time PCR assays at their most sensitive and efficient. Some manufacturers are now producing real time reaction mixes specifically designed for use with multiplex assays, and provide guidelines on the optimal primer and probe concentrations to use. abstract: The advent of PCR has transformed the utility of the virus diagnostic laboratory. In comparison to traditional gel based PCR assays, real time PCR offers increased sensitivity and specificity in a rapid format. Over the past 4 years, we have introduced a number of qualitative and quantitative real time PCR assays into our routine testing service. During this period, we have gained substantial experience relating to the development and implementation of real-time assays. Furthermore, we have developed strategies that have allowed us to increase our sample throughput while maintaining or even reducing turn around times. The issues resulting from this experience (some of it bad) are discussed in detail with the aim of informing laboratories that are only just beginning to investigate the potential of this technology. url: https://www.sciencedirect.com/science/article/pii/S1386653205003501 doi: 10.1016/j.jcv.2005.12.006 id: cord-354943-wxhbwcfr author: Guo, Li title: Profiling Early Humoral Response to Diagnose Novel Coronavirus Disease (COVID-19) date: 2020-03-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: The emergence of coronavirus disease 2019 (COVID-19) is a major healthcare threat. The current method of detection involves a quantitative polymerase chain reaction (qPCR)–based technique, which identifies the viral nucleic acids when present in sufficient quantity. False-negative results can be achieved and failure to quarantine the infected patient would be a major setback in containing the viral transmission. We aim to describe the time kinetics of various antibodies produced against the 2019 novel coronavirus (SARS-CoV-2) and evaluate the potential of antibody testing to diagnose COVID-19. METHODS: The host humoral response against SARS-CoV-2, including IgA, IgM, and IgG response, was examined by using an ELISA-based assay on the recombinant viral nucleocapsid protein. 208 plasma samples were collected from 82 confirmed and 58 probable cases (qPCR negative but with typical manifestation). The diagnostic value of IgM was evaluated in this cohort. RESULTS: The median duration of IgM and IgA antibody detection was 5 (IQR, 3–6) days, while IgG was detected 14 (IQR, 10–18) days after symptom onset, with a positive rate of 85.4%, 92.7%, and 77.9%, respectively. In confirmed and probable cases, the positive rates of IgM antibodies were 75.6% and 93.1%, respectively. The detection efficiency by IgM ELISA is higher than that of qPCR after 5.5 days of symptom onset. The positive detection rate is significantly increased (98.6%) when combining IgM ELISA assay with PCR for each patient compared with a single qPCR test (51.9%). CONCLUSIONS: The humoral response to SARS-CoV-2 can aid in the diagnosis of COVID-19, including subclinical cases. url: https://www.ncbi.nlm.nih.gov/pubmed/32198501/ doi: 10.1093/cid/ciaa310 id: cord-015683-a9a82of4 author: Gupta, Varsha title: Molecular Diagnostics date: 2016-10-23 words: 4774.0 sentences: 294.0 pages: flesch: 52.0 cache: ./cache/cord-015683-a9a82of4.txt txt: ./txt/cord-015683-a9a82of4.txt summary: Molecular diagnostics such as Western blot , ELISA , PCR , DNA, and protein microarrays are 7 revolutionizing the clinical practice of infectious diseases. Molecular diagnostics such as Western blot , ELISA , PCR , DNA, and protein microarrays are 7 revolutionizing the clinical practice of infectious diseases. Binding of another antigen-specifi c antibody linked with enzyme results in color formation upon addition of the substrate 9.2 Diagnosis of Bacterial, Viral, and Parasitic Diseases peptide may react in some assays but not in others as some regions of a peptide may be more immunogenic than others. Because of the specifi city, homogeneity, and unlimited availability of the MAbs, vast amount of work has been carried out on the production/development The immuno-diagnoses of protozoan and parasitic diseases have signifi cantly been improved by MAb technology because the tests involving MAb as diagnostic reagents overcome the limitations of polyclonal antibodies. The sensitivity and specifi city of a PCR assay is dependent on target genes, primer sequences, PCR techniques, DNA extraction procedures, and PCR product detection methods. abstract: Effective and early management of diseases requires record of the history, behavioral parameters, and travel information. These are helpful for the diagnosis, prevention, and control of the disease. There have been several advancements in the methods for diagnosing infectious diseases. The wide spectrum of tests such as biochemical evaluation, microbiological tools, immunological and molecular biology techniques, etc., is available. Each type of diagnostic technique is strong and reliable in its own sense but poses certain limitations. These limitations may be complemented by using a combination of tests. Older techniques such as microscopy and culturing of organisms from clinical specimens are error-free but are very labor intensive and extremely time consuming. There is a need to develop rapid and sensitive tests that can be used in both high- and low-resource settings. Molecular diagnostics such as Western blot, ELISA, PCR, DNA, and protein microarrays are revolutionizing the clinical practice of infectious diseases. Their effects are significant in acute-care settings where timely and accurate diagnostic tools are critical for patient treatment decisions and outcomes. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7115026/ doi: 10.1007/978-981-10-0875-7_9 id: cord-273829-t5cuop5c author: Görgülü, Özkan title: rRT-PCR Results of a Covid-19 Diagnosed Geriatric Patient date: 2020-10-17 words: 1482.0 sentences: 89.0 pages: flesch: 52.0 cache: ./cache/cord-273829-t5cuop5c.txt txt: ./txt/cord-273829-t5cuop5c.txt summary: Therefore, the COVID-19 pandemic control and filiation evaluation with the rRT-PCR test may produce false negative results. Patient with positive Covid-19 IgM Rapid Test performed on May 19, 2020, was subjected to the rRT-PCR test, repeated twice on the 19th of May which also resulted in positive. The nucleic acid test functions as the gold standard method for confirming the SARS-COV-2 infection; however, some recent studies have detected false negative results of real-time reverse transcriptase polymerase chain reaction (rRT-PCR) [4] . Similar to our case, there are case reports of reverse transcription-polymerase chain reaction (RT-PCR) test initially false negative and later positive in the literature [11] . Therefore, it can be argued that COVID-19 pandemic control and filiation evaluation with the rRT-PCR test may produce false negative results. A case report of COVID-19 with false negative RT-PCR test: necessity of chest CT abstract: In this study, we aimed to present a geriatric patient with the diagnosis of COVID-19 and with contradictory results in rRT-PCR examinations in short time intervals. A 69-year-old male patient was admitted to the emergency room on the 18th day of May 2020, with the complaints of fever, sweating, myalgia, dry cough that continued for 5 days, and the lack of taste that started on the day he applied to the emergency room. Comorbidity factors include diabetes mellitus, bronchial asthma, and hypertension. The patient has a history of 36 years of smoking 1.5 packs per day. High laboratory findings during hospitalization: monocytes, creatinine, CRP (C-reactive protein). In the thorax CT, in the parenchyma areas of both lungs, there are increases in attenuation with multilobe distributions (more visible at the level of the upper lobes) in the form of ground-glass opacities. May 19, 2020, was subjected to the rRT-PCR test, repeated twice on the 19th of May which also resulted in positive. Despite rRT-PCR tests, which were negative on 27th of May and positive on 28th of May, the patient, whose symptoms disappeared, and general condition improved, was discharged on June 1, 2020, with the recommendation for home isolation. In our case, unlike the incubation period only, we encountered a negative rRT-PCR result on the 8th day after diagnosis. Therefore, the COVID-19 pandemic control and filiation evaluation with the rRT-PCR test may produce false negative results. url: https://doi.org/10.1007/s42399-020-00590-9 doi: 10.1007/s42399-020-00590-9 id: cord-281529-2rec51xg author: Haagmans, Bart L title: Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation date: 2013-12-17 words: 4032.0 sentences: 205.0 pages: flesch: 57.0 cache: ./cache/cord-281529-2rec51xg.txt txt: ./txt/cord-281529-2rec51xg.txt summary: We tested for the presence of MERS-CoV in dromedary camels from a farm in Qatar linked to two human cases of the infection in October, 2013. 13 Both MERS-CoV spike protein binding antibodies and virus neutralising antibodies were reported in dromedary camels from diff erent regions, including Oman and Egypt, but no virus shedding could be detected and, therefore, the signifi cance of these observations remained an issue of debate. The camel MERS-CoV clustered with viral sequences obtained from the two human cases related to the farm and with a sequence from Hafr-Al-Batin as the next closest relative (fi gure 1). However, virological testing was unable to detect MERS-CoV viral sequences in camels, probably because only faecal and serum samples were analysed. Our report describes the fi rst detection of MERS-CoV in dromedary camels on a farm in Qatar that had been linked to human cases of the disease. abstract: BACKGROUND: Middle East respiratory syndrome coronavirus (MERS-CoV) causes severe lower respiratory tract infection in people. Previous studies suggested dromedary camels were a reservoir for this virus. We tested for the presence of MERS-CoV in dromedary camels from a farm in Qatar linked to two human cases of the infection in October, 2013. METHODS: We took nose swabs, rectal swabs, and blood samples from all camels on the Qatari farm. We tested swabs with RT-PCR, with amplification targeting the E gene (upE), nucleocapsid (N) gene, and open reading frame (ORF) 1a. PCR positive samples were tested by different MERS-CoV specific PCRs and obtained sequences were used for phylogentic analysis together with sequences from the linked human cases and other human cases. We tested serum samples from the camels for IgG immunofluorescence assay, protein microarray, and virus neutralisation assay. FINDINGS: We obtained samples from 14 camels on Oct 17, 2013. We detected MERS-CoV in nose swabs from three camels by three independent RT-PCRs and sequencing. The nucleotide sequence of an ORF1a fragment (940 nucleotides) and a 4·2 kb concatenated fragment were very similar to the MERS-CoV from two human cases on the same farm and a MERS-CoV isolate from Hafr-Al-Batin. Eight additional camel nose swabs were positive on one or more RT-PCRs, but could not be confirmed by sequencing. All camels had MERS-CoV spike-binding antibodies that correlated well with the presence of neutralising antibodies to MERS-CoV. INTERPRETATION: Our study provides virological confirmation of MERS-CoV in camels and suggests a recent outbreak affecting both human beings and camels. We cannot conclude whether the people on the farm were infected by the camels or vice versa, or if a third source was responsible. FUNDING: European Union projects EMPERIE (contract number 223498), ANTIGONE (contract number 278976), and the VIRGO consortium. url: https://www.ncbi.nlm.nih.gov/pubmed/24355866/ doi: 10.1016/s1473-3099(13)70690-x id: cord-307068-360qs3ov author: Hagiwara, Masanori title: Loop‐mediated isothermal amplification method for detection of human papillomavirus type 6, 11, 16, and 18 date: 2007-03-26 words: 3332.0 sentences: 194.0 pages: flesch: 56.0 cache: ./cache/cord-307068-360qs3ov.txt txt: ./txt/cord-307068-360qs3ov.txt summary: A new method was developed for detection of human papillomavirus (HPV) by loop‐mediated isothermal amplification (LAMP), which was compared with the polymerase chain reaction (PCR), and real‐time PCR for specificity and sensitivity. In order to evaluate the reliability of HPV type‐specific LAMP detecting HPV DNA from clinical samples, tissue specimens were obtained from 27 patients with external genital polypoid lesions. In this study, a LAMP-based HPV typespecific DNA amplification method was developed and were compared its specificity and sensitivity with PCR and real-time PCR. Type-specific real-time PCR was used to measure the quantity of the DNAs of HPV-6, -11, -16, and -18 in each sample. The sensitivity of HPV-6, -11, -16, and -18 type-specific LAMP determined by turbidity assay were 1,000 copies/tube (Fig. 3) . The sensitivity of amplification of LAMP for detection of viral DNA was nearly the same as that of real-time PCR. abstract: A new method was developed for detection of human papillomavirus (HPV) by loop‐mediated isothermal amplification (LAMP), which was compared with the polymerase chain reaction (PCR), and real‐time PCR for specificity and sensitivity. All initial validation studies with the control DNA proved to be type‐specific. In order to evaluate the reliability of HPV type‐specific LAMP detecting HPV DNA from clinical samples, tissue specimens were obtained from 27 patients with external genital polypoid lesions. The histologic diagnoses included condyloma acuminatum (n = 21), bowenoid papulosis (n = 2), seborrheic keratosis (n = 2), epidermolytic acanthoma (n = 1), and hairy nymphae (n = 1). HPV‐6 DNA and HPV‐11 DNA were detected in 18 and 3 of 21 condylomata acuminata, respectively, and there was no simultaneous infection. HPV‐16 DNA was detected in one of two bowenoid papuloses. HPV DNA was not detected in the seborrheic keratoses, epidermolytic acanthoma, and hairy nymphae. These results correlated perfectly with those from real‐time PCR analysis. Most positive samples contained high copy numbers of HPV DNA. HPV‐11 DNA was detected in one case that could not be detected by PCR. The average reaction time was about 59 min. There was a linear correlation between the genome quantity and reaction time to reach the threshold. The LAMP method has an additional advantage as a quantitative method, and is superior in terms of sensitivity, specificity, rapidity, and simplicity, and can potentially be a valuable tool for the detection of HPV DNA. J. Med. Virol. 79:605–615, 2007. © 2007 Wiley‐Liss, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/17385684/ doi: 10.1002/jmv.20858 id: cord-302024-zz7mt6be author: Hakhverdyan, Mikhayil title: Evaluation of a single-tube fluorogenic RT-PCR assay for detection of bovine respiratory syncytial virus in clinical samples date: 2004-11-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Bovine respiratory syncytial virus (BRSV) causes severe disease in naïve cattle of all ages and is a common pathogen in the respiratory disease complex of calves. Simplified methods for rapid BRSV diagnosis would encourage sampling during outbreaks and would consequently lead to an extended understanding of the virus. In this study, a BRSV fluorogenic reverse transcription PCR (fRT-PCR) assay, based on TaqMan principle, was developed and evaluated on a large number of clinical samples, representing various cases of natural and experimental BRSV infections. By using a single-step closed-tube format, the turn-around time was shortened drastically and results were obtained with minimal risk for cross-contamination. According to comparative analyses, the detection limit of the fRT-PCR was on the same level as that of a nested PCR and the sensitivity relatively higher than that of a conventional PCR, antigen ELISA (Ag-ELISA) and virus isolation (VI). Interspersed negative control samples, samples from healthy animals and eight symptomatically or genetically related viruses were all negative, confirming a high specificity of the assay. Taken together, the data indicated that the fRT-PCR assay can be applied to routine virus detection in clinical specimens and provides a rapid and valuable tool in BRSV research. url: https://www.ncbi.nlm.nih.gov/pubmed/15620402/ doi: 10.1016/j.jviromet.2004.09.016 id: cord-277659-afysef1e author: Hamilton, F. title: Kinetics and performance of the Abbott Architect SARS-CoV-2 IgG antibody assay date: 2020-07-04 words: 3096.0 sentences: 203.0 pages: flesch: 53.0 cache: ./cache/cord-277659-afysef1e.txt txt: ./txt/cord-277659-afysef1e.txt summary: Objectives: To assess the performance (sensitivity and specificity) of the Abbott Architect SARS-CoV-2 IgG antibody assay across three clinical settings. Methods: Antibody testing was performed on three clinical cohorts of COVID-19 disease: hospitalised patients with PCR confirmation, hospitalized patients with a clinical diagnosis but negative PCR, and symptomatic healthcare workers (HCWs). To assess the performance (sensitivity and specificity) of the Abbott Architect SARS-CoV-2 IgG antibody assay across three clinical settings. Antibody testing was performed on three clinical cohorts of COVID-19 disease: hospitalised patients with PCR confirmation, hospitalized patients with a clinical diagnosis but negative PCR, and symptomatic healthcare workers (HCW''s). In this paper, we report the kinetics and performance of this assay in three populations: confirmed (PCR +ve) and suspected COVID-19 patients, confirmed (PCR +ve) healthcare workers, and pre-pandemic controls with respiratory infection. The sensitivity of the Abbott SARS-CoV-2 IgG assay was estimated with 95% Confidence Intervals at different time points post symptom onset (DISCOVER patients) or first PCR positive result (healthcare workers). abstract: Objectives: To assess the performance (sensitivity and specificity) of the Abbott Architect SARS-CoV-2 IgG antibody assay across three clinical settings. Methods: Antibody testing was performed on three clinical cohorts of COVID-19 disease: hospitalised patients with PCR confirmation, hospitalized patients with a clinical diagnosis but negative PCR, and symptomatic healthcare workers (HCWs). Pre-pandemic respiratory infection sera were tested as negative controls. The sensitivity of the assay was calculated at different time points (<5 days, 5-9 days, 10-14 days, 15-19 days, >20 days, >42 days), and compared between cohorts. Results: Performance of the Abbot Architect SARS-CoV-2 assay varied significantly between cohorts. For PCR confirmed hospitalised patients (n = 114), early sensitivity was low: <5 days: 44.4% (95%CI: 18.9%-73.3%), 5-9 days: 32.6% (95%CI, 20.5%-47.5%), 10-14 days: 65.2% (95% CI 44.9%-81.2%), 15-20 days: 66.7% (95% CI: 39.1%-86.2%) but by day 20, sensitivity was 100% (95%CI, 86.2-100%). In contrast, 17 out of 114 symptomatic healthcare workers tested at >20 days had negative results, generating a sensitivity of 85.1% (95%CI, 77.4% - 90.5%). All pre-pandemic sera were negative, a specificity of 100%. Seroconversion rates were similar for PCR positive and PCR negative hospitalised cases. Conclusions: The sensitivity of the Abbot Architect SARS-CoV-2 IgG assay increases over time, with sensitivity not peaking until 20 days post symptoms. Performance varied markedly by setting, with sensitivity significantly worse in symptomatic healthcare workers than in the hospitalised cohort. Clinicians, policymakers, and patients should be aware of the reduced sensitivity in this setting. url: http://medrxiv.org/cgi/content/short/2020.07.03.20145722v1?rss=1 doi: 10.1101/2020.07.03.20145722 id: cord-023698-wvk200j0 author: Hammerschlag, Margaret R. title: Chlamydia pneumoniae date: 2014-10-31 words: 10016.0 sentences: 533.0 pages: flesch: 38.0 cache: ./cache/cord-023698-wvk200j0.txt txt: ./txt/cord-023698-wvk200j0.txt summary: Because the organism has been difficult to grow and because of the lack of a commercially available other diagnostic assay, most original associations with respiratory diseases have been use of serology with the microimmunofluorescence (MIF) test. 38, 39 For an example of the complexity of this issue, consider that two multicenter pneumonia treatment studies in children showed that although 7% to 13% of the patients in the study had positive culture results and 7% to 18% met the serologic criteria with the MIF test for acute infection, they were not the same patients. pneumoniae infection is that the MIF method used to detect serum antibodies is not standardized; recent studies have shown substantial interlaboratory variation in the performance of these tests. Multicenter comparison trial of DNA extraction methods and PCR assays for detection of Chlamydia pneumoniae in endarterectomy specimens Multicenter comparison trial of DNA extraction methods and PCR assays for detection of Chlamydia pneumoniae in endarterectomy specimens abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173483/ doi: 10.1016/b978-1-4557-4801-3.00184-3 id: cord-292575-vsswxwdi author: Hammou, Rahma Ait title: Chapter 7 Scientific Advances in the Diagnosis of Emerging and Reemerging Viral Human Pathogens date: 2020-12-31 words: 8496.0 sentences: 402.0 pages: flesch: 39.0 cache: ./cache/cord-292575-vsswxwdi.txt txt: ./txt/cord-292575-vsswxwdi.txt summary: It is in this context that this chapter aims to discuss the various scientific advances, particularly molecular, in terms of diagnosis of these diseases; the new discoveries in the role of nanotechnologies and nanobiosensors; and also the implication of biomarkers, especially microRNAs (miRNAs), since it was reported that a single miRNA has the ultimate capacity to target multiple genes simultaneously. The availability of nucleic acidÀbased technology, such as real-time PCR, along with conventional staining and culture methods and immunoassays, can provide laboratories of many sizes with a comprehensive and responsible approach for the detection of both commonly encountered and emerging or reemerging pathogens. As is the case for SARS, agents of bioterrorism, and the other pathogens, rapid diagnostic methods, such as real-time PCR, and microarray will likely play a major role in the early and sensitive detection of emerging and reemerging infectious diseases encountered in the future. abstract: Abstract Despite scientific advances, the diagnosis of infectious diseases is primarily possible through vaccination and later by antibiotics. Emerging and reemerging pathologies are still considered to be dangerous to humanity because of the unique nature of these diseases: it is the encounter between two living organisms that have coexisted for millions of years within the people on the same planet without being previously recognized. These infectious agents, such as bacteria, viruses, fungi, or parasites, pose no threat to humans. In fact, only a few hundred are able to inflict damage to the human host. In addition, the spectrum of human disease caused by a particular pathogen varies considerably depending on the factors related to the ecological agent, the host, and the infectious agents. Several emerging or reemerging infectious agents are organisms that could be used in biological control. The differentiation of a natural epidemic from a bioterrorian event is based on several epidemiological indices as well as on the molecular characterization of the pathogen(s) involved. The role of pathologists is indeed very important. It is in this context that this chapter aims to discuss the various scientific advances, particularly molecular, in terms of diagnosis of these diseases; the new discoveries in the role of nanotechnologies and nanobiosensors; and also the implication of biomarkers, especially microRNAs (miRNAs), since it was reported that a single miRNA has the ultimate capacity to target multiple genes simultaneously. In a viral infection context, miRNAs have been connected with the interplay between host and pathogen and occupy a major role in the host–parasite interaction and pathogenesis. It is in this context that various molecular and nanomethods for the detection of emerging viruses and experimental validation of miRNAs during quelling viruses target transcripts will be discussed in this chapter. url: https://www.sciencedirect.com/science/article/pii/B978012814966900007X doi: 10.1016/b978-0-12-814966-9.00007-x id: cord-266499-g1lajsp8 author: Han, Jae-Ik title: A multiplex quantitative real-time polymerase chain reaction panel for detecting neurologic pathogens in dogs with meningoencephalitis date: 2015-09-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Meningoencephalitis (ME) is a common inflammatory disorder of the central nervous system in dogs. Clinically, ME has both infectious and non-infectious causes. In the present study, a multiplex quantitative real-time polymerase chain reaction (mqPCR) panel was optimized for the detection of eight canine neurologic pathogens (Blastomyces dermatitidis, Cryptococcus spp., Neospora caninum, Borrelia burgdorferi, Bartonella spp., Toxoplasma gondii, Ehrlichia canis, and canine distemper virus [CDV]). The mqPCR panel was subsequently applied to 53 cerebrospinal fluid (CSF) samples collected from dogs with ME. The analytic sensitivity (i.e., limit of detection, expressed as molecules per 1 µL of recombinant vector) was 3.8 for CDV, 3.7 for Ehrlichia canis, 3.7 for Bartonella spp., 3.8 for Borrelia burgdorferi, 3.7 for Blastomyces dermatitidis, 3.7 for Cryptococcus spp., 38 for Neospora caninum, and 3.7 for Toxoplasma gondii. Among the tested CSF samples, seven (15%) were positive for the following pathogens in decreasing order of frequency: Cryptococcus spp. (3/7), Blastomyces dermatitidis (2/7), and Borrelia burgdorferi (2/7). In summary, use of an mqPCR panel with high analytic sensitivity as an initial screen for infectious agents in dogs with ME could facilitate the selection of early treatment strategies and improve outcomes. url: https://www.ncbi.nlm.nih.gov/pubmed/26040611/ doi: 10.4142/jvs.2015.16.3.341 id: cord-271669-dkg6229j author: Han, Seung Beom title: Respiratory Viral Infections in Children and Adolescents with Hematological Malignancies date: 2019-01-01 words: 3774.0 sentences: 213.0 pages: flesch: 41.0 cache: ./cache/cord-271669-dkg6229j.txt txt: ./txt/cord-271669-dkg6229j.txt summary: Because these conventional methods have low sensitivity for detecting rhinovirus and enterovirus, which are the most common causes of community-acquired respiratory viral infection (RVI), RVI was identified only in 6-22% of immune compromised children with respiratory symptoms in the past. 7, 10, 19, 23, [25] [26] [27] Even in rhinovirus infection, which causes milder respiratory illnesses compared to those of RSV, parainfluenza virus and influenza virus, mortality was significantly higher in patients with LRIs than that in those with URIs. 26 Therefore, the early detection of patients at risk of progression to LRIs and early application of proper management for LRIs are necessary to improve the outcome of RVI in immune compromised patients. Considering the confirmed RVI diagnosis in half of the immune compromised children and adolescents with respiratory symptoms in this study, the introduction of multiplex PCR tests for RV detection in this population should be encouraged, especially for patients complaining of rhinorrhea or sputum prominent over a cough. abstract: BACKGROUND: Despite the introduction of a polymerase chain reaction (PCR) test for the diagnosis of respiratory viral infection (RVI), guidance on the application of this test and the management of RVI in immunocompromised children is lacking. This study evaluated the clinical characteristics of RVI and established strategies for the PCR test in children and adolescents with hematological malignancies. METHODS: This study included children and adolescents with underlying hematological malignancies and respiratory symptoms, in whom a multiplex PCR test was performed. Patients in whom RVI was identified and not identified were categorized into Groups I and II, respectively. Group I was sub-divided into patients with upper and lower respiratory infections. The medical records of the enrolled patients were retrospectively reviewed. RESULTS: A total of 93 respiratory illnesses were included. Group I included 46 (49.5%) cases of RVI, including 31 (67.4%) upper and 15 (32.6%) lower respiratory infections. Rhinovirus (37.0%) was the most common viral pathogen. Significantly more patients in Group I had community-acquired respiratory illnesses (p=0.003) and complained of rhinorrhea (p<0.001) and sputum (p=0.008) than those in Group II. In Group I, significantly more patients with lower respiratory infections had uncontrolled underlying malignancies (p=0.038) and received re-induction or palliative chemotherapy (p=0.006) than those with upper respiratory infections. CONCLUSIONS: A multiplex PCR test should be considered for RVI diagnosis in immunocompromised children and adolescents with respiratory symptoms, especially in those with rhinorrhea or sputum prominent over a cough. The early application of the PCR test in patients with uncontrolled underlying malignancies may improve outcomes. url: https://doi.org/10.4084/mjhid.2019.006 doi: 10.4084/mjhid.2019.006 id: cord-284366-snajbvr9 author: Han, Zhiyong title: Discharged COVID‐19 Patients Testing Positive Again for SARS‐CoV‐2 RNA: A Minireview of Published Studies from China date: 2020-07-01 words: 2017.0 sentences: 133.0 pages: flesch: 61.0 cache: ./cache/cord-284366-snajbvr9.txt txt: ./txt/cord-284366-snajbvr9.txt summary: [3] [4] [5] The diagnosis of COVID-19 considers clinical symptoms, GGO lesions in chest CT or Xray images, and positive RT-PCR test results for the presence of SARS-CoV-2 RNA in patient samples. For example, the guidelines of the National Health Commission of China state that patients must meet the following 4 benchmarks before they can be discharged: (i) be afebrile for at least 3 consecutive days, (ii) have significantly improved respiratory function, (iii) produce two negative SARS-CoV-2 RT-PCR test results at least 24 hours apart, and (iv) have significant improvement in lung GGO lesions determined by chest CT or X-ray imaging. In Table 1 , we summarize the information about patients who tested positive for SARS-CoV-2 RNA in post-discharge, follow-up examinations in China as described in the 12 published reports. Our analysis indicates that many of the discharged patients tested positive for SARS-CoV-2 RNA when feces or anal swabs were employed, even though they tested negative at the same time when nasopharyngeal or oropharyngeal or sputum samples were examined. abstract: In the ongoing COVID‐19 pandemic, one potential cause of concern is that some discharged COVID‐19 patients are testing positive again for SARS‐CoV‐2 RNA. To better understand what is happening and to provide public health policy planners and clinicians timely information, we have searched and reviewed published studies about discharged patients testing positive again for the SARS‐CoV‐2 RNA. Our search found 12 reports, all of which described patients in China. Our review of these reports indicates the presence of discharged patients who remain asymptomatic but test positive. However, it is unclear whether they are contagious because a positive RT‐PCR test does not necessarily indicate the presence of replicating and transmissible virus. Our review suggests the need for timely, parallel testing of different samples, including for example, fecal specimens, from COVID‐19 patients before and after they are discharged from hospitals. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.26250 doi: 10.1002/jmv.26250 id: cord-279223-qvih5qas author: Hascoët, Jean-Michel title: Case Series of COVID-19 Asymptomatic Newborns With Possible Intrapartum Transmission of SARS-CoV-2 date: 2020-09-29 words: 3057.0 sentences: 165.0 pages: flesch: 50.0 cache: ./cache/cord-279223-qvih5qas.txt txt: ./txt/cord-279223-qvih5qas.txt summary: Another mother exhibited infection 6 weeks pre-delivery, confirmed by nasopharyngeal swab testing with positive RT-PCR, and positive antibody detection (IgM and IgG). Two additional mothers exhibited infection confirmed by positive RT-PCR testing at 28and 31-days pre-delivery but did not present detectable antibody reaction at the time of delivery. Thus, although the mother was considered cleared at 6 weeks after the onset of infection, which was confirmed by negative nasopharyngeal and stool SARS-CoV-2 RT-PCR tests after delivery, we tested stool and pharynx swab samples from asymptomatic baby-girl D. Two additional babies and their mothers were tested at birth because the mothers had symptomatic infection, documented with positive SARS-CoV-2 RT-PCR results, at 28 and 31 days before delivery, respectively. Despite the first newborn was asymptomatic and the screening performed as part of routine systematic testing, SARS-CoV-2 RNA detection through early nasopharyngeal sampling and the persistent detection of virus in stool strongly suggest possible vertical maternofetal infection. abstract: Background: Despite the pandemic, data are limited regarding COVID-19 infection in pregnant women and newborns. This report aimed to bring new information about presentation that could modify precautionary measures for infants born of mothers with a remote history of COVID-19. Methods: We report two infants with possible maternofetal transmission, and four mothers without immunologic reactions. Data were collected from the patient files. Results: One mother exhibited infection signs 10 days before uncomplicated delivery, with negative RT-PCR and no antibody detection thereafter. Another mother exhibited infection 6 weeks pre-delivery, confirmed by nasopharyngeal swab testing with positive RT-PCR, and positive antibody detection (IgM and IgG). Both newborns were asymptomatic but tested positive for nasopharyngeal and stool RT-PCR at 1 and 3 days of age for the first one and at 1 day of age for stool analysis for the second one. Two additional mothers exhibited infection confirmed by positive RT-PCR testing at 28- and 31-days pre-delivery but did not present detectable antibody reaction at the time of delivery. Conclusion: These observations raise concerns regarding contamination risk by asymptomatic newborns and the efficacy of immunologic reactions in pregnant mothers, questioning the reliability of antibody testing during pregnancy. url: https://doi.org/10.3389/fped.2020.568979 doi: 10.3389/fped.2020.568979 id: cord-352831-ydlix2o7 author: Hase, Ryota title: A case of imported COVID-19 diagnosed by PCR-positive lower respiratory specimen but with PCR-negative throat swabs date: 2020-04-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A 35-year-old woman presented with fever and mild diarrhoea without any respiratory symptoms 9 days after travelling to Japan from Wuhan, China. Her computed tomography scan revealed pneumonia. The first polymerase chain reaction (PCR) test on throat swab for the novel corona virus upon admission was negative. Therefore, she was treated for community-acquired pneumonia, but fever persisted. On hospital day 5, PCR test on induced sputum was positive, but a second polymerase chain reaction test on throat swab remained negative. She was discharged, fully recovered, on hospital day 12. A lower respiratory tract specimen should be obtained for better diagnosis of corona virus disease 2019, even in the absence of respiratory symptoms for patients with significant travel or exposure history. url: https://doi.org/10.1080/23744235.2020.1744711 doi: 10.1080/23744235.2020.1744711 id: cord-027498-cfzfgzqi author: Hattori, Takeshi title: Older age is associated with sustained detection of SARS-CoV-2 in nasopharyngeal swab samples date: 2020-06-21 words: 841.0 sentences: 49.0 pages: flesch: 56.0 cache: ./cache/cord-027498-cfzfgzqi.txt txt: ./txt/cord-027498-cfzfgzqi.txt summary: Currently, the standard for diagnosis of Severe Acute Respiratory Syndrome-Coronavirus-2 (SARSinfection is a positive result based on a polymerase chain reaction (PCR) test from nasopharyngeal swab samples. Although her clinical symptoms and radiological findings resolved within a few days, PCR results from nasopharyngeal swab samples remained positive for 50 days after the onset. We specifically hypothesized that old age could be a risk for prolonged duration of positive PCR results from nasopharyngeal swab samples. In our analysis, older age is significantly associated with prolonged duration of positive PCR tests from nasopharyngeal swab samples, irrespective of the disease severity and the used of medication ( Figure 1 ). In summary, we demonstrated that old age is significantly associated with prolonged duration of positive PCR results from nasopharyngeal swab samples; this is the case regardless of disease severity. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7306199/ doi: 10.1016/j.jinf.2020.06.046 id: cord-292364-jhiimglg author: Hayakawa, Jun title: Genetic and Antigenic Characterization and Retrospective Surveillance of Bovine Influenza D Viruses Identified in Hokkaido, Japan from 2018 to 2020 date: 2020-08-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Influenza D virus (IDV), which is a new member of the Orthomyxoviridae family, is potentially involved in bovine respiratory diseases (BRDs). Bovine IDVs (BIDVs) from Japan have been distributed nationwide since 2010 and are genetically distinct from foreign IDVs. We isolated BIDVs from three BRD outbreaks, in Hokkaido during 2018–2020, to understand their genetic and antigenic characteristics. Retrospective surveillance was performed using sera collected throughout the last decade in Hokkaido to investigate BIDV existence. Three BIDVs were isolated using cell culture. Comparative and phylogenetic analyses using sequence data of the three BIDVs and IDVs from Japan and other countries available in GenBank demonstrated that Japanese BIDVs, including the three BIDV isolates, were genetically distinct from other IDVs. Genotype classifications based on the rotavirus genotype classification revealed multiple genotypes of RNA segments 1–7. Two BIDVs were of a new genotype, different from those of other Japanese BIDVs. Neutralization assays against two BIDVs with different genotypes using sera collected in acute and recovery phases of BRD revealed differences in cross-reactivity to heterogenous BIDVs. Retrospective surveillance suggested that BIDV existed in Hokkaido, in 2009. Our findings suggest that BIDVs of different genotypes and antigenicity are distributed and maintained in Hokkaido and provide new insights into molecular characteristics and the evolution of IDVs. url: https://www.ncbi.nlm.nih.gov/pubmed/32796617/ doi: 10.3390/v12080877 id: cord-307261-0a3iztns author: Hayden, Randall T. title: Comparison of two broadly multiplexed PCR systems for viral detection in clinical respiratory tract specimens from immunocompromised children date: 2012-01-30 words: 4052.0 sentences: 206.0 pages: flesch: 48.0 cache: ./cache/cord-307261-0a3iztns.txt txt: ./txt/cord-307261-0a3iztns.txt summary: title: Comparison of two broadly multiplexed PCR systems for viral detection in clinical respiratory tract specimens from immunocompromised children Samples were de-identified and assayed in parallel using two different, broadly multiplexed PCR systems: ResPlex™ II Panel v2.0 (ResPlex), Qiagen, Hilden, Germany and FilmArray(®) Respiratory Panel (FilmArray), Idaho Technology Inc., Salt Lake City, UT. Two broadly multiplexed PCR systems were compared to each other and to a panel of laboratory developed tests for the detection of respiratory viral pathogens in clinical respiratory tract specimens from pediatric immunocompromised children. FilmArray detected viral targets: adenovirus, bocavirus, coronavirus 229E, HKU1, NL63, OC43, enterovirus, hMPV, human rhinovirus, influenza virus types A and B, parainfluenza viruses 1, 2, 3 and 4, and RSV. The current study, to our knowledge, is the first reported that compares the FilmArray with the ResPlex II v2.0 for the direct detection of viral agents in clinical respiratory tract specimens from immunocompromised children. abstract: BACKGROUND: The detection of viral respiratory tract infections has evolved greatly with the development of PCR based commercial systems capable of simultaneously detecting a wide variety of pathogens. OBJECTIVES: Evaluate the relative performance of two commercial broad range systems for the detection of viral agents in clinical respiratory tract specimens from immunocompromised children. STUDY DESIGN: A total of 176 patient samples were included in the analysis, representing only the first sample collected for each patient, and excluding failed reactions. Samples were de-identified and assayed in parallel using two different, broadly multiplexed PCR systems: ResPlex™ II Panel v2.0 (ResPlex), Qiagen, Hilden, Germany and FilmArray(®) Respiratory Panel (FilmArray), Idaho Technology Inc., Salt Lake City, UT. Method comparison was based upon pair-wise concordance of results according to patient age, viral target and number of targets detected. RESULTS: The two systems showed an overall concordance, by patient, of 83.8% (p = 0.0001). FilmArray detected at least one target in 68.8% of samples, while ResPlex detected at least one target in 56.8%. ResPlex failed to detect 20.7% of FilmArray positives, and FilmArray failed to detect 4% of ResPlex positives. The relative performance of each system (including which system detected a higher number of positive samples) varied when stratified by target viral pathogen. CONCLUSIONS: Broadly multiplexed PCR is an effective means of detecting large numbers of clinically relevant respiratory viral pathogens. url: https://www.sciencedirect.com/science/article/pii/S1386653211005531 doi: 10.1016/j.jcv.2011.12.020 id: cord-255013-njpuc475 author: He, Xiaocui title: Establishment of Myotis myotis Cell Lines - Model for Investigation of Host-Pathogen Interaction in a Natural Host for Emerging Viruses date: 2014-10-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Bats are found to be the natural reservoirs for many emerging viruses. In most cases, severe clinical signs caused by such virus infections are normally not seen in bats. This indicates differences in the virus-host interactions and underlines the necessity to develop natural host related models to study these phenomena. Due to the strict protection of European bat species, immortalized cell lines are the only alternative to investigate the innate anti-virus immune mechanisms. Here, we report about the establishment and functional characterization of Myotis myotis derived cell lines from different tissues: brain (MmBr), tonsil (MmTo), peritoneal cavity (MmPca), nasal epithelium (MmNep) and nervus olfactorius (MmNol) after immortalization by SV 40 large T antigen. The usefulness of these cell lines to study antiviral responses has been confirmed by analysis of their susceptibility to lyssavirus infection and the mRNA patterns of immune-relevant genes after poly I:C stimulation. Performed experiments indicated varying susceptibility to lyssavirus infection with MmBr being considerably less susceptible than the other cell lines. Further investigation demonstrated a strong activation of interferon mediated antiviral response in MmBr contributing to its resistance. The pattern recognition receptors: RIG-I and MDA5 were highly up-regulated during rabies virus infection in MmBr, suggesting their involvement in promotion of antiviral responses. The presence of CD14 and CD68 in MmBr suggested MmBr cells are microglia-like cells which play a key role in host defense against infections in the central nervous system (CNS). Thus the expression pattern of MmBr combined with the observed limitation of lyssavirus replication underpin a protective mechanism of the CNS controlling the lyssavirus infection. Overall, the established cell lines are important tools to analyze antiviral innate immunity in M. myotis against neurotropic virus infections and present a valuable tool for a broad spectrum of future investigations in cellular biology of M. myotis. url: https://www.ncbi.nlm.nih.gov/pubmed/25295526/ doi: 10.1371/journal.pone.0109795 id: cord-340883-zf8jbhdl author: He, Zhongping title: Using patient-collected clinical samples and sera to detect and quantify the severe acute respiratory syndrome coronavirus (SARS-CoV) date: 2007-03-27 words: 2892.0 sentences: 119.0 pages: flesch: 56.0 cache: ./cache/cord-340883-zf8jbhdl.txt txt: ./txt/cord-340883-zf8jbhdl.txt summary: title: Using patient-collected clinical samples and sera to detect and quantify the severe acute respiratory syndrome coronavirus (SARS-CoV) Reverse transcriptase polymerase chain reaction (RT-PCR) was used to detect and quantify SARS-CoV in 934 sera and self-collected throat washes and fecal samples from 271 patients with laboratory-confirmed SARS managed at a single institution. The highest SARS-CoV RT-PCR rates (70.4–86.3%) and viral loads (log(10 )4.5–6.1) were seen in fecal samples collected 2–4 weeks after the onset of clinical illness. The aim of this study was to detect and quantify SARS-CoV using RT-PCR in sera and throat washes and stools self-collected by 271 patients with laboratory confirmed SARS managed at a single institution. The use of patient self-collected throat washings may reduce risks to healthcare workers, although lower respiratory tract samples such as sputum, NPAs or bronchoalveolar lavage fluid are likely to have higher viral loads and offer increased likelihood of SARS-CoV detection by RT-PCR. abstract: BACKGROUND: Severe acute respiratory syndrome (SARS) caused a large outbreak of pneumonia in Beijing, China, in 2003. Reverse transcriptase polymerase chain reaction (RT-PCR) was used to detect and quantify SARS-CoV in 934 sera and self-collected throat washes and fecal samples from 271 patients with laboratory-confirmed SARS managed at a single institution. RESULTS: SARS-CoV detection rates in sera were highest in the first 9 days of illness, whereas detection was highest in throat washes 5–14 days after onset of symptoms. The highest SARS-CoV RT-PCR rates (70.4–86.3%) and viral loads (log(10 )4.5–6.1) were seen in fecal samples collected 2–4 weeks after the onset of clinical illness. Fecal samples were frequently SARS-CoV RT-PCR positive beyond 40 days, and occasional sera still had SARS-CoV detected after 3 weeks of illness. CONCLUSION: In the context of an extensive outbreak with major pressure on hospital resources, patient self-collected samples are an alternative to nasopharyngeal aspirates for laboratory confirmation of SARS-CoV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/17386116/ doi: 10.1186/1743-422x-4-32 id: cord-308867-mrtf8l4f author: Heaney, Jude title: Chapter 6 Low-Density TaqMan® Array Cards for the Detection of Pathogens date: 2015-12-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract Real-time PCR assays have revolutionised diagnostic microbiology over the past 15 years or more. Adaptations and improvements over that time frame have led to the development of multiplex assays. However, limitations in terms of available fluorophores has meant the number of assays which can be combined has remained in single figures. This latter limitation has led to the focus tending to be on individual pathogens and their detection. This chapter describes the development of TaqMan® Array Cards (TACs), technology which allows the detection of multiple pathogens (up to 48 targets) from a single nucleic acid extract, utilising small volumes and real-time PCR. This in turn lends itself to a syndromic approach to infectious disease diagnosis. Using the examples of TACs we have developed in our own laboratory, as well as others, we explain the design, optimisation and use of TACs for respiratory, gastrointestinal and liver infections. Refinement of individual assays is discussed as well as the incorporation of appropriate internal and process controls onto the array cards. Finally, specific examples are given of instances where the assays have had a direct, positive impact on patient care. url: https://api.elsevier.com/content/article/pii/S0580951715000112 doi: 10.1016/bs.mim.2015.06.002 id: cord-252694-36ijqwge author: Heidinger, Benedikt H. title: Radiologische Manifestationen von Lungenerkrankungen bei COVID-19 date: 2020-09-08 words: 2948.0 sentences: 368.0 pages: flesch: 39.0 cache: ./cache/cord-252694-36ijqwge.txt txt: ./txt/cord-252694-36ijqwge.txt summary: Der Referenzstandard für die Diagnose von COVID-19 ist eine positive "reverse transcription polymerase chain reaction" (RT-PCR) eines Nasen-/ Rachenabstriches oder einer Probe tiefen Bronchialsekrets [4] . Mehrere medizinische und radiologische Fachgesellschaften haben Empfehlungen für die Anwendung der verschiedenen Bildgebungsmodalitäten bei Patienten mit Verdacht auf oder bereits nachgewiesener SARS-CoV-2 publiziert [5] [6] [7] [8] [9] [10] . Sollten sich COVID-19-typische Lungenveränderungen als Zufallsbefund bei respiratorisch asymptomatischen Patienten zeigen, ist eine Bestätigung der Diagnose mittels RT-PCR notwendig [7, 8] . Im Thoraxröntgen untypisch für COVID-19 sind Kavitationen und Pleuraergüsse, die hinweisend auf Komplikationen oder andere Diagnosen wie beispielswei-se eine kardiale Dekompensation sein können [19] . Besteht jedoch eine hohe klinische Vortestwahrscheinlichkeit für COVID-19, beispielsweise bei typischen klinischen Symptomen und bekanntem Kontakt zu einer SARS-CoV2-positiven Person oder einer hohen Erkrankungsprävalenz in der Bevölkerung, sind diese jedoch als wahrscheinlich für das Vorliegen einer COVID-19-Pneumonie zu werten. abstract: CLINICAL ISSUE: Since its emergence in late 2019, the disease caused by the novel coronavirus, termed COVID-19, has been declared a pandemic by the World Health Organization. Reference standard for the diagnosis of COVID-19 is a positive reverse transcription polymerase chain reaction (RT-PCR) test. While the RT-PCR shows a high specificity, its sensitivity depends on the duration of symptoms, viral load, quality of the sample, and the assay used. STANDARD RADIOLOGICAL METHODS: Chest radiography and computed tomography (CT) of the chest are the imaging modalities primarily used for assessment of the lung manifestations, extent, and complications of COVID-19 pneumonia. PERFORMANCE: Sensitivity and specificity of chest radiography is low. While sensitivity of CT for detecting COVID-19 pneumonia is high—averaging around 90%—its specificity is low—between 25 and 33%. PRACTICAL RECOMMENDATIONS: Indications for imaging in patients with suspected or diagnosed COVID-19 infection should be carefully considered to minimize the risk of infection for medical personnel and other patients. Imaging, particularly CT, can assess disease extent, complications, and differential diagnoses. COVID-19 pneumonia typically presents with bilateral, subpleural areas of ground glass opacifications with or without consolidations. During the course of the disease features resembling organizing pneumonia can occur. Follow-up examinations after recovery from COVID-19 pneumonia should focus on fibrotic changes of the lung parenchyma. url: https://www.ncbi.nlm.nih.gov/pubmed/32897438/ doi: 10.1007/s00117-020-00749-4 id: cord-017199-dn413uud author: Heineman, M.J. title: 21 Infecties, ziekte en zwangerschap date: 2016 words: 36456.0 sentences: 3453.0 pages: flesch: 61.0 cache: ./cache/cord-017199-dn413uud.txt txt: ./txt/cord-017199-dn413uud.txt summary: Aan zwangeren met een positieve kweekuitslag of aan vrouwen van wie nog geen uitslag bekend is, moeten intrapartum profylactisch antibiotica intraveneus worden toegediend, bij voorkeur 2 miljoen IE penicilline G, of anders 2 g amoxicilline/ampicilline, zo mogelijk te geven minstens vier uur voor de te verwachten partus en daarna à 4 uur de helft tot de baby geboren is. Dit kan via seksueel contact, maar vaak blijkt de bron van infectie een kind uit het gezin te zijn dat door contact met andere geïnfecteerde kinderen besmet is geraakt. Onafhankelijke risicofactoren voor hiv-overdracht zijn: primo-infectie tijdens zwangerschap of lactatie, vroeggeboorte, andere geslachtsziekten wanneer die leiden tot ulceratie van de genitaliën, vitamine-A-deficiëntie, langer dan vier uur gebroken vliezen, invasieve diagnostiek bij het kind voor de geboorte en een vaginale geboorte. Bij gezonde zwangeren is de D-dimeer plasmaspiegel rondom de bevalling en vier weken post partum dermate verhoogd dat deze bepaling tijdens zwangerschap en kraambed niet kan worden gebruikt voor het vaststellen van een tromboembolisch proces. abstract: Chronische ziekten en infecties vormen een belangrijke oorzaak van maternale en foetale morbiditeit en mortaliteit. Een goede voorbereiding op de interactie tussen de zwangerschap en het onderliggend lijden kan dit mogelijk verbeteren. Preconceptionele advisering, multidisciplinaire behandeling en het treffen van goede voorzorgsmaatregelen in het geval van complicaties maken hier een belangrijk onderdeel van uit. Kennis van de fysiologische veranderingen die optreden tijdens de zwangerschap, is hiervoor onontbeerlijk. Infecties vormen tijdens de zwangerschap een reëel gevaar voor de gezondheid van moeder en kind. Preventie en zo mogelijk tijdige behandeling is obligaat. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121700/ doi: 10.1007/978-90-368-1191-0_21 id: cord-297432-2edncbgn author: Helleberg, Marie title: Persistent COVID-19 in an Immunocompromised Patient Temporarily Responsive to Two Courses of Remdesivir Therapy date: 2020-07-23 words: 2390.0 sentences: 139.0 pages: flesch: 46.0 cache: ./cache/cord-297432-2edncbgn.txt txt: ./txt/cord-297432-2edncbgn.txt summary: A man in his fifties treated with chemoimmunotherapy for chronic lymphocytic leukemia experienced a 9-week course of COVID-19 with high fever and severe viral pneumonia. Recently, preliminary results of the Adaptive COVID-19 Treatment Trial (ACTT), a multicenter randomized controlled trial of remdesivir versus placebo for treatment of coronavirus disease 2019 (COVID-19) in hospitalized patients, demonstrated that remdesivir reduced time to recovery, in particular for those not yet having experienced respiratory failure with need for assisted ventilation [1] . We here report the clinical course and findings in an immunocompromised patient with remission of COVID-19 during treatment with remdesivir but relapse soon after discontinuation. We present a case of severe COVID-19 in a patient with B-and T-lymphocyte impairment secondary to CLL treated with chemoimmunotherapy 3 months prior to the SARS-CoV-2 infection. The course and findings in this clinical case suggest that remdesivir has a rapid onset of action and can suppress, but may not eradicate, SARS-CoV-2 in immunocompromised patients. abstract: The antiviral drug remdesivir has been shown clinically effective for treatment of COVID-19. We here demonstrate suppressive but not curative effect of remdesivir in an immunocompromised patient. A man in his fifties treated with chemoimmunotherapy for chronic lymphocytic leukemia experienced a 9-week course of COVID-19 with high fever and severe viral pneumonia. During two 10-day courses of remdesivir starting 24 and 45 days after fever onset, pneumonia and spiking fevers remitted, but relapsed after discontinuation. Kinetics of temperature, C-reactive protein, and lymphocyte counts mirrored the remitting/relapsing SARS-CoV-2 infection. Combination therapy or longer treatment duration may be needed in immunocompromised patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32702095/ doi: 10.1093/infdis/jiaa446 id: cord-303289-qoukiqr7 author: Hemida, M. G. title: Coronavirus infections in horses in Saudi Arabia and Oman date: 2017-03-13 words: 2807.0 sentences: 151.0 pages: flesch: 61.0 cache: ./cache/cord-303289-qoukiqr7.txt txt: ./txt/cord-303289-qoukiqr7.txt summary: We carried out RT‐PCR on 306 nasal and 315 rectal swabs and tested 243 sera for antibodies to detect coronavirus infections in apparently healthy horses in Saudi Arabia and Oman. RNA extracts were tested for evidence of conserved coronavirus nucleic acid genetic sequences using previously reported RT-PCR assays (Chu et al., 2014) , RTqPCR assay for MERS-CoV upE gene (Corman et al., 2012) , RTqPCR assay for ECoV (Miszczak et al., 2014) , and a RTqPCR assay for HKU23 reported below. T A B L E 5 Cross-neutralization titres (denoted as reciprocal titres) for Middle East respiratory coronavirus (MERS-CoV), bovine coronavirus (BCoV) and equine coronavirus (ECoV) in hyperimmune or naturally infected sera known to be positive for different coronaviruses NR460pig antiserum to porcine respiratory coronavirus 1,200 a <20 <20 <20 <20 Similarly, a BCoV immune serum from an experimentally infected gnotobiotic calf showed detectable, but 16-fold reduced antibody titre with ECoV but no cross-reaction with MERS-CoV. abstract: Equine coronaviruses (ECoV) are the only coronavirus known to infect horses. So far, data on ECoV infection in horses remain limited to the USA, France and Japan and its geographic distribution is not well understood. We carried out RT‐PCR on 306 nasal and 315 rectal swabs and tested 243 sera for antibodies to detect coronavirus infections in apparently healthy horses in Saudi Arabia and Oman. We document evidence of infection with ECoV and HKU23 coronavirus by RT‐PCR. There was no conclusive evidence of Middle East respiratory syndrome coronavirus infection in horses. Serological data suggest that lineage A betacoronavirus infections are commonly infecting horses in Saudi Arabia and Oman but antibody cross‐reactivities between these viruses do not permit us to use serological data alone to identify which coronaviruses are causing these infections. url: https://doi.org/10.1111/tbed.12630 doi: 10.1111/tbed.12630 id: cord-315541-tirod4t6 author: Henriques, Ana Margarida title: Development and validation of a real-time PCR for the detection and quantification of porcine circovirus type 2 date: 2018-07-17 words: 3552.0 sentences: 167.0 pages: flesch: 51.0 cache: ./cache/cord-315541-tirod4t6.txt txt: ./txt/cord-315541-tirod4t6.txt summary: This paper reports the development and validation of a real-time PCR targeted to ORF1 and based on a TaqMan probe for the detection of porcine circovirus type 2 DNA in swine samples. The real-time PCR method described in this paper was performed with DNA from this strain, and an amplification curve with Ct 19.9 was obtained, confirming that such mutation in the probe annealing sequence had no effect in the reaction. The test performed with a plasmid containing the fragment to be amplified in the qPCR, with known The DNA samples used for the determination of the intra-and inter-assay variabilities for medium Ct values was not the same due to the lack of available DNA Fig. 2 Amplification curves obtained in the real-time PCR reaction performed for the determination of the limit of detection. abstract: Porcine circovirus type 2 (PCV2) is a spherical and non-enveloped virus belonging to the genus Circovirus of the Circoviridae family with a single stranded circular DNA genome. This virus, already detected worldwide, has been associated to several diseases and was implicated as the etiological agent of a disease named postweaning multisystemic wasting syndrome. Several methods have been described for the detection of PCV2, being real-time PCR the most simple and reliable. As far as we know, all the real-time PCR systems described until now are based on ORF2 gene, that exhibit the highest variability. This paper reports the development and validation of a real-time PCR targeted to ORF1 and based on a TaqMan probe for the detection of porcine circovirus type 2 DNA in swine samples. Due to the lack of PCV1 samples, the ability of the test to discriminate between PCV1 and PCV2 positive samples was evaluated in silico. Estimations of 100% specificity and 100% sensitivity were obtained based on the qPCR results with panel of 81 swine samples (known PCV2-positive (n = 50); known PCV2-negative (n = 17); samples positive to other common swine viral pathogens (n = 13) and one sample from a BFDV-positive parrot (n = 1)). Intra- and inter-assay coefficients of variation obtained with three positive samples of different viral charges in five replicates or in five independent assays were below the acceptance threshold. The limit of detection determined with a recombinant plasmid containing the amplicon, led to conclude that this assay can detect at least three plasmid copies. url: https://www.ncbi.nlm.nih.gov/pubmed/30159371/ doi: 10.1007/s13337-018-0476-y id: cord-349562-ivu632j2 author: Hernes, S. S. title: Swabbing for respiratory viral infections in older patients: a comparison of rayon and nylon flocked swabs date: 2010-09-18 words: 3364.0 sentences: 185.0 pages: flesch: 55.0 cache: ./cache/cord-349562-ivu632j2.txt txt: ./txt/cord-349562-ivu632j2.txt summary: The purpose of this study was to compare the sampling efficacy of rayon swabs and nylon flocked swabs, and of oropharyngeal and nasopharyngeal specimens for the detection of respiratory viruses in elderly patients. Regardless of the sampling site, a calculated 4.8 times higher viral load (95% confidence interval [CI] 1.3–17, p = 0.017) was obtained using the nylon flocked swabs as compared to the rayon swabs. Samples for the diagnosis of a respiratory viral infection can be obtained by swabbing the oropharynx, the nasal cavity, the nasopharynx or alternatively, by nasopharyngeal aspiration (NPA) or nasopharyngeal washings (NPW). The aim of this study was to compare the respective efficacies of rayon swabs and nylon flocked swabs in providing material for direct respiratory virus detection by real-time PCR in adults above 60 years of age. Using monoplex (RSV and human metapneumovirus) or multiplex (influenza A/B, adenovirus/internal control and parainfluenza virus 1-4) PCR methods, the specimens were examined for, in total, nine different respiratory viruses (Table 2) . abstract: The purpose of this study was to compare the sampling efficacy of rayon swabs and nylon flocked swabs, and of oropharyngeal and nasopharyngeal specimens for the detection of respiratory viruses in elderly patients. Samples were obtained from patients 60 years of age or above who were newly admitted to Sorlandet Hospital Arendal, Norway. The patients were interviewed for current symptoms of a respiratory tract infection. Using rayon swabs and nylon flocked swabs, comparable sets of mucosal samples were harvested from the nasopharynx and the oropharynx. The samples were analysed using real-time polymerase chain reaction (PCR) methods. A total of 223 patients (mean age 74.9 years, standard deviation [SD] 9.0 years) were swabbed and a virus was recovered from 11% of the symptomatic patients. Regardless of the sampling site, a calculated 4.8 times higher viral load (95% confidence interval [CI] 1.3–17, p = 0.017) was obtained using the nylon flocked swabs as compared to the rayon swabs. Also, regardless of the type of swab, a calculated 19 times higher viral load was found in the samples from the nasopharynx as compared to the oropharynx (95% CI 5.4–67.4, p < 0.001). When swabbing for respiratory viruses in elderly patients, nasopharyngeal rather than oropharyngeal samples should be obtained. Nylon flocked swabs appear to be more efficient than rayon swabs. url: https://doi.org/10.1007/s10096-010-1064-2 doi: 10.1007/s10096-010-1064-2 id: cord-352872-y1qh5nig author: Herpe, Guillaume title: Efficacy of Chest CT for COVID-19 Pneumonia in France date: 2020-09-01 words: 3832.0 sentences: 205.0 pages: flesch: 50.0 cache: ./cache/cord-352872-y1qh5nig.txt txt: ./txt/cord-352872-y1qh5nig.txt summary: In France, chest CT in combination with reverse transcriptase-polymerase chain reaction (RT-PCR) testing was effective as a diagnostic tool to assess coronavirus disease 2019 (COVID19) pneumonia in symptomatic patients. The final discharge diagnosis based on a multiparametric item including clinical findings, RT-PCR testing, chest CT imaging, risk level of exposure, local estimated prevalence and biological data, was used as reference standard. The survey included the following parameters: clinical patient data (age, sex), results of initial chest CT and initial and/or repeat RT-PCR tests, time intervals between chest CT and RT-PCR, and final discharge summary according to the hospital discharge report. The final discharge diagnosis was based on multiparametric items, risk level of exposure, local estimated prevalence, symptoms (fever, cough, fatigue, dyspnea, anosmia), evolution during hospitalization for inpatient, Diagnostic accuracy, including sensitivity, specificity, PPV, negative predictive value, and accuracy of chest CT imaging, were calculated using final report as the reference standard. abstract: BACKGROUND: The role and performance of chest CT in the diagnosis of the coronavirus disease 2019 (COVID-19) pandemic remains under active investigation. PURPOSE: To evaluate the French national experience using Chest CT for COVID-19, results of chest CT and RT-PCR were compared together and with the final discharge diagnosis used as reference standard. MATERIALS AND METHODS: A structured CT scan survey (NCT04339686) was sent to 26 hospital radiology departments in France between March 2 and April 24 2020. These dates correspond to the peak of the national COVID-19 epidemic. Radiology departments were selected to reflect the estimated geographical prevalence heterogeneities of the epidemic. All symptomatic patients suspected of having a COVID-19 pneumonia who underwent within 48 hours both initial chest CT and at least one RT-PCR testing were included. The final discharge diagnosis, based on multiparametric items, was recorded. Data for each center were prospectively collected and gathered each week. Test efficacy was determined by using Mann-Whitney Test, Student’s t-test, Chi-square test and Pearson’s correlation. A p value <.05 determined statistical significance. RESULTS: Twenty-six of 26 hospital radiology departments responded to the survey with 7500 patients entered; 2652 did not have RT-PCR results or had unknown or excess delay between RT-PCR and CT. After exclusions, 4824 patients (mean age 64, ± 19 yrs, 2669 males) were included. Using final diagnosis as the reference, 2564 of the 4824 patients were positive for COVID-19 (53%). Sensitivity, specificity, NPV and PPV of chest CT for diagnosing COVID-19 were 2319/2564 (90%, 95% confidence interval [CI]: 89, 91), 2056/2260 (91%, 95%CI: 91, 92%), 2056/2300 (89%, 95%CI; 87, 90%) and 2319/2524 (92%, 95%CI 91, 93%) respectively. There was no significant difference for chest CT efficacy among the 26 geographically separate sites, each with varying amounts of disease prevalence. CONCLUSION: Use of chest CT for the initial diagnosis and triage of suspected COVID-19 patients was successful. url: https://doi.org/10.1148/radiol.2020202568 doi: 10.1148/radiol.2020202568 id: cord-258250-zueo1xfa author: Hirotsu, Yosuke title: Comparison of Automated SARS-CoV-2 Antigen Test for COVID-19 Infection with Quantitative RT-PCR using 313 Nasopharyngeal Swabs Including from 7 Serially Followed Patients date: 2020-08-12 words: 3105.0 sentences: 184.0 pages: flesch: 55.0 cache: ./cache/cord-258250-zueo1xfa.txt txt: ./txt/cord-258250-zueo1xfa.txt summary: title: Comparison of Automated SARS-CoV-2 Antigen Test for COVID-19 Infection with Quantitative RT-PCR using 313 Nasopharyngeal Swabs Including from 7 Serially Followed Patients In summary, the LUMIPULSE antigen test can rapidly identify SARS-CoV-2-infected individuals with moderate to high viral loads and may be helpful for monitoring viral clearance in hospitalized patients. To date, 11 million individuals have been infected with SARS-CoV-2 and 0.52 million patients have died from coronavirus disease 2019 (COVID-19) [2] . We compared the quantitative RT-PCR (RT-qPCR) results for viral load with the CLEIA results for antigen level following testing of 313 nasopharyngeal swabs. We used 100 µL of the supernatant per sample of thawed viral transport media from each nasopharyngeal swab to measure the antigen level with the LUMIPULSE SARS-CoV-2 Ag kit (Fujirebio) on the LUMIPULSE G600II automated immunoassay analyzer (Fujirebio) based on the CLEIA method. We next examined the relationship between the SARS-CoV-2 viral loads (as determined by RT-qPCR) and the antigen levels (Fig 2) . abstract: Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is determined by reverse-transcription PCR (RT-PCR) in routine clinical practice. In the current pandemic situation, a more rapid and high-throughput method is in growing demand. Here, we validated the performance of a new antigen test (LUMIPULSE) based on the chemiluminescence enzyme immunoassay. A total of 313 nasopharyngeal swabs (82 serial samples from 7 infected patients, 231 individual samples from 4 infected patients and 215 non-infected individuals) were analyzed for SARS-CoV-2 by quantitative RT-PCR (RT-qPCR) and then subjected to LUMIPULSE. We determined the cutoff value for antigen detection using receiver operating characteristic curve analysis and compared the antigen test performance with that of RT-qPCR. Further, we compared the viral loads and antigen levels in serial samples from seven infected patients. When using RT-qPCR as the reference, the antigen test exhibited 55.2% sensitivity and 99.6% specificity with a 91.4% overall agreement rate (286/313). In specimens with > 100 viral copies and between 10 and 100 copies, the antigen test showed 100% and 85% concordance with RT-qPCR, respectively. This concordance declined with lower viral loads. In the serially followed patients, the antigen levels showed a steady decline along with viral clearance. This gradual decline was in contrast with the abrupt “positive-to-negative” and “negative-to-positive” status changes observed with RT-qPCR, particularly in the late phase of infection. In summary, the LUMIPULSE antigen test can rapidly identify SARS-CoV-2-infected individuals with moderate to high viral loads and may be helpful for monitoring viral clearance in hospitalized patients. url: https://doi.org/10.1016/j.ijid.2020.08.029 doi: 10.1016/j.ijid.2020.08.029 id: cord-257521-1amcsgmj author: Hirsilä, Maija title: Detection by Reverse Transcription–Polymerase Chain Reaction of Influenza C in Nasopharyngeal Secretions of Adults with a Common Cold date: 2001-04-15 words: 2297.0 sentences: 116.0 pages: flesch: 53.0 cache: ./cache/cord-257521-1amcsgmj.txt txt: ./txt/cord-257521-1amcsgmj.txt summary: All 7 patients had a significant increase in antibody titers between serum samples collected during the acute and convalescent phases of the illness. Only 1 of the 7 patients from whom these samples were obtained was still positive by PCR at the first control visit 1 week later, but a signal was detected only with the NS-1 primer pair. A у8-fold increase between acute-and convalescent-phase serum samples was found in all 7 individuals with PCR-positive results (table 2). All 7 individuals with PCR-positive results had a у8-fold increase in antibody titers between serum samples collected during the acute and convalescent phases of the illness. In addition, 1 study participant with PCR-negative results also had a significant increase in antibody titer (patient 160; table 2). NPAs obtained from the 7 patients with RT-PCR-positive results at the first control visit 1 week after study entry also were tested. abstract: The lack of practical methods for a laboratory diagnosis of influenza C virus infections and the seemingly benign nature of the virus contribute to the fact that 50 years after its first isolation, relatively little is known about the epidemiology and the clinical impact of this virus. Reverse transcription–polymerase chain reaction (RT-PCR) was used to amplify influenza C RNA fragments from clinical specimens. Two hundred otherwise healthy adults with recent onset of a common cold were studied. Nasopharyngeal aspirates were collected at entry to the study and 1 week later. Serum samples for antibody determinations were obtained at the first visit and after 3 weeks. Influenza C was detected in 7 of the 200 patients by 2 different RT-PCR formats. All 7 patients had a significant increase in antibody titers between serum samples collected during the acute and convalescent phases of the illness. Influenza C appears to be one of the many viruses that cause acute upper respiratory tract infections in adults url: https://www.ncbi.nlm.nih.gov/pubmed/11262210/ doi: 10.1086/319675 id: cord-255975-ymw9avlm author: Ho, Yen‐Peng title: Advances in mass spectrometry for the identification of pathogens date: 2011-05-09 words: 15945.0 sentences: 814.0 pages: flesch: 35.0 cache: ./cache/cord-255975-ymw9avlm.txt txt: ./txt/cord-255975-ymw9avlm.txt summary: The direct analysis of whole pathogenic microbial cells with matrix‐assisted laser desorption/ionization MS without sample separation reveals specific biomarkers for taxonomy, and has the advantages of simplicity, rapidity, and high‐throughput measurements. Matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) allows the fast and accurate identification and subtyping of bacterial species (Seng et al., 2009; Stevenson, Drake, & Murray, 2010) , fungi (Marinach-Patrice et al., 2009 , 2010 Santos et al., 2010) , and viruses Franco et al., 2010) . Direct bacterial profiling with MALDI-TOFMS is based mainly on a comparison of specific mass spectra of the proteins, peptides, and other cellular components that are obtained from microbial cells. The development of a matrix-assisted laser desorption/ionization mass spectrometry-based method for the protein fingerprinting and identification of Aeromonas species using whole cells On-probe sample pretreatment for direct analysis of lipids in gram-positive bacterial cells by matrix-assisted laser desorption ionization mass spectrometry Universal sample preparation method for characterization of bacteria by matrix-assisted laser desorption ionization-time of flight mass spectrometry abstract: Mass spectrometry (MS) has become an important technique to identify microbial biomarkers. The rapid and accurate MS identification of microorganisms without any extensive pretreatment of samples is now possible. This review summarizes MS methods that are currently utilized in microbial analyses. Affinity methods are effective to clean, enrich, and investigate microorganisms from complex matrices. Functionalized magnetic nanoparticles might concentrate traces of target microorganisms from sample solutions. Therefore, nanoparticle‐based techniques have a favorable detection limit. MS coupled with various chromatographic techniques, such as liquid chromatography and capillary electrophoresis, reduces the complexity of microbial biomarkers and yields reliable results. The direct analysis of whole pathogenic microbial cells with matrix‐assisted laser desorption/ionization MS without sample separation reveals specific biomarkers for taxonomy, and has the advantages of simplicity, rapidity, and high‐throughput measurements. The MS detection of polymerase chain reaction (PCR)‐amplified microbial nucleic acids provides an alternative to biomarker analysis. This review will conclude with some current applications of MS in the identification of pathogens. © 2010 Wiley Periodicals, Inc., Mass Spec Rev 30:1203–1224, 2011 url: https://doi.org/10.1002/mas.20320 doi: 10.1002/mas.20320 id: cord-274128-kgtr77e7 author: Hochstetter, Axel title: Lab-on-a-Chip Technologies for the Single Cell Level: Separation, Analysis, and Diagnostics date: 2020-04-29 words: 14656.0 sentences: 748.0 pages: flesch: 49.0 cache: ./cache/cord-274128-kgtr77e7.txt txt: ./txt/cord-274128-kgtr77e7.txt summary: Given the vast adaptability of microfluidics to any kind of single or multi-cellular assay [63] , the ability to combine it with various light microscopy techniques [64] , image processing [65] , optical or acoustic traps [53] , generation of chemical gradients [66] , and even cell culture [4, [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] , any cellular or subcellular target seems to be possible for future on-chip diagnostics. If the sample is in the continuous phase, we can separate the target cells either using deterministic lateral displacement (DLD), ratchets, dean-flow, di-electrophoresis, surface acoustic waves (SAW), optical and acoustic tweezers or by using optical density/refractive index. abstract: In the last three decades, microfluidics and its applications have been on an exponential rise, including approaches to isolate rare cells and diagnose diseases on the single-cell level. The techniques mentioned herein have already had significant impacts in our lives, from in-the-field diagnosis of disease and parasitic infections, through home fertility tests, to uncovering the interactions between SARS-CoV-2 and their host cells. This review gives an overview of the field in general and the most notable developments of the last five years, in three parts: 1. What can we detect? 2. Which detection technologies are used in which setting? 3. How do these techniques work? Finally, this review discusses potentials, shortfalls, and an outlook on future developments, especially in respect to the funding landscape and the field-application of these chips. url: https://www.ncbi.nlm.nih.gov/pubmed/32365567/ doi: 10.3390/mi11050468 id: cord-259717-e8ljkv2y author: Holtz, Lori R. title: Geographic variation in the eukaryotic virome of human diarrhea date: 2014-11-01 words: 6748.0 sentences: 349.0 pages: flesch: 49.0 cache: ./cache/cord-259717-e8ljkv2y.txt txt: ./txt/cord-259717-e8ljkv2y.txt summary: Viromes from Northern Territory children contained more viral families per sample than viromes from Melbourne, which could be attributed largely to an increased number of sequences from the families Adenoviridae and Picornaviridae (genus enterovirus). Viromes from Northern Territory children contained more viral families per sample than viromes from Melbourne, which could be attributed largely to an increased number of sequences from the families Adenoviridae and Picornaviridae (genus enterovirus). Because previous metagenomic studies demonstrated significant virus diversity in patients with diarrhea (Finkbeiner et al., 2008) we focused this study on comparing the eukaryotic virus populations in stools of children with diarrhea collected from two different locations, Melbourne, Australia and the Northern Territory, Australia. In order to independently confirm the sequencing results, we used PCR to define the prevalence of the most frequently detected viruses for which pan-family or pan-genus primers could be used including: adenovirus, astrovirus, enterovirus, norovirus, and rotavirus. abstract: Little is known about the population of eukaryotic viruses in the human gut (“virome”) or the potential role it may play in disease. We used a metagenomic approach to define and compare the eukaryotic viromes in pediatric diarrhea cohorts from two locations (Melbourne and Northern Territory, Australia). We detected viruses known to cause diarrhea, non-pathogenic enteric viruses, viruses not associated with an enteric reservoir, viruses of plants, and novel viruses. Viromes from Northern Territory children contained more viral families per sample than viromes from Melbourne, which could be attributed largely to an increased number of sequences from the families Adenoviridae and Picornaviridae (genus enterovirus). qRT-PCR/PCR confirmed the increased prevalence of adenoviruses and enteroviruses. Testing of additional diarrhea cohorts by qRT-PCR/PCR demonstrated statistically different prevalences in different geographic sites. These findings raise the question of whether the virome plays a role in enteric diseases and conditions that vary with geography. url: https://www.ncbi.nlm.nih.gov/pubmed/25262473/ doi: 10.1016/j.virol.2014.09.012 id: cord-029710-ythz9ax0 author: Homayounieh, Fatemeh title: CT Radiomics, Radiologists and Clinical Information in Predicting Outcome of Patients with COVID-19 Pneumonia date: 2020-07-23 words: 3090.0 sentences: 166.0 pages: flesch: 44.0 cache: ./cache/cord-029710-ythz9ax0.txt txt: ./txt/cord-029710-ythz9ax0.txt summary: PURPOSE: To compare prediction of disease outcome, severity, and patient triage in COVID-19 pneumonia with whole lung radiomics, radiologists'' interpretation, and clinical variables. CONCLUSION: Radiomics from non-contrast chest CT were superior to radiologists'' assessment of extent and type of pulmonary opacities in predicting COVID-19 pneumonia outcome, disease severity, and patient triage. We compared prediction of disease outcome, severity, and patient triage in COVID-19 pneumonia with whole lung radiomics, radiologists'' interpretation, and clinical variables. Although prior studies have reported on the ability of visual severity score of COVID-19 pneumonia on chest CT [16, 18, 20] , we found that such qualitative assessment was not as useful as radiomics in predicting ICU admission or patient outcome (recovery versus death). Another limitation of our study pertains to the fact that some patients may have been admitted to the hospital based on severity of symptoms, other comorbidities (such as immunodeficiencies) or positive CT findings rather than an extensive lung changes related to COVID-19 pneumonia. abstract: PURPOSE: To compare prediction of disease outcome, severity, and patient triage in COVID-19 pneumonia with whole lung radiomics, radiologists’ interpretation, and clinical variables. METHODS: Our IRB-approved retrospective study included 315 adult patients (mean age 56 (21-100) years, 190 males, 125 females) with COVID-19 pneumonia who underwent non-contrast chest CT. All patients (inpatients, n=210; outpatients, n=105) were followed up for at least two-weeks to record disease outcome. Clinical variables such as presenting symptoms, laboratory data, peripheral oxygen saturation, and comorbid diseases were recorded. Two radiologists assessed each CT in consensus and graded the extent of pulmonary involvement (by percentage of involved lobe) and type of opacities within each lobe. We obtained radiomics for the entire lung and multiple logistic regression analyses with areas under the curve (AUC) as outputs were performed. RESULTS: Most patients (276/315,88%) recovered from COVID-19 pneumonia; 36/315 patients (11%) died and 3/315 patients (1%) remain admitted in the hospital. Radiomics differentiated chest CT in outpatient vs inpatient with an AUC of 0.84 (p<0.005), while radiologists’ interpretations of disease extent and opacity type had an AUC of 0.69 (p<0.0001). Whole lung radiomics were superior to the radiologists’ interpretation for predicting patient outcome in terms of ICU admission (AUC:0.75 vs 0.68) and death (AUC:0.81 vs 0.68) (p<0.002). Addition of clinical variables to radiomics improved the AUC to 0.84 for predicting ICU admission. CONCLUSION: Radiomics from non-contrast chest CT were superior to radiologists’ assessment of extent and type of pulmonary opacities in predicting COVID-19 pneumonia outcome, disease severity, and patient triage. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7380121/ doi: 10.1148/ryct.2020200322 id: cord-307758-a4sgt66g author: Hong, Ching-Ye title: Acute respiratory symptoms in adults in general practice date: 2004-06-17 words: 3927.0 sentences: 241.0 pages: flesch: 56.0 cache: ./cache/cord-307758-a4sgt66g.txt txt: ./txt/cord-307758-a4sgt66g.txt summary: Community studies have shown that ∼30% of patients with acute respiratory tract symptoms have no identifiable infective aetiology. The purpose of this study was to determine the infective aetiology in patients who presented to primary care doctors with acute respiratory symptoms. Data collection was through interview using structured questionnaire, physical examination, throat swabs for bacterial culture and nasal swabs for virus identification by immunofluorescence (IF) and polymerase chain reaction (PCR). The main objective of our study was therefore to determine the aetiological cause in patients who presented with acute respiratory symptoms in nine primary care clinics in Singapore, using bacterial culture, IF and PCR. To our knowledge, this is the first practice-based study on the aetiological diagnosis of a large group of patients presenting with URTI in primary care clinics in Asia, using IF and PCR as identification methods. abstract: Background. Community studies have shown that ∼30% of patients with acute respiratory tract symptoms have no identifiable infective aetiology. This may not be applicable in general practice. Objective. The purpose of this study was to determine the infective aetiology in patients who presented to primary care doctors with acute respiratory symptoms. Methods. A prospective study was carried out in all nine primary care clinics belonging to the National Healthcare Group Polyclinics (NHGPs) in Singapore. The subjects comprised 594 consecutive patients (318 males, 276 females) aged ≥21 years who presented with complaints of any one of cough, nasal or throat symptoms of <7 days duration. Data collection was through interview using structured questionnaire, physical examination, throat swabs for bacterial culture and nasal swabs for virus identification by immunofluorescence (IF) and polymerase chain reaction (PCR). Additional PCR was performed on a subsample of 100 patients. Patients were followed-up until resolution of symptoms. Results. The aetiological diagnosis by infective agent is as follows: 150 patients (25.2%) had virus infections, of which 90.7% (136/150) were by rhinovirus. Fourteen patients (2.4%) had bacterial infections, of which 10 were due to group G streptococcus. Group A streptococcus was not detected. Nineteen patients with new pathogens were identified by further PCR. These included parainfluenza 4, human coronavirus OC43, adenovirus, enterovirus and Chlamydia pneumoniae. No pathogen could be identified in 49% of patients. There were no differences in clinical presentation and socio-demographic variables between patients who had viral infections and those in whom no pathogen could be identified. Conclusion. In about half of patients who presented at NHGPs, no pathogens could be identified even after PCR. A non-infective aetiology could be considered in these patients. url: https://www.ncbi.nlm.nih.gov/pubmed/15128697/ doi: 10.1093/fampra/cmh319 id: cord-303978-z3888e3g author: Hong, Ka Lok title: Single-Stranded DNA Aptamers against Pathogens and Toxins: Identification and Biosensing Applications date: 2015-06-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Molecular recognition elements (MREs) can be short sequences of single-stranded DNA, RNA, small peptides, or antibody fragments. They can bind to user-defined targets with high affinity and specificity. There has been an increasing interest in the identification and application of nucleic acid molecular recognition elements, commonly known as aptamers, since they were first described in 1990 by the Gold and Szostak laboratories. A large number of target specific nucleic acids MREs and their applications are currently in the literature. This review first describes the general methodologies used in identifying single-stranded DNA (ssDNA) aptamers. It then summarizes advancements in the identification and biosensing application of ssDNA aptamers specific for bacteria, viruses, their associated molecules, and selected chemical toxins. Lastly, an overview of the basic principles of ssDNA aptamer-based biosensors is discussed. url: https://doi.org/10.1155/2015/419318 doi: 10.1155/2015/419318 id: cord-287228-0qm939ve author: Hong, Ke title: Prolonged presence of viral nucleic acid in clinically recovered COVID-19 patients was not associated with effective infectiousness date: 2020-10-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Prolonged presence of viral nucleic acid was reported in certain patients with coronavirus disease 2019 (COVID-19), with unclear clinical and epidemiological significance. We here described the clinical and epidemiological characteristics of 37 recovered COVID-19 patients with prolonged presence of viral RNA in Wuhan, China. For those who had been discharged and re-admitted, their close contacts outside the hospital were traced and evaluated. The median age of the 37 patients was 62 years (IQR 50, 68), and 24 (64.9%) were men. They had common or severe COVID-19. With prolonged positive RT-PCR, most patients were clinically stable, 29 (78.4%) denied any symptoms. A total of 431 PCR tests were carried out, with each patient at a median of 8 time points. The median time of PCR positivity to April 18 was 78 days (IQR 67.7, 84.5), and the longest 120 days. 22 of 37 patients had been discharged at a median of 44 days (IQR 22.3, 50) from disease onset, and 9 had lived with their families without personal protections for a total of 258 person-days and no secondary infection was identified through epidemiological investigation, nucleic acid and antibody screening. Infectiousness in COVID-19 patients with prolonged presence of viral nucleic acid should not solely be evaluated by RT–PCR. Those patients who have clinically recovered and whose disease course has exceeded four weeks were associated with very limited infectiousness. Reconsideration of disease control in such patients is needed. url: https://www.ncbi.nlm.nih.gov/pubmed/32981485/ doi: 10.1080/22221751.2020.1827983 id: cord-254250-l0v602x9 author: Hooper, Chantelle title: A Novel RNA Virus, Macrobrachium rosenbergii Golda Virus (MrGV), Linked to Mass Mortalities of the Larval Giant Freshwater Prawn in Bangladesh date: 2020-10-02 words: 6440.0 sentences: 309.0 pages: flesch: 48.0 cache: ./cache/cord-254250-l0v602x9.txt txt: ./txt/cord-254250-l0v602x9.txt summary: title: A Novel RNA Virus, Macrobrachium rosenbergii Golda Virus (MrGV), Linked to Mass Mortalities of the Larval Giant Freshwater Prawn in Bangladesh De novo virus assembly revealed a 29 kb single-stranded positive-sense RNA virus with similarities in key protein motif sequences to yellow head virus (YHV), an RNA virus that causes mass mortalities in marine shrimp aquaculture, and other viruses in the Nidovirales order. rnaSPAdes assembly of combined libraries produced 38,826 contigs; 23 contigs, of average length 4560 bp, had similarity in protein sequence to YHV or gill-associated virus (GAV), but when the trimmed reads were aligned against the YHV genome (accession number GCA_003972805.1), no alignment was seen. rosenbergii were negative: MrNV and XSV, the causative agents of white tail disease [9, 10] ; MrTV, a virus associated with mass larval mortalities in China [15] , Spiroplasma eriocheiris [8] , and WSSV-shown to be able to infect M. abstract: Mass mortalities of the larval stage of the giant freshwater prawn, Macrobrachium rosenbergii, have been occurring in Bangladesh since 2011. Mortalities can reach 100% and have resulted in an 80% decline in the number of hatcheries actively producing M. rosenbergii. To investigate a causative agent for the mortalities, a disease challenge was carried out using infected material from a hatchery experiencing mortalities. Moribund larvae from the challenge were prepared for metatranscriptomic sequencing. De novo virus assembly revealed a 29 kb single-stranded positive-sense RNA virus with similarities in key protein motif sequences to yellow head virus (YHV), an RNA virus that causes mass mortalities in marine shrimp aquaculture, and other viruses in the Nidovirales order. Primers were designed against the novel virus and used to screen cDNA from larvae sampled from hatcheries in the South of Bangladesh from two consecutive years. Larvae from all hatcheries screened from both years were positive by PCR for the novel virus, including larvae from a hatchery that at the point of sampling appeared healthy, but later experienced mortalities. These screens suggest that the virus is widespread in M. rosenbergii hatchery culture in southern Bangladesh, and that early detection of the virus can be achieved by PCR. The hypothesised protein motifs of Macrobrachium rosenbergii golda virus (MrGV) suggest that it is likely to be a new species within the Nidovirales order. Biosecurity measures should be taken in order to mitigate global spread through the movement of post-larvae within and between countries, which has previously been linked to other virus outbreaks in crustacean aquaculture. url: https://doi.org/10.3390/v12101120 doi: 10.3390/v12101120 id: cord-000979-cav9n18w author: Hoppe, Sebastian title: Rapid Identification of Novel Immunodominant Proteins and Characterization of a Specific Linear Epitope of Campylobacter jejuni date: 2013-05-29 words: 10056.0 sentences: 595.0 pages: flesch: 50.0 cache: ./cache/cord-000979-cav9n18w.txt txt: ./txt/cord-000979-cav9n18w.txt summary: title: Rapid Identification of Novel Immunodominant Proteins and Characterization of a Specific Linear Epitope of Campylobacter jejuni The innovative approach presented herein of generating cDNAs of prokaryotes in combination with a microarray platform rendering time-consuming purification steps obsolete has helped to illuminate novel immunodominant proteins of C.jejuni. Additionally, the structure and antigenicity of the proteins and epitopes were modelled to analyze the suitability of the identified sequences for future applications like diagnostic tools or vaccine development. For a summary of the predicted characteristics, see S9: Transmembrane and antigenic potential of three potential epitope sites for cj0920c.Further, specificity control assays revealed that these signals do not drop significantly when using antibodies to Salmonella enterica indicative of nonspecific binding to occur, see S10: Specific vs. jejuni and were able to determine the important residue involved in antibody binding as well as modelling the epitope''s accessibility within the full-length protein. abstract: Campylobacter jejuni remains one of the major gut pathogens of our time. Its zoonotic nature and wide-spread distribution in industrialized countries calls for a quick and reliable diagnostic tool. Antibody-based detection presents a suitable means to identify pathogenic bacteria. However, the knowledge about immunodominant targets is limited. Thus, an approach is presented, which allows for the rapid screening of numerous cDNA derived expression clones to identify novel antigens. The deeper understanding of immunodominant proteins assists in the design of diagnostic tools and furthers the insight into the bacterium’s pathogenicity as well as revealing potential candidates for vaccination. We have successfully screened 1536 clones of an expression library to identify 22 proteins that have not been described as immunodominant before. After subcloning the corresponding 22 genes and expression of full-length proteins, we investigated the immunodominant character by microarrays and ELISA. Subsequently, seven proteins were selected for epitope mapping. For cj0669 and cj0920c linear epitopes were identified. For cj0669, specificity assays revealed a specific linear epitope site. Consequently, an eleven amino acid residue sequence TLIKELKRLGI was analyzed via alanine scan, which revealed the glycine residue to be significant for binding of the antibody. The innovative approach presented herein of generating cDNAs of prokaryotes in combination with a microarray platform rendering time-consuming purification steps obsolete has helped to illuminate novel immunodominant proteins of C.jejuni. The findings of a specific linear epitope pave the way for a plethora of future research and the potential use in diagnostic applications such as serological screenings. Moreover, the current approach is easily adaptable to other highly relevant bacteria making it a formidable tool for the future discovery of antigens and potential biomarkers. Consequently, it is desirable to simplify the identification of structural epitopes, as this would extend the spectrum of novel epitopes to be detected. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3667084/ doi: 10.1371/journal.pone.0065837 id: cord-001435-ebl8yc92 author: Hoppe, Sebastian title: Identification of Antigenic Proteins of the Nosocomial Pathogen Klebsiella pneumoniae date: 2014-10-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The continuous expansion of nosocomial infections around the globe has become a precarious situation. Key challenges include mounting dissemination of multiple resistances to antibiotics, the easy transmission and the growing mortality rates of hospital-acquired bacterial diseases. Thus, new ways to rapidly detect these infections are vital. Consequently, researchers around the globe pursue innovative approaches for point-of-care devices. In many cases the specific interaction of an antigen and a corresponding antibody is pivotal. However, the knowledge about suitable antigens is lacking. The aim of this study was to identify novel antigens as specific diagnostic markers. Additionally, these proteins might be aptly used for the generation of vaccines to improve current treatment options. Hence, a cDNA-based expression library was constructed and screened via microarrays to detect novel antigens of Klebsiella pneumoniae, a prominent agent of nosocomial infections well-known for its extensive antibiotics resistance, especially by extended-spectrum beta-lactamases (ESBL). After screening 1536 clones, 14 previously unknown immunogenic proteins were identified. Subsequently, each protein was expressed in full-length and its immunodominant character examined by ELISA and microarray analyses. Consequently, six proteins were selected for epitope mapping and three thereof possessed linear epitopes. After specificity analysis, homology survey and 3d structural modelling, one epitope sequence GAVVALSTTFA of KPN_00363, an ion channel protein, was identified harboring specificity for K. pneumoniae. The remaining epitopes showed ambiguous results regarding the specificity for K. pneumoniae. The approach adopted herein has been successfully utilized to discover novel antigens of Campylobacter jejuni and Salmonella enterica antigens before. Now, we have transferred this knowledge to the key nosocomial agent, K. pneumoniae. By identifying several novel antigens and their linear epitope sites, we have paved the way for crucial future research and applications including the design of point-of-care devices, vaccine development and serological screenings for a highly relevant nosocomial pathogen. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4205017/ doi: 10.1371/journal.pone.0110703 id: cord-328526-es8t6t0j author: Hoppes, Sharman title: The Isolation, Pathogenesis, Diagnosis, Transmission, and Control of Avian Bornavirus and Proventricular Dilatation Disease date: 2010-08-02 words: 5502.0 sentences: 326.0 pages: flesch: 54.0 cache: ./cache/cord-328526-es8t6t0j.txt txt: ./txt/cord-328526-es8t6t0j.txt summary: Since its discovery, avian bornavirus (ABV) has been successfully cultured from the brains of psittacines diagnosed with PDD, providing a source of antigen for serologic assays and nucleic acid for molecular assays. Subsequently the authors have isolated ABV by culture in duck embryo fibroblasts using material from the brains of 5 additional birds with necropsy-confirmed PDD (Fig. 2) . Lierz and colleagues 34 have also shown that apparently healthy birds within an aviary where clinical cases were occurring were also shedding ABV as detected by fecal swabs. Diagnostic tests such as Western blots or fecal PCR can identify many, but not all ABV-infected birds, and should be employed to control the spread of this disease. Advances in understanding of proventricular dilation disease (PDD): detection of virus and viral nucleic acid in infected birds Unususal and severe lesions of proventricular dilatation disease in Cockatiels (Nymphicus hollandicus) as healthy carriers of avian bornavirus and subsequently infected with a virulent strain of the same ABV genotype. abstract: Proventricular dilatation disease (PDD) is a common infectious neurologic disease of birds comprising a dilatation of the proventriculus by ingested food as a result of defects in intestinal motility, which affects more than 50 species of psittacines, and is also known as Macaw wasting disease, neuropathic ganglioneuritis, or lymphoplasmacytic ganglioneuritis. Definitive diagnosis of PDD has been problematic due to the inconsistent distribution of lesions. Since its discovery, avian bornavirus (ABV) has been successfully cultured from the brains of psittacines diagnosed with PDD, providing a source of antigen for serologic assays and nucleic acid for molecular assays. This article provides evidence that ABV is the etiologic agent of PDD. Recent findings on the transmission, epidemiology, pathogenesis, diagnosis, and control of ABV infection and PDD are also reviewed. url: https://api.elsevier.com/content/article/pii/S1094919410000769 doi: 10.1016/j.cvex.2010.05.014 id: cord-328409-px92ff89 author: Hornuss, Daniel title: COVID-19-assoziierte Pneumonie trotz persistierend negativen PCR-Tests aus oropharyngealen Abstrichen date: 2020-05-13 words: 1575.0 sentences: 172.0 pages: flesch: 42.0 cache: ./cache/cord-328409-px92ff89.txt txt: ./txt/cord-328409-px92ff89.txt summary: After the first PCR turned in negative another PCR-analysis for SARS-CoV-2 of a deep oral swab-sample was performed since the clinical, laboratory and radiological findings were typical for COVID-19. After the first PCR turned in negative another PCR-analysis for SARS-CoV-2 of a deep oral swab-sample was performed since the clinical, laboratory and radiological findings were typical for COVID-19. After a third attempt for a PCR-analysis of a deep oral swab-sample was negative, analysis of a sputum was performed which finally confirmed the diagnosis of COVID-19 associated pneumonia. After a third attempt for a PCR-analysis of a deep oral swab-sample was negative, analysis of a sputum was performed which finally confirmed the diagnosis of COVID-19 associated pneumonia. Als Diagnostik der Wahl zur schnellen Identifikation von COVID-19-Fällen hat sich dabei die PCR-Analyse auf SARS-CoV-2 aus tiefen nasopharyngealen oder oropharyngealen Abstrichen etabliert [3] . abstract: Patient history and clinical findings A 46-year old construction worker presented at the emergency department with two orthostatic syncopes. The patient complained of prolonged fever and coughs for 7 days which had not improved after oral treatment with sultamicillin for 5 days, prescribed by the patient’s general practitioner. Physical examination showed high blood pressure due to previously known hypertension. Other vital signs without pathological findings. Pulmonary auscultation showed basal soft crackling noises of the left lung Findings and Diagnosis Laboratory examination showed increased values for LDH, pro-BNP and CRP and normal values for leucocytes and procalcitonin. Conventional X-Ray of the chest showed bipulmonal lateral atypical infiltrates. After the first PCR turned in negative another PCR-analysis for SARS-CoV-2 of a deep oral swab-sample was performed since the clinical, laboratory and radiological findings were typical for COVID-19. Again, SARS-CoV-2-RNA was not detected. A CT-scan of the chest showed bipulmonal lateral ground-glass attenuation, again typical for COVID-19 associated pneumonia. After a third attempt for a PCR-analysis of a deep oral swab-sample was negative, analysis of a sputum was performed which finally confirmed the diagnosis of COVID-19 associated pneumonia. Therapy and Course of events The patient was admitted for evaluation of syncopes and suspect of COVID-19 associated pneumonia. The patient was prophylactically isolated while the result of SARS-CoV-2-PCR from a deep oral swab was pending. Suspecting a possible secondary bacterial infection at the beginning, intravenous antibiotic treatment with ampicillin/sulbactam was initiated. While further examinations showed no indication for bacterial infection, antibiotics were discontinued after 3 days. Due to clinical recovery antiviral therapy was not performed after confirming the diagnosis. The patient was discharged 17 days after onset of first symptoms without any requirements for further isolation. Conclusion This casuistic describes a case of COVID-19 associated pneumonia presenting with typical clinical features, laboratory and radiological findings. Detection of viral RNA was not successful from deep oral swab-samples despite repeated attempts. Finally, PCR-analysis of sputum confirmed the diagnosis. Analysis of deeper airway samples (sputum, bronchoalveolar lavage, tracheal secretions) or stool for SARS-CoV-2 should be performed in cases of evident clinical suspicion of COVID-19 and negative PCR results from deep oral swabs. url: https://doi.org/10.1055/a-1170-6061 doi: 10.1055/a-1170-6061 id: cord-276368-c9e93h0u author: Hosmillo, Myra D.T. title: Development of universal SYBR Green real-time RT-PCR for the rapid detection and quantitation of bovine and porcine toroviruses date: 2010-06-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Toroviruses (ToVs) are a group of emerging viruses that cause gastroenteritis in domestic animals and humans. Currently, methods such as real-time reverse transcription-polymerase chain reaction (real-time RT-PCR) have not yet been developed for the rapid detection and quantitation of bovine (BToV) and porcine (PToV) toroviruses. Using BToV and PToV RNA standards generated by in vitro transcription, the detection limit of the SYBR Green real-time RT-PCR assay was 2.54 × 10(2) BToV and 2.17 × 10(3) PToV copies/reaction (correlation coefficiency = 0.99 and 0.97, respectively), whereas those of RT-PCR and nested PCR were 2.54 × 10(5) and 2.54 × 10(4) (BToV) and 2.17 × 10(7) and 2.17 × 10(5) (PToV) cRNA viral copies/reaction, respectively. Archived diarrhea specimens of calves (n = 121) and piglets (n = 86) were subjected to RT-PCR, nested PCR and SYBR Green real-time RT-PCR. By conventional RT-PCR, 1 (0.8%) bovine and 7 (8.1%) porcine samples tested positive to BToV and PToV, respectively. With nested PCR, 13 (10.7%) bovine and 17 (19.8%) porcine samples tested positive. SYBR Green real-time RT-PCR assay detected BToV and PToV in 22 of 121 (18.2%) bovine and 31 of 86 (36.0%) porcine samples. These results indicate that SYBR Green real-time RT-PCR (P < 0.05) is a more sensitive assay, which can be reproduced as a reliable, sensitive, and rapid tool for the detection and quantitation of toroviruses. url: https://api.elsevier.com/content/article/pii/S0166093410002132 doi: 10.1016/j.jviromet.2010.06.001 id: cord-261237-0hbijukt author: Hou, Peili title: Development of a recombinase polymerase amplification combined with lateral-flow dipstick assay for detection of bovine ephemeral fever virus date: 2017-12-26 words: 4858.0 sentences: 254.0 pages: flesch: 51.0 cache: ./cache/cord-261237-0hbijukt.txt txt: ./txt/cord-261237-0hbijukt.txt summary: title: Development of a recombinase polymerase amplification combined with lateral-flow dipstick assay for detection of bovine ephemeral fever virus In this study, we described the development of lateral-flow dipstick isothermal recombinase polymerase amplification (LFD-RPA) assays for detection of BEFV. In this study, we aimed to develop the lateral flow dipsticks recombinase polymerase amplification (LFD-RPA) assays for rapid detection of BEFV. The results of those assays showed that a total of 83 clinical specimens were tested positive by conventional RT-PCR, while the similar performance that 96 specimens were detected positive by BEFV RPA nucleic acid amplification assays on LFD within 5 min, and 95 specimens were positive with the C t values below 35 using the real-time qPCR assay. As the applications of LFD-RPA, conventional RT-PCR and real time qPCR methods for detection BEFV genomes from clinical samples (Table 2) , the results clearly indicated the potential benefits of the developed assay over PCR-based methods. abstract: Bovine ephemeral fever virus (BEFV), identified as the causative pathogen of bovine ephemeral fever (BEF), is responsible for increasing numbers of epidemics/outbreaks and has a significant harmful effect on the livestock industry. Therefore, a rapid detection assay is imperative for BEFV diagnosis. In this study, we described the development of lateral-flow dipstick isothermal recombinase polymerase amplification (LFD-RPA) assays for detection of BEFV. RPA primers and LF probes were designed by targeting the specific G gene, and the amplification product can be visualized on a simple lateral flow dipstick with the naked eyes. The amplification reaction was performed at 38 °C for 20 min and LFD incubation time within 5 min. The detection limit of this assay was 8 copies per reaction, and there was no cross-reactivity with other bovine infectious viruses such as bovine viral diarrhea virus, infectious bovine rhinotracheitis virus, bovine respiratory syncytial virus, bovine coronavirus, bovine parainfluenza virus type 3, bovine vesicular stomatitis virus. In addition, the assay was performed with total 128 clinical specimens and the diagnostic results were compared with conventional RT-PCR, real-time quantative(q) PCR. The result showed that the coincidence rate of BEFV LFD-RPA and real-time qPCR was 96.09% (123/128), which was higher than conventional RT-PCR. The RPA combined with LFD assay probably provides a rapid and sensitive alternative for diagnosis of BEFV infections outbreak. url: https://api.elsevier.com/content/article/pii/S0890850817301214 doi: 10.1016/j.mcp.2017.12.003 id: cord-341141-bgrgzfoo author: Hou, Peili title: Rapid detection of infectious bovine Rhinotracheitis virus using recombinase polymerase amplification assays date: 2017-12-13 words: 4693.0 sentences: 234.0 pages: flesch: 51.0 cache: ./cache/cord-341141-bgrgzfoo.txt txt: ./txt/cord-341141-bgrgzfoo.txt summary: In this study, we described the development of a lateral flow dipstrip (LFD) of isothermal recombinase polymerase amplification (RPA) method for rapid detection of IBRV. The assay performance on acute-phase high fever clinical samples collected from cattle with no vaccine against IBRV, which were suspected to be infected with IBRV, was validated by detecting 24 fecal, 36 blood, 38 nasal swab and 8 tissue specimens, and compared with SYBR Green I based real-time PCR. The initial agarose gel result showed that Primer set 4-2F/4-2R/ 4-2LF yielded specific amplification efficiency for the RPA assay, and produced the expected size of the product was 250 base-pairs (Fig. 1a) , while the primers/probe targeting glycoprotein gB of the IBRV genome in this study could not be used to amplify effectively in the initial screen (data not show). abstract: BACKGROUND: Infectious bovine rhinotracheitis virus (IBRV) is a major pathogen in cattle and has led to significant economic losses to the dairy industry worldwide, and therefore a more optimal method for the rapid diagnosis of IBRV infection is highly needed. In this study, we described the development of a lateral flow dipstrip (LFD) of isothermal recombinase polymerase amplification (RPA) method for rapid detection of IBRV. METHODS: Distinct regions were selected as a candidate target for designing the LFD-RPA primers and probes. The analytical sensitivity of the RPA assay was determined using ten-fold serially diluted IBRV DNA. The specificity of the assay was assessed with other viral pathogens of cattle with similar clinic and other herpesviruses. The clinical performance was evaluated by testing 106 acute-phase high fever clinical specimens. RESULTS: RPA primers and probe were designed to target the specific conserved UL52 region fragment of IBRV. The detection could be completed at a constant temperature of 38 °C for 25 min, and the amplification products were easily visualized on a simple LFD. The detection limit of this assay was 5 copies per reaction of IBRV DNA and there was no cross-reactivity with other viruses causing bovine gastrointestinal and respiratory infections or other herpesviruses. The assay performance on acute-phase high fever clinical samples collected from cattle with no vaccine against IBRV, which were suspected to be infected with IBRV, was validated by detecting 24 fecal, 36 blood, 38 nasal swab and 8 tissue specimens, and compared with SYBR Green I based real-time PCR. The coincidence between IBRV LFD-RPA and real-time PCR was 100%. CONCLUSION: IBRV LFD-RPA was fast and much easier to serve as an alternative to the common measures used for IBRV diagnosis, as there is reduction in the use of instruments for identification of the infected animals. In addition, this assay may be the potential candidate to be used as point-of-care diagnostics in the field. url: https://www.ncbi.nlm.nih.gov/pubmed/29237466/ doi: 10.1186/s12917-017-1284-0 id: cord-296309-i1mpov7k author: Houldcroft, Charlotte J. title: Clinical and biological insights from viral genome sequencing date: 2017-01-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Whole-genome sequencing (WGS) of pathogens is becoming increasingly important not only for basic research but also for clinical science and practice. In virology, WGS is important for the development of novel treatments and vaccines, and for increasing the power of molecular epidemiology and evolutionary genomics. In this Opinion article, we suggest that WGS of viruses in a clinical setting will become increasingly important for patient care. We give an overview of different WGS methods that are used in virology and summarize their advantages and disadvantages. Although there are only partially addressed technical, financial and ethical issues in regard to the clinical application of viral WGS, this technique provides important insights into virus transmission, evolution and pathogenesis. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nrmicro.2016.182) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1038/nrmicro.2016.182 doi: 10.1038/nrmicro.2016.182 id: cord-278176-o9glkhyv author: Houng, Huo-Shu H title: Development and evaluation of an efficient 3′-noncoding region based SARS coronavirus (SARS-CoV) RT-PCR assay for detection of SARS-CoV infections date: 2004-09-01 words: 4782.0 sentences: 226.0 pages: flesch: 54.0 cache: ./cache/cord-278176-o9glkhyv.txt txt: ./txt/cord-278176-o9glkhyv.txt summary: The SARS-CoV cDNA preparations derived from viral RNA extract and the cloned recombinant plasmid both exhibit the identical amplification characteristics, i.e. amplification efficacy using the same PCR formulation developed in this study. The 3′-NCR based SARS-CoV assay demonstrated 100% diagnostic specificity testing samples of patients with acute respiratory disease from a non-SARS epidemic region. It was demonstrated that the RT-PCR assay with 91% amplification efficiency could be used for consistent detect ion of the SARS-CoV viral RNA extracted from samples containing as little as 0.005 pfu per reaction with an anticipated C T value of 40 cycles (data not shown). It was demonstrated in this study that the cloned pHCV1 plasmid could be used to replace viral cDNA as a stable and rational SARS-CoV copy number standard for the SARS-CoV RT-PCR assay. Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays abstract: The severe acute respiratory syndrome (SARS) epidemic originating from China in 2002 was caused by a previously uncharacterized coronavirus that could be identified by specific RT-PCR amplification. Efforts to control future SARS outbreaks depend on the accurate and early identification of SARS-CoV infected patients. A real-time fluorogenic RT-PCR assay based on the 3′-noncoding region (3′-NCR) of SARS-CoV genome was developed as a quantitative SARS diagnostic tool. The ideal amplification efficiency of a sensitive SARS-CoV RT-PCR assay should yield an E value (PCR product concentration increase per amplification cycle) equal to 2.0. It was demonstrated that the 3′-NCR SARS-CoV based RT-PCR reactions could be formulated to reach excellent E values of 1.81, or 91% amplification efficacy. The SARS-CoV cDNA preparations derived from viral RNA extract and the cloned recombinant plasmid both exhibit the identical amplification characteristics, i.e. amplification efficacy using the same PCR formulation developed in this study. The viral genomic copy (or genomic equivalences, GE) per infectious unit (GE/pfu) of SARS-CoV used in this study was also established to be approximate 1200–1600:1. The assay’s detection sensitivity could reach 0.005 pfu or 6–8 GE per assay. It was preliminarily demonstrated that the assay could efficiently detect SARS-CoV from clinical specimens of SARS probable and suspected patients identified in Taiwan. The 3′-NCR based SARS-CoV assay demonstrated 100% diagnostic specificity testing samples of patients with acute respiratory disease from a non-SARS epidemic region. url: https://www.ncbi.nlm.nih.gov/pubmed/15234807/ doi: 10.1016/j.jviromet.2004.04.008 id: cord-340046-kgbvld0y author: Houspie, Lieselot title: Exhaled breath condensate sampling is not a new method for detection of respiratory viruses date: 2011-03-04 words: 4081.0 sentences: 219.0 pages: flesch: 53.0 cache: ./cache/cord-340046-kgbvld0y.txt txt: ./txt/cord-340046-kgbvld0y.txt summary: BACKGROUND: Exhaled breath condensate (EBC) sampling has been considered an inventive and novel method for the isolation of respiratory viruses. RESULTS: Viral screening resulted in the detection of 4 different viruses in EBC and/or nasal swabs: Rhinovirus, Human Respiratory Syncytial Virus B, Influenza A and Influenza B. This observation has created a growing interest in the use of EBC as a new sampling method for the screening of respiratory viruses infecting the upper airways. The aim of this study was to investigate whether the EBC collection method was suited for the efficient condensation of aerosolised virus particles during normal breathing and to explore the isolation of respiratory viruses in the condensate. In this study, 102 EBCs were collected from otherwise healthy volunteers showing respiratory or flu-like symptoms (defined in Table 1 ), using a commercially available condenser (RTube™, Respiratory Research Inc., Charlottesville, Virginia, USA). Collection of exhaled breath condensates is a novel and non-invasive method for obtaining samples of the upper respiratory tract. abstract: BACKGROUND: Exhaled breath condensate (EBC) sampling has been considered an inventive and novel method for the isolation of respiratory viruses. METHODS: In our study, 102 volunteers experiencing upper airway infection were recruited over the winter and early spring of 2008/2009 and the first half of the winter of 2009/2010. Ninety-nine EBCs were successfully obtained and screened for 14 commonly circulating respiratory viruses. To investigate the efficiency of virus isolation from EBC, a nasal swab was taken in parallel from a subset of volunteers. The combined use of the ECoVent device with the RTube™ allowed the registration of the exhaled volume and breathing frequency during collection. In this way, the number of exhaled viral particles per liter air or per minute can theoretically be estimated. RESULTS: Viral screening resulted in the detection of 4 different viruses in EBC and/or nasal swabs: Rhinovirus, Human Respiratory Syncytial Virus B, Influenza A and Influenza B. Rhinovirus was detected in 6 EBCs and 1 EBC was Influenza B positive. We report a viral detection rate of 7% for the EBCs, which is much lower than the detection rate of 46.8% observed using nasal swabs. CONCLUSION: Although very promising, EBC collection using the RTube™ is not reliable for diagnosis of respiratory infections. url: https://www.ncbi.nlm.nih.gov/pubmed/21375748/ doi: 10.1186/1743-422x-8-98 id: cord-291916-5yqc3zcx author: Hozhabri, Hossein title: The Global Emergency of Novel Coronavirus (SARS-CoV-2): An Update of the Current Status and Forecasting date: 2020-08-05 words: 16737.0 sentences: 847.0 pages: flesch: 45.0 cache: ./cache/cord-291916-5yqc3zcx.txt txt: ./txt/cord-291916-5yqc3zcx.txt summary: abstract: Over the past two decades, there have been two major outbreaks where the crossover of animal Betacoronaviruses to humans has resulted in severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). In December 2019, a global public health concern started with the emergence of a new strain of coronavirus (SARS-CoV-2 or 2019 novel coronavirus, 2019-nCoV) which has rapidly spread all over the world from its origin in Wuhan, China. SARS-CoV-2 belongs to the Betacoronavirus genus, which includes human SARS-CoV, MERS and two other human coronaviruses (HCoVs), HCoV-OC43 and HCoV-HKU1. The fatality rate of SARS-CoV-2 is lower than the two previous coronavirus epidemics, but it is faster spreading and the large number of infected people with severe viral pneumonia and respiratory illness, showed SARS-CoV-2 to be highly contagious. Based on the current published evidence, herein we summarize the origin, genetics, epidemiology, clinical manifestations, preventions, diagnosis and up to date treatments of SARS-CoV-2 infections in comparison with those caused by SARS-CoV and MERS-CoV. Moreover, the possible impact of weather conditions on the transmission of SARS-CoV-2 is also discussed. Therefore, the aim of the present review is to reconsider the two previous pandemics and provide a reference for future studies as well as therapeutic approaches. url: https://doi.org/10.3390/ijerph17165648 doi: 10.3390/ijerph17165648 id: cord-350890-ajxvjkmq author: Hsieh, Yi-Fan title: A real-time convective PCR machine in a capillary tube instrumented with a CCD-based fluorometer date: 2013-07-05 words: 4214.0 sentences: 207.0 pages: flesch: 47.0 cache: ./cache/cord-350890-ajxvjkmq.txt txt: ./txt/cord-350890-ajxvjkmq.txt summary: This research reports the design, analysis, integration, and test of a prototype of a real-time convective polymerase chain reaction (RT-cPCR) machine that uses a color charged coupled device (CCD) for detecting the emission of fluorescence intensity from an RT-cPCR mix in a microliter volume glass capillary. The measured results from the image-processing scheme indicate that the RT-cPCR prototype with a CCD-based fluorometer can achieve similar DNA quantification reproducibility compared to commercial machines, even when the initial DNA concentration in the test PCR mix is reduced to 10 copies/μL To assess the performance of the prototype, a single DNA template, HBV 122 base pairs, with known concentrations and a single labeling dye, SYBR Green I, was used in the PCR mixes undergoing the same thermal cycling in both the prototype and commercial RT-PCR machines for comparing their measured and predicted fluorescence intensities emitted from the glass capillaries. abstract: This research reports the design, analysis, integration, and test of a prototype of a real-time convective polymerase chain reaction (RT-cPCR) machine that uses a color charged coupled device (CCD) for detecting the emission of fluorescence intensity from an RT-cPCR mix in a microliter volume glass capillary. Because of its simple mechanism, DNA amplification involves employing the cPCR technique with no need for thermocycling control. The flow pattern and temperature distribution can greatly affect the cPCR process in the capillary tube, a computational fluid dynamics (CFD) simulation was conducted in this study for the first time to estimate the required period of an RT-cPCR cycle. This study also tested the PCR mix containing hepatitis B virus (HBV) plasmid samples by using SYBR Green I fluorescence labeling dye to assess the prototype performance. The measured results from the image-processing scheme indicate that the RT-cPCR prototype with a CCD-based fluorometer can achieve similar DNA quantification reproducibility compared to commercial machines, even when the initial DNA concentration in the test PCR mix is reduced to 10 copies/μL url: https://doi.org/10.1016/j.snb.2013.04.003 doi: 10.1016/j.snb.2013.04.003 id: cord-260231-vayxg23a author: Hsien Koh, Tse title: Epidemiology of Clostridium difficile infection in a large teaching hospital in Singapore date: 2007-08-31 words: 3314.0 sentences: 224.0 pages: flesch: 58.0 cache: ./cache/cord-260231-vayxg23a.txt txt: ./txt/cord-260231-vayxg23a.txt summary: Summary Aims We undertook this study to define the incidence of toxigenic Clostridium difficile in our hospital and to characterise the isolates. Detection of tcdA and tcdB genes was carried out for A2B+ strains by polymerase chain reaction (PCR).The minimum inhibitory concentrations (MICs) of metronidazole, vancomycin and clindamycin for all isolates were tested using the Etest. All unformed stool from SGH inpatients sent to the Department of Pathology from 1 October 2002 to 28 February 2003 was tested for the presence of TcdA and TcdB using the Premier Toxin A and B enzyme immunoassay (EIA) kit (Meridian Diagnostics, USA) following the manufacturer''s instructions. Combining the numbers of toxigenic strains and culture negative/direct toxin positive specimens, the incidence of CDAD was 3.2 cases per 1000 admissions or discharges and 53.8 cases per 100 000 patient days. Clindamycin resistant strains of Clostridium difficile isolated from cases of C. abstract: Summary Aims We undertook this study to define the incidence of toxigenic Clostridium difficile in our hospital and to characterise the isolates. Methods All unformed stool was tested for the presence of Toxin A (TcdA) and Toxin B (TcdB), and cultured for C. difficile. Culture filtrates were also tested for TcdA and TcdB. Detection of tcdA and tcdB genes was carried out for A2B+ strains by polymerase chain reaction (PCR).The minimum inhibitory concentrations (MICs) of metronidazole, vancomycin and clindamycin for all isolates were tested using the Etest. PCR ribotyping was carried out on all isolates. Results The incidence of Clostridium difficile associated disease (CDAD) was 3.2 cases per 1000 admissions or discharges and 53.8 cases per 100000 patient days. Most cases occurred in renal and haematology patients. CDAD was more common in patients aged over 50 years and of male gender. The Indian population was under-represented. Fourteen (11.8%) isolates were A-B+. All strains were susceptible to metronidazole but one strain showed intermediate resistance to vancomycin. Only 12.8% of the isolates were susceptible to clindamycin. Thirty-five isolates had PCR ribotype A, of which 29 (83%) had a clindamycin MIC >256mg/L. Thirty-three had PCR ribotype B, of which only one (3%) had a clindamycin MIC >256mg/L. The 14 A-B+ strains were all PCR ribotype C, and had a range of MICs for clindamycin from 2 to >256mg/L. Conclusions: The incidence of CDAD in our hospital is relatively low. Isolates remain susceptible to metronidazole and vancomycin. url: https://api.elsevier.com/content/article/pii/S0031302516337679 doi: 10.1080/00313020701444507 id: cord-015941-4fz79wzf author: Hu, Yuan title: Molecular Techniques for Blood and Blood Product Screening date: 2018-11-10 words: 7210.0 sentences: 381.0 pages: flesch: 50.0 cache: ./cache/cord-015941-4fz79wzf.txt txt: ./txt/cord-015941-4fz79wzf.txt summary: Through the application of molecular biology, biological and biochemical analyses have been revolutionized, and nucleic acid, gene-based techniques have been developed to screen blood and plasma donations for evidence of very recent and earlier viral infections that might otherwise be missed by conventional serologic testing. Because NAT detects a virus''s genetic material instead of waiting for the body''s response, the formation of antibodies, as with many current tests, it offers the opportunity to reduce the window period during which an infecting agent is undetectable by traditional tests [21] , thus further improving blood safety. One reason for this is that currently available blood screening technologies detect core antibodies or surface antigens, which appear up to 8 weeks after infection. The anti-HBc test developed in 1987 detects an antibody to the hepatitis B virus that is produced during and after infection. Detection of HIV-1 and HCV infections among antibody-negative blood donors by nucleic acid-amplification testing abstract: Blood product safety is a high priority for manufacturing industries, hospitals, and regulatory agencies. An important step in ensuring safety is the screening of donated blood for infectious diseases. Molecular technologies for screening infectious diseases have improved remarkably over the years. Molecular biological assay significantly reduced the risk of transfusion-transmitted infections. Unlike previous methods, molecular technologies for screening infectious diseases are specific, efficient, easy to use, and economical. A new era in molecular biology is coming to the field of blood safety. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120069/ doi: 10.1007/978-3-319-95111-9_2 id: cord-017948-fqhl1qb4 author: Hu, Yuan title: Molecular Techniques for Blood and Blood Product Screening date: 2012-04-05 words: 7304.0 sentences: 372.0 pages: flesch: 54.0 cache: ./cache/cord-017948-fqhl1qb4.txt txt: ./txt/cord-017948-fqhl1qb4.txt summary: Currently, nucleic acid testing techniques have been developed to screen blood and plasma products for evidence of very recent viral infections that could be missed by conventional serologic tests. Through the application of molecular biology, biological and biochemical analyses have been revolutionized, and nucleic acid, gene-based techniques have been developed to screen blood and plasma donations for evidence of very recent and earlier viral infections that might otherwise be missed by conventional serologic testing. Because NAT detects a virus''s genetic material instead of waiting for the body''s response, the formation of antibodies, as with many current tests, it offers the opportunity to reduce the window period during which an infecting agent is undetectable by traditional tests [ 19 ] , thus further improving blood safety. Detection of HIV-1 and HCV infections among antibody-negative blood donors by nucleic acid-ampli fi cation testing abstract: The Food and Drug Administration (FDA) is responsible for ensuring the safety of the more than 15 million units of blood and blood components donated each year in the United States. “Blood banking has become a manufacturing industry, an industry that must conform to high standards and quality control requirements comparable to those of pharmaceutical companies or other regulated industries,” said David A. Kessler, MD, former FDA commissioner [1]. Screening donated blood for infectious diseases that can be transmitted through blood transfusion is a very important step in ensuring safety. The United States has the safest blood supply in the world [1] and the FDA is striving to keep it safe by decreasing the risk of infectious disease transmission. The regulatory agency is continuously updating its requirements and standards for collecting and processing blood. As mentioned earlier, an important step in ensuring safety is the screening of donated blood for infectious diseases. In the United States, tests for infectious diseases are routinely conducted on each unit of donated blood, and these tests are designed to comply with regulatory requirements (Table 28.1). The field of clinical microbiology and virology are now focusing on molecular technology. Currently, nucleic acid testing techniques have been developed to screen blood and plasma products for evidence of very recent viral infections that could be missed by conventional serologic tests. It is time for all blood safety procedures to include molecular detection techniques. This approach can significantly aid in blood safety to reduce the risk of transmission of serious disease by transfusion. This chapter reviews the current antigen/antibody-based technology, molecular biological technology, and published regulatory policy data for blood safety. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122649/ doi: 10.1007/978-1-4614-3970-7_28 id: cord-310095-1pxki8y8 author: Huang, Huanhuan title: Detection and clinical characteristics analysis of respiratory viruses in hospitalized children with acute respiratory tract infections by a GeXP‐based multiplex‐PCR assay date: 2019-11-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: The information regarding viral epidemiology and clinical characteristics in hospitalized children with acute respiratory tract infection (ARTI) in central Fujian is limited. In this study, we aimed at analyzing the viral epidemiology and clinical characteristics of ARTI in hospitalized children admitted to The First Affiliated Hospital of Fujian Medical University. METHODS: Cohort of 386 hospitalized children (31 days to 15 years) diagnosed with ARTI admitted to the Department of Pediatrics from January 1, 2018, to December 31, 2018, was enrolled in this study. Nasopharyngeal swab or sputum samples on the day of hospitalization were tested for 11 viruses via a GeXP‐based multiplex‐PCR assay. The viral profiles and clinical characteristics were analyzed. RESULTS: The overall positive rate of the samples was 43.26% (167/386). Among the 167 positive samples, 134 (80.24%, 134/167) had a single virus and 33 (19.76%, 33/167) had multiple viruses. There was a significant difference in the frequency of single vs mixed infections among positive samples (80.24% vs 19.76%; χ (2) = 122.168, P = .000) as well as among the total examined samples (34.72% vs 8.55%; χ (2) = 77.945, P = .000). Human rhinovirus was the most prevalent virus (17.36%, 67/386), followed by influenza A (5.96%, 23/386) and human adenovirus (5.70%, 22/386). There was no significant difference in the etiological distribution of viral pathogens between males and females (χ (2) = 0.480, P = .489). Viral infections were more likely to occur in the winter‐spring months than in the summer‐autumn months (52.51% vs 33.53%, χ (2) = 13.830, P = .000). CONCLUSIONS: The GeXP‐based multiplex PCR is an accurate and high‐throughput assay allows us to quickly detect multiple respiratory viruses simultaneously in pediatric patients. Our study provides information on the viral profiles and clinical characteristics in hospitalized children with ARTI, which would help better effective prevention strategies. url: https://www.ncbi.nlm.nih.gov/pubmed/31774213/ doi: 10.1002/jcla.23127 id: cord-303986-9g24xg9x author: Huang, W. title: A CRISPR-Cas12a-based specific enhancer for more sensitive detection of SARS-CoV-2 infection date: 2020-06-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: High Ct-values falling in the grey zone are frequently encountered in SARS-CoV-2 detection by real-time reverse transcription PCR (rRT-PCR) and have brought urgent challenges in diagnosis of samples with low viral load. Based on the single-stranded DNA reporter trans-cleavage activity by Cas12a upon target DNA recognition, we create a Specific Enhancer for detection of PCR-amplified Nucleic Acids (SENA) to confirm SARS-CoV-2 detection through specifically targeting its rRT-PCR amplicons. SENA is highly sensitive, with its limit of detection being at least 2 copies/reaction lower than that of the corresponding rRT-PCR, and highly specific, which identifies both false-negative and false-positive cases in clinic applications. SENA provides effective confirmation for nucleic acid amplification-based molecular diagnosis, and may immediately eliminate the uncertainty problems of rRT-PCR in SARS-CoV-2 clinic detection. url: http://medrxiv.org/cgi/content/short/2020.06.02.20119735v1?rss=1 doi: 10.1101/2020.06.02.20119735 id: cord-287931-cxqzac4a author: Huang, Weiwei title: An easy operating pathogen microarray (EOPM) platform for rapid screening of vertebrate pathogens date: 2013-09-20 words: 5161.0 sentences: 256.0 pages: flesch: 45.0 cache: ./cache/cord-287931-cxqzac4a.txt txt: ./txt/cord-287931-cxqzac4a.txt summary: RESULTS: Using multiple probes designed to specifically detect a microbial genus or species, EOPM can correctly identify known pathogens at the species or genus level in blinded testing. To facilitate the application of EOPM in multiple surveillance sites for infectious diseases, we designed software with a user-friendly interface, which is supported by a statistical analysis method based on a comprehensive microbial sequence identification database. Analysis of the enrichment results at the genus level revealed Cardiovirus as the number one match, showing significant enrichment ( The microarray raw data of other symptom-causing pathogens, such as streptococcus and mycoplasma, identified by EOPM in peripheral blood in infectious patients, were also submitted to the GEO database. These microarray platforms use long oligonucleotide probes (60-70-mer) and random PCR amplification, and have successfully identified unexpected pathogens in infectious disease outbreaks, even discovering novel viruses with homology to known species [8, 11] . abstract: BACKGROUND: Infectious diseases emerge frequently in China, partly because of its large and highly mobile population. Therefore, a rapid and cost-effective pathogen screening method with broad coverage is required for prevention and control of infectious diseases. The availability of a large number of microbial genome sequences generated by conventional Sanger sequencing and next generation sequencing has enabled the development of a high-throughput high-density microarray platform for rapid large-scale screening of vertebrate pathogens. METHODS: An easy operating pathogen microarray (EOPM) was designed to detect almost all known pathogens and related species based on their genomic sequences. For effective identification of pathogens from EOPM data, a statistical enrichment algorithm has been proposed, and further implemented in a user-friendly web-based interface. RESULTS: Using multiple probes designed to specifically detect a microbial genus or species, EOPM can correctly identify known pathogens at the species or genus level in blinded testing. Despite a lower sensitivity than PCR, EOPM is sufficiently sensitive to detect the predominant pathogens causing clinical symptoms. During application in two recent clinical infectious disease outbreaks in China, EOPM successfully identified the responsible pathogens. CONCLUSIONS: EOPM is an effective surveillance platform for infectious diseases, and can play an important role in infectious disease control. url: https://doi.org/10.1186/1471-2334-13-437 doi: 10.1186/1471-2334-13-437 id: cord-001843-ceatyj3o author: Huang, Yong title: Ultrasensitive Detection of RNA and DNA Viruses Simultaneously Using Duplex UNDP-PCR Assay date: 2015-11-06 words: 5184.0 sentences: 231.0 pages: flesch: 50.0 cache: ./cache/cord-001843-ceatyj3o.txt txt: ./txt/cord-001843-ceatyj3o.txt summary: PCV2 DNA and TGEV RNA were simultaneously released from the serum sample by boiling with lysis buffer, then magnetic beads and gold nanoparticles coated with single and/or duplex specific probes for TGEV and PCV2 were added to form a sandwich-like complex with nucleic acids released from viruses. This duplex UNDP-PCR assay could detect TGEV (RNA virus) and PCV2 (DNA virus) from large-scale serum samples simultaneously without the need for DNA/RNA extraction, purification and reverse transcription of RNA, and showed a significantly increased positive detection rate for PCV2 (29%) and TGEV (11.7%) preclinical infection than conventional duplex PCR/RT-PCR. The duplex UNDP-PCR assay is suitable for simultaneous detection of RNA and DNA viruses in early viral infection, providing an effective approach for diagnosis of swine diseases. The duplex UNDP-PCR assay developed in this study provided a useful tool for simultaneous detection of RNA (TGEV) and DNA viruses (PCV2) without the need for viral nucleic acid extraction, purification and reverse transcription. abstract: Mixed infection of multiple viruses is common in modern intensive pig rearing. However, there are no methods available to detect DNA and RNA viruses in the same reaction system in preclinical level. In this study, we aimed to develop a duplex ultrasensitive nanoparticle DNA probe-based PCR assay (duplex UNDP-PCR) that was able to simultaneously detect DNA and RNA viruses in the same reaction system. PCV2 and TGEV are selected as representatives of the two different types of viruses. PCV2 DNA and TGEV RNA were simultaneously released from the serum sample by boiling with lysis buffer, then magnetic beads and gold nanoparticles coated with single and/or duplex specific probes for TGEV and PCV2 were added to form a sandwich-like complex with nucleic acids released from viruses. After magnetic separation, DNA barcodes specific for PCV2 and TGEV were eluted using DTT and characterized by specific PCR assay for specific DNA barcodes subsequently. The duplex UNDP-PCR showed similar sensitivity as that of single UNDP-PCR and was able to detect 20 copies each of PCV2 and TGEV in the serum, showing approximately 250-fold more sensitivity than conventional duplex PCR/RT-PCR assays. No cross-reaction was observed with other viruses. The positive detection rate of single MMPs- and duplex MMPs-based duplex UNDP-PCR was identical, with 29.6% for PCV2, 9.3% for TGEV and 3.7% for PCV2 and TGEV mixed infection. This duplex UNDP-PCR assay could detect TGEV (RNA virus) and PCV2 (DNA virus) from large-scale serum samples simultaneously without the need for DNA/RNA extraction, purification and reverse transcription of RNA, and showed a significantly increased positive detection rate for PCV2 (29%) and TGEV (11.7%) preclinical infection than conventional duplex PCR/RT-PCR. Therefore, the established duplex UNDP-PCR is a rapid and economical detection method, exhibiting high sensitivity, specificity and reproducibility. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636378/ doi: 10.1371/journal.pone.0141545 id: cord-274954-06c3ymc3 author: Huang, Yu-Liang title: Development of a reverse transcription multiplex real-time PCR for the detection and genotyping of classical swine fever virus date: 2009-05-04 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A reverse transcription multiplex real-time PCR (RT-MRT-PCR) was developed for rapid detection and genotyping of classical swine fever virus (CSFV). The universal primers and specific TaqMan probes for each of the three genotypes, genotypes 1, 2, and 3, were designed within the 3′-UTR of the CSFV. Non-CSFV swine virus and clinical samples from specific pathogen-free (SPF) pigs were both demonstrated to be CSFV-negative by RT-MRT-PCR. The diagnostic sensitivity of RT-MRT-PCR was determined to be 1 viral copy/μl for each genotype of standard plasmid. For the analytical sensitivity experiment, 100 samples of 14 CSFV genotype 1 strains and 86 samples from CSFV outbreak farms were all detected as CSFV-positive by RT-MRT-PCR, and the genotype results were consistent with the results of sequencing from a previous study. The intra-assay and inter-assay variations of RT-MRT-PCR were below 3% in all experiments. The sensitivity of RT-MRT-PCR was the same as the reverse transcription nested PCR (RT-nPCR) and higher than reverse transcription PCR (RT-PCR) and viral isolation from clinical samples. This assay was used further to evaluate the duration of viremia of wild-type CSFV in vaccinated exposed pigs. The results indicated that pigs vaccinated with the E2 subunit vaccine had longer viremia than pigs given the C-strain vaccine, which is compatible with the findings of previous studies. Thus, the new RT-MRT-PCR is a rapid, reproducible, sensitive, and specific genotyping tool for CSFV detection. url: https://www.ncbi.nlm.nih.gov/pubmed/19414034/ doi: 10.1016/j.jviromet.2009.04.029 id: cord-322566-ye27nqj2 author: Huang, Yuxiang title: Stable Internal Reference Genes for Normalizing Real-Time Quantitative PCR in Baphicacanthus cusia under Hormonal Stimuli and UV Irradiation, and in Different Plant Organs date: 2017-05-03 words: 5805.0 sentences: 305.0 pages: flesch: 49.0 cache: ./cache/cord-322566-ye27nqj2.txt txt: ./txt/cord-322566-ye27nqj2.txt summary: title: Stable Internal Reference Genes for Normalizing Real-Time Quantitative PCR in Baphicacanthus cusia under Hormonal Stimuli and UV Irradiation, and in Different Plant Organs cusia in this study, and the expression stability was assessed across 60 samples representing different tissues and organs under various conditions, including ultraviolet (UV) irradiation, hormonal stimuli (jasmonic acid methyl ester and abscisic acid), and in different plant organs. However, it is necessary to select suitable reference genes as internal controls under different experimental conditions for accurate RT-qPCR evaluation because of the variability in initial material, RNA integrity, RT-PCR efficiency, and RT-qPCR efficiency (Derveaux et al., 2010) . cusia was evaluated by RNA-Seq (unpublished data) in this study to identify potential reference genes suitable for transcript normalization in experiments under UV irradiation and hormonal stimuli (MeJA and ABA), and also in different plant organs. abstract: Baphicacanthus cusia (Nees) Bremek, the plant source for many kinds of drugs in traditional Chinese medicine, is widely distributed in South China, especially in Fujian. Recent studies about B. cusia mainly focus on its chemical composition and pharmacological effects, but further analysis of the plant's gene functions and expression is required to better understand the synthesis of its effective compounds. Real-time quantitative polymerase chain reaction (RT-qPCR) is a powerful method for gene expression analysis. It is necessary to select a suitable reference gene for expression normalization to ensure the accuracy of RT-qPCR results. Ten candidate reference genes were selected from the transcriptome datasets of B. cusia in this study, and the expression stability was assessed across 60 samples representing different tissues and organs under various conditions, including ultraviolet (UV) irradiation, hormonal stimuli (jasmonic acid methyl ester and abscisic acid), and in different plant organs. By employing different algorithms, such as geNorm, NormFinder, and BestKeeper, which are complementary approaches based on different statistical procedures, 18S rRNA was found to be the most stable gene under UV irradiation and hormonal stimuli, whereas ubiquitin-conjugating enzyme E2 was the best suitable gene for different plant organs. This novel study aimed to screen for suitable reference genes and corresponding primer pairs specifically designed for gene expression studies in B. cusia, in particular for RT-qPCR analyses. url: https://doi.org/10.3389/fpls.2017.00668 doi: 10.3389/fpls.2017.00668 id: cord-261442-r4vgt0h3 author: Huh, Hee Jae title: Comparison of the AnyplexTM II RV16 and Seeplex® RV12 ACE assays for the detection of respiratory viruses date: 2014-08-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract The AnyplexTM II RV16 detection kit (RV16; Seegene, Seoul, South Korea) is a multiplex real-time PCR assay based on tagging oligonucleotide cleavage extension. In this prospective study, we evaluated the RV16 assay by comparing with the Seeplex® RV12 ACE detection kit (RV12; Seegene), a multiplex end-point PCR kit. A total of 365 consecutive respiratory specimens were tested with both RV16 and RV12 assays in parallel and detected 140 (38.4%) and 89 (24.4%) positive cases, respectively. The positive percent agreement, negative percent agreement, and kappa values for the 2 assays were 95.6% (95% confidence interval [CI], 89.4–98.3%), 80.4% (95% CI, 75.3–84.6%), and 0.64 (95% CI, 0.56–0.72), respectively. The monoplex PCR and sequencing for the samples with discrepant results revealed that majority of the results were concordant with the results from RV16 assays. In conclusion, the RV16 assay produces results comparable to the RV12 assay. url: https://www.sciencedirect.com/science/article/pii/S0732889314000583 doi: 10.1016/j.diagmicrobio.2014.01.025 id: cord-286096-h275nner author: Huijskens, Elisabeth G. W. title: Viral and bacterial aetiology of community‐acquired pneumonia in adults date: 2012-08-22 words: 3714.0 sentences: 192.0 pages: flesch: 47.0 cache: ./cache/cord-286096-h275nner.txt txt: ./txt/cord-286096-h275nner.txt summary: Methods Between April 2008 and April 2009, 408 adult patients (aged between 20 and 94 years) with community‐acquired pneumonia were tested for the presence of respiratory pathogens using bacterial cultures, real‐time PCR for viruses and bacteria, urinary antigen testing for Legionella and Pneumococci and serology for the presence of viral and bacterial pathogens. All samples were tested using real-time PCR for the presence of respiratory viruses and bacteria including adenovirus (AdV), human bocavirus (hBoV), KI-and WU polyomaviruses (KIPyV and WUPyV), human metapneumovirus (hMPV), human rhinovirus (HRV), human coronaviruses (HCoV) (OC43, NL63, HKU and 229E), parainfluenza viruses (PIV), 1-4 influenza viruses A and B (InfA, InfB), respiratory syncytial virus (RSV), Legionella pneumophila, Mycoplasma pneumoniae, Chlamydophila psittaci, Chlamydophila pneumoniae, Coxiella burnetii and Streptococcus pneumoniae. This study revealed the viral and bacterial aetiology in 263 (64AE5%) of 408 patients with community-acquired pneumonia. abstract: Please cite this paper as: Huijskens et al. (2012) Viral and bacterial aetiology of community‐acquired pneumonia in adults. Influenza and Other Respiratory Viruses 7(4), 567–573. Background Modern molecular techniques reveal new information on the role of respiratory viruses in community‐acquired pneumonia. In this study, we tried to determine the prevalence of respiratory viruses and bacteria in patients with community‐acquired pneumonia who were admitted to the hospital. Methods Between April 2008 and April 2009, 408 adult patients (aged between 20 and 94 years) with community‐acquired pneumonia were tested for the presence of respiratory pathogens using bacterial cultures, real‐time PCR for viruses and bacteria, urinary antigen testing for Legionella and Pneumococci and serology for the presence of viral and bacterial pathogens. Results Pathogens were identified in 263 (64·5%) of the 408 patients. The most common single organisms in these 263 patients were Streptococcus pneumoniae (22·8%), Coxiella burnetii (6·8%) and influenza A virus (3·8%). Of the 263 patients detected with pathogens, 117 (44·5%) patients were positive for one or more viral pathogens. Of these 117 patients, 52 (44·4%) had no bacterial pathogen. Multiple virus infections (≥2) were found in 16 patients. Conclusion In conclusion, respiratory viruses are frequently found in patients with CAP and may therefore play an important role in the aetiology of this disease. url: https://doi.org/10.1111/j.1750-2659.2012.00425.x doi: 10.1111/j.1750-2659.2012.00425.x id: cord-304457-8g36h1bz author: Idelsis, E.-M. title: Effect and safety of combination of interferon alpha-2b and gamma or interferon alpha-2b for negativization of SARS-CoV-2 viral RNA. Preliminary results of a randomized controlled clinical trial. date: 2020-08-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract Objectives: IFN-alpha2b and IFN-gamma combination has demonstrated favorable pharmacodynamics for genes underlying antiviral activity which might be involved in the defense of the organism from a SARS-CoV-2 infection. Considering this we conducted a randomized controlled clinical trial for efficacy and safety evaluation of subcutaneous IFN-alpha2b and IFN-gamma administration in patients positive to SARS-CoV-2. Methods: We enrolled 19-82 years-old inpatients at the Military Central Hospital Luis Diaz Soto, Havana, Cuba. They were hospitalized after confirmed diagnosis for SARS-CoV-2 RNA by real-time reverse transcription polymerase chain reaction. Patients were randomly assigned in a 1:1 ratio to receive either, subcutaneous treatment with a co-lyophilized combination of 3.0 MIU IFN-alpha2b and 0.5 MIU IFN-gamma (HeberFERON, CIGB, Havana, Cuba), twice a week for two weeks, or thrice a week intramuscular injection of 3.0 MIU IFN-alpha2b (Heberon Alpha R, CIGB, Havana, Cuba). Additionally, all patients received lopinavir-ritonavir 200/50 mg every 12 h and chloroquine 250 mg every 12 h (standard of care). The primary endpoints were the time to negativization of viral RNA and the time to progression to severe COVID-19, from the start of treatment. The protocol was approved by the Ethics Committee on Clinical Investigation from the Hospital and the Center for the State Control of Medicines, Equipment and Medical Devices in Cuba. Informed consent was obtained from each participant. Results: A total of 79 patients with laboratory-confirmed SARS-CoV-2 infection, including symptomatic or asymptomatic conditions, fulfilled the inclusion criteria and underwent randomization. Thirty-three subjects were assigned to the HeberFERON group, and 33 to the Heberon Alpha R group. Sixty-three patients were analyzed for viral negativization, of them 78.6% in the HeberFERON group negativized the virus after 4 days of treatment versus 40.6% of patients in the Heberon Alpha R groups (p=0.004). Time to reach the negativization of the SARS-CoV-2 measured by RT-PCR in real time was of 3.0 and 5.0 days for the HeberFERON and Heberon Alpha R groups, respectively. A significant improvement in the reduction of time for negativization was attributable to HeberFERON (p=0.0027, Log-rank test) with a Hazard Ratio of 3.2 and 95% CI of 1.529 to 6.948, as compared to Heberon Alpha R treated group. Worsening of respiratory symptoms was detected in two (6.6%) and one (3.3%) patients in HeberFERON and IFN-alpha2b groups, respectively. None of the subjects transit to severe COVID-19 during the study or the epidemiological follow-up for 21 more days. RT-PCR on day 14 after the start of the treatment was negative to SARS-CoV-2 in 100% and 91% of patients of the combination of IFNs and IFN-alpha2b, respectively. Negativization for HeberFERON treated patients was related to a significant increase in lymphocytes counts and an also significant reduction in CRP as early as 7 days after commencing the therapeutic schedule. All the patients in both cohorts recover by day 14 and were in asymptomatic condition and laboratory parameters return to normal values by day 14 after treatment initiation. Adverse events were identified in 31.5% of patients, 28.5% in the control group, and 34.4% in the HeberFERON group, and the most frequent were headaches (17.4%). Conclusions: In a cohort of 63 hospitalized patients between 19 to 82 years-old with positive SARS-CoV-2, HeberFERON significantly negativized the virus on day 4 of treatment when comparing with IFN-alpha2b. Heberon Alpha R also showed efficacy for the treatment of the viral infection. Both treatments were safe and positively impact on the resolution of the symptoms. None of the patients developed severe COVID-19. Key words: COVID-19, treatment, drug, virus negativization, antiviral, interferon combination, SARS CoV-2. url: https://doi.org/10.1101/2020.07.29.20164251 doi: 10.1101/2020.07.29.20164251 id: cord-312996-qzu8pkyt author: Iles, R. K. title: A clinical MALDI-ToF Mass spectrometry assay for SARS-CoV-2: Rational design and multi-disciplinary team work. date: 2020-08-22 words: 6845.0 sentences: 375.0 pages: flesch: 51.0 cache: ./cache/cord-312996-qzu8pkyt.txt txt: ./txt/cord-312996-qzu8pkyt.txt summary: Testing limitations, including reagent shortages, remain a bottleneck in the battle to curtail COVID-19 spread in even the wealthiest countries [1, 2] The development of new matrix assisted laser desorption time of flight mass spectrometry (MALDI-ToF MS) diagnostics for SARS-CoV-2 detection is driven by the need for greater diagnostic capacity and alternative applications to complement standard PCR and antibody based diagnostics. Consequently studies where swab samples have been split for simultaneous analysis by RT PCR detection systems of SARS-CoV-2 RNA and by MALDI-ToF mass spectrometry for viral proteins, are compromised [4] . virus grown in vitro and mass spectra of gargle/saliva spiked with culture media from cells infected with SARS-CoV-2: S proteolytic fragments S1 and S2 were seen in all preparations and S2b only in serum free samples. These confirmed PCR-negative gargle samples were analysed by MALDI-ToF mass spectrometry 40 times; the measured peak intensities of which acted as comparative controls to the viral spiked saliva/gargle. abstract: The COVID-19 pandemic caused by the SARS-CoV-2 Coronavirus has stretched national testing capacities to breaking points in almost all countries of the world. The need to rapidly screen vast numbers of a countrys population in order to control the spread of the infection is paramount. However, the logistical requirement for reagent supply (and associated cost) of RT-PCR based testing (the current front-line test) have been hugely problematic. Mass spectrometry-based methods using swab and gargle samples have been reported with promise, but have not approached the task from a systematic analysis of the entire diagnostic process. Here, the pipeline from sample processing, the biological characteristics of the pathogen in human biofluid, the downstream bio- and physical-chemistry and the all-important data processing with clinical interpretation and reporting, are carefully compiled into a single high throughput and reproducible rapid process. Utilizing MALDI-ToF mass spectrometric detection to viral envelope glycoproteins in a systems biology - multidisciplinary team approach, we have achieved a multifaceted clinical MALDI ToF MS screening test, primarily (but not limited to) SARS-CoV-2, with direct applicable to other future epidemics/pandemics that may arise. The clinical information generated not only includes SARS-CoV-2 Coronavirus detection (Spike protein fragments S1, S2b, S2a peaks), but other respiratory viral infections detected as well as an assessment of generalised oral upper respiratory immune response (elevated total Ig light chain peak) and a measure of the viral immune response (elevated intensity of IgA heavy chain peak). The advantages of the method include; 1) ease of sampling, 2) speed of analysis, and much reduced cost of testing. These features reveal the diagnostic utility of MALDI-ToF mass spectrometry as a powerful and economically attractive global solution. url: http://medrxiv.org/cgi/content/short/2020.08.22.20176669v1?rss=1 doi: 10.1101/2020.08.22.20176669 id: cord-300508-po2zolo8 author: Inoue, Gen title: Experience of an Orthopaedic Surgery Department Early During the COVID-19 Outbreak in Japan Including Real-Time Polymerase Chain Reaction Assay Results for SARS-CoV-2 date: 2020-10-24 words: 3942.0 sentences: 182.0 pages: flesch: 49.0 cache: ./cache/cord-300508-po2zolo8.txt txt: ./txt/cord-300508-po2zolo8.txt summary: With the need to develop an approach to manage orthopaedic surgeries, we aimed to evaluate the most current data on all the surgical cases in our department including the results of the reverse-transcriptase polymerase chain reaction (RT-PCR) assay for infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We also examined the results of PT-PCR for SARS-CoV-2, which was principally performed for all the surgical candidates in our department beginning May 13, and investigated their laboratory test results before surgery, their clinical signs and symptoms, which were reported to be related with COVID-19. evaluated 66 orthopaedic healthcare workers exposed to one patient who became positive for SARS-CoV-2 infection one week after admission, and reported that the RT-PCR assays were negative for all 66 healthcare workers, although 14 (21%) manifested clinical signs/symptoms suggestive of COVID-19, including cough (6.1%), sore throat (4.5%), nasal congestion (4.5%), dyspnoea (3.0%), fever (1.5%), headache, and myalgias (1.5%) [19] . abstract: Introduction The coronavirus disease 2019 (COVID-19) epidemic beginning December 2019 in China has now become a worldwide pandemic. With the need to develop an approach to manage orthopaedic surgeries, we aimed to evaluate the most current data on all the surgical cases in our department including the results of the reverse-transcriptase polymerase chain reaction (RT-PCR) assay for infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Methods The monthly number of surgical cases from 2016 were reviewed, and compared the numbers of surgical cases both in elective and emergency surgery during the pandemic with the pre-pandemic period. The results of RT-PCR for SARS-CoV-2 in 94 orthopaedic surgery cases from May 13 to June 30, 2020, and clinical signs/symptoms, and laboratory data of 48 consecutive cases within a month from May 13 were also evaluated. Results The mean monthly number of surgeries from January to May 2020 was significantly lower than the mean number in 2019 (73.8 vs 121.9, respectively, p=0.01). The proportion of emergency surgeries in all surgeries performed in May 2020 was 35.5%, which is significantly more than the mean rate of 20.4% in 2019 (p=0.04). Hip arthroplasties and spine surgeries showed the greatest reduction, at greater than 80% and 65%, respectively. Although none of the 94 patients were positive for SARS-CoV-2, 66.7% showed signs/symptoms typical of COVID-19. The most frequent signs/symptoms were production of nasal mucus (25.5%), followed by dry cough (19.1%); and fatigue, headache, and dizziness (17.0% each). The incidence of abnormal values, which are commonly noted in COVID-19 patients, were eosinopaenia 37.5%; lymphopaenia 18.8%; thrombocytopaenia 8.3%; and elevated prothrombin time 10.4%. Conclusions Our results show that our RT-PCR negative patients showed signs/symptoms and abnormal laboratory values typical of COVID-19, indicating surgeons should be aware of these abnormalities in patients and the need to rule out COVID-19 before proceeding with surgery. url: https://www.ncbi.nlm.nih.gov/pubmed/33133795/ doi: 10.7759/cureus.11140 id: cord-324012-q2ilk6gs author: Inui, Ken title: A field‐deployable insulated isothermal RT‐PCR assay for identification of influenza A (H7N9) shows good performance in the laboratory date: 2019-09-05 words: 1521.0 sentences: 78.0 pages: flesch: 55.0 cache: ./cache/cord-324012-q2ilk6gs.txt txt: ./txt/cord-324012-q2ilk6gs.txt summary: METHODS: A panel of 59 virus isolates, including H7N9, avian influenza viruses of subtype H1 to H13, swine and human influenza viruses, Newcastle disease virus, and infectious bursal disease virus, were tested by H7 and N9 iiRT‐PCR reagents, using probes and primers specific to H7 or N9, in comparison with laboratory‐based real‐time RT‐PCR assays to determine analytical sensitivity and specificity. Fifty oropharyngeal samples from experimentally infected chicken and ducks with H7N9 and 50 non‐infected control swabs were tested by the H7 iiRT‐PCR to determine diagnostic sensitivity and specificity. The H7 and N9 iiRT-PCR reagents yielded comparable levels of analytical sensitivity and specificity with real-time RT-PCR for the detection of H7N9 virus. Reverse transcription-insulated isothermal PCR (RT-iiRT-PCR) assay for rapid and sensitive detection of foot-and-mouth disease virus A rapid field-deployable reverse transcription-insulated isothermal polymerase chain reaction assay for sensitive and specific detection of bluetongue virus Rapid detection of equine influenza virus H3N8 subtype by insulated isothermal RT-PCR (iiRT-PCR) assay using the POCKIT nucleic acid analyzer abstract: BACKGROUND: Avian influenza A (H7N9) remains circulating in China. For countries at risk of introduction of H7N9, such as Vietnam, early detection of H7N9 virus is essential for the early containment of the virus. Insulated isothermal reverse transcriptase PCR (iiRT‐PCR) is a portable PCR system that can be deployed under field conditions to identify pathogens at the sampling site. Applying PCR at the sampling site will greatly reduce the time to obtain a diagnostic result which allows the veterinary authority to take immediate action to contain disease spreading. OBJECTIVE: To determine analytical and diagnostic sensitivity and specificity of the portable iiRT‐PCR for H7N9 virus detection. METHODS: A panel of 59 virus isolates, including H7N9, avian influenza viruses of subtype H1 to H13, swine and human influenza viruses, Newcastle disease virus, and infectious bursal disease virus, were tested by H7 and N9 iiRT‐PCR reagents, using probes and primers specific to H7 or N9, in comparison with laboratory‐based real‐time RT‐PCR assays to determine analytical sensitivity and specificity. Fifty oropharyngeal samples from experimentally infected chicken and ducks with H7N9 and 50 non‐infected control swabs were tested by the H7 iiRT‐PCR to determine diagnostic sensitivity and specificity. RESULTS: The H7 and N9 iiRT‐PCR reagents yielded comparable levels of analytical sensitivity and specificity with real‐time RT‐PCR for the detection of H7N9 virus. Diagnostic sensitivity and specificity of H7 iiRT‐PCR were 98% and 100%, respectively. CONCLUSION: The observed high sensitivity and specificity of iiRT‐PCR for H7N9 detection show its potential for early detection of H7N9 in risk‐based surveillance. url: https://www.ncbi.nlm.nih.gov/pubmed/31487118/ doi: 10.1111/irv.12646 id: cord-307070-tqxvu3pu author: Iqbal, Phool title: Should We Rely on Screening Tests for Further Management Alone in Polymerase Chain Reaction Negative COVID-19 Patients? A Case Series date: 2020-09-20 words: 2758.0 sentences: 150.0 pages: flesch: 49.0 cache: ./cache/cord-307070-tqxvu3pu.txt txt: ./txt/cord-307070-tqxvu3pu.txt summary: However, improvement was observed in the clinical condition of the patients who were managed as per COVID-19 protocol based upon the clinical signs and symptoms after correlating with diagnostic chest imaging studies. The infectious disease team advised testing with COVID-19 serology (immunoglobulin (Ig) M and IgG antibodies through lateral flow assay), the results of which were positive, indicating recent infection. The infectious disease team was consulted and based upon his clinical presentation and previous investigations, the patient was maintained on the local management protocol for COVID-19 infection. Moreover, biomarkers such as CRP, ferritin, lymphocyte counts, lactate dehydrogenase, and N-terminal pro b-type natriuretic peptide, along with radiological findings in CXR or features such as unilateral or bilateral pneumonia, ground-glass opacities, or consolidations in a chest CT scan, can suggest COVID-19 infection even in such patients where RT-PCR alone is negative [4] . abstract: Since the declaration of coronavirus disease 2019 (COVID-19) disease as a pandemic by the World Health Organization (WHO), it has been a challenge to the whole medical community. Researchers and clinicians have been trying to explain and explore its mechanism and pathophysiology to get a better understanding of this disease, as it has exhausted the healthcare resources and has impacted human life in general. Many tests have been developed including polymerase chain reaction (PCR) of the virus and rapid diagnostic testing in patients based on IgM/IgG serology. But owing to variable sensitivity and specificity of these tests, it has created a challenging situation to proceed with the further management plan. We are reporting a case series where we experienced the dilemma of diagnosing COVID-9 disease in our patients and further plan of care. url: https://www.ncbi.nlm.nih.gov/pubmed/33101802/ doi: 10.7759/cureus.10555 id: cord-316932-fia1w9jt author: Ireland, D. C. title: Improved detection of rhinoviruses in nasal and throat swabs by seminested RT‐PCR date: 2005-12-07 words: 4099.0 sentences: 232.0 pages: flesch: 61.0 cache: ./cache/cord-316932-fia1w9jt.txt txt: ./txt/cord-316932-fia1w9jt.txt summary: PCR tests in which a primary "touchdown" PCR was followed by secondary reactions using PV or HRV specific primers were able to differentiate HRVs of 48 serotypes from EVs. PVnRT‐PCR and HRVnRT‐PCR were then used to test nasal and throat swabs from adult subjects with naturally acquired respiratory virus infections. 2"PCRs using a primer of sequence A together with primers complementary to either B (HRVnRT-PCR) or C (PVnRT-PCR) are then used to differentiate between HRVs and other PVs. We have applied this test directly to nasal and throat swabs from controls and from individuals with naturally acquired colds and compared the rate of PV detection by PVnRT-PCR and by cell culture. This study has shown that PVnRT-PCR is a t least five times more sensitive than cell culture for the detection of PVs in nasal and throat swabs. abstract: A seminested RT‐PCR (nRT‐PCR) was used to detect picornavirus (PV) RNA in cell cultures inoculated with rhinoviruses (HRVs) and enteroviruses (EVs). PCR tests in which a primary "touchdown" PCR was followed by secondary reactions using PV or HRV specific primers were able to differentiate HRVs of 48 serotypes from EVs. PVnRT‐PCR and HRVnRT‐PCR were then used to test nasal and throat swabs from adult subjects with naturally acquired respiratory virus infections. The swabs were also analysed for respiratory viruses by cell culture techniques and the rates of PV identification by the two methods were compared. PVnRT‐PCR was found to be at least five times more sensitive than cell culture for the detection of PVs in these clinical specimens. Paired acute and convalescent serum samples were tested for complement fixing antibodies to adenovirus, influenza A and B, respiratory syncytial virus, parainfluenza viruses 1, 2, and 3, Myco plasma pneumoniae, and Chlamydia psittaci. An enzyme‐linked immunosorbent assay (ELISA) was used to detect rises in antibody level to coronavirus types 229E and OC43. The overall rate of pathogen identification in 159 swabs from adult asthmatics increased from 28% when only cell culture and serology were used to 57% when these methods were supplemented by PVnRT‐PCR. © 1993 Wiley‐Liss, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/8395557/ doi: 10.1002/jmv.1890400204 id: cord-260404-leifaqda author: Ishak, Anthony M. title: Prevalence of Mycoplasma haemofelis, ‘Candidatus Mycoplasma haemominutum’, Bartonella species, Ehrlichia species, and Anaplasma phagocytophilum DNA in the blood of cats with anemia date: 2006-07-17 words: 3401.0 sentences: 143.0 pages: flesch: 44.0 cache: ./cache/cord-260404-leifaqda.txt txt: ./txt/cord-260404-leifaqda.txt summary: In this retrospective study, we used polymerase chain reaction (PCR) assays to determine the prevalence rates of Mycoplasma haemofelis, ''Candidatus M haemominutum'', A phagocytophilum, Ehrlichia species, and Bartonella species DNA in the blood of cats with anemia and a control group of healthy cats. The purpose of this study was to determine whether there were differences in prevalence rates of M haemofelis, ''Candidatus M haemominutum'', A phagocytophilum, Ehrlichia species, and Bartonella species DNA in the blood of healthy cats and retrovirus-negative cats with anemia that did not have an apparent non-infectious (ie, blood loss, chronic disease) cause for their anemia. In this study, we reviewed the laboratory submission forms and medical records to attempt to eliminate cats with known causes of anemia including neoplasia, FeLV, FIV, suspected FIP, blood loss, chronic renal failure, bone marrow disease, other chronic diseases (eg, neoplasia), endocrinopathies, and previous cytologic evidence of hemoplasmosis to allow for selection of cases that were likely to have anemia from previously unrecognized infectious diseases or primary immune-mediated anemia. abstract: Hemoplasmas are known causes of anemia in some cats and some Bartonella species have been associated with anemia in people and in dogs. In this retrospective study, we used polymerase chain reaction (PCR) assays to determine the prevalence rates of Mycoplasma haemofelis, ‘Candidatus M haemominutum’, A phagocytophilum, Ehrlichia species, and Bartonella species DNA in the blood of cats with anemia and a control group of healthy cats. DNA of the organisms was amplified from 22 of 89 cats with anemia (24.7%) and 20 of 87 healthy cats (23.0%). DNA of a hemoplasma was amplified from 18 of 89 cats with anemia (20.2%) and 13 of 87 healthy cats (14.9%); DNA of a Bartonella species was amplified from five of 89 cats with anemia (5.6%) and seven of 87 healthy cats (8.0%). There were no statistically significant differences detected between groups. url: https://api.elsevier.com/content/article/pii/S1098612X06000702 doi: 10.1016/j.jfms.2006.05.003 id: cord-353253-kk2q71vg author: Itokawa, Kentaro title: Disentangling primer interactions improves SARS-CoV-2 genome sequencing by multiplex tiling PCR date: 2020-09-18 words: 3327.0 sentences: 179.0 pages: flesch: 52.0 cache: ./cache/cord-353253-kk2q71vg.txt txt: ./txt/cord-353253-kk2q71vg.txt summary: Soon after the pandemic was recognized by epidemiologists, a group of biologists comprising the ARTIC Network, has devised a multiplexed polymerase chain reaction (PCR) protocol and primer set for targeted whole-genome amplification of SARS-CoV-2. In our experience, the low to zero depth for those two amplicons was the most frequent bottleneck for using the ARTIC primer set V1 to sequence all targeted genomic regions from samples with middle to low viral load (Ct > 27). The results indicated that preventing primer dimerformation is an effective measure to improve coverage bias in the ARTIC Network''s SARS-CoV-2 genome sequencing protocol, and may be applicable to other PrimalSeq methods in general. The formation of primer-dimers is a major cause of coverage bias in the ARTIC Network''s multiplex PCR protocol for SARS-CoV-2 genome sequencing. A proposal of an alternative primer for the ARTIC Network''s multiplex PCR to improve coverage of SARS-CoV-2 genome sequencing (manuscript version 1) abstract: Since December 2019, the coronavirus disease 2019 (COVID-19) caused by a novel coronavirus SARS-CoV-2 has rapidly spread to almost every nation in the world. Soon after the pandemic was recognized by epidemiologists, a group of biologists comprising the ARTIC Network, has devised a multiplexed polymerase chain reaction (PCR) protocol and primer set for targeted whole-genome amplification of SARS-CoV-2. The ARTIC primer set amplifies 98 amplicons, which are separated only in two PCRs, across a nearly entire viral genome. The original primer set and protocol showed a fairly small amplification bias when clinical samples with relatively high viral loads were used. However, as sample’s viral load become low, rapid decrease in abundances of several amplicons were seen. In this report, we will show that dimer formations between some primers are the major cause of coverage bias in the multiplex PCR. Based on this, we propose 12 alternative primers in total in the ARTIC primer set that were predicted to be involved in 14 primer interactions. The resulting primer set, version N1 (NIID-1), exhibits improved overall coverage compared to the ARTIC Network’s original (V1) and modified (V3) primer set. url: https://doi.org/10.1371/journal.pone.0239403 doi: 10.1371/journal.pone.0239403 id: cord-260791-2gmrsm8q author: Iwata, Takanori title: PCR detection and new therapies for COVID-19 date: 2020-06-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://doi.org/10.5051/jpis.2020.50.3.133 doi: 10.5051/jpis.2020.50.3.133 id: cord-285323-473d7zvg author: Jang, Hyesun title: Altered pro-inflammatory cytokine mRNA levels in chickens infected with infectious bronchitis virus date: 2013-09-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Infectious bronchitis virus (IBV) replicates primarily in the respiratory tract and grows in various organs in chickens, with or without pathological effects. The diversity of this virus has been verified by sequence analysis of the S1 glycoprotein gene, but this method must be supplemented with further analysis for characterization of the agent. To increase our understanding of the pathogenesis of the disease caused by this virus, we investigated the response of chickens to 2 IBV with different genotypes, KIIa and ChVI. The clinical signs induced by the viruses were observed. In addition, the mRNA levels of the pro-inflammatory cytokines, IL-6, IL-1β, and lipopolysaccharide-induced tumor necrosis factor-α factor and the serum levels of α(1)-acid glycoprotein, which is a major acute phase protein, were measured. The KIIa genotype (Kr/ADL110002/2011) induced clinical signs accompanied by the excessive production of pro-inflammatory cytokines and a higher viral load. In chickens infected with this isolate, simultaneous peaks in the viral copy number and cytokine production were observed at 7 dpi in the trachea and 9 d postinoculation in the kidney. On the other hand, the chickens infected with the ChVI genotype (Kr/ADL120003/2012) did not show a response other than a mild upregulation of cytokines at 1 d postinoculation, which appears to indicate the invasion of the virus. In summary, we confirmed a differential innate response following infection with distinct IBV. We hypothesize that an excessive innate response contributes to the scale of the pathophysiologic effect in chickens. url: https://api.elsevier.com/content/article/pii/S0032579119394404 doi: 10.3382/ps.2013-03116 id: cord-011966-7k2cxy8a author: Jang, Seong Sik title: The Epidemiological Characteristics of the Korean Bat Paramyxovirus between 2016 and 2019 date: 2020-06-04 words: 2997.0 sentences: 190.0 pages: flesch: 58.0 cache: ./cache/cord-011966-7k2cxy8a.txt txt: ./txt/cord-011966-7k2cxy8a.txt summary: Phylogenetic analysis based on the partial nucleotide sequences of RdRp, F, and HN proteins suggested that the viruses belonged to the proposed genus Shaanvirus. The Hendra and Nipah viruses are emerging bat-borne infectious agents that are highly pathogenic paramyxoviruses, which have caused outbreaks of respiratory and neurological diseases in humans and domesticated mammals [13, 14] . In 2016, 121 bat fecal samples were collected and four positive samples were identified based on RT-semi-nested PCR using consensus primers targeting the RdRp region. Based on the partial RdRp, F, and HN nucleotide sequences, the Korean bat paramyxoviruses belonged to the proposed genus shaanvirus. The phylogenetic analysis based on partial RdRp nucleotide sequences indicated that Korean bat paramyxoviruses belonged to the unclassified proposed genera Shaanvirus (Figure 2 ). In addition, the phylogenetic analysis based on the partial nucleotide sequences of RdRp, F, and HN proteins suggested that the viruses belonged to the proposed genus Shaanvirus. abstract: Bats are considered reservoirs of severe emerging human pathogens. Notably, bats host major mammalian paramyxoviruses from the family Paramyxoviridae, order Mononegavirales. In this study, paramyxoviruses were investigated by reverse transcription semi-nested polymerase chain reaction (RT-semi-nested PCR) and reverse transcription polymerase chain reaction (RT-PCR), based on the RT-semi-nested PCR using the consensus paramyxovirus primers targeting the RNA dependent-RNA-polymerase (RdRp) region. In addition, RT-PCR was performed using newly designed primers targeting regions of the fusion protein (F) and hemagglutinin-neuraminidase (HN). The dominant bat species in the collection site of paramyxoviruses were Miniopterus schreibersii, Myotis macrodactylus, Myotis petax, and Rhinolophus ferrumequinum. Paramyxoviruses were detected in four samples in 2016 and six in 2019. Meanwhile, in samples collected in 2017 and 2018, no paramyxoviruses were detected. Phylogenetic analysis based on the partial nucleotide sequences of RdRp, F, and HN proteins suggested that the viruses belonged to the proposed genus Shaanvirus. In conclusion, this study revealed that bat paramyxoviruses in Korea belonged to a single genus and circulated sporadically in several provinces, including Chungbuk, Gangwon, Jeju, and Jeonnam. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7356101/ doi: 10.3390/microorganisms8060844 id: cord-322657-q4aeood2 author: Jartti, Tuomas title: Respiratory Picornaviruses and Respiratory Syncytial Virus as Causative Agents of Acute Expiratory Wheezing in Children date: 2004-06-17 words: 3169.0 sentences: 177.0 pages: flesch: 45.0 cache: ./cache/cord-322657-q4aeood2.txt txt: ./txt/cord-322657-q4aeood2.txt summary: We studied the viral etiology of acute expiratory wheezing (bronchiolitis, acute asthma) in 293 hospitalized children in a 2-year prospective study in Finland. To prevent and treat acute expiratory wheezing illnesses in children, efforts should be focused on RSV, enterovirus, and rhinovirus infections. The purpose of the study was to investigate the role of 11 respiratory viruses in children hospitalized for acute expiratory wheezing. The supernatants of cell cultures exhibiting a cytopathogenic effect were further studied by antigen detection for adenovirus; influenza A and B viruses; parainfluenza virus types 1, 2, and 3; and RSV or by reverse transcription (RT)-PCR for enterovirus-es and rhinovirus. First, respiratory virus infection was detected in up to 90% of hospitalized children with acute expiratory wheezing. In conclusion, this study showed that acute expiratory wheezing necessitating hospitalization was most often associated with RSV, enterovirus, and rhinovirus infections. abstract: We studied the viral etiology of acute expiratory wheezing (bronchiolitis, acute asthma) in 293 hospitalized children in a 2-year prospective study in Finland. A potential causative viral agent was detected in 88% of the cases. Eleven different viruses were represented. Respiratory syncytial virus (RSV) (27%), enteroviruses (25%), rhinovirus (24%), and nontypable rhino/enterovirus (16%) were found most frequently. In infants, RSV was found in 54% and respiratory picornaviruses (rhinovirus and enteroviruses) in 42% of the cases. In older children, respiratory picornaviruses dominated (65% of children ages 1-2 years and 82% of children ages >3 years). Human metapneumovirus was detected in 4% of all children and in 11% of infants. To prevent and treat acute expiratory wheezing illnesses in children, efforts should be focused on RSV, enterovirus, and rhinovirus infections. url: https://www.ncbi.nlm.nih.gov/pubmed/15207063/ doi: 10.3201/eid1006.030629 id: cord-302713-h3aoag4y author: Jauréguiberry, Stéphane title: Clinical and Microbiological Evaluation of Travel‐Associated Respiratory Tract Infections in Travelers Returning From Countries Affected by Pandemic A(H1N1) 2009 Influenza date: 2011-12-08 words: 3012.0 sentences: 184.0 pages: flesch: 51.0 cache: ./cache/cord-302713-h3aoag4y.txt txt: ./txt/cord-302713-h3aoag4y.txt summary: title: Clinical and Microbiological Evaluation of Travel‐Associated Respiratory Tract Infections in Travelers Returning From Countries Affected by Pandemic A(H1N1) 2009 Influenza BACKGROUND: Although acute respiratory tract infections (RTI) have been recognized as a significant cause of illness in returning travelers, few studies have specifically evaluated the etiologies of RTI in this population. Patients were included if they presented with signs suggestive of RTI that had occurred during travel or <7 days after their return from countries endemic for influenza virus A(H1N1) 2009. At the virology laboratory, the first step of the diagnostic evaluation was to identify influenza A(H1N1) 2009 virus infection by means of real-time reverse transcription-PCR (RT-PCR), as previously described 11 to assess whether or not the patient should remain isolated. In a study performed at San Francisco University Medical Center during the influenza season, a viral agent was identified (through shell vial assay and PCR) in 103 (39%) of the patients with RTI. abstract: BACKGROUND: Although acute respiratory tract infections (RTI) have been recognized as a significant cause of illness in returning travelers, few studies have specifically evaluated the etiologies of RTI in this population. METHODS: This prospective investigation evaluated travelers returning from countries with endemic influenza A(H1N1) 2009, and who were seen in our department at the onset of the outbreak (April–July 2009). Patients were included if they presented with signs of RTI that occurred during travel or less than 7 days after return from overseas travel. Patients were evaluated for microbial agents with RespiFinder plus assay, and throat culture according to clinical presentation. RESULTS: A total of 113 travelers (M/F ratio 1.2:1; mean age 39 y) were included. They were mainly tourists (n = 50; 44.2%) mostly returning from North America (n = 65; 58%) and Mexico (n = 21; 18.5%). The median duration of travel was 23 days (range 2–540 d). The median lag time between return and onset of illness was 0.2 days (range 10 d prior to 7 d after). The main clinical presentation of RTI was influenza‐like illness (n = 76; 67.3%). Among the 99 microbiologically evaluated patients, a pathogen was found by polymerase chain reaction (PCR) or throat culture in 65 patients (65.6%). The main etiological agents were influenza A(H1N1) 2009 (18%), influenza viruses (14%), and rhinovirus (20%). A univariate analysis was unable to show variables associated with influenza A(H1N1) 2009, whereas rhinorrhea was associated with viruses other than influenza (p = 0.04). CONCLUSION: Despite the A(H1N1) 2009 influenza pandemic, rhinovirus and other influenza viruses were also frequent causes of RTI in overseas travelers. Real‐time reverse transcription‐PCR and nasopharyngeal swab cultures are useful diagnostic tools for evaluating travelers with RTI. url: https://www.ncbi.nlm.nih.gov/pubmed/22221808/ doi: 10.1111/j.1708-8305.2011.00570.x id: cord-300399-21xozruq author: Jayamohan, Harikrishnan title: SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations date: 2020-10-18 words: 13003.0 sentences: 770.0 pages: flesch: 44.0 cache: ./cache/cord-300399-21xozruq.txt txt: ./txt/cord-300399-21xozruq.txt summary: This review paper examines current molecular diagnostic tools (Fig. 1) , such as amplification-based (including CRISPR-Cas based), antibody and antigen tests, and sequencing, utilized for the detection of SARS-CoV-2. In addition, we also discuss sample preparation aspects that are relevant to wider utilization and point-of-care (POC) deployment of COVID-19 diagnostic tests (PCR, isothermal amplification, and sequencing-including library preparation). RT-PCR broadly involves four steps-lysis of SARS-CoV-2 in the sample, purification of the viral RNA, reverse transcription to complementary DNA (cDNA), and amplification of specific regions of the cDNA, and finally, optical detection of the amplified cDNA. The assay can detect the virus from respiratory swab samples with sensitivity comparable to that of the US Centers for Disease Control and Prevention (CDC) SARS-CoV-2 real-time RT-PCR assay in 30-40 min. Evaluation of novel antigen-based rapid detection test for the diagnosis of SARS-CoV-2 in respiratory samples abstract: The unprecedented global pandemic known as SARS-CoV-2 has exercised to its limits nearly all aspects of modern viral diagnostics. In doing so, it has illuminated both the advantages and limitations of current technologies. Tremendous effort has been put forth to expand our capacity to diagnose this deadly virus. In this work, we put forth key observations in the functionality of current methods for SARS-CoV-2 diagnostic testing. These methods include nucleic acid amplification–, CRISPR-, sequencing-, antigen-, and antibody-based detection methods. Additionally, we include analysis of equally critical aspects of COVID-19 diagnostics, including sample collection and preparation, testing models, and commercial response. We emphasize the integrated nature of assays, wherein issues in sample collection and preparation could impact the overall performance in a clinical setting. url: https://www.ncbi.nlm.nih.gov/pubmed/33073312/ doi: 10.1007/s00216-020-02958-1 id: cord-274127-12x5cc8i author: Jeong, Ji Hun title: Comparison of sputum and nasopharyngeal swabs for detection of respiratory viruses date: 2014-05-06 words: 2721.0 sentences: 148.0 pages: flesch: 49.0 cache: ./cache/cord-274127-12x5cc8i.txt txt: ./txt/cord-274127-12x5cc8i.txt summary: Paired specimens of nasopharyngeal swabs and sputum were obtained from 154 subjects, and RNA was extracted and tested for 16 different respiratory viruses using the Anyplex II RV16 Detection kit (Seegene, Seoul, Korea). The detection rates of respiratory viruses from sputum samples were significantly higher than those from nasopharyngeal swabs in adults using real‐time multiplex RT‐PCR. The aim of this study was to compare the detection rates of respiratory viruses in paired nasopharyngeal swabs and sputum samples from adult patients with respiratory symptoms using multiplex real-time RT-PCR. The present study found that the overall detection rate from sputum samples in adults was significantly higher than from nasopharyngeal swabs using multiplex real-time RT-PCR. In conclusion, the detection rates of respiratory viruses from sputum samples are significantly higher than those from nasopharyngeal swabs in adults using multiple real-time RT-PCR. abstract: Diagnostic tests for respiratory viral infections use traditionally either nasopharyngeal washes or swabs. Sputum is representative of the lower respiratory tract but is used rarely for viral testing. The aim of this study was to compare the detection rates of respiratory viruses from nasopharyngeal swabs and sputum using a multiplex real‐time reverse transcription‐polymerase chain reaction (RT‐PCR). Adults who were admitted or presented to the clinics of Gil Medical Center with acute respiratory symptoms were recruited from 1 November 2012 to 31 March 2013. Paired specimens of nasopharyngeal swabs and sputum were obtained from 154 subjects, and RNA was extracted and tested for 16 different respiratory viruses using the Anyplex II RV16 Detection kit (Seegene, Seoul, Korea). The positive rate was 53% (81/154) for nasopharyngeal swabs and 68% (105/154) for sputum (P < 0.001). One hundred thirty‐four viruses were identified for 107 illnesses. Influenza A virus, RSV A, HRV, coronavirus OC43, and adenovirus were detected more frequently in sputum samples than in nasopharyngeal swabs (P < 0.001). Importantly, 12 of 44 (27%) influenza A infections and 11 of 27 (41%) RSV infections were positive in only sputum samples. The detection rates of respiratory viruses from sputum samples were significantly higher than those from nasopharyngeal swabs in adults using real‐time multiplex RT‐PCR. These findings suggest that sputum would benefit for the detection of respiratory viruses by nucleic acid amplification tests (NAATs) in patients who produce sputum. Further studies are needed to establish standardized RNA extraction methods from sputum samples. J. Med. Virol. 86:2122–2127, 2014. © 2014 Wiley Periodicals, Inc. url: https://doi.org/10.1002/jmv.23937 doi: 10.1002/jmv.23937 id: cord-001762-dtvzwin8 author: Jeong, Joojin title: Development of a Rapid Detection Method for Potato virus X by Reverse Transcription Loop-Mediated Isothermal Amplification date: 2015-09-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The primary step for efficient control of viral diseases is the development of simple, rapid, and sensitive virus detection. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) has been used to detect viral RNA molecules because of its simplicity and high sensitivity for a number of viruses. RT-LAMP for the detection of Potato virus X (PVX) was developed and compared with conventional reverse transcription polymerase chain reaction (RT-PCR) to demonstrate its advantages over RT-PCR. RT-LAMP reactions were conducted with or without a set of loop primers since one out of six primers showed PVX specificity. Based on real-time monitoring, RT-LAMP detected PVX around 30 min, compared to 120 min for RT-PCR. By adding a fluorescent reagent during the reaction, the extra step of visualization by gel electrophoresis was not necessary. RT-LAMP was conducted using simple inexpensive instruments and a regular incubator to evaluate whether RNA could be amplified at a constant temperature instead of using an expensive thermal cycler. This study shows the potential of RT-LAMP for the diagnosis of viral diseases and PVX epidemiology because of its simplicity and rapidness compared to RT-PCR. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4564147/ doi: 10.5423/ppj.oa.03.2015.0044 id: cord-335359-4rcj75tc author: Jia, Bei title: Evaluation of a PCR-electrospray ionization mass spectrometry platform for detection and identification of fungal pathogens directly from prospectively collected bronchoalveolar lavage specimens date: 2020-01-15 words: 5126.0 sentences: 238.0 pages: flesch: 40.0 cache: ./cache/cord-335359-4rcj75tc.txt txt: ./txt/cord-335359-4rcj75tc.txt summary: We report here the use of a diagnostic assay that utilizes a universal extraction method, broad spectrum PCR amplification and analysis via electrospray ionization mass spectrometry (PCR/ESI-MS) to detect and identify more than 200 pathogenic fungi directly from bronchoalveolar lavage (BAL) specimens in less than 8 hours. For the clinical performance, the PCR/ESI-MS method was applied to prospectively collected BAL specimens obtained from patients suspected of, or at high risk for, pulmonary fungal infections. All BAL samples were processed at the Johns Hopkins Hospital Microbiology Laboratory for the detection and identification of fungal pathogens using all standard of care reference tests including direct microscopic examination by calcofluor white staining, fungal culture, galactomannan (positive cutoff value: GMI 0.5), and direct fluorescent antibody (DFA) microscopic examination that is the only method used for the detection of Pneumocystis jirovecii. abstract: The incidence of invasive fungal infections is on the rise worldwide due to the growth of the immunocompromised population. We report here the use of a diagnostic assay that utilizes a universal extraction method, broad spectrum PCR amplification and analysis via electrospray ionization mass spectrometry (PCR/ESI-MS) to detect and identify more than 200 pathogenic fungi directly from bronchoalveolar lavage (BAL) specimens in less than 8 hours. In this study, we describe both analytical and clinical performance of the assay, when run with prospectively collected clinical BAL specimens. In 146 patients with probable and possible fungal infections defined by EORTC/MSG (European Organization for Research and Treatment of Cancer/Mycoses Study Group) criteria, the PCR/ESI-MS assay demonstrated a sensitivity of 90.9% (95% CI: 76.4–96.9%) and a specificity of 82.3% (95% CI: 74.2–88.2%). This data demonstrates the utility of a non-culture based broad fungal targets molecular diagnostic tool for rapid and accurate diagnosis of invasive fungal infections in patients at risk of developing fungal diseases. url: https://www.sciencedirect.com/science/article/pii/S0732889319308983 doi: 10.1016/j.diagmicrobio.2020.114988 id: cord-305473-w30hsr4m author: Jiang, Lili title: Detection of viral respiratory pathogens in mild and severe acute respiratory infections in Singapore date: 2017-02-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: To investigate the performance of laboratory methods and clinical case definitions in detecting the viral pathogens for acute respiratory infections (ARIs) from a prospective community cohort and hospital inpatients, nasopharyngeal swabs from cohort members reporting ARIs (community-ARI) and inpatients admitted with ARIs (inpatient-ARI) were tested by Singleplex Real Time-Polymerase Chain Reaction (SRT-PCR), multiplex RT-PCR (MRT-PCR) and pathogen-chip system (PathChip) between April 2012 and December 2013. Community-ARI and inpatient-ARI was also combined with mild and severe cases of influenza from a historical prospective study as mild-ARI and severe-ARI respectively to evaluate the performance of clinical case definitions. We analysed 130 community-ARI and 140 inpatient-ARI episodes (5 inpatient-ARI excluded because multiple pathogens were detected), involving 138 and 207 samples respectively. Detection by PCR declined with days post-onset for influenza virus; decrease was faster for community-ARI than for inpatient-ARI. No such patterns were observed for non-influenza respiratory virus infections. PathChip added substantially to viruses detected for community-ARI only. Clinical case definitions discriminated influenza from other mild-ARI but performed poorly for severe-ARI and for older participants. Rational strategies for diagnosis and surveillance of influenza and other respiratory virus must acknowledge the differences between ARIs presenting in community and hospital settings. url: https://doi.org/10.1038/srep42963 doi: 10.1038/srep42963 id: cord-349070-bqv03u2e author: Jiang, Shih Sheng title: Sensitive and Quantitative Detection of Severe Acute Respiratory Syndrome Coronavirus Infection by Real-Time Nested Polymerase Chain Reaction date: 2004-01-15 words: 2465.0 sentences: 110.0 pages: flesch: 51.0 cache: ./cache/cord-349070-bqv03u2e.txt txt: ./txt/cord-349070-bqv03u2e.txt summary: title: Sensitive and Quantitative Detection of Severe Acute Respiratory Syndrome Coronavirus Infection by Real-Time Nested Polymerase Chain Reaction In most of the cases, we and others have found that the single-step real time RT-PCR methods (as suggested by the World Health Organization [WHO] ; available at http://www.who.int/csr/sars/diagnostic tests/en/) could specifically detect SARS-CoV but were unable to proficiently detect !10 copies of virus per test, suggesting that the conventional RT-PCR assay may actually yield falsenegative results. In contrast, the second-round amplification by nested real-time PCR proficiently generated a signal of SARS-CoV DNA without apparent background, compared with no detectable signal for the negative control samples ( figure 1A ). After 25 cycles of first-round amplification and 25 cycles of nested PCR amplification, our assay could detect a theoretical single copy of extracted viral RNA (figure 1A), suggesting its superior sensitivity for detection of SARS-CoV. abstract: A quantitative, real-time, nested polymerase chain reaction (PCR) method, combining the high sensitivity of nested PCR with time-saving real-time instrumentation, was developed for large-scale screening for severe acute coronavirus (SARS) coronavirus. Forty-six clinical specimens were analyzed by this method, and results were compared with those obtained by conventional, single-round, real-time reverse-transcriptase PCR (RT-PCR) performed in parallel. Of the 17 positive results, 2 identified by our method were not detected by single-round, real-time RT-PCR, which suggests that real-time nested PCR has the potential for increased sensitivity, leading to earlier detection of SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/14699465/ doi: 10.1086/380841 id: cord-328373-cubp1cc1 author: Jiang, Yanfang title: Digital PCR is a sensitive new technique for SARS-CoV-2 detection in clinical applications date: 2020-11-04 words: 3564.0 sentences: 217.0 pages: flesch: 50.0 cache: ./cache/cord-328373-cubp1cc1.txt txt: ./txt/cord-328373-cubp1cc1.txt summary: In the current study the use of a novel digital PCR assay to detect SARS-CoV-2 in both clinical patient-derived samples and environmentally derived samples was investigated, with the ultimate aim of reducing the rate of false negative results. Thirty-two patient samples including nasopharyngeal swabs, throat swabs, oropharyngeal swabs, phlegm, plasma/blood, and eye conjunctiva were collected at multiple timepoints during the disease course, and tested for the presence of SARS-CoV-2 via RT-PCR. SARS-CoV-2 nucleic acid sequences were detected in all clinical patient samples (respiratory tract samples including nasopharyngeal and oropharyngeal swabs). To prevent false-negative SARS-CoV-2 nucleic acid-based test results, and develop a new sensitive detection assay, we evaluated the performance of real-time RT-PCR and digital PCR for detecting SARS-CoV-2 nucleic acid in clinical patient-derived samples and environmentally derived samples. Strikingly, digital PCR detected SARS-CoV-2 nucleic acids in several samples that had previously tested negative via real-time RT-PCR, including 3 patient-derived samples and 5 environmentally derived samples. abstract: The global coronavirus disease 2019 (COVID-19) pandemic has posed great challenges in people’s daily lives. Highly sensitive laboratory techniques played a critical role in clinical COVID-19 diagnosis and management. In this study the feasibility of using a new digital PCR-based detection assay for clinical COVID-19 diagnosis was investigated by comparing its performance with that of RT-PCR. Clinical patient samples and samples obtained from potentially contaminated environments were analyzed. The study included 10 patients with confirmed COVID-19 diagnoses, 32 validated samples of various types derived from different clinical timepoints and sites, and 148 environmentally derived samples. SARS-CoV-2 nucleic acids were more readily detected in respiratory tract samples (35.0%). In analyses of environmentally derived samples, the positivity rate of air samples was higher than that of surface samples, probably due to differences in virus concentrations. Digital PCR detected SARS–CoV–2 in several samples that had previously been deemed negative, including 3 patient-derived samples and 5 environmentally derived samples. In this study digital PCR exhibited higher sensitivity than conventional RT-PCR, suggesting that it may be a useful new method for clinical SARS-CoV-2 detection. Improvement of SARS-CoV-2 detection would substantially reduce the rates of false-negative COVID-19 test results, in particular those pertaining to asymptomatic carriers. url: https://doi.org/10.1016/j.cca.2020.10.032 doi: 10.1016/j.cca.2020.10.032 id: cord-012085-ubdzhkfq author: Jin, Tao title: Diversity and quantity of ammonia-oxidizing Archaea and Bacteria in sediment of the Pearl River Estuary, China date: 2011-02-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the sediment of the Pearl River Estuary were investigated by cloning and quantitative real-time polymerase chain reaction (qPCR). From one sediment sample S16, 36 AOA OTUs (3% cutoff) were obtained from three clone libraries constructed using three primer sets for amoA gene. Among the 36 OTUs, six were shared by all three clone libraries, two appeared in two clone libraries, and the other 28 were only recovered in one of the libraries. For AOB, only seven OTUs (based on 16S rRNA gene) and eight OTUs (based on amoA gene) were obtained, showing lower diversity than AOA. The qPCR results revealed that AOA amoA gene copy numbers ranged from 9.6 × 10(6) to 5.1 × 10(7) copies per gram of sediment and AOB amoA gene ranged from 9.5 × 10(4) to 6.2 × 10(5) copies per gram of sediment, indicating that the dominant ammonia-oxidizing microorganisms in the sediment of the Pearl River Estuary were AOA. The terminal restriction fragment length polymorphism results showed that the relative abundance of AOB species in the sediment samples of different salinity were significantly different, indicating that salinity might be a key factor shaping the AOB community composition. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00253-011-3107-8) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3076564/ doi: 10.1007/s00253-011-3107-8 id: cord-319324-zdpbrprg author: Jinks, Maggie R. title: Causes of endogenous uveitis in cats presented to referral clinics in North Carolina date: 2015-11-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVE: To investigate the causes of endogenous uveitis in cats presenting to referral ophthalmology clinics in North Carolina. PROCEDURE: Medical records of cats diagnosed with endogenous uveitis at North Carolina State University's College of Veterinary Medicine (NCSU‐CVM) or Animal Eye Care Associates of Cary, NC between 2003 and 2015 were reviewed. Inclusion criteria were cats that had complete diagnostic workups, including clinical, clinicopathological, serological, and histopathological data, as well as imaging modalities. Serology was consistently completed for feline leukemia virus (FeLV), feline immunodeficiency virus (FIV), feline coronavirus (FCoV), Toxoplasma gondii, and Bartonella spp. RESULTS: One hundred and twenty cats met the inclusion criteria. Seroprevalence of FeLV (2.7%), FIV (7.3%), FCoV (34.7%), T. gondii (23.7%), and Bartonella spp. (43.2%) was observed, with a combined seroprevalence of 59.2%. Nineteen cats (15.8%) were diagnosed with feline infectious peritonitis (FIP) based on clinical, hematological, serological, histopathological, and necropsy findings. The average age of all cases was 7.62 years, while the average age of cats diagnosed with FIP was 1.82 years. Neoplasia was diagnosed in six cats (5.0%). No underlying etiology was found in 49 cats (40.8%). CONCLUSIONS: Both idiopathic and neoplastic causes of uveitis were less prevalent than previously reported in studies, while seropositivity was higher than previously reported for the study area. This may be due to improved diagnostic capabilities or that cats with infectious disease were more likely to be referred. Because of the high prevalence of FIP, young cats with uveitis should be evaluated for hyperglobulinemia and FCoV serology should be performed as minimal diagnostics. url: https://doi.org/10.1111/vop.12324 doi: 10.1111/vop.12324 id: cord-350211-vuxs5wtt author: Johanna, Barón‐Sánchez title: Afectación del sentido del olfato y el gusto en la enfermedad leve por coronavirus (COVID-19) en pacientes españoles date: 2020-07-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Resumen Introducción: La enfermedad por coronavirus-2019 (Covid-19), se ha expandido con gran rapidez en todo el mundo. Las alteraciones del olfato y/o gusto han emergido como un síntoma muy frecuente a medida que la enfermedad se propagó en Europa. Uno de los países con mayor número de contagios en este continente ha sido España. Objetivo: Investigar la evolución clínica de los trastornos del olfato y el gusto en la enfermedad leve por COVID-19 en pacientes españoles. Métodos: Se realizó un estudio transversal a través de encuesta on‐line, en pacientes que presentaron afección súbita del olfato y/o el gusto, durante los dos meses de confinamiento total por COVID-19 en España. Resultados: El 91,18% de los sujetos con afectación del olfato y/o el gusto, que tuvieron a acceso a la realización de PCR, fueron positivos para COVID-19. El 6,5% presentó anosmia y ageusia de forma aislada. El 93,5% manifestó otros síntomas leves asociados: cefalea (51,6%), tos (51,6%), mialgias (45,2%), astenia (38,7%), congestión nasal o rinorrea (35,5%), fiebre (41,9%), febrícula (29,0%), odinofagia (25.8%) y diarrea (6,5%). La duración media de la anosmia fue de 8,33 días, posteriormente los pacientes manifestaron hiposmia, con resolución completa en 17,79 días de media. En el 22,6% de los pacientes el déficit olfatorio persistió. Todos los sujetos recuperaron el sentido del gusto. Conclusiones: Los trastornos olfativos y gustativos son síntomas prevalentes en la infección leve por COVID-19. Gran parte de los pacientes no presentan congestión nasal o rinorrea asociada y un grupo reducido de pacientes los presentan de forma aislada. Abstract Introduction: Coronavirus disease 2019 (COVID-19) has spread rapidly throughout the world. Smell and/or taste disorders have emerged as a very frequent symptom as the disease has spread in Europe. Spain is one of the European countries with the highest number of infections. Objective: This study aimed to investigate the clinical progression of smell and taste disorders in Spanish patients with mild COVID-19. Methods: An online survey was used to conduct a cross-sectional study of patients who presented sudden smell and/or taste disorders during the 2 months of total lockdown due to COVID-19 in Spain. Results: In our sample, 91.18% of respondents with impaired smell and/or taste and who were able to undergo PCR testing were positive for SARS-CoV-2 infection. Anosmia and ageusia presented in isolation in 6.5% of participants. The remaining 93.5% presented other mild symptoms: headache (51.6%), cough (51.6%), myalgia (45.2%), asthaenia (38.7%), nasal congestion or rhinorrhoea (35.5%), fever (41.9%), low-grade fever (29.0%), odynophagia (25.8%), or diarrhoea (6.5%). The mean duration of anosmia was 8.33 days, with patients subsequently manifesting hyposmia; complete resolution occurred after a mean of 17.79 days. In 22.6% of respondents, olfactory deficits persisted. All participants recovered their sense of taste. Conclusions: Olfactory and gustatory disorders are prevalent symptoms in mild COVID-19. Most patients do not present associated nasal congestion or rhinorrhoea and a small group of patients present these alterations in isolation. url: https://api.elsevier.com/content/article/pii/S0213485320302334 doi: 10.1016/j.nrl.2020.07.006 id: cord-276978-xl4u7n6r author: Jonassen, Christine Monceyron title: Detection and Sequence Characterization of the 3′-End of Coronavirus Genomes Harboring the Highly Conserved RNA Motif s2m date: 2007-11-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A remarkably conserved 43-nucleotide-long motif present at the 3′-end of the genomes of several members of the polyadenylated RNA virus families Astroviridae, Coronaviridae, and Picornaviridae can be used for the detection and sequence characterization of the viruses harboring it. The procedure makes use of a primer located in the most conserved core of s2m toward a generic anchored oligo(dT) primer in a semispecific PCR. This strategy allows the sequencing of some 50–100 nucleotides from the 3′-end of the virus genome, representing sufficient sequence information for initiation of further genomic characterization in a rapid amplification of cDNA ends (5′-RACE) and primer walking strategy. url: https://doi.org/10.1007/978-1-59745-181-9_3 doi: 10.1007/978-1-59745-181-9_3 id: cord-331740-yjt3q9ph author: Jones, R. M. title: Development and Validation of RT‐PCR Tests for the Detection and S1 Genotyping of Infectious Bronchitis Virus and Other Closely Related Gammacoronaviruses Within Clinical Samples date: 2011-04-07 words: 5863.0 sentences: 257.0 pages: flesch: 49.0 cache: ./cache/cord-331740-yjt3q9ph.txt txt: ./txt/cord-331740-yjt3q9ph.txt summary: This real-time RT-PCR test was used to examine a panel of field samples and its performance compared to virus isolation in embryonated fowls'' eggs. Design and calibration of IBV real-time RT-PCR To confirm that the modified test was suitable for detecting contemporary UK field strains of IBV, a panel of laboratory isolates of IBV representing the major genotypes currently circulating in the UK was tested . The validity of the result obtained for 38 of the 173 real-time RT-PCR positive, virus isolation negative samples could be confirmed by sequencing of the amplicon generated by the diagnostic RT-PCR. Infectious bronchitis virus RNA has been detected in tracheal swab samples by other real-time RT-PCRs for at least 21 days post-vaccination (Callison et al., 2006) and has been isolated from faecal samples in some infected birds as long as 227 days post-infection Gough, 1977, 1978) , making it essential to be able to differentiate between vaccine and field strains for diagnostic purposes. abstract: Two tests were developed that allow the detection and genotyping of infectious bronchitis virus (IBV) and other closely related gammacoronaviruses. The first test employs a one‐step, reverse transcription‐polymerase chain reaction (RT‐PCR) assay in which the amplification is monitored in real time using a TaqMan(®) probe. This real‐time RT‐PCR test was used to examine a panel of field samples and its performance compared to virus isolation in embryonated fowls’ eggs. A total of 323 field samples were tested; 176 samples were positive using the real‐time RT‐PCR method, but only three were positive by virus isolation. Sequencing was used to confirm the positive real‐time RT‐PCR results for a subset of samples. The test is suitable for swabs and post‐mortem samples and has been shown to be highly sensitive and specific. The second test, a genotyping method, was developed for identification of the strain of IBV present in field samples based on nucleotide variations within the gene encoding the S1 subunit of the surface spike (S) glycoprotein. This method was developed to provide a tool to inform vaccination decisions and for ongoing surveillance to detect new and emerging strains of IBV within the UK. The performance of the test was evaluated using laboratory isolates of IBV and field samples. Both tests are suitable for use in a high‐throughput diagnostic laboratory. url: https://doi.org/10.1111/j.1865-1682.2011.01222.x doi: 10.1111/j.1865-1682.2011.01222.x id: cord-006450-si5168pb author: Jouneau, S. title: Which patients should be tested for viruses on bronchoalveolar lavage fluid? date: 2012-12-14 words: 3119.0 sentences: 154.0 pages: flesch: 38.0 cache: ./cache/cord-006450-si5168pb.txt txt: ./txt/cord-006450-si5168pb.txt summary: The variables associated with positive viral tests on univariate analysis were immunosuppression [human immunodeficiency virus (HIV), corticosteroids >10 mg/day for ≥3 weeks, or other immunosuppressive therapy], ground-glass attenuations on computed tomography (CT) scanning, late-onset ventilator-associated pneumonia (VAP), and durations of (i) hospital stay, (ii) intensive care unit (ICU) stay, and (iii) mechanical ventilation before BAL (p < 0.01 for each comparison). The variables significantly associated with positive viral tests on univariate analysis were immunosuppression (i.e., HIV infection, corticosteroids >10 mg/day for ≥3 weeks, and/or other immunosuppressive therapy), ground-glass attenuations on chest CT scans, late-onset ventilator-associated pneumonia (VAP), and durations of (i) hospital stay, (ii) ICU stay, and (iii) mechanical ventilation before BAL was performed (p<0.01 for each comparison). This advocates for the systematic use of PCR techniques for viral tests in BALF, in accordance with previous studies [27, 28] , in the situations where viruses may reasonably be suspected (i.e., acute lower tract respiratory disease in immunocompromised patients and/or patients with unexplained bilateral ground-glass attenuations on CT scan). abstract: Bronchoalveolar lavage (BAL) is a major diagnostic tool in lung diseases, including viral respiratory infections. We aimed to better define the situations where viral tests should be performed on BAL fluid (BALF). We retrospectively studied all cases where viral tests [immunofluorescence, immunocytochemistry, viral culture, and/or polymerase chain reaction (PCR)] were performed on BALF during a period of 1 year (2008) in our institution. We compared the characteristics of patients with virus-positive versus virus-negative BALF. Of the 636 BALF samples sent to the microbiology laboratory, 232 underwent viral tests. Of these, 70 (30 %) were positive and identified 85 viruses: herpes simplex virus (HSV)-1 (n = 27), cytomegalovirus (CMV, n = 23), Epstein–Barr virus (EBV, n = 18), human herpesvirus (HHV)-6 (n = 12), respiratory syncytial virus (RSV, n = 3), rhinovirus (n = 1), and adenovirus (n = 1). The variables associated with positive viral tests on univariate analysis were immunosuppression [human immunodeficiency virus (HIV), corticosteroids >10 mg/day for ≥3 weeks, or other immunosuppressive therapy], ground-glass attenuations on computed tomography (CT) scanning, late-onset ventilator-associated pneumonia (VAP), and durations of (i) hospital stay, (ii) intensive care unit (ICU) stay, and (iii) mechanical ventilation before BAL (p < 0.01 for each comparison). On multivariate analysis, only immunosuppression [odds ratio (OR) 6.4, 95 % confidence interval (CI) [2.8–14.3], p < 0.0001] and ground-glass attenuations (OR 3.7, 95 % CI [1.8–7.7], p = 0.0004) remained associated with virus-positive BAL. None of the viral tests performed on BALF for the initial assessment of diffuse infiltrative lung disease (n = 15) was positive. PCR improved the diagnostic yield of viral tests on BALF by 50 %. Testing for viruses on BALF should be mostly restricted to immunocompromised patients with acute respiratory diseases and/or patients with unexplained ground-glass attenuations on CT scanning. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101843/ doi: 10.1007/s10096-012-1791-7 id: cord-309565-8syjr6k8 author: KANNO, Toru title: A long-term animal experiment indicating persistent infection of bovine coronavirus in cattle date: 2018-05-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A long-term animal experiment involving inoculation with bovine coronavirus (BCoV) was conducted to verify its persistent infection in cattle. Three colostrum-deprived Holstein calves were housed separately in individual rooms of a high-containment facility and inoculated with the BCoV strain Kumamoto/1/07. Until the end of the experiment (1,085, 700 and 280 days, respectively), viral RNAs were detected sporadically by RT-PCR and nested PCR from plasma, nasal discharge, and feces. Seroconversion and titer changes were validated by hemagglutination inhibition tests and neutralization tests. Among the samples, nasal discharge showed a higher viral positivity than feces, which seemed to be associated with positive detection in the plasma. These data demonstrate the existence of persistent infection of BCoV in the respiratory tissues of cattle. url: https://doi.org/10.1292/jvms.18-0050 doi: 10.1292/jvms.18-0050 id: cord-311748-yr2ep7uf author: Kahyaoglu, L. N. title: 11 New approaches in microbial pathogen detection date: 2013-12-31 words: 8020.0 sentences: 381.0 pages: flesch: 48.0 cache: ./cache/cord-311748-yr2ep7uf.txt txt: ./txt/cord-311748-yr2ep7uf.txt summary: In recent years, polymerase chain reaction (PCR)-based methods in particular, have become the gold standard for virus detection in food due to their high sensitivity, specifi city and potential to detect even a single virus particle (Bosch et al. In recent years, qRT-PCR has been widely used in food virology as the most promising nucleic acid detection method, since it offers several advantages over conventional RT-PCR, including high sensitivity, the possibility of simultaneous amplifi cation, detection and quantifi cation of the target nucleic acids in a single step, and with minimum risk of carry-over contamination through the use of a closed system (Mackay et al. The challenges associated with the detection of foodborne viruses, such as PCR inhibitors and low virus concentrations in foods, affect the effi ciency of realtime assay adversely, therefore, for process control (PC) an internal amplifi cation control (IAC), which is extracted and amplifi ed with the target sequence, is crucial in the evaluation of PCR and to prevent false negatives (Di Pasquale et al. abstract: Abstract: Viruses are common causes of foodborne outbreaks. Viral diseases have low fatality rates but transmission to humans via food is important due to the high probability of consuming fecally contaminated food or water because of poor food handling. Because of the low infectious doses of some foodborne viruses, there is a need for standardization and the development of new sensitive methods for detecting viruses. The focus is on molecular and non-molecular approaches, and emerging methods for the detection of foodborne viruses. The detection of noroviruses, hepatitis A and E viruses, rotaviruses and adenoviruses will be discussed. The chapter will conclude with insights into future research directions. url: https://api.elsevier.com/content/article/pii/B978085709438450011X doi: 10.1533/9780857098740.3.202 id: cord-260700-u12aa739 author: Kainulainen, Leena title: Recurrent and persistent respiratory tract viral infections in patients with primary hypogammaglobulinemia date: 2010-06-10 words: 3686.0 sentences: 248.0 pages: flesch: 46.0 cache: ./cache/cord-260700-u12aa739.txt txt: ./txt/cord-260700-u12aa739.txt summary: title: Recurrent and persistent respiratory tract viral infections in patients with primary hypogammaglobulinemia OBJECTIVE: We conducted a prospective 12-month follow-up study of respiratory tract infections in 12 adult patients with primary hypogammaglobulinemia. METHODS: Nasal swab samples and induced sputum samples were taken at the onset of acute respiratory tract infection and every 3 months thereafter. CONCLUSIONS: Despite adequate immunoglobulin replacement therapy, patients with primary hypogammaglobulinemia have increased susceptibility to respiratory tract viral infections. Using modern diagnostic techniques, we wanted to study the occurrence of respiratory tract infections, especially viral infections, in patients with primary hypogammaglobulinemia who were receiving regular immunoglobulin replacement therapy. If the spouse of the patient had acute symptoms of respiratory tract infection, she or he took nasal swabs at home according to the instructions of the research nurse and sent the vials by post. First, despite adequate immunoglobulin replacement therapy, most patients with primary hypogammaglobulinemia had increased susceptibility to respiratory tract viral infections. abstract: BACKGROUND: The occurrence of respiratory tract viral infections in patients with primary hypogammaglobulinemia has not been studied. OBJECTIVE: We conducted a prospective 12-month follow-up study of respiratory tract infections in 12 adult patients with primary hypogammaglobulinemia. METHODS: Nasal swab samples and induced sputum samples were taken at the onset of acute respiratory tract infection and every 3 months thereafter. Samples were tested for bacteria and viruses. PCR tests were performed for 15 respiratory tract viruses. In case the results for rhinovirus were positive, follow-up nasal swab samples were taken every 2 weeks until rhinoviral PCR results became negative. Patients completed symptom diaries, which were collected every month. The spouses of the patients served as healthy control subjects. RESULTS: During the 12-month period, the 12 patients had 65 episodes of acute respiratory tract infections, and the 11 spouses had 12 acute episodes (P < .001). Respiratory tract viruses were found in sputum in 54% of the infections. Rhinovirus was the most common virus. In more than half of our patients, rhinoviral PCR results stayed positive for more than 2 months. The most long-acting persistence with the same rhinovirus was 4 months. CONCLUSIONS: Despite adequate immunoglobulin replacement therapy, patients with primary hypogammaglobulinemia have increased susceptibility to respiratory tract viral infections. Rhinoviral infections are frequent and prolonged. url: https://api.elsevier.com/content/article/pii/S0091674910006652 doi: 10.1016/j.jaci.2010.04.016 id: cord-305657-ayqxesiv author: Kalra, Mannudeep K. title: Chest CT practice and protocols for COVID-19 from radiation dose management perspective date: 2020-07-03 words: 3958.0 sentences: 197.0 pages: flesch: 49.0 cache: ./cache/cord-305657-ayqxesiv.txt txt: ./txt/cord-305657-ayqxesiv.txt summary: Out of concern over the use of CT and associated radiation doses to patients with suspected or known COVID-19 infection, the International Atomic Energy Agency (IAEA) organized a survey and a webinar to discuss CT practice and protocol optimization for COVID-19 pneumonia on April 9, 2020. When these assays have limited availability, diagnostic imaging (chest radiographs or CT) can be used in patients with at least moderate to severe clinical features supportive of COVID-19 pneumonia. Although there are no specific publications or guidance on this matter, in pregnant patients with suspected complications or worsening respiratory status, a chest CT may be indicated and, when necessary, performed with single-phase, non-contrast, lowdose CT protocol. Most national and international organizations recommend against routine use of diagnostic imaging for the diagnosis of COVID-19 pneumonia unless there is a lack of availability or access to RT-PCR or immunoassays in patients with moderate to severe disease, worsening respiratory status, or a suspicion of cardiopulmonary complications. abstract: The global pandemic of coronavirus disease 2019 (COVID-19) has upended the world with over 6.6 million infections and over 391,000 deaths worldwide. Reverse-transcription polymerase chain reaction (RT-PCR) assay is the preferred method of diagnosis of COVID-19 infection. Yet, chest CT is often used in patients with known or suspected COVID-19 due to regional preferences, lack of availability of PCR assays, and false-negative PCR assays, as well as for monitoring of disease progression, complications, and treatment response. The International Atomic Energy Agency (IAEA) organized a webinar to discuss CT practice and protocol optimization from a radiation protection perspective on April 9, 2020, and surveyed participants from five continents. We review important aspects of CT in COVID-19 infection from the justification of its use to specific scan protocols for optimizing radiation dose and diagnostic information. Key Points • Chest CT provides useful information in patients with moderate to severe COVID-19 pneumonia. • When indicated, chest CT in most patients with COVID-19 pneumonia must be performed with non-contrast, low-dose protocol. • Although chest CT has high sensitivity for diagnosis of COVID-19 pneumonia, CT findings are non-specific and overlap with other viral infections including influenza and H1N1. url: https://www.ncbi.nlm.nih.gov/pubmed/32621238/ doi: 10.1007/s00330-020-07034-x id: cord-322937-lakdi3x8 author: Kang, Xiao-ping title: A duplex real-time RT-PCR assay for detecting H5N1 avian influenza virus and pandemic H1N1 influenza virus date: 2010-06-02 words: 2324.0 sentences: 143.0 pages: flesch: 61.0 cache: ./cache/cord-322937-lakdi3x8.txt txt: ./txt/cord-322937-lakdi3x8.txt summary: title: A duplex real-time RT-PCR assay for detecting H5N1 avian influenza virus and pandemic H1N1 influenza virus A duplex real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay was improved for simultaneous detection of highly pathogenic H5N1 avian influenza virus and pandemic H1N1 (2009) influenza virus, which is suitable for early diagnosis of influenza-like patients and for epidemiological surveillance. In this study, a duplex TaqMan real-time RT-PCR assay was improved by adjusting the concentrations of primers and probes in the WHO protocols. The protocol of real-time RT-PCR for influenza A (H1N1) recommended by WHO used a concentration of 1000 nM each of novel SW H1 primers and 250 nM of SW H1 probe [18] . Design of multiplexed detection assays for identification of avian influenza a virus subtypes pathogenic to humans by SmartCycler real-time reverse transcription-PCR A duplex real-time RT-PCR assay for detecting H5N1 avian influenza virus and pandemic H1N1 influenza virus Virology Journal 2010 abstract: A duplex real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay was improved for simultaneous detection of highly pathogenic H5N1 avian influenza virus and pandemic H1N1 (2009) influenza virus, which is suitable for early diagnosis of influenza-like patients and for epidemiological surveillance. The sensitivity of this duplex real-time RT-PCR assay was 0.02 TCID(50 )(50% tissue culture infective dose) for H5N1 and 0.2 TCID(50 )for the pandemic H1N1, which was the same as that of each single-target RT-PCR for pandemic H1N1 and even more sensitive for H5N1 with the same primers and probes. No cross reactivity of detecting other subtype influenza viruses or respiratory tract viruses was observed. Two hundred and thirty-six clinical specimens were tested by comparing with single real-time RT-PCR and result from the duplex assay was 100% consistent with the results of single real-time RT-PCR and sequence analysis. url: https://www.ncbi.nlm.nih.gov/pubmed/20515509/ doi: 10.1186/1743-422x-7-113 id: cord-267928-dflkggjt author: Kantola, Kalle title: Merkel cell polyomavirus DNA in tumor-free tonsillar tissues and upper respiratory tract samples: Implications for respiratory transmission and latency date: 2009-05-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Merkel cell polyomavirus (MCPyV) was discovered recently. It is considered a potential causative agent of Merkel cell carcinoma, a life-threatening skin cancer. OBJECTIVES: To study the prevalence of MCPyV in a large number of clinical samples of various types. Most of the samples were examined also for the other newly found polyomaviruses KI (KIPyV) and WU (WUPyV). STUDY DESIGN: Altogether 1390 samples from immunocompetent or immunocompromised patients, including (i) tonsillar tissues and sera from tonsillectomy patients; (ii) nasopharyngeal aspirates (NPAs) and sera from wheezing children and (iii) nasal swabs, sera and stools from febrile leukemic children were studied for MCPyV. The tonsils, nasal swabs and stools were also studied for KIPyV and WUPyV. RESULTS: MCPyV DNA was detected in 14 samples altogether; 8 of 229 (3.5%) tonsillar tissues, 3 of 140 (2.1%) NPAs, 2 of 106 (1.9%) nasal swabs and 1 of 840 (0.1%) sera. WUPyV and KIPyV were detected in 5 (2.2%) and 0 tonsils, 1 (0.9%) and 4 (3.8%) nasal swabs and 0 and 2 (2.7%) fecal samples, respectively. The patients carrying in tonsils MCPyV were of significantly higher age (median 42 years) than those carrying WUPyV (4 years, p < 0.001). CONCLUSIONS: MCPyV DNA occurs in tonsils more frequently in adults than in children. By contrast, WUPyV DNA is found preferentially in children. MCPyV occurs also in nasal swabs and NPAs, in a frequency similar to that of KIPyV and WUPyV. The tonsil may be an initial site of WUPyV infection and a site of MCPyV persistence. url: https://api.elsevier.com/content/article/pii/S138665320900167X doi: 10.1016/j.jcv.2009.04.008 id: cord-000235-782iew86 author: Kapoor, A title: Human bocaviruses are highly diverse, dispersed, recombination prone, and prevalent enteric infections date: 2010-06-01 words: 4182.0 sentences: 228.0 pages: flesch: 54.0 cache: ./cache/cord-000235-782iew86.txt txt: ./txt/cord-000235-782iew86.txt summary: The multiple species and high degree of genetic diversity seen among the human bocaviruses found in feces relative to the highly homogeneous HBoV1 suggest that this world-wide distributed respiratory pathogen may have recently evolved from an enteric bocavirus, perhaps after acquiring an expanded tropism favoring the respiratory track. Most PCR-positive stool samples contained HBoV2B (76 of 101), making this genotype the most commonly detected enteric human bocavirus (Table 1) . Based on the phylogenetic clustering observed for a large number of partial VP1 sequences ( Figure 1 ) and the distances among full genomes (Table 2) , we propose for future classification that HBoV strains showing 18% protein and 110% nucleotide difference in the complete VP1 gene should be considered different species, whereas those showing 11.5% protein and 15% nucleotide difference should be considered different genotypes. abstract: A new species of parvovirus tentatively named human bocavirus 4 (HBoV4) was genetically characterized. Among 641 feces samples from children and adults the most commonly detected bocaviruses species were HBoV2>HBoV3>HBoV4>HBoV1 with HBoV2 prevalence of 21% and 26% in Nigerian and Tunisian children. HBoV3 and HBoV4 species combined were found in 12/192 cases of non-polio acute flaccid paralysis (AFP) from Tunisia and Nigeria and 0/96 healthy Tunisian contacts (p=0.01). Evidence of extensive recombination at the NP1 and VP1 gene boundary between and within species was found. The multiple species and high degree of genetic diversity seen among the human bocaviruses found in feces relative to the highly homogeneous HBoV1 suggest that this world-wide distributed respiratory pathogen may have recently evolved from an enteric bocavirus, perhaps after acquiring an expanded tropism favoring the respiratory track. Elucidating the possible role of the newly identified enteric bocaviruses in human diseases including AFP and diarrhea will require further epidemiological studies. url: https://academic.oup.com/jid/article-pdf/201/11/1633/18059675/201-11-1633.pdf doi: 10.1086/652416 id: cord-268817-wx96wwpg author: Karp, Donna Grace title: Sensitive and Specific Detection of SARS-CoV-2 Antibodies Using a High-Throughput, Fully Automated Liquid-Handling Robotic System date: 2020-08-20 words: 3600.0 sentences: 182.0 pages: flesch: 47.0 cache: ./cache/cord-268817-wx96wwpg.txt txt: ./txt/cord-268817-wx96wwpg.txt summary: Here, we present an ultrasensitive and high-throughput automated liquid biopsy assay based on the Hamilton Microlab ADAP STAR automated liquid-handling platform, which was developed and validated for the qualitative detection of total antibodies against spike protein 1 (S1) of SARS-CoV-2 that uses as little as 4 µL of serum. 6 In this study, we report the development and validation of a highly sensitive and specific SARS-CoV-2 total antibody assay on a Hamilton MicroLab STAR liquid-handling platform (Fig. 1) , based on the ADAP STAR assay-ready workstation. The successful implementation of the automated high-throughput ADAP SARS-CoV-2 total antibody assay solution as described herein can help meet the surge in demand for COVID-19 infection testing. To evaluate the assay''s sensitivity, 57 serum specimens from COVID-19 patients were subjected to the ADAP SARS-CoV-2 total antibody analysis. abstract: As of July 22, 2020, more than 14.7 million infections of SARS-CoV-2, the virus responsible for Coronavirus Disease 2019 (COVID-19), have been confirmed globally. Serological assays are essential for community screening, assessing infection prevalence, aiding identification of infected patients, and enacting appropriate treatment and quarantine protocols in the battle against this rapidly expanding pandemic. Antibody detection by agglutination–PCR (ADAP) is a pure solution phase immunoassay that generates a PCR amplifiable signal when patient antibodies agglutinate DNA-barcoded antigen probes into a dense immune complex. Here, we present an ultrasensitive and high-throughput automated liquid biopsy assay based on the Hamilton Microlab ADAP STAR automated liquid-handling platform, which was developed and validated for the qualitative detection of total antibodies against spike protein 1 (S1) of SARS-CoV-2 that uses as little as 4 µL of serum. To assess the clinical performance of the ADAP assay, 57 PCR-confirmed COVID-19 patients and 223 control patients were tested. The assay showed a sensitivity of 98% (56/57) and a specificity of 99.55% (222/223). Notably, the SARS-CoV-2–negative control patients included individuals with other common coronaviral infections, such as CoV-NL63 and CoV-HKU, which did not cross-react. In addition to high performance, the hands-free automated workstation enabled high-throughput sample processing to reduce screening workload while helping to minimize analyst contact with biohazardous samples. Therefore, the ADAP STAR liquid-handling workstation can be used as a valuable tool to address the COVID-19 global pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32815769/ doi: 10.1177/2472630320950663 id: cord-310064-p8u424ch author: Katz, Andrew P. title: False‐positive reverse transcriptase polymerase chain reaction screening for SARS‐CoV‐2 in the setting of urgent head and neck surgery and otolaryngologic emergencies during the pandemic: Clinical implications date: 2020-06-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: No reports describe falsepositive reverse transcriptase polymerase chain reaction (RT‐PCR) for novel coronavirus in preoperative screening. METHODS: Preoperative patients had one or two nasopharyngeal swabs, depending on low or high risk of viral transmission. Positive tests were repeated. RESULTS: Forty‐three of 52 patients required two or more preoperative tests. Four (9.3%) had discrepant results (positive/negative). One of these left the coronavirus disease (COVID) unit against medical advice despite an orbital abscess, with unknown true disease status. The remaining 3 of 42 (7.1%) had negative repeat RT‐PCR. Although ultimately considered falsepositives, one was sent to a COVID unit postoperatively and two had urgent surgery delayed. Assuming negative repeat RT‐PCR, clear chest imaging, and lack of subsequent symptoms represent the “gold standard,” RT‐PCR specificity was 0.97. CONCLUSIONS: If false positives are suspected, we recommend computed tomography (CT) of the chest and repeat RT‐PCR. Validated serum immunoglobulin testing may ultimately prove useful. url: https://www.ncbi.nlm.nih.gov/pubmed/32530131/ doi: 10.1002/hed.26317 id: cord-346308-9h2fk9qt author: Kaur, Rajwinder title: Microbiology of hospital wastewater date: 2020-05-01 words: 14673.0 sentences: 648.0 pages: flesch: 34.0 cache: ./cache/cord-346308-9h2fk9qt.txt txt: ./txt/cord-346308-9h2fk9qt.txt summary: The study of hospital wastewater (HWW) microbiology is important to understand the pollution load, growth of particular pathogenic microbes, shift and drift in microbial community, development and spread of antibiotic resistance in microbes, and subsequent change in treatment efficiencies. Within past years, pieces of evidence have shown mobilization of these resistance genes from the environment into pathogenic bacteria causing health risks to humans and animals and also, demonstrating a link between environmental and clinical resistance [123] . The HWW has been reported to have two overexpressed β-lactam-resistance genes (bla GES and bla OXA ) as compared with the water collected from other aquatic bodies, which could be correlated with antibiotic usage over the time in hospitals and discharge of the residues of antibiotics in the wastewater [176] . Urban wastewater treatment plants as hotspots for antibiotic resistant bacteria and genes spread into the environment: a review abstract: The study of hospital wastewater (HWW) microbiology is important to understand the pollution load, growth of particular pathogenic microbes, shift and drift in microbial community, development and spread of antibiotic resistance in microbes, and subsequent change in treatment efficiencies. This chapter investigates the potential microbes such as bacteria, viruses, fungi, and parasites present in HWW along with the diseases associated and methods of treatment used. Due to the indiscriminate release of antibiotics from hospitals, HWW serves as a hotspot for emergence of antibiotic-resistance genes (ARGs) and antibiotic-resistance bacteria. This chapter discusses the ARGs occurrence in HWW, their prevalence in the environment, the molecular tools used for identification, and different mechanisms of horizontal gene transfer. Thus better understanding of the microbiology of HWW could further help in development of advanced treatment technologies for effective removal of microbes and their bioproducts (toxins and infectious nucleic acid) from HWW and contaminated water. url: https://www.sciencedirect.com/science/article/pii/B9780128197226000043 doi: 10.1016/b978-0-12-819722-6.00004-3 id: cord-279577-iwqr2d0r author: Kaur, Taranjit title: Descriptive epidemiology of fatal respiratory outbreaks and detection of a human‐related metapneumovirus in wild chimpanzees (Pan troglodytes) at Mahale Mountains National Park, Western Tanzania date: 2008-06-11 words: 6210.0 sentences: 301.0 pages: flesch: 49.0 cache: ./cache/cord-279577-iwqr2d0r.txt txt: ./txt/cord-279577-iwqr2d0r.txt summary: title: Descriptive epidemiology of fatal respiratory outbreaks and detection of a human‐related metapneumovirus in wild chimpanzees (Pan troglodytes) at Mahale Mountains National Park, Western Tanzania Here, we provide the descriptive epidemiology on respiratory outbreaks that were observed in 2003, 2005 and 2006 in the M-Group at MMNP, and present our findings that the probable causative agent responsible for the fatal 2006 illness is a human-related paramyxovirus. Also, shown is 2006 plus presumed cases, where nine additional chimpanzees, although not observed with clinical signs, have not been seen since the time of the outbreak as follows: one on May 25 (day -8), six on June 5 (day 3), one on June 6 (day 4) and one on June 28 (day 26); they are presumed dead possibly in association with the respiratory illness [Hanamura et al., 2008] . Clinical signs of respiratory illness were observed in all age groups of the M-Group chimpanzees consistent with those reported in humans infected with hMPV. abstract: Over the past several years, acute and fatal respiratory illnesses have occurred in the habituated group of wild chimpanzees at the Mahale Mountains National Park, Tanzania. Common respiratory viruses, such as measles and influenza, have been considered possible causative agents; however, neither of these viruses had been detected. During the fatal respiratory illnesses in 2003, 2005 and 2006, regular observations on affected individuals were recorded. Cause‐specific morbidity rates were 98.3, 52.4 and 33.8%, respectively. Mortality rates were 6.9, 3.2 and 4.6%; all deaths were observed in infants 2 months–2 years 9 months of age. Nine other chimpanzees have not been seen since the 2006 outbreak and are presumed dead; hence, morbidity and mortality rates for 2006 may be as high as 47.7 and 18.5%, respectively. During the 2005 and 2006 outbreaks, 12 fecal samples were collected from affected and nonaffected chimpanzees and analyzed for causative agents. Analysis of fecal samples from 2005 suggests the presence of paramyxovirus, and in 2006 a human‐related metapneumovirus was detected and identified in an affected chimpanzee whose infant died during the outbreak. Our findings provide preliminary evidence that the causative agent associated with these illnesses is viral and contagious, possibly of human origin; and that, possibly more than one agent may be circulating in the population. We recommend that baseline health data be acquired and food wadge and fecal samples be obtained and bio‐banked as early as possible when attempting to habituate new groups of chimpanzees or other great apes. For already habituated populations, disease prevention strategies, ongoing health monitoring programs and reports of diagnostic findings should be an integral part of managing these populations. In addition, descriptive epidemiology should be a major component of disease outbreak investigations. Am. J. Primatol. 70: 755–765, 2008. © 2008 Wiley‐Liss, Inc. url: https://doi.org/10.1002/ajp.20565 doi: 10.1002/ajp.20565 id: cord-318341-0827d8to author: Kaushik, Sulochana title: In-vitro and in silico activity of Cyamopsis tetragonoloba (Gaur) L. supercritical extract against the dengue-2 virus date: 2020-08-31 words: 3838.0 sentences: 209.0 pages: flesch: 51.0 cache: ./cache/cord-318341-0827d8to.txt txt: ./txt/cord-318341-0827d8to.txt summary: The aim of the present study is to check the in vitro and in silico anti-dengue activity of Cyamopsis tetragonoloba supercritical extract in cell lines. The antiviral assay was performed on C6/36 cell lines with 100 copies of dengue-2 virus and maximum non-toxic dose (31.25 µg/ml) of supercritical extract and their effect was detected by real-time RT-PCR. tetragonoloba extracts) as well as experimental well (cell with 100 copies of the dengue-2 virus treated by MNTD of C. The percentages of cell viability of supercritical plants extract concentrations and anti-dengue data was analyzed by Microsoft Excel 2007 with the help of Tukey''s test (each treatment mean value different from each other and compared to control). tetragonoloba show highly significant anti-viral activity against the dengue-2 virus quantitatively with the help of a real-time PCR assay. tetragonoloba extract was found 31.25 lg/ml effective against the DENV-2 virus on C6/36 cells. abstract: Our health and wealth are highly influenced by a number of viruses. Dengue is one of them having a global influence in absence of vaccines and antiviral. WHO suggested that the morbidity of dengue is increasing more than 6 times from 0.5 million in 2010 to over 3.34 million in 2016, following a sharp increase in 2019. The aim of the present study is to check the in vitro and in silico anti-dengue activity of Cyamopsis tetragonoloba supercritical extract in cell lines. The optimum yield of supercritical extract was obtained 0.13 g/10 g (1.3% w/w) at 40 °C temp and 15 MPa pressure and further characterized by GC–MS. The antiviral assay was performed on C6/36 cell lines with 100 copies of dengue-2 virus and maximum non-toxic dose (31.25 µg/ml) of supercritical extract and their effect was detected by real-time RT-PCR. This study revealed that C. tetragonoloba supercritical extract inhibited the dengue-2 virus (99.9%). GC–MS analysis of C. tetragonoloba supercritical extract showed the presence of 10 compounds. The major compounds identified were Hexadecanoic acid, 15-methyl–methyl ester (24.498%); 9,12-octadecadienoyl chloride, (z,z)- (23.718%); methyl dodecanoic acid (13.228%); methyl-stearate (8.696%); Tridecanoic acid, 12-methyl-, methyl-ester (8.426%), dodecanoic acid (6.102%). The study reveals that C. tetragonoloba can be exploited to develop an effective, inexpensive, and specific anti-dengue. The molecular docking study demonstrated the binding energy of 1,2-benzenedicarboxylic acid, bis(2-methylpropyl) ester (− 4.1 kcal/mol), 9,12-octadecadienoyl chloride (z,z) (− 4.0 kcal/mol) ligands were higher than others. It is concluded that C. tetragonoloba can play a major role to inhibit dengue-2 virus. url: https://doi.org/10.1007/s13337-020-00624-9 doi: 10.1007/s13337-020-00624-9 id: cord-344749-omzhhr0k author: Kaya, Sariye Irem title: Electrochemical virus detections with nanobiosensors date: 2020-02-14 words: 8402.0 sentences: 508.0 pages: flesch: 37.0 cache: ./cache/cord-344749-omzhhr0k.txt txt: ./txt/cord-344749-omzhhr0k.txt summary: Cell culture-based virus isolation has been accepted as a "gold standard" in the detection and identification of viruses and is the technique by which all other test methods have been compared [35] . A novel method for dengue virus detection and antibody screening using a graphene-polymer based electrochemical biosensor Chitosan-carbon nanofiber modified single-use graphite electrodes developed for electrochemical detection of DNA hybridization related to hepatitis B virus A sensitive electrochemical biosensor for specific DNA sequence detection based on flower-like VS2, graphene and Au nanoparticles signal amplification Electrochemical DNA biosensor based on a tetrahedral nanostructure probe for the detection of avian influenza A (H7N9) virus Electrochemical DNA biosensor based on gold nanorods for detecting hepatitis B virus Electrochemical-DNA biosensor development based on a modified carbon electrode with gold nanoparticles for influenza a (H1N1) detection: effect of spacer Magnetic nanoparticle-based immunosensor for electrochemical detection of hepatitis B surface antigen abstract: Infectious diseases are caused from pathogens, which need a reliable and fast diagnosis. Today, expert personnel and centralized laboratories are needed to afford much time in diagnosing diseases caused from pathogens. Recent progress in electrochemical studies shows that biosensors are very simple, accurate, precise, and cheap at virus detection, for which researchers find great interest in this field. The clinical levels of these pathogens can be easily analyzed with proposed biosensors. Their working principle is based on affinity between antibody and antigen in body fluids. The progress still continues on these biosensors for accurate, rapid, reliable sensors in future. url: https://www.sciencedirect.com/science/article/pii/B9780128198704000177 doi: 10.1016/b978-0-12-819870-4.00017-7 id: cord-287447-5lzzobl3 author: Keyaerts, Els title: In vitro inhibition of severe acute respiratory syndrome coronavirus by chloroquine date: 2004-10-08 words: 2159.0 sentences: 130.0 pages: flesch: 53.0 cache: ./cache/cord-287447-5lzzobl3.txt txt: ./txt/cord-287447-5lzzobl3.txt summary: Abstract We report on chloroquine, a 4-amino-quinoline, as an effective inhibitor of the replication of the severe acute respiratory syndrome coronavirus (SARS-CoV) in vitro. Glycyrrhizin (an active component of liquorice roots), niclosamide (an antihelminthic drug), nelfinavir (a human immunodeficiency deficiency virus (HIV) protease inhibitor), and SNAP (a nitric oxide donor) were reported to have an antiviral effect against SARS-CoV [12] [13] [14] [15] . In this study we report the in vitro antiviral activity of chloroquine against SARS-CoV Frankfurt 1 strain infection. The IC 50 of chloroquine inhibition of SARS-CoV replication in Vero E6 cells, 8.8 lM, is below (1000-fold) the plasma concentrations of chloroquine that are reached in human plasma, following treatment with chloroquine (for acute malaria) at a dose of 25 mg/kg over three days [27] . Our results show that chloroquine inhibits the replication of SARS-CoV in Vero E6 cells. abstract: Abstract We report on chloroquine, a 4-amino-quinoline, as an effective inhibitor of the replication of the severe acute respiratory syndrome coronavirus (SARS-CoV) in vitro. Chloroquine is a clinically approved drug effective against malaria. We tested chloroquine phosphate for its antiviral potential against SARS-CoV-induced cytopathicity in Vero E6 cell culture. Results indicate that the IC50 of chloroquine for antiviral activity (8.8±1.2μM) was significantly lower than its cytostatic activity; CC50 (261.3±14.5μM), yielding a selectivity index of 30. The IC50 of chloroquine for inhibition of SARS-CoV in vitro approximates the plasma concentrations of chloroquine reached during treatment of acute malaria. Addition of chloroquine to infected cultures could be delayed for up to 5h postinfection, without an important drop in antiviral activity. Chloroquine, an old antimalarial drug, may be considered for immediate use in the prevention and treatment of SARS-CoV infections. url: https://api.elsevier.com/content/article/pii/S0006291X0401839X doi: 10.1016/j.bbrc.2004.08.085 id: cord-333524-a6p6ma8r author: Khan, Pavana title: Isothermal SARS-CoV-2 Diagnostics: Tools for Enabling Distributed Pandemic Testing as a Means of Supporting Safe Reopenings date: 2020-09-23 words: 8841.0 sentences: 603.0 pages: flesch: 50.0 cache: ./cache/cord-333524-a6p6ma8r.txt txt: ./txt/cord-333524-a6p6ma8r.txt summary: 19 The current most common diagnostic method used to identify SARS-CoV-2 infection is a molecular technique for detecting viral RNA through nucleic acid amplification, RT-PCR. Nucleic acid amplification tests (NAATs) are the most common diagnostic tests used to detect pathogens, and many of the current SARS-CoV-2 detection techniques are primarily based on NAATs. 21 NAATs involve nucleic acid amplification, a process that initiates with a small quantity of starting nucleic acids and uses primers that target specific, short nucleic acid sequences in conjunction with enzymes to amplify or increase the quantity of starting nucleic acids. 34 This test incorporates a nested nucleic acid amplification technique showing higher sensitivity of detection than LAMP alone and conventional RT-PCR for minimally processed SARS-CoV-2 samples. 55 The technique first uses RT-LAMP for reverse transcription and isothermal amplification of viral RNA, and then employs the Cas12a enzyme to identify sequences of SARS-CoV-2, allowing cleavage of a reporter molecule ( Figure 5 ). abstract: [Image: see text] The COVID-19 pandemic, caused by the SARS-CoV-2 virus, poses grave threats to both the global economy and health. The predominant diagnostic screens in use for SARS-CoV-2 detection are molecular techniques such as nucleic acid amplification tests. In this Review, we compare current and emerging isothermal diagnostic methods for COVID-19. We outline the molecular and serological techniques currently being used to detect SARS-CoV-2 infection, past or present, in patients. We also discuss ongoing research on isothermal techniques, CRISPR-mediated detection assays, and point-of-care diagnostics that have potential for use in SARS-CoV-2 detection. Large-scale viral testing during a global pandemic presents unique challenges, chief among them the simultaneous need for testing supplies, durable equipment, and personnel in many regions worldwide, with each of these regions possessing testing needs that vary as the pandemic progresses. The low-cost isothermal technologies described in this Review provide a promising means by which to address these needs and meet the global need for testing of symptomatic individuals as well as provide a possible means for routine testing of asymptomatic individuals, providing a potential means of safely enabling reopenings and early monitoring of outbreaks. url: https://www.ncbi.nlm.nih.gov/pubmed/32966744/ doi: 10.1021/acssynbio.0c00359 id: cord-102511-7zgd45fl author: Khodakov, Dmitriy title: Donut PCR: a rapid, portable, multiplexed, and quantitative DNA detection platform with single-nucleotide specificity date: 2020-05-05 words: 4279.0 sentences: 214.0 pages: flesch: 44.0 cache: ./cache/cord-102511-7zgd45fl.txt txt: ./txt/cord-102511-7zgd45fl.txt summary: Here, we present the Donut PCR platform that features high multiplexing, rapid turnaround times, single nucleotide discrimination, and precise quantitation of DNA targets in a portable, affordable, and battery-powered instrument using closed consumables that minimize contamination. Here, we present the Donut PCR platform for DNA detection that combines scalable and massive multiplexing, rapid turnaround times, single nucleotide discrimination, and precise quantitation in a portable, affordable, and batterypowered instrument using closed consumables that minimize contamination risks ( Table 1 ). By engineering a donut-shaped reaction chamber in the PCR chip, we remove most of the dead volume, and are able to achieve similar PCR specificity on human genomic DNA as the commercial Bio-Rad CFX96 instrument (Fig. 2a) . The Donut PCR platform presented here achieves rapid, sensitive, and quantitative detection of many DNA targets from a single sample using a closed, portable, and affordable instrument. abstract: Current platforms for molecular analysis of DNA markers are either limited in multiplexing (qPCR, isothermal amplification), turnaround time (microarrays, NGS), quantitation accuracy (isothermal amplification, microarray, nanopore sequencing), or specificity against single-nucleotide differences (microarrays, nanopore sequencing). Here, we present the Donut PCR platform that features high multiplexing, rapid turnaround times, single nucleotide discrimination, and precise quantitation of DNA targets in a portable, affordable, and battery-powered instrument using closed consumables that minimize contamination. We built a bread-board instrument prototype and three assays/chips to demonstrate the capabilities of Donut PCR: (1) a 9-plex mammal identification panel, (2) a 15-plex bacterial identification panel, and (3) a 30-plex human SNP genotyping assay. The limit of detection of the platform is under 10 genomic copies in under 30 minutes, and the quantitative dynamic range is at least 4 logs. We envision that this platform would be useful for a variety of applications where rapid and highly multiplexed nucleic acid detection is needed at the point of care. url: https://doi.org/10.1101/2020.04.24.058453 doi: 10.1101/2020.04.24.058453 id: cord-343377-6muareue author: Kidszun, André title: Viral Infections in Neonates with Suspected Late-Onset Bacterial Sepsis—A Prospective Cohort Study date: 2016-05-16 words: 2356.0 sentences: 163.0 pages: flesch: 47.0 cache: ./cache/cord-343377-6muareue.txt txt: ./txt/cord-343377-6muareue.txt summary: Objective The aim of our study was to evaluate the occurrence of viral infections in infants with suspected late-onset bacterial sepsis in a neonatal intensive care unit. Methods In a prospective study, infants with suspected late-onset bacterial sepsis underwent viral testing alongside routine blood culture sampling. Bennett et al performed a surveillance study of viral respiratory infections in two NICUs. All infants of a gestational age < 33 weeks were tested twice a week using multiplex RT-PCR ELISA. Detection of respiratory viral infections in neonates treated for suspicion of nosocomial bacterial sepsis: a feasibility study Viral respiratory tract infections in the neonatal intensive care unit: the VIRIoN-I study Unrecognized viral respiratory tract infections in premature infants during their birth hospitalization: a prospective surveillance study in two neonatal intensive care units Viral respiratory tract infections in the Neonatal Intensive Care Unit abstract: Objective The aim of our study was to evaluate the occurrence of viral infections in infants with suspected late-onset bacterial sepsis in a neonatal intensive care unit. Methods In a prospective study, infants with suspected late-onset bacterial sepsis underwent viral testing alongside routine blood culture sampling. Using a multiplex reverse transcription-polymerase chain reaction enzyme-linked immunosorbent assay, nasopharyngeal aspirates were analyzed for adenovirus, respiratory syncytial virus (RSV), influenza virus A and B, H1N1 virus, parainfluenza virus 1 to 4, metapneumovirus, coronavirus, and picornavirus. Stools were examined for adenovirus, rotavirus, norovirus, and enterovirus. Results Between August 2010 and March 2014, data of 88 infants with 137 episodes of suspected late-onset bacterial sepsis were analyzed. Six infants were diagnosed with a respiratory viral infection (2 × RSV, 4 × picornavirus). Blood culture–proven bacterial sepsis was detected in 15 infants. Neither viral–bacterial coinfections nor polymerase chain reaction positive stool samples were found. Conclusion Respiratory viruses can be detected in a considerable number of neonates with suspected late-onset bacterial sepsis. In contrast, gastrointestinal viral or enterovirus infections appear uncommon in such cases. url: https://www.ncbi.nlm.nih.gov/pubmed/27182999/ doi: 10.1055/s-0036-1584150 id: cord-254450-ienq3aex author: Kim, Dae-Ki title: Tools to Detect Influenza Virus date: 2013-05-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In 2009, pandemic influenza A (H1N1) virus (H1N1 09) started to spread quickly in many countries. It causes respiratory infection with signs and symptoms of common infectious agents. Thus, clinicians sometimes may miss the H1N1 patient. Clinical laboratory tests are important for the diagnosis of the H1N1 infection. There are several tests available, however, the rapid test and direct fluorescence antigen test are unable to rule out the influenza virus infection and viral culture test is time consuming. Therefore, nucleic acid amplification techniques based on reverse transcription polymerase chain reaction assays are regarded as a specific diagnosis to confirm the influenza virus infection. Although the nucleic acid-based techniques are highly sensitive and specific, the high mutation rate of the influenza RNA-dependent RNA polymerase could limit the utility of the techniques. In addition, their use depends on the availability, cost and throughput of the diagnostic techniques. To overcome these drawbacks, evaluation and development of the techniques should be continued. This review provides an overview of various techniques for specific diagnosis of influenza infection. url: https://doi.org/10.3349/ymj.2013.54.3.560 doi: 10.3349/ymj.2013.54.3.560 id: cord-277125-s11obc7w author: Kim, Hyeong Rae title: An integrated system of air sampling and simultaneous enrichment for rapid biosensing of airborne coronavirus and influenza virus date: 2020-09-26 words: 3925.0 sentences: 240.0 pages: flesch: 66.0 cache: ./cache/cord-277125-s11obc7w.txt txt: ./txt/cord-277125-s11obc7w.txt summary: This study employed an electrostatic air sampler to capture aerosolized test viruses (human coronavirus 229E (HCoV-229E), influenza A virus subtype H1N1 (A/H1N1), and influenza A virus subtype H3N2 (A/H3N2)) in a continuously flowing liquid (aerosol-to-hydrosol (ATH) enrichment) and a concanavalin A (ConA)-coated magnetic particles (CMPs)-installed fluidic channel for simultaneous hydrosol-to-hydrosol (HTH) enrichment. Even though a liquid sample obtained via the ATH collection of virus particles of very low concentration in air is "non-detectable" in real-time qRT-PCR analysis, we demonstrate that subsequent HTH enrichment can cause a "non-detectable" sample to become "detectable." Human coronavirus 229E (HCoV-229E), Influenza A virus subtype H1N1 (A/H1N1), and Influenza A virus subtype H3N2 (A/H3N2) J o u r n a l P r e -p r o o f 6 were used as test viruses. abstract: Point-of-care risk assessment (PCRA) for airborne viruses requires a system that can enrich low-concentration airborne viruses dispersed in field environments into a small volume of liquid. In this study, airborne virus particles were collected to a degree above the limit of detection (LOD) for a real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). This study employed an electrostatic air sampler to capture aerosolized test viruses (human coronavirus 229E (HCoV-229E), influenza A virus subtype H1N1 (A/H1N1), and influenza A virus subtype H3N2 (A/H3N2)) in a continuously flowing liquid (aerosol-to-hydrosol (ATH) enrichment) and a concanavalin A (ConA)-coated magnetic particles (CMPs)-installed fluidic channel for simultaneous hydrosol-to-hydrosol (HTH) enrichment. The air sampler's ATH enrichment capacity (EC) was evaluated using the aerosol counting method. In contrast, the HTH EC for the ATH-collected sample was evaluated using transmission-electron-microscopy (TEM)-based image analysis and real-time qRT-PCR assay. For example, the ATH EC for HCoV-229E was up to 67,000, resulting in a viral concentration of 0.08 PFU/mL (in a liquid sample) for a viral epidemic scenario of 1.2 PFU/m(3) (in air). The real-time qRT-PCR assay result for this liquid sample was “non-detectable” however, subsequent HTH enrichment for 10 min caused the “non-detectable” sample to become “detectable” (cycle threshold (CT) value of 33.8 ± 0.06). url: https://api.elsevier.com/content/article/pii/S0956566320306461 doi: 10.1016/j.bios.2020.112656 id: cord-311639-zij2wbzs author: Kim, Hyun Soo title: Evaluation of the SD Bioline Norovirus rapid immunochromatography test using fecal specimens from Korean gastroenteritis patients date: 2012-08-30 words: 3674.0 sentences: 175.0 pages: flesch: 52.0 cache: ./cache/cord-311639-zij2wbzs.txt txt: ./txt/cord-311639-zij2wbzs.txt summary: This study was performed to evaluate the analytical and clinical performance of a newly developed rapid ICG test (SD Bioline Norovirus test) for detecting human norovirus genogroups GI and GII in stool specimens. In samples with negative ICG and positive real-time PCR results, 200 L of fecal suspension was mixed with 200 L diluent (1:1 dilution) instead of 1 mL diluent, and the test was repeated. In this study, therefore, in the case of samples with negative ICG and positive real-time PCR results, 200 L of fecal suspension was mixed with 200 L diluent instead of 1 mL diluent (total dilution titer was 1:10-1:20 dilution, which is similar to that of the original procedure of this assay using stool), and the test was repeated. Evaluation of rapid immunochromatography test for the detection of norovirus infection: comparison with ELISA and real time quantitative reverse transcription PCR assays abstract: The analytical and clinical performance of a new rapid immunochromatography test, the SD Bioline Norovirus test, was evaluated for the detection of human norovirus in fecal specimens. The analytical performance studies were performed for detection limit, reproducibility, cross-reactivity, and interference. For comparison, 92 norovirus-positive stool samples and 126 norovirus-negative samples for which the results were confirmed by 2 different real-time PCR kits were used. The rapid immunochromatography test detected the equivalent of 4.48 × 10(6) copies/mL of the norovirus genome in stool samples. On performing the repeatability/reproducibility test, samples above this concentration all provided positive results (100%) and 97.8% of the samples slightly below this concentration (2.45 × 10(6) copies/mL) provided negative results. No cross-reactivity or interference was detected. Positive percent agreement (sensitivity), negative percent agreement (specificity), and overall percent agreement of the rapid immunochromatography test compared with testing by real-time PCR were 90.2%, 100%, and 95.9%, respectively. In addition, the rapid immunochromatography test was completed within 20 min. The SD Bioline Norovirus test was, therefore, easier and more rapid to perform and showed excellent reproducibility, no cross-reactivity, no interference, and high agreement compared with real-time PCR. Thus, this test is useful for rapid screening to identity norovirus infection. url: https://api.elsevier.com/content/article/pii/S0166093412002935 doi: 10.1016/j.jviromet.2012.08.014 id: cord-306396-wci56l0c author: Kim, Jayoung title: Evaluation of an Immunochromatographic Assay for the Rapid and Simultaneous Detection of Rotavirus and Adenovirus in Stool Samples date: 2014-04-08 words: 2736.0 sentences: 142.0 pages: flesch: 46.0 cache: ./cache/cord-306396-wci56l0c.txt txt: ./txt/cord-306396-wci56l0c.txt summary: BACKGROUND: We evaluated the analytical and clinical performances of the SD BIOLINE Rota/Adeno Rapid kit (SD Rota/Adeno Rapid; Standard Diagnostics, Inc., Korea), an immunochromatographic assay (ICA), for the simultaneous detection of rotaviruses and adenoviruses in human stool samples. METHODS: We tested 400 clinical stool samples from patients with acute gastroenteritis and compared the ICA results with the results obtained by using ELISA, enzyme-linked fluorescent assays (ELFA), PCR, and multiplex reverse transcription-PCR (mRT-PCR). In this study, we evaluated the analytical and clinical performance of this ICA for the detection of rotaviruses and adenoviruses and compared the results with those of other tests, including ELISA, enzyme-linked fluorescent assays (ELFA), real-time PCR, and multiplex reverse transcription-PCR (mRT-PCR) assays. The SD Rota/Adeno Rapid test is a one-step lateral flow ICA that simultaneously detects group A rotavirus and adenovirus in stool samples. abstract: BACKGROUND: We evaluated the analytical and clinical performances of the SD BIOLINE Rota/Adeno Rapid kit (SD Rota/Adeno Rapid; Standard Diagnostics, Inc., Korea), an immunochromatographic assay (ICA), for the simultaneous detection of rotaviruses and adenoviruses in human stool samples. METHODS: We tested 400 clinical stool samples from patients with acute gastroenteritis and compared the ICA results with the results obtained by using ELISA, enzyme-linked fluorescent assays (ELFA), PCR, and multiplex reverse transcription-PCR (mRT-PCR). To assess the analytical performance of the SD BIOLINE Rota/Adeno Rapid kit, we determined its detection limit, reproducibility, cross-reactivity, and analytical reactivity for adenovirus subtypes, and performed interference studies. RESULTS: The overall agreement rates among the tested methods were 91.5% for rotavirus and 85.5% for adenovirus. On the basis of mRT-PCR, the overall agreement, positive agreement, and negative agreement rates of the ICA were 95.6%, 100%, and 94.9% for rotavirus, and 94.0%, 71.4%, and 94.8% for adenovirus, respectively. Using the ICA, we detected all the subtypes of adenovirus tested, but the analytical reactivities for adenovirus subtypes were different between the 4 adenovirus detection methods. The high reproducibility was confirmed, and no cross-reactivity or interference was detected. CONCLUSIONS: The SD BIOLINE Rota/Adeno Rapid kit showed acceptable analytical and clinical performances. However, interpretation of adenovirus positive/negative result should be cautious because of different detectability for adenovirus subtypes among adenovirus detection methods. url: https://www.ncbi.nlm.nih.gov/pubmed/24790909/ doi: 10.3343/alm.2014.34.3.216 id: cord-253826-63dgq551 author: Kim, Jisung title: State of diagnosing infectious pathogens using colloidal nanomaterials date: 2017-08-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Infectious diseases are a major global threat that accounts for one of the leading causes of global mortality and morbidity. Prompt diagnosis is a crucial first step in the management of infectious threats, which aims to quarantine infected patients to avoid contacts with healthy individuals and deliver effective treatments prior to further spread of diseases. This review article discusses current advances of diagnostic systems using colloidal nanomaterials (e.g., gold nanoparticles, quantum dots, magnetic nanoparticles) for identifying and differentiating infectious pathogens. The challenges involved in the clinical translation of these emerging nanotechnology based diagnostic devices will also be discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/28898761/ doi: 10.1016/j.biomaterials.2017.08.013 id: cord-254825-c5d0wul9 author: Kim, Sei Won title: Containment of a healthcare-associated COVID-19 outbreak in a university hospital in Seoul, Korea: A single-center experience date: 2020-08-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Our hospital experienced the first healthcare-associated COVID-19 outbreak in Seoul at the time the first COVID-19 cases were confirmed in Korea. The first confirmed COVID-19 patient was a hospital personnel who was in charge of transferring patients inside our hospital. To contain the virus spread, we shutdown our hospital, and tested all inpatients, medical staff members, and employees. METHODS: We retrospectively analyzed the results of SARS-CoV-2 RT-PCR testing according to the contact history, occupation, and presence of respiratory symptoms. Closed-circuit television (CCTV) was reviewed in the presence of an epidemiologist to identify individuals who came into contact with confirmed COVID-19 patients. RESULTS: A total of 3,091 respiratory samples from 2,924 individuals were obtained. Among 2,924 individuals, two inpatients, and one caregiver tested positive (positivity rate, 0.1%). Although all confirmed cases were linked to a general ward designated for pulmonology patients, no medical staff members, medical support personnel, or employees working at the same ward were infected. Contact with confirmed COVID-19 cases was frequent among inpatients and medical support personnel. The most common contact area was the general ward for pulmonology patients and medical support areas, including clinical and imaging examination rooms. Finally, the total number of hospital-associated infections was 14, consisting of four diagnosed at our hospital and ten diagnosed outside the hospital. CONCLUSIONS: The robust control of the COVID-19 outbreak further minimized the transmission of SARS-CoV-2 in the hospital and local communities. However, there was also a debate over the appropriate period of hospital shutdown and testing of all hospital staff and patients. Future studies are required to refine and establish the in-hospital quarantine and de-isolation guidelines based on the epidemiological and clinical settings. url: https://doi.org/10.1371/journal.pone.0237692 doi: 10.1371/journal.pone.0237692 id: cord-285527-1mceq6v0 author: Kinloch, Natalie N title: Suboptimal biological sampling as a probable cause of false-negative COVID-19 diagnostic test results date: 2020-06-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: False-negative SARS-CoV-2 test results can negatively impact the clinical and public health response to COVID-19. We used droplet digital PCR (ddPCR) to demonstrate that human DNA levels, a stable molecular marker of sampling quality, were significantly lower in samples from 40 confirmed or suspected COVID-19 cases that yielded negative diagnostic test results (i.e. suspected false-negative test results) compared to a representative pool of 87 specimens submitted for COVID-19 testing. Our results support suboptimal biological sampling as a contributor to false-negative COVID-19 test results and underscore the importance of proper training and technique in the collection of nasopharyngeal specimens. url: https://doi.org/10.1093/infdis/jiaa370 doi: 10.1093/infdis/jiaa370 id: cord-291486-5h96msv1 author: Kistler, Amy title: Pan-Viral Screening of Respiratory Tract Infections in Adults With and Without Asthma Reveals Unexpected Human Coronavirus and Human Rhinovirus Diversity date: 2007-09-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Background. Between 50% and 80% of asthma exacerbations are associated with viral respiratory tract infections (RTIs), yet the influence of viral pathogen diversity on asthma outcomes is poorly understood because of the limited scope and throughput of conventional viral detection methods. Methods. We investigated the capability of the Virochip, a DNA microarray—based viral detection platform, to characterize viral diversity in RTIs in adults with and without asthma. Results. The Virochip detected viruses in a higher proportion of samples (65%) than did culture isolation (17%) while exhibiting high concordance (98%) with and comparable sensitivity (97%) and specificity (98%) to pathogen-specific polymerase chain reaction. A similar spectrum of viruses was identified in the RTIs of each patient subgroup; however, unexpected diversity among human coronaviruses (HCoVs) and human rhinoviruses (HRVs) was revealed. All but one of the HCoVs corresponded to the newly recognized HCoV-NL63 and HCoV-HKU1 viruses, and >20 different serotypes of HRVs were detected, including a set of 5 divergent isolates that formed a distinct genetic subgroup. Conclusions. The Virochip can detect both known and novel variants of viral pathogens present in RTIs. Given the diversity detected here, larger-scale studies will be necessary to determine whether particular substrains of viruses confer an elevated risk of asthma exacerbation. url: https://www.ncbi.nlm.nih.gov/pubmed/17703411/ doi: 10.1086/520816 id: cord-257316-dmc8wjyl author: Ko, Fanny W.S. title: Viral Etiology of Acute Exacerbations of COPD in Hong Kong date: 2007-09-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Introduction Viral respiratory infections may precipitate acute exacerbations of COPD (AECOPD). However, little is known about viral etiology related to AECOPD in Asia. We aimed to study the viral etiology of AECOPD in Hong Kong. Methods Patients admitted to an acute hospital in Hong Kong with AECOPD were recruited prospectively from May 1, 2004, to April 30, 2005. Nasopharyngeal aspirate was collected and assessed by polymerase chain reaction (PCR) and viral culture. Spirometry was performed in the stable phase at 2 to 3 months after hospital discharge. Results There were 262 episodes of AECOPD among 196 patients (mean age, 75.7 ± 7.7 years [± SD]; 160 men). Mean FEV1 was 39.6 ± 18.9% of predicted normal, and FEV1/FVC ratio was 58.0 ± 15.2%. Fifty-eight episodes (22.1%) yielded positive viral PCR results. The viruses identified were influenza A (7.3%), coronavirus OC43 (4.6%), rhinovirus (3.1%), influenza B (2.7%), and respiratory syncytial virus (2.3%). The diagnostic yield of viral identification by PCR was 2.7 times higher than that based on conventional viral culture. The rates of identifying a positive viral etiology by PCR were similar among the subjects with FEV1 ≥ 50%, ≥ 30 to 50%, and < 30% of predicted normal. Viral infection appeared to have no effect on subsequent readmissions or mortality rate over a study period of 1 year Conclusion Influenza A and two less-attended viruses, coronavirus OC43 and rhinovirus, were the common etiologic agents in patients hospitalized with AECOPD in Hong Kong. These should be considered in developing diagnostic and intervening strategies pertaining to AECOPD. url: https://www.sciencedirect.com/science/article/pii/S0012369215366563 doi: 10.1378/chest.07-0530 id: cord-259324-g8kv4pvq author: Ko, Suk-Min title: Expression of the protective antigen for PEDV in transgenic duckweed, Lemna minor date: 2011-10-28 words: 2332.0 sentences: 121.0 pages: flesch: 50.0 cache: ./cache/cord-259324-g8kv4pvq.txt txt: ./txt/cord-259324-g8kv4pvq.txt summary: In this study, we assessed the feasibility of producing a protective antigen for the PEDV spike protein 1 using duckweed, Lemna minor. Transgene integration and expression of the PEDV spike protein 1 gene were confirmed by genomic PCR and RT-PCR and western blot analysis of transgenic Lemna, respectively. In this study, we report the stable transformation and expression of a protective antigen for PEDV in Lemna minor with potential for use as an effective complement to the diets of animals. Fronds were then blotted onto sterile filter paper, and co-cultivated with Agrobacterium tumefaciens strain EHA105 harboring the PEDV spike protein 1 gene fused to a c-myc tag for 72 h on antibiotic-free ½MS1BA medium. PCR products of the expected size (330 bp) corresponding to primers designed on the internal PEDV spike protein 1 gene were detected from kanamycin-resistant Lemna, whereas no DNA band corresponding to the target gene was detected in untransformed wild-type Lemna. abstract: Duckweeds are small, floating aquatic plants with a number of useful characteristics, including edibility, fast-growing, and a clonal proliferation. Duckweed is also fed to animals as a diet complement because of its high nutritional value. Porcine epidemic diarrhea virus (PEDV) is a major causative agent of fatal diarrhea in piglets and is a serious problem in the hog-raising industry. In this study, we assessed the feasibility of producing a protective antigen for the PEDV spike protein 1 using duckweed, Lemna minor. Stably transformed Lemna were obtained by co-cultivation with A. tumefaciens EHA105 harboring the PEDV spike protein gene. Transgene integration and expression of the PEDV spike protein 1 gene were confirmed by genomic PCR and RT-PCR and western blot analysis of transgenic Lemna, respectively. This is the first report of the expression of a vaccine antigen against an animal infectious disease in duckweed. url: https://www.ncbi.nlm.nih.gov/pubmed/32226733/ doi: 10.1007/s13580-011-0007-x id: cord-320854-ybah03kr author: Kongprajug, Akechai title: Suppression of PmRab11 inhibits YHV infection in Penaeus monodon date: 2017-05-17 words: 6782.0 sentences: 396.0 pages: flesch: 55.0 cache: ./cache/cord-320854-ybah03kr.txt txt: ./txt/cord-320854-ybah03kr.txt summary: Suppression of PmRab11 using dsRNA-PmRab11 either before or after YHV-challenge resulted in significant inhibition of YHV levels in the hemocytes and viral release in the supernatant in both mRNA and protein levels. Protein analysis revealed that an envelope glycoprotein gp64 of YHV cannot be detected in the hemocytes and supernatant of the PmRab11 knockdown group from 24 to 72 h post-YHV challenge. The low signals of PmRab11 protein and YHV glycoprotein 64 (gp64) can be observed inside the hemocytes of PmRab11 knockdown shrimp at 24 h post-infection (Fig. 8B) . In contrast, high signals of PmRab11 and gp64 can be detected in shrimp that was injected with dsRNA-GFP and NaCl followed by YHV challenge at this time point. Similar results of the delay in shrimp mortalities can be demonstrated for the knockdown effects of other Rab proteins including PmRab7 and PmRab5 during YHV infection [11, 12] . abstract: Yellow head virus (YHV) is one of the most serious pathogens that causes worldwide shrimp production loss. It enters the cells via clathrin-mediated endocytosis and utilizes small GTPase Rab proteins such as PmRab5 and PmRab7 for intracellular trafficking. In this study, molecular cloning and functional analysis of Rab11 during YHV infection were investigated. PmRab11 cDNA was cloned by Rapid amplification of cDNA ends (RACEs). It contained two forms of sizes 1200 and 1050 bp distinct at the 5ʹ UTR. The coding region of PmRab11 was 645 bp, encoding 214 amino acids. It also demonstrated the characteristics of Rab11 proteins containing five GTP-binding domains, five Rab family domains, four Rab subfamily domains and a prenylation site at the C-terminus. Suppression of PmRab11 using dsRNA-PmRab11 either before or after YHV-challenge resulted in significant inhibition of YHV levels in the hemocytes and viral release in the supernatant in both mRNA and protein levels. In addition, the silencing effect of PmRab11 in YHV-infected shrimps resulted in a delay in shrimp mortality for at least 2 days. Immunofluorescence study showed co-localization between PmRab11 and YHV at 24–72 h post YHV-challenge. In contrast, the co-localization signals were absence in the PmRab11 knockdown hemocytes and the YHV signals accumulated at the perinuclear region at 24 h post YHV-challenge. Then, accumulation of YHV was hardly observed after 48–72 h. These results suggested that PmRab11 is required for YHV infection in shrimp. url: https://doi.org/10.1016/j.fsi.2017.05.039 doi: 10.1016/j.fsi.2017.05.039 id: cord-349745-zlhu1jit author: Konrad, Regina title: Rapid establishment of laboratory diagnostics for the novel coronavirus SARS-CoV-2 in Bavaria, Germany, February 2020 date: 2020-03-05 words: 2417.0 sentences: 137.0 pages: flesch: 55.0 cache: ./cache/cord-349745-zlhu1jit.txt txt: ./txt/cord-349745-zlhu1jit.txt summary: The need for timely establishment of diagnostic assays arose when Germany was confronted with the first travel-associated outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Europe. We found that the SARS-CoV E gene screening assay with the QuantiTect Virus +Rox Vial kit showed moderate to high amounts of unspecific signals in late cycles in 61% (451/743) of the tested patient samples and also of negative extraction and non-template controls (Table, Figure 2 ), which complicated the evaluation of the qPCR result. The Public Health Microbiology Laboratory in Bavaria was confronted with SARS-CoV-2-related events very early: once the assays and control materials arrived and the PCR assays were performed for the first time, a large contact investigation around the first German COVID-19 patient (data not shown) was immediately started, with so far more than 700 samples. abstract: The need for timely establishment of diagnostic assays arose when Germany was confronted with the first travel-associated outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Europe. We describe our laboratory experiences during a large contact tracing investigation, comparing previously published real-time RT-PCR assays in different PCR systems and a commercial kit. We found that assay performance using the same primers and probes with different PCR systems varied and the commercial kit performed well. url: https://www.ncbi.nlm.nih.gov/pubmed/32156330/ doi: 10.2807/1560-7917.es.2020.25.9.2000173 id: cord-264716-igl25jhg author: Koo, B.S. title: Molecular survey of enteric viruses in commercial chicken farms in Korea with a history of enteritis date: 2013-11-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Several enteric viruses have increasingly received attention as potential causative agents of runting-stunting syndrome (RSS) in chickens. A molecular survey was performed to determine the presence of a broad range of enteric viruses, namely chicken astrovirus (CAstV), avian nephritis virus (ANV), chicken parvovirus (ChPV), infectious bronchitis virus (IBV), avian rotavirus (AvRV), avian reovirus (ARV), and fowl adenovirus (FAdV), in intestinal samples derived from 34 commercial chicken flocks that experienced enteritis outbreaks between 2010 and 2012. Using techniques such as PCR and reverse-transcription PCR, enteric viruses were identified in a total of 85.3% of investigated commercial chicken flocks in Korea. Furthermore, diverse combinations of 2 or more enteric viruses were simultaneously identified in 51.7% of chicken farms positive for enteric viruses. The rank order of positivity for enteric viruses was as follows: ANV (44.1%), CAstV (38.2%), ChPV (26.5%), IBV (20.6%), ARV (8.8%), AvRV (5.9%), and FAdV (2.9%). Additionally, other pathogens such as Escherichia coli, Salmonella spp., Eimeria spp., and FAdV were detected in 79% of chicken flocks positive for enteric viruses using PCR, bacterial isolation, and microscopic examination. The results of our study indicate the presence of several enteric viruses with various combinations in commercial chicken farms that experienced enteritis outbreaks. Experimental studies are required to further understand the roles of enteric viruses in RSS in commercial chickens. url: https://doi.org/10.3382/ps.2013-03280 doi: 10.3382/ps.2013-03280 id: cord-264944-7xj27r98 author: Koopmans, Marion title: Optimization of extraction and PCR amplification of RNA extracts from paraffin-embedded tissue in different fixatives date: 1993-07-31 words: 5182.0 sentences: 255.0 pages: flesch: 54.0 cache: ./cache/cord-264944-7xj27r98.txt txt: ./txt/cord-264944-7xj27r98.txt summary: The method was compared to existing extraction techniques by studying the quality of the templates for reverse-transcriptase polymerase chain reaction amplification (RT-PCR), using virus-infected and mock-infected paraffin-embedded cell pellets as a model. The method was compared to existing extraction techniques by studying the quality of the templates for rcvcrsetranscriptase polymerase chain reaction amplification (RT-PCR), using virusinfected and mock-infected paraffin-embedded cell pellets as a model. In the work reported here we used paraffin-embedded torovirus-infected cell pellets to compare the effect of different fixatives and RNA extraction methods on RT-PCR amplification of tissue extracts. abstract: Abstract A method was developed for fast and efficient isolation of RNA from paraffin-embedded tissue sections for subsequent PCR analysis. This method is based on the binding of RNA to acid-treated glass beads in the presence of a high molarity of guanidinium salt. It can be completed within an hour, and obviates the need for dewaxing and phenol/chloroform extractions. The effect of various fixatives and fixation times was tested and the amplification of actin mRNA fragments ranging in length from 82 to 507 bp was used to demonstrate the presence of RNA in the extracts. The method was compared to existing extraction techniques by studying the quality of the templates for reverse-transcriptase polymerase chain reaction amplification (RT-PCR), using virus-infected and mock-infected paraffin-embedded cell pellets as a model. PCR amplification of cellular and viral RNA was successful for RNA isolated by use of all extraction techniques, although the glass bead method was preferred for its simplicity and rapidity. Specimens fixed with formalin were found to be suitable for PCR, but the best results were obtained with acetone-fixed paraffin-embedded material. Dewaxing of tissue sections had no effect on the yield and quality of RNA extractions, and further purification of the extracts using gel filtration did not improve the results. After the protocols were optimized, rotavirus-infected cell pellets were used to demonstrate that extraction and amplification of dsRNA was possible. The information obtained from the studies with the model system was used for extraction of toroviral and rotaviral RNA from archival intestinal material. These data indicate that paraffin-embedded archival tissue can be used for RT-PCR analysis, adding an important technique to diagnostic pathology and retrospective studies. url: https://www.ncbi.nlm.nih.gov/pubmed/8396155/ doi: 10.1016/0166-0934(93)90076-4 id: cord-255465-sc1yzzsn author: Krasteva, Gabriela title: Caveolin-1 and -2 in airway epithelium: expression and in situ association as detected by FRET-CLSM date: 2006-08-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Caveolae are involved in diverse cellular functions such as signal transduction, cholesterol homeostasis, endo- and transcytosis, and also may serve as entry sites for microorganisms. Hence, their occurrence in epithelium of the airways might be expected but, nonetheless, has not yet been examined. METHODS: Western blotting, real-time quantitative PCR analysis of abraded tracheal epithelium and laser-assisted microdissection combined with subsequent mRNA analysis were used to examine the expression of cav-1 and cav-2, two major caveolar coat proteins, in rat tracheal epithelium. Fluorescence immunohistochemistry was performed to locate caveolae and cav-1 and -2 in the airway epithelium of rats, mice and humans. Electron-microscopic analysis was used for the identification of caveolae. CLSM-FRET analysis determined the interaction of cav-1α and cav-2 in situ. RESULTS: Western blotting and laser-assisted microdissection identified protein and transcripts, respectively, of cav-1 and cav-2 in airway epithelium. Real-time quantitative RT-PCR analysis of abraded tracheal epithelium revealed a higher expression of cav-2 than of cav-1. Immunoreactivities for cav-1 and for cav-2 were co-localized in the cell membrane of the basal cells and basolaterally in the ciliated epithelial cells of large airways of rat and human. However, no labeling for cav-1 or cav-2 was observed in the epithelial cells of small bronchi. Using conventional double-labeling indirect immunofluorescence combined with CLSM-FRET analysis, we detected an association of cav-1α and -2 in epithelial cells. The presence of caveolae was confirmed by electron microscopy. In contrast to human and rat, cav-1-immunoreactivity and caveolae were confined to basal cells in mice. Epithelial caveolae were absent in cav-1-deficient mice, implicating a requirement of this caveolar protein in epithelial caveolae formation. CONCLUSION: These results show that caveolae and caveolins are integral membrane components in basal and ciliated epithelial cells, indicating a crucial role in these cell types. In addition to their physiological role, they may be involved in airway infection. url: https://www.ncbi.nlm.nih.gov/pubmed/16904002/ doi: 10.1186/1465-9921-7-108 id: cord-256146-d599uera author: Kuiken, Thijs title: Newly discovered coronavirus as the primary cause of severe acute respiratory syndrome date: 2003-07-26 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: The worldwide outbreak of severe acute respiratory syndrome (SARS) is associated with a newly discovered coronavirus, SARS-associated coronavirus (SARSCoV). We did clinical and experimental studies to assess the role of this virus in the cause of SARS. METHODS: We tested clinical and postmortem samples from 436 SARS patients in six countries for infection with SARSCoV, human metapneumovirus, and other respiratory pathogens. We infected four cynomolgus macaques (Macaca fascicularis) with SARS-CoV in an attempt to replicate SARS and did necropsies on day 6 after infection. FINDINGS: SARS-CoV infection was diagnosed in 329 (75%) of 436 patients fitting the case definition of SARS; human metapneumovirus was diagnosed in 41 (12%) of 335, and other respiratory pathogens were diagnosed only sporadically. SARS-CoV was, therefore, the most likely causal agent of SARS. The four SARS-CoV-infected macaques excreted SARS-CoV from nose, mouth, and pharynx from 2 days after infection. Three of four macaques developed diffuse alveolar damage, similar to that in SARS patients, and characterised by epithelial necrosis, serosanguineous exudate, formation of hyaline membranes, type 2 pneumocyte hyperplasia, and the presence of syncytia. SARS-CoV was detected in pneumonic areas by virus isolation and RT-PCR, and was localised to alveolar epithelial cells and syncytia by immunohistochemistry and transmission electron microscopy. INTERPRETATION: Replication in SARS-CoV-infected macaques of pneumonia similar to that in human beings with SARS, combined with the high prevalence of SARS-CoV infection in SARS patients, fulfill the criteria required to prove that SARS-CoV is the primary cause of SARS. Published online July 22, 2003 http://image.thelancet.com/extras/03art6318web.pdf url: https://www.ncbi.nlm.nih.gov/pubmed/12892955/ doi: 10.1016/s0140-6736(03)13967-0 id: cord-325113-sou8xyld author: Kuiper, Johannes W. P. title: Detection of SARS-CoV-2 from raw patient samples by coupled high temperature reverse transcription and amplification date: 2020-11-02 words: 4973.0 sentences: 241.0 pages: flesch: 51.0 cache: ./cache/cord-325113-sou8xyld.txt txt: ./txt/cord-325113-sou8xyld.txt summary: The use of unprocessed swap samples is enabled by employing a heat-stable RNAand DNA-dependent DNA polymerase, which performs the double task of stringent reverse transcription of RNA at elevated temperatures as well as PCR amplification of a SARS-CoV-2 specific target gene. A RNA-and DNA-reading heat-stable polymerase reverse transcribes and amplifies viral RNA Evidence of an acute SARS-CoV-2 infection depends on the detection of viral RNA species in patient samples, which necessitates reverse transcription of RNA followed by PCR amplification of the resulting DNA. To evaluate the potential of the high-temperature RT-PCR protocol using Volvano3G for the detection of viral RNAs in patient material, we assessed the presence of SARS-CoV-2 in RNA isolated from a small cohort of COVID-19 suspected cases. Interestingly, for most positive samples detected by the high-temperature RT-PCR with Volcano3G, the cq-values were lower compared to the standard RT-PCR (Fig 3C and 3D) , indicating that the detection of SARS-CoV-2 from unprocessed patient material is not limited by the sensitivity of this direct approach. abstract: SARS-CoV-2 is spreading globally with unprecedented consequences for modern societies. The early detection of infected individuals is a pre-requisite to contain the virus. Currently, purification of RNA from patient samples followed by RT-PCR is the gold standard to assess the presence of this single-strand RNA virus. However, these procedures are time consuming, require continuous supply of specialized reagents, and are prohibitively expensive in resource-poor settings. Here, we report an improved nucleic-acid-based approach to detect SARS-CoV-2 with the ability to detect as little as five viral genome equivalents. The approach delivers results without the need to purify RNA, reduces handling steps, minimizes costs, and allows evaluation by non-specialized equipment. The use of unprocessed swap samples is enabled by employing a heat-stable RNA- and DNA-dependent DNA polymerase, which performs the double task of stringent reverse transcription of RNA at elevated temperatures as well as PCR amplification of a SARS-CoV-2 specific target gene. As results are obtained within 2 hours and can be read-out by a hand-held LED-screen, this novel protocol will be of particular importance for large-scale virus surveillance in economically constrained settings. url: https://doi.org/10.1371/journal.pone.0241740 doi: 10.1371/journal.pone.0241740 id: cord-256456-rg366bk2 author: Kulcsar, Gabor title: Testing for viral contaminants of veterinary vaccines in Hungary date: 2010-05-31 words: 2801.0 sentences: 147.0 pages: flesch: 50.0 cache: ./cache/cord-256456-rg366bk2.txt txt: ./txt/cord-256456-rg366bk2.txt summary: Contrary to group 1, group 2 agents like Torque Teno virus (TTV) or RD114, a replication-competent feline γ-retrovirus, have only recently been recognised and their role as contaminants needs further investigation. Since 2007, 12 batches of live Aujeszky''s disease vaccines have been tested for Pestivirus by reverse transcriptase-polymerase chain reaction (RT-PCR), in the framework of the Official Control Authority Batch Release (OCABR). In addition, 27 poultry vaccines, from eight different manufacturers, used in Hungary between 1996 and 2009 were randomly selected and examined by PCR for the presence of chicken anaemia virus (CAV) and egg drop syndrome virus (EDSV). Contrary to the wellknown Group 1 agents, Group 2 contains new potential contaminants, such as TTV and/or RD114 virus, recently found to be present in vaccines. Swine Torque Teno virus detection in pig commercial vaccines, enzymes for laboratory use and human drugs containing components of porcine origin abstract: Abstract The safety of veterinary vaccines is of paramount importance and it is significantly jeopardised by extraneous agents such as bacteria, mycoplasma, Chlamydia and viruses. Several critical steps of vaccine manufacture involve a potential risk of viral contamination. Viruses, as extraneous, agents can be divided into two main groups. Group 1 agents, such as Pestivirus, chicken anaemia virus (CAV), and egg drop syndrome virus (EDSV) are well-known to manufacturers and authorities. Compendial detection methods, clear guidelines and legislation have been established to minimise the risk of contamination with these agents. Contrary to group 1, group 2 agents like Torque Teno virus (TTV) or RD114, a replication-competent feline γ-retrovirus, have only recently been recognised and their role as contaminants needs further investigation. Randomly selected veterinary vaccines used between 1992 and 2009 were tested by nucleic acid amplification for CAV, EDSV, and TTV. Pestivirus contamination was examined in 33 vaccines used between 1996 and 2006 and a further 27 vaccines used between 2007 and 2009 based on random selection of these vaccines. In addition to random tests done on vaccines used from 2007 on, 12 batches of live Aujeszky's disease vaccines submitted to our laboratory for Official Control Authority Batch Release (OCABR) were also tested for Pestivirus. url: https://doi.org/10.1016/j.biologicals.2010.01.007 doi: 10.1016/j.biologicals.2010.01.007 id: cord-314937-jrxu65bl author: Kuwelker, K. title: High attack rates of SARS-CoV-2 infection through household-transmission: a prospective study date: 2020-11-04 words: 5868.0 sentences: 391.0 pages: flesch: 55.0 cache: ./cache/cord-314937-jrxu65bl.txt txt: ./txt/cord-314937-jrxu65bl.txt summary: The secondary attack rate of SARS-CoV-2 from index cases to household contacts reflects the natural spread of infection in immunologically naive populations with limited preventive measures to control transmission. Here, we estimated the secondary household attack rate of SARS-CoV-2 and identified the determinants of household transmission by measuring SARS-CoV-2-specific antibodies in household members of RT-PCR confirmed cases during the first month of the COVID-19 pandemic in Norway. Our study was specifically designed to assess household attack rates as measured by seropositivity in household members 6-8 weeks after onset of symptoms in the index case, with low prevalence of SARS-CoV-2 virus in the community. We calculated attack rates based on SARS-CoV-2-specific antibodies in household members, whereas the majority of previous studies have ascertained transmission based on RT-PCR, with estimates of 7·6% to 38% (11) (12) (13) (14) (15) (16) (17) (18) (19) (20) . abstract: Background: Household attack rates of SARS-CoV-2 ranging from 7% to 38% have been reported, using reverse transcription polymerase chain reaction (RT-PCR) of respiratory samples. Lower attack rates were described in children, but the importance of age in household transmission dynamics remains to be clarified. Methods: During the first month of the outbreak, we enrolled 112 households (291 participants) in a prospective case-ascertained study, collecting demographic and clinical data from index cases and household members. Sera were collected 6-8 weeks after index case symptom onset, to measure SARS-CoV-2-specific antibodies. Findings: The overall household attack rate was 45% assessed by seroconversion, and 47% when also including RT-PCR positives. Serology identified a significantly higher number of infected household members than RT-PCR. Attack rates were equally high in children (43%) and young adults (46%), but highest among household members aged [≥]60 years (72%). The attack rate was 16% in asymptomatic household members, and 42% in RT-PCR negative household members. Older adults generally had higher antibody titres than younger adults. The risk of household transmission was higher when the index case had fever or dyspnoea during acute illness but not associated with cough. Interpretation: Serological assays provide more accurate estimates of household secondary attack rate than RT-PCR, especially among children who have a lower RT-PCR positivity rate. Children are equally susceptible to infection as adults, but elderly show higher attack rates. Negative RT-PCR or lack of symptoms are not sufficient to rule out infection in household members. url: https://doi.org/10.1101/2020.11.02.20224485 doi: 10.1101/2020.11.02.20224485 id: cord-309763-8eywr57j author: Kuypers, Jane title: Detection and quantification of human metapneumovirus in pediatric specimens by real-time RT-PCR date: 2005-02-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Human metapneumovirus (hMPV), a recently identified virus, causes respiratory illness in children. OBJECTIVES: A real-time reverse transcription-polymerase chain reaction (RT-PCR) assay was developed and used to detect and quantify hMPV in respiratory specimens. STUDY DESIGN: The quantitative RT-PCR assay amplified an approximately 70 base pair fragment from the hMPV fusion protein gene. The assay was validated and used to test respiratory specimens obtained from children seen at a hospital in Seattle, Washington, from December 2002 through May 2003. RESULTS: The assay detected 1000 hMPV copies/mL of specimen, did not detect 19 other respiratory viruses, and was able to detect and accurately quantify isolates from the four known hMPV genetic lineages in a proficiency panel of 20 previously tested samples. hMPV was detected in 52 (7.2%) of 719 pediatric respiratory specimens. The mean log 10 copies/mL of hMPV in the 52 positive specimens was 7.67 (range = 4.59–10.60). Children aged 7–12 months had a significantly higher hMPV prevalence (12.4%) than did children younger than 7 months (4.7%) (P < 0.005). Children in this age group also had significantly higher levels of hMPV in their respiratory specimens (mean log 8.43 copies/mL) than did the younger children (mean log 6.93 copies/mL) (P = 0.0025). CONCLUSIONS: The rapid real-time RT-PCR assay described here is a sensitive test for clarifying the epidemiology of and diseases associated with hMPV. url: https://www.ncbi.nlm.nih.gov/pubmed/16036180/ doi: 10.1016/j.jcv.2004.11.023 id: cord-284037-nj5jo1ev author: Kwee, Thomas C. title: Chest CT in COVID-19: What the Radiologist Needs to Know date: 2020-10-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Chest CT has a potential role in the diagnosis, detection of complications, and prognostication of coronavirus disease 2019 (COVID-19). Implementation of appropriate precautionary safety measures, chest CT protocol optimization, and a standardized reporting system based on the pulmonary findings in this disease will enhance the clinical utility of chest CT. However, chest CT examinations may lead to both false-negative and false-positive results. Furthermore, the added value of chest CT in diagnostic decision making is dependent on several dynamic variables, most notably available resources (real-time reverse transcription–polymerase chain reaction [RT-PCR] tests, personal protective equipment, CT scanners, hospital and radiology personnel availability, and isolation room capacity) and the prevalence of both COVID-19 and other diseases with overlapping manifestations at chest CT. Chest CT is valuable to detect both alternative diagnoses and complications of COVID-19 (acute respiratory distress syndrome, pulmonary embolism, and heart failure), while its role for prognostication requires further investigation. The authors describe imaging and managing care of patients with COVID-19, with topics including (a) chest CT protocol, (b) chest CT findings of COVID-19 and its complications, (c) the diagnostic accuracy of chest CT and its role in diagnostic decision making and prognostication, and (d) reporting and communicating chest CT findings. The authors also review other specific topics, including the pathophysiology and clinical manifestations of COVID-19, the World Health Organization case definition, the value of performing RT-PCR tests, and the radiology department and personnel impact related to performing chest CT in COVID-19. (©)RSNA, 2020 url: https://doi.org/10.1148/rg.2020200159 doi: 10.1148/rg.2020200159 id: cord-316173-ocdlh310 author: LIU, Dafei title: One-step triplex PCR/RT-PCR to detect canine distemper virus, canine parvovirus and canine kobuvirus date: 2018-01-23 words: 997.0 sentences: 48.0 pages: flesch: 56.0 cache: ./cache/cord-316173-ocdlh310.txt txt: ./txt/cord-316173-ocdlh310.txt summary: title: One-step triplex PCR/RT-PCR to detect canine distemper virus, canine parvovirus and canine kobuvirus To rapidly distinguish Canine distemper virus (CDV), canine parvovirus (CPV), and canine kobuvirus (CaKoV) in practice, a one-step multiplex PCR/RT-PCR assay was developed, with detection limits of 10(2.1) TCID(50) for CDV, 10(1.9) TCID(50) for CPV and 10(3) copies for CaKoV. Therefore, the assay provides a sensitive tool for the rapid clinical detection and epidemiological surveillance of CDV, CPV and CaKoV in dogs. The viral DNA/RNA of fecal samples collected from dogs with clinical symptoms of diarrhea were extracted and tested in parallel with both the one-step multiplex PCR/RT-PCR and the commercial Rapid CDV/CPV Ag Test Kit (Bionote, Gyeonggi, Republic of Korea) for CDV or CPV, according to the manufacturer''s instruction, and a traditional simplex RT-PCR for CaKoV, as described previously with minor modification [4] . Detection of canine distemper virus in dogs by real-time RT-PCR abstract: To rapidly distinguish Canine distemper virus (CDV), canine parvovirus (CPV), and canine kobuvirus (CaKoV) in practice, a one-step multiplex PCR/RT-PCR assay was developed, with detection limits of 10(2.1) TCID(50) for CDV, 10(1.9) TCID(50) for CPV and 10(3) copies for CaKoV. This method did not amplify nonspecific DNA or RNA from other canine viruses. Therefore, the assay provides a sensitive tool for the rapid clinical detection and epidemiological surveillance of CDV, CPV and CaKoV in dogs. url: https://www.ncbi.nlm.nih.gov/pubmed/29367517/ doi: 10.1292/jvms.17-0442 id: cord-320787-dwyyjq6o author: La Rosa, Giuseppina title: First detection of SARS-CoV-2 in untreated wastewaters in Italy date: 2020-05-23 words: 2747.0 sentences: 141.0 pages: flesch: 54.0 cache: ./cache/cord-320787-dwyyjq6o.txt txt: ./txt/cord-320787-dwyyjq6o.txt summary: Italy is among the world''s worst-affected countries in the COVID-19 pandemic, but so far there are no studies assessing the presence of SARS-CoV-2 in Italian wastewaters. To this aim, twelve influent sewage samples, collected between February and April 2020 from Wastewater Treatment Plants in Milan and Rome, were tested adapting, for concentration, the standard WHO procedure for Poliovirus surveillance. SARS-CoV-2 RNA detection was accomplished in volumes of 250 mL of wastewaters collected in areas of high (Milan) and low (Rome) epidemic circulation, according to clinical data. Herein we report the results of the screening for SARS-CoV-2 presence in sewage samples collected between the end of February and the beginning of April 2020 from WWTPs in Milan (Northern Italy) and Rome (Central Italy). In the absence of a standardized method for SARS-CoV-2 detection in environmental samples, RNAs were tested for the presence of SARS-CoV-2 using three different nested RT-PCR assays and one real-time qPCR assay (Table 1 and Figure 1 b) a newly designed primer set specific for SARS-CoV-2. abstract: Abstract Several studies have demonstrated the advantages of environmental surveillance through the monitoring of sewage for the assessment of viruses circulating in a given community (wastewater-based epidemiology, WBE). During the COVID-19 public health emergency, many reports have described the presence of SARS-CoV-2 RNA in stools from COVID-19 patients, and a few studies reported the occurrence of SARS-CoV-2 in wastewaters worldwide. Italy is among the world's worst-affected countries in the COVID-19 pandemic, but so far there are no studies assessing the presence of SARS-CoV-2 in Italian wastewaters. To this aim, twelve influent sewage samples, collected between February and April 2020 from Wastewater Treatment Plants in Milan and Rome, were tested adapting, for concentration, the standard WHO procedure for Poliovirus surveillance. Molecular analysis was undertaken with three nested protocols, including a newly designed SARS-CoV-2 specific primer set. SARS-CoV-2 RNA detection was accomplished in volumes of 250 mL of wastewaters collected in areas of high (Milan) and low (Rome) epidemic circulation, according to clinical data. Overall, 6 out of 12 samples were positive. One of the positive results was obtained in a Milan wastewater sample collected a few days after the first notified Italian case of autochthonous SARS-CoV-2. The study confirms that WBE has the potential to be applied to SARS-CoV-2 as a sensitive tool to study spatial and temporal trends of virus circulation in the population. url: https://doi.org/10.1016/j.scitotenv.2020.139652 doi: 10.1016/j.scitotenv.2020.139652 id: cord-289744-suiqh3gv author: Lafolie, Jérémy title: Assessment of blood enterovirus PCR testing in paediatric populations with fever without source, sepsis-like disease, or suspected meningitis: a prospective, multicentre, observational cohort study date: 2018-10-30 words: 4727.0 sentences: 239.0 pages: flesch: 48.0 cache: ./cache/cord-289744-suiqh3gv.txt txt: ./txt/cord-289744-suiqh3gv.txt summary: The aim of our multicentre study was to assess detection of enterovirus by PCR in blood specimens of newborn babies, infants, and children with fever without source, sepsis-like disease, or suspected meningitis. Evidence before this study We searched PubMed up to Feb 7, 2018, for papers reporting paediatric enterovirus diseases and enterovirus PCR testing or molecular detection of viruses in cerebrospinal fluid (CSF) or blood specimens of patients with aseptic meningitis, sepsis and sepsis-like disease, or fever without source. Our study of 360 patients with laboratory findings of enterovirus infection is, as far as we are aware, the largest prospective, multicentre, observational study to assess PCR testing for enterovirus in both blood and CSF samples from newborn babies (aged ≤28 days) and infants (aged >28 days to ≤2 years) with fever without source, sepsis-like disease, or suspected meningitis, and children (aged >2 years to ≤16 years) with suspected meningitis. abstract: BACKGROUND: Enteroviruses are the most frequent cause of acute meningitis and are seen increasingly in sepsis-like disease and fever without source in the paediatric population. Detection of enterovirus in cerebrospinal fluid (CSF) specimens by PCR is the gold standard diagnostic test. Our aim was to assess a method of detecting enterovirus in blood specimens by PCR. METHODS: We did a prospective, multicentre, observational study at 35 French paediatric and emergency departments in 16 hospitals. We recruited newborn babies (aged ≤28 days) and infants (aged >28 days to ≤2 years) with fever without source, sepsis-like disease, or suspected meningitis, and children (aged >2 years to ≤16 years) with suspected meningitis, who were admitted to a participating hospital. We used a standardised form to obtain demographic, clinical, and laboratory data, which were anonymised. Enterovirus PCR testing was done in blood and CSF specimens. FINDINGS: Between June 1, 2015, and Oct 31, 2015, and between June 1, 2016, and Oct 31, 2016, we enrolled 822 patients, of whom 672 had enterovirus PCR testing done in blood and CSF specimens. Enterovirus was detected in 317 (47%) patients in either blood or CSF, or both (71 newborn babies, 83 infants, and 163 children). Detection of enterovirus was more frequent in blood samples than in CSF specimens of newborn babies (70 [99%] of 71 vs 62 [87%] of 71; p=0·011) and infants (76 [92%] of 83 vs 62 [75%] of 83; p=0·008), and was less frequent in blood samples than in CSF specimens of children (90 [55%] of 163 vs 148 [91%] of 163; p<0·0001). Detection of enterovirus was more frequent in blood samples than in CSF specimens of infants aged 2 years or younger with fever without source (55 [100%] of 55 vs 41 [75%] of 55; p=0·0002) or with sepsis-like disease (16 [100%] of 16 vs nine [56%] of 16; p=0·008). Detection of enterovirus was less frequent in blood than in CSF of patients with suspected meningitis (165 [67%] of 246 vs 222 [90%] of 246; p<0·0001). INTERPRETATION: Testing for enterovirus in blood by PCR should be an integral part of clinical practice guidelines for infants aged 2 years or younger. This testing could decrease the length of hospital stay and reduce exposure to antibiotics for low-risk patients admitted to the emergency department with febrile illness. FUNDING: University Hospital Clermont-Ferrand. url: https://doi.org/10.1016/s1473-3099(18)30479-1 doi: 10.1016/s1473-3099(18)30479-1 id: cord-340710-dmow5p7k author: Lagana, Stephen M. title: Hepatic pathology in patients dying of COVID-19: a series of 40 cases including clinical, histologic, and virologic data date: 2020-08-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The novel coronavirus SARS-CoV-2 (coronavirus disease 19, or COVID-19) primarily causes pulmonary injury, but has been implicated to cause hepatic injury, both by serum markers and histologic evaluation. The histologic pattern of injury has not been completely described. Studies quantifying viral load in the liver are lacking. Here we report the clinical and histologic findings related to the liver in 40 patients who died of complications of COVID-19. A subset of liver tissue blocks were subjected to polymerase chain reaction (PCR) for viral ribonucleic acid (RNA). Peak levels of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were elevated; median ALT peak 68 U/l (normal up to 46 U/l) and median AST peak 102 U/l (normal up to 37 U/l). Macrovesicular steatosis was the most common finding, involving 30 patients (75%). Mild lobular necroinflammation and portal inflammation were present in 20 cases each (50%). Vascular pathology, including sinusoidal microthrombi, was infrequent, seen in six cases (15%). PCR of liver tissue was positive in 11 of 20 patients tested (55%). In conclusion, we found patients dying of COVID-19 had biochemical evidence of hepatitis (of variable severity) and demonstrated histologic findings of macrovesicular steatosis and mild acute hepatitis (lobular necroinflammation) and mild portal inflammation. We also identified viral RNA in a sizeable subset of liver tissue samples. url: https://doi.org/10.1038/s41379-020-00649-x doi: 10.1038/s41379-020-00649-x id: cord-303665-l57e54hu author: Lahrich, S. title: Review on the contamination of wastewater by COVID-19 virus: Impact and treatment date: 2020-09-10 words: 5849.0 sentences: 329.0 pages: flesch: 48.0 cache: ./cache/cord-303665-l57e54hu.txt txt: ./txt/cord-303665-l57e54hu.txt summary: Under these circumstances, the passive, but effective, method of sewage or wastewater monitoring can be used to trace and track the presence of SARS-CoV-2, through their genetic material RNA, and screen entire community. Since wastewater contains viruses that are repelled by everyone, regardless of their health, monitoring for viruses in wastewater and environmental waters that receive effluent from wastewater treatment plants (WWTPs) can determine the true prevalence and molecular epidemiology of gastroenteritis viruses and the risks to human health (Guan et al., 2020; Huang et al., 2020; Wang et al., 2020a) in a given geographical area rather than clinical research (Prevost et al., 2015; Kazama et al., 2017) . Therefore, the safety of drinking water and wastewater depends on the appropriate selection of the disinfectant dose and contact time in the treated environment, which are very important analytical techniques and methods that can detect viruses. Understanding how the virus breaks down in the aquatic environment is also critical to assessing risks to human health at present; the stability of the SARS-CoV-2 genome in wastewater is unclear. abstract: Emerging viruses are a major public health problem. Most zoonotic pathogens originate in wildlife, including human immunodeficiency virus (HIV), influenza, Ebola, and coronavirus. Severe acute respiratory syndrome (SARS) is a viral respiratory illness caused by a coronavirus called SARS-associated coronavirus (SARS-CoV). Viruses are charged colloidal particles that have the ability to adsorb on surfaces depending on pH. Their sorptive interaction with solid particles has important implications for their behavior in aquatic environments, soils, sewage sludge, and other solid materials and their removal or concentration by water treatment processes. Current state of knowledge on the potential of wastewater surveillance to understand the COVID-19 pandemic is reviewed. This study also identified wastewater irrigation systems with a higher risk of COVID-19 transmission. Emphasis was placed on methodologies for the detection and quantification of SARS-CoV-2 in wastewater. url: https://doi.org/10.1016/j.scitotenv.2020.142325 doi: 10.1016/j.scitotenv.2020.142325 id: cord-338899-qt17jhg0 author: Lakshmi, Vemu title: Clinical Features and Molecular Diagnosis of Chikungunya Fever from South India date: 2008-05-01 words: 3623.0 sentences: 178.0 pages: flesch: 48.0 cache: ./cache/cord-338899-qt17jhg0.txt txt: ./txt/cord-338899-qt17jhg0.txt summary: Emergence or reemergence of severe arboviral hemorrhagic fevers caused by mosquitoborne viruses, such as dengue virus and Chikungunya (CHIK) virus, have been frequently reported in the Indian subcontinent in the past few years. We report clinical observations and laboratory investigations involving virus isolation methods and molecular assays performed for 296 clinically suspected cases of CHIK fever. Of particular interest was the applicability of a novel method of gene amplificatio called real-time loop-mediated isothermal amplifica tion (RT-LAMP) as a rapid, sensitive, and specifi real-time method to detect and quantify CHIK virus in the acute phase of the infection. All 132 patients who had clinically suspected CHIK virus but whose RT-PCR and RT-LAMP results were negative presented 17 days after the onset of fever; this may be the reason for the negative test results. The RT-LAMP allows rapid, realtime detection of CHIK virus in acute-phase serum samples, without requiring sophisticated equipment, and has potential usefulness for clinical diagnosis and surveillance of CHIK virus in developing countries. abstract: An epidemic of Chikungunya fever of unprecedented magnitude occurred in many parts of India in early 2006 after an interval of 33 years, and there has been a resurgence in some parts of South India since June 2007. The article highlights clinical manifestations of infection and various molecular tests that were used for diagnoses of Chikungunya virus infection. Of particular interest is the real-time loop-mediated isothermal amplification (RT LAMP) assay, which is rapid and cost-effective and can be adopted at ill-equipped laboratories. Clinical symptoms were characterized by a triad of fever, rash, and severe rheumatic manifestations. RT LAMP identified 20 additional Chikungunya virus—positive cases, compared with reverse-transcriptase polymerase chain reaction. Chikungunya virus was isolated from 20 randomly selected samples. Genotyping of the virus isolates revealed that the East Central South African genotype of Chikungunya virus was the etiologic agent of this epidemic. Molecular diagnosis is an important tool to identify such new vectorborne viral illnesses. url: https://www.ncbi.nlm.nih.gov/pubmed/18419449/ doi: 10.1086/529444 id: cord-264392-he1vekrt author: Lambeth, L. S. title: Complete genome sequence of Nariva virus, a rodent paramyxovirus date: 2008-12-23 words: 4363.0 sentences: 204.0 pages: flesch: 52.0 cache: ./cache/cord-264392-he1vekrt.txt txt: ./txt/cord-264392-he1vekrt.txt summary: This study confirmed the classification of NarPV as a member of the subfamily Paramyxovirinae and established the close genome organization and sequence relationship between the two rodent paramyxoviruses isolated almost a decade apart and from two locations separated by more than 15,000 km. This was then followed by PCR to fill in the ''''gaps'''' using specific primers designed from NarPV Nariva virus genome 201 sequences obtained from the cDNA subtraction or degenerate primers designed using highly conserved consensus sequences of known paramyxoviruses in the subfamily Paramyxovirinae. Overall comparison of deduced sizes and amino acid sequences of all proteins indicated that NarPV is most closely related to MosPV (Table 1) genome is significantly larger (16,650 nt) than that of NarPV due to the longer untranslated regions (UTRs) located at the 3 0 end of most genes ( Fig. 1b and Table 1 ). abstract: Nariva virus (NarPV) was isolated from forest rodents (Zygodontomys b. brevicauda) in eastern Trinidad in the early 1960s. Initial classification within the family Paramyxoviridae was based mainly on morphological observations including the structure of nucleocapsids and virion surface projections. Here, we report the characterization of the complete genome sequence of NarPV. The genome is 15,276 nucleotides in length, conforming to the rule-of-six, and has a genome organization typical of most members of the family, with six transcriptional units in the order 3′-N–P-M-F–H-L-5′. The gene junctions contain highly conserved gene start and stop signals and a tri-nucleotide intergenic sequence present in most members of the subfamily Paramyxovirinae. Sequence comparison studies indicate that NarPV is most closely related to Mossman virus, which was isolated from wild rats (Rattus leucopus) in Queensland, Australia, in 1970. This study confirmed the classification of NarPV as a member of the subfamily Paramyxovirinae and established the close genome organization and sequence relationship between the two rodent paramyxoviruses isolated almost a decade apart and from two locations separated by more than 15,000 km. url: https://doi.org/10.1007/s00705-008-0287-3 doi: 10.1007/s00705-008-0287-3 id: cord-291360-z19ri377 author: Lan, Fan-Yun title: COVID-19 symptoms predictive of healthcare workers’ SARS-CoV-2 PCR results date: 2020-06-26 words: 4339.0 sentences: 251.0 pages: flesch: 52.0 cache: ./cache/cord-291360-z19ri377.txt txt: ./txt/cord-291360-z19ri377.txt summary: Of 509 HCWs with initial negative SARS-CoV-2 assays, nine had symptom progression and positive re-tests, yielding an estimated negative predictive value of 98.2% (95% CI: 96.8–99.0%) for the exclusion of clinically relevant COVID-19. CONCLUSIONS: Symptom and temperature reports are useful screening tools for predicting SARS-CoV-2 assay results in HCWs. Anosmia/ageusia, fever, and myalgia were the strongest independent predictors of positive assays. Therefore, we investigated the presenting symptoms most predictive of positive/negative SARS-CoV-2 RT-PCR results among HCWs. Since March 9, 2020, the occupational health service of a Massachusetts community healthcare system has implemented a staff "hotline" system to maintain a viable/healthy workforce and operational continuity during the pandemic. The clinical COVID-19 attack rate during the study period was calculated as: (the number of initial positive SARS-CoV-2 assays + the number of false negatives) divided by the system''s estimated total HCW population (n = 4600). abstract: BACKGROUND: Coronavirus 2019 disease (COVID-19) is caused by the virus SARS-CoV-2, transmissible both person-to-person and from contaminated surfaces. Early COVID-19 detection among healthcare workers (HCWs) is crucial for protecting patients and the healthcare workforce. Because of limited testing capacity, symptom-based screening may prioritize testing and increase diagnostic accuracy. METHODS AND FINDINGS: We performed a retrospective study of HCWs undergoing both COVID-19 telephonic symptom screening and nasopharyngeal SARS-CoV-2 assays during the period, March 9—April 15, 2020. HCWs with negative assays but progressive symptoms were re-tested for SARS-CoV-2. Among 592 HCWs tested, 83 (14%) had an initial positive SARS-CoV-2 assay. Fifty-nine of 61 HCWs (97%) who were asymptomatic or reported only sore throat/nasal congestion had negative SARS-CoV-2 assays (P = 0.006). HCWs reporting three or more symptoms had an increased multivariate-adjusted odds of having positive assays, 1.95 (95% CI: 1.10–3.64), which increased to 2.61 (95% CI: 1.50–4.45) for six or more symptoms. The multivariate-adjusted odds of a positive assay were also increased for HCWs reporting fever and a measured temperature ≥ 37.5°C (3.49 (95% CI: 1.95–6.21)), and those with myalgias (1.83 (95% CI: 1.04–3.23)). Anosmia/ageusia (i.e. loss of smell/loss of taste) was reported less frequently (16%) than other symptoms by HCWs with positive assays, but was associated with more than a seven-fold multivariate-adjusted odds of a positive test: OR = 7.21 (95% CI: 2.95–17.67). Of 509 HCWs with initial negative SARS-CoV-2 assays, nine had symptom progression and positive re-tests, yielding an estimated negative predictive value of 98.2% (95% CI: 96.8–99.0%) for the exclusion of clinically relevant COVID-19. CONCLUSIONS: Symptom and temperature reports are useful screening tools for predicting SARS-CoV-2 assay results in HCWs. Anosmia/ageusia, fever, and myalgia were the strongest independent predictors of positive assays. The absence of symptoms or symptoms limited to nasal congestion/sore throat were associated with negative assays. url: https://doi.org/10.1371/journal.pone.0235460 doi: 10.1371/journal.pone.0235460 id: cord-263118-6sf41rsj author: Landry, Marie L. title: Real-time PCR compared to Binax NOW and cytospin-immunofluorescence for detection of influenza in hospitalized patients date: 2008-07-18 words: 2586.0 sentences: 137.0 pages: flesch: 56.0 cache: ./cache/cord-263118-6sf41rsj.txt txt: ./txt/cord-263118-6sf41rsj.txt summary: STUDY DESIGN: Binax NOW, cytospin-enhanced direct immunofluoroescence (DFA), and influenza A and B multiplex TaqMan RT-PCR were performed on 237 clinical samples. RESULTS: Binax NOW detected 70 (53.0%), cytospin-DFA detected 127 (96.2%), and TaqMan RT-PCR detected 132 (100%) influenza-positive samples. CONCLUSIONS: The accuracy of real-time RT-PCR should greatly improve the diagnosis of influenza in hospitals using simple rapid flu tests, but may have a more modest impact in hospitals with expertise in cytospin-DFA. In our hospital, cytospin-enhanced direct immunofluorescence (DFA) is performed on respiratory samples when Virology is open, and a rapid influenza test, Binax NOW, is used in the Core Laboratory when Virology is closed (Landry and Ferguson, 2000; Landry et al., 2004) . During the study period, reflex cultures were performed on 683 DFA-negative samples, but only three influenza A positives were detected. abstract: BACKGROUND: Rapid tests have had a significant impact on influenza diagnosis, but more accurate tests are needed for hospitalized patients who test negative by rapid methods. OBJECTIVE: We sought to determine the increased yield obtained from influenza RT-PCR in hospitalized patients compared to two rapid methods. STUDY DESIGN: Binax NOW, cytospin-enhanced direct immunofluoroescence (DFA), and influenza A and B multiplex TaqMan RT-PCR were performed on 237 clinical samples. RESULTS: Binax NOW detected 70 (53.0%), cytospin-DFA detected 127 (96.2%), and TaqMan RT-PCR detected 132 (100%) influenza-positive samples. The difference in sensitivity was significant between RT-PCR and Binax NOW (p < 0.0001), but not between RT-PCR and cytospin-DFA (p = 0.0736). Two samples testing positive for influenza B by all three methods, tested falsely positive for influenza A by Binax. Eight true positive samples did not become reactive by Binax until 30 min, and thus were counted as negative. CONCLUSIONS: The accuracy of real-time RT-PCR should greatly improve the diagnosis of influenza in hospitals using simple rapid flu tests, but may have a more modest impact in hospitals with expertise in cytospin-DFA. Further studies are needed to determine the effect of influenza RT-PCR on patient management and costs in hospitalized patients. url: https://www.ncbi.nlm.nih.gov/pubmed/18639488/ doi: 10.1016/j.jcv.2008.06.006 id: cord-022310-yc6xtw0s author: Lappin, Michael R. title: Microbiology and Infectious Disease date: 2011-12-15 words: 14109.0 sentences: 913.0 pages: flesch: 39.0 cache: ./cache/cord-022310-yc6xtw0s.txt txt: ./txt/cord-022310-yc6xtw0s.txt summary: 47 Because of these findings, it is currently recommended to combine serologic test results with those of blood culture or PCR assay results when evaluating clinically ill cats for bartonellosis. Because serologic test results do not accurately correlate with presence of bacteremia and individual culture or PCR assay results can be falsely negative, there is no indication for testing healthy cats for Bartonella spp. T. gondii-specific IgM is detectable in serum by ELISA in approximately 80% of subclinically ill cats 2 to 4 weeks after experimental induction of toxoplasmosis; these titers generally are negative less than 16 weeks after infection. The author, however, has demonstrated IgG antibody titers greater than 1 : 16,384 in subclinically ill cats 5 years after experimental induction In chronic disease or asymptomatic carriers, demonstration of organisms is unreliable, and a tentative diagnosis is based on clinical signs and a positive titer. gondii-specific antibodies can also be detected in the serum, CSF, and aqueous humor of healthy, infected animals, one cannot assay results in clinically ill dogs, E. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155555/ doi: 10.1016/b978-1-4377-0657-4.00015-6 id: cord-326017-qw4qynqv author: Laskar, Partha title: “Tomorrow Never Dies”: Recent Advances in Diagnosis, Treatment, and Prevention Modalities against Coronavirus (COVID-19) amid Controversies date: 2020-08-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The outbreak of novel coronavirus disease (2019-nCoV or COVID-19) is responsible for severe health emergency throughout the world. The attack of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is found to be responsible for COVID-19. The World Health Organization has declared the ongoing global public health emergency as a pandemic. The whole world fights against this invincible enemy in various capacities to restore economy, lifestyle, and safe life. Enormous amount of scientific research work(s), administrative strategies, and economic measurements are in place to create a successful step against COVID-19. Furthermore, differences in opinion, facts, and implementation methods laid additional layers of complexities in this battle against survival. Thus, a timely overview of the recent, important, and overall inclusive developments against this pandemic is a pressing need for better understanding and dealing with COVID-19. In this review, we have systematically summarized the epidemiological studies, clinical features, biological properties, diagnostic methods, treatment modalities, and preventive measurements related to COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32781617/ doi: 10.3390/diseases8030030 id: cord-270964-kxze0470 author: Lau, Kwok-Kwong title: Possible Central Nervous System Infection by SARS Coronavirus date: 2004-02-17 words: 1556.0 sentences: 93.0 pages: flesch: 57.0 cache: ./cache/cord-270964-kxze0470.txt txt: ./txt/cord-270964-kxze0470.txt summary: On day 22 of illness, generalized tonic-clonic convulsion developed in a 32-year-old woman with severe acute respiratory syndrome (SARS). In our patient, the occurrence of generalized convulsion with a positive RT-PCR for SARS-CoV in the CSF suggests possible infection of the central nervous system by SARS-CoV. The findings from our patient are not compatible with multiple sclerosis, and the PCR result suggests that the central nervous system (CNS) is affected by SARS-CoV. The possibility also remains that infection of the CNS never occurred, as suggested by the lack of focal neurologic deficit, normal CSF pressure, cell count, and biochemistry. Besides involvement of the lungs and possibly the CNS, no good alternative explanation exists for acute renal failure in this patient. Renal failure could possibly be caused by SARS-CoV involving the kidneys. Additionally, our patient had diarrhea from day 3 to day 20, with positive RT-PCR for SARS-CoV in stool specimens, suggesting involvement of the gastrointestinal tract as well. abstract: On day 22 of illness, generalized tonic-clonic convulsion developed in a 32-year-old woman with severe acute respiratory syndrome (SARS). Cerebrospinal fluid tested positive for SARS coronavirus (SARS-CoV) by reverse transcriptase–polymerase chain reaction. SARS-CoV may have caused an infection in the central nervous system in this patient. url: https://www.ncbi.nlm.nih.gov/pubmed/15030709/ doi: 10.3201/eid1002.030638 id: cord-353353-njvalb44 author: Lau, Susanna K. P. title: Identification of Novel Rosavirus Species That Infects Diverse Rodent Species and Causes Multisystemic Dissemination in Mouse Model date: 2016-10-13 words: 6982.0 sentences: 314.0 pages: flesch: 44.0 cache: ./cache/cord-353353-njvalb44.txt txt: ./txt/cord-353353-njvalb44.txt summary: Analysis of 13 complete genome sequences showed that "Rosavirus B" and "Rosavirus C" represent two potentially novel picornavirus species infecting different rodents. Rosavirus C isolated from 3T3 cells causes multisystemic diseases in a mouse model, with high viral loads and positive viral antigen expression in organs of infected mice after oral or intracerebral inoculation. Rosavirus C isolated from cell culture causes multisystemic diseases in a mouse model, with histopathological changes and positive viral antigen expression in lungs and liver of infected mice. A total of 13 complete genomes from samples of four different wild rodent species (chestnut spiny rat, Coxing''s white-bellied rat, roof rat and Indochinese forest rat) positive for "Rosavirus C" and one street rodent species (Norway rat) positive for "Rosavirus B" were sequenced directly from the positive respiratory or alimentary samples and characterized. Infected cell lines and tissues from challenged mice that were tested positive for rosavirus C RASM14A by RT-PCR were subject to viral load studies and immunohistochemical staining for viral VP1 protein as described previously [28, 69] . abstract: While novel picornaviruses are being discovered in rodents, their host range and pathogenicity are largely unknown. We identified two novel picornaviruses, rosavirus B from the street rat, Norway rat, and rosavirus C from five different wild rat species (chestnut spiny rat, greater bandicoot rat, Indochinese forest rat, roof rat and Coxing's white-bellied rat) in China. Analysis of 13 complete genome sequences showed that “Rosavirus B” and “Rosavirus C” represent two potentially novel picornavirus species infecting different rodents. Though being most closely related to rosavirus A, rosavirus B and C possessed distinct protease cleavage sites and variations in Yn-Xm-AUG sequence in 5’UTR and myristylation site in VP4. Anti-rosavirus B VP1 antibodies were detected in Norway rats, whereas anti-rosavirus C VP1 and neutralizing antibodies were detected in Indochinese forest rats and Coxing's white-bellied rats. While the highest prevalence was observed in Coxing's white-bellied rats by RT-PCR, the detection of rosavirus C from different rat species suggests potential interspecies transmission. Rosavirus C isolated from 3T3 cells causes multisystemic diseases in a mouse model, with high viral loads and positive viral antigen expression in organs of infected mice after oral or intracerebral inoculation. Histological examination revealed alveolar fluid exudation, interstitial infiltration, alveolar fluid exudate and wall thickening in lungs, and hepatocyte degeneration and lymphocytic/monocytic inflammatory infiltrates with giant cell formation in liver sections of sacrificed mice. Since rosavirus A2 has been detected in fecal samples of children, further studies should elucidate the pathogenicity and emergence potential of different rosaviruses. url: https://www.ncbi.nlm.nih.gov/pubmed/27737017/ doi: 10.1371/journal.ppat.1005911 id: cord-274707-mxh38hwd author: Laureano, Ana Flávia Santarine title: The different tests for the diagnosis of COVID-19 - A review in Brazil so far date: 2020 words: 3736.0 sentences: 204.0 pages: flesch: 50.0 cache: ./cache/cord-274707-mxh38hwd.txt txt: ./txt/cord-274707-mxh38hwd.txt summary: The virus is now widespread and causing the current pandemic of COVID-19, a highly pathogenic viral pneumonia, commonly presented with fever and cough, which frequently lead to lower respiratory tract disease with poor clinical outcomes associated with older age and underlying health conditions. Most rapid tests use colloidal gold particles in a technique known as immunochromatography, also called lateral flow immunoassay, a type of sandwich assay that relies on a pair of antibodies used to recognize two independent epitopes of a protein, and therefore it can achieve high specificity (Zhou et al., 2012) . One of the first rapid tests (lateral flow immunoassay) for SARS-CoV-2 IgG and IgM immune responses was developed by professor''s Feng Ye group at the National Clinical Research Centre for Respiratory Disease in Guangzhou, China. Development and Clinical Application of A Rapid IgM-IgG Combined Antibody Test for SARS-CoV-2 Infection Diagnosis abstract: SARS-CoV-2 is a novel virus from the coronavirus family that emerged in the end of December 2019 in Wuhan, China. The virus is now widespread and causing the current pandemic of COVID-19, a highly pathogenic viral pneumonia, commonly presented with fever and cough, which frequently lead to lower respiratory tract disease with poor clinical outcomes associated with older age and underlying health conditions. Supportive care for patients is typically the standard protocol because no specific effective antiviral therapies have been identified so far. The current outbreak is challenging governments and health authorities all over the world. In here we present a comparison among the current diagnostic tools and kits being used to test Brazilian population. url: https://www.ncbi.nlm.nih.gov/pubmed/32491306/ doi: 10.5935/1518-0557.20200046 id: cord-004717-41ui4lqc author: Laurin, Marc-André title: Detection and genetic characterization of a novel pig astrovirus: relationship to other astroviruses date: 2011-09-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Emerging viruses represent a continuous threat to human health and to farmed animals, as evidenced on multiple occasions by outbreaks of influenza, henipavirus and SARS. Knowledge about the diversity of viromes present in reservoir species can lead to a better understanding of the origin of emerging pathogens. In this study, we extend the knowledge of astrovirus diversity in pigs by reporting the genetic characterization of an unknown astrovirus lineage. Phylogenetic analyses provided evidence that this porcine astrovirus lineage is unique and does not appear to share a recent common ancestor with any known mamastrovirus. The data reported in this study extend the number of porcine astrovirus lineages to a total of five, all of which most likely represent distinct species of different origins. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086720/ doi: 10.1007/s00705-011-1088-7 id: cord-332042-bqtflk7r author: LeBlanc, J. J. title: Validation of the Seegene RV15 multiplex PCR for the detection of influenza A subtypes and influenza B lineages during national influenza surveillance in hospitalized adults date: 2019-07-02 words: 4562.0 sentences: 227.0 pages: flesch: 44.0 cache: ./cache/cord-332042-bqtflk7r.txt txt: ./txt/cord-332042-bqtflk7r.txt summary: Influenza A and B viruses are identified and characterized using real-time reverse-transcriptase polymerase chain reaction (RT-PCR), and multiplex testing has been performed on a subset of patients to identify other respiratory virus aetiologies. The CIRN SOS Network comprises 15 to 45 acute care (depending on the year) hospitals across Canada, and influenza testing is performed using real-time reverse-transcriptase polymerase chain reaction (RT-PCR) methods derived from the World Health Organization (WHO) [12] [13] [14] . While WHO-based real-time RT-PCRs methods are often viewed as the reference standard for influenza virus detection, diagnostic laboratories and surveillance studies often test for other viral aetiologies of respiratory illness [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] . This study''s strengths include prospectively collected specimens from a defined patient population (adults hospitalized with acute respiratory illness), comparison of results against reference methods for influenza A and B detection, and analyses performed on influenza viruses characterized by subtyping or lineage determination. abstract: BACKGROUND: The Serious Outcomes Surveillance Network of the Canadian Immunization Research Network (CIRN SOS) has been performing active influenza surveillance since 2009 (ClinicalTrials.gov identifier: NCT01517191). Influenza A and B viruses are identified and characterized using real-time reverse-transcriptase polymerase chain reaction (RT-PCR), and multiplex testing has been performed on a subset of patients to identify other respiratory virus aetiologies. Since both methods can identify influenza A and B, a direct comparison was performed. METHODS: Validated real-time RT-PCRs from the World Health Organization (WHO) to identify influenza A and B viruses, characterize influenza A viruses into the H1N1 or H3N2 subtypes and describe influenza B viruses belonging to the Yamagata or Victoria lineages. In a subset of patients, the Seeplex RV15 One-Step ACE Detection assay (RV15) kit was also used for the detection of other respiratory viruses. RESULTS: In total, 1111 nasopharyngeal swabs were tested by RV15 and real-time RT-PCRs for influenza A and B identification and characterization. For influenza A, RV15 showed 98.0 % sensitivity, 100 % specificity and 99.7 % accuracy. The performance characteristics of RV15 were similar for influenza A subtypes H1N1 and H3N2. For influenza B, RV15 had 99.2 % sensitivity, 100 % specificity and 99.8 % accuracy, with similar assay performance being shown for both the Yamagata and Victoria lineages. CONCLUSIONS: Overall, the detection of circulating subtypes of influenza A and lineages of influenza B by RV15 was similar to detection by real-time RT-PCR. Multiplex testing with RV15 allows for a more comprehensive respiratory virus surveillance in hospitalized adults, without significantly compromising the reliability of influenza A or B virus detection. url: https://doi.org/10.1099/jmm.0.001032 doi: 10.1099/jmm.0.001032 id: cord-290976-dhwlr2ui author: Lednicky, John A title: Isolation and genetic characterization of human coronavirus NL63 in primary human renal proximal tubular epithelial cells obtained from a commercial supplier, and confirmation of its replication in two different types of human primary kidney cells date: 2013-06-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Cryopreserved primary human renal proximal tubule epithelial cells (RPTEC) were obtained from a commercial supplier for studies of Simian virus 40 (SV40). Within twelve hrs after cell cultures were initiated, cytoplasmic vacuoles appeared in many of the RPTEC. The RPTEC henceforth deteriorated rapidly. Since SV40 induces the formation of cytoplasmic vacuoles, this batch of RPTEC was rejected for the SV40 study. Nevertheless, we sought the likely cause(s) of the deterioration of the RPTEC as part of our technology development efforts. METHODS: Adventitious viruses in the RPTEC were isolated and/or detected and identified by isolation in various indicator cell lines, observation of cytopathology, an immunoflurorescence assay, electron microscopy, PCR, and sequencing. RESULTS: Cytomegalovirus (CMV) was detected in some RPTEC by cytology, an immunofluorescence assay, and PCR. Human Herpesvirus 6B was detected by PCR of DNA extracted from the RPTEC, but was not isolated. Human coronavirus NL63 was isolated and identified by RT-PCR and sequencing, and its replication in a fresh batch of RPTEC and another type of primary human kidney cells was confirmed. CONCLUSIONS: At least 3 different adventitious viruses were present in the batch of contaminated RPTEC. Whereas we are unable to determine whether the original RPTEC were pre-infected prior to their separation from other kidney cells, or had gotten contaminated with HCoV-NL63 from an ill laboratory worker during their preparation for commercial sale, our findings are a reminder that human-derived biologicals should always be considered as potential sources of infectious agents. Importantly, HCoV-NL63 replicates to high titers in some primary human kidney cells. url: https://doi.org/10.1186/1743-422x-10-213 doi: 10.1186/1743-422x-10-213 id: cord-287104-4k8pqbc0 author: Lee, J. Y. title: Development of Rapid and Specific Detection for the Human Aichivirus A Using the Loop-Mediated Isothermal Amplification from Water Samples date: 2019-04-04 words: 2019.0 sentences: 108.0 pages: flesch: 53.0 cache: ./cache/cord-287104-4k8pqbc0.txt txt: ./txt/cord-287104-4k8pqbc0.txt summary: title: Development of Rapid and Specific Detection for the Human Aichivirus A Using the Loop-Mediated Isothermal Amplification from Water Samples In this study, developed a LAMP method to achieve a rapid, specific and highly sensitive detection of AiV-A. A newly developed method was more rapid (approximately 2–8 h), specific and equivalent detection of AiV-A than with the conventional PCRs. In addition, confirm system of positive LAMP reaction was developed by using the restriction enzyme Aci I and Hae III. A method for detecting AiV-A specific genes by using reverse transcription nested polymerase chain reaction (RT-PCR) assay, have been reported [15] [16] [17] . In this study, developed a rapid, specific and highly sensitive detection of AiV-A by using a LAMP assay. In this study, developed a LAMP assay that could rapid, specific, and sensitive detection of AiV-A from water samples. abstract: Human Aichivirus A (AiV-A) is classified as a Kobuvirus, group IV positive sense single strand RNA viruses. The first outbreak of AiV-A was reported from Aichi Prefecture, Japan in 1989. AiV-A exists not only among clinical patients, such as diarrhea, but also in a variety of water environments, as its occurrence is reported across a wide geographical range, from developing to advanced countries. For diagnose of AiV-A from water samples, mostly polymerase chain reaction (PCR) system have been developed. However, loop-mediated isothermal amplification (LAMP) assay has not been applied. In this study, developed a LAMP method to achieve a rapid, specific and highly sensitive detection of AiV-A. The method developed in this study is aimed specifically at AiV-A. Through a specific and non-specific selection and sensitivity test process for the five prepared LAMP primer sets, one primer set and optimum reaction temperature were selected. A newly developed method was more rapid (approximately 2–8 h), specific and equivalent detection of AiV-A than with the conventional PCRs. In addition, confirm system of positive LAMP reaction was developed by using the restriction enzyme Aci I and Hae III. For evaluation and verification of developing LAMP assay, a was applied to twenty cDNA from groundwater samples. This study proved rapid and specific diagnosis of AiV-A from water samples, and it is also demanded to be applicable to other environmental, clinical and food samples. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12088-019-00803-3) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s12088-019-00803-3 doi: 10.1007/s12088-019-00803-3 id: cord-004003-rlgzgyzn author: Lee, Jeewon title: Applying a Linear Amplification Strategy to Recombinase Polymerase Amplification for Uniform DNA Library Amplification date: 2019-11-12 words: 3386.0 sentences: 200.0 pages: flesch: 51.0 cache: ./cache/cord-004003-rlgzgyzn.txt txt: ./txt/cord-004003-rlgzgyzn.txt summary: Thus, to amplify the size-variable DNA library uniformly, we introduced a linear amplification strategy with RPA and successfully improved the uniformity. Also, the average percentages of bases in the uniform range (uniformity value between 0.5 and 1.5) about the triplet experiment was improved from 56.3 and 49.2% by two-primer RPA to 73.6 and 75.7% by linear RPA for the small and large DNA libraries, respectively (Figures 2b and S5) . Taken together, the data show that RPA uniformly amplifies DNA libraries of the same size and has different amplification preferences than PCR. However, during the experiment, an accelerated small-sized DNA amplification by two-primer RPA reaction caused lower uniformity compared to PCR. It was noted that during the analysis, different amplification preferences were found between the PCR and RPA amplified oligo library sequencing data. Taken together, we show that single-primer linear RPA can be one of the alternative methods to PCR for DNA library amplification. abstract: [Image: see text] Recombinase polymerase amplification (RPA) is an isothermal DNA amplification method with broad applications as a point-of-care test and in molecular biology techniques. Currently, most of the applications are focused on target-specific amplification. Because RPA has the advantage of amplifying DNA under isothermal conditions, we utilized RPA as a DNA library amplification tool. In this study, we used a sheared genomic DNA library and an oligonucleotide (oligo) library for the comparison of polymerase chain reaction and RPA. For the sheared DNA library, we observed biased amplification after RPA was conducted. Thus, to amplify the size-variable DNA library uniformly, we introduced a linear amplification strategy with RPA and successfully improved the uniformity. On the other hand, using the same-sized oligo library, we confirmed that RPA amplified this library uniformly without modification of the protocol. These results demonstrate that RPA can be applied not only to amplify a specific target as previously demonstrated but also to amplify a complex DNA library composed of a large number of different DNA molecules. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6882106/ doi: 10.1021/acsomega.9b02886 id: cord-337206-jo29nx9b author: Lee, Jong-Han title: Identification of Adenovirus, Influenza Virus, Parainfluenza Virus, and Respiratory Syncytial Virus by Two Kinds of Multiplex Polymerase Chain Reaction (PCR) and a Shell Vial Culture in Pediatric Patients with Viral Pneumonia date: 2010-09-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: PURPOSE: Early identification of causative agents in lower respiratory infection of pediatric patients can reduce morbidity and prevent an overuse of antimicrobials. Two kinds of multiplex polymerase chain reaction (PCR) and a commercial shell vial viral culture were performed to identify causative agents in pediatric patients. MATERIALS AND METHODS: Nasopharyngeal aspirates of 220 children diagnosed with viral pneumonia were obtained. Two kinds of multiplex PCR (Seeplex™ RV detection kit, and Labopass™ RV detection kit), and a shell vial culture by R-Mix were performed. RESULTS: Positive samples from 220 total samples by two multiplex PCRs were 52.7% and 46.4%, respectively. We also cultured 103 samples that showed positive results of the adenovirus, influenza virus, parainfluenza virus, and respiratory syncytial virus (RSV) by two multiplex PCR. The RSV was most frequently detected in 53.0% (Seeplex) and 51.7% (Labopass) of patients. The detection rate of adenovirus (AdV) was 10.3% and 12.1%, influenza virus (IFV) A and B was 12.5% and 3.4%, and parainfluenza virus (PIFV) 1, 2, and 3 were 2.9% and 2.6%. Shell vial cultures showed concordant results with each multiplex PCR by 96.1% and 77.7%, respectively. Sequencing results were 90% consistent with multiplex PCR. CONCLUSION: Multiplex PCR showed more positivity than the shell vial culture and it can be an effective primary test. Other complementary efforts such as viral cultures and sequencing analysis could be considered, according to clinical and laboratory conditions. url: https://www.ncbi.nlm.nih.gov/pubmed/20635453/ doi: 10.3349/ymj.2010.51.5.761 id: cord-255871-dau9tz6u author: Lee, Mi-Kyung title: Survey of Clinical Laboratory Practices for 2015 Middle East Respiratory Syndrome Coronavirus Outbreak in the Republic of Korea date: 2015-12-18 words: 2610.0 sentences: 130.0 pages: flesch: 48.0 cache: ./cache/cord-255871-dau9tz6u.txt txt: ./txt/cord-255871-dau9tz6u.txt summary: BACKGROUND: It is crucial to understand the current status of clinical laboratory practices for the largest outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infections in the Republic of Korea to be well prepared for future emerging infectious diseases. The number of MERS-CoV rRT-PCR tests performed was collected from 32 medical institutions and five referral medical laboratories. A total of 27,009 MERS-CoV rRT-PCR tests were performed at 32 medical institutions (N = 11,502) and five referral medical laboratories (N = 15,507) (Table 1 and Fig. 1 ). The proportion of medical institutions was significantly underestimated because one tertiary care hospital submitted responses for the survey but not the specimen list, and the numbers of MERS-CoV rRT-PCR tests and positive specimens at this institution would have been predominant in the reporting medical institutions. Table 2 shows the current status of clinical laboratories in medical institutions with respect to their response to the outbreak of MERS-CoV infections. abstract: BACKGROUND: It is crucial to understand the current status of clinical laboratory practices for the largest outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infections in the Republic of Korea to be well prepared for future emerging infectious diseases. METHODS: We conducted a survey of 49 clinical laboratories in medical institutions and referral medical laboratories. A short questionnaire to survey clinical laboratory practices relating to MERS-CoV diagnostic testing was sent by email to the directors and clinical pathologists in charge of the clinical laboratories performing MERS-CoV testing. The survey focused on testing volume, reporting of results, resources, and laboratory safety. RESULTS: A total of 40 clinical laboratories responded to the survey. A total of 27,009 MERS-CoV real-time reverse transcription PCR (rRT-PCR) tests were performed. Most of the specimens were sputum (73.5%). The median turnaround time (TAT) was 5.29 hr (first and third quartile, 4.11 and 7.48 hr) in 26 medical institutions. The median TAT of more than a half of the laboratories (57.7%) was less than 6 hr. Many laboratories were able to perform tests throughout the whole week. Laboratory biosafety preparedness included class II biosafety cabinets (100%); separated pre-PCR, PCR, and post-PCR rooms (88.6%); negative pressure pretreatment rooms (48.6%); and negative pressure sputum collection rooms (20.0%). CONCLUSIONS: Clinical laboratories were able to quickly expand their diagnostic capacity in response to the 2015 MERS-CoV outbreak. Our results show that clinical laboratories play an important role in the maintenance and enhancement of laboratory response in preparation for future emerging infections. url: https://www.ncbi.nlm.nih.gov/pubmed/26709263/ doi: 10.3343/alm.2016.36.2.154 id: cord-004810-g0y7ied0 author: Lee, S. K. title: S1 glycoprotein gene analysis of infectious bronchitis viruses isolated in Korea date: 2003-11-13 words: 3750.0 sentences: 190.0 pages: flesch: 59.0 cache: ./cache/cord-004810-g0y7ied0.txt txt: ./txt/cord-004810-g0y7ied0.txt summary: The S1 glycoprotein gene of IBV isolates were amplified by reverse transcriptase – polymerase chain reaction (RT-PCR) and analyzed by restriction fragment length polymorphism (RFLP) analysis. And these IBV isolates showed different patterns from each other and non-Korean IBV isolates in reverse transcriptase-polymerase chain reaction-restriction fragment length polymorphism (RT-PCR-RFLP) analysis [29] . Amplified S1 genes were first classified by RFLP analysis and then the representative strains were cloned, sequenced and compared to other non-Korean published IBV sequences. Phylogenetic trees were constructed from the nucleotide and deduced amino acid sequences of the S1 glycoprotein genes of Korean IBV isolates and non-Korean IBV strains (Fig. 3) . Korean IBV K281-01 and K210-02 isolates formed distinct clusters that were related to non-Korean IBV Ark99, Ark DPI, Gray and JMK strains although K281-01 and K210-02 isolates were classified into the Arkansas type by PCR-RFLP analysis. abstract: Fifteen isolates of Infectious bronchitis virus (IBV) were obtained from the kidney, trachea, and cecal tonsil of IB suspected chickens between 2001 and 2002 years in Korea. The S1 glycoprotein gene of IBV isolates were amplified by reverse transcriptase – polymerase chain reaction (RT-PCR) and analyzed by restriction fragment length polymorphism (RFLP) analysis. Fifteen Korean IBV isolates were classified into 4 groups by their RFLP patterns using restriction enzymes, HaeIII, BstYI, and XcmI. The RFLP patterns for 3, 1, and 1 of 15 isolates corresponded to the patterns of IBV Arkansas, Connecticut, and Massachusetts strains, respectively. Ten of 15 isolates generated unique KM91 RFLP pattern that was observed in the IBV KM 91 strain previously isolated in Korea. To confirm genetic diversity in the S1 genes of IBV isolates, viral RNAs of representative 9 of 15 IBV isolates were amplified, cloned, sequenced and compared with published sequences for non-Korean IBV strains. Korean IBV isolates showed amino acid sequence similarity between 61.8% (K446-01 and K161-02) and 96.1% (K281-01 and K210-02) with each other and they showed amino acid sequence similarity between 42.9% (K161-02 and GA980470) and 96.5% (K203-02 and KB8523) compared to non-Korean IBV strains. By phylogenetic tree analysis, Korean IBV field isolates were branched into five clusters in which 3 clusters were differentiated from non-Korean IBV strains. Especially, Korean IBV isolates K069-01, K507-01, K774-01 and K142-02 formed a separate cluster. It seems that IBVs continue to evolve and IBVs showing various genetic differences may cocirculate in Korea. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087141/ doi: 10.1007/s00705-003-0225-3 id: cord-351125-asrezu1f author: Lee, Sangmin title: Identification of Cystoisospora ohioensis in a Diarrheal Dog in Korea date: 2018-08-31 words: 1718.0 sentences: 115.0 pages: flesch: 50.0 cache: ./cache/cord-351125-asrezu1f.txt txt: ./txt/cord-351125-asrezu1f.txt summary: Although multiplex real-time PCR was positive for Cyclospora cayetanensis, the final diagnosis was Cystoisospora ohioensis infection, confirmed by phylogenetic analysis of 18S rRNA. ohioensis was identified in a Korean dog, using microscopy of diarrheal stools and confirmed using phylogenetic analysis of 18S ribosomal RNA (rRNA). Blood chemistry and hematology profile were analyzed using the Fuji DRI-CHEM NX500 automated clinical chemistry analyzer (Fuji, Tokyo, Japan) and veterinary hematology analyzer PE-Identification of Cystoisospora ohioensis in a Diarrheal Dog in Korea 6800 VET (Prokan, Shenzhen, China), respectively. Immunochromatographic assay, multiplex real-time polymerase chain reaction (PCR), and reverse transcription PCR (RT-PCR) were performed at POBANILAB using POBGEN canine enteric pathogen detection kits ( In order to confirm coccidian organisms in fecal samples, sequence analysis was performed as described previously [7] . Based on multiplex real-time PCR and fecal smear analyses, trimethoprim-sulfamethoxazole and metronidazole were initially administered to the puppy for treatment of the condition tentatively diagnosed as canine cyclosporiasis. abstract: A 3-month-old female Maltese puppy was hospitalized with persistent diarrhea in a local veterinary clinic. Blood chemistry and hematology profile were analyzed and fecal smear was examined. Diarrheal stools were examined in a diagnostic laboratory, using multiplex real-time polymerase chain reaction (PCR) against 23 diarrheal pathogens. Sequence analysis was performed using nested PCR amplicon of 18S ribosomal RNA. Coccidian oocysts were identified in the fecal smear. Although multiplex real-time PCR was positive for Cyclospora cayetanensis, the final diagnosis was Cystoisospora ohioensis infection, confirmed by phylogenetic analysis of 18S rRNA. To our knowledge, this the first case report of C. ohioensis in Korea, using microscopic examination and phylogenetic analysis. url: https://doi.org/10.3347/kjp.2018.56.4.371 doi: 10.3347/kjp.2018.56.4.371 id: cord-035280-z0bbz19b author: Lee, Seung Hun title: First identification of Anaplasma phagocytophilum in both a biting tick Ixodes nipponensis and a patient in Korea: a case report date: 2020-11-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Human granulocytic anaplasmosis (HGA) is a tick-borne infectious disease caused by Anaplasma phagocytophilum. To date, there have been no reported cases of A. phagocytophilum infection found in both the biting tick and the patient following a tick bite. CASE PRESENTATION: An 81-year-old woman presented with fever following a tick bite, with the tick still intact on her body. The patient was diagnosed with HGA. The tick was identified as Ixodes nipponensis by morphological and molecular biological detection methods targeting the 16S rRNA gene. The patient’s blood was cultured after inoculation into the human promyelocytic leukemia cell line HL-60. A. phagocytophilum growth was confirmed via culture and isolation. A. phagocytophilum was identified in both the tick and the patient’s blood by Anaplasma-specific groEL- and ankA-based nested polymerase chain reaction followed by sequencing. Moreover, a four-fold elevation in antibodies was observed in the patient’s blood. CONCLUSION: We report a case of a patient diagnosed with HGA following admission for fever due to a tick bite. A. phagocytophilum was identified in both the tick and the patient, and A. phagocytophilum was successfully cultured. The present study suggests the need to investigate the possible incrimination of I. nipponensis as a vector for HGA in Korea. SUPPLEMENTARY INFORMATION: Supplementary information accompanies this paper at 10.1186/s12879-020-05522-5. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7656494/ doi: 10.1186/s12879-020-05522-5 id: cord-274676-wtizb7hk author: Lee, Seung-Hun title: Multilocus typing of Cryptosporidium spp. in young calves with diarrhea in Korea date: 2016-10-15 words: 4374.0 sentences: 272.0 pages: flesch: 56.0 cache: ./cache/cord-274676-wtizb7hk.txt txt: ./txt/cord-274676-wtizb7hk.txt summary: Cryptosporidium prevalence was assessed by PCR and ELISA, and molecular characterization was performed by targeting the 18S rRNA, heat-shock protein 70 (hsp70), and glycoprotein 60 (gp60) genes. Previous studies using different methods found variable prevalence rates of Cryptosporidium in cattle: 49.4% (39/79) in Hungary using IFA (Plutzer and Karanis, 2007) , 11.9% (68/571) in the United States using PCR (Fayer et al., 2006) , 75.0% (60/80) in Japan using PCR (Karanis et al., 2010) , 20.0% (15/60) in New Zealand using IFA (Shrestha et al., 2014) , 5.1% (150/2945) in China using PCR (Zhang et al., 2015) , 21.5-22.5% in Ireland using direct fluorescence antibody testing (Mirhashemi et al., 2016) , and 10.2% (49/480) in Egypt using microscopy with staining (Ibrahim et al., 2016) . In addition, the PCR and ELISA results showed the same statistically significant differences with respect to the higher prevalence in the central region and lower prevalence in the case of hemorrhagic diarrhea. In addition, a higher prevalence at the farm level than the individual level was observed, regardless of the PCR or ELISA results, indicating a wide distribution of Cryptosporidium in calves in Korea. abstract: We assessed the prevalence and performed molecular analysis of Cryptosporidium spp. in diarrheal feces of calves in Korea. Diarrheal fecal samples were collected from 951 young calves (<3 months) on 425 farms. Cryptosporidium prevalence was assessed by PCR and ELISA, and molecular characterization was performed by targeting the 18S rRNA, heat-shock protein 70 (hsp70), and glycoprotein 60 (gp60) genes. Data were analyzed according to the sex, type of cattle, region, season, and type of diarrhea. PCR analysis revealed Cryptosporidium spp. in 9.9% (94/951) of diarrheal fecal samples. C. parvum and C. bovis/ryanae were present in 6.1% (58/951) and 4.1% (39/951) of diarrheal fecal samples, respectively. In addition, ELISA showed positive results for C. parvum in 9.7% (92/951) samples. Statistical analysis of the PCR and ELISA results revealed a lower prevalence of C. parvum in the hemorrhagic diarrheal samples (P < 0.05). For C. bovis/ryanae, seasonality and high prevalence in hemorrhagic diarrhea were observed (P < 0.05). Of the 951 samples tested for C. parvum, 903 samples showed agreement with a κ value of 0.65, indicating good agreement between the two tests. Although C. bovis and C. ryanae share highly similar 18S rRNA sequences, PCR based on hsp70 successfully distinguished C. bovis from C. ryanae. Sequence analysis of gp60 revealed that C. parvum belonged to the IIa families and was further subtyped as IIaA18G3R1 and IIaA16G3R1, which have not been previously reported in Asia. These findings indicate that Cryptosporidium spp. play an important role in diarrhea in young calves in Korea. Considering the zoonotic significance of C. parvum IIa subtype and dense rearing system of cattle in Korea, prevention and continuous monitoring of Cryptosporidium are required. url: https://api.elsevier.com/content/article/pii/S0304401716303934 doi: 10.1016/j.vetpar.2016.09.019 id: cord-339419-b6tr2zyx author: Lee, Thomas Ming-Hung title: DNA-based bioanalytical microsystems for handheld device applications date: 2006-01-18 words: 5425.0 sentences: 331.0 pages: flesch: 49.0 cache: ./cache/cord-339419-b6tr2zyx.txt txt: ./txt/cord-339419-b6tr2zyx.txt summary: Recent progresses in the miniaturization of various biological processing steps for the sample preparation, DNA amplification (polymerase chain reaction), and product detection are delineated in detail. The organization of the following contents is based upon the three basic DNA processing modules of sample preparation, target amplification, and product detection. Thermal lysis can be easily adapted to microfabricated amplification systems as the initial high-temperature step (∼95 • C) employed to denature the double-stranded (ds) DNA template is powerful enough to open up the cell membranes [10, 12, 19] . The sensing protocol basically involves the immobilization of an oligonucleotide onto a transducer surface, and upon the hybridization of complementary target sequence, the binding event is detected by optical, microgravimetric (mass-sensitive), or electrochemical methods. To further increase the sensitivity of the gold nanoparticle-based assay, a signal amplification step Pictorial representation of the working principle of the molecular beacon-type capture probe labeled with ferrocene group for the reagentless sequence-specific DNA detection. abstract: Abstract This article reviews and highlights the current development of DNA-based bioanalytical microsystems for point-of-care diagnostics and on-site monitoring of food and water. Recent progresses in the miniaturization of various biological processing steps for the sample preparation, DNA amplification (polymerase chain reaction), and product detection are delineated in detail. Product detection approaches utilizing “portable” detection signals and electrochemistry-based methods are emphasized in this work. The strategies and challenges for the integration of individual processing module on the same chip are discussed. url: https://www.sciencedirect.com/science/article/pii/S0003267005009438 doi: 10.1016/j.aca.2005.05.075 id: cord-316309-8xe7cg8q author: Lee, Wah Heng title: LOMA: A fast method to generate efficient tagged-random primers despite amplification bias of random PCR on pathogens date: 2008-09-10 words: 5895.0 sentences: 296.0 pages: flesch: 53.0 cache: ./cache/cord-316309-8xe7cg8q.txt txt: ./txt/cord-316309-8xe7cg8q.txt summary: We build on our previous paper [14] describing in further detail the AES algorithm that identifies genomics sequences that can be successfully amplified by random primers, facilitating the design of appropriate microarray probes for detection of the pathogen. In our paper, we reported an observation that experiments using random priming amplification often resulted in incomplete hybridization of the pathogen genome marked by interspersed genomic regions not detected by tiling probes on the microarray (Figure 1. Since our pathogen detection chip contains tiling 40-mer probes of both RSV and HMPV, the number and distribution of the probes with high signal intensities would give a good indication of the amount of PCR products generated across the target genome by a tagged-random primer. We expect that a tagged-random primer with desirable amplification efficiency that generates sufficient PCR products uniformly across the whole target genome would result in high signal intensity probes distributed evenly across the whole genome. abstract: BACKGROUND: Pathogen detection using DNA microarrays has the potential to become a fast and comprehensive diagnostics tool. However, since pathogen detection chips currently utilize random primers rather than specific primers for the RT-PCR step, bias inherent in random PCR amplification becomes a serious problem that causes large inaccuracies in hybridization signals. RESULTS: In this paper, we study how the efficiency of random PCR amplification affects hybridization signals. We describe a model that predicts the amplification efficiency of a given random primer on a target viral genome. The prediction allows us to filter false-negative probes of the genome that lie in regions of poor random PCR amplification and improves the accuracy of pathogen detection. Subsequently, we propose LOMA, an algorithm to generate random primers that have good amplification efficiency. Wet-lab validation showed that the generated random primers improve the amplification efficiency significantly. CONCLUSION: The blind use of a random primer with attached universal tag (random-tagged primer) in a PCR reaction on a pathogen sample may not lead to a successful amplification. Thus, the design of random-tagged primers is an important consideration when performing PCR. url: https://www.ncbi.nlm.nih.gov/pubmed/18783594/ doi: 10.1186/1471-2105-9-368 id: cord-252347-vnn4135b author: Lee, Wai-Ming title: A Diverse Group of Previously Unrecognized Human Rhinoviruses Are Common Causes of Respiratory Illnesses in Infants date: 2007-10-03 words: 5672.0 sentences: 271.0 pages: flesch: 51.0 cache: ./cache/cord-252347-vnn4135b.txt txt: ./txt/cord-252347-vnn4135b.txt summary: METHODS AND FINDINGS: To directly type HRVs in nasal secretions of infants with frequent respiratory illnesses, we developed a sensitive molecular typing assay based on phylogenetic comparisons of a 260-bp variable sequence in the 5'' noncoding region with homologous sequences of the 101 known serotypes. The degenerate primers EV292 and EV222 for PCR amplification of NIm-1A region were not sensitive enough for direct detection of small amount of HRV in original clinical samples (data not shown), and high titer infected cell lysates of cultured isolates were needed to produce enough PCR product for cloning and sequencing. This new assay had 3 key components: sensitive pan-HRV primers and semi-nested PCR to amplify P1-P2 region from cDNA prepared from original clinical specimens, a sequence database of 260-bp P1-P2 region of 5''NCR of all 101 HRV serotypes to serve as standard references for HRV identification, and phylogenetic tree reconstruction of the new P1-P2 sequences and the 101 homologous reference sequences. abstract: BACKGROUND: Human rhinoviruses (HRVs) are the most prevalent human pathogens, and consist of 101 serotypes that are classified into groups A and B according to sequence variations. HRV infections cause a wide spectrum of clinical outcomes ranging from asymptomatic infection to severe lower respiratory symptoms. Defining the role of specific strains in various HRV illnesses has been difficult because traditional serology, which requires viral culture and neutralization tests using 101 serotype-specific antisera, is insensitive and laborious. METHODS AND FINDINGS: To directly type HRVs in nasal secretions of infants with frequent respiratory illnesses, we developed a sensitive molecular typing assay based on phylogenetic comparisons of a 260-bp variable sequence in the 5' noncoding region with homologous sequences of the 101 known serotypes. Nasal samples from 26 infants were first tested with a multiplex PCR assay for respiratory viruses, and HRV was the most common virus found (108 of 181 samples). Typing was completed for 101 samples and 103 HRVs were identified. Surprisingly, 54 (52.4%) HRVs did not match any of the known serotypes and had 12–35% nucleotide divergence from the nearest reference HRVs. Of these novel viruses, 9 strains (17 HRVs) segregated from HRVA, HRVB and human enterovirus into a distinct genetic group (“C”). None of these new strains could be cultured in traditional cell lines. CONCLUSIONS: By molecular analysis, over 50% of HRV detected in sick infants were previously unrecognized strains, including 9 strains that may represent a new HRV group. These findings indicate that the number of HRV strains is considerably larger than the 101 serotypes identified with traditional diagnostic techniques, and provide evidence of a new HRV group. url: https://www.ncbi.nlm.nih.gov/pubmed/17912345/ doi: 10.1371/journal.pone.0000966 id: cord-287843-snra23sy author: Lee, Wan‐Ji title: Prevalence and molecular epidemiology of human coronavirus HKU1 in patients with acute respiratory illness date: 2012-11-14 words: 2715.0 sentences: 157.0 pages: flesch: 56.0 cache: ./cache/cord-287843-snra23sy.txt txt: ./txt/cord-287843-snra23sy.txt summary: In this study, a Taq-Man 1 -based real-time polymerase chain reaction (PCR) method that targets the HCoV-HKU1 open reading frame (ORF) 1a and ORF 1b genes with high sensitivity and specificity was developed and evaluated. Fifty HCoV-HKU1-positive cases were detected (2.5%) out of 1,985 clinical specimens using real-time PCR assays targeting ORF 1a and ORF 1b. To circumvent these limitations, a quantitative real-time PCR was developed and targeted a study group of 1,985 throat swab specimens collected from patients with an acute respiratory illness from January 2007 to May 2008. The aim of the real-time PCR assays developed in this study was to detect both of the HCoV-HKU1 ORF 1a and ORF 1b genes. One limitation of this study was that because clinical specimens were chosen from negative cases of acute respiratory illness in the ARI-Net laboratory surveillance system [Chun et al., 2009] , dual or multiple infections of HCoV-HKU1 with other respiratory viruses could not be detected. abstract: In 2005, human coronavirus HKU1 (HCoV‐HKU1) was isolated and identified from a 71‐year‐old man with pneumonia in Hong Kong. To identify and classify genotypes of HCoV‐HKU1 in Korea, a sensitive, specific, and quantitative real‐time polymerase chain reaction (PCR) assay was developed and analyzed the sequences of HCoV‐HKU1 isolated in Korea. A total of 1,985 respiratory specimens taken from patients with acute respiratory illness were tested for HCoV‐HKU1 from January 2007 to May 2008. The major clinical symptoms associated with HCoV‐HKU1 infection were examined statistically and sequence variations of the RNA‐dependent RNA polymerase (RdRp), spike, and nucleocapsid genes were also analyzed. Fifty cases (2.5%) HCoV‐HKU1 were identified by real‐time PCR and viral loads ranged from 6.7 × 10(4) to 1.6 × 10(9) copies/ml. The clinical symptoms of HCoV‐HKU1 infection included rhinorrhea (72%), cough (64%), nasal congestion (56%), fever (32%), sputum (30%), sore throat (18%), chills (16%), postnasal discharge (14%), and tonsillar hypertrophy (10%). There was a seasonal distribution of HCoV‐HKU1 infection, peaking in winter and spring. Both genotypes A and B were detected but no recombination between them was found. This is the first report on the identification and genotyping of HCoV‐HKU1 as a causative agent of acute respiratory illness in Korea. The data suggest that at least two genotypes, A and B, of HCoV‐HKU1 with scattered silent mutations were circulating in Korea from 2007 to 2008. J. Med. Virol. 85:309–314, 2013. © 2012 Wiley Periodicals, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/23161446/ doi: 10.1002/jmv.23465 id: cord-352554-hsbyznex author: Lee, Yeon Joo title: Quality of Ribonucleic Acid Extraction for Real-Time Reverse Transcription-PCR (rRT-PCR) of SARS-CoV-2: Importance of Internal Control Monitoring date: 2020-11-01 words: 1122.0 sentences: 64.0 pages: flesch: 56.0 cache: ./cache/cord-352554-hsbyznex.txt txt: ./txt/cord-352554-hsbyznex.txt summary: On 6th February 2020, Emergency Use Authorization (EUA) for COVID-19 testing was implemented in Korea, permitting rapid expansion of capacity in clinical and public health laboratories [5] . To evaluate the performance of the RNA extraction step, 31 and 35 samples were prepared using the Real-Prep-in-use and the new Real-Prep system, respectively, and all 66 eluates were submitted to the same run of rRT-PCR. As the experience of the Middle East Respiratory Syndrome outbreak of 2015 in Korea, an epidemic of emerging infectious diseases necessitates clinical laboratories to conduct new tests at a large scale in a short period of time with kits and equipment that have not been thoroughly validated [10] . Analytical and clinical validation of six commercial Middle East Respiratory Syndrome coronavirus RNA detection kits based on real-time reverse-transcription PCR Comparative evaluation of three homogenization methods for isolating Middle East Respiratory Syndrome coronavirus nucleic acids from sputum samples for real-time reverse transcription PCR abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32539306/ doi: 10.3343/alm.2020.40.6.490 id: cord-290867-akurajpf author: Legrand, Loïc title: Epidemiological and phylogenic study of human metapneumovirus infections during three consecutive outbreaks in Normandy, France date: 2011-01-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Human metapneumovirus (hMPV) is responsible for respiratory tract disease, particularly in the young and elderly population. An epidemiological and phylogenic study was performed on children admitted to hospital with an acute lower respiratory tract infection (LRI). Data were obtained and analyzed over three consecutive winters, from 2002–2003 to 2004–2005. Each year during the winter period, from November to March, 2,415 nasal swabs were tested by a direct immunofluorescence assay (DFA) for influenza viruses A and B, respiratory syncytial virus, parainfluenza viruses, and adenoviruses. Rhinoviruses, enteroviruses, and coronaviruses OC43 and 229E were detected by RT‐PCR. A RT‐PCR designed for the M gene was performed on negative samples for hMPV detection and phylogenic analyses. For the three consecutive winters, hMPV represented 10%, 22.6%, and 8.8% of virus‐negative samples, respectively. In most cases, clinical symptoms indicated a LRI with a final diagnosis of bronchiolitis. During the winter of 2003–2004, all viral clusters (A1, A2, B1, and B2) that circulated in France shifted progressively from the A group to the B group. This study determined the prevalence of hMPV in Normandy, its clinical impact and permitted the analysis of the molecular evolution during the successive outbreaks. J. Med. Virol. 83:517–524, 2011. © 2011 Wiley‐Liss, Inc. url: https://doi.org/10.1002/jmv.22002 doi: 10.1002/jmv.22002 id: cord-271341-fszljnax author: Lei, Pinggui title: COVID-19 Carrier or Pneumonia: Positive Real-Time Reverse-Transcriptase Polymerase Chain Reaction but Negative or Positive Chest CT Results date: 2020-05-06 words: 1011.0 sentences: 59.0 pages: flesch: 43.0 cache: ./cache/cord-271341-fszljnax.txt txt: ./txt/cord-271341-fszljnax.txt summary: title: COVID-19 Carrier or Pneumonia: Positive Real-Time Reverse-Transcriptase Polymerase Chain Reaction but Negative or Positive Chest CT Results Dear Editor, We have read the articles published in the Korean Journal of Radiology with great interest concerning the real-time reverse-transcriptase polymerase chain reaction (rRT-PCR) amplification of the viral deoxyribonucleic acid (DNA) and chest computed tomography (CT) results for screening or detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (1, 2) . Based on the aforementioned situation, patients with positive rRT-PCR but negative chest CT results should be classified as SARS-CoV-2 carriers. To the Editor, Thank you for your comments on our online article focusing on the false-negative results of real-time reversetranscriptase polymerase chain reaction (rRT-PCR) and the possible complementary approaches for screening coronavirus disease 2019 (COVID-19). With the rapid and extensive spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), patients with positive rRT-PCR but negative chest CT results emerged. abstract: nan url: https://doi.org/10.3348/kjr.2020.0360 doi: 10.3348/kjr.2020.0360 id: cord-342785-55r01n0x author: Lemmon, Gordon H title: Predicting the sensitivity and specificity of published real-time PCR assays date: 2008-09-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: In recent years real-time PCR has become a leading technique for nucleic acid detection and quantification. These assays have the potential to greatly enhance efficiency in the clinical laboratory. Choice of primer and probe sequences is critical for accurate diagnosis in the clinic, yet current primer/probe signature design strategies are limited, and signature evaluation methods are lacking. METHODS: We assessed the quality of a signature by predicting the number of true positive, false positive and false negative hits against all available public sequence data. We found real-time PCR signatures described in recent literature and used a BLAST search based approach to collect all hits to the primer-probe combinations that should be amplified by real-time PCR chemistry. We then compared our hits with the sequences in the NCBI taxonomy tree that the signature was designed to detect. RESULTS: We found that many published signatures have high specificity (almost no false positives) but low sensitivity (high false negative rate). Where high sensitivity is needed, we offer a revised methodology for signature design which may designate that multiple signatures are required to detect all sequenced strains. We use this methodology to produce new signatures that are predicted to have higher sensitivity and specificity. CONCLUSION: We show that current methods for real-time PCR assay design have unacceptably low sensitivities for most clinical applications. Additionally, as new sequence data becomes available, old assays must be reassessed and redesigned. A standard protocol for both generating and assessing the quality of these assays is therefore of great value. Real-time PCR has the capacity to greatly improve clinical diagnostics. The improved assay design and evaluation methods presented herein will expedite adoption of this technique in the clinical lab. url: https://www.ncbi.nlm.nih.gov/pubmed/18817537/ doi: 10.1186/1476-0711-7-18 id: cord-007564-ljqrxjvv author: Leroy, O. title: 04 – Apport des explorations microbiologiques au diagnostic des infections des voies respiratoires basses date: 2006-11-13 words: 13542.0 sentences: 1229.0 pages: flesch: 54.0 cache: ./cache/cord-007564-ljqrxjvv.txt txt: ./txt/cord-007564-ljqrxjvv.txt summary: Trentetrois examens directs et 46 Ces données montrent que l''examen direct et la culture de l''expectoration dès lors qu''ils sont correctement effectués chez un patient sans antibiothérapie sont fréquemment positifs au cours des PAC à pneumocoque les plus graves, c''est-à-dire bactériémiques. Ces données ne doivent pas toutefois faire perdre de vue, comme le souligne Pesola [37] que dans plus de 10 % des cas, les PAC ont une étiologie plurimicrobienne et qu''il n''est peut être pas raisonnable de focaliser l''antibiothérapie uniquement sur le pneumocoque en cas de test positif. À partir d''échantillons provenant du tractus respiratoire inférieur (expectoration, voire prélèvements endoscopiques) ou supérieur (prélèvement nasopharyngé), un certain nombre de techniques ont été mises au point pour le diagnostic des infections liées à des germes tels que Chlamydia pneumoniae, Mycoplasma pneumoniae ou Legionella spp. abstract: The diagnosis of community-acquired pneumonia is usually based on clinical and radiological criteria. The identification of a causative organism is not required for the diagnosis. Although numerous microbiological techniques are available, their sensitivity and specificity are not high enough to guide first-line antimicrobial therapy. Consequently, this treatment remains most often empiric. If the causative organism is identified, the antimicrobial treatment is adapted. Sputum analysis may be proposed as a diagnostic tool for patients with an acute exacerbation of chronic obstructive pulmonary disease, in specific cases (prior antibiotherapy, hospitalization, failure of the empiric antimicrobial treatment). url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119138/ doi: 10.1016/j.medmal.2006.07.008 id: cord-253502-v2hh3w3r author: Leung, C.W. title: Clinical picture, diagnosis, treatment and outcome of severe acute respiratory syndrome (SARS) in children date: 2004-11-05 words: 8625.0 sentences: 524.0 pages: flesch: 45.0 cache: ./cache/cord-253502-v2hh3w3r.txt txt: ./txt/cord-253502-v2hh3w3r.txt summary: authors: Leung, C.W.; Chiu, W.K. title: Clinical picture, diagnosis, treatment and outcome of severe acute respiratory syndrome (SARS) in children [5] [6] [7] [8] [9] [10] [11] Superspreading events including a major hospital outbreak, in-flight transmission on board commercial PAEDIATRIC RESPIRATORY REVIEWS (2004) Summary Children are susceptible to infection by SARS-associated coronavirus (SARS-CoV) but the clinical picture of SARS is milder than in adults. abstract: Children are susceptible to infection by SARS-associated coronavirus (SARS-CoV) but the clinical picture of SARS is milder than in adults. Teenagers resemble adults in presentation and disease progression and may develop severe illness requiring intensive care and assisted ventilation. Fever, malaise, cough, coryza, chills or rigor, sputum production, headache, myalgia, leucopaenia, lymphopaenia, thrombocytopaenia, mildly prolonged activated partial thromboplastin times and elevated lactate dehydrogenase levels are common presenting features. Radiographic findings are non-specific but high-resolution computed tomography of the thorax in clinically suspected cases may be an early diagnostic aid when initial chest radiographs appear normal. The improved reverse transcription-polymerase chain reaction (RT-PCR) assays are critical in the early diagnosis of SARS, with sensitivity approaching 80% in the first 3 days of illness when performed on nasopharyngeal aspirates, the preferred specimens. Absence of seroconversion to SARS-CoV beyond 28 days from disease onset generally excludes the diagnosis. The best treatment strategy for SARS among children remains to be determined. No case fatality has been reported in children and the short- to medium-term outcome appears to be good. The importance of continued monitoring for any long-term complications due to the disease or its empiric treatment, cannot be overemphasised. url: https://www.sciencedirect.com/science/article/pii/S152605420400079X doi: 10.1016/j.prrv.2004.07.010 id: cord-299672-dq1y1gkc author: Leung, Ting Fan title: Multiplex Molecular Detection of Respiratory Pathogens in Children With Asthma Exacerbation date: 2010-02-28 words: 3642.0 sentences: 221.0 pages: flesch: 51.0 cache: ./cache/cord-299672-dq1y1gkc.txt txt: ./txt/cord-299672-dq1y1gkc.txt summary: Conclusions Respiratory viral infections are commonly found in children with asthma exacerbation, with HRV being the most important pathogen in our patients. Our primary outcome was the difference in detection rate for any respiratory pathogen between children with asthma with acute exacerbation and controls (ie, stable asthma). Secondary outcomes consisted of differences in the clinical severity of asthma exacerbation, lung function parameters, and fractional exhaled nitric oxide concentration (FeNO) in relation to patients with different respiratory pathogens. HRV infection was associated with asthma exacerbation in the children, which is consistent with FeNO was the only parameter that differed between patients with and without HRV, being signifi cantly lower in the former group ( P 5 .018). Identifi cation of viral and atypical bacterial pathogens in children hospitalized with acute respiratory infections in Hong Kong by multiplex PCR assays abstract: Background Up to 80% of asthma exacerbations in white children are associated with viral upper respiratory infections. The relative importance of different respiratory pathogens and relevant microbiological data in Asian children are unclear. This study elucidated the epidemiology of respiratory infections in Hong Kong children with asthma exacerbation. Methods A total of 209 children aged 3-18 years with asthma exacerbations and 77 controls with stable asthma were recruited. The severity of asthma exacerbations was assessed according to Global Initiative for Asthma guideline, and subjects aged 6 years or older performed exhaled nitric oxide and spirometric measurements. Nested multiplex polymerase chain reaction was used to detect 20 different respiratory pathogens. Results Respiratory pathogens were detected in 105 (51.0%) subjects. The presence of any respiratory pathogen was associated with asthma exacerbation (odds ratio [OR], 2.77; 95% CI, 1.51–5.11; P < .001). Specifically, human rhinovirus (HRV) infection was more common among children with asthma exacerbation (OR, 2.38; 95% CI, 1.09–5.32; P = .018). All other pathogens or coinfections were not associated with asthmatic attacks. None of these respiratory infections was associated with the severity of asthma exacerbation (P > .15 for all). During peak HRV season in the winter of 2007 to 2008, this virus was detected in 46.4% of children with asthma exacerbations. Conclusions Respiratory viral infections are commonly found in children with asthma exacerbation, with HRV being the most important pathogen in our patients. Respiratory viral infection is a triggering factor for asthma exacerbation but does not correlate with its severity. url: https://doi.org/10.1378/chest.09-1250 doi: 10.1378/chest.09-1250 id: cord-021772-5v4gor2v author: Levine, Gwendolyn J. title: Cerebrospinal Fluid and Central Nervous System Cytology date: 2019-05-31 words: 12646.0 sentences: 768.0 pages: flesch: 46.0 cache: ./cache/cord-021772-5v4gor2v.txt txt: ./txt/cord-021772-5v4gor2v.txt summary: 45, 46 In a recent study of 106 canine CSF samples without pleocytosis (TNCC <5/μL) but containing at least 500 RBCs/μL, the mean percentage of neutrophils (45.2% versus 5.7%), percentage of samples with eosinophils present (36.8% versus 6.8%), and mean protein concentration (40 mg/dL versus 26 mg/dL) were found to be significantly increased in the samples with blood contamination when compared with controls. 4 A study of cats with CNS cryptococcosis showed organisms in 9 of 11 of the CSF samples, and a majority of cases (9 of 10) had neutrophilic pleocytosis and increased protein concentration (8 of 10). A case series of five cats showed CSF ranging from normal to marked neutrophilic pleocytosis with moderately elevated protein concentration and variable correlation to clinical outcome. 85 A study of eight dogs with natural infection (confirmed by CNS tissue-PCR and histopathology) showed lymphocytic pleocytosis in all samples and normal protein concentrations. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151995/ doi: 10.1016/b978-0-323-53314-0.00014-6 id: cord-338205-sy91rnse author: Li, Chenxi title: Laboratory Diagnosis of Coronavirus Disease-2019 (COVID-19) date: 2020-07-02 words: 7515.0 sentences: 436.0 pages: flesch: 51.0 cache: ./cache/cord-338205-sy91rnse.txt txt: ./txt/cord-338205-sy91rnse.txt summary: With limited understanding of COVID-19, it is difficult to exclude SARS-CoV-2 infection based on a single negative PCR result, especially when testing was used for upper respiratory tract specimens. The study found that SARS-CoV-2 could be detected in all primer-probe sets applied in the qRT-PCR tests, but significant discrepancy was observed in the detection limit and the ability to identify negatives and positives with a lower viral load. Compared with the qRT-PCR kit, nested RT-PCR analysis showed higher sensitivity and specificity, indicating that it is more suitable for clinical application to detect SARS-CoV-2 in cases with low viral load. In cases where RT-PCR assays are negative and there is a strong epidemiological link to SARS-CoV-2 infection, paired serum samples (in the acute and convalescent-phase) could support diagnosis once validated serology tests are available with the initial samples collected in the first week of COVID-19 and the second collected after 2-4 weeks [28] . abstract: Abstract The outbreak of Coronavirus Disease-2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has threatened health worldwide. As of the end of 2020, there were nearly 10 million confirmed cases and nearly 5 million deaths associated with COVID-19. Rapid and early laboratory diagnosis of COVID-19 is the main focus of treatment and control. Molecular tests are the basis for confirmation of COVID-19, but serological tests for SARS-CoV-2 are widely available and play an increasingly important role in understanding the epidemiology of the virus and in identifying populations at higher risk for infection. Point-of-care tests have the advantage of rapid, accurate, portable, low cost and non-specific device requirements, which provide great help for disease diagnosis and detection. This review will discuss the performance of different laboratory diagnostic tests and platforms, as well as suitable clinical samples for testing, and related biosafety protection. This review shall guide for the diagnosis of COVID-19 caused by SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32621814/ doi: 10.1016/j.cca.2020.06.045 id: cord-325124-0hxan9rw author: Li, Chenyu title: Highly sensitive and full-genome interrogation of SARS-CoV-2 using multiplexed PCR enrichment followed by next-generation sequencing date: 2020-05-18 words: 6119.0 sentences: 364.0 pages: flesch: 53.0 cache: ./cache/cord-325124-0hxan9rw.txt txt: ./txt/cord-325124-0hxan9rw.txt summary: However, it has been reported that only 47-59% of the positive cases were identified by some RT-PCR methods, probably due to low viral load, timing of sampling, degradation of virus RNA in the sampling process, or possible mutations spanning the primer binding sites. With the goal of improving sensitivity and accommodating various application settings, we developed a multiplex-PCR-based method comprised of 343 pairs of specific primers, and demonstrated its efficiency to detect SARS-CoV-2 at low copy numbers. We further amplified the entire SARS-CoV-2 genome from 8 to half a million viral copies purified from 13 COVID-19 positive specimens, and detected mutations through next generation sequencing. Finally, we developed a multiplex-PCR-based metagenomic method in parallel, that required modest sequencing depth for uncovering SARS-CoV-2 mutational diversity and potentially novel or emerging isolates. To overcome this constraint, we developed a multiplex-PCR-based metagenomic method that achieved >96% coverage of the S and N genes of SARS-CoV-2 in the contest of human gDNA, while only required ~0.6M of total reads per library. abstract: Many detection methods have been used or reported for the diagnosis and/or surveillance of COVID-19. Among them, reverse transcription polymerase chain reaction (RT-PCR) is the most commonly used because of its high sensitivity, typically claiming detection of about 5 copies of viruses. However, it has been reported that only 47-59% of the positive cases were identified by some RT-PCR methods, probably due to low viral load, timing of sampling, degradation of virus RNA in the sampling process, or possible mutations spanning the primer binding sites. Therefore, alternative and highly sensitive methods are imperative. With the goal of improving sensitivity and accommodating various application settings, we developed a multiplex-PCR-based method comprised of 343 pairs of specific primers, and demonstrated its efficiency to detect SARS-CoV-2 at low copy numbers. The assay produced clean characteristic target peaks of defined sizes, which allowed for direct identification of positives by electrophoresis. We further amplified the entire SARS-CoV-2 genome from 8 to half a million viral copies purified from 13 COVID-19 positive specimens, and detected mutations through next generation sequencing. Finally, we developed a multiplex-PCR-based metagenomic method in parallel, that required modest sequencing depth for uncovering SARS-CoV-2 mutational diversity and potentially novel or emerging isolates. url: https://doi.org/10.1101/2020.03.12.988246 doi: 10.1101/2020.03.12.988246 id: cord-305399-98sqovwb author: Li, Hao title: Development of a reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for the detection of porcine pegivirus date: 2019-04-22 words: 2854.0 sentences: 136.0 pages: flesch: 56.0 cache: ./cache/cord-305399-98sqovwb.txt txt: ./txt/cord-305399-98sqovwb.txt summary: A simple and accurate reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay was developed and evaluated for the detection of porcine pegivirus (PPgV). The results indicated that RT-LAMP assay developed in this study could be a highly specific, sensitive, and cost-effective alternative for a rapid detection of PPgV in field settings. The final volume of 25 μl reaction mixtures for RT-LAMP was prepared, which contained 1 μl of Bst DNA polymerase (NEB, USA) (8000 U/ml), 2.5 μl of 10 × Isothermal Amplification Buffer, 5 μl of Betaine (5 M), 1 μl of MgSO 4 (100 mM), 5 μl of dNTP (2.5 mM), 2 μl of each inner primers FIP and BIP (10 μmol), 0.25 μl of each outer primers F3 and B3 (10 μmol), 0.25 μl of each loop primers LF and LB (10 μmol), 1.25 μl of AMV reverse transcriptase (TaKaRa, China) (40 U/μl), 2 μl of RNA template, and the sterile distilled water was set as a negative control template. abstract: A simple and accurate reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay was developed and evaluated for the detection of porcine pegivirus (PPgV). The specific RT-LAMP primers targeting the conserved regions of NS5A genes were designed and used to detect PPgV. The optimal reaction parameter for RT-LAMP assay was 63℃ for 60 min. The detection limit of the RT-LAMP assay was 10 copies of PPgV genome, which was 100 times more sensitive than that of the conventional RT-PCR and comparable to nested RT-PCR and quantitative RT-PCR (qRT-PCR). There was no cross amplification with other related RNA viruses. In the clinical evaluation, the RT-LAMP assay exhibited a similar sensitivity with nested RT-PCR and qRT-PCR. The results indicated that RT-LAMP assay developed in this study could be a highly specific, sensitive, and cost-effective alternative for a rapid detection of PPgV in field settings. url: https://doi.org/10.1016/j.jviromet.2019.04.019 doi: 10.1016/j.jviromet.2019.04.019 id: cord-305336-wxiazglk author: Li, Ji Lian title: Systemic Spread and Propagation of a Plant-Pathogenic Virus in European Honeybees, Apis mellifera date: 2014-01-21 words: 6907.0 sentences: 319.0 pages: flesch: 50.0 cache: ./cache/cord-305336-wxiazglk.txt txt: ./txt/cord-305336-wxiazglk.txt summary: In the present study, we showed that a plant-pathogenic RNA virus, tobacco ringspot virus (TRSV), could replicate and produce virions in honeybees, Apis mellifera, resulting in infections that were found throughout the entire body. While intracellular life cycle, species-level genetic variation, and pathogenesis of the virus in honeybee hosts remain to be determined, the increasing prevalence of TRSV in conjunction with other bee viruses from spring toward winter in infected colonies was associated with gradual decline of host populations and winter colony collapse, suggesting the negative impact of the virus on colony survival. Conventional RT-PCR was performed on RNA samples extracted from adult bees, Varroa mites, different tissues, and bee bread collected from the same colony for the presence and distribution of TRSV. abstract: Emerging and reemerging diseases that result from pathogen host shifts are a threat to the health of humans and their domesticates. RNA viruses have extremely high mutation rates and thus represent a significant source of these infectious diseases. In the present study, we showed that a plant-pathogenic RNA virus, tobacco ringspot virus (TRSV), could replicate and produce virions in honeybees, Apis mellifera, resulting in infections that were found throughout the entire body. Additionally, we showed that TRSV-infected individuals were continually present in some monitored colonies. While intracellular life cycle, species-level genetic variation, and pathogenesis of the virus in honeybee hosts remain to be determined, the increasing prevalence of TRSV in conjunction with other bee viruses from spring toward winter in infected colonies was associated with gradual decline of host populations and winter colony collapse, suggesting the negative impact of the virus on colony survival. Furthermore, we showed that TRSV was also found in ectoparasitic Varroa mites that feed on bee hemolymph, but in those instances the virus was restricted to the gastric cecum of Varroa mites, suggesting that Varroa mites may facilitate the spread of TRSV in bees but do not experience systemic invasion. Finally, our phylogenetic analysis revealed that TRSV isolates from bees, bee pollen, and Varroa mites clustered together, forming a monophyletic clade. The tree topology indicated that the TRSVs from arthropod hosts shared a common ancestor with those from plant hosts and subsequently evolved as a distinct lineage after transkingdom host alteration. This study represents a unique example of viruses with host ranges spanning both the plant and animal kingdoms. url: https://www.ncbi.nlm.nih.gov/pubmed/24449751/ doi: 10.1128/mbio.00898-13 id: cord-048359-lz37rh82 author: Li, Jin title: s-RT-MELT for rapid mutation scanning using enzymatic selection and real time DNA-melting: new potential for multiplex genetic analysis date: 2007-06-01 words: 6258.0 sentences: 299.0 pages: flesch: 49.0 cache: ./cache/cord-048359-lz37rh82.txt txt: ./txt/cord-048359-lz37rh82.txt summary: Subsequently, melting curve analysis, on conventional or nano-technology real-time PCR platforms, detects the samples that contain mutations in a high-throughput and closed-tube manner. Following denaturation and re-annealing of PCR products that leads to formation of cross-hybridized sequences at the positions of mutations ( Figure 1A ) the sample is exposed to Surveyor TM endonuclease that recognizes base pair mismatches or small loops with high specificity (28) and generates a break on both DNA strands 3 0 to the mismatch. Finally, because the amplified mutated sequences contain defined primers at their ends, direct sequencing of enzymatically selected PCR products is readily possible following the real-time melting step, enabling sequencing of low-level mutations identified by Surveyor TM . Here we enabled Surveyor TM , an endonuclease that recognizes selectively mismatches formed by mutations and small deletions following ''cross-hybridized sequence'' formation, to generate mutation-specific DNA fragments that are amplified and screened via differential melting curve analysis. abstract: The rapidly growing understanding of human genetic pathways, including those that mediate cancer biology and drug response, leads to an increasing need for extensive and reliable mutation screening on a population or on a single patient basis. Here we describe s-RT-MELT, a novel technology that enables highly expanded enzymatic mutation scanning in human samples for germline or low-level somatic mutations, or for SNP discovery. GC-clamp-containing PCR products from interrogated and wild-type samples are hybridized to generate mismatches at the positions of mutations over one or multiple sequences in-parallel. Mismatches are converted to double-strand breaks using a DNA endonuclease (Surveyor™) and oligonucleotide tails are enzymatically attached at the position of mutations. A novel application of PCR enables selective amplification of mutation-containing DNA fragments. Subsequently, melting curve analysis, on conventional or nano-technology real-time PCR platforms, detects the samples that contain mutations in a high-throughput and closed-tube manner. We apply s-RT-MELT in the screening of p53 and EGFR mutations in cell lines and clinical samples and demonstrate its advantages for rapid, multiplexed mutation scanning in cancer and for genetic variation screening in biology and medicine. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1919510/ doi: 10.1093/nar/gkm403 id: cord-263735-sos2ovng author: Li, K. title: Diagnostic performance of CT and its key signs for COVID-19: A systematic review and meta-analysis date: 2020-05-26 words: 5251.0 sentences: 310.0 pages: flesch: 69.0 cache: ./cache/cord-263735-sos2ovng.txt txt: ./txt/cord-263735-sos2ovng.txt summary: Furthermore, several studies reported that CT had high sensitivity for COVID-19 [7, 9, 10] , but a recent study including 121 cases found 56% of patients had a normal CT finding in the early stage of infection [11] . Furthermore, there are 10 studies reported the diagnostic sensitivity of the initial PCR assay [7, 10, 11, 18, 22, 29, 32, [34] [35] [36] , while 5 of them mentioned the rate of missed diagnosis after the second tests [10, 22, 29, 32, 35] . For these 25 studies, the diagnostic sensitivity and specificity of CT for COVID-19 ranged from 69% to 100% and from 0% to 96%, with pooled estimates of 93% (95% CI, 89-96%) and 44% (95% CI, 27-62%) (Figure 4 ), respectively. For the 10 studies with repeated PCR assay, the pooled sensitivity of the initial RT-PCR test in diagnosis of COVID-19 was 76% (95% CI: 59-89%; I 2 =96%). abstract: Abstract Purpose: To evaluate the diagnostic value of chest CT in 2019 novel coronavirus disease (COVID-19), using the reverse transcription polymerase chain reaction(RT-PCR)as a reference standard. At the same time, the imaging features of CT in confirmed COVID-19 patients would be summarized. Methods: A comprehensive literature search of 5 electronic databases was performed. The pooled sensitivity, specificity, positive predictive value, and negative predictive value were calculated using the random-effects model and the summary receiver operating characteristic (SROC) curve. We also conducted a meta-analysis to estimate the pooled incidence of the chest CT imaging findings and the 95% confidence interval (95%CI). Meta-regression analysis was used to explore the source of heterogeneity. Results: Overall, 25 articles comprising 4,857 patients were included. The pooled sensitivity of CT was 93% (95% CI, 89-96%) and specificity was 44% (95% CI, 27-62%). The area under the SROC curve was 0.94 (95% CI, 0.91-0.96). For the RT-PCR assay, the pooled sensitivity of the initial test and the missed diagnosis rate after the second-round test were 76% (95% CI: 59-89%; I2=96%) and 26% (95% CI: 14-39%; I2=45%), respectively. According to the subgroup analysis, the diagnostic sensitivity of CT in Hubei was higher than that in other regions. Besides, the most common patterns on CT imaging finding was ground glass opacities (GGO) 58% (95% CI: 49-70%), followed by air bronchogram 51% (95% CI: 31-70%). Lesions were inclined to distribute in peripheral 64% (95% CI: 49-78%), and the incidence of bilateral lung involvement was 69% (95% CI: 58-79%). Conclusions: There were still several cases of missed diagnosis after multiple RT-PCR examinations. In high-prevalence areas, CT could be recommended as an auxiliary screening method for RT-PCR. url: https://doi.org/10.1101/2020.05.24.20111773 doi: 10.1101/2020.05.24.20111773 id: cord-284262-lddmo1sv author: Li, Linlin title: Circovirus in Tissues of Dogs with Vasculitis and Hemorrhage date: 2013-04-17 words: 4159.0 sentences: 218.0 pages: flesch: 46.0 cache: ./cache/cord-284262-lddmo1sv.txt txt: ./txt/cord-284262-lddmo1sv.txt summary: We identified a canine circovirus in the liver of a dog that had necrotizing vasculitis and granulomatous lymphadenitis, both of which are described in PCV2-infected pigs (4) . A fourth sample cohort consisted of tissue samples from 21 necropsy cases of dogs whose clinical signs or microscopic lesions matched the sentinel animal (i.e., hemorrhagic diarrhea, vasculitis, and/or granulomatous disease); these samples were selected from the tissue archives of Anatomic Pathology at the UC Davis Veterinary Medical Teaching Hospital. To establish tissue distribution and investigate whether DogCV contributes to canine disease, we developed and validated an ISH oligomeric probe and examined the sentinel dog and dogs from 21 suspected, retrospective cases that included >2 of these 3 signs: vasculitis, hemorrhage, or granulomatous disease. We characterized the genome of multiple DogCV strains, determined DogCV prevalence in dog fecal and plasma samples and tissue distribution in infected animals, and detected paracrystalline arrays in inclusion bodies in macrophages. abstract: We characterized the complete genome of a novel dog circovirus (DogCV) from the liver of a dog with severe hemorrhagic gastroenteritis, vasculitis, and granulomatous lymphadenitis. DogCV was detected by PCR in fecal samples from 19/168 (11.3%) dogs with diarrhea and 14/204 (6.9%) healthy dogs and in blood from 19/409 (3.3%) of dogs with thrombocytopenia and neutropenia, fever of unknown origin, or past tick bite. Co-infection with other canine pathogens was detected for 13/19 (68%) DogCV-positive dogs with diarrhea. DogCV capsid proteins from different dogs varied by up to 8%. In situ hybridization and transmission electron microscopy detected DogCV in the lymph nodes and spleens of 4 dogs with vascular compromise and histiocytic inflammation. The detection of a circovirus in tissues of dogs expands the known tropism of these viruses to a second mammalian host. Our results indicate that circovirus, alone or in co-infection with other pathogens, might contribute to illness and death in dogs. url: https://doi.org/10.3201/eid1904.121390 doi: 10.3201/eid1904.121390 id: cord-287054-zmxpuynv author: Li, Ning title: Molecular diagnosis of COVID-19: Current situation and trend in China (Review) date: 2020-08-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: COVID-19 is caused by a novel coronavirus (2019-nCoV or SARS-CoV-2) and has become a global public health emergency. Rapid and accurate molecular diagnostic technologies are crucial for the screening, isolation, treatment, prevention and control of COVID-19. Currently, nucleic acid detection-based techniques and rapid diagnostic tests that detect antigens or antibodies specific to 2019-nCoV infections are the primary diagnostic tools. China National Medical Products Administration has opened a special channel for approval of new pharmaceuticals owing to urgent clinical needs, with 18 nucleic acid detection kits, 11 protein detection kits and 1 sequencing-related equipment and supporting software having been approved until April 23, 2020. The current review summarizes the application situation, advantages, disadvantages and associated technology improvement trends of molecular diagnostics for COVID-19 in China, identifies knowledge gaps and indicates future priorities for research in this field. The most effective way to prevent and control COVID-19 is early detection, diagnosis, isolation and treatment. In the clinical application of molecular diagnosis technology, it is necessary to combine pathogenic microbiology, immunology and other associated detection technologies, advocate the combination of multiple technologies, determine how they complement each other, enhance practicability and improve the ability of rapid and accurate diagnosis and differential diagnosis of COVID-19. url: https://doi.org/10.3892/etm.2020.9142 doi: 10.3892/etm.2020.9142 id: cord-343441-z849jvq5 author: Li, Yan title: Simultaneous detection of hemagglutinin and neuraminidase genes of novel influenza A (H7N9) by duplex real-time reverse transcription polymerase chain reaction date: 2013-09-01 words: 2236.0 sentences: 112.0 pages: flesch: 54.0 cache: ./cache/cord-343441-z849jvq5.txt txt: ./txt/cord-343441-z849jvq5.txt summary: In this study, a duplex real-time reverse transcription polymerase chain reaction (rRT-PCR) assay was developed for the simultaneous detection of hemagglutinin (HA) and neuraminidase (NA) genes of H7N9 influenza viruses. In this study, a duplex real-time reverse transcription polymerase chain reaction (rRT-PCR) assay was developed for the simultaneous detection of hemagglutinin (HA) and neuraminidase (NA) genes of H7N9 influenza viruses. The analytic sensitivity of the duplex TaqMan rRT-PCR assay was compared with the WHO TaqMan assay and a commercial single H7N9 rRT-PCR kit (bioPerfectus technologies, Taizhou, China) with a 10-fold dilution series of a nasopharyngeal aspirate (NPA) from a patient infected with the H7N9 virus (approximately 4.8 × 10 6 copies of the viral genome/mL). To determine the actual detection limit (number of copies per reaction) of the duplex TaqMan rRT-PCR assay, in vitro RNA transcripts of HA and NA genes from the H7N9 virus were prepared with T7 RNA polymerase (TaKaRa Biotechnology Co. Ltd., Dalian, China) according to the manufacturer''s instructions using influenza A/Nanjing/1/2013 (H7N9) RNA as a template. abstract: A novel reassortant influenza A (H7N9) virus emerged recently in China. In this study, a duplex real-time reverse transcription polymerase chain reaction (rRT-PCR) assay was developed for the simultaneous detection of hemagglutinin (HA) and neuraminidase (NA) genes of H7N9 influenza viruses. The sensitivity of the assay was determined to be 10 RNA copies per reaction for both HA and NA genes. No cross-reactivity was observed with other influenza virus subtypes or respiratory tract viruses. One hundred and forty-six clinical and environmental specimens were tested and compared with reference methods and were found to be consistent. The assay is suitable for large-scale screening due to short turnaround times and high specificity, sensitivity, and reproducibility. url: https://doi.org/10.1016/j.jviromet.2013.08.021 doi: 10.1016/j.jviromet.2013.08.021 id: cord-288556-o8i6j3b2 author: Li, Yanpeng title: Virome of a Feline Outbreak of Diarrhea and Vomiting Includes Bocaviruses and a Novel Chapparvovirus date: 2020-05-04 words: 5872.0 sentences: 325.0 pages: flesch: 53.0 cache: ./cache/cord-288556-o8i6j3b2.txt txt: ./txt/cord-288556-o8i6j3b2.txt summary: We characterized from fecal samples the genome of a novel chapparvovirus we named fechavirus that was shed by 8/17 affected cats and identified three different feline bocaviruses shed by 9/17 cats. Epidemiological investigation of disease signs, time of onset, and transfers of affected cats between three facilities support a possible role for this new chapparvovirus in a highly contagious feline diarrhea and vomiting disease. Here, we analyzed a multi-facility outbreak of vomiting and diarrhea in cats using the following approaches: a commercial feline diarrhea panel of PCR tests for known enteric pathogens; viral metagenomics; and follow-up PCRs. Multiple mammalian viruses of varied origins were detected. DNA was extracted from each individual fecal sample (and one pool of 3, cat#973-975) shown in Table 3 plus 4 vomit samples using the QIAamp MinElute Virus Spin Kit (Qiagen, Hilden, Germany), and PCR assays were used for the detection of different viral nucleic acids in each sample. abstract: An unexplained outbreak of feline diarrhea and vomiting, negative for common enteric viral and bacterial pathogens, was subjected to viral metagenomics and PCR. We characterized from fecal samples the genome of a novel chapparvovirus we named fechavirus that was shed by 8/17 affected cats and identified three different feline bocaviruses shed by 9/17 cats. Also detected were nucleic acids from attenuated vaccine viruses, members of the normal feline virome, viruses found in only one or two cases, and viruses likely derived from ingested food products. Epidemiological investigation of disease signs, time of onset, and transfers of affected cats between three facilities support a possible role for this new chapparvovirus in a highly contagious feline diarrhea and vomiting disease. url: https://www.ncbi.nlm.nih.gov/pubmed/32375386/ doi: 10.3390/v12050506 id: cord-011436-ud35mf5l author: Li, Yingying title: Interferon-λ Attenuates Rabies Virus Infection by Inducing Interferon-Stimulated Genes and Alleviating Neurological Inflammation date: 2020-04-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Rabies, caused by rabies virus (RABV), is a fatal neurological disease that still causes more than 59,000 human deaths each year. Type III interferon IFN-λs are cytokines with type I IFN-like antiviral activities. Although IFN-λ can restrict the infection for some viruses, especially intestinal viruses, the inhibitory effect against RABV infection remains undefined. In this study, the function of type III IFN against RABV infection was investigated. Initially, we found that IFN-λ2 and IFN-λ3 could inhibit RABV replication in cells. To characterize the role of IFN-λ in RABV infection in a mouse model, recombinant RABVs expressing murine IFN-λ2 or IFN-λ3, termed as rB2c-IFNλ2 or rB2c-IFNλ3, respectively, were constructed and rescued. It was found that expression of IFN-λ could reduce the pathogenicity of RABV and limit viral spread in the brains by different infection routes. Furthermore, expression of IFN-λ could induce the activation of the JAK-STAT pathway, resulting in the production of interferon-stimulated genes (ISGs). It was also found that rRABVs expressing IFN-λ could reduce the production of inflammatory cytokines in primary astrocytes and microgila cells, restrict the opening of the blood-brain barrier (BBB), and prevent excessive infiltration of inflammatory cells into the brain, which could be responsible for the neuronal damage caused by RABV. Consistently, IFN-λ was found to maintain the integrity of tight junction (TJ) protein ZO-1 of BBB to alleviate neuroinflammation in a transwell model. Our study underscores the role of IFN-λ in inhibiting RABV infection, which potentiates IFN-λ as a possible therapeutic agent for the treatment of RABV infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7232327/ doi: 10.3390/v12040405 id: cord-264880-0tmd9knh author: Li, Zhao title: Picoliter Well Array Chip-Based Digital Recombinase Polymerase Amplification for Absolute Quantification of Nucleic Acids date: 2016-04-13 words: 5347.0 sentences: 260.0 pages: flesch: 46.0 cache: ./cache/cord-264880-0tmd9knh.txt txt: ./txt/cord-264880-0tmd9knh.txt summary: We developed a picoliter well array (PWA) chip with 27,000 consistently sized picoliter reactions (314 pL) for isothermal DNA quantification using digital RPA (dRPA) at 39°C. To avoid thermal cycling, different isothermal amplification methods have been developed that rapidly amplify nucleic acids to detectable levels at a single temperature [42, 43] , such as loop-mediated amplification (LAMP) [44] , rolling circle amplification (RCA) [45] , helicasedependent amplification (HDA) [46] , nucleic acid sequence-based amplification (NASBA) [47] , recombinase polymerase amplification (RPA) [48] , transcription-mediated amplification (TMA) [49] , multiple displacement amplification (MDA) [50] , and strand-displacement amplification (SDA) [51] . Finally, we sealed the PWA chip in a homemade copper chamber filled with oil and successfully performed real-time dRPA on an isothermal incubation setup for the absolute quantification of serial dilutions of a Listeria monocytogenes gDNA stock solution. abstract: Absolute, precise quantification methods expand the scope of nucleic acids research and have many practical applications. Digital polymerase chain reaction (dPCR) is a powerful method for nucleic acid detection and absolute quantification. However, it requires thermal cycling and accurate temperature control, which are difficult in resource-limited conditions. Accordingly, isothermal methods, such as recombinase polymerase amplification (RPA), are more attractive. We developed a picoliter well array (PWA) chip with 27,000 consistently sized picoliter reactions (314 pL) for isothermal DNA quantification using digital RPA (dRPA) at 39°C. Sample loading using a scraping liquid blade was simple, fast, and required small reagent volumes (i.e., <20 μL). Passivating the chip surface using a methoxy-PEG-silane agent effectively eliminated cross-contamination during dRPA. Our creative optical design enabled wide-field fluorescence imaging in situ and both end-point and real-time analyses of picoliter wells in a 6-cm(2) area. It was not necessary to use scan shooting and stitch serial small images together. Using this method, we quantified serial dilutions of a Listeria monocytogenes gDNA stock solution from 9 × 10(-1) to 4 × 10(-3) copies per well with an average error of less than 11% (N = 15). Overall dRPA-on-chip processing required less than 30 min, which was a 4-fold decrease compared to dPCR, requiring approximately 2 h. dRPA on the PWA chip provides a simple and highly sensitive method to quantify nucleic acids without thermal cycling or precise micropump/microvalve control. It has applications in fast field analysis and critical clinical diagnostics under resource-limited settings. url: https://doi.org/10.1371/journal.pone.0153359 doi: 10.1371/journal.pone.0153359 id: cord-274289-8g9tuyrc author: Liang, Xiao title: Evaluation of Fast Technology Analysis (FTA) Cards as an improved method for specimen collection and shipment targeting viruses associated with Bovine Respiratory Disease Complex date: 2014-06-15 words: 3438.0 sentences: 139.0 pages: flesch: 42.0 cache: ./cache/cord-274289-8g9tuyrc.txt txt: ./txt/cord-274289-8g9tuyrc.txt summary: The study assessed the stability of nucleic acids stored on FTA cards at a temperature range representing the extremes of environmental heat (13 • to 46 • C) and cold specimen handling conditions (−7 • to −27 • C), and a timeframe from specimen collection to laboratory processing consistent with the expected extremes of diagnostic sample shipping (7-14 days). Bovine Coronavirus was the most prevalent virus detected by realtime PCR during this phase of the study, with 60% animals testing Table 2 Kappa values (95% CI) and percentage agreement for specimens collected into viral transport media compared to specimens collected onto FTA Cards. Bovine Respiratory Syncytial virus was detected using both the specimens in viral transport media and those on FTA Cards for 100% agreement; however the realtime PCR positive test result was for only one animal (Tables 1 and 2) . abstract: In order to improve the analytic quality of respiratory specimens collected from cattle for nucleic acid-based diagnosis, a study was undertaken to verify realtime PCR efficiency of specimens collected and stabilized on FTA Cards™, filter paper which is treated chemically. Nucleic acids collected using FTA Cards without the need for a cold-chain or special liquid media handling provided realtime PCR results consistent (96.8% agreement, kappa 0.923 [95% CI = 0.89–0.96]) with the same specimens collected using traditional viral transport media and shipped on ice using the U.S. Department of Transportation mandated liquid handling requirements. Nucleic acid stabilization on FTA Cards was evaluated over a temperature range (−27 °C to +46 °C) for up to 14 days to mimic environmental conditions for diagnostic sample handling between collection and processing in a routine veterinary laboratory. No significant difference (P ≥ 0.05) was observed in realtime PCR cycle threshold values over the temperature range and time storage conditions for Bovine Viral Diarrhea virus, Bovine Respiratory Syncytial virus, Bovine Coronavirus, and Bovine Herpesvirus I. The four viruses evaluated in the study are associated with Bovine Respiratory Disease Complex where improvements in ease and reliability of specimen collection and shipping would enhance the diagnostic quality of specimens collected in the field, and ultimately improve diagnostic efficiency. url: https://api.elsevier.com/content/article/pii/S0166093414000755 doi: 10.1016/j.jviromet.2014.02.022 id: cord-302207-ljpfgih2 author: Lichtmannsperger, Katharina title: Molecular characterization of Giardia intestinalis and Cryptosporidium parvum from calves with diarrhoea in Austria and evaluation of point-of-care tests date: 2019-07-12 words: 4491.0 sentences: 241.0 pages: flesch: 52.0 cache: ./cache/cord-302207-ljpfgih2.txt txt: ./txt/cord-302207-ljpfgih2.txt summary: title: Molecular characterization of Giardia intestinalis and Cryptosporidium parvum from calves with diarrhoea in Austria and evaluation of point-of-care tests Validation of two immunochromatographic point-of-care tests resulted in a sensitivity of 29.2% and 77.6%; a specificity of 98.4% and 91.1% for the detection of Giardia intestinalis and Cryptosporidium parvum, respectively. It was hypothesized that diarrhoeic calves from Austria harbour Giardia and Cryptosporidium genotypes/subtypes which have the potential to cause human infection, and that immunochromatographic point-of-care tests are valid methods for the detection of these parasites in calf faeces. This is in sharp contrast to a previous study on the possible causes of diarrhoea in calves from Austria which only detected 4.4-6.1% Giardia-and 11.7-25.6% Cryptosporidium-positive samples by sugar-flotation [19, 37] . In Southern Germany 101/110 Giardia intestinalis-positive faecal samples from calves were positive for genotype assemblage E, eight for A and one had a mixed infection with A and E [13] . abstract: To obtain information about the occurrence and genotype distribution of G. intestinalis and C. parvum in Austrian cattle, faecal samples from diarrhoeic calves younger than 180 days of age originating from 70 farms were examined. Of the 177 faecal samples, 27.1% were positive for Giardia cysts (immunofluorescence microscopy) and 55.4% for Cryptosporidium oocysts (phase-contrast microscopy). Positive samples were characterized by nested PCR for Giardia, 83.3% (triosephosphate isomerase; tpi) and 89.6% (β-giardin; bg) were positive, while the Cryptosporidium nested PCR returned 92.5% (60-kDa glycoprotein) positive results. Sequence analysis revealed one assemblage A-positive sample and 30 (bg) respectively 29 (tpi) assemblage E-positive samples for G. intestinalis. For C. parvum four subtypes within the IIa family (IIaA15G2R1, n = 29; IIaA19G2R2, n = 3; IIaA21G2R1, n = 2; IIaA14G1R1, n = 1) could be differentiated. Validation of two immunochromatographic point-of-care tests resulted in a sensitivity of 29.2% and 77.6%; a specificity of 98.4% and 91.1% for the detection of Giardia intestinalis and Cryptosporidium parvum, respectively. Results confirm the widespread occurrence of both protozoa in diarrhoeic calves in Austria. url: https://doi.org/10.1016/j.cimid.2019.101333 doi: 10.1016/j.cimid.2019.101333 id: cord-333413-8buawes0 author: Liebing, J. title: Health status of free-ranging ring-necked pheasant chicks (Phasianus colchicus) in North-Western Germany date: 2020-06-16 words: 5556.0 sentences: 306.0 pages: flesch: 51.0 cache: ./cache/cord-333413-8buawes0.txt txt: ./txt/cord-333413-8buawes0.txt summary: Being a typical ground-breeding bird of the agricultural landscape in Germany, the pheasant has experienced a strong and persistent population decline with a hitherto unexplained cause. In the present study, 62 free-ranging pheasant chicks were caught within a two-year period in three federal states of Germany; Lower Saxony, North Rhine-Westphalia and Schleswig-Holstein. Pheasant chick deaths may often have been triggered by poor nutritional status, probably in association with inflammatory changes in various tissues and organs as well as bacterial and parasitic pathogens. In 2014 and 2015, the Institute for Terrestrial and Aquatic Wildlife Research (ITAW), University of Veterinary Medicine Hannover, Foundation, Hannover and the Wildlife Research Institute, State Office for Nature, Environment and Consumer Protection of North Rhine-Westphalia caught free-living Ring-necked Pheasant chicks from Lower Saxony (Cuxhaven, Grafschaft Bentheim, Emsland, Osnabrück, Vechta), North Rhine-Westphalia (Coesfeld, Warendorf) and Schleswig-Holstein (Dithmarschen) to assess the health state by means of pathological, microbiological, virological, parasitological and toxicological investigations. abstract: Being a typical ground-breeding bird of the agricultural landscape in Germany, the pheasant has experienced a strong and persistent population decline with a hitherto unexplained cause. Contributing factors to the ongoing negative trend, such as the effects of pesticides, diseases, predation, increase in traffic and reduced fallow periods, are currently being controversially discussed. In the present study, 62 free-ranging pheasant chicks were caught within a two-year period in three federal states of Germany; Lower Saxony, North Rhine-Westphalia and Schleswig-Holstein. The pheasant chicks were divided into three age groups to detect differences in their development and physical constitution. In addition, pathomorphological, parasitological, virological, bacteriological and toxicological investigations were performed. The younger chicks were emaciated, while the older chicks were of moderate to good nutritional status. However, the latter age group was limited to a maximum of three chicks per hen, while the youngest age class comprised up to ten chicks. The majority of chicks suffered from dermatitis of the periocular and caudal region of the head (57–94%) of unknown origin. In addition, intestinal enteritis (100%), pneumonia (26%), hepatitis (24%), perineuritis (6%), tracheitis (24%), muscle degeneration (1%) and myositis (1%) were found. In 78% of the cases, various Mycoplasma spp. were isolated. Mycoplasma gallisepticum (MG) was not detected using an MG-specific PCR. Parasitic infections included Philopteridae (55%), Coccidia (48%), Heterakis/Ascaridia spp. (8%) and Syngamus trachea (13%). A total of 8% of the chicks were Avian metapneumovirus (AMPV) positive using RT-PCR, 16% positive for infectious bronchitis virus (IBV) using RT-PCR, and 2% positive for haemorrhagic enteritis virus (HEV) using PCR. All samples tested for avian encephalomyelitis virus (AEV), infectious bursal disease virus (IBDV) or infectious laryngotracheitis virus (ILTV) were negative. The pool samples of the ten chicks were negative for all acid, alkaline-free and derivative substances, while two out of three samples tested were positive for the herbicide glyphosate. Pheasant chick deaths may often have been triggered by poor nutritional status, probably in association with inflammatory changes in various tissues and organs as well as bacterial and parasitic pathogens. Theses impacts may have played a major role in the decline in pheasant populations. url: https://www.ncbi.nlm.nih.gov/pubmed/32544211/ doi: 10.1371/journal.pone.0234044 id: cord-302296-7ge92p69 author: Lilleeng, Einar title: Comparison of intestinal gene expression in Atlantic cod (Gadus morhua) fed standard fish meal or soybean meal by means of suppression subtractive hybridization and real-time PCR date: 2007-07-03 words: 6481.0 sentences: 351.0 pages: flesch: 57.0 cache: ./cache/cord-302296-7ge92p69.txt txt: ./txt/cord-302296-7ge92p69.txt summary: The selected clones were sequences showing similarity to the following genes: fatty acid binding protein (FABP, clone ID GH4A-F142), putative transmembrane 4 superfamily member protein (TM4, clone ID GH4A-F103), polypeptide N-acetylgalactosaminyltransferase (ppGaNTase, clone ID GH4A-F107), Aminopeptidase M (Alanyl aminopeptidase)(CD13)/Aminopeptidase N (APN, clone ID GH4A-F77), transcobalamin I precursor (TCI, clone ID GH4A-F84), Sec61-alpha (SEC61, clone ID GH4A-F137), F-box protein 44 (F-BOX, clone ID GH4A-F138), glutathione peroxidase (GPx, clone ID GH4A-F127), peroxiredoxin 4 (Prx4, clone ID GH4A-F167), cytochrome P450 3A40 (CYP3A40, clone ID GH4A-F166), ras-related nuclear protein (Ran, clone ID GH4A-F53), and 14-3-3B2 protein (14-3-3, clone ID GH4A-F159). Mean normalized calibrated ratios from real-time PCR of 12 clones, selected based on their similarity to genes involved in processes such as protein-and lipid metabolism, growth and antioxidant functions, showed that expression of 4 out of the 12 clones tested were significantly up regulated (P b 0.05) in intestine from cod fed SBM compared to intestines from cod fed FM. abstract: Gene expression was studied in Atlantic cod fed two different diets, fish meal (FM) and dehulled and extracted soybean meal (SBM). RNA was isolated from the distal part of the mid-intestine of Atlantic cod and suppression subtractive hybridization (SSH) was employed to screen for genes that showed changes in expression in response to the two dietary treatments. We made a cDNA subtracted library, isolated and sequenced 192 clones. Identification of 157 clones was predicted by BLAST. Most of the clones were previously unidentified in cod. Expression of 12 selected clones was further studied by quantitative PCR. Expression of four clones showing similarity to aminopeptidase N, transcobalamin I precursor, cytochrome P450 3A40, and ras-related nuclear protein was significantly up regulated in intestine of cod fed SBM compared to cod fed FM. A trend towards up regulation of a clone with similarity to fatty acid binding protein in SBM-fed cod was also observed. No significant differences in expression were observed for: transmembrane 4 superfamily protein member, polypeptide N-acetylgalactosaminyltransferase, glutathione peroxidase, peroxiredoxin 4, SEC61, F-BOX, and 14-3-3. url: https://doi.org/10.1016/j.aquaculture.2007.01.048 doi: 10.1016/j.aquaculture.2007.01.048 id: cord-001134-8ljgxnhf author: Lin, Chao-Nan title: Comparison of viremia of type II porcine reproductive and respiratory syndrome virus in naturally infected pigs by zip nucleic acid probe-based real-time PCR date: 2013-09-12 words: 2978.0 sentences: 165.0 pages: flesch: 52.0 cache: ./cache/cord-001134-8ljgxnhf.txt txt: ./txt/cord-001134-8ljgxnhf.txt summary: title: Comparison of viremia of type II porcine reproductive and respiratory syndrome virus in naturally infected pigs by zip nucleic acid probe-based real-time PCR In this study, we developed a sensitive and specific zip nucleic acid probe-based real-time PCR assay to evaluate the viremia of natural PRRSV-infected pigs in Taiwan. CONCLUSIONS: ZNA probe-based real-time PCR can be a useful tool to diagnose symptomatic and asymptomatic PRRSV-infected pigs. ZNA probe-based real-time PCR amplification and the limit of detection Tenfold serial plasmid dilutions (10 1 to 10 6 copies/μl) were tested and used to construct the standard curve by plotting the logarithm of the plasmid copy number against the measured quantification cycles (Cq) values. However, this is first study to report the viral load using serum samples in asymptomatic PRRSV-infected pigs using ZNA probebased real-time PCR. Development of a onestep real-time quantitative PCR assay based on primer-probe energy transfer for the detection of porcine reproductive and respiratory syndrome virus abstract: BACKGROUND: Porcine reproductive and respiratory syndrome virus (PRRSV) is a RNA virus with high genetic variation. This virus causes significant economic losses in most pig-producing countries. The clinical presentation of PRRSV ranges from asymptomatic to devastating. In this study, we developed a sensitive and specific zip nucleic acid probe-based real-time PCR assay to evaluate the viremia of natural PRRSV-infected pigs in Taiwan. Serum samples were collected from 577 pigs aged 5–12 weeks. These include 444 clinically healthy pigs and 133 symptomatic pigs were confirmed to have porcine respiratory disease complex (PRDC). RESULTS: Viremia was quantified in 79 of the 444 (17.8%) clinically healthy pigs and in 112 of the 133 (84.2%) PRDC cases. Viremias were significantly more common in pigs with PRDC compared with the clinically healthy pigs (P <0.0001). These results suggest that a high viral load is a major feature of PRRSV-affected pigs. CONCLUSIONS: ZNA probe-based real-time PCR can be a useful tool to diagnose symptomatic and asymptomatic PRRSV-infected pigs. The presence of this marker in a sample of animals with high PRRSV loads (>10(4.2) PRRSV genomes/μl of serum) seems to indicate that it correlates with the presence of PRDC in pigs. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3847877/ doi: 10.1186/1746-6148-9-181 id: cord-315037-lmur80te author: Lin, Chien-Yu title: Increased Detection of Viruses in Children with Respiratory Tract Infection Using PCR date: 2020-01-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Respiratory viruses are a common cause of respiratory tract infection (RTI), particularly in neonates and children. Rapid and accurate diagnosis of viral infections could improve clinical outcomes and reduce the use of antibiotics and treatment sessions. Advances in diagnostic technology contribute to the accurate detection of viruses. We performed a multiplex real-time polymerase chain reaction (PCR) to investigate the viral etiology in pediatric patients and compared the detection rates with those determined using traditional antigen tests and virus cultures. Fifteen respiratory viruses were included in our investigation: respiratory syncytial virus A/B (RSV), influenza virus A (FluA) and influenza virus B (FluB), human metapneumovirus (MPV), enterovirus (EV), human parainfluenza virus (PIV) types 1–4, human rhinovirus (RV), human coronavirus OC43, NL63, and 229E, human adenovirus (ADV), and human bocavirus (Boca). In total, 474 specimens were collected and tested. Respiratory viruses were detected more frequently by PCR (357, 75.3%) than they were by traditional tests (229, 49.3%). The leading pathogens were RSV (113, 23.8%), RV (72, 15.2%), PIV3 (53, 11.2%), FluA (51, 10.8%), and ADV (48, 10.1%). For children younger than 5 years, RSV and RV were most prevalent; for children older than 5 years, FluA and ADV were the most frequently detected. Of the specimens, 25.8% (92/357) were coinfected with two or more viruses. RV, Boca, PIV2, FluB, and PIV4 had higher rates of coinfection; MPV and PIV1 had the lowest rates of coinfection (9.1% and 5.3%). To conclude, the detection power of PCR was better than that of traditional antigen tests and virus cultures when considering the detection of respiratory viruses. RSV and RV were the leading viral pathogens identified in the respiratory specimens. One-quarter of the positive specimens were coinfected with two or more viruses. In the future, further application of PCR may contribute to the rapid and accurate diagnosis of respiratory viruses and could improve patient outcomes. url: https://www.ncbi.nlm.nih.gov/pubmed/31952364/ doi: 10.3390/ijerph17020564 id: cord-298462-xpx3orvs author: Lin, Feng title: Quantification of human bocavirus in lower respiratory tract infections in China date: 2007-01-31 words: 1455.0 sentences: 82.0 pages: flesch: 52.0 cache: ./cache/cord-298462-xpx3orvs.txt txt: ./txt/cord-298462-xpx3orvs.txt summary: A quantitative PCR method was established to quantify human bocavirus (HBoV) genomic copies in clinical specimens from children with lower respiratory tract infections (LRTI) in China. Recently, a reliable quantitative PCR (Q-PCR) method has been developed to detect HBoV genomic copies in clinical samples, and this has demonstrated a presence of HBoV DNA in children with pneumonia-like symptoms in Thailand [14] . In this study, we used a Q-PCR with the amplicon targeted to the NS coding region of HBoV to detect the presence of HBoV DNA in children with respiratory tract infection in China. All 7 positive samples were either sputum or aspirated sputum, indicating a significant presence of HBoV DNA in lower respiratory tract. HBoV (Human bocavirus); LTRI (Lower respiratory tract infection); Q-PCR (Quantitative polymerase chain reaction). Detection of human bocavirus in Japanese children with lower respiratory tract infections abstract: A quantitative PCR method was established to quantify human bocavirus (HBoV) genomic copies in clinical specimens from children with lower respiratory tract infections (LRTI) in China. A total of 257 respiratory tract specimens were tested, and 7 (2.7%) of these (all sputum samples) were positive, with genomic copies that ranged from 8.0 × 10(3 )to 8.0 × 10(9 )in the samples. The main clinical symptom of patients who were positive for HBoV DNA was a pneumonia-like syndrome represented by high fever and cough. Our results suggest that HBoV may be an important etiological agent of LRTI in children in China. url: https://www.ncbi.nlm.nih.gov/pubmed/17266760/ doi: 10.1186/1750-9378-2-3 id: cord-005752-tur57xd9 author: Linden, Saara title: Parechovirus infection preceding Guillain–Barré syndrome date: 2012-05-12 words: 1307.0 sentences: 87.0 pages: flesch: 49.0 cache: ./cache/cord-005752-tur57xd9.txt txt: ./txt/cord-005752-tur57xd9.txt summary: Since the near global eradication of poliomyelitis, Guillain-Barré syndrome (GBS) has become the most common cause of acute neuromuscular paralysis. Recent Campylobacter jejuni infection is discovered in 30 % of GBS patients (Poropatich et al. In this case report, we describe a 36-year-old male Finnish patient with GBS, who had a parechovirus infection preceding the neurological illness. Picornavirus PCR was positive from a stool sample taken on the day following hospitalization. Our patient had a mild clinical parechovirus infection preceding GBS. jejuni infection preceding GBS include serological evidence of C. jejuni IgG antibody titer≥1:2,000 by ELISA test) and a definite history of diarrhea within the previous 3 weeks of GBS onset (Kuwabara et al. It remains unproven whether HPeV had any causative role in triggering autoimmunity in our patient, but no other acute or recent microbial infections were detected. Epidemiology and clinical associations of human parechovirus respiratory infections abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095366/ doi: 10.1007/s13365-012-0104-3 id: cord-017959-g0nf1iwm author: Lipkin, W. Ian title: Diagnosis, Discovery and Dissection of Viral Diseases date: 2014-02-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Only a few years ago, viral diagnosis was largely an exercise for academic researchers and public health practitioners with focus on epidemiologic analyses and outbreak prevention, detection, and control. Opportunities for therapeutic intervention were limited to only a few applications such as herpesvirus infections, influenza, and HIV/AIDS; hence, once a bacterial or fungal infection was excluded, clinicians were limited to providing supportive care for what was presumed to be a viral syndrome. Public health organizations tracked the incidence of viral infections and the development of resistance to the few antiviral drugs in use and provided input to governments and the pharmaceutical industry regarding selection of vaccine targets. More recently, interest in viral diagnostics has burgeoned with the advent of new tools for detection and discovery, global recognition of pandemic risk, high-throughput drug screening, rational drug design, and immunotherapeutics. An additional impetus has been the implication of viruses in chronic illnesses not previously attributed to infection. The objective of this chapter is to review the factors responsible for the rise in awareness of viral infections, methods for diagnosis and monitoring viral infections, and future prospects for improvements in discovery, detection, and response to the challenges of clinical virology. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122662/ doi: 10.1007/978-1-4899-7448-8_2 id: cord-347443-0evqo01m author: Litwin, Christine M. title: Seasonality and prevalence of respiratory pathogens detected by multiplex PCR at a tertiary care medical center date: 2013-07-24 words: 3991.0 sentences: 218.0 pages: flesch: 50.0 cache: ./cache/cord-347443-0evqo01m.txt txt: ./txt/cord-347443-0evqo01m.txt summary: Seasonality has been reported for many viruses, including influenza virus, respiratory syncytial virus (RSV), and the recently described human metapneumovirus (hMPV). Major causes of bronchiolitis and lower respiratory tract illnesses in children include respiratory syncytial virus (RSV), parainfluenza viruses, influenza virus, and human metapneumovirus (hMPV). The organism/viruses detected by the FilmArray included adenovirus, influenza A virus (FluA), influenza B virus (FluB), parainfluenza virus 1 (Para 1), parainfluenza virus 2 (Para 2), parainfluenza virus 3 (Para 3), parainfluenza virus 4 (Para 4), respiratory syncytial virus (RSV), coronavirus 229E (CoronaV 229E), CoronaV NL63, CoronaV HKU1, CoronaV OC43, human metapneumovirus (hMPV), Bordetella pertussis, Chlamydophila pneumoniae and Mycoplasma pneumoniae. In our study, 939 specimens were analyzed over the course of a year using a respiratory pathogen multiplex PCR that yielded a positivity rate of 65 % with multiple analytes detected in 12 % of specimens, especially in children. RSV and hMPV PCR-positive cases were statistically much more likely than Rhino/Entero PCR-positive infections to initially present with pneumonia or bronchiolitis in our study. abstract: Respiratory tract infections (RTIs) are a leading cause of mortality and morbidity. Seasonality has been reported for many viruses, including influenza virus, respiratory syncytial virus (RSV), and the recently described human metapneumovirus (hMPV). We hypothesize that the availability of rapid, multiplex PCR diagnostics will provide better clinical care and new insights into the etiology and clinical spectrum of RTIs. We conducted a retrospective analysis of the incidence of respiratory pathogens at a 500-bed adult and 154-bed pediatric hospital tertiary care center. A total of 939 specimens from patients with an age range of 5 days to 91 years (median, 2 years) were tested by a multiplex respiratory pathogen PCR from November 14, 2011 to November 13, 2012. Sixty-five percent of specimens were positive for at least one pathogen. As the age of the patient increased, the positivity rate for the PCR decreased proportionately. Rhinoviruses/enteroviruses (Rhino/Entero) were the most prevalent (34.3 %) followed by RSV (19.2 %) and hMPV (6.2 %). Twelve percent of the positive samples were positive for multiple analytes, with Rhino/Entero and RSV being the most common combination. The peak months were September and May for Rhino/Entero infections, January for RSV and February for coronavirus. hMPV peaked 2 months after RSV, as has been observed recently in other studies. Multiplex PCR provides rapid diagnostic information that can be used to make knowledgeable clinical decisions and potentially reduce the use of antibiotics. Active respiratory PCR surveillance could also predict seasonal respiratory epidemics to allow for adequate planning of additional infection control measures. url: https://www.ncbi.nlm.nih.gov/pubmed/23881085/ doi: 10.1007/s00705-013-1794-4 id: cord-301167-101lnq4f author: Liu, Quanjun title: Microarray-in-a-Tube for Detection of Multiple Viruses date: 2007-02-01 words: 3248.0 sentences: 177.0 pages: flesch: 48.0 cache: ./cache/cord-301167-101lnq4f.txt txt: ./txt/cord-301167-101lnq4f.txt summary: Methods: We developed a novel PCR assay, the microarray-in-a-tube system, which integrates multiple PCR processes and DNA microarrays for multiple virus detection. A 5 × 5 oligonucleotide microarray for detecting 4 respiratory tract viruses (severe acute respiratory syndrome–associated coronavirus, influenza A virus, influenza B virus, and enterovirus) with inner controls was arranged on the inner surface of a specially designed Eppendorf cap with a flat, optically transparent window. We aimed to develop a microarray-in-a-tube that integrates RT-PCR and a DNA microarray for detecting and distinguishing 4 viruses causing human acute respiratory tract infection, SARS coronavirus, influenza A and B viruses, and enterovirus. The system (Fig. 1 ) has 3 parts, which include an optically transparent plastic cap with an oligonucleotide microarray on the inner surface, a black inner vessel that contains hybridization solution, and the body of the Eppendorf tube. abstract: Background: The detection of multiple viruses is important for pathogenic diagnosis and disease control. Microarray detection is a good method, but requires complex procedures for multiple virus detection. Methods: We developed a novel PCR assay, the microarray-in-a-tube system, which integrates multiple PCR processes and DNA microarrays for multiple virus detection. A 5 × 5 oligonucleotide microarray for detecting 4 respiratory tract viruses (severe acute respiratory syndrome–associated coronavirus, influenza A virus, influenza B virus, and enterovirus) with inner controls was arranged on the inner surface of a specially designed Eppendorf cap with a flat, optically transparent window. Results: We were able to perform all detection processes in the encapsulated system without opening the cap. The 4 viruses were successfully amplified by one-step reverse transcription–PCR in the encapsulated tube. After the PCR process, the microarray-in-a-tube was inverted, and the fluorescence-labeled PCR products were directly hybridized on the microarray. Hybridization signals were obtained with an ordinary fluorescent microscope. The sensitivity of the system for virus detection reached 10(2) copies/μL. With the help of inner controls, the system provided reliable results without false negatives and false positives. Conclusions: The microarray-in-a-tube system is a rapid, labor-saving tool for multiple virus detection with several advantages, such as convenience, prevention of cross-contamination of the PCR products, and potential for multiple-gene detection. url: https://www.ncbi.nlm.nih.gov/pubmed/17158198/ doi: 10.1373/clinchem.2006.071720 id: cord-312139-g1hczx54 author: Liu, Wei title: Non-specific Primers Reveal False-negative Risk in Detection of COVID-19 Infections date: 2020-04-11 words: 3347.0 sentences: 212.0 pages: flesch: 60.0 cache: ./cache/cord-312139-g1hczx54.txt txt: ./txt/cord-312139-g1hczx54.txt summary: Based on the primers provided by research institutes from different countries, especially primers from China, detailed analysis of non-specificity of primer sequences had been conducted, and interference of human mRNA targeted by the primer was discussed deeply for RT-PCR detection of COVID-19 infections. https://doi.org/10.1101/2020.04.07.20056804 doi: medRxiv preprint 8 Although many patients tested one or more negative before receiving positive results for SARS-CoV-2 virus in China, it was difficult to understand the extent to which this abnormal phenomenon occurs. To eliminate the host interference in RT-PCR detection of COVID-19 infections, specific amplification of the intended target of SARS-Cov-2 sequence required that primers matched as little as possible to any human RNA transcript. Hence it was not difficult to draw a conclusion that non-specificity of the primer designed for SARS-CoV-2 virus might be an important factor resulting in so many false-negative diagnoses for COVID-19 infections in China. abstract: Background: A novel coronavirus disease 2019 (COVID-19) broke out in Wuhan of Hubei province and had spread throughout the world since December 2019. Because the clinically diagnosed cases in Hubei province were reported for the first time on February 13, 2020, a very high peak of new cases in China was observed. The reason why so many clinically diagnosed cases appeared was not clear. Methods: All data of new cases in China were acquired from WHO situation reports. Linear fitting was used to infer the ability to detect COVID-19 infections. Primer-BLAST and nucleotide blast were applied to check the specificity of primers. Expression data of human mRNA in different tissues was obtained from Human Protein Atlas. Finding: Based on the data and analysis of changes of new laboratory-confirmed cases and new clinically diagnosed cases, it was inferred that there were many false-negative results in all clinically diagnosed cases in Hubei province. There were eight non-specific primers in dozens of primers used in clinical or research detection of COVID-19. Among them, a pair of primer for the ORF1ab regions of SARS-CoV-2 genome, which widely applied to detect SARS-CoV-2 virus in China, well matched some human mRNAs such as Cathepsin C transcripts. Compared to other transcripts, Cathepsin C mRNA had a high abundance in tonsil, lung and small intestine. Interpretation: Some non-specific RT-PCR primers could cause the serious interference during RT-PCR amplification so as to increase the risk of false-negative diagnoses for COVID-19 infections. Funding Key Research Project of the Higher Education of Henan Province url: https://doi.org/10.1101/2020.04.07.20056804 doi: 10.1101/2020.04.07.20056804 id: cord-001787-lj1nd922 author: Liu, Ying title: Enhancing production of ergosterol in Pichia pastoris GS115 by over-expression of 3-hydroxy-3-methylglutaryl CoA reductase from Glycyrrhiza uralensis date: 2014-04-02 words: 3105.0 sentences: 174.0 pages: flesch: 56.0 cache: ./cache/cord-001787-lj1nd922.txt txt: ./txt/cord-001787-lj1nd922.txt summary: title: Enhancing production of ergosterol in Pichia pastoris GS115 by over-expression of 3-hydroxy-3-methylglutaryl CoA reductase from Glycyrrhiza uralensis pastoris strains containing different copy numbers of the GuHMGR gene were obtained and the content of ergosterol was analyzed by HPLC. In this study, we investigated how copy number variation (CNV) of the GuHMGR gene affects the formation of ergosterol. pastoris strains containing different copy numbers of the GuHMGR gene were induced to express the gene; P. pastoris strains was 1.07-2.51 times higher than in the negative control but with increase in the copy number of GuHMGR gene; the content of ergosterol showed an increasing-decreasingincreasing pattern. pastoris strain containing 44 copies of the GuHMGR gene. In this study, the dependence of the content of ergosterol on the copy number of the GuHMGR gene suggests that an increase in the latter could lead to an increase in the production of GA in G. abstract: The rate-limiting enzyme in the mevalonic acid (MVA) pathway which can lead to triterpenoid saponin glycyrrhizic acid (GA) is 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR). In order to reveal the effect of copy number variation in the HMGR gene on the MVA pathway, the HMGR gene from Glycyrrhiza uralensis Fisch. (GuHMGR) was cloned and over-expressed in Pichia pastoris GS115. Six recombinant P. pastoris strains containing different copy numbers of the GuHMGR gene were obtained and the content of ergosterol was analyzed by HPLC. The results showed that all the recombinant P. pastoris strains contained more ergosterol than the negative control and the strains with 8 and 44 copies contained significantly more ergosterol than the other strains. However, as the copy number increased, the content of ergosterol showed an increasing–decreasing–increasing pattern. This study provides a rationale for increasing the content of GA through over-expressing the GuHMGR gene in cultivars of G. uralensis. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4590296/ doi: 10.1016/j.apsb.2014.02.007 id: cord-017894-8iahlshj author: Loa, Chien Chang title: A Multiplex Polymerase Chain Reaction for Differential Detection of Turkey Coronavirus from Chicken Infectious Bronchitis Virus and Bovine Coronavirus date: 2015-09-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A multiplex polymerase chain reaction (PCR) method for differential detection of turkey coronavirus (TCoV), infectious bronchitis virus (IBV), and bovine coronavirus (BCoV) is presented in this chapter. Primers are designed from the conserved or variable regions of nucleocapsid (N) or spike (S) protein genes of TCoV, IBV, and BCoV and used in the same PCR reaction. Reverse transcription followed by PCR reaction is used to amplify a portion of N or S gene of the corresponding coronaviruses. Two PCR products, a 356-bp band corresponding to N gene and a 727-bp band corresponding to S gene, are obtained for TCoV. In contrast, one PCR product of 356 bp corresponding to a fragment of N gene is obtained for IBV strains and one PCR product of 568 bp corresponding to a fragment of S gene is obtained for BCoV. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122580/ doi: 10.1007/978-1-4939-3414-0_12 id: cord-316537-f5rto51t author: Loens, Katherine title: Mycoplasma pneumoniae: Current Knowledge on Nucleic Acid Amplification Techniques and Serological Diagnostics date: 2016-03-31 words: 4207.0 sentences: 190.0 pages: flesch: 34.0 cache: ./cache/cord-316537-f5rto51t.txt txt: ./txt/cord-316537-f5rto51t.txt summary: The clinical significance of a serologic test, both for IgM and IgG, should be defined by studies of patients with a documented infection and for whom detailed information concerning the time lapses between onset of disease and the collection of the serum specimens are known. Comparison of real-time polymerase chain reaction and serological tests for the confirmation of Mycoplasma pneumoniae infection in children with clinical diagnosis of atypical pneumonia Evaluation of five real-time PCR assays for detection of Mycoplasma pneumoniae Sensitive detection of Mycoplasma pneumoniae in human respiratory tract samples by optimized real-time PCR approach Diagnostic sensitivity of a rapid antigen test for the detection of Mycoplasma pneumoniae: comparison with real-time PCR Development of a multiplex real-time PCR assay for detection of Mycoplasma pneumoniae, Chlamydia pneumoniae and mutations associated with macrolide resistance in Mycoplasma pneumoniae from respiratory clinical specimens Real-time PCR detection of Mycoplasma pneumoniae in respiratory specimens Evaluation of a new real-time PCR assay for detection of Mycoplasma pneumoniae in clinical specimens abstract: Mycoplasma pneumoniae (M. pneumoniae) belongs to the class Mollicutes and has been recognized as a common cause of respiratory tract infections (RTIs), including community-acquired pneumonia (CAP), that occur worldwide and in all age groups. In addition, M. pneumoniae can simultaneously or sequentially lead to damage in the nervous system and has been associated with a wide variety of other acute and chronic diseases. During the past 10 years, the proportion of LRTI in children and adults, associated with M. pneumoniae infection has ranged from 0 to more than 50%. This variation is due to the age and the geographic location of the population examined but also due to the diagnostic methods used. The true role of M. pneumoniae in RTIs remains a challenge given the many limitations and lack of standardization of the applied diagnostic tool in most cases, with resultant wide variations in data from different studies. Correct and rapid diagnosis and/or management of M. pneumoniae infections is, however, critical to initiate appropriate antibiotic treatment and is nowadays usually done by PCR and/or serology. Several recent reviews, have summarized current methods for the detection and identification of M. pneumoniae. This review will therefore provide a look at the general principles, advantages, diagnostic value, and limitations of the most currently used detection techniques for the etiological diagnosis of a M. pneumoniae infection as they evolve from research to daily practice. url: https://www.ncbi.nlm.nih.gov/pubmed/27064893/ doi: 10.3389/fmicb.2016.00448 id: cord-322234-1zyy536y author: Lorusso, Alessio title: One-step real-time RT-PCR for pandemic influenza A virus (H1N1) 2009 matrix gene detection in swine samples date: 2009-12-17 words: 4162.0 sentences: 195.0 pages: flesch: 51.0 cache: ./cache/cord-322234-1zyy536y.txt txt: ./txt/cord-322234-1zyy536y.txt summary: To evaluate the applicability of the test as a diagnostic tool in the screening of field specimens from swine, 64 field isolates of North American swine, 5 equine and 48 avian influenza viruses collected during diagnostic investigations were analyzed retrospectively as well as samples collected during an experimental in vivo infection with two novel H1N1 isolates, A/California/04/2009 (H1N1)v virus and A/Mexico/4108/2009 (H1N1)v. Swine and equine influenza virus isolates and the clinical samples from pigs infected experimentally with 2009 (H1N1)v were subjected to the USDA-validated qRT-PCR procedure for the general detection of type A influenza virus RNA (matrix screening assay), following procedures described previously (Spackman and Suarez, 2008) . All endemic North American swine influenza virus isolates were negative for (H1N1) 2009 specific matrix gene RNA using the present qRT-PCR assay, whereas the (H1N1) 2009 strains used as positive control were positive. abstract: In the spring of 2009, a novel (H1N1) influenza A virus began to spread among humans worldwide. Although the 2009 H1N1 is related genetically to swine influenza viruses, human infection has not been connected to pig exposure. Because the virus is now circulating widely in the human population, swine herds are at increased risk of becoming infected. In order to investigate potential outbreaks of the 2009 pandemic virus in pigs, a quantitative real-time reverse transcriptase-polymerase chain reaction (qRT-PCR) for the detection of the (H1N1) 2009 RNA in clinical specimens was developed. To evaluate the applicability of the test as a diagnostic tool in the screening of field specimens from swine, 64 field isolates of North American swine, 5 equine and 48 avian influenza viruses collected during diagnostic investigations were analyzed retrospectively as well as samples collected during an experimental in vivo infection with two novel H1N1 isolates, A/California/04/2009 (H1N1)v virus and A/Mexico/4108/2009 (H1N1)v. The sensitivity of the qRT-PCR was shown to be higher with respect to standard techniques such as virus isolation and the reproducibility was satisfactory. The present unique and highly sensitive assay is able to detect as little as 1 × 10(1) copies of RNA per μl of template and it represents a rapid and useful approach for the screening and quantitation of (H1N1) 2009 RNA in porcine specimens. url: https://www.sciencedirect.com/science/article/pii/S0166093409005205 doi: 10.1016/j.jviromet.2009.12.002 id: cord-279496-3be5tlnw author: Losurdo, Michele title: Long-term shedding of Canine alphaherpesvirus 1 in naturally infected newborn pups date: 2018-07-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The long-term shedding of Canine alphaherpesvirus 1 (CaHV-1) by neonatal pups with natural infection is reported. The pups belonged to a litter of 11 pointers of a breeding kennel in southern Italy, 9 of which developed a fatal form of systemic infection, as resulted by the detection of CaHV-1 in internal organs (kidney, liver, lung and brain) of one of this dogs and in the vaginal swab of their mother. The two remaining animals displayed a milder form of disease, with one pup showing ocular involvement, and underwent a progressive recovery. These pups were monitored from 11 to 36 days of age, showing a long-term shedding of the virus through the nasal and ocular secretions and the faeces. CaHV-1 shedding, as assessed by means of a specific and sensitive real-time PCR assay, occurred mainly through the nasal secretions, although the pup displaying ocular disease shed the virus at high titres and for a long period even in the ocular secretions. url: https://api.elsevier.com/content/article/pii/S003452881830167X doi: 10.1016/j.rvsc.2018.07.001 id: cord-314051-dr27bsvt author: Lother, Sylvain A. title: Preoperative SARS-CoV-2 screening: Can it really rule out COVID-19? date: 2020-06-23 words: 3121.0 sentences: 259.0 pages: flesch: 56.0 cache: ./cache/cord-314051-dr27bsvt.txt txt: ./txt/cord-314051-dr27bsvt.txt summary: If viral carriage is not detected by testing, patients may proceed with elective surgery whereby signs and symptoms of coronavirus disease (COVID-19) may arise in the postoperative period, leading to adverse outcomes. 3 While screening with RT-PCR may detect some presymptomatic preoperative patients, the window of diagnostic utility is small, and careful interpretation of negative and positive test results must be considered prior to altering the course of therapy. A positive RT-PCR result identifies a group of patients who may be infected with SARS-CoV-2 and should have elective surgeries delayed. Si la présence virale n''est pas dépistée par un test, les patients peuvent aller de l''avant avec leur chirurgie non urgente, à la suite de laquelle les signes et symptômes d''une atteinte au coronavirus (COVID-19) pourraient survenir en période postopératoire, entraînant des devenirs défavorables. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32578049/ doi: 10.1007/s12630-020-01746-w id: cord-298051-ej8qxkce author: Louten, Jennifer title: Detection and Diagnosis of Viral Infections date: 2016-05-06 words: 11204.0 sentences: 602.0 pages: flesch: 57.0 cache: ./cache/cord-298051-ej8qxkce.txt txt: ./txt/cord-298051-ej8qxkce.txt summary: Cell lines can be infected with patient samples to allow viral replication within the cells; observable cytopathic effects can help to identify the identity of the virus. Infected cells can also be used for immunofluorescence assays, which use fluorescently labeled virus-specific antibodies to identify viruses in fixed cells or tissues. In the process of PCR, DNA (including any viral DNA present) is isolated from the clinical specimen, generally blood cells or tissue, and added to a tube containing primers, DNA polymerase, and nucleotides ( Fig. 7.14) . The diagnostic techniques described in this chapter identify the presence of a virus in a sample, or even the amount of viral nucleic acid, but these assays cannot determine the amount of virus present that is capable of productively infecting cells. Fluorescently labeled antibodies bind to viral antigens present in infected cells. abstract: Diagnostic tests are paramount in determining the etiology of viral infections. Direct diagnostic methods assay for the presence of the virus, while indirect methods test for effects of the virus. Cell culture is the process of growing cells or tissues in the laboratory. Cell lines can be infected with patient samples to allow viral replication within the cells; observable cytopathic effects can help to identify the identity of the virus. Infected cells can also be used for immunofluorescence assays, which use fluorescently labeled virus-specific antibodies to identify viruses in fixed cells or tissues. A variety of diagnostic immunoassays exist, including enzyme-linked immunosorbent assays/enzyme immunoassays, western blots, lateral flow immunoassays, and agglutination reactions. Assays that detect viral nucleic acids are based upon the principles of PCR or nucleic acid hybridization, are extremely sensitive, and are specific for a particular virus. url: https://api.elsevier.com/content/article/pii/B9780128009475000077 doi: 10.1016/b978-0-12-800947-5.00007-7 id: cord-009376-a35a92gh author: Lovatt, Archie title: Applications of quantitative PCR in the biosafety and genetic stability assessment of biotechnology products date: 2002-01-07 words: 9214.0 sentences: 523.0 pages: flesch: 48.0 cache: ./cache/cord-009376-a35a92gh.txt txt: ./txt/cord-009376-a35a92gh.txt summary: Applications of Q-PCR within biotechnology are discussed with particular emphasis on the following areas of biosafety and genetic stability testing: (a) determination of the biodistribution of gene therapy vectors in animals; (b) quantification of the residual DNA in final product therapeutics; (c) detection of viral and bacterial nucleic acid in contaminated cell banks and final products; (d) quantification of the level of virus removal in process validation viral clearance studies; (e) specific detection of retroviral RT activity in vaccines with high sensitivity; and (f) transgene copy number determination for monitoring genetic stability during production. We are developing Q-PCR assays for these repeat regions for rodent and primate residual DNA to obtain sensitivity in the fg range, however, one advantage of using a gene such as ␤-actin is gene stability, as this target should not undergo copy number changes within a stable cell line. abstract: High throughput screening, increased accuracy and the coupling of real-time quantitative PCR (Q-PCR) to robotic set-up systems are beginning to revolutionise biotechnology. Applications of Q-PCR within biotechnology are discussed with particular emphasis on the following areas of biosafety and genetic stability testing: (a) determination of the biodistribution of gene therapy vectors in animals; (b) quantification of the residual DNA in final product therapeutics; (c) detection of viral and bacterial nucleic acid in contaminated cell banks and final products; (d) quantification of the level of virus removal in process validation viral clearance studies; (e) specific detection of retroviral RT activity in vaccines with high sensitivity; and (f) transgene copy number determination for monitoring genetic stability during production. Methods employed for Q-PCR assay validation as required in ICH Topic Q2A Validation of Analytical Methods: Definitions and Terminology (1st June 1995) are also reviewed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7148957/ doi: 10.1016/s1389-0352(01)00043-5 id: cord-284275-bqo203pf author: Lu, Roujian title: Characterization of Human Coronavirus Etiology in Chinese Adults with Acute Upper Respiratory Tract Infection by Real-Time RT-PCR Assays date: 2012-06-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: In addition to SARS associated coronaviruses, 4 non-SARS related human coronaviruses (HCoVs) are recognized as common respiratory pathogens. The etiology and clinical impact of HCoVs in Chinese adults with acute upper respiratory tract infection (URTI) needs to be characterized systematically by molecular detection with excellent sensitivity. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we detected 4 non-SARS related HCoV species by real-time RT-PCR in 981 nasopharyngeal swabs collected from March 2009 to February 2011. All specimens were also tested for the presence of other common respiratory viruses and newly identified viruses, human metapneumovirus (hMPV) and human bocavirus (HBoV). 157 of the 981 (16.0%) nasopharyngeal swabs were positive for HCoVs. The species detected were 229E (96 cases, 9.8%), OC43 (42 cases, 4.3%), HKU1 (16 cases, 1.6%) and NL63 (11 cases, 1.1%). HCoV-229E was circulated in 21 of the 24 months of surveillance. The detection rates for both OC43 and NL63 were showed significantly year-to-year variation between 2009/10 and 2010/11, respectively (P<0.001 and P = 0.003), and there was a higher detection frequency of HKU1 in patients aged over 60 years (P = 0.03). 48 of 157(30.57%) HCoV positive patients were co-infected. Undifferentiated human rhinoviruses and influenza (Flu) A were the most common viruses detected (more than 35%) in HCoV co-infections. Respiratory syncytial virus (RSV), human parainfluenza virus (PIV) and HBoV were detected in very low rate (less than 1%) among adult patients with URTI. CONCLUSIONS/SIGNIFICANCE: All 4 non-SARS-associated HCoVs were more frequently detected by real-time RT-PCR assay in adults with URTI in Beijing and HCoV-229E led to the most prevalent infection. Our study also suggested that all non-SARS-associated HCoVs contribute significantly to URTI in adult patients in China. url: https://www.ncbi.nlm.nih.gov/pubmed/22719912/ doi: 10.1371/journal.pone.0038638 id: cord-252838-av7ducrk author: Lucchi, Naomi W. title: Real-Time Fluorescence Loop Mediated Isothermal Amplification for the Diagnosis of Malaria date: 2010-10-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Molecular diagnostic methods can complement existing tools to improve the diagnosis of malaria. However, they require good laboratory infrastructure thereby restricting their use to reference laboratories and research studies. Therefore, adopting molecular tools for routine use in malaria endemic countries will require simpler molecular platforms. The recently developed loop-mediated isothermal amplification (LAMP) method is relatively simple and can be improved for better use in endemic countries. In this study, we attempted to improve this method for malaria diagnosis by using a simple and portable device capable of performing both the amplification and detection (by fluorescence) of LAMP in one platform. We refer to this as the RealAmp method. METHODOLOGY AND SIGNIFICANT FINDINGS: Published genus-specific primers were used to test the utility of this method. DNA derived from different species of malaria parasites was used for the initial characterization. Clinical samples of P. falciparum were used to determine the sensitivity and specificity of this system compared to microscopy and a nested PCR method. Additionally, directly boiled parasite preparations were compared with a conventional DNA isolation method. The RealAmp method was found to be simple and allowed real-time detection of DNA amplification. The time to amplification varied but was generally less than 60 minutes. All human-infecting Plasmodium species were detected. The sensitivity and specificity of RealAmp in detecting P. falciparum was 96.7% and 91.7% respectively, compared to microscopy and 98.9% and 100% respectively, compared to a standard nested PCR method. In addition, this method consistently detected P. falciparum from directly boiled blood samples. CONCLUSION: This RealAmp method has great potential as a field usable molecular tool for diagnosis of malaria. This tool can provide an alternative to conventional PCR based diagnostic methods for field use in clinical and operational programs. url: https://doi.org/10.1371/journal.pone.0013733 doi: 10.1371/journal.pone.0013733 id: cord-320547-law20pmw author: Luchsinger, Vivian title: Comparison of Luminex xTAG® RVP fast assay and real time RT‐PCR for the detection of respiratory viruses in adults with community‐acquired pneumonia date: 2016-02-02 words: 3944.0 sentences: 222.0 pages: flesch: 60.0 cache: ./cache/cord-320547-law20pmw.txt txt: ./txt/cord-320547-law20pmw.txt summary: The detection rates of respiratory viruses by Luminex xTAG® RVP fast assay, real time RT‐PCR (rtRT‐PCR) (Sacace®), and immunofluorescence assay (IFA) in adult CAP were performed in nasopharyngeal swabs (NPS) and aspirates (NPA) from 179 hospitalized adults. The aim of this study was to compare the respiratory viruses detection by Luminex xTAG 1 RVP, rtRT-PCR, and IFA in adults presenting with CAP, in secretions obtained by two nasopharyngeal secretion samples, swabs, and aspirates. Although detection rate for each virus by rtRT-PCR and by Luminex 1 were similar in NPS (P > 0.2), 10 viruses were additionally positive by rtRT-PCR (eight RV, one AdV, and one PIV) and 15 by xTAG 1 RVP Fast (eleven RV-EV, two Flu A,one hMPV, and one PIV-4) ( Table SII) , totalizing 24 patients with discordant viral detection. In the adult CAP cases herein studied the overall respiratory viruses detection rate, by both the new Luminex xTAG 1 RVP Fast and the rtRT-PCR technique was similar (51.9% vs. abstract: Community‐acquired pneumonia (CAP) is the third cause of death worldwide. Viruses are frequently detected in adult CAP. Highly sensitive diagnostic techniques should be used due to poor viral shedding. Different sampling methods can affect viral detection, being necessary to establish the optimal type of sample for identifying respiratory viruses in adults. The detection rates of respiratory viruses by Luminex xTAG® RVP fast assay, real time RT‐PCR (rtRT‐PCR) (Sacace®), and immunofluorescence assay (IFA) in adult CAP were performed in nasopharyngeal swabs (NPS) and aspirates (NPA) from 179 hospitalized adults. Positivity was 47.5% for Luminex®, 42.5% for rtRT‐PCR (P = 0.3), and 2.7% for IFA (2.7%) (P < 0.0). The sensitivity, specificity, and kappa coefficient of xTAG® RVP compared with rtRT‐PCR were 84.2%, 79.6%, and 0.62%, respectively. Luminex® and rtRT‐PCR detected 65 (58.0%) and 57 (50.9%) viruses in 112 NPA and 35 (34.3%) and 31 (30.4%) in 102 NPS, respectively (P < 0.01). xTAG® RVP is appropriate for detecting respiratory viruses in CAP adults. Both molecular techniques yielded better results with nasopharyngeal aspirate than swabs. J. Med. Virol. 88:1173–1179, 2016. © 2016 Wiley Periodicals, Inc. url: https://doi.org/10.1002/jmv.24463 doi: 10.1002/jmv.24463 id: cord-273859-tr4s5i7h author: Luis García Garmendia, José title: DETECCIÓN VIRAL Y RESPUESTA SEROLÓGICA EN PACIENTES CRÍTICOS INTUBADOS CON SARS-CoV-2. IMPLICACIONES PARA RETIRADA DE AISLAMIENTO date: 2020-04-29 words: 1379.0 sentences: 139.0 pages: flesch: 61.0 cache: ./cache/cord-273859-tr4s5i7h.txt txt: ./txt/cord-273859-tr4s5i7h.txt summary: En las formas clínicas menos graves, la detección de ARN viral es máxima durante las dos primeras semanas desde el inicio de los síntomas(4), y a partir de los 7-10 días se produce respuesta inmunológica de IgM y después de IgG (5) . El CDC propone como una pauta segura la determinación de 2 rRT-PCR negativas consecutivas para valorar la necesidad de aislamiento de los pacientes con COVID-19 (8). A estos pacientes se les hicieron 2 determinaciones de rRT-PCR de Coronavirus a partir de 21 días del inicio de síntomas, separadas por 24 h, para comprobar si persistía eliminación del virus. La detección del ARN viral mediante técnicas de rRT-PCR parece ser una forma adecuada de determinar la necesidad de aislamiento de los pacientes con SARS-CoV-2(8, 12). Seguimiento de negativización de rRT-PCR a coronavirus en 10 pacientes críticos con SARS-CoV-2 bajo ventilación mecánica. Seguimiento de negativización de rRT-PCR a coronavirus en 10 pacientes críticos con SARS-CoV-2 bajo ventilación mecánica. abstract: nan url: https://api.elsevier.com/content/article/pii/S0210569120301534 doi: 10.1016/j.medin.2020.04.014 id: cord-291026-99cit4ig author: Lung, O. title: Insulated Isothermal Reverse Transcriptase PCR (iiRT‐PCR) for Rapid and Sensitive Detection of Classical Swine Fever Virus date: 2015-01-27 words: 4566.0 sentences: 206.0 pages: flesch: 55.0 cache: ./cache/cord-291026-99cit4ig.txt txt: ./txt/cord-291026-99cit4ig.txt summary: In this study, we describe validation of a new probe‐based insulated isothermal reverse transcriptase PCR (iiRT‐PCR) assay for rapid detection of classical swine fever virus (CSFV) on a compact, user‐friendly device (POCKIT (™) Nucleic Acid Analyzer) that does not need data interpretation by the user. Archived viral nucleic acid from 18 laboratory-amplified non-CSF viruses including eight other pestiviruses (BVDV 1-Hastings, Singer and NY1 strains; BVDV 2-Ames 125c, 890, 24515 strains; BDV-Coos Bay; HoBi atypical pestivirus), African swine fever virus-Lisbon, swine vesicular disease virus-ITL 19/92, porcine respiratory and reproductive syndrome virus-YNL, swine influenza virus (H3N2), porcine circovirus 1 (PCV1, derived from infectious clone based on GenBank accession no. The iiRT-PCR assay accurately detected all CSFV RNA samples which represented all three genotypes, and eight of 11 subgenotypes that were available for testing and gave negative results for three BVDV type 1 strains, three BVDV type 2 strains, BDV, HoBi atypical pestivirus, ASFV and nine other viruses that affect livestock. abstract: Classical swine fever (CSF) is an OIE‐listed disease that can have a severe impact on the swine industry. User‐friendly, sensitive, rapid diagnostic tests that utilize low‐cost field‐deployable instruments for CSF diagnosis can be useful for disease surveillance and outbreak monitoring. In this study, we describe validation of a new probe‐based insulated isothermal reverse transcriptase PCR (iiRT‐PCR) assay for rapid detection of classical swine fever virus (CSFV) on a compact, user‐friendly device (POCKIT (™) Nucleic Acid Analyzer) that does not need data interpretation by the user. The assay accurately detected CSFV RNA from a diverse panel of 33 CSFV strains representing all three genotypes plus an additional in vitro‐transcribed RNA from cloned sequences representing a vaccine strain. No cross‐reactivity was observed with a panel of 18 viruses associated with livestock including eight other pestivirus strains (bovine viral diarrhoea virus type 1 and type 2, border disease virus, HoBi atypical pestivirus), African swine fever virus, swine vesicular disease virus, swine influenza virus, porcine respiratory and reproductive syndrome virus, porcine circovirus 1, porcine circovirus 2, porcine respiratory coronavirus, vesicular exanthema of swine virus, bovine herpes virus type 1 and vesicular stomatitis virus. The iiRT‐PCR assay accurately detected CSFV as early as 2 days post‐inoculation in RNA extracted from serum samples of experimentally infected pigs, before appearance of clinical signs. The limit of detection (LOD (95%)) calculated by probit regression analysis was 23 copies per reaction. The assay has a sample to answer turnaround time of less than an hour using extracted RNA or diluted or low volume of neat serum. The user‐friendly, compact device that automatically analyses and displays results could potentially be a useful tool for surveillance and monitoring of CSF in a disease outbreak. url: https://doi.org/10.1111/tbed.12318 doi: 10.1111/tbed.12318 id: cord-331932-oujdl459 author: Lung, O. title: Multiplex PCR and Microarray for Detection of Swine Respiratory Pathogens date: 2015-12-12 words: 6362.0 sentences: 293.0 pages: flesch: 44.0 cache: ./cache/cord-331932-oujdl459.txt txt: ./txt/cord-331932-oujdl459.txt summary: The user‐friendly assay detected and differentiated between four viruses [porcine reproductive and respiratory syndrome virus (PRRSV), influenza A virus, porcine circovirus type 2, porcine respiratory corona virus], four bacteria (Mycoplasma hyopneumoniae, Pasteurella multocida, Salmonella enterica serovar Choleraesuis, Streptococcus suis), and further differentiated between type 1 and type 2 PRRSV as well as toxigenic and non‐toxigenic P. Here, a microarray assay with associated multiplex RT-PCRs for detection and differentiation of four viruses and four bacteria involved in PRDC using a novel user-friendly electronic microarray in which capture probe printing, hybridization, washing and reporting are fully integrated and automated is described. Similarly, representative whole-genome sequences, as well as full and partial sequences of homologous genes from related and unrelated non-targets such as TGEV, porcine circovirus type 1 (PCV1), as well as other Salmonella enterica serovars, and Mycoplasma species were downloaded for in silico analysis of probe specificity. The analytical specificity of the viral and bacterial multiplex PCR assays was assessed by amplifying panels of 14 non-target viruses and 21 bacteria, respectively (Table 3) . abstract: Porcine respiratory disease complex (PRDC) is one of the most important health concerns for pig producers and can involve multiple viral and bacterial pathogens. No simple, single‐reaction diagnostic test currently exists for the simultaneous detection of major pathogens commonly associated with PRDC. Furthermore, the detection of most of the bacterial pathogens implicated in PRDC currently requires time‐consuming culture‐based methods that can take several days to obtain results. In this study, a novel prototype automated microarray that integrates and automates all steps of post‐PCR microarray processing for the simultaneous detection and typing of eight bacteria and viruses commonly associated with PRDC is described along with associated multiplex reverse transcriptase PCR. The user‐friendly assay detected and differentiated between four viruses [porcine reproductive and respiratory syndrome virus (PRRSV), influenza A virus, porcine circovirus type 2, porcine respiratory corona virus], four bacteria (Mycoplasma hyopneumoniae, Pasteurella multocida, Salmonella enterica serovar Choleraesuis, Streptococcus suis), and further differentiated between type 1 and type 2 PRRSV as well as toxigenic and non‐toxigenic P. multocida. The assay accurately identified and typed a panel of 34 strains representing the eight targeted pathogens and was negative when tested with 34 relevant and/or closely related non‐target bacterial and viral species. All targets were also identified singly or in combination in a panel of clinical lung samples and/or experimentally inoculated biological material. url: https://doi.org/10.1111/tbed.12449 doi: 10.1111/tbed.12449 id: cord-316343-u1uup5da author: Luo, Yun title: Longitudinal Surveillance of Betacoronaviruses in Fruit Bats in Yunnan Province, China During 2009–2016 date: 2018-02-01 words: 3493.0 sentences: 200.0 pages: flesch: 58.0 cache: ./cache/cord-316343-u1uup5da.txt txt: ./txt/cord-316343-u1uup5da.txt summary: Total RNA was extracted from the hearts, livers, spleens, lungs, kidneys, brains, and intestines of six bats infected with bat coronaviruses HKU9 or GCCDC1 using the High Pure Viral RNA Kit. Partial RdRp representing HKU9 or GCCDC1 were cloned into the pGEM-T-easy Vector (Promega, Madison, WI, USA) and used as a positive control for quantitative analysis. By RT-PCR detection targeting partial RdRP, 46 (8.29%) samples were positive for HKU9 and 13 (2.34%) were positive for GCCDC1 or closely related viruses (Table 1) . A phylogenetic tree was conducted based on the alignment of partial RdRp sequences along with previously reported HKU9, GCCDC1, and related stains, as well as representative strains of other betacoronaviruses. In this study, we identified all bat species positive for coronavirus by sequencing the Cytb gene and found that HKU9 and GCCDC1 were from two different genera, Rousettus and Eonycteris, respectively. abstract: Previous studies indicated that fruit bats carry two betacoronaviruses, BatCoV HKU9 and BatCoV GCCDC1. To investigate the epidemiology and genetic diversity of these coronaviruses, we conducted a longitudinal surveillance in fruit bats in Yunnan province, China during 2009–2016. A total of 59 (10.63%) bat samples were positive for the two betacorona-viruses, 46 (8.29%) for HKU9 and 13 (2.34%) for GCCDC1, or closely related viruses. We identified a novel HKU9 strain, tentatively designated as BatCoV HKU9-2202, by sequencing the full-length genome. The BatCoV HKU9-2202 shared 83% nucleotide identity with other BatCoV HKU9 stains based on whole genome sequences. The most divergent region is in the spike protein, which only shares 68% amino acid identity with BatCoV HKU9. Quantitative PCR revealed that the intestine was the primary infection organ of BatCoV HKU9 and GCCDC1, but some HKU9 was also detected in the heart, kidney, and lung tissues of bats. This study highlights the importance of virus surveillance in natural reservoirs and emphasizes the need for preparedness against the potential spill-over of these viruses to local residents living near bat caves. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12250-018-0017-2) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s12250-018-0017-2 doi: 10.1007/s12250-018-0017-2 id: cord-271504-t3y1w9ef author: Luo, Zichao title: Combating the Coronavirus Pandemic: Early Detection, Medical Treatment, and a Concerted Effort by the Global Community date: 2020-06-16 words: 14361.0 sentences: 795.0 pages: flesch: 42.0 cache: ./cache/cord-271504-t3y1w9ef.txt txt: ./txt/cord-271504-t3y1w9ef.txt summary: A confirmed case should have at least one of the following criteria: (i) a positive result for 2019-nCoV nucleic acid, using real-time PCR tests from respiratory or blood samples; (ii) a high homogeneity between viral gene sequencing from respiratory or blood samples and known 2019-nCoV; and (iii) serum samples positive for IgM or IgG to 2019-nCoV, or seroconversion in IgG, or a fourfold or more significant increase in IgG antibody titer to 2019-nCoV in the recovery phase than in the acute phase [25] . Using blood samples taken from alleged COVID-19 patients, the researchers detected antibodies targeting the spike protein that prevented the virus from killing cells in laboratory tests. showed a promising in vitro inhibitory effect of this serine protease inhibitor in SARS-CoV and 2019-nCoV on human lung cells, showing potential as a viable option for COVID-19 treatment [113] . Given that antiviral drugs have previously demonstrated reasonable inhibition of coronaviruses and therapeutic efficacy against coronavirus outbreaks, umifenovir, chloroquine, hydroxychloroquine, lopinavir-ritonavir, and ribavirin have been recommended in the latest guidelines for diagnosis and treatment of COVID-19, updated on 17 February 2020 [189] . abstract: The World Health Organization (WHO) has declared the outbreak of 2019 novel coronavirus, known as 2019-nCoV, a pandemic, as the coronavirus has now infected over 2.6 million people globally and caused more than 185,000 fatalities as of April 23, 2020. Coronavirus disease 2019 (COVID-19) causes a respiratory illness with symptoms such as dry cough, fever, sudden loss of smell, and, in more severe cases, difficulty breathing. To date, there is no specific vaccine or treatment proven effective against this viral disease. Early and accurate diagnosis of COVID-19 is thus critical to curbing its spread and improving health outcomes. Reverse transcription-polymerase chain reaction (RT-PCR) is commonly used to detect the presence of COVID-19. Other techniques, such as recombinase polymerase amplification (RPA), loop-mediated isothermal amplification (LAMP), clustered regularly interspaced short palindromic repeats (CRISPR), and microfluidics, have allowed better disease diagnosis. Here, as part of the effort to expand screening capacity, we review advances and challenges in the rapid detection of COVID-19 by targeting nucleic acids, antigens, or antibodies. We also summarize potential treatments and vaccines against COVID-19 and discuss ongoing clinical trials of interventions to reduce viral progression. url: https://www.ncbi.nlm.nih.gov/pubmed/32607499/ doi: 10.34133/2020/6925296 id: cord-317042-dll3qt4g author: Lv, Jun title: Detection of SARS-CoV-2 RNA residue on object surfaces in nucleic acid testing laboratory using droplet digital PCR date: 2020-06-19 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract The rapid development of global COVID-19 pandemic poses an unprecedented challenge to the safety and quality of laboratory diagnostic testing. Little is known about the laboratory surface areas and operation behaviors that may cause potential contamination in SARS-CoV-2 nucleic acid testing. This study aims to provide reference basis for the improvement of laboratory disinfection programs and personal operating protocols. In this study, we compared the qRT-PCR and ddPCR in detecting of residual virus that existed on the object surfaces from sample transportation and reception related facilities, testing related instruments, personal protective equipment and other facilities in nucleic acid testing laboratory. All samples were negative by qRT-PCR, in contrast, 13 of 61 samples were positive for SARS-CoV-2 by ddPCR. The areas with highest density of SARS-CoV-2 nucleic acid were the outer gloves of operator A (37.4 copies/cm2), followed by door handle of 4 °C refrigerator (26.25 copies/cm2), goggles of operator A (22.16 copies/cm2), outer cover of high speed centrifuge (19.95 copies/cm2), inner wall of high speed centrifuge (14.70 copies/cm2) and others. We found that all the positive objects were directly or indirectly contacted by the operator's gloved hands, suggesting that hands contact was the main transmission pathway that led to laboratory environmental contamination. In summary, ddPCR has an advantage over qRT-PCR in tracing laboratory contamination. We evaluated the risk areas and operation behaviors that may easily cause contamination, and provided recommendation for improving the laboratory disinfection programs and personal operating specifications. url: https://api.elsevier.com/content/article/pii/S0048969720338924 doi: 10.1016/j.scitotenv.2020.140370 id: cord-298401-4szmu1dh author: Lyoo, Kwang-Soo title: Development of rapid immunochromatographic strip test for the detection of porcine epidemic diarrhoea virus date: 2017-12-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Porcine epidemic diarrhoea virus (PEDV) causes acute and severe watery diarrhoea and dehydration, as well as 50–100 per cent mortality in piglets. For the PEDV diagnosis, a rapid test kit that is specific and sensitive to PEDV is critical to monitor this disease at pig farms. The present study aimed to develop an immunochromatographic assay (ICA) strip test for detecting PEDV in faecal swabs. The newly developed diagnostic test showed a detection limit of 10(4.0) TCID(50)/ml of PEDV. Using faecal swab samples, the relative sensitivity and specificity of the ICA kit were 95.0 per cent and 98.6 per cent, respectively, compared with those of real-time RT-PCR. In samples from piglets experimentally infected with PEDV, the results showed 100 per cent agreement with those found by real-time RT-PCR. Our developed test strip will be useful for rapid diagnosis and can be used for epidemiological surveillance of PEDV infection. url: https://doi.org/10.1136/vr.103959 doi: 10.1136/vr.103959 id: cord-284367-cy61pjcb author: MULEYA, Walter title: Molecular Epidemiology of Paramyxoviruses in Frugivorous Eidolon helvum Bats in Zambia date: 2013-12-31 words: 1565.0 sentences: 92.0 pages: flesch: 53.0 cache: ./cache/cord-284367-cy61pjcb.txt txt: ./txt/cord-284367-cy61pjcb.txt summary: In this study, we describe the detection of novel paramyxoviruses from the Eidolon helvum species of fruit bats. Semi-nested RT-PCR detected a total of 25 (8%) positive samples for paramyxoviruses which were then directly sequenced and analyzed using phylogenetic analysis. Our study identified novel Henipavirus-related and unrelated viruses using RT-PCR in fruit bats from Kansaka National Park and indicated the presence of similar Bat paramyxoviruses originating from wide geographic areas, suggesting the ability of bats to harbor and transmit viruses. This has been as a result of the high detection rate of previously unknown viral sequences in bats coupled with the emergence of pathogens, such as Hendra, Nipah, Severe acute respiratory syndrome (SARS)-Corona, Ebola and Marburg viruses, all of which are highly virulent and pose a great zoonotic risk [2, 3, 8, 9, 17] . The samples from Zambia formed clusters with the Henipavirus-related viruses and with the unclassified Bat paramyxoviruses (Fig. 1) . abstract: In this study, we describe the detection of novel paramyxoviruses from the Eidolon helvum species of fruit bats. We extracted RNA from 312 spleen samples from bats captured in Zambia over a period of 4 years (2008–2011). Semi-nested RT-PCR detected a total of 25 (8%) positive samples for paramyxoviruses which were then directly sequenced and analyzed using phylogenetic analysis. Among the positive samples, seven novel paramyxoviruses were detected. Five viruses were closely related to the genus Henipavirus, while two viruses were related to the unclassified Bat paramyxoviruses from Ghana and Congo Brazzaville. Our study identified novel Henipavirus-related and unrelated viruses using RT-PCR in fruit bats from Kansaka National Park and indicated the presence of similar Bat paramyxoviruses originating from wide geographic areas, suggesting the ability of bats to harbor and transmit viruses. The presence of these viruses in fruit bats might pose a public health risk. url: https://www.ncbi.nlm.nih.gov/pubmed/24389743/ doi: 10.1292/jvms.13-0518 id: cord-273179-bpnak9ov author: Ma, Fen-lian title: Quantitative detection of human Malawi polyomavirus in nasopharyngeal aspirates, sera, and feces in Beijing, China, using real-time TaqMan-based PCR date: 2017-08-14 words: 4116.0 sentences: 218.0 pages: flesch: 60.0 cache: ./cache/cord-273179-bpnak9ov.txt txt: ./txt/cord-273179-bpnak9ov.txt summary: METHODS: We used real-time TaqMan-based PCR to detect MWPyV in the feces (n = 174) of children with diarrhea, nasopharyngeal aspirates (n = 887) from children with respiratory infections, and sera (n = 200) from healthy adults, and analyzed its clinical characteristics statistically. Therefore, in this study, we used realtime qPCR and DNA sequencing to investigate the presence of MWPyV in fecal samples from 174 children with diarrhea, nasopharyngeal aspirate (NPA) samples from 887 children with acute respiratory tract infections (ARIs), and sera from 200 healthy adults in China. In brief, the analysis of 1261 clinical samples only detected MWPyV in respiratory and fecal specimens from children, suggesting that the establishment of the primary infection occurs at an early age, and that the gastrointestinal and respiratory tracts are sites of viral persistence. abstract: BACKGROUND: Human Malawi polyomavirus (MWPyV) was discovered in 2012, but its prevalence and clinical characteristics are largely unknown. METHODS: We used real-time TaqMan-based PCR to detect MWPyV in the feces (n = 174) of children with diarrhea, nasopharyngeal aspirates (n = 887) from children with respiratory infections, and sera (n = 200) from healthy adults, and analyzed its clinical characteristics statistically. All the MWPyV-positive specimens were also screened for other common respiratory viruses. RESULTS: Sixteen specimens were positive for MWPyV, including 13 (1.47%) respiratory samples and three (1.7%) fecal samples. The samples were all co-infected with other respiratory viruses, most commonly with influenza viruses (69.2%) and human coronaviruses (30.7%). The MWPyV-positive children were diagnosed with bronchopneumonia or viral diarrhea. They ranged in age from 12 days to 9 years, and the most frequent symptoms were cough and fever. CONCLUSIONS: Real-time PCR is an effective tool for the detection of MWPyV in different types of samples. MWPyV infection mainly occurs in young children, and fecal–oral transmission is a possible route of its transmission. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12985-017-0817-2) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/28806976/ doi: 10.1186/s12985-017-0817-2 id: cord-261419-8dcqnifn author: Ma, Qing-Hu title: Overexpression of a wheat jasmonate-regulated lectin increases pathogen resistance date: 2009-12-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Jasmonates are known to induce the transcriptional activation of plant defense genes, which leads to the production of jasmonate-regulated proteins (JRP). We previously cloned and characterized a novel jacalin-like lectin gene (Ta-JA1) from wheat (Triticum aestivum L.), which codes a modular JRP with disease response and jacalin-related lectin (JRL) domains and is present only in the Gramineae family. The function of this protein is still unclear. Phylogenetic analysis indicated that Ta-JA1 and related proteins from cereals grouped together, which diverged from JRL with an additional N-terminal disease response domain. The recombinant Ta-JA1 proteins agglutinated rabbit erythrocytes, and this hemagglutination activity was preferentially inhibited by mannose. The Ta-JA1 protein was able to inhibit E. coli cell growth. Overexpression of Ta-JA1 in transgenic tobacco plants increased their resistance to infection by tobacco bacterial, fungal and viral pathogens. Our results suggest that Ta-JA1 belongs to a mannose-specific lectin, which may confer a basal but broad-spectrum resistance to plant pathogens. Ta-JA1 and its homologues in maize, rice, sorghum and creeping bentgrass may represent a new type of monocot lectin with a modular structure and diversity of physiological functions in biotic and abiotic stress responses. url: https://www.ncbi.nlm.nih.gov/pubmed/19958808/ doi: 10.1016/j.biochi.2009.11.008 id: cord-016144-280kwlev author: Maan, Sushila title: Novel Molecular Diagnostics and Therapeutic Tools for Livestock Diseases date: 2018-04-26 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Recent novelties in diverse diagnostics and therapeutic tools in animal health sector have paved a brighter and clearer way ahead. These are proved to be better in detection, management, control and eradication of animal sufferings caused by various infectious and non-infectious diseases. These innovations have potential impact that extends beyond the animal health and welfare. The advancements have significantly contributed towards improvement in the economy of the country as well as food security. In the present competitive era of evolution, the organisms have inculcated a number of new strategies for survival and spread. Therefore, science needs to continuously evolve more sensitive, specific and high-throughput tools to overcome pathogen cleverness to escape from host immune surveillance. For visible or remarkable changes, it is necessary to use full potential of these advanced molecular techniques into current animal health standards and practices. Under ‘One Health’ concept, the health of animals and humans has to be taken care simultaneously. At present, these advanced molecular diagnostic methods play a significant role in the detection of new and emerging pathogens of livestock. The acquired information also helps to study the interrelationships of pathogens, their hosts and their surroundings. Additionally new vaccines bridging human and animal health development may be discovered. Latest developments in the field of diagnostics and vaccine design through genomics approach have also laid the foundation to enhance the diagnosis and surveillance and in turn helped in the control of infectious diseases. Latest high-throughput DNA sequencing platforms are currently being used for identification and detailed analysis of both disease pathogen and host genomes. The high-throughput data generated using these platforms need to be analysed adopting the bioinformatics and computational genomics that have taken a very high pace nowadays. In the context of animal health, the data analysis may provide some key opportunities for the development of better diagnostic and therapeutic tools for emerging or re-emerging diseases. Such novel and potent technologies put forward a significantly new scenario of disease knowledge, which enables more accurate predictions leading to faster and greater management responses to combat potentially devastating disease crises. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120337/ doi: 10.1007/978-981-10-4702-2_14 id: cord-000180-howix091 author: MacLeod, Iain J. title: Binding of Herpes Simplex Virus Type-1 Virions Leads to the Induction of Intracellular Signalling in the Absence of Virus Entry date: 2010-03-05 words: 6788.0 sentences: 316.0 pages: flesch: 49.0 cache: ./cache/cord-000180-howix091.txt txt: ./txt/cord-000180-howix091.txt summary: By taking advantage of the entry-defective phenotype of glycoprotein-deficient HSV-1 virus particles, the results presented here show that binding of virions to cellular receptors on the plasma membrane is sufficient to stimulate a change in cellular gene expression. As induction of the NF-kB reporter construct occurred within one hour of inoculation with DgH virions and peaked at around two-and-a-half hours post-inoculation, then the transcripts previHFFs were stimulated with 1000 particles/cell of DgB, DgD or DgH HSV-1 for six hours and a cDNA microarray corresponding to targets of 19 signalling pathways was used to detect changes in cellular gene expression when compared to mock-infected. Real-time PCR confirmed that changes in transcription associated with the NF-kB, JAK/STAT, JAK/Src and PI3K pathways were modulated as a result of virion binding, all of which required gD on the envelope surface To demonstrate that signalling occurred at physiologically relevant multiplicities of infection, HFFs were inoculated with either 1000, 100, 10 or 1 particles per cell of entry-defective HSV-1. abstract: The envelope of HSV-1 contains a number of glycoproteins, four of which are essential for virus entry. Virus particles lacking gB, gD, gH or gL are entry-defective, although these viruses retain the ability to bind to the plasma membrane via the remaining glycoproteins. Soluble forms of gD have been shown to trigger the nuclear translocation of the NF-κB transcriptional complex in addition to stimulating the production of Type I interferon. By taking advantage of the entry-defective phenotype of glycoprotein-deficient HSV-1 virus particles, the results presented here show that binding of virions to cellular receptors on the plasma membrane is sufficient to stimulate a change in cellular gene expression. Preliminary microarray studies, validated by quantitative real-time PCR, identified the differential expression of cellular genes associated with the NF-κB, PI3K/Akt, Jak/Stat and related Jak/Src pathways by virions lacking gB or gH but not gD. Gene induction occurred at a few particles per cell, corresponding to physiological conditions during primary infection. Reporter assay studies determined that NF-κB transcriptional activity is stimulated within an hour of HSV-1 binding, peaks between two and three hours post-binding and declines to background levels by five hours after induction. The immediate, transient nature of these signalling events suggests that HSV-1 glycoproteins, particularly gD, may alter the cellular environment pre-entry so as to condition the cell for viral replication. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832691/ doi: 10.1371/journal.pone.0009560 id: cord-336453-cbq0ui4p author: Machitori, Akihiro title: Computed tomography surveillance helps tracking COVID-19 outbreak date: 2020-08-07 words: 3802.0 sentences: 186.0 pages: flesch: 49.0 cache: ./cache/cord-336453-cbq0ui4p.txt txt: ./txt/cord-336453-cbq0ui4p.txt summary: PURPOSE: To reveal that a computed tomography surveillance program (CT-surveillance) could demonstrate the epidemiologic features of COVID-19 infection and simultaneously investigate the type and frequency of CT findings using clinical CT data. Using an online questionnaire, we asked Japanese board-certified radiologists to register their patients'' information including patient age and sex, the CT examination date, the results of PCR test for COVID-19 infection, CT findings, and the postal code of the medical institution that performed the CT. We conducted the present study to reveal that CT-surveillance could demonstrate the epidemiologic features of COVID-19 infection as well as simultaneously investigate the type and frequency of characteristic imaging findings on CT by using clinical CT data. CT findings in CT surveillance might distinguish the group that is considered Fig. 2 The epidemic curve of the diurnal patient number in the CT surveillance (a) shows a distribution similar to that of the PCR surveillance (b). abstract: PURPOSE: To reveal that a computed tomography surveillance program (CT-surveillance) could demonstrate the epidemiologic features of COVID-19 infection and simultaneously investigate the type and frequency of CT findings using clinical CT data. MATERIALS AND METHODS: We targeted individuals with possible CT findings of viral pneumonia. Using an online questionnaire, we asked Japanese board-certified radiologists to register their patients’ information including patient age and sex, the CT examination date, the results of PCR test for COVID-19 infection, CT findings, and the postal code of the medical institution that performed the CT. We compared the diurnal patient number and the cumulative regional distribution map of registrations in CT-surveillance to those of the PCR-positive patient surveillance (PCR-surveillance). RESULTS: A total of 637 patients was registered from January 1 to April 17, 2020 for CT-surveillance. Their PCR test results were positive (n = 62.5–398%), negative (n = 8.9–57%), unknown (n = 26.2–167%), and other disease (n = 2.4–15%). An age peak at 60–69 years and male dominance were observed in CT-surveillance. The most common CT finding was bilaterally distributed ground-glass opacities. The diurnal number and the cumulative regional distribution map by CT-surveillance showed tendencies that were similar to those revealed by PCR-surveillance. CONCLUSION: Using clinical CT data, CT-surveillance program delineated the epidemiologic features of COVID-19 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32766927/ doi: 10.1007/s11604-020-01026-z id: cord-016499-5iqpl23p author: Mackay, Ian M. title: Rhinoviruses date: 2014-02-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Picornaviruses, which include the human rhinoviruses (HRVs) and enteroviruses (EVs), are the most frequent cause of acute human illness worldwide. HRVs are the most prevalent cause of acute respiratory tract illnesses (ARIs) which usually commence in the upper respiratory tract (URT). ARIs are the leading cause of morbidity in children under 5 years and occur in all seasons. ARIs linked to HRV infections are associated with excessive and perhaps inappropriate antibiotic prescribing and with significant direct and indirect healthcare expenditure. ARI incidence is highest in the first 2 years of life, with up to thirteen episodes per year including up to six positive for an HRV, and it is not uncommon to average one infection per child-month. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120790/ doi: 10.1007/978-1-4899-7448-8_29 id: cord-317244-4su5on6s author: Maganga, Gael D. title: Identification of an Unclassified Paramyxovirus in Coleura afra: A Potential Case of Host Specificity date: 2014-12-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Bats are known to harbor multiple paramyxoviruses. Despite the creation of two new genera, Aquaparamyxovirus and Ferlavirus, to accommodate this increasing diversity, several recently isolated or characterized viruses remain unclassified beyond the subfamily level. In the present study, among 985 bats belonging to 6 species sampled in the Belinga caves of Gabon, RNA of an unclassified paramyxovirus (Belinga bat virus, BelPV) was discovered in 14 African sheath-tailed bats (Coleura afra), one of which exhibited several hemorrhagic lesions at necropsy, and viral sequence was obtained in two animals. Phylogenetically, BelPV is related to J virus and Beilong virus (BeiPV), two other unclassified paramyxoviruses isolated from rodents. In the diseased BelPV-infected C. afra individual, high viral load was detected in the heart, and the lesions were consistent with those reported in wild rodents and mice experimentally infected by J virus. BelPV was not detected in other tested bat species sharing the same roosting sites and living in very close proximity with C. afra in the two caves sampled, suggesting that this virus may be host-specific for C. afra. The mode of transmission of this paramyxovirus in bat populations remains to be discovered. url: https://doi.org/10.1371/journal.pone.0115588 doi: 10.1371/journal.pone.0115588 id: cord-314201-6njwigco author: Maher-Sturgess, Sheryl L title: Universal primers that amplify RNA from all three flavivirus subgroups date: 2008-01-24 words: 4625.0 sentences: 253.0 pages: flesch: 54.0 cache: ./cache/cord-314201-6njwigco.txt txt: ./txt/cord-314201-6njwigco.txt summary: Tanaka [3] published the first universal primer pair specific for mosquito borne flaviviruses in 1993; the YF1 and YF3 primers targeted the NS5/3''UTR of the genome and were based upon the six flavivirus sequences available at the time. In 2005 Gaunt and Gould designed a universal nested PCR, using six primers targeting the E gene, capable of amplifying cDNA from 60 flavivirus strains. In the present study, we identified conserved sites and developed a universal, non-nested primer pair that amplifies cDNA from each of the major subgroups of flaviviruses, and also TABV, under standard reaction conditions. Since the amplified products represent 8% of the genome, this is sufficient sequence to determine the species of the virus and thus potentially to identify unrecognised flaviviruses. Rapid subgroup identification of the flaviviruses using degenerate primer E-gene RT-PCR and site specific restriction enzyme analysis abstract: BACKGROUND: Species within the Flavivirus genus pose public health problems around the world. Increasing cases of Dengue and Japanese encephalitis virus in Asia, frequent outbreaks of Yellow fever virus in Africa and South America, and the ongoing spread of West Nile virus throughout the Americas, show the geographical burden of flavivirus diseases. Flavivirus infections are often indistinct from and confused with other febrile illnesses. Here we review the specificity of published primers, and describe a new universal primer pair that can detect a wide range of flaviviruses, including viruses from each of the recognised subgroups. RESULTS: Bioinformatic analysis of 257 published full-length Flavivirus genomes revealed conserved regions not previously targeted by primers. Two degenerate primers, Flav100F and Flav200R were designed from these regions and used to generate an 800 base pair cDNA product. The region amplified encoded part of the methyltransferase and most of the RNA-dependent-RNA-polymerase (NS5) coding sequence. One-step RT-PCR testing was successful using standard conditions with RNA from over 60 different flavivirus strains representing about 50 species. The cDNA from each virus isolate was sequenced then used in phylogenetic analyses and database searches to confirm the identity of the template RNA. CONCLUSION: Comprehensive testing has revealed the broad specificity of these primers. We briefly discuss the advantages and uses of these universal primers. url: https://doi.org/10.1186/1743-422x-5-16 doi: 10.1186/1743-422x-5-16 id: cord-298600-cnolne6k author: Majeed, Talal title: The Role of the Computed Tomography (CT) Thorax in the Diagnosis of COVID-19 for Patients Presenting with Acute Surgical Emergencies. A Single Institute Experience date: 2020-10-20 words: 3221.0 sentences: 164.0 pages: flesch: 48.0 cache: ./cache/cord-298600-cnolne6k.txt txt: ./txt/cord-298600-cnolne6k.txt summary: Our aim was to determine the diagnostic accuracy in terms of sensitivity and specificity of CT chest in diagnosing and confirming COVID-19 infection in patients presenting with acute surgical and medical pathologies. Patients admitted for acute surgical emergencies were treated according to RCS guidelines and subjected to RT-PCR test and/or CT scan of the thorax. Patients admitted for acute surgical emergencies were treated according to RCS guidelines and subjected to RT-PCR test and/or CT scan of the thorax. CT imaging was found to have a high false positive rate making it an unreliable tool for a definitive diagnosis in the presence of concomitant respiratory pathologies, but with a strong negative predictive value at 82.4% makes it a useful tool for the exclusion of COVID-19 infection and can be helpful in surgical decision making for asymptomatic patients (Table 1 ).In our study, more than 70% of all acute surgical presentations which are normally treated surgically were treated conservatively with good outcome. abstract: The current Coronavirus disease 2019 (COVID-19) pandemic has had a huge impact on emergency surgical services in the UK. The Royal College of Surgeons (RCS) published guidelines about COVID-19 pandemic in March, 2020 to aid decision making for the surgeons. These guidelines recommended that all patients requiring urgent surgery should have reverse transcriptase polymerase chain reaction (RT-PCR) and/or computed tomography (CT) thorax pre-operatively. However, it is currently unclear whether the use of CT thorax is a sensitive and specific diagnostic test. The objective of this study was to find out whether CT thorax is a reliable and accurate test in the diagnosis of COVID-19 compared to RT-PCR. This is particularly important in surgical patients where there is no time to wait for RT-PCR results. A prospective cohort study of patients presented with acute surgical emergencies at a University Teaching Hospital was conducted. Data was collected from March 23, to May 15, 2020, during the peak of the crisis in the UK. All adult patients presented with operable general surgical emergencies were considered eligible. Another group of patients, admitted with acute medical emergencies but with suspected COVID-19 infection, was used for comparison. Data was manually collected, and sensitivity, specificity and predictive value were calculated using the MedCalc statistical software version 19.2.6. Standard reporting for COVID-19 infection for CT chest based on guidelines from British Society of Thoracic Imaging (BSTI) and Radiological Society of North America (RSNA) was used. Patients who had their CT thorax reported as typical or classic of COVID 19 (high probability) were treated as infected cases with extra precautions in the wards and surgical theatres as suggested by health and safety executive (HSE). These patients had serial RT-PCR during their admissions or in the post-operative phase, if the first swab was negative. For the study, 259 patients were considered eligible for inclusion from both groups. Patients admitted for acute surgical emergencies were treated according to RCS guidelines and subjected to RT-PCR test and/or CT scan of the thorax. There were 207 patients with high clinical suspicion of COVID-19. Of those 207 patients, 77 patients had CT thorax with radiographic features consistent with COVID-19 pneumonia. However, only 40 patients had a positive RT-PCR result. CT thorax was normal in 130 patients, out of which 29 patients were found to have COVID-19 diagnosis after swab test. Sensitivity of CT scan to diagnose COVID-19 infection was found to be 58% (95% CI; 45.48% to 69.76%) whilst specificity was 73% (95% CI; 64.99% to 80.37%) with a negative predictive value of 77.69% (95% CI; 72.17% to 82.39%). CT scan was found to be a reliable tool in the diagnosis of COVID-19. With a negative predictive value of up to 82.4%, CT thorax can play an important role to help surgeons in their decision making for asymptomatic suspected cases of COVID-19. However, over-reliance on CT scan which also has a high false positive rate for diagnosis of COVID-19 infections can lead to overtreatment, overuse of resources and delays in decision-making process. Hence, results should be interpreted with caution and correlated with clinical presentation and swab test results. url: https://www.ncbi.nlm.nih.gov/pubmed/33100739/ doi: 10.1007/s12262-020-02626-9 id: cord-289216-g4kqi560 author: Malecki, M. title: Analysis of external quality assessment samples revealed crucial performance differences between commercial RT-PCR assays for SARS-CoV-2 detection when taking extraction methods and real-time-PCR instruments into account date: 2020-09-23 words: 1927.0 sentences: 127.0 pages: flesch: 51.0 cache: ./cache/cord-289216-g4kqi560.txt txt: ./txt/cord-289216-g4kqi560.txt summary: title: Analysis of external quality assessment samples revealed crucial performance differences between commercial RT-PCR assays for SARS-CoV-2 detection when taking extraction methods and real-time-PCR instruments into account The aim of this study was to compare the performance of the overall analytical matrix including the extraction kit (BD MAX, Promega, Qiagen), the PCR instrument (Agilent Mx3005P, BD MAX, Qiagen Rotor-Gene, Roche Cobas z 480) and the RT-PCR assay (Altona Diagnostics, CerTest Biotec, R-Biopharm AG) using predefined samples from proficiency testing organizers. In this study, two diagnostic laboratories of a tertiary care hospital equipped with different PCR systems validated the available kits on the respective systems for SARS-CoV-2 testing. In order to evaluate the performance of analytical components used for SARS-CoV-2 diagnostic we compared three commercially available RT-PCR kits, six extraction kits and four PCR cyclers in all possible combinations using predefined EQA samples. abstract: In limelight of the ongoing pandemic SARS-CoV-2 testing is critical for the diagnosis of infected patients, contact-tracing and mitigating the transmission. Diagnostic laboratories are expected to provide appropriate testing with maximum accuracy. Real-time reverse transcriptase PCR (RT-PCR) is the diagnostic standard yet many commercial diagnostic kits have become available. However, only a handful of studies have reviewed their performance in clinical settings. The aim of this study was to compare the performance of the overall analytical matrix including the extraction kit (BD MAX, Promega, Qiagen), the PCR instrument (Agilent Mx3005P, BD MAX, Qiagen Rotor-Gene, Roche Cobas z 480) and the RT-PCR assay (Altona Diagnostics, CerTest Biotec, R-Biopharm AG) using predefined samples from proficiency testing organizers. The greatest difference of the Ct values between the matrices was 9 cycles. One borderline sample could not be detected by 3 out of 12 analytical matrices and yielded a false negative result. We therefore conclude that diagnostic laboratories should take the complete analytical matrix in addition to the performance values published by the manufacturer for a respective RT-PCR kit into account. With limited resources laboratories have to validate a wide range of kits to determine appropriate analytical matrices for detecting SARS-CoV-2 reliably. The interpretation of clinical results has to be adapted accordingly. url: http://medrxiv.org/cgi/content/short/2020.09.18.20185744v1?rss=1 doi: 10.1101/2020.09.18.20185744 id: cord-277265-p8pns7r9 author: Malik, Yashpal Singh title: Biotechnological innovations in farm and pet animal disease diagnosis date: 2019-09-20 words: 7286.0 sentences: 346.0 pages: flesch: 37.0 cache: ./cache/cord-277265-p8pns7r9.txt txt: ./txt/cord-277265-p8pns7r9.txt summary: However, utilizing the principles of ELISA and PCR, several serological and molecular technologies have been developed to achieve higher sensitivity, rapid, and point-of-care (POC) detection such as lateral flow assays, biosensors, loop-mediated isothermal amplification, recombinase polymerase amplification, and molecular platforms for field-level detection of animal pathogens. Since then, biotechnological applications have been making significant contributions in the development of novel powerful diagnostic assays for the efficient diagnosis and control of animal infectious diseases. Presently, molecular detection-based methods such as polymerase chain reaction (PCR) or its variants, and serological methods such as enzyme-linked immunosorbent assay (ELISA), are being used worldwide for the accurate diagnosis of many animal diseases. Although, yet not been adopted for animal disease diagnosis, but novel platforms such as smartphonebased diagnosis (which expands nucleic acid-based detection assays toward POCD) like RT-LAMP and fluorescent lateral flow immunoassay (already developed for Zika virus and Dengue virus) provide exciting opportunities for veterinary diagnostics in the near future (Rong et al., 2019) . abstract: The application of innovative diagnostic technologies for the detection of animal pathogens at an early stage is essential in restricting the economic loss incurred due to emerging infectious animal diseases. The desirable characteristics of such diagnostic methods are easy to use, cost-effective, highly sensitive, and specific, coupled with the high-throughput detection capabilities. The enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) are still the most common assays used for the detection of animal pathogens across the globe. However, utilizing the principles of ELISA and PCR, several serological and molecular technologies have been developed to achieve higher sensitivity, rapid, and point-of-care (POC) detection such as lateral flow assays, biosensors, loop-mediated isothermal amplification, recombinase polymerase amplification, and molecular platforms for field-level detection of animal pathogens. Furthermore, animal disease diagnostics need to be updated regularly to capture new, emerging and divergent infectious pathogens, and biotechnological innovations are helpful in fulfilling the rising demand for such diagnostics for the welfare of the society. Therefore, this chapter primarily describes and discusses in detail the serological, molecular, novel high-throughput, and POC assays to detect pathogens affecting farm and companion animals. url: https://www.sciencedirect.com/science/article/pii/B9780128163528000138 doi: 10.1016/b978-0-12-816352-8.00013-8 id: cord-332053-df44guu7 author: Malka, Jonathan title: The Effect of Viral Infection on Exhaled Nitric Oxide in Children with Acute Asthma Exacerbations date: 2015-07-26 words: 4754.0 sentences: 257.0 pages: flesch: 54.0 cache: ./cache/cord-332053-df44guu7.txt txt: ./txt/cord-332053-df44guu7.txt summary: The Effect of Viral Infection on Exhaled Nitric Oxide in Children with Acute Asthma Exacerbations Jonathan Malka, MD a,b , Ronina Covar, MD c,d , Anna Faino, MS e , Jennifer Fish, CPNP f , Paige Pickering, BS g , Preveen Ramamoorthy, MD g , Melanie Gleason, PAC b,h , and Joseph D. All patients who presented to the Urgent Care Clinic at National Jewish Health for an acute asthma exacerbation and who had undergone spirometry and FENO measurements within the last 6 months when clinically stable (visit 1) were approached to participate in the study (Figure 1 ). We found FENO levels to be the highest in children with acute asthma exacerbations that were not associated with viral infections [PCR(À)]. B, Change in exhaled nitric oxide levels from baseline, during an exacerbation, and following a course of prednisone in adjusted models. abstract: BACKGROUND: Fraction of exhaled nitric oxide (Feno) level is used as an aid in the diagnosis and management of chronic asthma. Its role in acute asthma remains to be studied. OBJECTIVE: To determine whether Feno levels are elevated in children with asthma exacerbations compared with baseline, and whether there is a difference in Feno levels based on PCR positive (+) (respiratory virus isolated by PCR analysis) versus PCR negative (−) (respiratory virus not isolated by PCR analysis) status. METHODS: Children with a previous Feno level measurement while stable and who presented to an urgent care facility with an asthma exacerbation were enrolled. Feno levels, spirometry, and nasal swabs for viral PCR were obtained at the time of the exacerbation and following a course of prednisone. Data were available on 66 children. Linear mixed models were used to regress the outcomes of interest (FEV(1), FEV(1)/forced vital capacity, forced expiratory flow at 25% to 75% of forced vital capacity, and natural log Feno) on detected virus (yes/no), visit (baseline, exacerbation, follow-up), and the interaction between the detected virus and visit. RESULTS: Compared with baseline, higher Feno values and lower lung function were found at the time of an exacerbation. A respiratory virus was detected in 59% of the exacerbations. The interaction between PCR (+) and PCR (−) groups and visit on log Feno was marginally significant (P = .07). There was no difference in log Feno between the PCR (+) and PCR (−) groups at baseline, while higher log Feno was found in the PCR (−) group at the time of exacerbation and following prednisone (P = .05 and .001, respectively). CONCLUSIONS: Higher Feno concentration in PCR (−) exacerbations suggests an eosinophilic predominance in nonviral compared with viral exacerbations. url: https://doi.org/10.1016/j.jaip.2015.05.029 doi: 10.1016/j.jaip.2015.05.029 id: cord-346859-r1v6ir8u author: Mallett, Sue title: At what times during infection is SARS-CoV-2 detectable and no longer detectable using RT-PCR-based tests? A systematic review of individual participant data date: 2020-11-04 words: 5020.0 sentences: 277.0 pages: flesch: 52.0 cache: ./cache/cord-346859-r1v6ir8u.txt txt: ./txt/cord-346859-r1v6ir8u.txt summary: BACKGROUND: Tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral ribonucleic acid (RNA) using reverse transcription polymerase chain reaction (RT-PCR) are pivotal to detecting current coronavirus disease (COVID-19) and duration of detectable virus indicating potential for infectivity. METHODS: We conducted an individual participant data (IPD) systematic review of longitudinal studies of RT-PCR test results in symptomatic SARS-CoV-2. Because testing is pivotal to management and containment of COVID-19, we performed an individual participant data (IPD) systematic review of emerging evidence about test accuracy by anatomical sampling site to inform optimal sampling strategies for SARS-CoV-2. Previous studies have established that in COVID-19 infection, viral loads typically peak just before symptoms and at symptom onset [4] and estimated false negative test results over time since exposure from upper respiratory tract samples [2] . • Participants included will be biased to over-represent people with detectable virus in respiratory tract sampling sites and at times frequently used for testing (post symptom onset or at admission to hospital). abstract: BACKGROUND: Tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral ribonucleic acid (RNA) using reverse transcription polymerase chain reaction (RT-PCR) are pivotal to detecting current coronavirus disease (COVID-19) and duration of detectable virus indicating potential for infectivity. METHODS: We conducted an individual participant data (IPD) systematic review of longitudinal studies of RT-PCR test results in symptomatic SARS-CoV-2. We searched PubMed, LitCOVID, medRxiv, and COVID-19 Living Evidence databases. We assessed risk of bias using a QUADAS-2 adaptation. Outcomes were the percentage of positive test results by time and the duration of detectable virus, by anatomical sampling sites. RESULTS: Of 5078 studies screened, we included 32 studies with 1023 SARS-CoV-2 infected participants and 1619 test results, from − 6 to 66 days post-symptom onset and hospitalisation. The highest percentage virus detection was from nasopharyngeal sampling between 0 and 4 days post-symptom onset at 89% (95% confidence interval (CI) 83 to 93) dropping to 54% (95% CI 47 to 61) after 10 to 14 days. On average, duration of detectable virus was longer with lower respiratory tract (LRT) sampling than upper respiratory tract (URT). Duration of faecal and respiratory tract virus detection varied greatly within individual participants. In some participants, virus was still detectable at 46 days post-symptom onset. CONCLUSIONS: RT-PCR misses detection of people with SARS-CoV-2 infection; early sampling minimises false negative diagnoses. Beyond 10 days post-symptom onset, lower RT or faecal testing may be preferred sampling sites. The included studies are open to substantial risk of bias, so the positivity rates are probably overestimated. url: https://doi.org/10.1186/s12916-020-01810-8 doi: 10.1186/s12916-020-01810-8 id: cord-266466-5sgfx7oq author: Mansour, Amani title: First Case of an Infant with COVID-19 in the Middle East date: 2020-04-03 words: 1504.0 sentences: 97.0 pages: flesch: 55.0 cache: ./cache/cord-266466-5sgfx7oq.txt txt: ./txt/cord-266466-5sgfx7oq.txt summary: Here, we report the case of a 16-month-old female infant from Lebanon who presented with fever and severe diarrhea and tested positive for COVID-19. Her RT-PCR test was negative after five days of treatment, suggesting that children can clear the virus faster than adults. Most severe illness occurs in older adults but comparison with the pediatric population can be challenging as documented cases in infants and children have been scarce [3, 4] . On day 5, the RT-PCR test of the infant was negative, and the patient''s symptoms had resolved. Uniquely, our patient presented with fever and diarrhea; cough and other respiratory symptoms were not reported. Similarly, previous research in children indicates that the RT-PCR test becomes negative within 12 days (range: 6-22) after the presentation of symptoms [6] . This is the first case reported from the Middle East on an infant presenting with fever and diarrhea that tested positive for COVID-19. abstract: The novel coronavirus (COVID-19) has been declared a worldwide pandemic. It was initially thought to spare children and adolescents as significantly smaller number of cases have been reported in the pediatric population in comparison to adults. Here, we report the case of a 16-month-old female infant from Lebanon who presented with fever and severe diarrhea and tested positive for COVID-19. Her symptoms started six days prior to presentation with no cough, rhinorrhea, or other respiratory manifestations reported. Chest radiography showed lobar consolidation and bronchial infiltrates. Blood culture was positive for Streptococcus pneumoniae. Stool and urine cultures were negative. She was treated with ceftriaxone and metronidazole. Her RT-PCR test was negative after five days of treatment, suggesting that children can clear the virus faster than adults. The patient likely contracted the virus from her parents, who because of the fear of social stigma hide recent history of respiratory illness. These findings serve as a practical reference for the clinical diagnosis and medical treatment of children with COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32377468/ doi: 10.7759/cureus.7520 id: cord-264107-6doie8pj author: Marando, Marco title: False-Negative Nasopharyngeal Swab RT-PCR Assays in Typical COVID-19: Role of Ultra-low-dose Chest CT and Bronchoscopy in Diagnosis date: 2020-04-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: On 11 March 2020, the WHO declared COVID-19 a pandemic and global health emergency. We describe the clinical features and role of ultra-low-dose chest computed tomography (CT) and bronchoscopy in the diagnosis of coronavirus disease (COVID-19). In our patient, who was highly suggestive clinically and radiologically for COVID-19, we had two false-negative results for nasopharyngeal and oral swab reverse-transcriptase polymerase chain reaction (RT-PCR) assays for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Eventually, we confirmed the diagnosis using bronchoscopy and bronchoalveolar lavage (BAL). LEARNING POINTS: Clinical and laboratory findings in COVID-19 are unspecific. Chest CT has a diagnostic sensitivity comparable to nasopharyngeal swab RT-PCR assay but lacks specificity. RT-PCR assays on biological specimens, particularly nasopharyngeal swabs, are considered the diagnostic gold standard. Bronchoscopy and bronchoalveolar lavage can help confirm the diagnosis and should be performed in patients in whom diagnostic-driven treatment for COVID-19, such as tocilizumab or remdesivir, is being considered. url: https://www.ncbi.nlm.nih.gov/pubmed/32670990/ doi: 10.12890/2020_001680 id: cord-258438-6exkwp52 author: Marcone, Débora N. title: Diagnóstico de virus respiratorios utilizando un sistema automatizado de PCR múltiples (FilmArray) y su comparación con métodos convencionales date: 2015-03-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Resumen Las infecciones respiratorias agudas producen una importante morbimortalidad y comúnmente son causadas por virus. En Argentina, los programas de vigilancia epidemiológica se basan en la detección de antígenos virales por inmunofluorescencia (IF), aunque es bien conocido que los métodos moleculares son más sensibles. El panel respiratorio (PR) FilmArray (PR-FilmArray) es un equipo comercial automatizado de PCR múltiples que detecta 17 virus respiratorios y 3 bacterias, en un sistema cerrado que requiere 5min de procesamiento y una 1h de instrumentación. Se evaluó un total de 315 muestras respiratorias de niños menores de 6 años con infecciones respiratorias agudas por IF para 8 virus respiratorios y por RT-PCR para rinovirus. Posteriormente, estas muestras se estudiaron con el PR-FilmArray. La frecuencia de positividad al considerar los 9 virus estudiados por IF y RT-PCR fue del 75%; por PR-FilmArray fue del 92%. El porcentaje de acuerdo positivo entre ambas metodologías fue del 70,5% y el de acuerdo negativo fue del 99,6% (intervalo de confianza 95%: 65,5-75,1 y 99,2-99,8, respectivamente). El PR-FilmArray permitió obtener un mayor diagnóstico positivo (97%) y detectó otros virus, como los coronavirus NL63, 229E, OC43 y HKU1 (10%) y los bocavirus (18%). Además, permitió identificar coinfecciones múltiples (39%) con 2, 3, 4 y hasta 5 virus. Actualmente, la IF continúa siendo el método más utilizado en los países latinoamericanos para el diagnóstico de virus respiratorios por su bajo costo, por su capacidad para procesar un alto número de muestras simultáneamente y porque los resultados de los virus más frecuentes están disponibles en 5h. Sin embargo, la futura incorporación de métodos moleculares aumentaría notablemente la capacidad diagnóstica. Abstract Acute respiratory infections, which are commonly caused by viruses, are an important cause of morbidity and mortality in children. In Argentina, national surveillance programs for the detection of respiratory viruses are usually performed by using immunofluorescence (IF) assays, although it is well known that molecular methods are more sensitive. An automated multiplex PCR device, the FilmArray-Respiratory Panel (FilmArray-RP), can detect 17 viral and 3 bacterial pathogens in a closed system that requires only 5min of hands-on time and 1h of instrumentation time. A total of 315 respiratory samples from children under 6 years of age suffering from acute respiratory infections, were studied by IF for 8 respiratory viruses and by RT-PCR for rhinoviruses. Later, these samples were tested by the FilmArray-RP. The positivity frequency obtained for the 9 viruses tested was 75% by IF/RT-PCR and 92% by the FilmArray-RP. The positive and negative percent agreement between both methods was 70.5% whereas the negative percent agreement was 99.6% (95% confidence interval:65.5-75.1 and 99.2-99.8 respectively). The FilmArray-RP allowed a higher positive diagnosis (97%) and detected other viruses such as coronavirus NL63, 229E, OC43, HKU1 (10%) and bocavirus (18%). In addition, this method identified multiple coinfections (39%) with 2, 3, 4 and up to 5 different viruses. At present, IF is still the most frequently used method in most Latin American countries for respiratory viruses diagnosis due to its low cost, its capability to process a high number of samples simultaneously and the fast determination of results for the most frequent viruses, which are available within 5h. However, the coming incorporation of molecular methods in routine procedures will significantly increase the diagnostic yield of these infections. url: https://www.ncbi.nlm.nih.gov/pubmed/25735216/ doi: 10.1016/j.ram.2014.12.003 id: cord-354308-ol8twpay author: Mardani, title: COVID-19 infection recurrence presented with meningoencephalitis date: 2020-07-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract COVID- 19 infection can involve many organs such as central nervous system and also would be relapse. In this article we presented a 64-year-old woman with microbiological confirmed COVID-19 induced respiratory distress that treated resulted by negative nasopharyngeal swab RT-PCR for COVID-19. But, after a few weeks; relapse occurred by symptoms of acute meningoencephalitis. Results for COVID-19 RT-PCR from her cerebrospinal fluid, nasopharyngeal and tracheal aspiration specimens became positive again whereas, negative COVID-19 serum antibodies. So, it should be mentioned that neurological involvement symptoms can be one of COVID-19 first or relapse presentation. So, regular evaluation of patients during the convalescence seems necessary. url: https://www.ncbi.nlm.nih.gov/pubmed/32789020/ doi: 10.1016/j.nmni.2020.100732 id: cord-288701-nx9fg4yn author: Mari, Viviana title: Multiplex real-time RT-PCR assay for bovine viral diarrhea virus type 1, type 2 and HoBi-like pestivirus date: 2015-12-17 words: 4827.0 sentences: 227.0 pages: flesch: 53.0 cache: ./cache/cord-288701-nx9fg4yn.txt txt: ./txt/cord-288701-nx9fg4yn.txt summary: The aim of the present study was to develop a multiplex real-time RT-PCR assay, based on the TaqMan technology, for the rapid and unambiguous characterisation of all bovine pestiviruses, including the emerging HoBi-like strains. Analysis of field samples tested positive for BVDV-1, BVDV-2 or HoBi-like virus by a nested PCR protocol revealed that the developed TaqMan assay had equal or higher sensitivity and was able to discriminate correctly the viral species in all tested samples, whereas a real-time RT-PCR assay previously developed for HoBi-like pestivirus detection showed cross-reactivity with few high-titre BVDV-2 samples. To overcome these limitations, we have developed a multiplex real-time RT-PCR assay for simultaneous detection of the different species of bovine pestiviruses, including the emerging HoBi-like group, allowing a rapid, sensitive and specific diagnosis of pestivirus infection and characterisation of the viral species. abstract: HoBi-like pestiviruses are emerging pestiviruses that infect cattle causing clinical forms overlapping to those induced by bovine viral diarrhea virus (BVDV) 1 and 2. As a consequence of their widespread distribution reported in recent years, molecular tools for rapid discrimination among pestiviruses infecting cattle are needed. The aim of the present study was to develop a multiplex real-time RT-PCR assay, based on the TaqMan technology, for the rapid and unambiguous characterisation of all bovine pestiviruses, including the emerging HoBi-like strains. The assay was found to be sensitive, specific and repeatable, ensuring detection of as few as 10(0)–10(1) viral RNA copies. No cross-reactions between different pestiviral species were observed even in samples artificially contaminated with more than one pestivirus. Analysis of field samples tested positive for BVDV-1, BVDV-2 or HoBi-like virus by a nested PCR protocol revealed that the developed TaqMan assay had equal or higher sensitivity and was able to discriminate correctly the viral species in all tested samples, whereas a real-time RT-PCR assay previously developed for HoBi-like pestivirus detection showed cross-reactivity with few high-titre BVDV-2 samples. url: https://api.elsevier.com/content/article/pii/S0166093415003870 doi: 10.1016/j.jviromet.2015.12.003 id: cord-318013-5om35tu8 author: Marie, Tré-Hardy title: The role of serology for COVID-19 control: Population, kinetics and test performance do matter date: 2020-05-15 words: 944.0 sentences: 59.0 pages: flesch: 48.0 cache: ./cache/cord-318013-5om35tu8.txt txt: ./txt/cord-318013-5om35tu8.txt summary: (1-4) The authors of these reports or correspondence highlighted the added value of serological testing, which, if captured within the correct timeframe after disease onset, can detect both active and past infections.(1) By providing estimates of who is and is not immune to SARS-CoV-2, serological data can be used to estimate epidemiological variables, such as the attack rate or case-fatality rate, which are necessary to assess how much community transmission has occurred and its burden.(5) They can also be used to strategically deploy immune health-care workers to reduce exposure of the virus to susceptible individuals or to assess the effect of non-pharmaceutical interventions at the population level and inform policy changes to release such measures. After two weeks, all tests demonstrate a sensitivity of 100%, as reported by other groups, (8, 10) except when the cut-off provided by the manufacturer were used for IgG detection (i.e. one of our 15 patients was never considered as positive). abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0163445320302978?v=s5 doi: 10.1016/j.jinf.2020.05.019 id: cord-325736-gs9d8y55 author: Marin, J title: Persistence of Viruses in Upper Respiratory Tract of Children with Asthma date: 2000-07-31 words: 1874.0 sentences: 135.0 pages: flesch: 61.0 cache: ./cache/cord-325736-gs9d8y55.txt txt: ./txt/cord-325736-gs9d8y55.txt summary: title: Persistence of Viruses in Upper Respiratory Tract of Children with Asthma Conclusions: The persistent presence of viruses in the upper respiratory tract of asthmatic children shows a possible connection between viral infections and asthma. 4 In this study nasopharyngeal swabs were taken from asthmatic children whose asthma was well controlled, and when they were at least 3 weeks free of any respiratory infections. The samples were examined for the presence of adenovirus DNA and rhinovirus and coronavirus RNA. Five microlitres of c-DNA product were subsequently amplified in 50µl PCR reaction mixture consisting of 10 reaction buffer, 25 mM MgCl 2 , 20 mM dNTP, 5 U/l of DNA Taq polymerase (all reagents provided by Perkin Elmer, New Jersey, USA) and 50 µM of each specific primer for rhinoviruses and coronaviruses (TIB MOLBIOL, Berlin, Germany) (Table I) . found that upper respiratory tract viruses were associated with over 80% of asthma exacerbations in children. abstract: Abstract Objectives: Nasopharyngeal swabs of 50 asthmatic children in the symptom-free period were examined for the presence of adenoviruses, rhinoviruses and coronaviruses. A control group of 20 healthy individuals was included in this study. Methods: A polymerase chain reaction was used to detect adenovirus DNA and rhinovirus and coronavirus complementary DNA. The fragments of amplified genetic material were visualized with the use of agarose gel electrophoresis. Results: Adenovirus DNA was found in 78.4% of asthmatic children, rhinovirus RNA in 32.4% and coronavirus RNA in 2.7%. Adenovirus DNA was detected in one of the 20 nasopharyngeal swabs of healthy controls; the rest of the control samples were negative. Conclusions: The persistent presence of viruses in the upper respiratory tract of asthmatic children shows a possible connection between viral infections and asthma. url: https://www.ncbi.nlm.nih.gov/pubmed/10942643/ doi: 10.1053/jinf.2000.0688 id: cord-012461-v8d91fdo author: Marnissi, Boutheina title: Generation of ssDNA aptamers as diagnostic tool for Newcastle avian virus date: 2020-08-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Aptamers are short single-stranded DNA (ssDNA), RNA or synthetic XNA molecules, which are used as a class of affinity binders recognizing target molecules with a very high affinity and specificity. The aim of this study was to generate and characterize ssDNA aptamers for the detection of Newcastle disease virus (NDV). These aptamers were selected using systematic evolution of ligands by exponential enrichment (SELEX) in combination with quantitative high-throughput DNA sequencing. After three rounds of selections, a highly enriched ssDNA pool was sequenced, and the results were analyzed using FASTAptamer Toolkit. Sequencing reads were sorted by copy numbers and clustered into groups, according to their sequence homology. Top aptameric sequences were used to develop a sandwich enzymatic linked aptamer assay (ELAA) for rapid and sensitive detection of NDV in farm samples. The selected aptamers have an affinity within the nanomolar range, and a high specificity with no cross-reactivity towards other avian viruses. Following optimization of the sandwich ELAA method, the results demonstrated that both selected aptamers Apt_NDV01 and Apt_NDV03 with dissociation constant values of 31 nM and 78.1 nM, respectively, showed the highest specificity and affinity for NDV detection. The ELAA results were verified by quantitative real-time PCR, demonstrating strong concordance, and showing outstanding accuracy for detection of NDV in field sample. In summary, combination of SELEX with high-throughput DNA sequencing allowed rapid screening and selection of aptamers. The selected aptamers allowed recognition of NDV with high affinities. This is the first report that uses a validated sandwich ELAA for rapid and specific detection of NDV in poultry samples. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7425888/ doi: 10.1371/journal.pone.0237253 id: cord-140318-xtx8hl14 author: Martin, Alexandra title: High-sensitivity COVID-19 group testing by digital PCR date: 2020-06-03 words: 4252.0 sentences: 213.0 pages: flesch: 58.0 cache: ./cache/cord-140318-xtx8hl14.txt txt: ./txt/cord-140318-xtx8hl14.txt summary: Methods: We implemented RT-dPCR based COVID-19 group testing on commercially available system and assay (Naica System from Stilla Technologies) and investigated the sensitivity of the method in real life conditions of a university hospital in Paris, France, in May 2020. The results for SARS-CoV-2 detection by RT-dPCR in groups of 8 samples, detailed in Tables 1 and 2 , are in concordance with the reference individual RT-PCR testing for 52 groups (corresponding for 416 samples), out of which 32 were RT-PCR negative groups and 20 groups contained at least one RT-PCR+ sample. In this work, we assessed the sensitivity and specificity of group testing combined with digital PCR for SARS-CoV-2 detection. abstract: Background: Worldwide demand for SARS-CoV-2 RT-PCR testing is increasing as more countries are impacted by COVID-19 and as testing remains central to contain the spread of the disease, both in countries where the disease is emerging and in countries that are past the first wave but exposed to re-emergence. Group testing has been proposed as a solution to expand testing capabilities but sensitivity concerns have limited its impact on the management of the pandemic. Digital PCR (RT-dPCR) has been shown to be more sensitive than RT-PCR and could help in this context. Methods: We implemented RT-dPCR based COVID-19 group testing on commercially available system and assay (Naica System from Stilla Technologies) and investigated the sensitivity of the method in real life conditions of a university hospital in Paris, France, in May 2020. We tested the protocol in a direct comparison with reference RT-PCR testing on 448 samples split into groups of 3 sizes for RT-dPCR analysis: 56 groups of 8 samples, 28 groups of 16 samples and 14 groups of 32 samples. Results: Individual RT-PCR testing identified 25 positive samples. Using groups of 8, testing by RT-dPCR identified 23 groups as positive, corresponding to 26 true positive samples including 2 samples not initially detected by individual RT-PCR but confirmed positive by further RT-PCR and RT-dPCR investigation. For groups of 16, 15 groups tested positive, corresponding to 25 true positive samples identified. 100% concordance is found for groups of 32 but with limited data points. url: https://arxiv.org/pdf/2006.02908v1.pdf doi: nan id: cord-286343-s8n1ldol author: Martin, Javier title: Tracking SARS-CoV-2 in Sewage: Evidence of Changes in Virus Variant Predominance during COVID-19 Pandemic date: 2020-10-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), responsible for the ongoing coronavirus disease (COVID-19) pandemic, is frequently shed in faeces during infection, and viral RNA has recently been detected in sewage in some countries. We have investigated the presence of SARS-CoV-2 RNA in wastewater samples from South-East England between 14th January and 12th May 2020. A novel nested RT-PCR approach targeting five different regions of the viral genome improved the sensitivity of RT-qPCR assays and generated nucleotide sequences at sites with known sequence polymorphisms among SARS-CoV-2 isolates. We were able to detect co-circulating virus variants, some specifically prevalent in England, and to identify changes in viral RNA sequences with time consistent with the recently reported increasing global dominance of Spike protein G614 pandemic variant. Low levels of viral RNA were detected in a sample from 11th February, 3 days before the first case was reported in the sewage plant catchment area. SARS-CoV-2 RNA concentration increased in March and April, and a sharp reduction was observed in May, showing the effects of lockdown measures. We conclude that viral RNA sequences found in sewage closely resemble those from clinical samples and that environmental surveillance can be used to monitor SARS-CoV-2 transmission, tracing virus variants and detecting virus importations. url: https://www.ncbi.nlm.nih.gov/pubmed/33050264/ doi: 10.3390/v12101144 id: cord-268251-mcg1v24t author: Martins, Ronaldo Bragança title: Detection of respiratory viruses by real-time polymerase chain reaction in outpatients with acute respiratory infection date: 2014-09-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Viruses are the major contributors to the morbidity and mortality of upper and lower acute respiratory infections (ARIs) for all age groups. The aim of this study was to determine the frequencies for a large range of respiratory viruses using a sensitive molecular detection technique in specimens from outpatients of all ages with ARIs. Nasopharyngeal aspirates were obtained from 162 individuals between August 2007-August 2009. Twenty-three pathogenic respiratory agents, 18 respiratory viruses and five bacteria were investigated using multiplex real-time reverse transcriptase polymerase chain reaction (RT-PCR) and indirect immunofluorescence assay (IIF). Through IIF, 33 (20.4%) specimens with respiratory virus were recognised, with influenza virus representing over half of the positive samples. Through a multiplex real-time RT-PCR assay, 88 (54.3%) positive samples were detected; the most prevalent respiratory viral pathogens were influenza, human rhinovirus and respiratory syncytial virus (RSV). Six cases of viral co-detection were observed, mainly involving RSV. The use of multiplex real-time RT-PCR increased the viral detection by 33.9% and revealed a larger number of respiratory viruses implicated in ARI cases, including the most recently described respiratory viruses [human bocavirus, human metapneumovirus, influenza A (H1N1) pdm09 virus, human coronavirus (HCoV) NL63 and HCoV HKU1]. url: https://www.ncbi.nlm.nih.gov/pubmed/25317699/ doi: 10.1590/0074-0276140046 id: cord-334688-0i1pu8wc author: Martos Pérez, F. title: Comorbidity and prognostic factors on admission in a COVID-19 cohort of a general hospital date: 2020-08-19 words: 3445.0 sentences: 208.0 pages: flesch: 57.0 cache: ./cache/cord-334688-0i1pu8wc.txt txt: ./txt/cord-334688-0i1pu8wc.txt summary: Material and methods Retrospective cohort study of patients with COVID-19 admitted from 26th February 2020, who had been discharged or died up to 29th April 2020. Conclusions The presence of cardiopathy, levels of LDH ≥ 345 IU/L and age ≥ 65 years, are associated with a higher risk of death during hospital stay for COVID-19. In this study, we describe the first cases of COVID-19 in patients hospitalized in a general hospital and analyze the characteristics upon admission associated with in-hospital death. Our model shows that a medical history of cardiopathy, LDH levels ≥345 IU/L upon admission, and age ≥65 years are associated with greater in-hospital mortality due to COVID-19. Predictors of Mortality for Patients with COVID-19 Pneumonia Caused by SARS-CoV-2: A Prospective Cohort Study Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study. abstract: Abstract Antecedents and objective To describe clinical features, comorbidity, and prognostic factors associated with in-hospital mortality in a cohort of COVID-19 admitted to a general hospital. Material and methods Retrospective cohort study of patients with COVID-19 admitted from 26th February 2020, who had been discharged or died up to 29th April 2020. A descriptive study and an analysis of factors associated with intrahospital mortality were performed. Results Out of the 101 patients, 96 were analysed. Of these, 79 (82%) recovered and were discharged, and 17 (18%) died in the hospital. Diagnosis of COVID-19 was confirmed by polymerase chain reaction to SARS-CoV2 in 92 (92.5%). The mean age was 63 years, and 66% were male. The most frequent comorbidities were hypertension (40%), diabetes mellitus (16%) y cardiopathy (14%). Patients who died were older (mean 77 vs 60 years), had higher prevalence of hypertension (71% vs 33%), and cardiopathy (47% vs 6%), and higher levels of lactate dehydrogenase (LDH) and reactive C protein (mean 662 vs 335 UI/L, and 193 vs 121 mg/L respectively) on admission. In a multivariant analysis the variables significantly associated to mortality were the presence of cardiopathy (CI 95% OR 2,58-67,07), levels of LDH ≥ 345 IU/L (CI 95% OR 1,52-46,00), and age ≥ 65 years (CI 95% OR 1,23-44,62). Conclusions The presence of cardiopathy, levels of LDH ≥ 345 IU/L and age ≥ 65 years, are associated with a higher risk of death during hospital stay for COVID-19. This model should be validated in prospective cohorts. url: https://www.sciencedirect.com/science/article/pii/S2254887420300928?v=s5 doi: 10.1016/j.rceng.2020.05.010 id: cord-320002-25ivll3q author: Mathew, Joseph L. title: Etiology of community acquired pneumonia among children in India: prospective, cohort study date: 2015-10-21 words: 4151.0 sentences: 220.0 pages: flesch: 44.0 cache: ./cache/cord-320002-25ivll3q.txt txt: ./txt/cord-320002-25ivll3q.txt summary: BACKGROUND: Childhood community acquired pneumonia (CAP) is a significant problem in developing countries, and confirmation of microbial etiology is important for individual, as well as public health. The Pneumonia Research for Child Health (PERCH) project [15] is a 7-site case-control study to identify the cause of pneumonia among children in developing countries. Currently, there is no study from India reporting etiology of CAP in a large cohort of children, using multiple biological samples, and various sensitive as well as specific microbiologic methods. We initiated the Community Acquired Pneumonia Etiology Study (CAPES) to address this knowledge gap by determining the microbiologic etiology of CAP in a cohort of Indian children using multiple biological specimens (blood, nasopharyngeal aspirates, bronchoalveolar lavage) and the relationship between etiology and pneumonia severity. Lower respiratory infections among hospitalized children in New Caledonia: a pilot study for the Pneumonia Etiology Research for Child Health project abstract: BACKGROUND: Childhood community acquired pneumonia (CAP) is a significant problem in developing countries, and confirmation of microbial etiology is important for individual, as well as public health. However, there is paucity of data from a large cohort, examining multiple biological specimens for diverse pathogens (bacteria and viruses). The Community Acquired Pneumonia Etiology Study (CAPES) was designed to address this knowledge gap. METHODS: We enrolled children with CAP (based on WHO IMCI criteria of tachypnea with cough or breathing difficulty) over 24 consecutive months, and recorded presenting symptoms, risk factors, clinical signs, and chest radiography. We performed blood and nasopharyngeal aspirate (NPA) bacterial cultures, and serology (Mycoplasma pneumoniae, Chlamydophila pneumoniae). We also performed multiplex PCR for 25 bacterial/viral species in a subgroup representing 20% of the cohort. Children requiring endotracheal intubation underwent culture and PCR of bronchoalveolar lavage (BAL) specimens. FINDINGS: We enrolled 2345 children. NPA and blood cultures yielded bacteria in only 322 (13.7%) and 49 (2.1%) children respectively. In NPA, Streptococcus pneumoniae (79.1%) predominated, followed by Haemophilus influenzae (9.6%) and Staphylococcus aureus (6.8%). In blood, S. aureus (30.6%) dominated, followed by S. pneumoniae (20.4%) and Klebsiella pneumoniae (12.2%). M. pneumoniae and C. pneumoniae serology were positive in 4.3% and 1.1% respectively. Multiplex PCR in 428 NPA specimens identified organisms in 422 (98.6%); of these 352 (82.2%) had multiple organisms and only 70 (16.4%) had a single organism viz. S. pneumoniae: 35 (50%), Cytomegalovirus (CMV): 13 (18.6%), Respiratory Syncytial Virus (RSV): 9 (12.9%), other viruses: 6 (8.7%), S. aureus: 5 (7.1%), and H. influenzae: 2 (2.9%). BAL PCR (n = 30) identified single pathogens in 10 (S. pneumoniae–3, CMV–3, S. aureus–2, H. influenzae–2) and multiple pathogens in 18 children. There were 108 (4.6%) deaths. The pattern of pathogens identified did not correlate with pneumonia severity or mortality. CONCLUSIONS: The majority of children with CAP have multiple pathogens (bacteria and viruses). S. pneumoniae and S. aureus predominate in NPA and blood respectively. CMV and RSV were the dominant respiratory viruses in NPA and BAL. The presence of multiple pathogens, especially organisms associated with nasopharyngeal carriage, precludes confirmation of a causal relationship in most cases. url: https://www.ncbi.nlm.nih.gov/pubmed/26528392/ doi: 10.7189/jogh.05.020418 id: cord-302459-grs2x26l author: Matin, Farhana title: A Plasma Biomarker Panel of Four MicroRNAs for the Diagnosis of Prostate Cancer date: 2018-04-27 words: 8311.0 sentences: 413.0 pages: flesch: 48.0 cache: ./cache/cord-302459-grs2x26l.txt txt: ./txt/cord-302459-grs2x26l.txt summary: In this study we profiled 372 cancer-associated miRNAs in plasma collected before (~60% patients) and after/during commencement of treatment (~40% patients), from age-matched prostate cancer patients and healthy controls, and observed elevated levels of 4 miRNAs miR-4289, miR-326, miR-152-3p and miR-98-5p, which were validated in an independent cohort. Analysis of published miRNA transcriptomic data from clinical samples in the TCGA dataset demonstrated low expression of miR-152-3p in tumour compared to adjacent non-malignant tissues (p = 0.001) (Wilcoxon test, p ≤ 0.05) (Fig. 4) Figure S3) . Similarly, other groups have assessed the diagnostic performance of plasma or serum miRNAs in patients with localised or metastatic prostate cancer, BPH and healthy controls, and in most instances the specificity and sensitivity of the miRNA biomarkers have outperformed the accuracy of the PSA test 23, 28, 29 . abstract: Prostate cancer is diagnosed in over 1 million men every year globally, yet current diagnostic modalities are inadequate for identification of significant cancer and more reliable early diagnostic biomarkers are necessary for improved clinical management of prostate cancer patients. MicroRNAs (miRNAs) modulate important cellular processes/pathways contributing to cancer and are stably present in body fluids. In this study we profiled 372 cancer-associated miRNAs in plasma collected before (~60% patients) and after/during commencement of treatment (~40% patients), from age-matched prostate cancer patients and healthy controls, and observed elevated levels of 4 miRNAs - miR-4289, miR-326, miR-152-3p and miR-98-5p, which were validated in an independent cohort. The miRNA panel was able to differentiate between prostate cancer patients and controls (AUC = 0.88). Analysis of published miRNA transcriptomic data from clinical samples demonstrated low expression of miR-152-3p in tumour compared to adjacent non-malignant tissues. Overexpression of miR-152-3p increased proliferation and migration of prostate cancer cells, suggesting a role for this miRNA in prostate cancer pathogenesis, a concept that was supported by pathway analysis of predicted miR-152-3p target genes. In summary, a four miRNA panel, including miR-152-3p which likely targets genes with key roles in prostate cancer pathogenesis, has the potential to improve early prostate cancer diagnosis. url: https://doi.org/10.1038/s41598-018-24424-w doi: 10.1038/s41598-018-24424-w id: cord-002178-ggtxuulg author: Mauk, Michael G. title: Integrated Microfluidic Nucleic Acid Isolation, Isothermal Amplification, and Amplicon Quantification date: 2015-10-20 words: 5753.0 sentences: 257.0 pages: flesch: 39.0 cache: ./cache/cord-002178-ggtxuulg.txt txt: ./txt/cord-002178-ggtxuulg.txt summary: A portable, miniaturized POC NAAT with performance comparable to conventional PCR (polymerase-chain reaction)-based tests in clinical laboratories can be realized with a disposable, palm-sized, plastic microfluidic chip in which: (1) nucleic acids (NAs) are extracted from relatively large (~mL) volume sample lysates using an embedded porous silica glass fiber or cellulose binding phase ("membrane") to capture sample NAs in a flow-through, filtration mode; (2) NAs captured on the membrane are isothermally (~65 °C) amplified; (3) amplicon production is monitored by real-time fluorescence detection, such as with a smartphone CCD camera serving as a low-cost detector; and (4) paraffin-encapsulated, lyophilized reagents for temperature-activated release are pre-stored in the chip. abstract: Microfluidic components and systems for rapid (<60 min), low-cost, convenient, field-deployable sequence-specific nucleic acid-based amplification tests (NAATs) are described. A microfluidic point-of-care (POC) diagnostics test to quantify HIV viral load from blood samples serves as a representative and instructive example to discuss the technical issues and capabilities of “lab on a chip” NAAT devices. A portable, miniaturized POC NAAT with performance comparable to conventional PCR (polymerase-chain reaction)-based tests in clinical laboratories can be realized with a disposable, palm-sized, plastic microfluidic chip in which: (1) nucleic acids (NAs) are extracted from relatively large (~mL) volume sample lysates using an embedded porous silica glass fiber or cellulose binding phase (“membrane”) to capture sample NAs in a flow-through, filtration mode; (2) NAs captured on the membrane are isothermally (~65 °C) amplified; (3) amplicon production is monitored by real-time fluorescence detection, such as with a smartphone CCD camera serving as a low-cost detector; and (4) paraffin-encapsulated, lyophilized reagents for temperature-activated release are pre-stored in the chip. Limits of Detection (LOD) better than 10(3) virons/sample can be achieved. A modified chip with conduits hosting a diffusion-mode amplification process provides a simple visual indicator to readily quantify sample NA template. In addition, a companion microfluidic device for extracting plasma from whole blood without a centrifuge, generating cell-free plasma for chip-based molecular diagnostics, is described. Extensions to a myriad of related applications including, for example, food testing, cancer screening, and insect genotyping are briefly surveyed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4996405/ doi: 10.3390/microarrays4040474 id: cord-292742-mio4przi author: McAloose, Denise title: From People to Panthera: Natural SARS-CoV-2 Infection in Tigers and Lions at the Bronx Zoo date: 2020-10-13 words: 6364.0 sentences: 309.0 pages: flesch: 47.0 cache: ./cache/cord-292742-mio4przi.txt txt: ./txt/cord-292742-mio4przi.txt summary: KEYWORDS One Health, Panthera leo, Panthera tigris, SARS-CoV-2, in situ hybridization, lion, rRT-PCR, tiger, virus isolation, whole-genome sequencing, zoo, zoonotic infection C oronaviruses are a recognized cause of disease in humans and animals (1) . Subsequent to confirmation of SARS-CoV-2 infection in the animals, an epidemiologic investigation of zoo staff identified 10 zoo keepers and two managers who provided care for and had close (Յ1.8-m) but not direct contact with the tigers or lions between 16 March 2020 (the date on which the zoo was closed to the public due to the pandemic) and 27 March to 3 April 2020 (timeline of disease onset in the animals). Nine complete SARS-CoV-2 genome sequences (from four tigers, three lions, and two keepers) and eight full-length S gene sequences (from seven symptomatic animals and one asymptomatic animal) were generated directly from respiratory and/or fecal samples (Data Sets 3 and 4). abstract: Despite numerous barriers to transmission, zoonoses are the major cause of emerging infectious diseases in humans. Among these, severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and ebolaviruses have killed thousands; the human immunodeficiency virus (HIV) has killed millions. Zoonoses and human-to-animal cross-species transmission are driven by human actions and have important management, conservation, and public health implications. The current SARS-CoV-2 pandemic, which presumably originated from an animal reservoir, has killed more than half a million people around the world and cases continue to rise. In March 2020, New York City was a global epicenter for SARS-CoV-2 infections. During this time, four tigers and three lions at the Bronx Zoo, NY, developed mild, abnormal respiratory signs. We detected SARS-CoV-2 RNA in respiratory secretions and/or feces from all seven animals, live virus in three, and colocalized viral RNA with cellular damage in one. We produced nine whole SARS-CoV-2 genomes from the animals and keepers and identified different SARS-CoV-2 genotypes in the tigers and lions. Epidemiologic and genomic data indicated human-to-tiger transmission. These were the first confirmed cases of natural SARS-CoV-2 animal infections in the United States and the first in nondomestic species in the world. We highlight disease transmission at a nontraditional interface and provide information that contributes to understanding SARS-CoV-2 transmission across species. url: https://doi.org/10.1128/mbio.02220-20 doi: 10.1128/mbio.02220-20 id: cord-273343-als886fe author: McClenahan, Shasta D. title: Discovery of a Bovine Enterovirus in Alpaca date: 2013-08-12 words: 4596.0 sentences: 214.0 pages: flesch: 51.0 cache: ./cache/cord-273343-als886fe.txt txt: ./txt/cord-273343-als886fe.txt summary: A cytopathic virus was isolated using Madin-Darby bovine kidney (MDBK) cells from lung tissue of alpaca that died of a severe respiratory infection. To identify the virus, the infected cell culture supernatant was enriched for virus particles and a generic, PCR-based method was used to amplify potential viral sequences. The new alpaca virus sequence was most similar to recently designated Enterovirus species F, previously bovine enterovirus (BEVs), viruses that are globally prevalent in cattle, although they appear not to cause significant disease. Analysis of the full polyprotein and the individual capsid, 2A protease, 3C protease, and polymerase proteins of the alpaca-infecting virus relative to sequences of other representative enteroviruses from bovine EV-E (BEV-A serotypes 1-4) and EV-F (BEV-B serotypes 1-4), and sequences from three unclassified EV-F viruses [16] , two from bovine sources (AY724744 and AY724745) [20] , and one from a capped langur (JX538037) [21] , possum, porcine (PEV), and human (HEV) hosts. abstract: A cytopathic virus was isolated using Madin-Darby bovine kidney (MDBK) cells from lung tissue of alpaca that died of a severe respiratory infection. To identify the virus, the infected cell culture supernatant was enriched for virus particles and a generic, PCR-based method was used to amplify potential viral sequences. Genomic sequence data of the alpaca isolate was obtained and compared with sequences of known viruses. The new alpaca virus sequence was most similar to recently designated Enterovirus species F, previously bovine enterovirus (BEVs), viruses that are globally prevalent in cattle, although they appear not to cause significant disease. Because bovine enteroviruses have not been previously reported in U.S. alpaca, we suspect that this type of infection is fairly rare, and in this case appeared not to spread beyond the original outbreak. The capsid sequence of the detected virus had greatest homology to Enterovirus F type 1 (indicating that the virus should be considered a member of serotype 1), but the virus had greater homology in 2A protease sequence to type 3, suggesting that it may have been a recombinant. Identifying pathogens that infect a new host species for the first time can be challenging. As the disease in a new host species may be quite different from that in the original or natural host, the pathogen may not be suspected based on the clinical presentation, delaying diagnosis. Although this virus replicated in MDBK cells, existing standard culture and molecular methods could not identify it. In this case, a highly sensitive generic PCR-based pathogen-detection method was used to identify this pathogen. url: https://doi.org/10.1371/journal.pone.0068777 doi: 10.1371/journal.pone.0068777 id: cord-350593-bvmg7f15 author: McDonald, R.S. title: Proportional mouse model for aerosol infection by influenza date: 2012-08-21 words: 6550.0 sentences: 324.0 pages: flesch: 49.0 cache: ./cache/cord-350593-bvmg7f15.txt txt: ./txt/cord-350593-bvmg7f15.txt summary: CONCLUSIONS: MID (50) for inspired H1N1 aerosols in CD‐1 mice is between 12 and 40 TCID (50); proportionality to dose of weight loss and viral populations makes the CD‐1 mouse a useful model for measuring infectivity by inhalation. Although a few publications have documented the transmissibility of influenza A through inhalation routes (Tellier 2006 (Tellier , 2009 , few studies to date have utilized a mouse model to investigate susceptibility to and pathogenicity of measured aerosol exposures. Table 2 Results of three assays [PCR, direct fluorescent antibody assay (DFA) and CPE] from the homogenates of CD-1 murine lung tissue exposed to an aerosol generated from 1Á58 9 10 6 TCID 50 ml À1 At the 3-min exposure time, no mice were positive for influenza virus as determined by Ct value. abstract: AIMS: The aim of this study was to demonstrate a prototype tool for measuring infectivity of an aerosolized human pathogen – influenza A/PR/8/34 (H1N1) virus – using a small‐animal model in the Controlled Aerosol Test System (CATS). METHODS AND RESULTS: Intranasal inoculation of nonadapted H1N1 virus into C57BL, BALB/c and CD‐1 mice caused infection in all three species. Respiratory exposure of CD‐1 mice to the aerosolized virus at graduated doses was accomplished in a modified rodent exposure apparatus. Weight change was recorded for 7 days postexposure, and viral populations in lung tissue homogenates were measured post mortem by DNA amplification (qRT‐PCR), direct fluorescence and microscopic evaluation of cytopathic effect. Plots of weight change and of PCR cycle threshold vs delivered dose were linear to threshold doses of ~40 TCID (50) and ~12 TCID (50), respectively. CONCLUSIONS: MID (50) for inspired H1N1 aerosols in CD‐1 mice is between 12 and 40 TCID (50); proportionality to dose of weight loss and viral populations makes the CD‐1 mouse a useful model for measuring infectivity by inhalation. SIGNIFICANCE AND IMPACT OF THE STUDY: In the CATS, this mouse–virus model provides the first quantitative method to evaluate the ability of respiratory protective technologies to attenuate the infectivity of an inspired pathogenic aerosol. url: https://www.ncbi.nlm.nih.gov/pubmed/22809111/ doi: 10.1111/j.1365-2672.2012.05402.x id: cord-258768-bjjfkfgg author: McElligott, Susan title: Detection and genetic characterization of canine parvoviruses and coronaviruses in southern Ireland date: 2010-11-24 words: 4380.0 sentences: 220.0 pages: flesch: 53.0 cache: ./cache/cord-258768-bjjfkfgg.txt txt: ./txt/cord-258768-bjjfkfgg.txt summary: Two hundred fifty samples were collected in total, Fig. 2 Phylogenetic tree based on partial S gene nucleotide sequences of CCoVs described in this study and reference strains. As a result of RNA recombination, insertions, deletions and a high susceptibility to frequent mutation, coronaviruses can mutate rapidly, leading to new genotypes (CCoV-I), biotypes (pantropic CCoV) and host variants (canine respiratory coronavirus), all of which may present possible difficulties regarding successful vaccination of dogs. As a result of this study, it can be concluded that although it appears that the viral evolution of CPV type 2 is not yet a significant problem for the canine population in Ireland, vaccine efficacy may need to be re-evaluated by the animal healthcare industry, as it is a possibility that the new CPV-2c strain will eventually emerge into the population as a result of importing dogs from other parts of the world. abstract: Canine parvovirus (CPV) and canine coronavirus (CCoV) are considered the main pathogens responsible for acute gastroenteritis in dogs. From a collection of 250 samples, seven CPV strains and three CCoV strains were identified in symptomatic Irish dogs. Samples were screened for the viruses using polymerase chain reaction (PCR) and typed via DNA sequence analysis. Three CPV strains were characterized as CPV-2a, while four others were characterized as CPV-2b. To date, CPV-2c remains unreported in Ireland. Two CCoV strains were characterized as CCoV-II and one as CCoV-I. In the case of one sample, PH4/09/Ire, a mixed infection with CPV and CCoV was detected. url: https://www.ncbi.nlm.nih.gov/pubmed/21107617/ doi: 10.1007/s00705-010-0861-3 id: cord-307602-2cmgu7rf author: McErlean, P. title: Characterisation of a newly identified human rhinovirus, HRV-QPM, discovered in infants with bronchiolitis date: 2007-05-07 words: 3269.0 sentences: 172.0 pages: flesch: 50.0 cache: ./cache/cord-307602-2cmgu7rf.txt txt: ./txt/cord-307602-2cmgu7rf.txt summary: BACKGROUND: Human rhinoviruses (HRVs) are some of the earliest identified and most commonly detected viruses associated with acute respiratory tract infections (ARTIs) and yet the molecular epidemiology and genomic variation of individual serotypes remains undefined. RESULTS: Phylogenetic studies of complete coding sequences defined HRV-QPM as a novel member the genus Rhinovirus residing within the previously described HRV-A2 sub-lineage. CONCLUSIONS: We present the molecular characterisation and preliminary clinical impact of a newly identified HRV along with sequences representing additional new HRVs. Acute respiratory tract infections (ARTIs) are a leading cause of human morbidity worldwide and are most frequently viral in origin. We further investigated one of these putative viruses and herein present the complete polyprotein coding sequence of a novel HRV, HRV-QPM, which was first detected in an infant with bronchiolitis. abstract: BACKGROUND: Human rhinoviruses (HRVs) are some of the earliest identified and most commonly detected viruses associated with acute respiratory tract infections (ARTIs) and yet the molecular epidemiology and genomic variation of individual serotypes remains undefined. OBJECTIVES: To molecularly characterise a novel HRV and determine its prevalence and clinical impact on a predominantly paediatric population. STUDY DESIGN: Nucleotide sequencing was employed to determine the complete HRV-QPM coding sequence. Two novel real-time RT-PCR diagnostic assays were designed and employed to retrospectively screen a well-defined population of 1244 specimen extracts to identify the prevalence of HRV-QPM during 2003. RESULTS: Phylogenetic studies of complete coding sequences defined HRV-QPM as a novel member the genus Rhinovirus residing within the previously described HRV-A2 sub-lineage. Investigation of the relatively short VP1 sequence suggest that the virus is resistant to Pleconaril, setting it apart from the HRV A species. Sixteen additional HRV-QPM strains were detected (1.4% of specimens) often as the sole micro-organism present among infants with suspected bronchiolitis. HRV-QPM was also detected in Europe during 2006, and a closely related virus circulated in the United States during 2004. CONCLUSIONS: We present the molecular characterisation and preliminary clinical impact of a newly identified HRV along with sequences representing additional new HRVs. url: https://api.elsevier.com/content/article/pii/S1386653207001278 doi: 10.1016/j.jcv.2007.03.012 id: cord-294138-h7sfd1wa author: McIver, David J. title: Coronavirus surveillance of wildlife in the Lao People’s Democratic Republic detects viral RNA in rodents date: 2020-06-01 words: 2780.0 sentences: 130.0 pages: flesch: 56.0 cache: ./cache/cord-294138-h7sfd1wa.txt txt: ./txt/cord-294138-h7sfd1wa.txt summary: Both countries were involved in the United States Agency for International Development''s (USAID) Emerging Pandemic Threats PREDICT program, and surveillance of bats in wildlife markets in rural areas in Laos using family-level PCR assays revealed the presence of CoV RNA in 41 animals [5] . Considering the significant interactions of wildlife and especially rodents with humans in Laos, we were interested in investigating the presence of CoVs in these animals, which can be primary or intermediate hosts for CoVs with zoonotic potential. Since there are abundant contact opportunities for wildlife pathogens and humans in Laos, and considering that coronavirus-zoonotic events can involve intermediate hosts, as in the cases of SARS and MERS, we focused our screening on non-bat species potentially capable of playing that role. It is worth noting that we targeted rodents most likely to be in contact with humans and transmit virus and found fewer CoV-RNA-positive animals than in other studies of rodents in the region or elsewhere. abstract: Coronaviruses can become zoonotic, as in the case of COVID-19, and hunting, sale, and consumption of wild animals in Southeast Asia increases the risk for such incidents. We sampled and tested rodents (851) and other mammals and found betacoronavirus RNA in 12 rodents. The sequences belong to two separate genetic clusters and are closely related to those of known rodent coronaviruses detected in the region and distantly related to those of human coronaviruses OC43 and HKU1. Considering the close human-wildlife contact with many species in and beyond the region, a better understanding of virus diversity is urgently needed for the mitigation of future risks. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-020-04683-7) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00705-020-04683-7 doi: 10.1007/s00705-020-04683-7 id: cord-277988-dhzln0n3 author: Mcheik, Jiad N. title: Infantile hypertrophic pyloric stenosis: Are viruses involved? date: 2010-10-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Infantile hypertrophic pyloric stenosis (IHPS) is characterized by abnormal thickening of the internal circular muscle layer. IHPS is known to be due to a combination of genetic and environmental factors, but its precise causes and pathophysiology are poorly understood. The objective of the study is to determine the prevalence of the principal viruses targeting the respiratory and digestive tracts in children with IHPS. Nasopharyngeal fluids, stools, vomit, and surgical pyloric muscle fragments and swabs were tested by cell culture, viral antigen assay and PCR. IHPS was diagnosed in 23 boys and 8 girls with a mean (±SD) age of 42 ± 15 days (range 20–88 days). There was no seasonal pattern of diagnosis. Twenty‐two children (71%) lost weight (mean 246 ± 164 g, range 30–600 g) after the onset of vomiting, and five (16.1%) were dehydrated. Seven (22.6%) infants had been exposed to an infectious contact within 15 days before admission, and one on the day of admission (3.2%). Ear, nose and throat samples and pyloric muscle specimens were negative for all the viruses tested. An adenovirus type 3 was recovered from one stool sample, and RT‐PCR was positive for an enterovirus on one vomit sample. This study suggests that the principal viruses targeting the respiratory and digestive tracts are not responsible for IHPS. J. Med. Virol. 82:2087–2091, 2010. © 2010 Wiley‐Liss, Inc. url: https://doi.org/10.1002/jmv.21913 doi: 10.1002/jmv.21913 id: cord-316376-76beuk0c author: Medeiros, Augusto Kreling title: Higher frequency of hepatic steatosis at CT among COVID-19-positive patients date: 2020-07-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: PURPOSE: Recent studies have demonstrated that obesity is significantly associated with increased disease severity, hospitalizations and mortality in COVID-19, with a potential role in the pathogenesis and prevalence in the new pandemic. The association with hepatic steatosis, however, a condition closely related to obesity within the spectrum of systemic metabolic dysfunctions, remains to be elucidated. We aimed to evaluate the frequency of hepatic steatosis as incidentally detected in chest CT examinations of COVID-19 positive patients in comparison to non-infected controls. METHODS: A retrospective study was performed with 316 patients (204 RT-PCR positive; 112 RT-PCR negative and chest CT negative). Steatosis was measured with placement of a single ROI in the right lobe of the liver (segments VI-VII) and defined as a liver attenuation value ≤ 40 HU. RESULTS: The frequency of hepatic steatosis was higher in the RT-PCR positive group in comparison to controls (31.9% vs. 7.1%, p < 0.001). Logistic linear regression analysis showed a 4.7 times odds of steatosis in the COVID-19 positive group as compared to controls after adjusting for age and sex (OR 4.698; 95% IC 2.12–10.41, p < 0.001). CONCLUSION: A significantly higher prevalence of steatosis was found among COVID-19 positive individuals. These findings are in accordance with other recent studies linking obesity and COVID-19 infection, as there is an intricate relationship between liver steatosis, metabolic syndrome and obesity. Further studies are required to confirm if such association remains after accounting for multiple variables, as well as possible relationships with disease severity and worst clinical outcomes. url: https://doi.org/10.1007/s00261-020-02648-7 doi: 10.1007/s00261-020-02648-7 id: cord-342380-lihz7h1k author: Meguid Kassem, Abdel title: SARS-CoV-2 infection among healthcare workers of a gastroenterological service in a tertiary care facility date: 2020-07-21 words: 3044.0 sentences: 164.0 pages: flesch: 51.0 cache: ./cache/cord-342380-lihz7h1k.txt txt: ./txt/cord-342380-lihz7h1k.txt summary: BACKGROUND AND STUDY AIMS: Frontlines healthcare workers (HCWs) during the coronavirus disease 2019 (COVID-19) pandemic are at increased risk of infection by SARS-CoV-2, but there are limited data on the prevalence of COVID-19 among HCWs in Egypt. SUBJECTS AND METHODS: Seventy-four HCWs at the gastroenterological service of Al-Manial University Hospital, the main hospital of the largest tertiary university hospitals complex in Egypt (Kasr Al-Ainy Faculty of Medicine, Cairo University) were tested using real-time reverse transcription–polymerase chain reaction (RT-PCR) on nasopharyngeal samples, and rapid serological IgM/IgG tests (RST). This work has been conducted to determine the extent of infection by realtime reverse transcription polymerase chain reaction (RT-PCR) and rapid serological test (RST) for SARS-CoV-2 among frontline HCWs providing gastrointestinal services. Previous studies in developed countries reported variable infection rates in HCWs. In a study on 957 employees in a German university hospital, 52 of them (5.4%) tested positive for SARS-CoV-2 by PCR [13] . abstract: BACKGROUND AND STUDY AIMS: Frontlines healthcare workers (HCWs) during the coronavirus disease 2019 (COVID-19) pandemic are at increased risk of infection by SARS-CoV-2, but there are limited data on the prevalence of COVID-19 among HCWs in Egypt. This study aimed to assess SARS-CoV-2 infection among HCWs providing gastroenterological services. SUBJECTS AND METHODS: Seventy-four HCWs at the gastroenterological service of Al-Manial University Hospital, the main hospital of the largest tertiary university hospitals complex in Egypt (Kasr Al-Ainy Faculty of Medicine, Cairo University) were tested using real-time reverse transcription–polymerase chain reaction (RT-PCR) on nasopharyngeal samples, and rapid serological IgM/IgG tests (RST). A questionnaire was used to collect demographic, occupational and clinical data. RESULTS: Of the 74 HCWs, 10 tested positive by RT-PCR (13.5%). In 9/74 (12.2 %) HCWs, antibodies could be detected by RST: three with both IgM and IgG lines; six with IgM line only and none with IgG line only. Frequency of positive tests was more among subjects with minor symptoms compared to completely asymptomatic HCWs (50% vs 16.1%, respectively). Neither age, gender or occupation was a risk factor for SARS-CoV-2 infection. CONCLUSIONS: Point prevalence of COVID-19 in gastroenterology HCWs is 13.5% by RT-PCR. Continued measures are warranted to assure HCWs safety and reduce transmission from healthcare settings to the community during COVID-19 pandemic. Presence of positive test results among asymptomatic HCWs illustrates the importance of screening all HCWs irrespective of symptoms. url: https://www.ncbi.nlm.nih.gov/pubmed/32732168/ doi: 10.1016/j.ajg.2020.07.005 id: cord-337003-7ygcfzii author: Mehrbod, Parvaneh title: Association of IFITM3 rs12252 polymorphisms, BMI, diabetes, and hypercholesterolemia with mild flu in an Iranian population date: 2017-11-09 words: 4411.0 sentences: 250.0 pages: flesch: 49.0 cache: ./cache/cord-337003-7ygcfzii.txt txt: ./txt/cord-337003-7ygcfzii.txt summary: METHODS: We conducted a case-control study, including 79 mild flu and 125 flu-negative individuals attending primary care centers of three provinces of Iran (i.e, Markazi, Semnan, and Zanjan). Lack of significant association between C allele homozygous and mild flu, observed in this study, might be the result of small sample size in this group. Therefore, we performed this study to identify the association between mild flu and IFITM3 rs12252-C polymorphism, BMI, diabetes and hypercholesterolemia. In this study, we investigated the association between mild flu and IFITM3 rs12252 variant, BMI, diabetes, and hypercholesterolemia in an Iranian population. To control for the effect of residual population admixture on our results, we adjusted genetic association between IFITM3-SNP rs12252 and susceptibility to mild flu for participants'' residence area. To the best of our knowledge, this is the first study evaluating the association between IFITM3 rs12252 polymorphism, diabetes, hypercholesterolemia and BMI with susceptibility to mild flu in an Iranian sample. abstract: BACKGROUND: IFITM3 has been suggested to be associated with infection in some ethnic groups. Diabetes and hypercholesterolemia are also important clinical conditions that can predispose individuals to infection. The aim of this study was to investigate the association of rs12252 C polymorphism, BMI, diabetes, and hypercholesterolemia with mild flu in an Iranian population. METHODS: We conducted a case-control study, including 79 mild flu and 125 flu-negative individuals attending primary care centers of three provinces of Iran (i.e, Markazi, Semnan, and Zanjan). Pharyngeal swab specimens were collected from all participants, and were subjected to RNA and DNA extractions for Real-time PCR and PCR tests. All PCR products were then sequenced to find T/C polymorphisms in the rs12252 region. Data on demographic, anthropometric, and clinical variables were collected from participants’ medical records available in the primary care centers. The data was analyzed using DNASIS (v. 2.5) and Stata (v.11) software. RESULTS: All participants were of Fars ethnic background. The allele frequency for rs12252-C was found to be 9.49% among cases and 2.40% among controls. Carriers of the rs12252 C allele (CT + CC genotypes) showed 5.92 folds increase in the risk of mild flu comparing to the T allele homozygotes (P value: 0.007). We also found a significant positive association between rs12252 C allele heterozygote and mild flu (OR: 7.62, P value: 0.008), but not in C allele homozygote group (OR: 2.71, P value: 0.406). Similarly, we did not find a significant association between mild flu and BMI (OR: 1.06, P value: 0.087), diabetes (OR: 0.61, P value: 0.392), and hypercholesterolemia (OR: 0.50, P value: 0.393) in multivariable logistic regression. CONCLUSIONS: This is the first study evaluating the association between rs12252 polymorphisms, diabetes, hypercholesterolemia, and BMI and susceptibility to mild flu in an Iranian population. Our results suggest a significant positive association between mild flu and rs12252 C allele heterozygous and carriage. Future replication of the strong association observed here between rs12252 C allele carriage and mild flu might candidate this polymorphism as a genetic marker for early screening of susceptibility to mild flu. Lack of significant association between C allele homozygous and mild flu, observed in this study, might be the result of small sample size in this group. TRIAL REGISTRATION: IR.PII.REC.1395.3. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12985-017-0884-4) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/29121968/ doi: 10.1186/s12985-017-0884-4 id: cord-319921-uxtydu60 author: Meli, Marina L. title: Feline Leukemia Virus and Other Pathogens as Important Threats to the Survival of the Critically Endangered Iberian Lynx (Lynx pardinus) date: 2009-03-09 words: 5506.0 sentences: 259.0 pages: flesch: 48.0 cache: ./cache/cord-319921-uxtydu60.txt txt: ./txt/cord-319921-uxtydu60.txt summary: METHODOLOGY/ PRINCIPAL FINDINGS: We systematically analyzed the prevalence and importance of seven viral, one protozoan (Cytauxzoon felis), and several bacterial (e.g., hemotropic mycoplasma) infections in 77 of approximately 200 remaining free-ranging Iberian lynxes of the Doñana and Sierra Morena areas, in Southern Spain, between 2003 and 2007. Furthermore, the presence of feline leukemia virus (FeLV) provirus was recently reported in six samples originating from both the Doñ ana and Sierra Morena areas in southern Spain between 1994 and 2003 [29] . Thus, in the present study, we report on the prevalence of the aforementioned pathogens and we describe a dramatic FeLV epidemic, which most likely led to the death of 6 Iberian lynxes within a 6-months period in 2007, its possible origin, and its relationship to other infectious agents. However, endogenous FeLV sequences related to those of domestic cats are apparently not present in Iberian lynxes: only 5 of the 77 lynxes tested displayed weak signals by quantitative realtime PCR, which is not compatible with presence of enFeLV sequences. abstract: BACKGROUND: The Iberian lynx (Lynx pardinus) is considered the most endangered felid species in the world. In order to save this species, the Spanish authorities implemented a captive breeding program recruiting lynxes from the wild. In this context, a retrospective survey on prevalence of selected feline pathogens in free-ranging lynxes was initiated. METHODOLOGY/ PRINCIPAL FINDINGS: We systematically analyzed the prevalence and importance of seven viral, one protozoan (Cytauxzoon felis), and several bacterial (e.g., hemotropic mycoplasma) infections in 77 of approximately 200 remaining free-ranging Iberian lynxes of the Doñana and Sierra Morena areas, in Southern Spain, between 2003 and 2007. With the exception of feline immunodeficiency virus (FIV), evidence of infection by all tested feline pathogens was found in Iberian lynxes. Fourteen lynxes were feline leukemia virus (FeLV) provirus-positive; eleven of these were antigenemic (FeLV p27 positive). All 14 animals tested negative for other viral infections. During a six-month period in 2007, six of the provirus-positive antigenemic lynxes died. Infection with FeLV but not with other infectious agents was associated with mortality (p<0.001). Sequencing of the FeLV surface glycoprotein gene revealed a common origin for ten of the eleven samples. The ten sequences were closely related to FeLV-A/61E, originally isolated from cats in the USA. Endogenous FeLV sequences were not detected. CONCLUSIONS/SIGNIFICANCE: It was concluded that the FeLV infection most likely originated from domestic cats invading the lynx's habitats. Data available regarding the time frame, co-infections, and outcome of FeLV-infections suggest that, in contrast to the domestic cat, the FeLV strain affecting the lynxes in 2007 is highly virulent to this species. Our data argue strongly for vaccination of lynxes and domestic cats in and around lynx's habitats in order to prevent further spread of the virus as well as reduction the domestic cat population if the lynx population is to be maintained. url: https://doi.org/10.1371/journal.pone.0004744 doi: 10.1371/journal.pone.0004744 id: cord-285587-rggfg60a author: Meligy, Bassant title: Detection of viral acute lower respiratory tract infection in hospitalized infants using real-time PCR date: 2015-12-30 words: 3534.0 sentences: 212.0 pages: flesch: 50.0 cache: ./cache/cord-285587-rggfg60a.txt txt: ./txt/cord-285587-rggfg60a.txt summary: title: Detection of viral acute lower respiratory tract infection in hospitalized infants using real-time PCR Detection of viral acute lower respiratory tract infection in hospitalized infants using real-time PCR Introduction Viral pathogens account for a large proportion of community acquired pneumonia cases. 6, 7 The present study aims at investigating the epidemiology of viral infection using multiplex real time PCR, and exploring the clinical spectrum of the affected children in relation to viral type, during the winter season in hospitalized children with viral pneumonia. 19 Although RSV is well recognized as the main agent associated with severe ALRTIs, recent data indicate that other viruses may play a significant role in these clinical outcomes, RV seems to be of particular interest, as the most prevalent virus in respiratory illnesses even in the first years of life, being associated with severe acute bronchiolitis. Viral etiology of hospitalized acute lower respiratory infections in children under 5 years of age -a systematic review and metaanalysis abstract: INTRODUCTION: Acute lower respiratory tract infection in children causes significant morbidity in the developing countries. Documentation of virus infection using PCR and clinical characteristics of patients affected with viral pneumonia are reviewed in this study. METHODS: 51 children less than three years admitted to the Pediatric Hospital, Cairo University with viral pneumonia were included. All patients had undergone nasopharyngeal aspirate for PCR viral detection. RESULTS: A total of 51 cases were enrolled in the study, of which 7 cases were negative while 44 children were positive for viruses. The most common respiratory virus was Rhinovirus in 32 patients (72.2%), then parainfluenza virus (PIV) in 12 (27.3%), of which subtypes PIV1 were 2 (4.5%), PIV3 were 5 (11.4%) and PIV4 were 5 (11.4%) cases. The third common viruses were respiratory syncytial virus (RSV) in 9 (20.5%) cases of which 3 (6.8%) were RSVA and 6 (13.6%) were RSVB and adenovirus in 9 cases (20.5%). Boca virus was found in 8 (18.2%) patients, corona virus 2 (4.5%) patients, H1N1 2 (4.5%) patients, enterovirus 2 patients (4.5%) and human metapneumovirus in one case (2.3%). Influenza B and PIV2 were not detected. Coinfection was found in 28 (63.7%). Mortality occurred in 12 (23.5%). There was no significant relation between virus type or coinfection with disease severity. CONCLUSIONS: RV was the most commonly detected virus in children under 3 years admitted with acute lower respiratory tract infections. Coinfection was present in the majority of our patients; however it was not related significantly to parameters of disease severity. url: https://api.elsevier.com/content/article/pii/S1110663815000622 doi: 10.1016/j.epag.2015.11.005 id: cord-342344-jjnf4yje author: Mello, C. J. title: Absolute quantification and degradation evaluation of SARS-CoV-2 RNA by droplet digital PCR date: 2020-06-26 words: 3122.0 sentences: 190.0 pages: flesch: 55.0 cache: ./cache/cord-342344-jjnf4yje.txt txt: ./txt/cord-342344-jjnf4yje.txt summary: Diagnostic assays for the presence of SARS-CoV-2 currently use real-time reverse transcriptase PCR (RT-qPCR) to yield a binary (positive or negative) result based on an amplification cycle threshold (Ct) value 9-12 . Current PCR-based assays can detect the presence of very short SARS-CoV-2 RNA sequences but do not distinguish whether these sequences are derived from longer molecules present in the sample at the time of collection. To address these issues, we explored using droplet digital PCR (ddPCR) 19, 20 to more precisely quantify SARS-CoV-2 RNA in biological samples and evaluate the extent to which positive results reflect larger, intact viral nucleic acids. The results yielded definitive evidence of linkage: although only 822 of the 12,220 droplets (6.7%) were positive for either N1 or N2, 75% of the droplets that were positive for N2 (HEX) were also positive for N1 (FAM) (Fig. 2a, Table 1 ); we estimate (using a formula we previously described 21 , which accounts for chance co-encapsulation) that 71% of the detected RNA sequences were physically linked. abstract: Quantifying SARS-CoV-2 infectivity, formulating well-calibrated public-health policy, and managing the safety of workplaces would all be facilitated by precise measurement of the extent to which SARS-CoV-2 RNA is present in an intact form in biological specimens and human environments. We describe assays that use digital PCR in nanoliter droplets (droplet digital PCR) to measure these properties. Such assays could be broadly deployed to inform COVID-19 epidemiology, measure symptomatic and asymptomatic infectivity, and help manage the safety of environments in which people live, move, and work. url: http://medrxiv.org/cgi/content/short/2020.06.24.20139584v1?rss=1 doi: 10.1101/2020.06.24.20139584 id: cord-355489-tkvfneje author: Mendez, Jairo A title: Phylogenetic history demonstrates two different lineages of dengue type 1 virus in Colombia date: 2010-09-14 words: 4615.0 sentences: 235.0 pages: flesch: 48.0 cache: ./cache/cord-355489-tkvfneje.txt txt: ./txt/cord-355489-tkvfneje.txt summary: Yet, the phylogenetic relationships between strains isolated along the covered period of time suggests that viral strains detected in some years, although belonging to the same genotype V, have different recent origins corresponding to multiple re-introduction events of viral strains that were circulating in neighbor countries. Due to the importance of DENV in public health, the particular goals of this research were to reconstruct the phylogenetic history of DENV-1 and to date the phylogenetic tree using isolation time as calibration points to establish date of introduction of virus and rate evolution patterns of virus in Colombia. Previously reported genotypes were represented in the tree and placed most of the Colombian isolates nesting in the genotype V clade (America, Africa) and were closely related to Argentina, Brazil and Paraguay virus strains. abstract: BACKGROUND: Dengue Fever is one of the most important viral re-emergent diseases affecting about 50 million people around the world especially in tropical and sub-tropical countries. In Colombia, the virus was first detected in the earliest 70's when the disease became a major public health concern. Since then, all four serotypes of the virus have been reported. Although most of the huge outbreaks reported in this country have involved dengue virus serotype 1 (DENV-1), there are not studies about its origin, genetic diversity and distribution. RESULTS: We used 224 bp corresponding to the carboxyl terminus of envelope (E) gene from 74 Colombian isolates in order to reconstruct phylogenetic relationships and to estimate time divergences. Analyzed DENV-1 Colombian isolates belonged to the formerly defined genotype V. Only one virus isolate was clasified in the genotype I, likely representing a sole introduction that did not spread. The oldest strains were closely related to those detected for the first time in America in 1977 from the Caribbean and were detected for two years until their disappearance about six years later. Around 1987, a split up generated 2 lineages that have been evolving separately, although not major aminoacid changes in the analyzed region were found. CONCLUSION: DENV-1 has been circulating since 1978 in Colombia. Yet, the phylogenetic relationships between strains isolated along the covered period of time suggests that viral strains detected in some years, although belonging to the same genotype V, have different recent origins corresponding to multiple re-introduction events of viral strains that were circulating in neighbor countries. Viral strains used in the present study did not form a monophyletic group, which is evidence of a polyphyletic origin. We report the rapid spread patterns and high evolution rate of the different DENV-1 lineages. url: https://doi.org/10.1186/1743-422x-7-226 doi: 10.1186/1743-422x-7-226 id: cord-315598-qwh72inx author: Mendoza, Jose Luis Accini title: ACTUALIZACION DE LA DECLARACIÓN DE CONSENSO EN MEDICINA CRITICA PARA LA ATENCIÓN MULTIDISCIPLINARIA DEL PACIENTE CON SOSPECHA O CONFIRMACIÓN DIAGNÓSTICA DE COVID-19 date: 2020-10-06 words: 69640.0 sentences: 6489.0 pages: flesch: 54.0 cache: ./cache/cord-315598-qwh72inx.txt txt: ./txt/cord-315598-qwh72inx.txt summary: De otorgarse un Consentimiento Informado amplio, éste debería ser única y exclusivamente para los procesos asociados con COVID-19".(71) AMCI ® Se recomienda considerar la transición del cuidado intensivo al cuidado paliativo en todo paciente con sospecha o diagnóstico de COVID-19 sin mejoría a pesar de las intervenciones óptimas, con empeoramiento progresivo de su pronóstico vital y ante un evidente deterioro; aplicando medidas generales en control de síntomas ( Manejo de secreciones -Tratamiento del dolor -Tratamiento de la disnea -Sedación paliativa), así como apoyo espiritual, siempre acompañando al paciente y nunca abandonarlo en el final de la vida. En cuanto hace referencia a la situación actual de pandemia por SARS-CoV-2 y compromiso pulmonar; Wu y cols, en Marzo de 2.020 realizaron un estudio retrospectivo de 201 pacientes con COVID-19 en China; para aquellos pacientes que desarrollaron SDRA, el tratamiento con metilprednisolona estuvo asociado con una disminución del riesgo de muerte (23/50 [46%] con esteroides vs 21/34 [62%] sin esteroides; HR, 0.38 [IC 95%, 0.20-0.72]), con las limitaciones de los estudios retrospectivo, de un solo centro, con un limitado número de pacientes (400). abstract: Antecedentes y objetivos: La enfermedad por coronavirus de 2019 (COVID-19) es una enfermedad ocasionada por el nuevo coronavirus del síndrome respiratorio agudo grave (SARS-CoV-2). Se identificó por primera vez en diciembre de 2019 en la ciudad de Wuhan, en los meses siguientes se expandió rápidamente a todos los continentes y la Organización Mundial de la Salud (OMS), la reconoció como una pandemia global el 11 de marzo de 2020. La mayoría de los individuos son asintomáticos pero una baja proporción ingresan a cuidados intensivos con una alta morbilidad y mortalidad. Este consenso tiene como objetivo actualizar la declaratoria inicial emitida por la Asociación Colombiana de Medicina Crítica (AMCI) para el manejo del paciente críticamente enfermo con COVID-19 dentro de las áreas críticas de las instituciones de salud. Métodos: Este estudio utilizó dos técnicas de consenso formal para construir las recomendaciones finales: Delphi modificada y grupos nominales. Se construyeron preguntas por la estrategia PICO. 10 grupos nominales desarrollaron recomendaciones para cada unidad temática. El producto del consenso fue evaluado y calificado en una ronda Delphi y se discutió de forma virtual por los relatores de cada núcleo y los representantes de sociedades médicas científicas afines al manejo del paciente con COID-19. Resultados: 80 expertos nacionales participaron en la actualización del consenso AMCI, especialistas en Medicina Critica y Cuidados Intensivos, Nefrología, Neurología, Neumología, bioeticistas, Medicina interna, Anestesia, Cirugía General, Cirugía de cabeza y cuello, Cuidados Paliativos, Enfermeras Especialistas en Medicina crítica, Terapeutas respiratorias especialistas en medicina crítica y Fisioterapia, con experiencia clínica en la atención del paciente críticamente enfermo. La declaratoria emite recomendaciones en los ámbitos más relevantes para la atención en salud de los casos de COVID-19 al interior de las unidades de cuidados intensivos en el contexto nacional de Colombia. Conclusiones: un grupo significativo multidisciplinario de profesionales expertos en medicina crítica emiten mediante técnicas de consenso formal recomendaciones sobre la mejor práctica para la atención del paciente críticamente enfermo con COVID-19. Las recomendaciones deben ser adaptadas a las condiciones específicas, administrativas y estructurales de las distintas unidades de cuidados intensivos del país. Background and objectives: The 2019 coronavirus disease (COVID-19) is caused by the new severe acute respiratory syndrome coronavirus (SARS-CoV-2). It was first identified in December 2019 in Wuhan, China. In the following months it spread quickly to all continents and was recognised as a global pandemic by the World Health Organization (WHO) on March 11th, 2020. Most cases of infection remain asymptomatic, while a low proportion require intensive care, experiencing high morbidity and mortality. This consensus aims to update the initial statement issued by the Colombian Association of Critical Medicine (AMCI) for the management of the critically ill patient with COVID-19 within the critical areas of health institutions. Methods: This study used two formal consensus techniques to construct the final recommendations: modified Delphi and nominal groups. Questions were constructed using the PICO strategy. Recommendations for each thematic unit were developed by 10 nominal groups. The consensus product was evaluated and qualified in a Delphi round, and was discussed virtually by the speaker of each nucleus, as well as the representatives of scientific medical societies related to the management of the patient with COVID-19. Results: A total of 80 national experts participated in the update of the AMCI consensus, all specialists in Critical and Intensive Care Medicine, Nephrologists, Neurologists, Chest physician, bioethicists, Internal medicine specialists, Anaesthetists, General Surgeons, head and neck surgery, palliative care, Nurses Specialised in Critical Medicine, Respiratory therapists specialised in critical medicine and Physiotherapy, with clinical experience in the care of critically ill patients. This update issues recommendations in the most relevant areas for health care of COVID-19 patients within the intensive care units, contextualised for Colombia. Conclusions: A significant multidisciplinary group of professionals, who are experts in critical medicine, reviewed and issued recommendations on best practice for the care of critically ill patients with COVID-19 through formal consensus techniques. Recommendations must be adapted to the specific, administrative, and structural conditions of the different intensive care units in the country. url: https://www.sciencedirect.com/science/article/pii/S0122726220300859?v=s5 doi: 10.1016/j.acci.2020.09.004 id: cord-257398-fmkfo5ju author: Meng, Qing-Bin title: Clinical application of combined detection of SARS-CoV-2-specific antibody and nucleic acid date: 2020-10-06 words: 3231.0 sentences: 190.0 pages: flesch: 49.0 cache: ./cache/cord-257398-fmkfo5ju.txt txt: ./txt/cord-257398-fmkfo5ju.txt summary: In the present study, we collected clinical data from 652 suspected COVID-19 patients and 206 non-COVID-19 patients to investigate the diagnostic value of SARS-CoV-2 IgM/IgG antibody test kits with colloidal gold immunoassays and nucleic acid RT-PCR test kits. As recently reported, a rapid IgM/IgG October 6, 2020 Volume 8 Issue 19 combined antibody test was used for the diagnosis of SARS-CoV-2 infection, showing 88.66% sensitivity and 90.63% specificity [15] . Of the 415 suspected COVID-19 patients who were negative for the SARS-CoV-2 nucleic acid tests, 366 patients were positive for the SARS-CoV-2specific IgM and/or IgG antibody tests with a positive detection rate of 88.2%. Of the 415 suspected COVID-19 patients who were negative for the SARS-CoV-2 nucleic acid tests, 366 patients were positive for the SARS-CoV-2specific IgM and/or IgG antibody tests with a positive detection rate of 88.2%. abstract: BACKGROUND: The global outbreak of human severe acute respiratory syndrome coronavirus (SARS-CoV)-2 infection represents an urgent need for readily available, accurate and rapid diagnostic tests. Nucleic acid testing of respiratory tract specimens for SARS-CoV-2 is the current gold standard for diagnosis of coronavirus disease 2019 (COVID-19). However, the diagnostic accuracy of reverse transcription polymerase chain reaction (RT-PCR) tests for detecting SARS-CoV-2 nucleic acid may be lower than optimal. The detection of SARS-CoV-2-specific antibodies should be used as a serological non-invasive tool for the diagnosis and management of SARS-CoV-2 infection. AIM: To investigate the diagnostic value of SARS-CoV-2 IgM/IgG and nucleic acid detection in COVID-19. METHODS: We retrospectively analyzed 652 suspected COVID-19 patients, and 206 non-COVID-19 patients in Wuhan Integrated TCM and Western Medicine Hospital. Data on SARS-CoV-2 nucleic acid tests and serum antibody tests were collected to investigate the diagnostic value of nucleic acid RT-PCR test kits and immunoglobulin (Ig)M/IgG antibody test kits. The χ2 test was used to compare differences between categorical variables. A 95% confidence interval (CI) was provided by the Wilson score method. All analyses were performed with IBM SPSS Statistics version 22.0 (IBM Corp., Armonk, NY, United States). RESULTS: Of the 652 suspected COVID-19 patients, 237 (36.3%) had positive nucleic acid tests, 311 (47.7%) were positive for IgM, and 592 (90.8%) were positive for IgG. There was a significant difference in the positive detection rate between the IgM and IgG test groups (P < 0.001). Using the RT-PCR results as a reference, the specificity, sensitivity, and accuracy of IgM/IgG combined tests for SARS-CoV-2 infection were 98.5%, 95.8%, and 97.1%, respectively. Of the 415 suspected COVID-19 patients with negative nucleic acid test results, 366 had positive IgM/IgG tests with a positive detection rate of 88.2%. CONCLUSION: Our data indicate that serological IgM/IgG antibody combined test had high sensitivity and specificity for the diagnosis of SARS-CoV-2 infection, and can be used in combination with RT-PCR for the diagnosis of SARS-CoV-2 infection. url: https://doi.org/10.12998/wjcc.v8.i19.4360 doi: 10.12998/wjcc.v8.i19.4360 id: cord-350172-w3yoxhsg author: Mertens, Pascal title: Development and Potential Usefulness of the COVID-19 Ag Respi-Strip Diagnostic Assay in a Pandemic Context date: 2020-05-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Introduction: COVID-19 Ag Respi-Strip, an immunochromatographic (ICT) assay for the rapid detection of SARS-CoV-2 antigen on nasopharyngeal specimen, has been developed to identify positive COVID-19 patients allowing prompt clinical and quarantine decisions. In this original research article, we describe the conception, the analytical and clinical performances as well as the risk management of implementing the COVID-19 Ag Respi-Strip in a diagnostic decision algorithm. Materials and Methods: Development of the COVID-19 Ag Respi-Strip resulted in a ready-to-use ICT assay based on a membrane technology with colloidal gold nanoparticles using monoclonal antibodies directed against the SARS-CoV and SARS-CoV-2 highly conserved nucleoprotein antigen. Four hundred observations were recorded for the analytical performance study and thirty tests were analyzed for the cross-reactivity study. The clinical performance study was performed in a retrospective multi-centric evaluation on aliquots of 328 nasopharyngeal samples. COVID-19 Ag Respi-Strip results were compared with qRT-PCR as golden standard for COVID-19 diagnostics. Results: In the analytical performance study, the reproducibility showed a between-observer disagreement of 1.7%, a robustness of 98%, an overall satisfying user friendliness and no cross-reactivity with other virus-infected nasopharyngeal samples. In the clinical performance study performed in three different clinical laboratories during the ascendant phase of the epidemiological curve, we found an overall sensitivity and specificity of 57.6 and 99.5%, respectively with an accuracy of 82.6%. The cut-off of the ICT was found at CT <22. User-friendliness analysis and risk management assessment through Ishikawa diagram demonstrate that COVID-19 Ag Respi-Strip may be implemented in clinical laboratories according to biosafety recommendations. Conclusion: The COVID-19 Ag Respi-Strip represents a promising rapid SARS-CoV-2 antigen assay for the first-line diagnosis of COVID-19 in 15 min at the peak of the pandemic. Its role in the proposed diagnostic algorithm is complementary to the currently-used molecular techniques. url: https://doi.org/10.3389/fmed.2020.00225 doi: 10.3389/fmed.2020.00225 id: cord-286065-x0g67pnb author: Metzgar, David title: The IRIDICA BAC BSI Assay: Rapid, Sensitive and Culture-Independent Identification of Bacteria and Candida in Blood date: 2016-07-06 words: 5925.0 sentences: 240.0 pages: flesch: 38.0 cache: ./cache/cord-286065-x0g67pnb.txt txt: ./txt/cord-286065-x0g67pnb.txt summary: We describe the analytical characteristics of the IRIDICA BAC BSI Assay and compare its pre-clinical performance to current standard-of-care methods in a collection of prospectively collected blood specimens from patients with symptoms of sepsis. During the clinical sample study, performed following the sterility and personal protective equipment recommendations of the manufacturer, 61 negative controls were tested and yielded no Other reportable organisms excluding potential contaminants (n = 550) 0 0 0 207 A These 11 culture-negative, IRIDICA BAC BSI Assay-positive detections were supported by later organism-specific ID data which identified the same species as agents of infection (as noted on the subjects'' charts). The broad-spectrum nature of the IRIDICA BAC BSI Assay primers, paired with a signal analysis method capable of sensitive and specific detection and identification of one or more species signatures in samples with high background levels of human DNA, make it uniquely suited as a molecular test for bacterial and Candida DNA in blood samples. abstract: Bloodstream infection (BSI) and sepsis are rising in incidence throughout the developed world. The spread of multi-drug resistant organisms presents increasing challenges to treatment. Surviving BSI is dependent on rapid and accurate identification of causal organisms, and timely application of appropriate antibiotics. Current culture-based methods used to detect and identify agents of BSI are often too slow to impact early therapy and may fail to detect relevant organisms in many positive cases. Existing methods for direct molecular detection of microbial DNA in blood are limited in either sensitivity (likely the result of small sample volumes) or in breadth of coverage, often because the PCR primers and probes used target only a few specific pathogens. There is a clear unmet need for a sensitive molecular assay capable of identifying the diverse bacteria and yeast associated with BSI directly from uncultured whole blood samples. We have developed a method of extracting DNA from larger volumes of whole blood (5 ml per sample), amplifying multiple widely conserved bacterial and fungal genes using a mismatch- and background-tolerant PCR chemistry, and identifying hundreds of diverse organisms from the amplified fragments on the basis of species-specific genetic signatures using electrospray ionization mass spectrometry (PCR/ESI-MS). We describe the analytical characteristics of the IRIDICA BAC BSI Assay and compare its pre-clinical performance to current standard-of-care methods in a collection of prospectively collected blood specimens from patients with symptoms of sepsis. The assay generated matching results in 80% of culture-positive cases (86% when common contaminants were excluded from the analysis), and twice the total number of positive detections. The described method is capable of providing organism identifications directly from uncultured blood in less than 8 hours. Disclaimer: The IRIDICA BAC BSI Assay is not available in the United States. url: https://www.ncbi.nlm.nih.gov/pubmed/27384540/ doi: 10.1371/journal.pone.0158186 id: cord-345518-athy5yg7 author: Meurs, Kathryn M title: Molecular Screening by Polymerase Chain Reaction Detects Panleukopenia Virus DNA in Formalin-Fixed Hearts from Cats with Idiopathic Cardiomyopathy and Myocarditis date: 2000-04-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract Viral myocarditis has been suggested as an etiology for cardiomyopathy in several mammalian species. Myocarditis and idiopathic cardiomyopathy have been reported in the domestic cat, although a viral etiology has not been demonstrated. Because of the continuing interest in the potential relationship between viral myocarditis and cardiomyopathy, we evaluated hearts from cats with spontaneous, idiopathic cardiomyopathy for viral genomic material within myocytes by polymerase chain reaction, and for the presence of myocarditis by light microscopy. Thirty-one (31) formalin-fixed hearts from domestic cats who died of idiopathic cardiomyopathy were randomly selected from pathology archives. Seventeen (17) formalin-fixed hearts from healthy cats were similarly selected as normal controls. The polymerase chain reaction (PCR) was used to evaluate myocardial tissue for the presence of viral genome from feline panleukopenia virus, herpes virus, calici virus, and corona virus. Hearts were examined using light microscopy for histologic evidence of myocarditis according to the Dallas criteria. Panleukopenia virus was identified by PCR in 10 of 31 cats with cardiomyopathy but in none of the controls. Neither cardiomyopathic or control cats tested positive by PCR for herpes virus, calici virus, and corona virus. Myocarditis was detected by histologic examination in 18 of 31 cardiomyopathic cats and in none of 17 control cats. Myocarditis and or feline panleukopenia virus genome was detected in felines with idiopathic hypertrophic, dilated, and restrictive cardiomyopathy, suggesting a possible role of viral infection and inflammation in the pathogenesis of cardiomyopathy in this species. url: https://www.sciencedirect.com/science/article/pii/S1054880700000314 doi: 10.1016/s1054-8807(00)00031-4 id: cord-339456-82iks0xf author: Mikel, P. title: Methods for Preparation of MS2 Phage-Like Particles and Their Utilization as Process Control Viruses in RT-PCR and qRT-PCR Detection of RNA Viruses From Food Matrices and Clinical Specimens date: 2015-02-25 words: 10033.0 sentences: 499.0 pages: flesch: 53.0 cache: ./cache/cord-339456-82iks0xf.txt txt: ./txt/cord-339456-82iks0xf.txt summary: title: Methods for Preparation of MS2 Phage-Like Particles and Their Utilization as Process Control Viruses in RT-PCR and qRT-PCR Detection of RNA Viruses From Food Matrices and Clinical Specimens The technology for production of MS2 phage-like particles is theoretically well established, uses the knowledge gained from the study of the familiar bacteriophage MS2 and utilizes many different approaches for the construction of the various process control viruses. Also MS2 phage-like particles have been used as the process control virus for the detection of pathogenic RNA viruses in clinical samples. prepared MS2 phage-like particles, also called armored RNA (aRNA), that carried the consensus RNA sequence from human immunodeficiency virus type 1 (HIV-1) packaged in the capsid which can serve as quantitative standard in detection of HIV-1 (Pasloske et al. MS2 phage-like particles carrying the plant-specific ribulose-1,5-bisphosphate carboxyl small subunit (rbcs) gene fragment were used as the process control virus in qRT-PCR detection of severe acute respiratory syndrome coronavirus (SARS-CoV) . abstract: RNA viruses are pathogenic agents of many serious infectious diseases affecting humans and animals. The detection of pathogenic RNA viruses is based on modern molecular methods, of which the most widely used methods are the reverse transcription polymerase chain reaction (RT-PCR) and the real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). All steps of RT-PCR and qRT-PCR should be strictly controlled to ensure the validity of obtained results. False-negative results may be caused not only by inhibition of RT or/and PCR steps but also by failure of the nucleic acid extraction step, particularly in the case of viral RNA extraction. The control of nucleic acid extraction generally involves the utilization of a non-pathogenic virus (process control virus) of similar structural properties to those of the target virus. Although in clinical samples the use of such process control virus is only recommended, in other kinds of settings such as food matrices its use is necessary. Currently, several different process control viruses are used for these purposes. Process control viruses can also be constructed artificially using technology for production of MS2 phage-like particles, which have many advantages in comparison with other used controls and are especially suited for controlling the detection and quantification of certain types of RNA viruses. The technology for production of MS2 phage-like particles is theoretically well established, uses the knowledge gained from the study of the familiar bacteriophage MS2 and utilizes many different approaches for the construction of the various process control viruses. Nevertheless, the practical use of MS2 phage-like particles in routine diagnostics is relatively uncommon. The current situation with regard to the use of MS2 phage-like particles as process control viruses in detection of RNA viruses and different methods of their construction, purification and use are summarized and discussed in this review. url: https://www.ncbi.nlm.nih.gov/pubmed/25711389/ doi: 10.1007/s12560-015-9188-2 id: cord-002376-970934vm author: Mikel, Pavel title: Preparation of MS2 Phage-Like Particles and Their Use As Potential Process Control Viruses for Detection and Quantification of Enteric RNA Viruses in Different Matrices date: 2016-12-01 words: 6581.0 sentences: 311.0 pages: flesch: 52.0 cache: ./cache/cord-002376-970934vm.txt txt: ./txt/cord-002376-970934vm.txt summary: The quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay is nowadays considered as the gold standard method for detection and quantification of enteric RNA viruses such as hepatitis A virus (HAV), hepatitis E virus (HEV) or human noroviruses (NoV) (Mattison et al., 2009; Blaise-Boisseau et al., 2010; Di Pasquale et al., 2010; Vasickova et al., 2012; Hennechart-Collette et al., 2014) . The present article is a followup study of a previously published theoretical concept (Mikel et al., 2015) and describes a method of preparation of MS2 PLP carrying a specific control sequence and their use as a PCV in RT-qPCR detection and quantification of enteric RNA viruses in swab, liver tissue, serum, feces, and vegetable samples. MS2 PLP were added in the amount of 5 × 10 6 particles to the different types of matrices (swabs, liver tissue, serum, feces, and leafy green vegetables) to reveal their ability to serve as PCV in the RT-qPCR detection of enteric RNA viruses. abstract: The detection and quantification of enteric RNA viruses is based on isolation of viral RNA from the sample followed by quantitative reverse transcription polymerase chain reaction (RT-qPCR). To control the whole process of analysis and in order to guarantee the validity and reliability of results, process control viruses (PCV) are used. The present article describes the process of preparation and use of such PCV– MS2 phage-like particles (MS2 PLP) – in RT-qPCR detection and quantification of enteric RNA viruses. The MS2 PLP were derived from bacteriophage MS2 carrying a unique and specific de novo-constructed RNA target sequence originating from the DNA of two extinct species. The amount of prepared MS2 particles was quantified using four independent methods – UV spectrophotometry, fluorimetry, transmission electron microscopy and a specifically developed duplex RT-qPCR. To evaluate the usefulness of MS2 PLP in routine diagnostics different matrices known to harbor enteric RNA viruses (swab samples, liver tissue, serum, feces, and vegetables) were artificially contaminated with specific amounts of MS2 PLP. The extraction efficiencies were calculated for each individual matrix. The prepared particles fulfill all requirements for PCV – they are very stable, non-infectious, and are genetically distinct from the target RNA viruses. Due to these properties they represent a good morphological and physiochemical model. The use of MS2 PLP as a PCV in detection and quantification of enteric RNA viruses was evaluated in different types of matrices. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5234545/ doi: 10.3389/fmicb.2016.01911 id: cord-266156-xmf4emln author: Miller, Tyler E. title: Clinical sensitivity and interpretation of PCR and serological COVID‐19 diagnostics for patients presenting to the hospital date: 2020-08-28 words: 4329.0 sentences: 221.0 pages: flesch: 45.0 cache: ./cache/cord-266156-xmf4emln.txt txt: ./txt/cord-266156-xmf4emln.txt summary: Our goal was to examine the clinical sensitivity of two most common SARS‐CoV‐2 diagnostic test modalities, polymerase chain reaction (PCR) and serology, over the disease course to provide insight into their clinical interpretation in patients presenting to the hospital. The goal of this study is to examine the clinical sensitivity and provide insights into the interpretation of the two most common SARS-CoV-2 diagnostic test modalities: polymerase chain reaction (PCR) and serology. Serologic analysis of IgM, IgA and IgG status was performed in a subset of the above SARS-CoV-2 PCR-positive patients for which we had excess material in the MGH core laboratories for clinical validation studies. To assess the sensitivity of our serology assay over time, we tested for IgM, IgG, and IgA antibodies against the RBD of SARS-CoV-2 spike protein in 157 SARS-CoV-2 PCR-positive patients using an in-house ELISA (Table 1) . abstract: The diagnosis of COVID‐19 requires integration of clinical and laboratory data. Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) diagnostic assays play a central role in diagnosis and have fixed technical performance metrics. Interpretation becomes challenging because the clinical sensitivity changes as the virus clears and the immune response emerges. Our goal was to examine the clinical sensitivity of two most common SARS‐CoV‐2 diagnostic test modalities, polymerase chain reaction (PCR) and serology, over the disease course to provide insight into their clinical interpretation in patients presenting to the hospital. We conducted a single‐center, retrospective study. To derive clinical sensitivity of PCR, we identified 209 PCR‐positive SARS‐CoV‐2 patients with multiple PCR test results (624 total PCR tests) and calculated daily sensitivity from date of symptom onset or first positive test. Clinical sensitivity of PCR decreased with days post symptom onset with >90% clinical sensitivity during the first 5 days after symptom onset, 70%‐71% from Days 9 to 11, and 30% at Day 21. To calculate daily clinical sensitivity by serology, we utilized 157 PCR‐positive patients with a total of 197 specimens tested by enzyme‐linked immunosorbent assay for IgM, IgG, and IgA anti‐SARS‐CoV‐2 antibodies. In contrast to PCR, serological sensitivity increased with days post symptom onset with >50% of patients seropositive by at least one antibody isotype after Day 7, >80% after Day 12, and 100% by Day 21. Taken together, PCR and serology are complimentary modalities that require time‐dependent interpretation. Superimposition of sensitivities over time indicate that serology can function as a reliable diagnostic aid indicating recent or prior infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32856766/ doi: 10.1096/fj.202001700rr id: cord-324944-ixh3ykrc author: Mitsakakis, Konstantinos title: Diagnostic tools for tackling febrile illness and enhancing patient management date: 2018-12-05 words: 20805.0 sentences: 961.0 pages: flesch: 45.0 cache: ./cache/cord-324944-ixh3ykrc.txt txt: ./txt/cord-324944-ixh3ykrc.txt summary: This review gives an overview of diagnostic technologies featuring a platform based approach: (i) assay (nucleic acid amplification technologies are examined); (ii) cartridge (microfluidic technologies are presented); (iii) instrument (various detection technologies are discussed); and at the end proposes a way that such technologies can be interfaced with electronic clinical decision-making algorithms towards a broad and complete diagnostic ecosystem. In studies that have recorded the clinical presentation of patients (and not only their laboratory results), the causes of fever in outpatients could be classified into four main syndromes: 1) acute respiratory infections (ARI, of any type); 2) diarrhea (gastroenteritis); 3) fever with another clear focus (e.g. meningitis or skin infection); and 4) non-specific fevers [13] (each diagnostic platform described in Section 5 focuses on at least one of the aforementioned cases). abstract: Most patients with acute infectious diseases develop fever, which is frequently a reason to visit health facilities in resource-limited settings. The symptomatic overlap between febrile diseases impedes their diagnosis on clinical grounds. Therefore, the World Health Organization promotes an integrated management of febrile illness. Along this line, we present an overview of endemic and epidemic etiologies of fever and state-of-the-art diagnostic tools used in the field. It becomes evident that there is an urgent need for the development of novel technologies to fulfill end-users' requirements. This need can be met with point-of-care and near-patient diagnostic platforms, as well as e-Health clinical algorithms, which co-assess test results with key clinical elements and biosensors, assisting clinicians in patient triage and management, thus enhancing disease surveillance and outbreak alerts. This review gives an overview of diagnostic technologies featuring a platform based approach: (i) assay (nucleic acid amplification technologies are examined); (ii) cartridge (microfluidic technologies are presented); (iii) instrument (various detection technologies are discussed); and at the end proposes a way that such technologies can be interfaced with electronic clinical decision-making algorithms towards a broad and complete diagnostic ecosystem. url: https://www.sciencedirect.com/science/article/pii/S0167931718304556 doi: 10.1016/j.mee.2018.10.001 id: cord-312477-2y88gzji author: Mlcochova, P. title: Combined point of care nucleic acid and antibody testing for SARS-CoV-2: a prospective cohort study in suspected moderate to severe COVID-19 disease. date: 2020-06-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract Background Rapid COVID-19 diagnosis in hospital is essential for patient management and identification of infectious patients to limit the potential for nosocomial transmission. The diagnosis is complicated by 30-50% of COVID-19 hospital admissions with negative nose/throat swabs negative for SARS-CoV-2 nucleic acid, frequently after the first week of illness when SARS-CoV-2 antibody responses become detectable. We assessed the diagnostic accuracy of combined rapid antibody point of care (POC) and nucleic acid assays for suspected COVID-19 disease in the emergency department. Methods We developed (i) an in vitro neutralization assay using a lentivirus expressing a genome encoding luciferase and pseudotyped with spike protein and (ii) an ELISA test to detect IgG antibodies to nucleocapsid (N) and spike (S) proteins from SARS-CoV-2. We tested two promising candidate lateral flow rapid fingerprick test with bands for IgG and IgM. We then prospectively recruited participants with suspected moderate to severe COVID-19 and tested for SARS-CoV-2 nucleic acid in a combined nasal/throat swab using the standard laboratory RT-PCR and a validated rapid nucleic acid test. Additionally, serum collected at admission was retrospectively tested by in vitro neutralization, ELISA and the candidate POC antibody tests. We determined the sensitivity and specificity of the individual and combined rapid POC diagnostic tests against a composite gold standard of neutralisation and the standard laboratory RT-PCR. Results 45 participants had specimens tested for nucleic acid in nose/throat swabs as well as stored sera for antibodies. Serum neutralisation assay, SARS-CoV-2 Spike IgG ELISA and the POC antibody test results were concordant. Using the composite gold standard, prevalence of COVID-19 disease was 53.3% (24/45). Median age was 73.5 (IQR 54.0-86.5) years in those with COVID-19 disease by our gold standard and 63.0 (IQR 41.0-72.0) years in those without disease. Median duration of symptoms was 7 days (IQR 1-8) in those with infection. The overall sensitivity of rapid NAAT diagnosis was 79.2% (95CI 57.8-92.9%) and 50.0% (11.8-88.2) at days 8-28. Sensitivity and specificity of the combined rapid POC diagnostic tests reached 100% (95CI 85.8-100) and 94.7% (95CI 74.0-99.0) overall. Conclusions Dual point of care SARS-CoV-2 testing can significantly improve diagnostic sensitivity, whilst maintaining high specificity. Rapid combined tests have the potential to transform our management of COVID-19, including inflammatory manifestations where nucleic acid test results are negative. A rapid combined approach will also aid recruitment into clinical trials and in prescribing therapeutics, particularly where potentially harmful immune modulators (including steroids) are used. url: http://medrxiv.org/cgi/content/short/2020.06.16.20133157v1?rss=1 doi: 10.1101/2020.06.16.20133157 id: cord-300316-r54ksiy3 author: Moesker, F.M. title: Diagnostic performance of influenza viruses and RSV rapid antigen detection tests in children in tertiary care date: 2016-03-25 words: 3350.0 sentences: 201.0 pages: flesch: 56.0 cache: ./cache/cord-300316-r54ksiy3.txt txt: ./txt/cord-300316-r54ksiy3.txt summary: authors: Moesker, F.M.; van Kampen, J.J.A.; Aron, G.; Schutten, M.; van de Vijver, D.A.M.C.; Koopmans, M.P.G.; Osterhaus, A.D.M.E.; Fraaij, P.L.A. title: Diagnostic performance of influenza viruses and RSV rapid antigen detection tests in children in tertiary care OBJECTIVES: Comparing diagnostic performances of BinaxNow Influenza AB(®) (BNI) and BinaxNow RSV(®) (BNR), to those of real-time reverse transcriptase PCR (RT-PCR), virus isolation and direct immunofluorescence (D-IF) in paediatric patients. Comparing diagnostic performances of two RADTs, BinaxNow Influenza AB ® (BNI) and BinaxNow RSV ® (BNR), with those of RT-PCR in samples of paediatric patients attending our tertiary care centre with ARTIs for a period of almost eight consecutive years. The main outcomes of this study were the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the BNI and BNR rapid test results compared to RT-PCR during the total study period and during viral season (October 1st through March 31st). abstract: BACKGROUND: Rapid antigen detection tests (RADTs) are increasingly used to detect influenza viruses and respiratory syncytial virus (RSV). However, their sensitivity and specificity are a matter of debate, challenging their clinical usefulness. OBJECTIVES: Comparing diagnostic performances of BinaxNow Influenza AB(®) (BNI) and BinaxNow RSV(®) (BNR), to those of real-time reverse transcriptase PCR (RT-PCR), virus isolation and direct immunofluorescence (D-IF) in paediatric patients. STUDY DESIGN: Between November 2005 and September 2013, 521 nasal washings from symptomatic children (age <5 years) attending our tertiary care centre were tested, with a combination of the respective assays using RT-PCR as gold standard. RESULTS: Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of BNI were 69% (confidence interval [CI] [51–83]), 96% [94–97], 55% [39–70] and 98% [96–99] respectively. Of eleven false-negative samples, RT-PCR Ct-values were higher than all RT-PCR positive test results (27 vs 22, p = 0.012). Of twenty false-positive samples, none were culture positive and two tested positive in D-IF. Sensitivity, specificity, PPV and NPV for BNR were 79% [73–85], 98% [96–99], 97% [93–99] and 88% [84–91]. Of the 42 false-negative samples the median Ct-value was higher than that of all RT-PCR positive samples (31 vs 23, p < 0.0001). Five false-positive samples were detected. Three of these tested positive for RSV in virus isolation and D-IF. CONCLUSIONS: RADTs have a high specificity with BNR being superior to BNI. However, their relative low sensitivity limits their usefulness for clinical decision making in a tertiary care paediatric hospital. url: https://api.elsevier.com/content/article/pii/S1386653216300506 doi: 10.1016/j.jcv.2016.03.022 id: cord-029183-3aotgq6m author: Monard, Céline title: Multicenter evaluation of a syndromic rapid multiplex PCR test for early adaptation of antimicrobial therapy in adult patients with pneumonia date: 2020-07-14 words: 5858.0 sentences: 301.0 pages: flesch: 37.0 cache: ./cache/cord-029183-3aotgq6m.txt txt: ./txt/cord-029183-3aotgq6m.txt summary: We evaluated the relevance of a new syndromic rapid multiplex PCR test (rm-PCR) on respiratory samples to guide empirical antimicrobial therapy in adult patients with community-acquired pneumonia (CAP), hospital-acquired pneumonia (HAP), and ventilator-acquired pneumonia (VAP). CONCLUSIONS: Use of a syndromic rm-PCR test has the potential to reduce unnecessary antimicrobial exposure and increase the appropriateness of empirical antibiotic therapy in adult patients with pneumonia. Therefore, in pneumonia patients, international guidelines state that an attempt should be made to obtain respiratory samples and recommend to start early empirical treatment while awaiting for the results of culture and antimicrobial susceptibility testing (AST) [3] . The BioFire® FilmArray® Pneumonia Panel (bioMerieux S.A., Marcy-l''Etoile, France) is a novel assay able to simultaneously identify 27 of the most common pathogens involved in lower respiratory tract infections (semi-quantitative results for 11 Gram-negative and 4 Gram-positive bacteria, qualitative results for 3 atypical bacteria and 9 viruses) as well as 7 antibiotic resistance genes (Fig. 1) . abstract: BACKGROUND: Improving timeliness of pathogen identification is crucial to allow early adaptation of antibiotic therapy and improve prognosis in patients with pneumonia. We evaluated the relevance of a new syndromic rapid multiplex PCR test (rm-PCR) on respiratory samples to guide empirical antimicrobial therapy in adult patients with community-acquired pneumonia (CAP), hospital-acquired pneumonia (HAP), and ventilator-acquired pneumonia (VAP). METHODS: This retrospective multicenter study was conducted in four French university hospitals. Respiratory samples were obtained from patients with clinical and radiological signs of pneumonia and simultaneously tested using conventional microbiological methods and the rm-PCR. A committee composed of an intensivist, a microbiologist, and an infectious diseases specialist retrospectively assessed all medical files and agreed on the most appropriate antimicrobial therapy for each pneumonia episode, according to the results of rm-PCR and blinded to the culture results. The rm-PCR-guided antimicrobial regimen was compared to the empirical treatment routinely administered to the patient in standard care. RESULTS: We included 159 pneumonia episodes. Most patients were hospitalized in intensive care units (n = 129, 81%), and episodes were HAP (n = 68, 43%), CAP (n = 54, 34%), and VAP (n = 37, 23%). Conventional culture isolated ≥ 1 microorganism(s) at significant level in 95 (60%) patients. The syndromic rm-PCR detected at least one bacteria in 132 (83%) episodes. Based on the results of the rm-PCR, the multidisciplinary committee proposed a modification of the empirical therapy in 123 (77%) pneumonia episodes. The modification was a de-escalation in 63 (40%), an escalation in 35 (22%), and undetermined in 25 (16%) patients. In microbiologically documented episodes (n = 95), the rm-PCR increased appropriateness of the empirical therapy to 83 (87%), as compared to 73 (77%) in routine care. CONCLUSIONS: Use of a syndromic rm-PCR test has the potential to reduce unnecessary antimicrobial exposure and increase the appropriateness of empirical antibiotic therapy in adult patients with pneumonia. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7359443/ doi: 10.1186/s13054-020-03114-y id: cord-291749-revhbd0q author: Mongan, Arthur Elia title: Portable sequencer in the fight against infectious disease date: 2019-10-03 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Infectious disease is still a major threat in the world today. Five decades ago, it was considered soon to be eradicated, but the adaptation of pathogens to environmental pressure, such as antimicrobials, encouraged the emergence and reemergence of infectious disease. The fight with infectious disease starts with prevention, diagnosis, and treatment. Diagnosis can be upheld by observing the cause of disease under the microscope or detecting the presence of nucleic acid and proteins of the pathogens. The molecular techniques span from classical polymerase chain reaction (PCR) to sequencing the nucleic acid composition. Here, we are reviewing the works have been undertaken to utilize a portable sequencer, MinION, in various aspects of infectious disease management. url: https://www.ncbi.nlm.nih.gov/pubmed/31582773/ doi: 10.1038/s10038-019-0675-4 id: cord-274567-xd37wxxf author: Monpoeho, S. title: Application of a Real-Time Polymerase Chain Reaction with Internal Positive Control for Detection and Quantification of Enterovirus in Cerebrospinal Fluid date: 2002-07-13 words: 3284.0 sentences: 161.0 pages: flesch: 47.0 cache: ./cache/cord-274567-xd37wxxf.txt txt: ./txt/cord-274567-xd37wxxf.txt summary: title: Application of a Real-Time Polymerase Chain Reaction with Internal Positive Control for Detection and Quantification of Enterovirus in Cerebrospinal Fluid A quantitative real-time reverse transcriptase-polymerase chain reaction (RT-PCR) method based on TaqMan technology was developed to determine the presence and amount of enterovirus RNA. Amplification of the internal positive control was effective in all but two specimens, confirming the absence of PCR inhibitors and allowing the results of amplification to be validated. Detection of EVs by amplification of viral RNA from CSF using reverse transcriptase-polymerase chain reaction (RT-PCR) assay has already been reported [4, 5, 6 ]. The fluorogenic RT-PCR was applied to detection of EVs in the CSF of 104 patients presenting with signs of meningitis. Amplicor enterovirus polymerase chain reaction in patients with aseptic meningitis: a sensitive test limited by amplification inhibitors Comparison of use of cerebrospinal fluid, serum, and throat swab specimens in diagnosis of enteroviral acute neurological infection by a rapid RNA detection PCR assay abstract: A quantitative real-time reverse transcriptase-polymerase chain reaction (RT-PCR) method based on TaqMan technology was developed to determine the presence and amount of enterovirus RNA. In order to prevent false-negative results, a one-step multiplex RT-PCR was optimized. It contains two dual-labelled fluorogenic probes to quantify the 5′ noncoding region of enterovirus and detect an internal positive control. In the present study, 104 cerebrospinal fluid samples collected during an outbreak of enteroviral meningitis were analyzed using this method. Amplification of the internal positive control was effective in all but two specimens, confirming the absence of PCR inhibitors and allowing the results of amplification to be validated. The sensitivity of the RT-PCR was 96.8%, while that of cell culture was 34.9%. Genomic viral loads found ranged between 3.3 and 5.9 log(10) copies per milliliter of cerebrospinal fluid (mean, 4.8 log(10) copies/ml). This fluorogenic enterovirus RT-PCR allows large numbers of samples to be screened rapidly. Moreover, its sensitivity and reproducibility make it highly reliable. With these characteristics, the enterovirus RT-PCR can be a useful tool that may offer considerable benefit in the clinical management of patients with enteroviral infections. url: https://www.ncbi.nlm.nih.gov/pubmed/12172744/ doi: 10.1007/s10096-002-0766-5 id: cord-332333-vw5ogccq author: Montenegro-López, Diego title: Uso de tecnologías en el lugar de atención para el manejo de la pandemia por COVID-19 en Colombia date: 2020-08-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVE. To propose a health care model that integrates point-of-care technologies and artificial intelligence for the management of the COVID-19 pandemic. METHODS. A theoretical model was used in which one million people accessed the mobile application CoronApp-Colombia, which collects personal data, signs, symptoms and epidemiological links compatible with COVID-19. With the information from the app artificial intelligence techniques (data science) were applied in a virtual situation room. RESULTS. Users compatible with COVID-19 were prioritized and subjected to a rapid diagnostic test for anti-SARS-CoV-2 antibodies. Screening with the rapid diagnostic test would allow detection of sero-reactive individuals, for whom diagnostic confirmation would be carried out using molecular biology (PCR). Information from positive cases confirmed by PCR would be re-screened using artificial intelligence and spatial statistical techniques to identify geographical foci of infection. These foci could be actively searched for contacts with positive index cases and the diagnostic route would be followed again using the rapid diagnostic test and PCR. CONCLUSION. This model may be useful for countries in the region with weak or absent technological platforms for PCR diagnosis to maximize existing resources, estimate the epidemiological burden of COVID-19 (infection, morbidity, mortality and lethality) and implement containment, mitigation and control plans according to their needs. url: https://doi.org/10.26633/rpsp.2020.97 doi: 10.26633/rpsp.2020.97 id: cord-007068-vcfs41eb author: Moradi, Tony title: Use of Procalcitonin and a Respiratory Polymerase Chain Reaction Panel to Reduce Antibiotic Use via an Electronic Medical Record Alert date: 2019-10-22 words: 3669.0 sentences: 197.0 pages: flesch: 38.0 cache: ./cache/cord-007068-vcfs41eb.txt txt: ./txt/cord-007068-vcfs41eb.txt summary: We sought to determine whether an automated electronic medical record best practice alert (BPA) based on procalcitonin and respiratory polymerase chain reaction (PCR) results could help reduce inappropriate antibiotic use in patients with likely viral respiratory illness. In the study group, a BPA alerted providers of the diagnostic results suggesting viral infection and prompted them to reassess the need for antibiotics. CONCLUSIONS: The automated antimicrobial stewardship BPA effectively reduced antibiotic use and discharge prescribing rates when diagnostics suggested viral respiratory tract infection, without a higher rate for reinitiation of antibiotics after discontinuation. The aim of our study was to determine if antibiotic use could be reduced by deploying an automated antimicrobial stewardship provider alert that prompted antibiotic de-escalation if 3 criteria were met: PCT <0.25 ng/mL, virus detected on respiratory PCR, and active use of systemic antibiotics. abstract: BACKGROUND: Respiratory tract infections are often viral and but are frequently treated with antibiotics, providing a significant opportunity for antibiotic de-escalation in patients. We sought to determine whether an automated electronic medical record best practice alert (BPA) based on procalcitonin and respiratory polymerase chain reaction (PCR) results could help reduce inappropriate antibiotic use in patients with likely viral respiratory illness. METHODS: This multisite, pre–post, quasi-experimental study included patients 18 years and older with a procalcitonin level <0.25 ng/mL and a virus identified on respiratory PCR within 48 hours of each other, and 1 or more systemic antibiotics ordered. In the study group, a BPA alerted providers of the diagnostic results suggesting viral infection and prompted them to reassess the need for antibiotics. The primary outcome measured was total antibiotic-days of therapy. RESULTS: The BPA reduced inpatient antibiotic-days of therapy by a mean of 2.2 days compared with patients who met criteria but did not have the alert fire (8.0 vs 5.8 days, respectively, P < .001). The BPA also reduced the percentage of patients prescribed antibiotics on discharge (20% vs 47.8%, P < .001), whereas there was no difference in need for antibiotic escalation after initial discontinuation (7.6% vs 4.3%, P = .198). CONCLUSIONS: The automated antimicrobial stewardship BPA effectively reduced antibiotic use and discharge prescribing rates when diagnostics suggested viral respiratory tract infection, without a higher rate for reinitiation of antibiotics after discontinuation. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7108168/ doi: 10.1093/cid/ciz1042 id: cord-337636-3yc0ribg author: Morehouse, Zachary P. title: A novel two-step, direct-to-PCR method for virus detection off swabs using human coronavirus 229E date: 2020-08-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Currently, one of the most reliable methods for viral infection detection are polymerase chain reaction (PCR) based assays. This process is time and resource heavy, requiring multiple steps of lysis, extraction, purification, and amplification procedures. Herein, we have developed a method to detect virus off swabs using solely shaker-mill based mechanical lysis and the transfer of the viral lysate directly to a PCR assay for virus detection, bypassing the substantial reagent and time investments required for extraction and purification steps. METHODS: Using Human Coronavirus 229E (HCoV-229E) as a model system, we spiked swabs in vitro for proof-of-concept testing. Swabs were spiked in serial dilutions from 1.2 × 10(6) to 1.2 × 10(1) copies/mL and then placed in 2 mL tubes with viral transport media (VTM) to mimic the specimen collection procedures in the clinic prior to processing via shaker-mill homogenization. After homogenization, 1 μL of lysate was processed using RT-qPCR for amplification of the nucleocapsid (N) gene, qualifying viral detection. RESULTS: HCoV-229E in vitro spiked swabs were processed in a novel two-step, direct-to-PCR methodology for viral detection. After running 54 swabs, we confidently determined our limit of detection to be 1.2 × 10(3) viral copies/mL with 96.30% sensitivity. CONCLUSION: We have proven that the shaker-mill homogenization-based two-step, direct-to-PCR procedures provides sufficient viral lysis off swabs, where the resulting lysate can be used directly in PCR for the detection of HCoV-229E. This finding allows for reductions in the time and resources required for PCR based virus detection in comparison to the traditional extraction-to-PCR methodology. url: https://doi.org/10.1186/s12985-020-01405-y doi: 10.1186/s12985-020-01405-y id: cord-102411-0mo1198e author: Moreno Borraz, LA title: PREVALENCIA DE INFECCIÓN POR CORONAVIRUS SARS-CoV-2 EN PACIENTES Y PROFESIONALES DE UN HOSPITAL DE MEDIA Y LARGA ESTANCIA EN ESPAÑA date: 2020-11-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Antecedentes y Objetivo: El objetivo de este estudio fue conocer la prevalencia de la infección por SARS-CoV-2 en pacientes y profesionales de un hospital de media y larga estancia en el periodo del pico de la pandemia en España en la primavera de 2020. Material y Métodos: A finales de febrero de 2020, se diseñó en el hospital una estrategia para el diagnóstico de la infección por SARS-CoV-2 consistente en complementar la realización de PCR a tiempo real con una técnica rápida de inmunocromatografía de flujo lateral para la detección de anticuerpos IgG e IgM frente al virus. Se protocolizó la realización de dichas pruebas diagnósticas y se consideró como infección (actual o pasada) un resultado positivo de alguna de ellas. Se incluyeron en el estudio 524 participantes (230 pacientes y 294 profesionales). Los pacientes se agruparon en ingresados y en ambulatorios para terapia de hemodiálisis. Los trabajadores se agruparon en asistenciales y no asistenciales. El periodo de tiempo que se documenta, es el comprendido entre el 20 de marzo y el 21 de abril de 2020. Resultados: En 26 de los 230 pacientes el resultado fue positivo en alguna de las técnicas, con una prevalencia del 11,30%. Por grupos, en ingresados fue del 14,38% frente al 5,95% de los ambulatorios (p=0,055), siendo significativamente superior el riesgo en pacientes ingresados tras ajustar por sexo y edad (OR=3,309 (IC95%:1,154-9,495). En 24 de los 294 profesionales el resultado fue positivo en alguna de las técnicas, con una prevalencia del 8,16%. Por grupos, en asistenciales fue del 8,91% frente al 4,26% de los no asistenciales (p=0,391), OR ajustado=2,502 (IC95%: 0,559-11,202) Conclusiones: Se ha encontrado una tasa de prevalencia baja frente a SARS-CoV-2 tanto en pacientes como en profesionales. La prevalencia en pacientes hospitalizados es mayor que en ambulatorios, también es superior la prevalencia de sanitarios asistenciales respecto a los no asistenciales. Background and goals: The aim of the study is to know the prevalence of SARS-CoV-2 infection in patients and professional staff of a medium or long-stay hospital during the peak period of the pandemic in Spain, spring 2020. Equipment and methods: At the end of February 2020, we developed at the hospital a strategy to diagnose the SARS-CoV-2 infection consisting of complementing the realization of PCR tests at real time with a quick technique of lateral flow immunochromatography to detect IgG and IgM antibodies against the virus. We also developed a protocol to realize those diagnostic tests and considered an infection (current or past) a positive result in any of the above tests. We included 524 participants in the study (230 patients and 294 hospital staff), and divided them into hospital patients and Hemodialysis outpatients. Furthermore, we divided the hospital staff into healthcare and non-healthcare staff. The documented period was from March, 20th to April, 21st, 2020. Results: 26 out of 230 patients tested positive in any of the diagnostic techniques (PCR, antibodies IgG, IgM) with a 11.30% prevalence. According to patients groups, we got a 14.38% prevalence in hospital patients vs. 5.95% in outpatients, with a significantly higher risk in admitted patients after adjustment for age and gender (OR=3,309 (IC95%:1,154-9,495). 24 out of 294 hospital staff tested positive in any of the diagnostic techniques, with a 8.16% prevalence. According to the groups, we got a 8.91% prevalence in healthcare staff vs. 4.26% in non-healthcare staff. Thus, we do not see any statistically significant differences between hospital staff and patients as far as prevalence is concerned (p=0,391), (OR=2,200 IC95 %: 0,500-9,689). Conclusions: The result of the study was a quite low prevalence rate of SARS-CoV-2 infection, in both patients and hospital staff, being the hospital patients’ prevalence rate higher than the outpatients’, and the healthcare staff higher than the non-healthcare’s. Combining PCR tests (gold standard) with antibodies tests proved useful as a diagnostic strategy. url: https://api.elsevier.com/content/article/pii/S0211139X20301803 doi: 10.1016/j.regg.2020.10.005 id: cord-002560-pue5q5wp author: Moreno, Paloma S. title: Characterisation of the canine faecal virome in healthy dogs and dogs with acute diarrhoea using shotgun metagenomics date: 2017-06-01 words: 5137.0 sentences: 265.0 pages: flesch: 50.0 cache: ./cache/cord-002560-pue5q5wp.txt txt: ./txt/cord-002560-pue5q5wp.txt summary: Recently, due to the advent of molecular enrichment protocols, high throughput sequencing and new metagenomic analytical methods we are now able to explore, identify and characterise viruses from different biological and environmental samples with a greater capacity [2, [5] [6] [7] [8] [9] [10] [11] In studies of human faeces, the virome has been shown to include viruses that infect eukaryotic organisms and viruses that infect prokaryotes (bacteriophages) [2, 5, [12] [13] [14] [15] [16] [17] [18] . Another eukaryotic viral family found in one healthy dog sample was Parvoviridae, genetic analysis of the 3 contigs/singletons showed a coverage of approximately 3.5% of the complete genome of canine parvovirus reference sequence (NC_001539), or 9.3% of the polyprotetin Ns1-Ns2. Nucleic acids from a single faecal sample from a dog with acute diarrhoea (DD1), which had 18 contigs/singletons of canine astrovirus (after tBLASTx analysis) was used to determine the complete genome sequence. abstract: The virome has been increasingly investigated in numerous animal species and in different sites of the body, facilitating the identification and discovery of a variety of viruses. In spite of this, the faecal virome of healthy dogs has not been investigated. In this study we describe the faecal virome of healthy dogs and dogs with acute diarrhoea in Australia, using a shotgun metagenomic approach. Viral sequences from a range of different virus families, including both RNA and DNA families, and known pathogens implicated in enteric disease were documented. Twelve viral families were identified, of which four were bacteriophages. Eight eukaryotic viral families were detected: Astroviridae, Coronaviridae, Reoviridae, Picornaviridae, Caliciviridae, Parvoviridae, Adenoviridae and Papillomaviridae. Families Astroviridae, Picornaviridae and Caliciviridae were found only in dogs with acute diarrhoea, with Astroviridae being the most common family identified in this group. Due to its prevalence, characterisation the complete genome of a canine astrovirus was performed. These studies indicate that metagenomic analyses are useful for the investigation of viral populations in the faeces of dogs. Further studies to elucidate the epidemiological and biological relevance of these findings are warranted. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5453527/ doi: 10.1371/journal.pone.0178433 id: cord-274656-dngumjns author: Mori, Masahiro title: Detection of mumps virus RNA in cerebrospinal fluid of patients with neuromyelitis optica date: 2011-04-06 words: 1985.0 sentences: 112.0 pages: flesch: 49.0 cache: ./cache/cord-274656-dngumjns.txt txt: ./txt/cord-274656-dngumjns.txt summary: To investigate the relationship between NMO and viruses that have special affinity for the central nervous system, we performed a nested polymerase chain reaction (PCR) to detect mumps virus or enterovirus RNA in cerebrospinal fluid samples from 13 patients with MS, 8 with NMO and 20 with other neurological diseases (ONDs). The aim of this study was to investigate using nested polymerase chain reaction (PCR) the relationship between NMO and the two causative agents of polio-like disease, mumps virus [9] and enteroviruses, which have specific affinity for the central nervous system. PCR tests for detection of the mumps virus and the enterovirus genomes CSF samples were tested for the presence of the mumps virus and enterovirus genomes by a nested PCR method (PCR-FMU), as described elsewhere [13, 14] , blindly with respect to clinical information and the results of NMO-IgG or anti-aquaporin-4 antibody assays. abstract: Neuromyelitis optica (NMO) is an acute inflammatory disease that preferentially involves the optic nerves and spinal cord. Although many infectious agents, including mumps virus, are postulated to have a role in the pathogenesis of multiple sclerosis (MS), the relationship between NMO and infectious agents remains uncertain. To investigate the relationship between NMO and viruses that have special affinity for the central nervous system, we performed a nested polymerase chain reaction (PCR) to detect mumps virus or enterovirus RNA in cerebrospinal fluid samples from 13 patients with MS, 8 with NMO and 20 with other neurological diseases (ONDs). Nested PCR was positive for mumps virus in 2 (25%) of NMO patients, but in none of those with MS and ONDs. Moreover, nested PCR results became negative in the remission phase in the two PCR-positive NMO patients. Mumps virus may have some role in the pathogenesis of NMO. url: https://doi.org/10.1007/s10072-011-0564-x doi: 10.1007/s10072-011-0564-x id: cord-325137-6c6er06a author: Moser, Lindsey A. title: A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses date: 2016-06-07 words: 9945.0 sentences: 514.0 pages: flesch: 53.0 cache: ./cache/cord-325137-6c6er06a.txt txt: ./txt/cord-325137-6c6er06a.txt summary: Our data demonstrate that this approach provides full-length genomic sequence information not only from high-titer virion preparations but it can also recover specific viral sequence from samples with limited starting material in the background of cellular RNA, and it can be used to identify pathogens from unknown samples. NGS data from this SOP can provide complete genome coverage from viral stocks and can also detect virus-specific reads from limited starting material. Thus, in some instances, large cDNAs, double-stranded DNAs (dsDNAs), or clones containing at least two-thirds of the genome may also be regulated as SAs. Positive-sense RNA viruses span multiple virus families, and the infectious nature of these genomic RNAs coupled with SA/biosafety/biosecurity concerns inhibit rapid removal from BSL-3/4 containment (7) or transport and handling of RNA samples that are known to contain viral genomes from outbreak settings. abstract: Several biosafety level 3 and/or 4 (BSL-3/4) pathogens are high-consequence, single-stranded RNA viruses, and their genomes, when introduced into permissive cells, are infectious. Moreover, many of these viruses are select agents (SAs), and their genomes are also considered SAs. For this reason, cDNAs and/or their derivatives must be tested to ensure the absence of infectious virus and/or viral RNA before transfer out of the BSL-3/4 and/or SA laboratory. This tremendously limits the capacity to conduct viral genomic research, particularly the application of next-generation sequencing (NGS). Here, we present a sequence-independent method to rapidly amplify viral genomic RNA while simultaneously abolishing both viral and genomic RNA infectivity across multiple single-stranded positive-sense RNA (ssRNA+) virus families. The process generates barcoded DNA amplicons that range in length from 300 to 1,000 bp, which cannot be used to rescue a virus and are stable to transport at room temperature. Our barcoding approach allows for up to 288 barcoded samples to be pooled into a single library and run across various NGS platforms without potential reconstitution of the viral genome. Our data demonstrate that this approach provides full-length genomic sequence information not only from high-titer virion preparations but it can also recover specific viral sequence from samples with limited starting material in the background of cellular RNA, and it can be used to identify pathogens from unknown samples. In summary, we describe a rapid, universal standard operating procedure that generates high-quality NGS libraries free of infectious virus and infectious viral RNA. IMPORTANCE This report establishes and validates a standard operating procedure (SOP) for select agents (SAs) and other biosafety level 3 and/or 4 (BSL-3/4) RNA viruses to rapidly generate noninfectious, barcoded cDNA amenable for next-generation sequencing (NGS). This eliminates the burden of testing all processed samples derived from high-consequence pathogens prior to transfer from high-containment laboratories to lower-containment facilities for sequencing. Our established protocol can be scaled up for high-throughput sequencing of hundreds of samples simultaneously, which can dramatically reduce the cost and effort required for NGS library construction. NGS data from this SOP can provide complete genome coverage from viral stocks and can also detect virus-specific reads from limited starting material. Our data suggest that the procedure can be implemented and easily validated by institutional biosafety committees across research laboratories. url: https://www.ncbi.nlm.nih.gov/pubmed/27822536/ doi: 10.1128/msystems.00039-15 id: cord-328633-c31xsyeo author: Moser, Michael J. title: Thermostable DNA Polymerase from a Viral Metagenome Is a Potent RT-PCR Enzyme date: 2012-06-04 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Viral metagenomic libraries are a promising but previously untapped source of new reagent enzymes. Deep sequencing and functional screening of viral metagenomic DNA from a near-boiling thermal pool identified clones expressing thermostable DNA polymerase (Pol) activity. Among these, 3173 Pol demonstrated both high thermostability and innate reverse transcriptase (RT) activity. We describe the biochemistry of 3173 Pol and report its use in single-enzyme reverse transcription PCR (RT-PCR). Wild-type 3173 Pol contains a proofreading 3′-5′ exonuclease domain that confers high fidelity in PCR. An easier-to-use exonuclease-deficient derivative was incorporated into a PyroScript RT-PCR master mix and compared to one-enzyme (Tth) and two-enzyme (MMLV RT/Taq) RT-PCR systems for quantitative detection of MS2 RNA, influenza A RNA, and mRNA targets. Specificity and sensitivity of 3173 Pol-based RT-PCR were higher than Tth Pol and comparable to three common two-enzyme systems. The performance and simplified set-up make this enzyme a potential alternative for research and molecular diagnostics. url: https://doi.org/10.1371/journal.pone.0038371 doi: 10.1371/journal.pone.0038371 id: cord-002852-m4l2l2r1 author: Munyua, Peninah M. title: Detection of influenza A virus in live bird markets in Kenya, 2009–2011 date: 2012-04-19 words: 3991.0 sentences: 240.0 pages: flesch: 60.0 cache: ./cache/cord-002852-m4l2l2r1.txt txt: ./txt/cord-002852-m4l2l2r1.txt summary: authors: Munyua, Peninah M.; Githinji, Jane W.; Waiboci, Lilian W.; Njagi, Leonard M.; Arunga, Geoffrey; Mwasi, Lydia; Murithi Mbabu, R.; Macharia, Joseph M.; Breiman, Robert F.; Kariuki Njenga, M.; Katz, Mark A. Background Surveillance for influenza viruses within live bird markets (LBMs) has been recognized as an effective tool for detecting circulating avian influenza viruses (AIVs). Efforts should be made to promote practices that could limit the maintenance and transmission of AIVs in LBMs. Influenza A viruses are zoonotic pathogens that infect a variety of domestic poultry such as chickens, turkeys, ducks, and geese. 2, 4, 5 Surveillance for influenza viruses within live bird markets (LBMs) has been recognized as an effective tool for detecting circulating influenza subtypes in the poultry population. 7, 8 Influenza viruses have also been detected in various environmental specimens collected in contaminated areas in LBMs including drinking water troughs, and surfaces in the delivery, holding and slaughter areas in markets. abstract: Please cite this paper as: Munyua et al. (2013) Detection of influenza A virus in live bird markets in Kenya, 2009–2011. Influenza and Other Respiratory Viruses 7(2), 113–119. Background Surveillance for influenza viruses within live bird markets (LBMs) has been recognized as an effective tool for detecting circulating avian influenza viruses (AIVs). In Sub‐Saharan Africa, limited data exist on AIVs in animal hosts, and in Kenya the presence of influenza virus in animal hosts has not been described. Objectives This surveillance project aimed to detect influenza A virus in poultry traded in five LBMs in Kenya. Methods We visited each market monthly and collected oropharyngeal and cloacal specimens from poultry and environmental specimens for virological testing for influenza A by real time RT‐PCR. On each visit, we collected information on the number and types of birds in each market, health status of the birds, and market practices. Results During March 24, 2009–February 28, 2011, we collected 5221 cloacal and oropharyngeal swabs. Of the 5199 (99·6%) specimens tested, influenza A virus was detected in 42 (0·8%), including 35/4166 (0·8%) specimens from chickens, 3/381 (0·8%) from turkeys, and 4/335 (1·2%) from geese. None of the 317 duck specimens were positive. Influenza was more commonly detected in oropharyngeal [33 (1·3%)] than in cloacal [9 (0·4%)] specimens. None of the 485 environmental specimens were positive. Virus was detected in all five markets during most (14/22) of the months. Ducks and geese were kept longer at the market (median 30 days) than chickens (median 2 days). Conclusions Influenza A was detected in a small percentage of poultry traded in LBMs in Kenya. Efforts should be made to promote practices that could limit the maintenance and transmission of AIVs in LBMs. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5780755/ doi: 10.1111/j.1750-2659.2012.00365.x id: cord-345211-4ivqlsgt author: Murdoch, David R. title: How recent advances in molecular tests could impact the diagnosis of pneumonia date: 2016-03-07 words: 5994.0 sentences: 295.0 pages: flesch: 35.0 cache: ./cache/cord-345211-4ivqlsgt.txt txt: ./txt/cord-345211-4ivqlsgt.txt summary: Guidelines for the management of community-acquired pneumonia in children are even more restrictive, again recommending that tests should mainly be used on patients with severe disease, with a focus on blood cultures and detection of respiratory viruses [11, 12] . While not exactly new (polymerase chain reaction (PCR) assays for respiratory pathogens have been around for over 20 years), the widespread adoption of nucleic acid detection tests (NATs) by diagnostic laboratories has been relatively slow. The NATs that are most widely used in diagnostic laboratories are those that detect potential pneumonia pathogens that are not part of the normal flora, namely respiratory viruses and selected non-colonizing bacteria. Quantitative multiplex PCR has been used to determine the etiology of community-acquired pneumonia in adults using cutoffs developed for interpretation of culture results from lower respiratory tract specimens [85, 86] . abstract: Molecular diagnostic tests have been the single major development in pneumonia diagnostics over recent years. Nucleic acid detection tests (NATs) have greatly improved the ability to detect respiratory viruses and bacterial pathogens that do not normally colonize the respiratory tract. In contrast, NATs do not yet have an established role for diagnosing pneumonia caused by bacteria that commonly colonize the nasopharynx due to difficulties discriminating between pathogens and coincidental carriage strains. New approaches are needed to distinguish infection from colonization, such as through use of quantitative methods and identification of discriminating cut-off levels. The recent realization that the lung microbiome exists has provided new insights into the pathogenesis of pneumonia involving the interaction between multiple microorganisms. New developments in molecular diagnostics must account for this new paradigm. url: https://www.ncbi.nlm.nih.gov/pubmed/26891612/ doi: 10.1586/14737159.2016.1156536 id: cord-268233-ibxufjrv author: Nagappa, Bharathnag title: Seroconversion rate and diagnostic accuracy of serological tests for COVID-19 date: 2020-05-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://doi.org/10.1093/cid/ciaa676 doi: 10.1093/cid/ciaa676 id: cord-274568-flqc3jjd author: Naguib, Michael title: The use of radiological imaging alongside reverse transcriptase PCR in diagnosing novel coronavirus disease 2019: a narrative review date: 2020-07-08 words: 2821.0 sentences: 148.0 pages: flesch: 49.0 cache: ./cache/cord-274568-flqc3jjd.txt txt: ./txt/cord-274568-flqc3jjd.txt summary: Many studies have reported high sensitivities of CT scans and suggested that they can be used in the diagnosis of COVID-19 alongside reverse transcriptase PCR. In this report, we will discuss the clinical relevance of each test and the current Centers for Disease Control and Prevention and American College of Radiology recommendations regarding the use of imaging in the diagnosis of COVID-19. Sensitivity of CT scans • Many studies have reported high sensitivity of CT scans and suggested its valuable use in aiding the diagnosis of novel coronavirus disease 2019 (COVID-19) alongside reverse transcriptase PCR. • Centers for Disease Control & Prevention and the American College of Radiology recommend against the use of CT as well as CXR for diagnosis and that reverse transcriptase PCR is the reference test for diagnosing of COVID-19. Discusses the importance of background chest computed tomography (CT) being used for diagnosis of novel coronavirus disease 2019 (COVID-19) alongside reverse transcriptase PCR. abstract: The diagnosis of novel coronavirus disease 2019 (COVID-19) has been a challenge in many countries due to nonspecific symptoms and variable incubation period. The current reference test is reverse transcriptase PCR. Many studies have reported high sensitivities of CT scans and suggested that they can be used in the diagnosis of COVID-19 alongside reverse transcriptase PCR. The current data about CT scans are highly variable and incoherent. Therefore, new multicentric studies in different countries are needed to better understand the role of CT scans in COVID-19 diagnosis. In this report, we will discuss the clinical relevance of each test and the current Centers for Disease Control and Prevention and American College of Radiology recommendations regarding the use of imaging in the diagnosis of COVID-19. url: https://doi.org/10.2217/fmb-2020-0098 doi: 10.2217/fmb-2020-0098 id: cord-318991-tw7wgpsi author: Nair, A. title: A British Society of Thoracic Imaging statement: considerations in designing local imaging diagnostic algorithms for the COVID-19 pandemic date: 2020-05-31 words: 2949.0 sentences: 134.0 pages: flesch: 46.0 cache: ./cache/cord-318991-tw7wgpsi.txt txt: ./txt/cord-318991-tw7wgpsi.txt summary: In accordance with guidance from the Chief Medical Officer''s office and the Royal College of Radiologists, the British Society of Thoracic Imaging (BSTI) recognises that based on the available evidence computed tomography (CT) currently has no upfront role in the diagnostic work-up of 2019 novel coronavirus (COVID-19) infection (https://www. 2 As such, in the minority of patients with high clinical suspicion but negative initial RT-PCR, the presence of typical CT appearances, such as peripheral ground-glass opacity, could be used to rapidly diagnose COVID-19 infection, until such time as multiple negative testing is sufficient to exclude or change the diagnosis. Therefore, we regard the role of CT in COVID-19 confirmed cases following RT-PCR results to be the same as in any other viral infection, in that it could be used to: (1) find co-existing or underlying diagnoses; (2) help diagnose complications, or investigate a clinically discordant picture (e.g., CRP decline, but increasing hypoxia); and (3) add value in patients with pre-existing lung diseases. abstract: nan url: https://api.elsevier.com/content/article/pii/S0009926020300969 doi: 10.1016/j.crad.2020.03.008 id: cord-263426-l32gyiky author: Najafi, Hamideh title: Molecular and clinical study on prevalence of feline herpesvirus type 1 and calicivirus in correlation with feline leukemia and immunodeficiency viruses date: 2014 words: 3437.0 sentences: 200.0 pages: flesch: 59.0 cache: ./cache/cord-263426-l32gyiky.txt txt: ./txt/cord-263426-l32gyiky.txt summary: In clinically normal cats, prevalence rates of FCV and FHV were about 50.00%, but FIV and FeLV rates (42.00% and 65.00% respectively) were higher compared to other studies. Feline herpesvirus1 (FHV-1), a double-stranded DNA virus, member of the Varicellovirus, genus of the subfamily Alphaherpesvirinae combine with, feline calicivirus (FCV) that is a single-stranded positive-sense RNA virus, in the family Caliciviridae, genus Vesivirus are considered as the main agents involved in upper respiratory tract diseases (URTD) in cats. 1 However, it is important to determine the prevalence of FHV-1 and FCV and evaluation of their clinical signs, especially in relation with FIV and FeLV, to identify agents involved in URTD in Iran. For better understanding the role of FIV and FeLV viruses in induction of FCV and FHV infections, the prevalence rates of these infections were investigated in healthy and diseased cats. Association between clinical signs in cats with URTD and infection with FIV, FeLV, FCV, FHV-1. abstract: Upper respiratory tract diseases (URTD) are common clinical problem in cats worldwide. Feline calicivirus (FCV) and feline herpesvirus type 1 (FHV-1) are the main primary pathogens. Feline immunodeficiency virus (FIV) and Feline leukemia virus (FeLV) are also among the most common infectious diseases of cats which suppress the immunity. Oropharyngeal and conjunctival swabs and blood samples were taken from 16 cats with clinical signs of URTD and 26 clinically healthy cats. PCR and RT-PCR were used to detect FHV/FIV or FCV/FeLV infections, respectively. Feline calicivirus was detected in all cats with URTD and 87.00% and 93.00% of them were positive for FIV and FeLV, respectively. Feline herpesvirus rate of infection was 43.00% in sick cats. In clinically normal cats, prevalence rates of FCV and FHV were about 50.00%, but FIV and FeLV rates (42.00% and 65.00% respectively) were higher compared to other studies. Stomatitis was observed in 50.00% of cats with URTD. The main causative agent of corneal ulcers is FHV-1, but in 50.00% of cats with corneal ulcers, FCV was detected alone. It seems new variants of Caliciviruses are the main causative agents to attack uncommon tissues like cornea, although retroviral infections may be in the background of these various signs. The high retroviral prevalence may be due to existence of large population of stray cats. This is the first molecular study of FeLV and FCV in Iran and seems that FCV and FHV prevalence rates in FIV or FeLV infected cats is more than other non-infected ones. url: https://www.ncbi.nlm.nih.gov/pubmed/25610576/ doi: nan id: cord-331413-fejho1of author: Nakayama, Eiichi title: Rapid optimization of antimicrobial chemotherapy given to pediatric patients with community-acquired pneumonia using PCR techniques with serology and standard culture date: 2007-12-31 words: 3955.0 sentences: 198.0 pages: flesch: 44.0 cache: ./cache/cord-331413-fejho1of.txt txt: ./txt/cord-331413-fejho1of.txt summary: title: Rapid optimization of antimicrobial chemotherapy given to pediatric patients with community-acquired pneumonia using PCR techniques with serology and standard culture Abstract Children (n =117; mean age 2.4 ± 2.9 years) were diagnosed as having community-acquired pneumonia (CAP) using clinical symptoms, chest X-rays, and hematological data. The causative pathogen was determined using real-time polymerase chain reaction (PCR) (6 bacteria), multiple reverse transcription-PCR (MPCR; 11 viruses), bacterial culture, and serology. [7] [8] [9] In Japan, antimicrobial chemotherapy for patients with CAP is begun empirically based on (1) chest X-rays, (2) clinical fi ndings including respiratory status, (3) age, and (4) laboratory tests such as white blood cell count (WBC) and C-reactive protein concentration (CRP). The bacteria suspected to be the causative pathogens was determined by standard culture and real-time PCR for six pathogens: Streptococcus pneumoniae, Haemophilus infl uenzae, Mycoplasma pneumoniae, Chlamydophila pneumoniae, Streptococcus pyogenes, and Legionella pneumophila (Table 3) In the patients suspected of having an infection caused by S. abstract: Abstract Children (n =117; mean age 2.4 ± 2.9 years) were diagnosed as having community-acquired pneumonia (CAP) using clinical symptoms, chest X-rays, and hematological data. The causative pathogen was determined using real-time polymerase chain reaction (PCR) (6 bacteria), multiple reverse transcription-PCR (MPCR; 11 viruses), bacterial culture, and serology. The initial chemotherapy was evaluated based on the pathogens identified using PCR. We found 27 viral cases (23.1%), 25 bacterial cases (21.4%), 45 mixed infections with virus and bacteria (38.5%), 10 Mycoplasma pneumoniae (8.5%), 7 mixed infections with M. pneumoniae and another pathogen (6.0%), 1 Chlamydophila pneumoniae (0.9%), and 2 unknown pathogens (1.7%). Streptococcus pneumoniae and Haemophilus influenzae accounted for 58 (49.5%) and 27 (23.0%) of the cases, respectively. The median values (50%) of the white blood cell count (WBC) and C-reactive protein (CRP) using the box-and-whisker and plot method, respectively, were 11.7 × 103 mm−3 and 1.4mg/dl in viral infections, 15.6 × 103 mm−3 and 4.8mg/dl in mixed infections with virus and bacteria, 17.8 × 103 mm−3 and 6.3mg/dl in bacterial infections, 6.7 × 103 mm−3 and 1.4mg/dl in M. pneumoniae infections, and 21.5 × 103 mm−3 and 6.4mg/dl in mixed infections with M. pneumoniae and other bacterial infections. Sulbactam/ampicillin (n =61), carbapenems (n =12), and ceftriaxone (n =7) were selected for the patients suspected of having bacterial infections alone or mixed infections with bacterial and viruses in accordance with our criteria defined tentatively. For those with M. pneumoniae and C. pneumoniae infections, azithromycin or minocycline was initially used. Treatments averaged 3–5 days. The empirical chemotherapy was improper in 9.4% of cases in relation to the etiologic agents finally identified. We conclude that rapid and comprehensive identification using PCR can provide optimal antimicrobial chemotherapy for CAP patients. url: https://www.sciencedirect.com/science/article/pii/S1341321X07708309 doi: 10.1007/s10156-007-0535-6 id: cord-276718-3lujp0oy author: Neeraja, M. title: Rapid detection and differentiation of dengue virus serotypes by NS1 specific reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay in patients presenting to a tertiary care hospital in Hyderabad, India date: 2014-10-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Early and rapid detection of dengue virus (DENV) infection during the acute phase of illness is crucial for proper patient management and prevention of the spread of the infection. In the present study, the standardization and validation of a one step, four tube reverse transcription loop-mediated isothermal amplification assay (RT-LAMP) for rapid detection and serotyping of the DENV targeting NS1 gene using the Genie® II flourometer was carried out. The performance of the RT-LAMP was compared to RT-PCR, CDC 1-4 Real time PCR and the NS1 antigen ELISA, IgM and IgG anti DENV antibodies. Acute DENV infection was confirmed in 250/300 patients suspected clinically of DENV infection. RT- LAMP and CDC 1-4 Real time PCR assay was positive in 148/250 patients, while 92/250 patients were positive for anti- Dengue IgM and IgG antibodies. The RT-LAMP assay and the CDC real-time RT-PCR assay showed high concordance (k = 1.0). The detection rate of acute DENV infection improved to 96% (240/250) when the results of RT-LAMP were combined with NS1 Ag, IgM and IgG ELISA. The RT-LAMP had a detection limit of 100 copies for DEN-1 and DEN-2, 10 copies for DEN-3 and DEN-4 compared to 1000 copies for DEN-1 and DEN-2, 100 copies for DEN-3 and DEN-4 by the conventional RT-PCR. The assay showed 100% specificity. The RT-LAMP assay developed in this study has potential use for early clinical diagnosis, serotyping and surveillance of DENV infection in endemic countries such as India. url: https://www.ncbi.nlm.nih.gov/pubmed/25455901/ doi: 10.1016/j.jviromet.2014.10.005 id: cord-297396-r1p7xn3a author: Ng, Ming-Yen title: Development and Validation of Risk Prediction Models for COVID-19 Positivity in a Hospital Setting date: 2020-09-15 words: 3251.0 sentences: 182.0 pages: flesch: 53.0 cache: ./cache/cord-297396-r1p7xn3a.txt txt: ./txt/cord-297396-r1p7xn3a.txt summary: OBJECTIVES: To develop:(1) two validated risk prediction models for COVID-19 positivity using readily available parameters in a general hospital setting; (2) nomograms and probabilities to allow clinical utilisation.  Developed two simple-to use nomograms for identifying COVID-19 positive patients  Probabilities are provided to allow healthcare leaders to decide suitable cut-offs  Variables are age, white cell count, chest x-ray appearances and contact history  Model variables are easily available in the general hospital setting. To develop: (1) two validated risk prediction models for COVID-19 positivity using readily available parameters in a general hospital setting; (2) nomograms and probabilities to allow clinical utilisation. Thus, a COVID-19 prediction model based on clinical, laboratory and radiological findings which presents the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) would allow public healthcare systems to decide a suitable strategy on prioritizing tests when such RT-PCR availability is constrained. abstract: OBJECTIVES: To develop:(1) two validated risk prediction models for COVID-19 positivity using readily available parameters in a general hospital setting; (2) nomograms and probabilities to allow clinical utilisation. METHODS: Patients with and without COVID-19 were included from 4 Hong Kong hospitals. Database was randomly split 2:1 for model development database (n = 895) and validation database (n = 435). Multivariable logistic regression was utilised for model creation and validated with the Hosmer-Lemeshow (H-L) test and calibration plot. Nomograms and probabilities set at 0.1, 0.2, 0.4, 0.6 were calculated to determine sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV). RESULTS: 1330 patients (mean age 58.2 ± 24.5 years; 50.7% males; 296 COVID-19 positive) were recruited. First prediction model developed had age, total white blood cell count, chest x-ray appearances and contact history as significant predictors (AUC = 0.911 [CI = 0.880-0.941]). Second model developed has same variables except contact history (AUC = 0.880 [CI = 0.844-0.916]). Both were externally validated on H-L test (p = 0.781 and 0.155 respectively) and calibration plot. Models were converted to nomograms. Lower probabilities give higher sensitivity and NPV; higher probabilities give higher specificity and PPV. CONCLUSION: Two simple-to-use validated nomograms were developed with excellent AUCs based on readily available parameters and can be considered for clinical utilisation. url: https://api.elsevier.com/content/article/pii/S1201971220307384 doi: 10.1016/j.ijid.2020.09.022 id: cord-353190-7qcoxl81 author: Nicklas, Werner title: Viral Infections of Laboratory Mice date: 2012-05-17 words: 27775.0 sentences: 1482.0 pages: flesch: 39.0 cache: ./cache/cord-353190-7qcoxl81.txt txt: ./txt/cord-353190-7qcoxl81.txt summary: This chapter covers infections of mice with the following viruses: herpesviruses, mousepox virus, murine adenoviruses, polyomaviruses, parvoviruses, lactate dehydrogenase-elevating virus, lymphocytic choriomeningitis virus, mammalian orthoreovirus serotype 3, murine hepatitis virus, murine norovirus, murine pneumonia virus, murine rotavirus, Sendai virus, and Theiler''s murine encephalomyelitis virus. These results are very difficult to summarize because the outcome of experimental infection in laboratory mice depends on various factors such as mouse strain and age, virus strain and passage history [26] , virus dose and route of inoculation [24] . Experimental infection of laboratory mice with MHV-68 is a frequently used model system for the study of human gammaherpesvirus pathogenesis, e.g. of Kaposi''s sarcoma-associated herpesvirus or Epstein-Barr virus (EBV) [62, 63] which are members of the same subfamily. Early descriptions of naturally occurring disease may have been complicated by concurrent infections such as MHV (murine hepatitis virus) or murine rotavirus A (MuRV-A)/epizootic diarrhoea of infant mice (EDIM) virus that contributed to the severity of the lesions especially in liver, pancreas, CNS and intestine. abstract: Viral infections of laboratory mice have considerable impact on research results, and prevention of such infections is therefore of crucial importance. This chapter covers infections of mice with the following viruses: herpesviruses, mousepox virus, murine adenoviruses, polyomaviruses, parvoviruses, lactate dehydrogenase-elevating virus, lymphocytic choriomeningitis virus, mammalian orthoreovirus serotype 3, murine hepatitis virus, murine norovirus, murine pneumonia virus, murine rotavirus, Sendai virus, and Theiler’s murine encephalomyelitis virus. For each virus, there is a description of the agent, epizootiology, clinical symptoms, pathology, methods of diagnosis and control, and its impact on research. url: https://api.elsevier.com/content/article/pii/B9780123820082000192 doi: 10.1016/b978-0-12-382008-2.00019-2 id: cord-261329-k1p7fo0e author: Nidzworski, Dawid title: Detection and differentiation of virulent and avirulent strains of Newcastle disease virus by real-time PCR date: 2010-12-28 words: 3156.0 sentences: 199.0 pages: flesch: 58.0 cache: ./cache/cord-261329-k1p7fo0e.txt txt: ./txt/cord-261329-k1p7fo0e.txt summary: A rapid diagnostic method based on the melting curve SYBR Green I real-time PCR analysis was developed to detect and differentiate Newcastle disease virus (NDV) strains. The results obtained in this study demonstrate the possible applications for melting curve real-time PCR analysis in laboratory practice for the diagnosis and differentiation of avirulent and virulent strains of Newcastle disease virus. (2005) described a SYBR Green I real-time PCR melting curve analysis assay for differentiation, although the differences in the Tm values between the three genotypes were not very significant and could cause false characterization of the virus. Using the SYBR Green I real-time PCR melting peak analysis, it was possible to detect and differentiate virulent and avirulent strains of Newcastle disease virus. In this study, a method for the rapid detection and differentiation of Newcastle disease virus by SYBR Green I melting-curve analysis was described. abstract: A rapid diagnostic method based on the melting curve SYBR Green I real-time PCR analysis was developed to detect and differentiate Newcastle disease virus (NDV) strains. Degenerated primers based on the cleavage site sequence of the F0 gene were designed to detect specific sequences characteristic of virulent and avirulent strains of NDV. Eighteen strains of NDV from four lineages were identified and grouped into virulent and avirulent strains. Peaks on the melting temperature graph with melting temperature values between 80.00 and 83.80 °C were observed for lentogenic (avirulent) strains. T(m) values higher than 83.80 were observed for virulent (mesogenic and velogenic) strains. The detection limit of real-time PCR was 2 × 10(2) plasmid copies per reaction or 10(2) EID(50) for velogenic strains and 10(3) EID(50) for lentogenic strains. The results obtained in this study demonstrate the possible applications for melting curve real-time PCR analysis in laboratory practice for the diagnosis and differentiation of avirulent and virulent strains of Newcastle disease virus. url: https://doi.org/10.1016/j.jviromet.2010.12.015 doi: 10.1016/j.jviromet.2010.12.015 id: cord-328534-66c2tg5r author: Nidzworski, Dawid title: Detection of avian influenza virus and newcastle disease virus by duplex one step RT PCR date: 2013-03-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Newcastle disease Virus (NDV), a member of the Paramyxoviridae family, and Influenza virus, from the Orthomyxoviridae family, are two main avian pathogens that cause serious economic problems in poultry farming. NDV strains are classified into three major pathotypes: velogenic, mesogenic, and lentogenic. Avian influenza viruses (AIV) are also divided into: low pathogenic (LPAI) and highly pathogenic (HPAI) strains. Both viruses are enveloped, single stranded, negative-sense RNA viruses which give similar symptoms ranging from sub-clinical infections to severe disease, including loss in egg production, acute respiratory syndrome, and high mortality, depending on their level of pathogenicity. This similarity hinders diagnosis when based solely on clinical and post mortem examination. Most of the currently available molecular detection methods are also pathogenspecific, so that more than one RT-PCR is then required to confirm or exclude the presence of both pathogens. To overcome this disadvantage, we have applied a One Step Duplex RT-PCR method to distinguish between those two pathogens. The main objective of the project was to develop a universal, fast, and inexpensive method which could be used in any veterinary laboratory. url: https://doi.org/10.2478/s11535-013-0164-7 doi: 10.2478/s11535-013-0164-7 id: cord-346054-k84rcpav author: Niespodziana, Katarzyna title: PreDicta chip-based high resolution diagnosis of rhinovirus-induced wheeze date: 2018-06-18 words: 7405.0 sentences: 349.0 pages: flesch: 47.0 cache: ./cache/cord-346054-k84rcpav.txt txt: ./txt/cord-346054-k84rcpav.txt summary: Here, we develop a chip containing 130 different micro-arrayed RV proteins and peptides and demonstrate in a cohort of 120 pre-school children, most of whom had been hospitalized due to acute wheeze, that it is possible to determine the culprit RV species with a minute blood sample by serology. The analysis of IgG reactivity to structural and non-structural proteins and to recombinant fragments and synthetic peptides spanning VP1, VP2, and VP3 from RV89 is shown in Supplementary Fig. 2a for all 120 children and in Supplementary Fig. 2b for those children (n = 41) who had shown increases of RV89-specific antibody responses in follow-up serum samples taken after recovery. Based on our previous observations that antibody increases specific for the N-terminal portion of VP1 can be detected in serum samples obtained from subjects after RV infection 36 , the PreDicta chip was equipped with a VP1 peptide set which should allow detecting species-specific immune responses at high resolution ( Fig. 1 ). abstract: Rhinovirus (RV) infections are major triggers of acute exacerbations of severe respiratory diseases such as pre-school wheeze, asthma and chronic obstructive pulmonary disease (COPD). The occurrence of numerous RV types is a major challenge for the identification of the culprit virus types and for the improvement of virus type-specific treatment strategies. Here, we develop a chip containing 130 different micro-arrayed RV proteins and peptides and demonstrate in a cohort of 120 pre-school children, most of whom had been hospitalized due to acute wheeze, that it is possible to determine the culprit RV species with a minute blood sample by serology. Importantly, we identify RV-A and RV-C species as giving rise to most severe respiratory symptoms. Thus, we have generated a chip for the serological identification of RV-induced respiratory illness which should be useful for the rational development of preventive and therapeutic strategies targeting the most important RV types. url: https://www.ncbi.nlm.nih.gov/pubmed/29915220/ doi: 10.1038/s41467-018-04591-0 id: cord-353246-q9qpec7t author: Nijhuis, R. H. T. title: Comparison of ePlex Respiratory Pathogen Panel with Laboratory-Developed Real-Time PCR Assays for Detection of Respiratory Pathogens date: 2017-05-23 words: 3431.0 sentences: 147.0 pages: flesch: 47.0 cache: ./cache/cord-353246-q9qpec7t.txt txt: ./txt/cord-353246-q9qpec7t.txt summary: The objective of this study was to compare the performance of the RP panel with those of laboratory-developed real-time PCR assays, using a variety of previously collected clinical respiratory specimens. In the current study, the performance of the syndromic RP panel was compared to those of laboratory-developed real-time PCR assays, using clinical specimens previously submitted for diagnosis of respiratory pathogens. The 323 positive clinical specimens contained a total of 464 respiratory pathogens as detected by laboratory-developed real-time PCR assays (Table 1) . Owing to the lack of clinical specimens containing MERS-CoV, dilutions of two different culture isolates were tested in this study, of which dilutions with C T values of Ͻ30 as shown by the laboratory-developed real-time PCR assay could be detected consistently. In conclusion, this study shows excellent performance of the GenMark ePlex RP panel in comparison to laboratory-developed real-time PCR assays for the detection of respiratory pathogens from multiple types of clinical specimens and EQA samples. abstract: Infections of the respiratory tract can be caused by a diversity of pathogens, both viral and bacterial. Rapid microbiological diagnosis ensures appropriate antimicrobial therapy as well as effective implementation of isolation precautions. The ePlex respiratory pathogen panel (RP panel) is a novel molecular biology-based assay, developed by GenMark Diagnostics, Inc. (Carlsbad, CA), to be performed within a single cartridge for the diagnosis of 25 respiratory pathogens (viral and bacterial). The objective of this study was to compare the performance of the RP panel with those of laboratory-developed real-time PCR assays, using a variety of previously collected clinical respiratory specimens. A total of 343 clinical specimens as well as 29 external quality assessment (EQA) specimens and 2 different Middle East respiratory syndrome coronavirus isolates have been assessed in this study. The RP panel showed an agreement of 97.4% with the real-time PCR assay regarding 464 pathogens found in the clinical specimens. All pathogens present in clinical samples and EQA samples with a threshold cycle (C(T)) value of <30 were detected correctly using the RP panel. The RP panel detected 17 additional pathogens, 7 of which could be confirmed by discrepant testing. In conclusion, this study shows excellent performance of the RP panel in comparison to real-time PCR assays for the detection of respiratory pathogens. The ePlex system provided a large amount of useful diagnostic data within a short time frame, with minimal hands-on time, and can therefore potentially be used for rapid diagnostic sample-to-answer testing, in either a laboratory or a decentralized setting. url: https://doi.org/10.1128/jcm.00221-17 doi: 10.1128/jcm.00221-17 id: cord-000322-8ctsa9sd author: Ninove, Laetitia title: RNA and DNA Bacteriophages as Molecular Diagnosis Controls in Clinical Virology: A Comprehensive Study of More than 45,000 Routine PCR Tests date: 2011-02-09 words: 2892.0 sentences: 130.0 pages: flesch: 46.0 cache: ./cache/cord-000322-8ctsa9sd.txt txt: ./txt/cord-000322-8ctsa9sd.txt summary: Subsequently, T4 and MS2 ICs were evaluated in routine real-time PCR or RT-PCR virological diagnostic tests, using a series of 8,950 clinical samples (representing 36 distinct specimen types) sent to our laboratory for the detection of a variety of DNA and RNA viruses. It represents a valuable strategy for enhancing the quality of routine molecular diagnosis in laboratories that use in-house designed diagnostic systems, which can conveniently be associated to the use of specific synthetic ECs. The high rate of inhibitors observed in a variety of specimen types should stimulate the elaboration of improved technical protocols for the extraction and amplification of nucleic acids. Monitoring rt-PCR and rt-RT-PCR assays and validation of the results rely on the use of relevant external or internal controls (ECs or ICs) [1, 2] and commercial kits including such control systems are being increasingly improved for the molecular diagnosis of a number of pathogens such as HIV, hepatitis viruses, influenza viruses etc.. abstract: Real-time PCR techniques are now commonly used for the detection of viral genomes in various human specimens and require for validation both external and internal controls (ECs and ICs). In particular, ICs added to clinical samples are necessary to monitor the extraction, reverse transcription, and amplification steps in order to detect false-negative results resulting from PCR-inhibition or errors in the technical procedure. Here, we performed a large scale evaluation of the use of bacteriophages as ICs in routine molecular diagnosis. This allowed to propose simple standardized procedures (i) to design specific ECs for both DNA and RNA viruses and (ii) to use T4 (DNA) or MS2 (RNA) phages as ICs in routine diagnosis. Various technical formats for using phages as ICs were optimised and validated. Subsequently, T4 and MS2 ICs were evaluated in routine real-time PCR or RT-PCR virological diagnostic tests, using a series of 8,950 clinical samples (representing 36 distinct specimen types) sent to our laboratory for the detection of a variety of DNA and RNA viruses. The frequency of inefficient detection of ICs was analyzed according to the nature of the sample. Inhibitors of enzymatic reactions were detected at high frequency in specific sample types such as heparinized blood and bone marrow (>70%), broncho-alveolar liquid (41%) and stools (36%). The use of T4 and MS2 phages as ICs proved to be cost-effective, flexible and adaptable to various technical procedures of real-time PCR detection in virology. It represents a valuable strategy for enhancing the quality of routine molecular diagnosis in laboratories that use in-house designed diagnostic systems, which can conveniently be associated to the use of specific synthetic ECs. The high rate of inhibitors observed in a variety of specimen types should stimulate the elaboration of improved technical protocols for the extraction and amplification of nucleic acids. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3036576/ doi: 10.1371/journal.pone.0016142 id: cord-330594-uq2h8rmv author: Nishizono, Akira title: A simple and rapid immunochromatographic test kit for rabies diagnosis date: 2008-04-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In rabies endemic countries, funds and infrastructure are often insufficient to employ the approved gold standard for the definitive diagnosis of rabies: the direct fluorescent test. In the present study, two types (type 1 and 2) of an ICT kit were evaluated for detection of rabies. These were developed using monoclonal antibodies which recognize epitope II and III of the nucleoprotein of rabies virus. Both kits specifically detected all rabies virus strains and there was no cross reactivity with Lyssaviruses (Lagos, Mokola and Duvenhage), Rhabdovirus (VSV and Oita 296/1972) and other common canine‐pathogenic viruses. In type 1, a single type of monoclonal antibody was used. It was capable of detecting recombinant nucleoprotein and showed sensitivity of 95.5% (42/44) and specificity of 88.9% (32/36) using brain samples from rabid dogs. In contrast, type 2 which was made of two different monoclonal antibodies had a lower sensitivity of 93.2% (41/44) and higher specificity of 100% (36/36). These ICT kits provide a simple and rapid method for rabies detection. They need neither cold chain for transportation nor complicated training for personnel. This diagnostic test is suitable for rabies screening, particularly in areas with a high prevalence of rabies and where the fluorescent antibody test is not available. url: https://www.ncbi.nlm.nih.gov/pubmed/18426399/ doi: 10.1111/j.1348-0421.2008.00031.x id: cord-314386-cxq9v218 author: Nitsche, Andreas title: SARS Coronavirus Detection date: 2004-07-17 words: 1904.0 sentences: 96.0 pages: flesch: 55.0 cache: ./cache/cord-314386-cxq9v218.txt txt: ./txt/cord-314386-cxq9v218.txt summary: We developed a set of three real-time reverse transcription–polymerase chain reaction (PCR) assays that amplify three different regions of the SARS-associated coronavirus (SARS-CoV), can be run in parallel or in a single tube, and can detect <10 genome equivalents of SARS-CoV. To improve the ability to detect SARS-CoV safely and reduce the risk of eliciting false-negative results caused by genome sequence variations, we established three individual real-time RT-PCR assays. Target sequences were chosen by using the following criteria: 1) the regions are distributed over the whole genome, including the nonstructural polyprotein 1a and 1ab genes and the spike glycoprotein gene (Table 1) ; 2) the regions are highly conserved among the 89, 90, and 100 respective sequences available in public sequence databases; 3) the regions are suitable for the design of a real-time RT-PCR assay; and 4) the designed primers, 5′-nuclease probes, and amplicons displayed no considerable homology to other viruses, including human CoV OC43 and 229E in BLAST searches (available from http://www.ncbi.nlm.nih.gov/BLAST/). abstract: We developed a set of three real-time reverse transcription–polymerase chain reaction (PCR) assays that amplify three different regions of the SARS-associated coronavirus (SARS-CoV), can be run in parallel or in a single tube, and can detect <10 genome equivalents of SARS-CoV. The assays consider all currently available SARS-CoV sequences and are optimized for two prominent real-time PCR platforms. url: https://www.ncbi.nlm.nih.gov/pubmed/15324554/ doi: 10.3201/eid1007.030678 id: cord-348209-rkkhv4mw author: Noerz, Dominik title: Clinical evaluation of a SARS-CoV-2 RT-PCR assay on a fully automated system for rapid on-demand testing in the hospital setting date: 2020-04-11 words: 1643.0 sentences: 125.0 pages: flesch: 61.0 cache: ./cache/cord-348209-rkkhv4mw.txt txt: ./txt/cord-348209-rkkhv4mw.txt summary: title: Clinical evaluation of a SARS-CoV-2 RT-PCR assay on a fully automated system for rapid on-demand testing in the hospital setting In this study we evaluated a SARS-CoV-2 LDT for the NeuMoDx 96 system, a fully automated (sample to result) RT-PCR platform offering random-access capabilities and good clinical performance for SARS-CoV-2 testing. In this study we evaluated a SARS-CoV-2 LDT for the NeuMoDx 96 30 system, a fully automated device performing extraction and real-time PCR. Due to its random-access workflow concept and rapid time-to-39 result of about 80 minutes, the device is very well suited for providing fast-tracked SARS-CoV-2 40 diagnostics for urgent clinical samples in the hospital setting. For the assay presented in this study, we used a fully automated random-access platform for molecular 56 diagnostics, handling everything from extraction, amplification, signal detection to reporting of results 57 (10). Evaluation of a quantitative RT-PCR assay for 180 the detection of the emerging coronavirus SARS-CoV-2 using a high throughput system abstract: The ongoing SARS-CoV-2 pandemic presents a unique challenge for diagnostic laboratories around the world. Automation of workflows in molecular diagnostics is instrumental for coping with the large number of tests ordered by clinicians, as well as providing fast-tracked rapid testing for urgent cases. In this study we evaluated a SARS-CoV-2 LDT for the NeuMoDx 96 system, a fully automated (sample to result) RT-PCR platform offering random-access capabilities and good clinical performance for SARS-CoV-2 testing. url: https://doi.org/10.1101/2020.04.07.20056234 doi: 10.1101/2020.04.07.20056234 id: cord-256130-zhlvvuj4 author: Nordén, Rickard title: Quantification of Torque Teno Virus and Epstein-Barr Virus Is of Limited Value for Predicting the Net State of Immunosuppression After Lung Transplantation date: 2018-03-06 words: 4853.0 sentences: 230.0 pages: flesch: 47.0 cache: ./cache/cord-256130-zhlvvuj4.txt txt: ./txt/cord-256130-zhlvvuj4.txt summary: Here, we evaluated quantification of torque teno virus (TTV) and Epstein-Barr virus (EBV) as biomarkers for defining the net state of immunosuppression in lung-transplanted patients. The aim of the present study was to evaluate levels of TTV and EBV in relation to the frequency of infectious events and acute rejections over time in a prospective manner in a single-center cohort of lung-transplanted patients. The total nucleic acid content was isolated from serum or whole blood samples and analyzed for TTV-, EBV-, and CMV-DNA load by real-time PCR. Comparison of TTV-and EBV-DNA levels in lung transplant recipients who received either Tacrolimus-or Cyclosporinebased therapy revealed that Cyclosporine-treated patients had significantly lower TTV-DNA levels in serum at month 6 post-LTx and onwards, compared with the Tacrolimustreated patients (Figure 1 ). However, we found no association between either TTV-or EBV-DNA load and infectious events or acute rejections, which suggests a limited clinical applicability as biomarkers predicting short-term outcomes related to the net state of immunosuppression. abstract: BACKGROUND: Major hurdles for survival after lung transplantation are rejections and infectious complications. Adequate methods for monitoring immune suppression status are lacking. Here, we evaluated quantification of torque teno virus (TTV) and Epstein-Barr virus (EBV) as biomarkers for defining the net state of immunosuppression in lung-transplanted patients. METHODS: This prospective single-center study included 98 patients followed for 2 years after transplantation. Bacterial infections, fungal infections, viral respiratory infections (VRTI), cytomegalovirus (CMV) viremia, and acute rejections, as well as TTV and EBV levels, were monitored. RESULTS: The levels of torque teno virus DNA increased rapidly after transplantation, likely due to immunosuppressive treatment. A modest increase in levels of Epstein-Barr virus DNA was also observed after transplantation. There were no associations between either TTV or EBV and infectious events or acute rejection, respectively, during follow-up. When Tacrolimus was the main immunosuppressive treatment, TTV DNA levels were significantly elevated 6–24 months after transplantation as compared with Cyclosporine treatment. CONCLUSIONS: Although replication of TTV, but not EBV, appears to reflect the functionality of the immune system, depending on the type of immunosuppressive treatment, quantification of TTV or EBV as biomarkers has limited potential for defining the net state of immune suppression. url: https://www.ncbi.nlm.nih.gov/pubmed/29644247/ doi: 10.1093/ofid/ofy050 id: cord-340021-pj6fywwc author: Norooznezhad, Amir Hossein title: Primary Symptoms, Comorbidities, and Outcomes of 431 Hospitalized Patients with Confirmative RT-PCR Results for COVID-19 date: 2020-06-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: This study aimed to evaluate the primary symptoms, comorbidities, and outcomes of inpatients with confirmed reverse transcription–PCR (RT-PCR) for SARS-CoV-2 infection among 2077 suspected/diagnosed cases of COVID-19. Based on the results of Least Absolute Shrinkage and Selection Operator (LASSO) logistic regression, age, and suggestive chest X-ray (CXR) findings for SARS-CoV-2 infection, cardiovascular diseases, diabetes mellitus, chronic lung diseases, and intensive care units admission had significant associations with positive RT-PCR results for COVID-19 infection. Also, the highest area under the curve (AUC) was related to cough (AUC = 0.53, 95% CI: 0.51–0.56), dyspnea (AUC = 0.52, 95% CI: 0.50–0.54), and abnormal CXR (AUC = 0.52, 95% CI: 0.50–0.54), as significant predictors. This study showed that some symptoms including cough and dyspnea, as well as abnormal CXR, could be proper predictors of positive RT-PCR result for SARS-CoV-2 infection. It seems that patients with underlying disease(s), such as cardiovascular diseases, diabetes mellitus, and chronic lung diseases, had a higher probability to have positive RT-PCR for SARS-CoV-2 infection than those with no underlying disease(s). url: https://doi.org/10.4269/ajtmh.20-0512 doi: 10.4269/ajtmh.20-0512 id: cord-341434-2xrdv92m author: Nowland, Megan H. title: Biology and Diseases of Rabbits date: 2015-07-10 words: 31591.0 sentences: 1921.0 pages: flesch: 47.0 cache: ./cache/cord-341434-2xrdv92m.txt txt: ./txt/cord-341434-2xrdv92m.txt summary: Etiology Pasteurella multocida is a Gram-negative nonmotile coccobacillus that causes pasteurellosis, also known as ''snuffles'', the primary respiratory disease affecting domestic rabbits (Deeb and DiGiacomo, 2000; Guo et al., 2012) . Research Complications Pasteurellosis can cause considerable economic losses (El Tayeb et al., 2004; Ferreira et al., 2012; Stahel et al., 2009 ) and has the potential to affect different types of research studies using rabbits due to the multisystemic nature of the disease, and the possibility of high morbidity and mortality. piliforme is a pleomorphic, Gramnegative, spore-forming, motile, obligate intracellular rod-shaped bacterium that causes Tyzzer''s disease and infects various animals including mice, nonhuman primates, gerbils, rats, rabbits, and others (Allen et al., 1965; Ganaway et al., 1971; Pritt et al., 2010) . Research Complications EPEC infection can cause high morbidity and mortality in laboratory rabbit colonies and can affect studies involving intestinal physiology in rabbits. abstract: Beginning in 1931, an inbred rabbit colony was developed at the Phipps Institute for the Study, Treatment and Prevention of Tuberculosis at the University of Pennsylvania. This colony was used to study natural resistance to infection with tuberculosis (Robertson et al., 1966). Other inbred colonies or well-defined breeding colonies were also developed at the University of Illinois College of Medicine Center for Genetics, the Laboratories of the International Health Division of The Rockefeller Foundation, the University of Utrecht in the Netherlands, and Jackson Laboratories. These colonies were moved or closed in the years to follow. Since 1973, the U.S. Department of Agriculture has reported the total number of certain species of animals used by registered research facilities (1997). In 1973, 447,570 rabbits were used in research. There has been an overall decrease in numbers of rabbits used. This decreasing trend started in the mid-1990s. In 2010, 210,172 rabbits were used in research. Despite the overall drop in the number used in research, the rabbit is still a valuable model and tool for many disciplines. url: https://www.sciencedirect.com/science/article/pii/B9780124095274000109 doi: 10.1016/b978-0-12-409527-4.00010-9 id: cord-257217-f9sdt7ax author: Nunes, Marta C. title: Clinical Epidemiology of Bocavirus, Rhinovirus, Two Polyomaviruses and Four Coronaviruses in HIV-Infected and HIV-Uninfected South African Children date: 2014-02-03 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Advances in molecular diagnostics have implicated newly-discovered respiratory viruses in the pathogenesis of pneumonia. We aimed to determine the prevalence and clinical characteristics of human bocavirus (hBoV), human rhinovirus (hRV), polyomavirus-WU (WUPyV) and –KI (KIPyV) and human coronaviruses (CoV)-OC43, -NL63, -HKU1 and -229E among children hospitalized with lower respiratory tract infections (LRTI). METHODS: Multiplex real-time reverse-transcriptase polymerase chain reaction was undertaken on archived nasopharyngeal aspirates from HIV-infected and –uninfected children (<2 years age) hospitalized for LRTI, who had been previously investigated for respiratory syncytial virus, human metapneumovirus, parainfluenza I–III, adenovirus and influenza A/B. RESULTS: At least one of these viruses were identified in 274 (53.0%) of 517 and in 509 (54.0%) of 943 LRTI-episodes in HIV-infected and -uninfected children, respectively. Human rhinovirus was the most prevalent in HIV-infected (31.7%) and –uninfected children (32.0%), followed by CoV-OC43 (12.2%) and hBoV (9.5%) in HIV-infected; and by hBoV (13.3%) and WUPyV (11.9%) in HIV-uninfected children. Polyomavirus-KI (8.9% vs. 4.8%; p = 0.002) and CoV-OC43 (12.2% vs. 3.6%; p<0.001) were more prevalent in HIV-infected than –uninfected children. Combined with previously-tested viruses, respiratory viruses were identified in 60.9% of HIV-infected and 78.3% of HIV-uninfected children. The newly tested viruses were detected at high frequency in association with other respiratory viruses, including previously-investigated viruses (22.8% in HIV-infected and 28.5% in HIV–uninfected children). CONCLUSIONS: We established that combined with previously-investigated viruses, at least one respiratory virus was identified in the majority of HIV-infected and HIV-uninfected children hospitalized for LRTI. The high frequency of viral co-infections illustrates the complexities in attributing causality to specific viruses in the aetiology of LRTI and may indicate a synergetic role of viral co-infections in the pathogenesis of childhood LRTI. url: https://doi.org/10.1371/journal.pone.0086448 doi: 10.1371/journal.pone.0086448 id: cord-103563-7a3wdduq author: Nunez-Bajo, Estefania title: Ultra-Low-Cost Integrated Silicon-based Transducer for On-Site, Genetic Detection of Pathogens date: 2020-03-25 words: 4535.0 sentences: 211.0 pages: flesch: 44.0 cache: ./cache/cord-103563-7a3wdduq.txt txt: ./txt/cord-103563-7a3wdduq.txt summary: Unlike other silicon-based technologies, TriSilix can be produced at wafer-scale in a standard laboratory; we have developed a series of methodologies based on metal-assisted chemical (wet) etching, electroplating, thermal bonding and laser-cutting to enable a cleanroom-free low-cost fabrication that does not require processing in an advanced semiconductor foundry. To create an ultra-low-cost device, the architecture proposed exploits the intrinsic properties of silicon and integrates three modes of operation in a single chip: i) electrical (Joule) heater, ii) temperature sensor (i.e. thermistor) with a negative temperature coefficient that can provide the precise temperature of the sample solution during reaction and iii) electrochemical sensor for detecting target NA. Using TriSilix, the sample solution can be maintained at a single, specific temperature (needed for isothermal amplification of NA such as Recombinase Polymerase Amplification (RPA) or cycled between different temperatures (with a precision of ±1.3°C) for Polymerase Chain Reaction (PCR) while the exact concentration of amplicons is measured quantitatively and in real-time electrochemically. abstract: Rapid screening and low-cost diagnosis play a crucial role in choosing the correct course of intervention e.g., drug therapy, quarantine, no action etc. when dealing with highly infectious pathogens. This is especially important if the disease-causing agent has no effective treatment, such as the novel coronavirus SARS-CoV-2 (the pathogen causing COVID-19), and shows no or similar symptoms to other common infections. We report a silicon-based integrated Point-of-Need (PoN) transducer (TriSilix) that can chemically-amplify and detect pathogen-specific sequences of nucleic acids (NA) quantitatively in real-time. Unlike other silicon-based technologies, TriSilix can be produced at wafer-scale in a standard laboratory; we have developed a series of methodologies based on metal-assisted chemical (wet) etching, electroplating, thermal bonding and laser-cutting to enable a cleanroom-free low-cost fabrication that does not require processing in an advanced semiconductor foundry. TriSilix is, therefore, resilient to disruptions in the global supply chain as the devices can be produced anywhere in the world. To create an ultra-low-cost device, the architecture proposed exploits the intrinsic properties of silicon and integrates three modes of operation in a single chip: i) electrical (Joule) heater, ii) temperature sensor (i.e. thermistor) with a negative temperature coefficient that can provide the precise temperature of the sample solution during reaction and iii) electrochemical sensor for detecting target NA. Using TriSilix, the sample solution can be maintained at a single, specific temperature (needed for isothermal amplification of NA such as Recombinase Polymerase Amplification (RPA) or cycled between different temperatures (with a precision of ±1.3°C) for Polymerase Chain Reaction (PCR) while the exact concentration of amplicons is measured quantitatively and in real-time electrochemically. A single 4-inch Si wafer yields 37 TriSilix chips of 10×10×0.65 mm in size and can be produced in 7 hours, costing ~US $0.35 per device. The system is operated digitally, portable and low power – capable of running up to 35 tests with a 4000 mAh battery (a typical battery capacity of a modern smartphone). We were able to quantitatively detect a 563-bp fragment (Insertion Sequence IS900) of the genomic DNA of M. avium subsp. paratuberculosis (extracted from cultured field samples) through PCR in real-time with a Limit-of-Detection of 20 fg, equivalent to a single bacterium, at the 30th cycle. Using TriSilix, we also detected the cDNA from SARS-CoV-2 (1 pg), through PCR, with high specificity against SARS-CoV (2003). url: https://doi.org/10.1101/2020.03.23.002931 doi: 10.1101/2020.03.23.002931 id: cord-034746-uxhpufnv author: Nusshag, Christian title: Glomerular filtration barrier dysfunction in a self-limiting, RNA virus-induced glomerulopathy resembles findings in idiopathic nephrotic syndromes date: 2020-11-05 words: 3642.0 sentences: 194.0 pages: flesch: 36.0 cache: ./cache/cord-034746-uxhpufnv.txt txt: ./txt/cord-034746-uxhpufnv.txt summary: We therefore analyzed standard markers of glomerular proteinuria (e.g. immunoglobulin G [IgG]), urinary nephrin excretion (podocyte injury) and serum levels of the soluble urokinase plasminogen activator receptor (suPAR), a proposed pathomechanically involved molecule in INS, in PUUV-infected patients. On admission, patients suffering from hantavirus infection showed significantly increased urinary nephrin, IgG, α1-MG and serum suPAR levels compared to healthy controls (Fig. 3A ). Though, urinary biomarker levels decreased in both groups over time, patients with severe PCR showed significantly higher levels of nephrin, IgG, ACR and PCR during the first 48 h after admission ( Table 2 ). Our data show a strong association between urinary nephrin levels and the extent of (non-selective) glomerular proteinuria, suggesting that hantavirus infection causes a pronounced podocyte damage and subsequent impairment of the GFB. To date, one other study showed significantly elevated blood suPAR levels and their association with hantavirus disease severity but did not include nephrinuria and the extent of proteinuria in their analysis 19 . abstract: Podocyte injury has recently been described as unifying feature in idiopathic nephrotic syndromes (INS). Puumala hantavirus (PUUV) infection represents a unique RNA virus-induced renal disease with significant proteinuria. The underlying pathomechanism is unclear. We hypothesized that PUUV infection results in podocyte injury, similar to findings in INS. We therefore analyzed standard markers of glomerular proteinuria (e.g. immunoglobulin G [IgG]), urinary nephrin excretion (podocyte injury) and serum levels of the soluble urokinase plasminogen activator receptor (suPAR), a proposed pathomechanically involved molecule in INS, in PUUV-infected patients. Hantavirus patients showed significantly increased urinary nephrin, IgG and serum suPAR concentrations compared to healthy controls. Nephrin and IgG levels were significantly higher in patients with severe proteinuria than with mild proteinuria, and nephrin correlated strongly with biomarkers of glomerular proteinuria over time. Congruently, electron microcopy analyses showed a focal podocyte foot process effacement. suPAR correlated significantly with urinary nephrin, IgG and albumin levels, suggesting suPAR as a pathophysiological mediator in podocyte dysfunction. In contrast to INS, proteinuria recovered autonomously in hantavirus patients. This study reveals podocyte injury as main cause of proteinuria in hantavirus patients. A better understanding of the regenerative nature of hantavirus-induced glomerulopathy may generate new therapeutic approaches for INS. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7644703/ doi: 10.1038/s41598-020-76050-0 id: cord-319253-8bssrn9o author: OKINO, Cintia Hiromi title: Rapid detection and differentiation of avian infectious bronchitis virus: an application of Mass genotype by melting temperature analysis in RT-qPCR using SYBR Green I date: 2018-02-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A method based on Melting Temperature analysis of Hypervariable regions (HVR) of S1 gene within a RT-qPCR was developed to detect different genotypes of avian infectious bronchitis virus (IBV) and identify the Mass genotype. The method was able to rapidly identify the Mass genotype among IBV field isolates, vaccine attenuated strains and reference M41 strain in allantoic liquid and also directly in tissues. The RT-qPCR developed detected the virus in both tracheal and pulmonary samples from M41-infected or H120-infected birds, in a larger post-infection period compared to detection by standard method of virus isolation. RT-qPCR method tested provided a sensitivity and rapid approach for screening on IBV detection and Mass genotyping from IBV isolates. url: https://www.ncbi.nlm.nih.gov/pubmed/29491226/ doi: 10.1292/jvms.17-0566 id: cord-022034-o27mh4wz author: OLANO, JUAN P. title: Distinguishing Tropical Infectious Diseases from Bioterrorism date: 2009-05-15 words: 10720.0 sentences: 642.0 pages: flesch: 41.0 cache: ./cache/cord-022034-o27mh4wz.txt txt: ./txt/cord-022034-o27mh4wz.txt summary: They include presence of disease outbreaks of the same illness in noncontiguous areas, disease outbreaks with zoonotic impact, different attack rates in different environments (indoor versus outdoor), presence of large epidemics in small populations, increased number of unexplained deaths, unusually high severity of a disease for a particular pathogen, unusual clinical manifestations owing to route of transmission for a given pathogen, presence of a disease (vector-borne or not) in an area not endemic for that particular disease, multiple epidemics with different diseases in the same population, a case of a disease by an uncommon agent (smallpox, viral hemorrhagic fevers, inhalational anthrax), unusual strains of microorganisms when compared to conventional strains circulating in the same affected areas, and genetically homogenous organisms isolated from different locations. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152372/ doi: 10.1016/b978-0-443-06668-9.50124-1 id: cord-304610-6o3hydg6 author: Odeyemi, Festus Ayotunde title: Gauging the laboratory responses to coronavirus disease (COVID‐19) in Africa date: 2020-08-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The rampaging effect of coronavirus disease (COVID‐19) in Africa is huge and have impacted almost every area of life. Across African states, there exist variations in the laboratory measures adopted, and these heterogeneous approaches, in turn, determines the successes or otherwise recorded. In this study, we assessed the various forms of laboratory responses to the containment, risk analyses, structures and features of COVID‐19 in high incidence African countries (Nigeria, South Africa, Egypt, Ghana, Algeria, Morocco, etc.) to aid better and efficient laboratory responses to the highly infectious diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/32904876/ doi: 10.1002/pa.2280 id: cord-337396-g69bb60d author: Ogawa, Yoshihiko title: Assessing the effects of exposure to a SARS-CoV-2 re-positive patient in healthcare personnel date: 2020-11-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVE: To evaluate whether patients with COVID-19 who have tested re-positive with the PCR test for the SARS-CoV-2 virus are infectious is a challenge in the current circumstances. A follow-up survey was conducted with healthcare personnel (HCP) who were exposed to a patient whose PCR test results for SARS-CoV-2 were re-positive 18 days after the initial confirmation of negative PCR results. RESULTS: We studied a total of 15 HCP who had contact exposures (15/15) and aerosol exposures (7/15). None of them tested positive for IgG against SARS-CoV-2 on blood examination. None of them had any symptoms during 10 days of active isolation. All PCR tests conducted using the nasopharyngeal swabs collected from the HCP on day 10 were negative. No apparent infection was found in any of the HCP who had contact exposure with and/or aerosol exposure to the patient whose PCR test results for SARS-CoV-2 were re-positive 18 days after the initial confirmation of negative results of PCR tests for SARS-CoV-2. Clinical trial: Trial Registration: No. 170, approved June 10th, 2020 by the ethics committee of Sakai City Medical Center. url: https://doi.org/10.1186/s13104-020-05365-y doi: 10.1186/s13104-020-05365-y id: cord-029775-mntcor5d author: Oka, Tomoichiro title: Polymerase chain reaction primer sets for the detection of genetically diverse human sapoviruses date: 2020-07-27 words: 1827.0 sentences: 100.0 pages: flesch: 58.0 cache: ./cache/cord-029775-mntcor5d.txt txt: ./txt/cord-029775-mntcor5d.txt summary: For the initial reactivity test, double-stranded DNA fragments (gBlocks® Gene Fragments) including the sequence targeted by the PCR primers (approximately 1700 bp each) of the human sapovirus genotypes GI.1 (GenBank accession number X86560), GI.2 (AB614356), GI.3 (AB623037), GI.4 (AJ606693), GI.5 (DQ366345), GI.6 (AJ606694), GI.7 (AB522390), GII.1 (AJ249939), GII.2 (AY237420), GII.3 (AB630068), GII.4 (AB522397), GII.5 (LC190463), GII.6 (AY646855), GII.7 (AB630067), GII.8 (KX894315), GIV.1 (DQ058829), GV.1 (DQ366344), and GV.2 (AB775659) were synthesized (Integrated DNA Technologies, Coralville, IA), and 1.0 × 10 4 copies of these fragments were used. The target regions of HuSaV-F1, -F2, and -F3 recently designed as forward primers in a broadly reactive real-time PCR for human sapoviruses [11] are similar to those of SV-F13 and SV-F14 (Fig. 2) , and the sapovirus-specific sequence of M13R-HuSaV5498R (5′-CCCCANCCNGCVHACAT-3′) ( [11] are shown in parentheses. The assay including two primers (M13F-HuSaV-5159F and M13R-HuSaV-5498R) generated similar-sized PCR products (approximately 380 bp) for all of the sapovirus genotypes tested (Fig. 1A, right panel, and Fig. 1B) . abstract: Sapoviruses are increasingly being recognized as pathogens associated with gastroenteritis in humans. Human sapoviruses are currently assigned to 18 genotypes (GI.1-7, GII.1-8, GIV.1, and GV.1-2) based on the sequence of the region encoding the major structural protein. In this study, we evaluated 11 polymerase chain reaction (PCR) assays using published and newly designed/modified primers and showed that four PCR assays with different primer combinations amplified all of the tested human sapovirus genotypes using either synthetic DNA or cDNA prepared from human sapovirus-positive fecal specimens. These assays can be used as improved broadly reactive screening tests or as tools for molecular characterization of human sapoviruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7383071/ doi: 10.1007/s00705-020-04746-9 id: cord-337096-ulc7mnwb author: Okazawa, Mitsushi title: Japanese tactics for suppressing COVID-19 spread date: 2020-07-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract COVID-19 infection is overwhelming the world and death toll is steadily increasing. The first wave in Japan seemed to converge with lower death rate than that in most developed countries. In this letter, we describe how Japanese government suppressed the first wave of COPD-19 spread. url: https://www.ncbi.nlm.nih.gov/pubmed/32726639/ doi: 10.1016/j.puhe.2020.07.012 id: cord-350296-6bq0tps2 author: Olsvik, Pål A title: Selection of reference genes for qRT-PCR examination of wild populations of Atlantic cod Gadus morhua date: 2008-07-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Extensive sequencing efforts have been taking place for the Atlantic cod (Gadus morhua) in recent years, the number of ESTs in the Genbank has reached more than 140.000. Despite its importance in North Atlantic fisheries and potential use in aquaculture, relatively few gene expression examination exists for this species, and systematic evaluations of reference gene stability in quantitative real-time RT-PCR (qRT-PCR) studies are lacking. RESULTS: The stability of 10 potential reference genes was examined in six tissues of Atlantic cod obtained from four populations, to determine the most suitable genes to be used in qRT-PCR analyses. Relative transcription levels of genes encoding β-actin (ACTB), elongation factor 1A (EF1A), actin-related protein-2 (ARP-2), glyceraldehyde-3P-dehydrogenase (GAPDH), ubiquitin (Ubi), acidic ribosomal protein (ARP), ribosomal protein S9 (S9), ribosomal protein L4 (RPL4), RPL22 and RPL37 were quantified in gills, brain, liver, head kidney, muscle and middle intestine in six juvenile fish from three wild populations and from farmed Atlantic cod. Reference gene stability was investigated using the geNorm and NormFinder tools. Based on calculations performed with the geNorm, which determines the most stable genes from a set of tested genes in a given cDNA sample, ARP, Ubi, S9 and RPL37 were among the most stable genes in all tissues. When the same calculations were done with NormFinder, the same genes plus RPL4 and EF1A were ranked as the preferable genes. CONCLUSION: Overall, this work suggests that the Ubi and ARP can be useful as reference genes in qRT-PCR examination of gene expression studying wild populations of Atlantic cod. url: https://doi.org/10.1186/1756-0500-1-47 doi: 10.1186/1756-0500-1-47 id: cord-252198-gs52k4lq author: Onions, David title: Validation of the safety of MDCK cells as a substrate for the production of a cell-derived influenza vaccine date: 2010-09-30 words: 6592.0 sentences: 290.0 pages: flesch: 41.0 cache: ./cache/cord-252198-gs52k4lq.txt txt: ./txt/cord-252198-gs52k4lq.txt summary: We conclude that the theoretical risks arising from manufacturing seasonal influenza vaccine using MDCK-33016PF cells are reduced to levels that are effectively zero by the multiple, orthogonal processes used during production. In order to quantitatively assess potential risks represented by adventitious viruses, data were collected about growth properties of various relevant viruses in MDCK-33016PF cells, about the virus inactivating and virus clearance of the vaccine manufacturing process, and about the detection limits of applied PCR methods to detect adventitious viruses. Combining all data on the virus growth in MDCK-33016PF cells, on the inactivation or process removal of various model viruses, and with consideration of applicable detection limits for virus exclusion tests, a process-specific risk assessment was made using quantitative data relative to infectious doses. First a rigorous analysis of the MDCK-33016PF cells was undertaken to exclude the presence of infectious oncogenic viruses or infectious oncogenic viral genomes; secondly the manufacturing process was shown to be capable of inactivating potential virus contaminants at very high levels. abstract: Abstract Cell culture-based production methods may assist in meeting increasing demand for seasonal influenza vaccines and developing production flexibility required for addressing influenza pandemics. MDCK-33016PF cells are used in propagation of a cell-based seasonal influenza vaccine (Optaflu®); but, like most continuous cell lines, can grow in immunocompromised mice to produce tumors. It is, therefore, essential that no residual cells remain within the vaccine, that cell lysates or DNA are not oncogenic, and that the cell substrate does not contain oncogenic viruses or oncogenic DNA. Multiple, redundant processes ensure the safety of influenza vaccines produced in MDCK-33016PF cells. The probability of a residual cell being present in a dose of vaccine is approximately 1 in 1034. Residual MDCK-DNA is ≤10ng per dose and the ß-propiolactone used to inactivate influenza virus results in reduction of detectable DNA to less than 200base pairs (bp). Degenerate PCR and specific PCR confirm exclusion of oncogenic viruses. The manufacturing process has been validated for its capacity to remove and inactivate viruses. We conclude that the theoretical risks arising from manufacturing seasonal influenza vaccine using MDCK-33016PF cells are reduced to levels that are effectively zero by the multiple, orthogonal processes used during production. url: https://api.elsevier.com/content/article/pii/S1045105610000989 doi: 10.1016/j.biologicals.2010.04.003 id: cord-274805-b3mqkfhh author: Onodera, Kenji title: Selection for 3′ end triplets for polymerase chain reaction primers date: 2004-12-31 words: 2271.0 sentences: 112.0 pages: flesch: 58.0 cache: ./cache/cord-274805-b3mqkfhh.txt txt: ./txt/cord-274805-b3mqkfhh.txt summary: We analyzed 3′ end triplets of PCR primer sequences obtained from refereed journal articles, to test those recommendations and to make empirical recommendations for primer design. The frequencies of the 64 possible 3′end triplets among 2137 PCR primers from the VirOligo database were not uniformly distributed. The analysis results revealed preferred and disfavored 3 0 end triplets in successful primer sequences, and led to recommendations for primer design based on experience rather than theory. Since the primer sequence data set contained 134 BHV-1, 237 BVDV and 121 FMV primers, these viruses were used to test whether genome compositions determined the 3 0 end triplet frequencies. Low GCC contents in the 3 0 end triplets of PCR primers were not frequently reported in the VirOligo database. We suggest that primer design software incorporate scores based on empirical frequencies of 3 0 end triplets, such as those reported here, into the evaluation of oligonucleotides as primers. abstract: Abstract The 3′ end of a primer is a key component of PCR primer design. Many recommendations for the composition and sequence of the 3′ end have been suggested based on theoretical considerations, but have not been verified experimentally. We analyzed 3′ end triplets of PCR primer sequences obtained from refereed journal articles, to test those recommendations and to make empirical recommendations for primer design. The frequencies of the 64 possible 3′end triplets among 2137 PCR primers from the VirOligo database were not uniformly distributed. From the analysis, we found that unfavored and preferred 3′ end triplets existed, and that the apparent preferences were not due to base compositions in viral genome sequences. Comparison of the sequences preferred by practitioners to those recommended, suggested that no single recommendation is entirely satisfactory. We suggest that recommendations be replaced with a scoring system incorporating empirical frequencies such as those reported here. url: https://api.elsevier.com/content/article/pii/S0890850804000520 doi: 10.1016/j.mcp.2004.05.007 id: cord-346436-p61mpc6t author: Onodera, Kenji title: Selection for 3′-End Triplets for Polymerase Chain Reaction Primers date: 2007 words: 3709.0 sentences: 225.0 pages: flesch: 72.0 cache: ./cache/cord-346436-p61mpc6t.txt txt: ./txt/cord-346436-p61mpc6t.txt summary: Over 2000 primer sequences from successful PCR experiments used with varieties of templates and conditions were analyzed for finding frequencies of the 3′-end triplets. This chapter discusses a trend in 3′-end triplet frequencies in primers used in successful PCR experiments and proposes requirements for the 3′-end of a primer. From the VirOligo database, 2137 PCR primer sequences were retrieved for detailed analysis of the 3 -end triplets of successful PCR primers (8; see Note 1). The analysis of the 3 -end triplets of primers (8; see Fig. 5 and Table 1) showed all 64 types were used in successful PCR experiments from the VirOligo database. 3. When primers are obtained by a primer design program, the user needs to note that some primer search settings such as 3 -end "GC clamp" interfere with the 3 -end triplet selection. abstract: Primer extension by thermostable DNA polymerase in PCR starts from the 3′-end of a primer. If the PCR starting process fails, the entire PCR fails. Primer sequences at the 3′-end often interfere with success in PCR experiments. Over 2000 primer sequences from successful PCR experiments used with varieties of templates and conditions were analyzed for finding frequencies of the 3′-end triplets. This chapter discusses a trend in 3′-end triplet frequencies in primers used in successful PCR experiments and proposes requirements for the 3′-end of a primer. Finally, a method break to select primers with the best 3′-end triplets is introduced based on the 3′-end analysis result. url: https://www.ncbi.nlm.nih.gov/pubmed/17951790/ doi: 10.1007/978-1-59745-528-2_3 id: cord-340627-xyvzgkxl author: Ornaghi, Sara title: Performance of an extended triage questionnaire to detect suspected cases of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection in obstetric patients: Experience from two large teaching hospitals in Lombardy, Northern Italy date: 2020-09-15 words: 3804.0 sentences: 228.0 pages: flesch: 51.0 cache: ./cache/cord-340627-xyvzgkxl.txt txt: ./txt/cord-340627-xyvzgkxl.txt summary: title: Performance of an extended triage questionnaire to detect suspected cases of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection in obstetric patients: Experience from two large teaching hospitals in Lombardy, Northern Italy Initially, a targeted SARS-CoV-2 screening approach triggered by a positive questionnaire and based on RT-PCR testing of nasopharyngeal swabs was used in women with hospital admission after accessing the Emergency Department. On April 8 th , we changed our policy and started testing all women for SARS-CoV-2 infection independent of the type of hospital admission and the questionnaire result, in agreement with a disposition of the Lombardy Region Health Care Authority. Our study investigated the accuracy of a comprehensive questionnaire thoroughly assessing obstetric patients upon hospital admission to identify cases suspected for SARS-CoV-2 infection. Our data show that thorough assessment of obstetric patients upon hospital admission by means of an exhaustive questionnaire is feasible and effective in discriminating women at low risk of SARS-CoV-2 infection in the context of both a targeted and a universal screening abstract: OBJECTIVES: 1. To assess the performance of an extended questionnaire in identifying cases of SARS-CoV-2 infection among obstetric patients. 2. To evaluate the rate of infection among healthcare workers involved in women’s care. STUDY DESIGN: A prospective cohort study of obstetric patients admitted to MBBM Foundation and Buzzi Hospital (Lombardy, Northern Italy) from March 16(th) to May 22(nd), 2020. Women were screened on admission by a questionnaire investigating major and minor symptoms of infection and high-risk contacts in the last 14 days. SARS-CoV-2 assessment was performed by RT-PCR on nasopharyngeal swabs. Till April 7(th), a targeted SARS-CoV-2 testing triggered by a positive questionnaire was used; from April 8(th), a universal testing approach was implemented. RESULTS: There were 1,177 women screened by the questionnaire, which yielded a positive result in 130 (11.0%) cases. SARS-CoV-2 RT-PCR was performed in 865 (73.5%) patients, identifying 51 (5.9%) infections. During the first period, there were 29 infected mothers, 4 (13.8%) of whom had a negative questionnaire. After universal testing implementation, there were 22 (3%, 95% CI 1.94% - 4.04%) infected mothers, 13 (59.1%) of whom had a negative questionnaire; rate of infection among asymptomatic women was 1.9%. Six of the 17 SARS-CoV-2-positive women with a negative questionnaire reported symptoms more than 14 but within 30 days before admission. Isolated olfactory or taste disorders were identified in 15.7% of infected patients. Rate of infection among healthcare workers was 5.8%. CONCLUSIONS: An exhaustive triage questionnaire can effectively discriminate women at low risk of SARS-CoV-2 infection in the context of a targeted and a universal viral testing approach. In 15.7% of infected women, correct classification as a suspected case of infection was due to investigation of olfactory and taste disorders. Extension of the assessed time-frame to 30 days may be worth considering to increase the questionnaire’s performance. url: https://www.ncbi.nlm.nih.gov/pubmed/32931524/ doi: 10.1371/journal.pone.0239173 id: cord-298805-ntpm68cg author: Otašević, S. title: Non-culture based assays for the detection of fungal pathogens date: 2018-03-29 words: 9284.0 sentences: 402.0 pages: flesch: 34.0 cache: ./cache/cord-298805-ntpm68cg.txt txt: ./txt/cord-298805-ntpm68cg.txt summary: Therefore, in order to overcome the limitations, many researchers have focused on the development of new immunological and molecular based rapid assays that could enable early diagnosis of infection and accurate identification of fungal pathogens causing superficial and invasive infection. Therefore, in order to overcome the limitations, many researchers have focused on the development of new immunological and molecular based rapid assays that could enable early diagnosis of infection and accurate identification of fungal pathogens causing superficial and invasive infection. As for the use of GM in diagnosis of invasive aspergilosis, recently published data suggest that detection of this Aspergillus Ag in blood and parallel PCR diagnostics provide very high sensitivity of 99% with specificity of 64% which influence 100% negative predictive value in high risk patients and enable the consideration of no-existing invasive aspergillosis in these patients and no need for antifungal therapy. abstract: Traditional, culture based methods for the diagnosis of fungal infections are still considered as gold standard, but they are time consuming and low sensitive. Therefore, in order to overcome the limitations, many researchers have focused on the development of new immunological and molecular based rapid assays that could enable early diagnosis of infection and accurate identification of fungal pathogens causing superficial and invasive infection. In this brief review, we highlighted the advantages and disadvantages of conventional diagnostic methods and possibility of non-culture based assays in diagnosis of superficial fungal infections and presented the overview on currently available immunochromatographic assays as well as availability of biomarkers detection by immunodiagnostic procedures in prompt and accurate diagnosis of invasive fungal infections. In addition, we presented diagnostic efficiency of currently available molecular panels and researches in this area. url: https://api.elsevier.com/content/article/pii/S1156523318300076 doi: 10.1016/j.mycmed.2018.03.001 id: cord-259458-o2yts5pq author: O’Grady, Kerry‐Ann F. title: Successful application of a simple specimen transport method for the conduct of respiratory virus surveillance in remote Indigenous communities in Australia date: 2011-03-21 words: 3636.0 sentences: 176.0 pages: flesch: 49.0 cache: ./cache/cord-259458-o2yts5pq.txt txt: ./txt/cord-259458-o2yts5pq.txt summary: This study assessed the sensitivity of a simple method for transporting respiratory samples from a remote setting for viral PCR compared with frozen specimens. To inform the design of surveillance and intervention studies addressing respiratory infections in remote communities, we compared the sensitivity of a simple, cost-efficient method for transporting respiratory samples from a remote setting for viral real-time PCR with transport using frozen specimens. Given the sensitivity and specificity of real-time PCR diagnosis, we considered a specimen from either nostril positive for any virus to represent a true-positive, similar to previous studies (Lambert et al. Determining the aetiology and burden of viral respiratory infections in remote communities has to date been limited by the inability to store and transport clinical specimens requiring freezing ⁄ refrigeration to urban laboratories. We propose that this method, combining standard clinic refrigeration and weekly surface mailing of specimens combined with real-time PCR, can be used for viral respiratory research in remote locations. abstract: Objective Surveillance programs and research for acute respiratory infections in remote Aboriginal communities are complicated by difficulties in the storage and transport of frozen samples to urban laboratories for testing. This study assessed the sensitivity of a simple method for transporting respiratory samples from a remote setting for viral PCR compared with frozen specimens. Methods We sampled every individual who presented to a remote Aboriginal community clinic in a non‐epidemic respiratory season. Two anterior nasal swabs were collected from each participant. The left nare specimen was mailed to the laboratory via routine postal services. The right nare specimen was transported frozen. Testing for 16 viruses was undertaken using real‐time multiplex PCR. Results A total of 140 participants were enrolled who contributed 150 study visits. Respiratory illnesses accounted for 10% of the reasons for presentation. Sixty‐one viruses were identified in 50 (33.3%) presentations for 40 (28.6%) individuals; bocavirus and rhinovirus were the most common viruses identified (14.0% and 12.6% of episodes respectively). The sensitivity for any virus detected in mailed specimens was 67.2% (95%CI 55.4, 78.9) compared to 65.6% (95%CI 53.7, 77.5) for frozen specimens. Conclusion The mailing of unfrozen nasal specimens from remote communities does not compromise the viability of the specimen for viral studies. url: https://www.ncbi.nlm.nih.gov/pubmed/21418445/ doi: 10.1111/j.1365-3156.2011.02757.x id: cord-313994-l15qa9tr author: Pabbaraju, Kanti title: Detection of enteroviruses and parechoviruses by a multiplex real-time RT-PCR assay date: 2015-02-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Detection of all enteroviruses while excluding cross-detection of rhinoviruses is challenging because of sequence similarities in the commonly used conserved targets for molecular assays. In addition, simultaneous detection and differentiation of enteroviruses and parechoviruses would be beneficial because of a similar clinical picture presented by these viruses. A sensitive and specific real-time RT-PCR protocol that can address these clinical needs would be valuable to molecular diagnostic laboratories. Here we report a multiplex nucleic acid based assay using hydrolysis probes targeting the 5′ non-translated region for the detection and differentiation of enteroviruses and parechoviruses without cross-detection of rhinoviruses. This assay has been shown to detect enteroviruses belonging to the different species in a variety of specimen types without detecting the different species of rhinoviruses. Laboratory validation shows the assay to be sensitive, specific, reproducible, easy to set up and uses generic cycling conditions. This assay can be implemented for diagnostic testing of patient samples in a high throughput fashion. url: https://doi.org/10.1016/j.mcp.2015.02.001 doi: 10.1016/j.mcp.2015.02.001 id: cord-005687-gj6q0ft0 author: Paiva, José-Artur title: Real -time PCR for early microbiological diagnosis: is it time? date: 2017-05-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095199/ doi: 10.1007/s00134-017-4793-1 id: cord-255711-8lojw5cz author: Palmu, Arto A. title: Nasal swab bacteriology by PCR during the first 24‐months of life: A prospective birth cohort study date: 2019-01-04 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Most respiratory bacterial carriage studies in children are based on cross‐sectional samples or longitudinal studies with infrequent sampling points. The prospective Observational Research in Childhood Infectious Diseases birth cohort study intensively evaluated the community‐based epidemiology of respiratory viruses and bacteria during the first 2‐years of life. Here we report the bacteriologic findings. METHODS: Pregnant women in Brisbane, Australia were recruited between September 2010 and October 2012, and their healthy newborn children were followed for the first 2‐years of life. Parents kept a daily symptom diary for the study child, collected a weekly anterior nose swab and completed an illness burden diary when their child met pre‐defined illness criteria. Specimens were tested for respiratory bacteria by real‐time polymerase chain reaction (PCR) assays and those containing human genomic DNA, deemed as high‐quality, were analyzed. RESULTS: Altogether 8100 high‐quality nasal swab specimens from 158 enrolled children were analyzed. Streptococcus pneumoniae, Moraxella catarrhalis, and Haemophilus influenzae were detected in 42.4%, 38.9%, and 14.8% of these samples, respectively. Concomitant detection of bacteria was common. In contrast, Bordetella pertussis, B. parapertussis, Mycoplasma pneumoniae, Chlamydia pneumoniae, and Simkania negevensis were rarely identified. The prevalence of the three major bacteria was higher with increasing age and in the winter and spring months. Siblings and childcare attendance were the other risk factors identified. CONCLUSIONS: We confirmed the feasibility of frequent nasal swabbing by parents for studying bacterial colonization. PCR detected the major respiratory tract bacteria with expected high frequencies, but atypical bacteria were found rarely in this cohort. url: https://www.ncbi.nlm.nih.gov/pubmed/30609299/ doi: 10.1002/ppul.24231 id: cord-276542-lxwls664 author: Pan, Zhongzhou title: Development of a TaqMan-probe-based multiplex real-time PCR for the simultaneous detection of emerging and reemerging swine coronaviruses date: 2020-06-03 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: With the outbreak of the recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019, coronaviruses have become a global research hotspot in the field of virology. Coronaviruses mainly cause respiratory and digestive tract diseases, several coronaviruses are responsible for porcine diarrhea, such as porcine epidemic diarrhea virus (PEDV), porcine deltacoronavirus (PDCoV), and emerging swine acute diarrhea syndrome coronavirus (SADS-CoV). Those viruses have caused huge economic losses and are considered as potential public health threats. Porcine torovirus (PToV) and coronaviruses, sharing similar genomic structure and replication strategy, belong to the same order Nidovirales. Here, we developed a multiplex TaqMan-probe-based real-time PCR for the simultaneous detection of PEDV, PDCoV, PToV, and SADS-CoV for the first time. Specific primers and TaqMan fluorescent probes were designed targeting the ORF1a region of PDEV, PToV, and SADS-CoV and the ORF1b region of PDCoV. The method showed high sensitivity and specificity, with a detection limit of 1 × 10(2) copies/μL for each pathogen. A total of 101 clinical swine samples with signs of diarrhea were analyzed using this method, and the result showed good consistency with conventional reverse transcription PCR (RT-PCR). This method improves the efficiency for surveillance of these emerging and reemerging swine enteric viruses and can help reduce economic losses to the pig industry, which also benefits animal and public health. url: https://www.ncbi.nlm.nih.gov/pubmed/32490723/ doi: 10.1080/21505594.2020.1771980 id: cord-313375-rs3jjiuj author: Panning, Marcus title: Singleplex real-time RT-PCR for detection of influenza A virus and simultaneous differentiation of A/H1N1v and evaluation of the RealStar influenza kit date: 2010-11-13 words: 2309.0 sentences: 159.0 pages: flesch: 57.0 cache: ./cache/cord-313375-rs3jjiuj.txt txt: ./txt/cord-313375-rs3jjiuj.txt summary: Study design: A real-time RT-PCR assay targeting the matrix gene of influenza A viruses was developed and validated using in vitro transcribed RNA derived from influenza A/H1N1v, A/H1N1 and A/H3N2 virus as well as plaque-quantified influenza A/H1N1v, A/H1N1 and A/H3N2 virus samples. Study design: A real-time RT-PCR assay targeting the matrix gene of influenza A viruses was developed and validated using in vitro transcribed RNA derived from influenza A/H1N1v, A/H1N1 and A/H3N2 virus as well as plaque-quantified influenza A/H1N1v, A/H1N1 and A/H3N2 virus samples. After validation of the in-house version the commercial RealStar kit was used to assess the clinical performance and specificity on a panel of influenza viruses including A/H1N1v, A/H1N1, swine A/H1N1, A/H3N2, avian A/H5N1 as well as patient specimens. After validation of the in-house version the commercial RealStar kit was used to assess the clinical performance and specificity on a panel of influenza viruses including A/H1N1v, A/H1N1, swine A/H1N1, A/H3N2, avian A/H5N1 as well as patient specimens. abstract: BACKGROUND: A novel influenza A virus, subtype A/H1N1v emerged in April 2009 and caused the first influenza pandemic of the 21st century. Reliable detection and differentiation from seasonal influenza viruses is mandatory for appropriate case management as well as public health. OBJECTIVES: To develop and technically validate a novel one-step real-time RT-PCR assay which can be used for influenza A virus screening and subtyping of A/H1N1v in a singleplex fashion. To assess the clinical performance of a novel commercial influenza RT-PCR kit based on the in-house version. STUDY DESIGN: A real-time RT-PCR assay targeting the matrix gene of influenza A viruses was developed and validated using in vitro transcribed RNA derived from influenza A/H1N1v, A/H1N1 and A/H3N2 virus as well as plaque-quantified influenza A/H1N1v, A/H1N1 and A/H3N2 virus samples. After validation of the in-house version the commercial RealStar kit was used to assess the clinical performance and specificity on a panel of influenza viruses including A/H1N1v, A/H1N1, swine A/H1N1, A/H3N2, avian A/H5N1 as well as patient specimens. RESULTS: The lower limit of detection of the in-house version was 2149, 1376 and 2994 RNA copies/ml for A/H1N1v, A/H1N1 and A/H3N2, respectively. The RealStar kit displayed 100% sensitivity and specificity and could reliably discriminate influenza A viruses from A/H1N1v. No cross reaction with swine A/H1N1 and A/H1N2 was observed with the RealStar A/H1N1v specific probe. CONCLUSION: Both assays demonstrated high sensitivity and specificity and might assist in the diagnosis of suspected influenza cases. url: https://www.ncbi.nlm.nih.gov/pubmed/21075679/ doi: 10.1016/j.jcv.2010.10.010 id: cord-339804-hktedla3 author: Papillard‐Marechal, Solesne title: Monitoring epidemic viral respiratory infections using one‐step real‐Time Triplex RT‐PCR targeting influenza A and B viruses and respiratory syncytial virus date: 2011-02-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Rapid and specific diagnosis of influenza A/B and respiratory syncytial virus (RSV) viruses is needed for optimal management of patients with acute respiratory infections. In this study, a one‐step triplex real‐time RT‐PCR assay was developed for rapid diagnosis of influenza A/B and RSV infections to optimize diagnosis efficiency of acute respiratory infections. Cell‐culture supernatants and clinical samples were used to evaluate specificity and sensitivity of the assay. The assay was used routinely during two winter epidemics for testing respiratory specimens from 2,417 patients. The limit of detection in cell‐culture supernatant was 1–10 plaque forming units/input (influenza A/B) and 2 × 10(−2) 50% tissue culture infectious dose/input (RSV). In clinical samples, the assay was as sensitive as commercial molecular assays for the detection of each influenza A/B and RSV (Flu‐A/B and RSV‐A/B r‐gene™) individually, and far more sensitive than antigen detection. During the winter 2008–2009, the assay identified 145 RSV, 42 influenza A, and one mixed RSV‐influenza A infections among 298 patients. The next winter, the assay was used in two independent hospital laboratory settings. 776 patients were tested in one hospital and 1,343 in the other, resulting in 184 and 501 RSV, 133 and 150 influenza A, and 1 and 11 mixed RSV‐influenza A infections, respectively, being detected. This new user‐friendly assay allows rapid (within hours), effective molecular diagnosis of single or mixed infections involving influenza A (including seasonal A H1N1 and H3N2, and A(H1N1) 2009), influenza B, and RSV(A/B). The assay is very valuable for managing patients during winter epidemics when influenza and respiratory syncytial viruses co‐circulate. J. Med. Virol. 83:695–701, 2011. © 2011 Wiley‐Liss, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/21328385/ doi: 10.1002/jmv.22006 id: cord-285203-ilxd0ih9 author: Paradiso, Angelo Virgilio title: Clinical meanings of rapid serological assay in patients tested for SARS-Co2 RT-PCR date: 2020-04-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Background RT-PCR test for identifiction of viral nucleic acid is the current standard diagnostic method for the diagnosis of COVID-19 disease but technical reasons limit the utilization of this assay on large scale screenings. Method We verified in a consecutive series of 191 symptomatic patients the clinical information that new rapid serological colorimetric test qualitatively analyzing IgM/IgG expression can provide with respect to standard assay and with respect to clinical outcome of patients. Results Rapid serological test showed a sensitivity of 30% and a specificity of 89% with respect to the standard assay but, interestingly, these performances improve after 8 days of symptoms appearance. After 10 days of symptoms the predictive value of rapid serological test is higher than that of standard assay. When the behaviour of the two immunoglobulins was evaluated with respect to time length of symptoms appearance, no significant difference in immunoglobulins behaviour was shown. Conclusions The rapid serological test analyzed in the present study is candidate to provide information on immunoreaction of the subject to COVID-19 exposure. url: https://doi.org/10.1101/2020.04.03.20052183 doi: 10.1101/2020.04.03.20052183 id: cord-307874-0obomty2 author: Pardon, Bart title: Bovine Respiratory Disease Diagnosis: What Progress Has Been Made in Infectious Diagnosis? date: 2020-05-23 words: 7061.0 sentences: 388.0 pages: flesch: 43.0 cache: ./cache/cord-307874-0obomty2.txt txt: ./txt/cord-307874-0obomty2.txt summary: Evidence-based guidelines for precise interpretation of microbiologic tests results are lacking; however, approaches that have been practically useful for the management of bovine respiratory disease outbreaks are presented. However, naturally resistant to fluoroquinolones 71 Escherichia coli, Gallibacterium anatis, Enterobacter hormaechei, staphylococci, streptococci, fungi Secondary Single reports on cattle-specific strains isolated in pure culture in an outbreak of pneumonia in calves 52, [72] [73] [74] Multiple other bacterial species can be detected in the bovine respiratory tract. 10, 35, 54 However, with current knowledge on the interpretation of DNS results at the individual or group level, samples of the lower respiratory tract are likely a better option to evaluate potential involvement of opportunistic pathogens. In the example where the pathogen is causing the disease in 100% of affected calves, the risk of not finding an infected animal after sampling n cases is (1-Se)n , where Se is the test sensitivity. abstract: When it is desired to identify infectious agents involved in an outbreak of bovine respiratory disease, a variety of possible sampling methods may be used. For field use, the deep nasopharyngeal swab, transtracheal wash, and nonendoscopic bronchoalveolar lavage are most feasible. At present, bacterial culture and polymerase chain reaction testing are most commonly used to identify infectious agents. Interpretation of test results can be challenging, particularly for opportunistic pathogens. Evidence-based guidelines for precise interpretation of microbiologic tests results are lacking; however, approaches that have been practically useful for the management of bovine respiratory disease outbreaks are presented. url: https://api.elsevier.com/content/article/pii/S0749072020300220 doi: 10.1016/j.cvfa.2020.03.005 id: cord-324094-23kzr8rq author: Parida, M. M. title: Rapid and real-time detection technologies for emerging viruses of biomedical importance date: 2008-11-01 words: 5709.0 sentences: 243.0 pages: flesch: 46.0 cache: ./cache/cord-324094-23kzr8rq.txt txt: ./txt/cord-324094-23kzr8rq.txt summary: We have developed two real-time assays ie., SYBR green I based real time reverse transcription polymerase chain reaction (RT-PCR) and RT-loop-mediated isothermal amplification (LAMP) assay for rapid detection as well as typing of some of the emerging viruses of biomedical importance viz. We have developed two real-time assays ie., SYBR green I based real time reverse transcription polymerase chain reaction (RT-PCR) and RT-loop-mediated isothermal amplifi cation (LAMP) assay for rapid detection as well as typing of some of the emerging viruses of biomedical importance viz. A one-step single tube real-time accelerated reverse transcription loop mediated isothermal amplifi cation (RT-LAMP) assays for rapid detection of some of the recently emerged human viral pathogens viz. Rapid detection and differentiation of dengue virus serotypes by a real-time reverse transcription-loop-mediated isothermal amplifi cation assay Development and evaluation of reverse transcription Loop mediated isothermal amplifi cation assay for rapid and Real-time detection of Japanese encephalitis virus abstract: The development of technologies with rapid and sensitive detection capabilities and increased throughput have become crucial for responding to greater number threats posed by emerging and re-emerging viruses in the recent past. The conventional identification methods require time-consuming culturing, and/ or detection of antibodies, which are not very sensitive and specific. The recent advances in molecular biology techniques in the field of genomics and proteomics greatly facilitate the rapid identification with more accuracy. We have developed two real-time assays ie., SYBR green I based real time reverse transcription polymerase chain reaction (RT-PCR) and RT-loop-mediated isothermal amplification (LAMP) assay for rapid detection as well as typing of some of the emerging viruses of biomedical importance viz. dengue, Japanese encephalitis, chikungunya, west Nile, severe acute respiratory syndrome virus (SARS) etc. Both these techniques are capable of detection and differentiation as well as quantifying viral load with higher sensitivity, rapidity, specificity. One of the most important advantages of LAMP is its field applicability, without requirement of any sophisticated equipments. Both these assays have been extensively evaluated and validated with clinical samples of recent epidemics from different parts of India. The establishment of these real time molecular assays will certainly facilitate the rapid detection of viruses with high degree of precision and accuracy in future. url: https://www.ncbi.nlm.nih.gov/pubmed/19208986/ doi: 10.1007/s12038-008-0079-7 id: cord-288253-wqrhiq08 author: Park, Jung-Eun title: Development of transgenic mouse model expressing porcine aminopeptidase N and its susceptibility to porcine epidemic diarrhea virus date: 2015-02-02 words: 5318.0 sentences: 289.0 pages: flesch: 51.0 cache: ./cache/cord-288253-wqrhiq08.txt txt: ./txt/cord-288253-wqrhiq08.txt summary: Because the major pathological changes of the porcine coronaviruses (e.g., TGEV and PEDV) involves enteric diseases, we measured porcine APN expression in the small intestine by RT-PCR, immunoblotting, and IHC. An immunohistochemical analysis, with both anti-Flag and anti-porcine APN antibodies, clearly confirmed porcine APN expression in the brush borders of the absorptive cells in the small intestines of the mouse model (Fig. 4C) . For these purposes, many transgenic mouse models have been developed to study viral pathogenesis, immune responses, and vaccines (Darling et Both wild type and porcine APN transgenic mice were infected with PEDV (5X TCID5010 6 ) orally on day 0. Although significant clinical illness was not observed when the transgenic mice were infected with PEDV, their susceptibility to the virus was confirmed by the detection of viral RNA in various organs with RT-PCR and viral proteins in the small intestines with IHC. abstract: Porcine coronavirus infections have known as they are specific to pigs with predominantly enteric or respiratory diseases. No laboratory animal model is yet been developed in porcine coronaviruses study. Here, we report that development of a transgenic mouse model expressing porcine APN which is susceptible to porcine coronavirus infection. The porcine APN transgene was constructed by fusing with mouse proximal APN promoter at 5′ terminus and bovine growth hormone polyadenylation site at its 3′ terminus. After screen on pubs from the microinjected mice, we confirmed two transgenic lines expressing porcine APN in various organs. We confirmed the susceptibility to porcine epidemic diarrhea virus, one of the porcine coronaviruses. These transgenic mice will be an important tool for research into the porcine coronaviruses. url: https://doi.org/10.1016/j.virusres.2014.12.024 doi: 10.1016/j.virusres.2014.12.024 id: cord-007066-zn10rnrm author: Park, Noh Jin title: Characterization of RNA in Saliva date: 2006-06-01 words: 4637.0 sentences: 285.0 pages: flesch: 62.0 cache: ./cache/cord-007066-zn10rnrm.txt txt: ./txt/cord-007066-zn10rnrm.txt summary: RNA can enter the oral cavity through various routes, including saliva secretions from the 3 major salivary glands (the parotid, submandibular, and sublingual glands) and minor glands, gingival crevice fluid (GCF), and desquamated oral epithelial cells. It is therefore possible that the RPS9 PCR products in panels B and C of Fig. 1 are produced from both RPS9 and RPS9P2 mRNAs. Previous expression-based microarray analysis showed that 185 different transcripts were consistently detected in the supernatants of 10 healthy human saliva samples (6 ) . Although individual variations exist, we detected ␤-actin mRNA in all 3 major salivary glands, GCF, and desquamated oral epithelial cells ( Fig. 2A) , suggesting that RNA enters the oral cavity from different sites. In addition to the saliva samples, we also measured RNA-macromolecule associations in serum and found that ϳ8% and Ͻ1% of ␤-actin mRNA could be detected in serum filtered through 0.45 and 0.22 m pores, respectively (see Fig. 1c in the online Data Supplement). abstract: Background: We have previously shown that human mRNAs are present in saliva and can be used as biomarkers of oral cancer. In this study, we analyzed the integrity, sources, and stability of salivary RNA. Methods: We measured the integrity of salivary RNA with reverse transcription followed by PCR (RT-PCR) or RT-quantitative PCR (RT-qPCR). To study RNA entry sites into the oral cavity, we used RT-PCR analysis of salivary RNA from the 3 major salivary glands, gingival crevice fluid, and desquamated oral epithelial cells. We measured stability of the salivary β-actin mRNA by RT-qPCR of salivary RNA incubated at room temperature for different periods of time. We measured RNA association with other macromolecules by filtering saliva through pores of different sizes before performing RT-qPCR. To assess RNA–macromolecule interaction, we incubated saliva with Triton X-100 for different periods of time before performing RT-qPCR. Results: In most cases, we detected partial- to full-length salivary mRNAs and smaller amounts of middle and 3′ gene amplicons compared with the 5′. RNA was present in all oral fluids examined. Endogenous salivary β-actin mRNA degraded more slowly than exogenous β-actin mRNA, with half-lives of 12.2 and 0.4 min, respectively (P <0.001). Salivary RNA could not pass through 0.22 or 0.45 μm pores. Incubation of saliva with Triton X-100 accelerated degradation of salivary RNA. Conclusions: Saliva harbors both full-length and partially degraded forms of mRNA. RNA enters the oral cavity from different sources, and association with macromolecules may protect salivary RNA from degradation. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7108156/ doi: 10.1373/clinchem.2005.063206 id: cord-289676-tjy7f9rk author: Park, Sang-Ik title: Development of SYBR Green real-time RT-PCR for rapid detection, quantitation and diagnosis of unclassified bovine enteric calicivirus date: 2009-03-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Unclassified bovine enteric calicivirus (BECV) is a newly recognized bovine enteric calicivirus that differs from bovine norovirus, and which causes diarrhea in the small intestines of calves. To date, methods such as real-time reverse transcription-polymerase chain reaction (RT-PCR) have not been developed for the rapid detection, quantitation and diagnosis of BECV. Presently, a BECV-specific SYBR Green real-time RT-PCR assay was evaluated and optimized. Diarrheic specimens (n = 118) collected from 2004 to 2005 were subjected to RT-PCR, nested PCR and SYBR Green real-time RT-PCR. By conventional RT-PCR and nested PCR, 9 (7.6%) and 59 (50%) samples tested positive, respectively, whereas the SYBR Green assay detected BECV in 91 (77.1%) samples. Using BECV RNA standards generated by in vitro transcription, the SYBR Green real-time RT-PCR assay sensitively detected BECV RNA to 1.1 × 10(0) copies/μl (correlation coefficiency = 0.98). The detection limits of the RT-PCR and nested PCR were 1.1 × 10(5) and 1.1 × 10(2) copies/μl, respectively. These results indicate that the SYBR Green real-time RT-PCR assay is more sensitive than conventional RT-PCR and nested PCR assays, and has potential as a reliable, reproducible, specific, sensitive and rapid tool for the detection, quantitation and diagnosis of unclassified BECV. url: https://api.elsevier.com/content/article/pii/S0166093409001050 doi: 10.1016/j.jviromet.2009.03.001 id: cord-320769-qcpua9ck author: Park, Su-Jin title: Molecular epidemiology of bovine toroviruses circulating in South Korea date: 2008-01-25 words: 2807.0 sentences: 147.0 pages: flesch: 61.0 cache: ./cache/cord-320769-qcpua9ck.txt txt: ./txt/cord-320769-qcpua9ck.txt summary: These results suggest that the BToV infections are sporadic in diarrheic calves in South Korea, and the Korean BToV strains are more closely related to the Japanese and Dutch BToVs than to the American and Italian BToVs. Toroviruses within the family Coronaviridae are spherical, oval, elongated, or kidney-shaped enveloped viruses that possess a positive-sense single-stranded, polyadenylated RNA genome of approximately 25-30 kb in length (Cornelissen et al., 1997; Horzinek, 1999; Snijder and Horzinek, 1993) . Based on the partial sequence of the BToV M gene, the Korean BToVs were more closely related to the Japanese and Dutch BToVs than to the American and Italian BToVs. To our knowledge, this is the first report of the detection of BToV shedding and its genetic diversity in diarrheic calves in South Korea. abstract: The prevalence of the bovine torovirus (BToV) and its genetic characterization have been reported in North America, Europe and Japan. Therefore, this study examined the prevalence and genetic diversity of the BToV in a total of 645 diarrheic fecal samples from 629 Korean native beef calf herds using RT-PCR and nested PCR with the primer pairs specific to a part of the BToV membrane (M) gene. Overall, 19 (2.9%) out of 645 diarrheic samples from 19 herds (6.9%) tested positive for BToVs by either RT-PCR or nested PCR. A comparison of the nucleotide (nt) and amino acid (aa) sequences of a part of the BToV M gene (409 bp) among the BToVs showed the Korean BToVs to have comparatively higher sequence homology to the Japanese and Dutch BToVs than to the American and Italian BToVs. Generally, the Korean BToV strains clustered with the Japanese and Dutch BToV strains. However, the American and Italian BToV strains clustered on a separate major branch, suggesting that these are more distantly related to other known BToV strains. These results suggest that the BToV infections are sporadic in diarrheic calves in South Korea, and the Korean BToV strains are more closely related to the Japanese and Dutch BToVs than to the American and Italian BToVs. url: https://www.ncbi.nlm.nih.gov/pubmed/17719729/ doi: 10.1016/j.vetmic.2007.07.012 id: cord-302819-oj33i2ma author: Pasick, J title: Investigation into the Role of Potentially Contaminated Feed as a Source of the First-Detected Outbreaks of Porcine Epidemic Diarrhea in Canada date: 2014-08-07 words: 7941.0 sentences: 363.0 pages: flesch: 55.0 cache: ./cache/cord-302819-oj33i2ma.txt txt: ./txt/cord-302819-oj33i2ma.txt summary: On the SDPP sample that was tested, the following N gene rRT-PCR results were observed: C t of 35.84 for PBS supernatant after 10 000 g, C t of 36.74 for the PBS pellet after 10 000 g, C t of 38.83 for the PBS + Nonidet P-40 Comparison of S protein gene sequences obtained from bioassay piglets versus those of field cases. No significant difference was observed in the kinetics of N gene rRT-PCR positivity in animals that were inoculated with the three SDPP samples that were tested, suggesting that each contained infectious virus. Negative contrast staining electron microscopy of fecal samples collected at 4 dpi from the SDPP-inoculated piglets and the positive control group piglets showed the presence of virus-like particles consistent with coronavirus virions. Similar virus-like particles were also found in the content of the small intestine of a SDPP-inoculated piglet at 7 dpi and a positive control group contact piglet at 5 days post-contact. abstract: SUMMARY: In January 2014, approximately 9 months following the initial detection of porcine epidemic diarrhea (PED) in the USA, the first case of PED was confirmed in a swine herd in south-western Ontario. A follow-up epidemiological investigation carried out on the initial and 10 subsequent Ontario PED cases pointed to feed as a common risk factor. As a result, several lots of feed and spray-dried porcine plasma (SDPP) used as a feed supplement were tested for the presence of PEDV genome by real-time RT-PCR assay. Several of these tested positive, supporting the notion that contaminated feed may have been responsible for the introduction of PEDV into Canada. These findings led us to conduct a bioassay experiment in which three PEDV-positive SDPP samples (from a single lot) and two PEDV-positive feed samples supplemented with this SDPP were used to orally inoculate 3-week-old piglets. Although the feed-inoculated piglets did not show any significant excretion of PEDV, the SDPP-inoculated piglets shed PEDV at a relatively high level for ≥9 days. Despite the fact that the tested PEDV genome positive feed did not result in obvious piglet infection in our bioassay experiment, contaminated feed cannot be ruled out as a likely source of this introduction in the field where many other variables may play a contributing role. url: https://www.ncbi.nlm.nih.gov/pubmed/25098383/ doi: 10.1111/tbed.12269 id: cord-315780-uhi66unn author: Paton, David title: Detection of transmissible gastroenteritis virus by RT-PCR and differentiation from porcine respiratory coronavirus date: 1997-07-31 words: 2905.0 sentences: 149.0 pages: flesch: 53.0 cache: ./cache/cord-315780-uhi66unn.txt txt: ./txt/cord-315780-uhi66unn.txt summary: Abstract An RT-PCR method was developed that amplified genetic material from the 5′ end of the S protein gene of both transmissible gastroenteritis virus (TGEV) and porcine respiratory coronavirus (PRCV), but discriminated between the two by the size of the product generated. Detection of TGEV in clinical specimens was possible using a spin column method to extract RNA and sensitivity was compared to virus isolation and antigen detection ELISA. There are also reports of the use of DNA probes and of RT-PCR as detectors of TGEV RNA (Bae et al., 1991; Vaughn et al., 1996; Wesley et al., 1991; Jackwood et al., 1995) but the methods were not shown to be suitable for the direct detection of virus in clinical samples. Differentiation of transmissible gastroenteritis virus from porcine respiratory coronavirus and other antigenically related coronaviruses by using cDNA probes specific for the 5'' region of the S glycoprotein gene abstract: Abstract An RT-PCR method was developed that amplified genetic material from the 5′ end of the S protein gene of both transmissible gastroenteritis virus (TGEV) and porcine respiratory coronavirus (PRCV), but discriminated between the two by the size of the product generated. A number of restriction endonuclease enzymes were assessed for recognition of the amplicons so produced. The assay was shown to detect viral RNA from all of the 26 different TGEV and PRCV isolates examined, covering a period from 1946 to 1996. Detection of TGEV in clinical specimens was possible using a spin column method to extract RNA and sensitivity was compared to virus isolation and antigen detection ELISA. The method could provide a means of confirming positive results from immunological screening tests such as FAT and ELISA, reducing the need for virus isolation and convalescent serology. url: https://www.ncbi.nlm.nih.gov/pubmed/9255741/ doi: 10.1016/s0166-0934(97)00055-4 id: cord-342383-ckswlo9o author: Pawlowski, C. title: Exploratory analysis of immunization records highlights decreased SARS-CoV-2 rates in individuals with recent non-COVID-19 vaccinations date: 2020-07-28 words: 5479.0 sentences: 273.0 pages: flesch: 51.0 cache: ./cache/cord-342383-ckswlo9o.txt txt: ./txt/cord-342383-ckswlo9o.txt summary: Furthermore, age, race/ethnicity, and blood group stratified analyses reveal significantly lower SARS-CoV-2 rate among black individuals who have taken the PCV13 vaccine, with relative risk of 0.45 at the 5 year time horizon (n: 653, 95% CI: (0.32, 0.64), p-value: 6.9e-05). Given this study population, we assess the rates of SARS-CoV-2 infection among individuals who did and did not receive one of 18 vaccines in the past 1, 2, and 5 years relative to the date of PCR testing. In Figure 6 , we present the results from the tipping point analysis on the statistically significant associations between vaccination and reduced rates of SARS-CoV-2 infection in the overall study population. For example, for the polio vaccine at the 1 year time horizon, an unobserved confounder with a relative risk of 2.78 which is prevalent in 17.8% of the vaccinated cohort and 0% of the unvaccinated cohort could explain the differences in SARS-CoV-2 infection rates that we observe in the data. abstract: Multiple clinical studies are ongoing to assess whether existing vaccines may afford protection against SARS-CoV-2 infection through trained immunity. In this exploratory study, we analyze immunization records from 137,037 individuals who received SARS-CoV-2 PCR tests. We find that polio, Hemophilus influenzae type-B (HIB), measles-mumps-rubella (MMR), varicella, pneumococcal conjugate (PCV13), geriatric flu, and hepatitis A / hepatitis B (HepA-HepB) vaccines administered in the past 1, 2, and 5 years are associated with decreased SARS-CoV-2 infection rates, even after adjusting for geographic SARS-CoV-2 incidence and testing rates, demographics, comorbidities, and number of other vaccinations. Furthermore, age, race/ethnicity, and blood group stratified analyses reveal significantly lower SARS-CoV-2 rate among black individuals who have taken the PCV13 vaccine, with relative risk of 0.45 at the 5 year time horizon (n: 653, 95% CI: (0.32, 0.64), p-value: 6.9e-05). These findings suggest that additional pre-clinical and clinical studies are warranted to assess the protective effects of existing non-COVID-19 vaccines and explore underlying immunologic mechanisms. We note that the findings in this study are preliminary and are subject to change as more data becomes available and as further analysis is conducted. url: https://doi.org/10.1101/2020.07.27.20161976 doi: 10.1101/2020.07.27.20161976 id: cord-158252-l43ztxsl author: Pawlowski, Colin title: Longitudinal laboratory testing tied to PCR diagnostics in COVID-19 patients reveals temporal evolution of distinctive coagulopathy signatures date: 2020-05-21 words: 6126.0 sentences: 221.0 pages: flesch: 35.0 cache: ./cache/cord-158252-l43ztxsl.txt txt: ./txt/cord-158252-l43ztxsl.txt summary: We found that compared to COVIDneg at the time of clinical presentation and diagnostic testing, COVIDpos patients tended to have higher plasma fibrinogen levels and similarly low platelet counts, with approximately 25% of patients in both cohorts showing outright thrombocytopenia. To this end, we instituted a holistic data science platform across an academic health care system that enables machine intelligence to augment the curation of phenotypes and outcomes from 15.2 million EHR clinical notes and associated 3 million lab tests from 1,192 COVID-19positive (COVIDpos) and 47,344 confirmed COVID-19-negative (COVIDneg) patients over a retrospectively defined 2-month observation period straddling the date of the PCR test (see Methods). Conversely, platelet counts were lower in the COVIDpos cohort at the time of clinical presentation but tended to increase over the subsequent 10 days to levels significantly higher than those in COVIDneg patients (Cohen''s D = 0.361, BH-adjusted Mann-Whitney p-value = 0.008, Table 2, Figure 2B ). abstract: Temporal inference from laboratory testing results and their triangulation with clinical outcomes as described in the associated unstructured text from the providers notes in the Electronic Health Record (EHR) is integral to advancing precision medicine. Here, we studied 181 COVIDpos and 7,775 COVIDneg patients subjected to 1.3 million laboratory tests across 194 assays during a two-month observation period centered around their SARS-CoV-2 PCR testing dates. We found that compared to COVIDneg at the time of clinical presentation and diagnostic testing, COVIDpos patients tended to have higher plasma fibrinogen levels and similarly low platelet counts, with approximately 25% of patients in both cohorts showing outright thrombocytopenia. However, these measures show opposite longitudinal trends as the infection evolves, with declining fibrinogen and increasing platelet counts to levels that are lower and higher compared to the COVIDneg cohort, respectively. Our EHR augmented curation efforts suggest a minority of patients develop thromboembolic events after the PCR testing date, including rare cases with disseminated intravascular coagulopathy (DIC), with most patients lacking the platelet reductions typically observed in consumptive coagulopathies. These temporal trends present, for the first time, fine-grained resolution of COVID-19 associated coagulopathy (CAC), via a digital framework that synthesizes longitudinal lab measurements with structured medication data and neural network-powered extraction of outcomes from the unstructured EHR. This study demonstrates how a precision medicine platform can help contextualize each patients specific coagulation profile over time, towards the goal of informing better personalization of thromboprophylaxis regimen. url: https://arxiv.org/pdf/2005.10938v1.pdf doi: nan id: cord-268721-n6dsc4ig author: Pawlowski, Colin title: Inference from longitudinal laboratory tests characterizes temporal evolution of COVID-19-associated coagulopathy (CAC) date: 2020-08-17 words: 6967.0 sentences: 296.0 pages: flesch: 41.0 cache: ./cache/cord-268721-n6dsc4ig.txt txt: ./txt/cord-268721-n6dsc4ig.txt summary: . Summary of lab tests significantly different between COVID pos and propensity score-matched COVID neg cohorts during at least one clinical time window. Conversely, platelet counts were lower in the COVID pos cohort at the time of clinical presentation but tended to increase over the subsequent 10 days to levels significantly higher than those in COVID neg patients (Cohen''s D = 0.229, BH-adjusted Mann-Whitney p-value = 3.6e-3, Table 2, Figure 3B ). This approach offers the advantage of increased granularity at the cost of sample size per time point, but we did identify similar lab tests as altered in COVID pos patients using each approach including the fibrinogen decline and platelet increase in the COVID pos cohort after diagnosis ( Figure 4 ). Our study focusing on COVID-19 patients with longitudinal lab data suggests that COVID-19 is indeed associated with modulation of coagulation related parameters such as platelet counts, fibrinogen levels, and clotting time ( Figure 2) . abstract: Temporal inference from laboratory testing results and triangulation with clinical outcomes extracted from unstructured electronic health record (EHR) provider notes is integral to advancing precision medicine. Here, we studied 246 SARS-CoV-2 PCR-positive (COVID(pos)) patients and propensity-matched 2460 SARS-CoV-2 PCR-negative (COVID(neg)) patients subjected to around 700,000 lab tests cumulatively across 194 assays. Compared to COVID(neg) patients at the time of diagnostic testing, COVID(pos) patients tended to have higher plasma fibrinogen levels and lower platelet counts. However, as the infection evolves, COVID(pos) patients distinctively show declining fibrinogen, increasing platelet counts, and lower white blood cell counts. Augmented curation of EHRs suggests that only a minority of COVID(pos) patients develop thromboembolism, and rarely, disseminated intravascular coagulopathy (DIC), with patients generally not displaying platelet reductions typical of consumptive coagulopathies. These temporal trends provide fine-grained resolution into COVID-19 associated coagulopathy (CAC) and set the stage for personalizing thromboprophylaxis. url: https://doi.org/10.7554/elife.59209 doi: 10.7554/elife.59209 id: cord-327894-b0bsseui author: Pecellín, Lidia Gestoso title: Recomendaciones y uso de los diferentes tipos de test para detección de infección por SARS-COV-2 date: 2020-10-14 words: 4897.0 sentences: 446.0 pages: flesch: 56.0 cache: ./cache/cord-327894-b0bsseui.txt txt: ./txt/cord-327894-b0bsseui.txt summary: En respuesta a la COVID-19, el gobierno español inicialmente instó a limitar el contacto social como medida general, sin embargo, otros países, además, implementaron pruebas generalizadas para la infección por SARS-COV-2 desde el principio de la pandemia. Son test sencillos de hacer, pero deben ser interpretados con prudencia, en relación con el curso de la infección, sobre todo por la tasa de falsos negativos en la detección de IgM ya que la respuesta de IgM en un enfermo COVID-19 puede tardar en aparecer desde varios días a dos semanas 21 Algunos estudios han mostrado que durante los primeros 7 días desde el inicio de síntomas, menos de un 40% de pacientes presentan anticuerpos IgM detectables. abstract: En la actual crisis provocada por el SARS-CoV-2, surge la necesidad global de conocer y combatir el virus. Una de las estrategias es rastrear y diagnosticar los casos con el fin de aislar e interrumpir la cadena epidemiológica. Por ello, el objetivo de este artículo es describir las distintas pruebas diagnósticas más utilizadas y analizar su validez y recomendaciones de uso según la evidencia científica y las principales recomendaciones nacionales e internacionales de sociedades científicas y organismos de referencia. Desde el inicio de la pandemia la disponibilidad de test ha estado supeditada a las condiciones del propio mercado de fabricación y a las directrices marcadas en cada país. Entre los tipos de test más utilizados cabe destacar la PCR, los Tests de detección de anticuerpos (IgG e IGM) y anticuerpos totales (Ab), también conocidos como tests rápidos, y los tests de detección de antígenos en exudado naso-faríngeo u otras muestras respiratorias de vías altas/bajas. Para cada uno de estos tests, es necesario conocer sus recomendaciones de uso y el procedimiento para la toma de muestras, siendo fundamental para minimizar las alteraciones en los resultados debido a una manipulación deficitaria. Asimismo, se recomienda determinar el momento más adecuado para la toma de muestras y su adecuada interpretación de los resultados obtenidos, que siempre ha de ser considerada junto con la sintomatología del paciente para la toma de decisiones clínicas. In the current crisis caused by SARS-CoV-2, there is a global need to know and combat the virus. One of the strategies is to track and diagnose cases in order to isolate and interrupt the epidemiological chain. Therefore, the aim of this article is to describe the different most used diagnostic tests and analyze their validity and recommendations for use according to scientific evidence and the main national and international recommendations of scientific societies and reference organizations. Since the beginning of the pandemic, the availability of tests has been subject to the conditions of the manufacturing market itself and to the guidelines set in each country. Among the most used types of tests, it is worth highlighting PCR, antibody detection tests (IgG and IGM) and total antibodies (Ab), also known as rapid tests, and tests for the detection of antigens in nasopharyngeal exudate or other upper / lower respiratory samples. For each of these tests, it is necessary to know their recommendations for use and the procedure for taking samples, which is essential to minimize alterations in the results due to poor handling. Likewise, it is recommended to determine the most appropriate moment for taking samples and their adequate interpretation of the results obtained, which must always be considered together with the patient's symptoms for clinical decision-making. url: https://api.elsevier.com/content/article/pii/S1130862120304952 doi: 10.1016/j.enfcli.2020.10.001 id: cord-022053-idft1p6d author: Pecora, Nicole title: New Technologies for the Diagnosis of Infection date: 2017-07-21 words: 11496.0 sentences: 610.0 pages: flesch: 40.0 cache: ./cache/cord-022053-idft1p6d.txt txt: ./txt/cord-022053-idft1p6d.txt summary: Organisms commonly identified this way include spirochetes, mycobacteria, DNA viruses, Aspergillus, Candida, and Toxoplasma, although special reference laboratories (e.g., The Infectious Disease Pathology Branch at the Centers for Disease Control and Prevention) have a wide range of antibodies for common to exotic pathogens for tissue confirmation. These include highly sensitive probes for use in direct specimens, to alternative amplification methods, rapid assays of single targets, and multiplexed systems that allow for the detection of many organisms in one assay. Application of RNA-ISH to Aspergillus and Candida in FFPE showed less sensitivity than real-time PCR with sequencing (gold standard), although some FISH-positive, PCRnegative cases with obvious fungal elements were seen, suggesting refinements of this technique may be valuable for rapid identification of these common organisms, especially if mucormycosis is in the differential. Comparative evaluation of the Bruker Biotyper and Vitek MS matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry systems for identification of yeasts of medical importance abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152403/ doi: 10.1016/b978-0-323-44585-6.00006-0 id: cord-325068-j1lfq60o author: Pene, Frédéric title: Coronavirus 229E-Related Pneumonia in Immunocompromised Patients date: 2003-10-01 words: 2583.0 sentences: 134.0 pages: flesch: 35.0 cache: ./cache/cord-325068-j1lfq60o.txt txt: ./txt/cord-325068-j1lfq60o.txt summary: The results of inoculation tests performed with HUH7 cells were also positive, revealing corona-like particles that were subsequently identified as coronavirus 229E by RT-PCR performed on both culture supernatant and BAL fluid specimens. However, respiratory symptoms only appeared after completion of antiviral treatment and improvement of skin eruptions, and both viral culture and PCR for VZV performed on BAL fluid specimens were negative. The prevalence of coronavirus pulmonary infections among immunocompromised patients is unknown, and it is probably largely underestimated in the absence of the routine performance of sensitive cell culture, RT-PCR, or electron microscopy on BAL fluid specimens. Thus, only 1 case of coronavirus-associated pneumonia was previously described in an immunocompromised patient following autologous bone marrow transplantation, with the diagnosis based on the presence of viral particles in BAL fluid specimens [22] . abstract: Coronaviruses strains 229E and OC43 have been associated with various respiratory illnesses ranging from the self-resolving common cold to severe pneumonia. Although chronic underlying conditions are major determinants of severe respiratory virus infections, few data about coronavirus-related pneumonia in immunocompromised patients are available. Here we report 2 well-documented cases of pneumonia related to coronavirus 229E, each with a different clinical presentation. Diagnosis was made on the basis of viral culture and electron microscopy findings that exhibited typical crown-like particles and through amplification of the viral genome by reverse transcriptase—polymerase chain reaction. On the basis of this report, coronaviruses should be considered as potential causative microorganisms of pneumonia in immunocompromised patients. url: https://www.ncbi.nlm.nih.gov/pubmed/13130404/ doi: 10.1086/377612 id: cord-340336-u59l0taa author: Perchetti, Garrett A. title: Multiplexing primer/probe sets for detection of SARS-CoV-2 by qRT-PCR date: 2020-06-08 words: 1390.0 sentences: 99.0 pages: flesch: 50.0 cache: ./cache/cord-340336-u59l0taa.txt txt: ./txt/cord-340336-u59l0taa.txt summary:  -Of all 356 samples tested, triplexing demonstrated 99.2% (n=353/356) assay agreement Abstract: Background -The novel respiratory virus SARS-CoV-2, responsible for over 380,000 COVID-19 related deaths, has caused significant strain on healthcare infrastructure and clinical laboratories globally. Methods -Nasopharyngeal swabs submitted to UW Virology for SARS-CoV-2 clinical testing were extracted, amplified by our laboratory developed test (LDT) -a CDC-based quantitative reverse transcriptase PCR reaction -and analyzed for agreement between the multiplexed assay. Methods -Nasopharyngeal swabs submitted to UW Virology for SARS-CoV-2 clinical testing were extracted, amplified by our laboratory developed test (LDT) -a CDC-based quantitative reverse transcriptase PCR reaction -and analyzed for agreement between the multiplexed assay. To increase throughput of SARS-CoV-2 testing in clinical laboratories, we designed a multiplexed real-time quantitative reverse transcription PCR (qRT-PCR) assay utilizing primers and probe sets from the CDC combined with an internal extraction control. abstract: BACKGROUND: The novel respiratory virus SARS-CoV-2, responsible for over 380,000 COVID-19 related deaths, has caused significant strain on healthcare infrastructure and clinical laboratories globally. The pandemic's initial challenges include broad diagnostic testing, consistent reagent supply lines, and access to laboratory instruments and equipment. In early 2020, primer/probe sets distributed by the CDC utilized the same fluorophore for molecular detection - requiring multiple assays to be run in parallel - consuming valuable and limited resources. METHODS: Nasopharyngeal swabs submitted to UW Virology for SARS-CoV-2 clinical testing were extracted, amplified by our laboratory developed test (LDT) - a CDC-based quantitative reverse transcriptase PCR reaction - and analyzed for agreement between the multiplexed assay. Laboratory- confirmed respiratory infection samples were included to evaluate assay cross-reaction specificity. RESULTS: Triplexing correctly identified SARS-CoV-2 in 98.4% of confirmed positive or inconclusive patient samples by single-plex LDT (n = 183/186). All 170 SARS-CoV-2 negative samples tested by single-plex LDT were negative by triplexing. Other laboratory-confirmed respiratory infections did not amplify for SARS-CoV-2 in the triplex reaction. CONCLUSIONS: Multiplexing two virus-specific gene targets and an extraction control was found to be comparable to running parallel assays independently, while significantly improving assay throughput. url: https://www.sciencedirect.com/science/article/pii/S1386653220302419?v=s5 doi: 10.1016/j.jcv.2020.104499 id: cord-315476-7rdiesav author: Peret, Teresa C. T. title: Characterization of Human Metapneumoviruses Isolated from Patients in North America date: 2002-06-01 words: 1959.0 sentences: 119.0 pages: flesch: 54.0 cache: ./cache/cord-315476-7rdiesav.txt txt: ./txt/cord-315476-7rdiesav.txt summary: In this study, 11 isolates from 10 patients with respiratory disease from Quebec, Canada, were tested by a reverse-transcriptase polymerase chain reaction based on the fusion protein gene. In this study, 11 isolates from 10 patients with respiratory disease from Quebec, Canada, were tested by a reverse-transcriptase polymerase chain reaction based on the fusion protein gene. In the present article, we describe polymerase chain reaction (PCR) and sequencing studies done on 11 isolates from respiratory specimens from 10 Canadian patients with acute respiratory tract illness. Published nucleocapsid (N) and fusion (F) gene sequences of HMPV and avian pneumovirus were used to develop primers for detection and sequencing of HMPV at the Respiratory Virus Section (Centers for Disease Control and Prevention, Atlanta). We detected virus in isolates from children with acute respiratory tract infection, as described in the first report of HMPV [1] . abstract: Human metapneumovirus (HMPV) was recently identified in The Netherlands and was linked to acute respiratory tract illness. In this study, 11 isolates from 10 patients with respiratory disease from Quebec, Canada, were tested by a reverse-transcriptase polymerase chain reaction based on the fusion protein gene. Identified sequences were consistent with HMPV. The patients were 2 months to 87 years of age (median age, 58 years) and presented with acute respiratory tract illness during the winter season. Sequence studies of the nucleocapsid, fusion, and polymerase genes identified 2 main lineages of HMPV and cocirculation of both lineages during the same year. These findings support a previous finding that HMPV is a human respiratory pathogen that merits further study. url: https://www.ncbi.nlm.nih.gov/pubmed/12023774/ doi: 10.1086/340518 id: cord-023830-w218ogsk author: Perlin, David title: Rapid Detection of Bioterrorism Pathogens date: 2008-09-10 words: 6048.0 sentences: 292.0 pages: flesch: 38.0 cache: ./cache/cord-023830-w218ogsk.txt txt: ./txt/cord-023830-w218ogsk.txt summary: The inadequacy of phenotypic-based diagnostic assays is illustrated graphically by the ''''gold standard'''' public health laboratory-testing algorithm that was in place for positive identification of Bacillus anthracis from environmental samples during the October 2001 anthrax outbreak (Fig. 16.1a) . Genomic differences between microbes offer an alternative to culturing for detection and identification of pathogens by providing species-specific DNA targets that can be accurately resolved by molecular methodology. Polymerase chain reaction (PCR)-based amplification of highly conserved ribosomal RNA (rRNA) genes, intergenic sequences, and specific toxin genes is currently the most reliable approach for identification of bacterial, fungal and many viral pathogenic agents. Most importantly, these genetic probing systems offer rapid turn around time (1-6 h) and are suitable for high throughput, automated multiplex operations critical for use in clinical diagnostic laboratories. Rapid diagnostic assays in the genomic biology era: detection and identification of infectious disease and biological weapon agents abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7176176/ doi: 10.1007/978-1-59745-326-4_16 id: cord-292772-xdic7rcy author: Petini, Matteo title: Nested–polymerase chain reaction detection of Pneumocystis carinii f. sp. canis in a suspected immunocompromised Cavalier King Charles spaniel with multiple infections date: 2019-04-26 words: 2467.0 sentences: 158.0 pages: flesch: 45.0 cache: ./cache/cord-292772-xdic7rcy.txt txt: ./txt/cord-292772-xdic7rcy.txt summary: Bordetella bronchiseptica, Mycoplasma spp., and Pneumocystis carinii were identified by polymerase chain reaction testing, and Klebsiella pneumonia was cultured from the bronchoalveolar lavage fluid. canis in a suspected immunocompromised Cavalier King Charles Spaniel with concurrent pulmonary and urinary tract infections involving four different pathogens, and highlights the importance of the use of polymerase chain reaction testing to detect canine Pneumocystis spp. 1 In the veterinary literature, there are many published cases of confirmed canine pneumocystosis-most of which described cases of young to middle-age dogs with suspected immunodeficiency, with the Miniature Dachshund, and the Cavalier King Charles Spaniel (CKCS) breeds most commonly reported. This case report, in the authors'' opinion, highlights four points about the diagnosis and clinical presentation of dogs with Pneumocystis spp. Second, the detection of the fungal pathogen was achieved through PCR testing of a BAL sample which was negative with microscopic visualization for Pneumocystis spp. abstract: A 7-month-old Cavalier King Charles Spaniel female was referred due to a chronic cough refractory to antibiotic treatments. Laboratory findings showed leukocytosis, increased serum C-reactive protein, hypogammaglobulinemia, and decreased total serum immunoglobulin G concentration. Thoracic radiographs showed a mild bronchial pattern. Cytology of the bronchoalveolar lavage fluid revealed a septic inflammation. Bordetella bronchiseptica, Mycoplasma spp., and Pneumocystis carinii were identified by polymerase chain reaction testing, and Klebsiella pneumonia was cultured from the bronchoalveolar lavage fluid. Moreover, Escherichia coli was also cultured from urine. Pneumocystis spp. identification was done by sequencing of genetic amplicons. The dog died due to cardiopulmonary arrest secondary to a spontaneous pneumothorax on the day following the procedure. This report documents the detection of Pneumocystis carinii f. sp. canis in a suspected immunocompromised Cavalier King Charles Spaniel with concurrent pulmonary and urinary tract infections involving four different pathogens, and highlights the importance of the use of polymerase chain reaction testing to detect canine Pneumocystis spp. in cases with negative bronchoalveolar lavage cytology. url: https://doi.org/10.1177/2050313x19841169 doi: 10.1177/2050313x19841169 id: cord-001858-nmi39n6h author: Petriccione, Milena title: Reference gene selection for normalization of RT-qPCR gene expression data from Actinidia deliciosa leaves infected with Pseudomonas syringae pv. actinidiae date: 2015-11-19 words: 5567.0 sentences: 286.0 pages: flesch: 50.0 cache: ./cache/cord-001858-nmi39n6h.txt txt: ./txt/cord-001858-nmi39n6h.txt summary: title: Reference gene selection for normalization of RT-qPCR gene expression data from Actinidia deliciosa leaves infected with Pseudomonas syringae pv. Primer sequence (5′-3′) BestKeeper and the deltaCt method) were used to evaluate the stability of expression of selected RGs. The analyses were performed for three comparison groups considering both low-and high-dose bacterial inocula in the leaves and their combined dataset. In kiwifruit leaves with a high dose of bacterial inoculum, BestKeeper revealed that only the expression of TUB overcame the stability threshold; CYP and GAPDH were considered to be the most stable genes, with SD values of 0.50 and 0.61, respectively (Table 3 ). The expression of three genes encoding the reactive oxygen species (ROS) scavenging enzymes ascorbate peroxidase (APX), superoxide dismutase (SOD) and catalase (CAT), induced during the systemic infection of kiwifruit leaves with PSA, were chosen to further validate the reliability of the selected RGs for the normalization of RT-qPCR data. abstract: Normalization of data, by choosing the appropriate reference genes (RGs), is fundamental for obtaining reliable results in reverse transcription-quantitative PCR (RT-qPCR). In this study, we assessed Actinidia deliciosa leaves inoculated with two doses of Pseudomonas syringae pv. actinidiae during a period of 13 days for the expression profile of nine candidate RGs. Their expression stability was calculated using four algorithms: geNorm, NormFinder, BestKeeper and the deltaCt method. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and protein phosphatase 2A (PP2A) were the most stable genes, while β-tubulin and 7s-globulin were the less stable. Expression analysis of three target genes, chosen for RGs validation, encoding the reactive oxygen species scavenging enzymes ascorbate peroxidase (APX), superoxide dismutase (SOD) and catalase (CAT) indicated that a combination of stable RGs, such as GAPDH and PP2A, can lead to an accurate quantification of the expression levels of such target genes. The APX level varied during the experiment time course and according to the inoculum doses, whereas both SOD and CAT resulted down-regulated during the first four days, and up-regulated afterwards, irrespective of inoculum dose. These results can be useful for better elucidating the molecular interaction in the A. deliciosa/P. s. pv. actinidiae pathosystem and for RGs selection in bacteria-plant pathosystems. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4652207/ doi: 10.1038/srep16961 id: cord-286555-rz88g3ze author: Petrovan, Vlad title: Evaluation of Commercial qPCR Kits for Detection of SARS-CoV-2 in Pooled Samples date: 2020-07-11 words: 3527.0 sentences: 156.0 pages: flesch: 55.0 cache: ./cache/cord-286555-rz88g3ze.txt txt: ./txt/cord-286555-rz88g3ze.txt summary: The most widely used molecular method approved by the World Health Organization (WHO) and the Centers for Disease Control and Prevention (CDC) to detect SARS-CoV-2 is the real-time reverse transcription polymerase chain reaction (qRT-PCR) [4] . The protocol for the COVID-19 PCR Diatheva Detection Kit used with Fast Gene Probe One Step Mix uses 5 µL of mix 1 mixed with 0.625 µL of mix 2, 9.375 µL of primer/probe mix, and 5 µL of RNA template, with a total volume of 20 µL. An initial interlaboratory validation was performed by the Molecular Pathology Laboratory from the University Emergency Hospital Bucharest, using the PowerCheck 2019-nCoV Real-Time PCR Kit. This study was conducted as part of a surveillance program for COVID-19 implemented by the Romanian government. To determine the analytical sensitivity of the COVID-19 commercial assays used in Romanian hospitals (PowerCheck Kogene 2019-nCoV, COVID-19 PCR Diatheva Detection Kit, and 2019-nCoV CDC EUA), we first evaluated their limit of detection (LOD) by performing 10-fold serial dilutions of the controls provided by the kits. abstract: Due to the current pandemic, a global shortage of reagents has drawn interest in developing alternatives to increase the number of coronavirus tests. One such alternative is sample pooling. We compared commercial kits that are used in COVID-19 diagnostics in terms of their sensitivity and feasibility for use in pooling. In this preliminary study, we showed that pooling of up to 80 samples did not affect the efficacy of the kits. Additionally, the RNA-dependent RNA polymerase (RdRp) gene is a more suitable target in pooled samples than the envelope (E) gene. This approach could provide an easy method of screening a large number of samples and help adjust different governmental regulations. url: https://doi.org/10.3390/diagnostics10070472 doi: 10.3390/diagnostics10070472 id: cord-293590-0xn6mqh6 author: Peña, Andrea A title: An evaluation of potential reference genes for stability of expression in two salmonid cell lines after infection with either Piscirickettsia salmonis or IPNV date: 2010-04-14 words: 3724.0 sentences: 187.0 pages: flesch: 48.0 cache: ./cache/cord-293590-0xn6mqh6.txt txt: ./txt/cord-293590-0xn6mqh6.txt summary: FINDINGS: The expression stability of five commonly used housekeeping genes [beta-actin (ACTB), elongation factor 1-alpha (EF1A), ubiquitin (UBQ), glyceraldehyd-3-phosphate dehydrogenase (GAPDH) and tubulin alpha (TUBA)] were monitored in salmonid cell lines CHSE-214 and RTS11 after infection with two of the most fastidious fish pathogens, the facultative bacterium Piscirickettsia salmonis and the aquabirnavirus IPNV (Infectious Pancreatic Necrosis Virus). CONCLUSION: Based on the data presented here with the cell culture models CHSE-214 and RTS11, we suggest the initial choice of UBQ, ACTB and EF1A as reference genes in qRT-PCR assays for studying the effect of P. Prior validation of the selected reference gene candidates (ACTB, EF1A, GAPDH, UBQ and TUBA), general expression levels based on mean qPCR threshold cycle (Ct) values in control CHSE-214 and RTS11 cells were determined, since extremely high or low expression levels might preclude their usefulness as internal controls ( Figure 3) . abstract: BACKGROUND: Due to the limited number of species specific antibodies against fish proteins, differential gene expression analyses are vital for the study of host immune responses. Quantitative real-time reverse transcription PCR (qRT-PCR) is one of the most powerful tools for this purpose. Nevertheless, the accuracy of the method will depend on the careful selection of genes whose expression are stable and can be used as internal controls for a particular experimental setting. FINDINGS: The expression stability of five commonly used housekeeping genes [beta-actin (ACTB), elongation factor 1-alpha (EF1A), ubiquitin (UBQ), glyceraldehyd-3-phosphate dehydrogenase (GAPDH) and tubulin alpha (TUBA)] were monitored in salmonid cell lines CHSE-214 and RTS11 after infection with two of the most fastidious fish pathogens, the facultative bacterium Piscirickettsia salmonis and the aquabirnavirus IPNV (Infectious Pancreatic Necrosis Virus). After geNorm analysis, UBQ and EF1A appeared as the most stable, although EF1A was slightly upregulated at late stages of P. salmonis infection in RTS11. ACTB instead, showed a good performance in each case, being always considered within the three most stable genes of the panel. In contrast, infection-dependent differential regulation of GAPDH and TUBA was also demonstrated. CONCLUSION: Based on the data presented here with the cell culture models CHSE-214 and RTS11, we suggest the initial choice of UBQ, ACTB and EF1A as reference genes in qRT-PCR assays for studying the effect of P. salmonis and IPNV on the host immune response. url: https://www.ncbi.nlm.nih.gov/pubmed/20398263/ doi: 10.1186/1756-0500-3-101 id: cord-277025-gmy51dx4 author: Pfefferle, Susanne title: Complete Genome Sequence of a SARS-CoV-2 Strain Isolated in Northern Germany date: 2020-06-04 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Here, we describe the complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain isolated from an oropharyngeal swab sample from a female patient with COVID-19 who was infected in Hamburg, northern Germany. url: https://www.ncbi.nlm.nih.gov/pubmed/32499358/ doi: 10.1128/mra.00520-20 id: cord-304058-i8cywew0 author: Pfefferle, Susanne title: Reverse genetic characterization of the natural genomic deletion in SARS-Coronavirus strain Frankfurt-1 open reading frame 7b reveals an attenuating function of the 7b protein in-vitro and in-vivo date: 2009-08-24 words: 9548.0 sentences: 514.0 pages: flesch: 53.0 cache: ./cache/cord-304058-i8cywew0.txt txt: ./txt/cord-304058-i8cywew0.txt summary: title: Reverse genetic characterization of the natural genomic deletion in SARS-Coronavirus strain Frankfurt-1 open reading frame 7b reveals an attenuating function of the 7b protein in-vitro and in-vivo To study the role of ORF 7b in the context of virus replication, we cloned a full genome cDNA copy of Frankfurt-1 in a bacterial artificial chromosome downstream of a T7 RNA polymerase promoter. In the context of viral host switching, it is interesting that several SARS-CoV proteins encoded on subgenomic (sg) RNAs seem to be dispensable for virus replication in cultured cells of primate or rodent origin, as well as in rodent models [17] [18] [19] . Both BACs were sequenced, confirming presence of all marker mutations and absence of any further mutations (refer to Influence on apoptosis and type I interferon induction by overexpression of ORF 7a, ORF 7b, and ORF 7b with the Frankfurt-1-specific deletion Interferon beta promoter-specific reporter gene expression (y-axis), shown as the factor of induction as compared to the mock-transfected, non-superinfected control (see below). abstract: During the outbreak of SARS in 2002/3, a prototype virus was isolated from a patient in Frankfurt/Germany (strain Frankfurt-1). As opposed to all other SARS-Coronavirus strains, Frankfurt-1 has a 45-nucleotide deletion in the transmembrane domain of its ORF 7b protein. When over-expressed in HEK 293 cells, the full-length protein but not the variant with the deletion caused interferon beta induction and cleavage of procaspase 3. To study the role of ORF 7b in the context of virus replication, we cloned a full genome cDNA copy of Frankfurt-1 in a bacterial artificial chromosome downstream of a T7 RNA polymerase promoter. Transfection of capped RNA transcribed from this construct yielded infectious virus that was indistinguishable from the original virus isolate. The presumed Frankfurt-1 ancestor with an intact ORF 7b was reconstructed. In CaCo-2 and HUH7 cells, but not in Vero cells, the variant carrying the ORF 7b deletion had a replicative advantage against the parental virus (4- and 6-fold increase of virus RNA in supernatant, respectively). This effect was neither associated with changes in the induction or secretion of type I interferon, nor with altered induction of apoptosis in cell culture. However, pretreatment of cells with interferon beta caused the deleted virus to replicate to higher titers than the parental strain (3.4-fold in Vero cells, 7.9-fold in CaCo-2 cells). In Syrian Golden Hamsters inoculated intranasally with 10e4 plaque forming units of either virus, mean titers of infectious virus and viral RNA in the lungs after 24 h were increased 23- and 94.8-fold, respectively, with the deleted virus. This difference could explain earlier observations of enhanced virulence of Frankfurt-1 in Hamsters as compared to other SARS-Coronavirus reference strains and identifies the SARS-CoV 7b protein as an attenuating factor with the SARS-Coronavirus genome. Because attenuation was focused on the early phase of infection in-vivo, ORF 7b might have contributed to the delayed accumulation of virus in patients that was suggested to have limited the spread of the SARS epidemic. url: https://www.ncbi.nlm.nih.gov/pubmed/19698190/ doi: 10.1186/1743-422x-6-131 id: cord-320085-n9i54wzh author: Pfefferle, Susanne title: Evaluation of a quantitative RT-PCR assay for the detection of the emerging coronavirus SARS-CoV-2 using a high throughput system date: 2020-03-05 words: 2032.0 sentences: 116.0 pages: flesch: 52.0 cache: ./cache/cord-320085-n9i54wzh.txt txt: ./txt/cord-320085-n9i54wzh.txt summary: We evaluated the performance of a molecular assay for the detection of SARS-CoV-2 on a high-throughput platform, the cobas 6800, using the ''open channel'' for integration of a laboratory-developed assay. We evaluated the performance of a molecular assay for the detection of SARS-CoV-2 on a high-throughput platform, the cobas 6800, using the ''open channel'' for integration of a laboratory-developed assay. The ability to quickly confirm or clear suspected cases is crucial during global outbreak scenarios, especially when clinical manifestations are difficult to distinguish from other respiratory infections such as influenza, molecular diagnostics is key for detection of the emerging virus. In this study, we demonstrated good analytical performance of an adapted SARS-CoV-2 assay on swab samples with an LoD of 689.3 copies/mL (e.g. 275.72 copies/process) at 95% detection probability, which is roughly in line with results published by Corman et al. abstract: Facing the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), high-volume respiratory testing is demanded in laboratories worldwide. We evaluated the performance of a molecular assay for the detection of SARS-CoV-2 on a high-throughput platform, the cobas 6800, using the ‘open channel’ for integration of a laboratory-developed assay. We observed good analytical performance in clinical specimens. The fully automated workflow enables high-throughput testing with minimal hands-on time, while offering fast and reliable results. url: https://doi.org/10.2807/1560-7917.es.2020.25.9.2000152 doi: 10.2807/1560-7917.es.2020.25.9.2000152 id: cord-017600-4e7mw041 author: Pfister, H. -W. title: Infektionen date: 2008 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Trotz Weiterentwicklung moderner Antibiotika in den letzten Jahren sind die Letalitätszahlen der bakteriellen (eitrigen) Meningitis weiterhin hoch; Überlebende haben häufig neurologische Residuen. Die ungünstigen klinischen Verläufe der bakteriellen Meningitis sind meist Folge intrakranieller Komplikationen, wie z. B. eines generalisierten Hirnödems, einer zerebrovaskulären arteriellen oder venösen Beteiligung oder eines Hydrozephalus. Als Folge dieser Komplikationen kommt es häufig zu einem Anstieg des intrakraniellen Drucks. Bei schweren, komplizierten klinischen Verläufen der bakteriellen Meningitis kommen oft adjuvante Therapiemaßnahmen (z. B. intravenöse Gabe von hyperosmolaren Substanzen, externe Ventrikeldrainage) zum Einsatz. Bei Nachweis einer meningitisassoziierten septischen Sinus-/Venenthrombose erfolgt die dosisadaptierte intravenöse Heparintherapie. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122197/ doi: 10.1007/978-3-540-68317-9_35 id: cord-308945-i2agpvhk author: Phipps, William S title: SARS-CoV-2 Antibody Responses Do Not Predict COVID-19 Disease Severity date: 2020-07-15 words: 3167.0 sentences: 174.0 pages: flesch: 50.0 cache: ./cache/cord-308945-i2agpvhk.txt txt: ./txt/cord-308945-i2agpvhk.txt summary: METHODS: A total of 967 subjects were tested for IgG antibodies reactive to SARS-CoV-2, including 172 suspected cases of SARS-CoV-2, 656 plasma samples from healthy donors, 49 sera from patients with rheumatic disease, and 90 specimens from individuals positive for polymerase chain reaction (PCR)–based respiratory viral panel. Long et al 8 have described a variable antiviral IgM and IgG immune response to SARS-CoV-2 infection in a Chinese population in which seroconversion in a group of 285 patients from 3 hospitals showed IgG positivity for all cases beyond 17 to 19 days. The goals of this study were to ascertain key performance metrics of analytical specificity and cross-reactivity for a SARS-CoV-2 IgG serologic assay, perform a detailed cross-sectional and serial assessment of IgG and IgM antibody responses in suspected COVID-19 patients, and determine their relation to disease severity. SARS-CoV-2 IgG antibody results agreed with the PCR-negative samples for 96 of 97 (99%) of cases, including 55 instances of patients with new or acute-on-chronic symptoms suspicious for COVID-19 and with known time of onset. abstract: OBJECTIVES: Initial reports indicate adequate performance of some serology-based severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) assays. However, additional studies are required to facilitate interpretation of results, including how antibody levels impact immunity and disease course. METHODS: A total of 967 subjects were tested for IgG antibodies reactive to SARS-CoV-2, including 172 suspected cases of SARS-CoV-2, 656 plasma samples from healthy donors, 49 sera from patients with rheumatic disease, and 90 specimens from individuals positive for polymerase chain reaction (PCR)–based respiratory viral panel. A subgroup of SARS-CoV-2 PCR-positive cases was tested for IgM antibodies by proteome array method. RESULTS: All specificity and cross-reactivity specimens were negative for SARS-CoV-2 IgG antibodies (0/795, 0%). Positive agreement of IgG with PCR was 83% of samples confirmed to be more than 14 days from symptom onset, with less than 100% sensitivity attributable to a case with severe immunosuppression. Virus-specific IgM was positive in a higher proportion of cases less than 3 days from symptom onset. No association was observed between mild and severe disease course with respect to IgG and IgM levels. CONCLUSIONS: The studied SARS-CoV-2 IgG assay had 100% specificity and no adverse cross-reactivity. Measures of IgG and IgM antibodies did not predict disease severity in our patient population. url: https://www.ncbi.nlm.nih.gov/pubmed/32666092/ doi: 10.1093/ajcp/aqaa123 id: cord-005865-7lohh5ty author: Pipper, Juergen title: Catching bird flu in a droplet date: 2007-09-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: It is assumed that a timely mass administration of antiviral drugs, backed by quarantines and social distancing, could contain a nascent influenza epidemic at its source, provided that the first clusters of cases were localized within a short time. However, effective routine surveillance may be impossible in countries lacking basic public health resources. For a global containment strategy to be successful, low-cost, easy-to-use handheld units that permit decentralized testing would be vital. Here we present a microfluidic platform that can detect the highly pathogenic avian influenza virus H5N1 in a throat swab sample by using magnetic forces to manipulate a free droplet containing superparamagnetic particles. In a sequential process, the viral RNA is isolated, purified, preconcentrated by 50,000% and subjected to ultrafast real-time RT-PCR. Compared to commercially available tests, the bioassay is equally sensitive and is 440% faster and 2,000–5,000% cheaper. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nm1634) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095864/ doi: 10.1038/nm1634 id: cord-008678-zi3aunqz author: Piñana, José Luis title: Clinical significance of Pneumocystis jirovecii DNA detection by real-time PCR in hematological patient respiratory specimens date: 2020-01-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133636/ doi: 10.1016/j.jinf.2020.01.001 id: cord-351643-8ce807ub author: Poon, LLM title: Rapid detection of reassortment of pandemic H1N1/2009 influenza virus date: 2010-08-01 words: 2085.0 sentences: 111.0 pages: flesch: 52.0 cache: ./cache/cord-351643-8ce807ub.txt txt: ./txt/cord-351643-8ce807ub.txt summary: It should be noted that all of the PCR-positive viral segments fall into the sister group of pandemic H1N1 (see online Supplemental Fig. 2) , which demonstrates the feasibility of using these real-time RT-PCR assays to detect genes from contemporary TR (PB2, PB1, PA, HA, NP, and NS) and EA (NA and M) swine viruses (2 ) . In contrast, melting-curve signals of the HA gene derived from the TR-H1 swine viruses were found to be different from that of the pandemic H1N1/ 2009 virus (Fig. 1B The sequence similarity and diversity of influenza viruses were the major hurdles for the primer design of this study. By use of the 8 established real-time PCR assays we tested RNA from 2 randomly selected samples of the original swine swab specimens that contained the pandemic H1N1/2009 virus. It should be noted that none of these assays can detect viral genes derived from seasonal human influenza viruses. abstract: BACKGROUND: Influenza viruses can generate novel reassortants in co-infected cells. The global circulation and occasional introductions of pandemic H1N1/2009 virus in humans and in pigs, respectively, might provide opportunities for this virus to reassort with other influenza viruses. These possible reassortment events might alter virulence and/or transmissibility of the new reassortants. Investigations that can detect such possible reassortants should therefore be included as a part of pandemic influenza surveillance plans. METHODS: We established a real-time RT-PCR-based strategy for the detection of reassortment of pandemic H1N1/2009 virus. Singleplex SYBR green-based RT-PCR assays specific for each gene segment of pandemic H1N1/2009 were developed. These assays were evaluated by influenza viruses with different genetic backgrounds. RESULTS: All human pandemic H1N1 (N=27) and all seasonal human (N=58) isolates were positive and negative, respectively, for all 8 segments. Of 48 swine influenza viruses isolated from our on-going surveillance program of influenza viruses in swine, 10 were positive in all reactions. All 8 viral segments of these 10 samples were confirmed to be of pandemic H1N1 origin, indicating that these were caused by zoonotic transmissions from human to pigs. The 38 swine viruses that are non-pandemic H1N1/2009 had 1 to 6 gene segments positive in the tests. Further characterization of these non-pandemic H1N1/2009 swine viruses indicated that these PCR positive genes are the precursor genes of pandemic H1N1/2009 virus. CONCLUSIONS: Our results demonstrated that these assays can detect re-introductions of pandemic H1N1/2009 virus in pigs. These assays might be useful screening tools for identifying viral reassortants derived from pandemic H1N1/2009 or its precursors. url: https://www.ncbi.nlm.nih.gov/pubmed/20567024/ doi: 10.1373/clinchem.2010.149179 id: cord-300685-bcjnujlj author: Poon, Leo L M title: Rapid Diagnosis of a Coronavirus Associated with Severe Acute Respiratory Syndrome (SARS) date: 2003-06-01 words: 2425.0 sentences: 115.0 pages: flesch: 54.0 cache: ./cache/cord-300685-bcjnujlj.txt txt: ./txt/cord-300685-bcjnujlj.txt summary: The detection of live virus (4 ) and the detection of high copy numbers of viral sequence from NPA samples in the current study clearly support that the concept that cough and sneeze droplets from SARS patients are a major route of spread of this infectious agent. Interestingly, two of four available stool samples from the SARS patients in this study were positive in the assay (data not shown). RNA samples from this study were subjected to nested reverse transcription-PCR (4 ), and no evidence of metapneumovirus infection was detected in any of the patients in this study (data not shown), suggesting that the novel coronavirus is the key player in the pathogenesis of SARS. The PCR products from all 23 positive cases in this study had the same melting point, strongly suggesting that there was no viral sequence variation in the target region of samples collected at the two Hong Kong hospitals during the 1-month period of patient accrual. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/12765993/ doi: 10.1373/49.6.953 id: cord-017072-qwe1ne3q author: Poritz, Mark A. title: Multiplex PCR for Detection and Identification of Microbial Pathogens date: 2018-11-10 words: 7205.0 sentences: 299.0 pages: flesch: 41.0 cache: ./cache/cord-017072-qwe1ne3q.txt txt: ./txt/cord-017072-qwe1ne3q.txt summary: Multiplex respiratory panels have the potential to improve patient management and lower overall healthcare costs by improving use of influenza antivirals, reducing inappropriate use of antibiotics and antivirals, reducing use of healthcare resource (e.g., additional laboratory or imaging procedures), informing appropriate infection control practices, and reducing length of hospital, emergency department, and intensive care unit (ICU) stay. In another study evaluating adult patients with a positive influenza result on a multiplex respiratory panel, Rappo [21] reported a significantly lower odds ratio for hospital admission (p = 0.046), a reduced length of stay (p = 0.040), reductions in antimicrobial duration (p = 0.032), and a reduction in the number of chest radiographs (p = 0.005). As with the individual molecular assays and the MALDI-TOF identification, numerous studies have shown that use of multiplex molecular blood culture panels dramatically reduces the time to organism identification [29] [30] [31] [32] which drives more appropriate pathogen-directed therapy. A retrospective study of the impact of rapid diagnostic testing on time to pathogen identification and antibiotic use for children with positive blood cultures abstract: Multiplexed nucleic acid-based tests for infectious disease have become a standard part of clinical laboratory practice. These tests provide a comprehensive syndrome-based approach to determine the etiological agent of disease. The technology underlying these different systems is reviewed here with a special focus on the BioFire FilmArray® platform. The literature on the clinical utility and cost-effectiveness of these platforms for respiratory, blood culture, and gastrointestinal infections is discussed. Although there are reports showing a clear benefit to the patient or to the healthcare system from adopting a syndromic molecular approach, it is also apparent that clinical laboratories and healthcare providers are still learning how to take full advantage of the new systems. Finally, some improvements to this technology that should appear in the next few years are discussed. These include automated pathogen-specific surveillance based on aggregating the data from these systems, a move toward point-of-care syndromic testing, and further decreases in time to result of the tests. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121544/ doi: 10.1007/978-3-319-95111-9_19 id: cord-319685-dw0qsl4s author: Porter, Emily title: Amino acid changes in the spike protein of feline coronavirus correlate with systemic spread of virus from the intestine and not with feline infectious peritonitis date: 2014-04-25 words: 5690.0 sentences: 272.0 pages: flesch: 58.0 cache: ./cache/cord-319685-dw0qsl4s.txt txt: ./txt/cord-319685-dw0qsl4s.txt summary: Recent evidence suggests that a mutation in the spike protein gene of feline coronavirus (FCoV), which results in an amino acid change from methionine to leucine at position 1058, may be associated with feline infectious peritonitis (FIP). Tissue and faecal samples collected post mortem from cats diagnosed with or without FIP were subjected to RNA extraction and quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR) to detect FCoV RNA. Data evaluating FCoV relative copy numbers in tissue and faecal samples from cats with and without FIP were analysed using a multilevel modelling approach (MLwiN v2.27) [25] , to account for the repeated measures within cats, and a non-parametric Mann-Whitney U test. Moreover, the majority (77%) of FCoV RNA sequences in faecal samples from cats with FIP had a methionine codon at position 1058 in the FCoV S protein gene, suggesting that these animals were shedding an enteric form of the virus. abstract: Recent evidence suggests that a mutation in the spike protein gene of feline coronavirus (FCoV), which results in an amino acid change from methionine to leucine at position 1058, may be associated with feline infectious peritonitis (FIP). Tissue and faecal samples collected post mortem from cats diagnosed with or without FIP were subjected to RNA extraction and quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR) to detect FCoV RNA. In cats with FIP, 95% of tissue, and 81% of faecal samples were PCR-positive, as opposed to 22% of tissue, and 60% of faecal samples in cats without FIP. Relative FCoV copy numbers were significantly higher in the cats with FIP, both in tissues (P < 0.001) and faeces (P = 0.02). PCR-positive samples underwent pyrosequencing encompassing position 1058 of the FCoV spike protein. This identified a methionine codon at position 1058, consistent with the shedding of an enteric form of FCoV, in 77% of the faecal samples from cats with FIP, and in 100% of the samples from cats without FIP. In contrast, 91% of the tissue samples from cats with FIP and 89% from cats without FIP had a leucine codon at position 1058, consistent with a systemic form of FCoV. These results suggest that the methionine to leucine substitution at position 1058 in the FCoV spike protein is indicative of systemic spread of FCoV from the intestine, rather than a virus with the potential to cause FIP. url: https://www.ncbi.nlm.nih.gov/pubmed/24767677/ doi: 10.1186/1297-9716-45-49 id: cord-340481-i3qrxnpr author: Pozo, Francisco title: Aplicación de los métodos moleculares al diagnóstico y el estudio epidemiológico de las infecciones respiratorias causadas por virus date: 2008-07-31 words: 9085.0 sentences: 740.0 pages: flesch: 48.0 cache: ./cache/cord-340481-i3qrxnpr.txt txt: ./txt/cord-340481-i3qrxnpr.txt summary: En comparación con las técnicas de diagnóstico clásicas, como son el cultivo de virus en líneas celulares (CC) o la detección de antígenos mediante ensayos de inmunofluorescencia (IF) u otros métodos, la reacción en cadena de la polimerasa (PCR), en sus múltiples variantes, ha permitido incre-mentar de manera considerable el número de muestras respiratorias en las que se detecta la presencia de alguno de los virus asociados con IRA. La elevada sensibilidad de los ensayos de PCR también comporta algunos inconvenientes para el diagnóstico etiológico de la IRA, como son la detección de virus que se encuentran colonizando la mucosa respiratoria de personas asintomáticas o la detección, a consecuencia de excreción prolongada, del virus en secreciones de pacientes que ya se han recuperado de una infección. abstract: Hasta la fecha se han identificado más de 200 virus pertenecientes a 6 familias taxonómicas diferentes asociados con la infección del tracto respiratorio humano. La utilización generalizada de métodos moleculares en los laboratorios de microbiología clínica no sólo ha aportado grandes ventajas al diagnóstico de estas infecciones, sino también está permitiendo profundizar en el conocimiento de la enfermedad y el comportamiento epidemiológico de los virus causantes. Esta tecnología incrementa de manera notable el rendimiento de detección de virus en las muestras respiratorias, debido a su elevada sensibilidad en comparación con las técnicas clásicas y a la posibilidad de identificar virus no cultivables o de crecimiento fastidioso en las líneas celulares habituales, lo que permite realizar el diagnóstico etiológico con mayor rapidez. Sin embargo, también comporta algunos inconvenientes, como son detectar virus que se encuentran colonizando la mucosa respiratoria de personas asintomáticas, o en secreciones de pacientes que ya se han recuperado de una infección pasada, a consecuencia de excreción prolongada de éstos. La secuenciación de los productos obtenidos en la reacción de amplificación genómica permite caracterizar de forma adicional los virus detectados mediante su genotipado, realizar estudios de epidemiología molecular e identificar resistencias a determinados antivirales, por citar sólo algunos ejemplos. To date, more than two hundred viruses, belonging to six different taxonomic families, have been associated with human respiratory tract infection. The widespread incorporation of molecular methods into clinical microbiology laboratories has not only led to notable advances in the etiological diagnosis of viral respiratory infections but has also increased insight into the pathology and epidemiological profiles of the causative viruses. Because of their high sensitivity, molecular techniques markedly increase the efficiency of viral detection in respiratory specimens, particularly those that fail to propagate successfully in common cell cultures, thus allowing more rapid etiologic diagnosis. However, there are also some disadvantages in the use of these new technologies such as detection of viruses that merely colonize the respiratory tract of healthy people, or those found in the nasopharyngeal secretions of patients who have recovered from respiratory infections, due to longterm viral shedding, when the viruses are unlikely to act as pathogens. Additionally, sequencing of the amplification products allows further characterization of detected viruses, including molecular epidemiology, genotyping, or detection of antiviral resistance, to cite only a few examples. url: https://www.sciencedirect.com/science/article/pii/S0213005X08765376 doi: 10.1016/s0213-005x(08)76537-6 id: cord-006960-9pho3hk6 author: Prakash, R. title: Droplet Microfluidic Chip Based Nucleic Acid Amplification and Real-Time Detection of Influenza Viruses date: 2013-12-27 words: 6279.0 sentences: 286.0 pages: flesch: 51.0 cache: ./cache/cord-006960-9pho3hk6.txt txt: ./txt/cord-006960-9pho3hk6.txt summary: In this work, we have utilized electro-actuation based DMF technology, integrated with suitably tailored resistive micro-heaters and temperature sensors, to achieve chip based real-time, quantitative PCR (qRT-PCR). Performance of the integrated DMF device was analyzed in real-time chip based qRT-PCR detection of in-vitro synthesized influenza A and C virus RNAs during 30-35 PCR cycles. Among the contact temperature control methods, the micro-fabricated resistive heaters/RTDs have smaller power requirement, faster thermal response and higher heating ramp rates and are therefore preferred for the proposed qRT-PCR micro-device. Mixing of the influenza C RNA sample and the off-chip prepared PCR reagents, followed by the RT reaction and thermal cycling over Micro-electrode 1, is shown in Figure 7 . This article demonstrates the design and micro-fabrication of integrated droplet microfluidic device, with nano-textured superhydrophobic top surface, that is capable of electro-handling of PCR samples/reagents, facilitating chip based mixing/sample preparation and chip based qRT-PCR amplification and detection of influenza viruses. abstract: Miniaturized bio-diagnostic devices have the potential to allow for rapid pathogen screening in clinical patient samples, as a low cost and portable alternative to conventional bench-top equipment. Miniaturization of key bio-diagnostic techniques, such as: nucleic acid detection and quantification, polymerase chain reaction (PCR), DNA fingerprinting, enzyme linked immunosorbent assay (ELISA), results in substantial reduction of reaction volumes (expensive samples/reagents) and shorter reaction times. Droplet microfluidics (DMF) is one of several miniaturized bio-sample handling techniques available for manipulating clinical samples and reagents in microliter (10(−6) L) to picoliter (10(−12) L) volume regime. Electro-actuation of sample and reagent in the form of droplets in the aforementioned volume regime, using dielectrophoresis (DEP) and/or Electrowetting (EW) are achieved by means of patterned, insulated metal electrodes on one or more substrates. In this work, we have utilized electro-actuation based DMF technology, integrated with suitably tailored resistive micro-heaters and temperature sensors, to achieve chip based real-time, quantitative PCR (qRT-PCR). This qRT-PCR micro-device was utilized to detect and quantify the presence of influenza A and C virus nucleic acids, using in-vitro synthesized viral RNA segments. The experimental analysis of the DMF micro-device confirms its capabilities in qRT-PCR based detection and quantification of pathogen samples, with accuracy levels comparable to established commercial bench-top equipment (PCR efficiency ∼95%). The limit of detection (LOD) of the chip based qRT-PCR technique was estimated to be ∼5 copies of template RNA per PCR reaction. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7105149/ doi: 10.1149/2.013402jes id: cord-286360-wrrqb387 author: Pratelli, A title: Development of a nested PCR assay for the detection of canine coronavirus date: 1999-06-02 words: 1677.0 sentences: 97.0 pages: flesch: 63.0 cache: ./cache/cord-286360-wrrqb387.txt txt: ./txt/cord-286360-wrrqb387.txt summary: A diagnostic test for canine coronavirus (CCV) infection based on a nested polymerase chain reaction (n-PCR) assay was developed and tested using the following coronavirus strains: CCV (USDA strain), CCV (45/93, field strain), feline infectious peritonitis virus (FIPV, field strain), trasmissible gastroenteritis virus (TGEV, Purdue strain), bovine coronavirus (BCV, 9WBL-77 strain), infectious bronchitis virus (IBV, M-41 strain) and fecal samples of dogs with CCV enteritis. The test described in the present study was able to amplify both CCV and TGEV strains and also gave positive results on fecal samples from CCV infected dogs. Recently a nested polymerase chain reaction (n-PCR) assay was developed for detection of feline infectious peritonitis virus (FIPV), a coronavirus closely related to CCV, in clinical specimens (Gamble et al., 1997) . PCR carried out with CCV1 and CCV2 primers specific for the target sequence 337 -746 of M gene revealed high sensitivity; tests performed on corresponding viral dilutions, which also were inoculated into cell cultures, gave positive results to the 10 − 4 dilution (approximately 10 -50 TCID 50 of virus). abstract: A diagnostic test for canine coronavirus (CCV) infection based on a nested polymerase chain reaction (n-PCR) assay was developed and tested using the following coronavirus strains: CCV (USDA strain), CCV (45/93, field strain), feline infectious peritonitis virus (FIPV, field strain), trasmissible gastroenteritis virus (TGEV, Purdue strain), bovine coronavirus (BCV, 9WBL-77 strain), infectious bronchitis virus (IBV, M-41 strain) and fecal samples of dogs with CCV enteritis. A 230-bp segment of the gene encoding for transmembrane protein M of CCV is the target sequence of the primer. The test described in the present study was able to amplify both CCV and TGEV strains and also gave positive results on fecal samples from CCV infected dogs. n-PCR has a sensitivity as high as isolation on cell cultures, and can therefore be used for the diagnosis of CCV infection in dogs. url: https://www.ncbi.nlm.nih.gov/pubmed/10403671/ doi: 10.1016/s0166-0934(99)00017-8 id: cord-292281-fui9all6 author: Pratelli, A. title: High‐cell‐passage canine coronavirus vaccine providing sterilising immunity date: 2007-09-14 words: 3532.0 sentences: 177.0 pages: flesch: 54.0 cache: ./cache/cord-292281-fui9all6.txt txt: ./txt/cord-292281-fui9all6.txt summary: Clinical Significance: This study showed the efficacy of a high‐cell‐passage canine coronavirus vaccine in preventing infection of dogs by virulent virus and, specifically, its ability to induce sterilising immunity. Faecal samples collected from the vaccinated and control dogs were tested by virus isolation and PCR assays. After challenge with field strain 144/ 01, the vaccinated dogs did not develop clinical signs, and virus isolation and PCR did not detect viral shedding. In a recent study, it was found that the inactivated vaccine had poor efficacy in reducing faecal shedding of CCoV following infection with a field strain of the virus (Pratelli and others 2003b) . After challenge at 14 dpsv, protection from CCoV infection was complete because no viral shedding was observed by either virus isolation or PCR tests. The present study has shown the efficacy of a high-cell-passage CCoV vaccine in preventing infection of dogs by virulent virus and, specifically, its ability to induce sterilising immunity. abstract: Objectives: To evaluate the ability of a high‐cell‐passage canine coronavirus vaccine to immunise dogs against challenge with a field isolate of the virus. Methods: Three dogs that had previously tested seronegative and virus‐negative for canine coronavirus were inoculated twice, at 21‐day intervals, with the vaccine and kept under observation. Two seronegative and virus‐negative dogs served as unvaccinated controls. For safety tests, two additional dogs were inoculated oronasally with 10 times the vaccinal dose and no reactions were observed. Faecal samples were collected daily from the vaccinated dogs after the first and second inoculations. Both vaccinated and control dogs were challenged two weeks after the second vaccination with a field canine coronavirus strain. Blood samples were collected for serological tests before vaccination and at weekly intervals after vaccinations and challenge. Results: Virus was not detected in faecal samples after the first or second vaccinations by virus isolation assays and PCR. Significantly, the vaccinated dogs did not have clinical signs after challenge and no virus shedding was observed. The two unvaccinated control dogs had moderate enteritis, and virus was detected in cell cultures starting from three days postchallenge (dog 1) and two days postchallenge (dog 2), and by PCR for 23 median days. Clinical Significance: This study showed the efficacy of a high‐cell‐passage canine coronavirus vaccine in preventing infection of dogs by virulent virus and, specifically, its ability to induce sterilising immunity. url: https://www.ncbi.nlm.nih.gov/pubmed/17877547/ doi: 10.1111/j.1748-5827.2007.00416.x id: cord-328961-waxtb759 author: Pratelli, Annamaria title: PCR assay for the detection and the identification of atypical canine coronavirus in dogs date: 2002-10-01 words: 1889.0 sentences: 95.0 pages: flesch: 57.0 cache: ./cache/cord-328961-waxtb759.txt txt: ./txt/cord-328961-waxtb759.txt summary: Comparative sequence analysis of the PCR products of the M gene and fragments of the pol1a and pol1b genes of canine coronavirus (CCoV) have demonstrated that two separate clusters of CCoV are present in dogs. The sequence analysis of the PCR products of the M and S genes carried out on the faecal samples from the two pups confirmed that the FCoV-like CCoV had caused the disease (personal observations). On the basis of these preliminary results, a PCR assay was developed to detect and identify the FCoV-like CCoV strains from faecal samples of infected dogs. In a previous study, similar nucleotide substitutions in the binding site of the internal primer CCoV3 used for the n-PCR were demonstrated in the sequence analysis of the PCR products from five faecal samples of pups with diarrhoea. abstract: Comparative sequence analysis of the PCR products of the M gene and fragments of the pol1a and pol1b genes of canine coronavirus (CCoV) have demonstrated that two separate clusters of CCoV are present in dogs. This note describes a PCR assay to identify atypical CCoV strains with nucleotide substitutions in the M gene. A total of 177 faecal samples from dogs CCoV positive previously with the PCR assay were analysed. Sixty-two of the 177 samples were amplified with the PCR described in the present study and were thus considered atypical CCoVs. The specificity of the PCR typing assay was confirmed by sequence analysis of the PCR products. url: https://api.elsevier.com/content/article/pii/S0166093402001659 doi: 10.1016/s0166-0934(02)00165-9 id: cord-342783-85b4lwh3 author: Prazuck, T. title: Evaluation of performance of two SARS-CoV-2 Rapid whole-blood finger-stick IgM-IgGCombined Antibody Tests date: 2020-05-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Background The SARS-CoV-2 virus is responsible for the infectious respiratory disease called COVID-19 (COronaVIrus Disease). In response to the growing COVID-19 pandemic, Rapid Diagnostic Tests (RDTs) have been developed to detect specific antibodies, IgG and IgM, to SARS-CoV-2 virus in human whole blood. We conducted a real-life study to evaluate the performance of two RDTs, COVID-PRESTO and COVID-DUO, compared to the gold standard, RT-PCR. Methods RT-PCR testing of SARS-Cov-2 was performed from nasopharyngeal swab specimens collected in adult patients visiting the infectious disease department at the hospital (Orleans, France). Fingertip whole blood samples taken at different time points after onset of the disease were tested with RDTs. The specificity and sensitivity of the rapid test kits compared to test of reference (RT-PCR) were calculated. Results Among 381 patients with symptoms of COVID-19 who went to the hospital for a diagnostic, 143 patients were RT-PCR negative. Results of test with RDTs were all negative for these patients, indicating a specificity of 100% for both RDTs. In the RT-PCR positive subgroup (n=238), 133 patients were tested with COVID-PRESTO and 129 patients were tested with COVID-DUO (24 patients tested with both). The further the onset of symptoms was from the date of collection, the greater the sensitivity. The sensitivity of COVID-PRESTO test ranged from 10.00% for patients having experienced their 1st symptoms from 0 to 5 days ago to 100% in patients where symptoms had occurred more than 15 days before the date of tests. For COVID-DUO test, the sensitivity ranged from 35.71% [0-5 days] to 100% (> 15 days). Conclusion COVID-PRESTO and DUO RDTs turned out to be very specific (none false positive) and to be sensitive enough after 15 days from onset of symptom. These easy to use IgG/IgM combined test kits are the first ones allowing a screening with capillary blood sample, by typing from a finger prick. These rapid tests are particularly interesting for screening in low resource settings. url: https://doi.org/10.1101/2020.05.27.20112888 doi: 10.1101/2020.05.27.20112888 id: cord-294546-0otd1heg author: Prendki, V. title: Accuracy of comprehensive PCR analysis of nasopharyngeal and oropharyngeal swabs for CT-scan-confirmed pneumonia in elderly patients: a prospective cohort study date: 2019-01-12 words: 3021.0 sentences: 169.0 pages: flesch: 39.0 cache: ./cache/cord-294546-0otd1heg.txt txt: ./txt/cord-294546-0otd1heg.txt summary: CONCLUSION: Comprehensive molecular testing of NPS increases the number of pathogens detected compared with routine methods, but results are poorly predictive of the presence of pneumonia. showed in a randomized controlled trial (107 individuals with lower respiratory tract infections, mean age 65 years) that PCR for viruses and atypical bacteria in nasopharyngeal and oropharyngeal swabs (NPS) allowed the identification of additional pathogens but did not reduce antibiotic use or costs [7] . Individuals admitted to hospital for suspected pneumonia had NPS collected at inclusion for the detection of multiple bacterial and viral pathogens using multiplex PCR (comprehensive molecular testing), in addition to routine testing. Demographic data, co-morbidities, vital signs, clinical findings, severity scores, results of standard laboratory tests, blood, sputum and urine cultures, urinary antigen detection, PCR for respiratory viruses on NPS, and antimicrobial therapy administered were recorded prospectively. abstract: OBJECTIVES: We aimed to assess the accuracy of PCR detection of viruses and bacteria on nasopharyngeal and oropharyngeal swabs (NPS) for the diagnosis of pneumonia in elderly individuals. METHODS: We included consecutive hospitalized elderly individuals suspected of having pneumonia. At inclusion, NPS were collected from all participants and tested by PCR for the presence of viral and bacterial respiratory pathogens (index test, defined as comprehensive molecular testing). Routine diagnostic tests (blood and sputum culture, urine antigen detection) were also performed. The reference standard was the presence of pneumonia on a low-dose CT scan as assessed by two independent expert radiologists. RESULTS: The diagnosis of pneumonia was confirmed in 127 of 199 (64%) included patients (mean age 83 years, community-acquired pneumonia in 105 (83%)). A pathogen was identified by comprehensive molecular testing in 114 patients (57%) and by routine methods in 22 (11%). Comprehensive molecular testing was positive for viruses in 62 patients (31%) and for bacteria in 73 (37%). The sensitivity and specificity were 61% (95% CI 53%–69%) and 50% (95% CI 39%–61%) for comprehensive molecular testing, and 14% (95% CI 82%–21%) and 94% (95% CI 86%–98%) for routine testing, respectively. Positive likelihood ratio was 2.55 for routine methods and 1.23 for comprehensive molecular testing. CONCLUSION: Comprehensive molecular testing of NPS increases the number of pathogens detected compared with routine methods, but results are poorly predictive of the presence of pneumonia. Hence, comprehensive molecular testing is unlikely to impact clinical decision-making (NCT02467192). CLINICAL TRIALS REGISTRATION: NCT02467192. url: https://doi.org/10.1016/j.cmi.2018.12.037 doi: 10.1016/j.cmi.2018.12.037 id: cord-301102-jbjysyqm author: Priestnall, Simon L. title: Quantification of mRNA encoding cytokines and chemokines and assessment of ciliary function in canine tracheal epithelium during infection with canine respiratory coronavirus (CRCoV) date: 2009-01-15 words: 6022.0 sentences: 296.0 pages: flesch: 48.0 cache: ./cache/cord-301102-jbjysyqm.txt txt: ./txt/cord-301102-jbjysyqm.txt summary: title: Quantification of mRNA encoding cytokines and chemokines and assessment of ciliary function in canine tracheal epithelium during infection with canine respiratory coronavirus (CRCoV) This study aimed to quantify pro-inflammatory cytokine mRNAs following infection of canine air-interface tracheal cultures with CRCoV. This study aimed to quantify pro-inflammatory cytokine mRNAs following infection of canine air-interface tracheal cultures with CRCoV. The quantification of canine IL-6, IL-8 and TNF-a mRNA copies in CRCoV-inoculated cultures was presented as the logarithm of the fold change relative to control-inoculated cultures in the same dog at the same time point. In response to LPS, mRNA levels of TNF-a, IL-6 and IL-8 in cultures, were significantly increased from 24 h post-inoculation, relative to controls, indicating that the assay was sensitive enough to detect changes in cytokine mRNAs within this system. IHC revealed coronavirus antigen positive intra-cytoplasmic staining of ciliated epithelial and goblet cells within canine tracheas of both CRCoV-inoculated cultures and from naturally infected cases of CIRD. abstract: One of the first lines of defence against viral infection is the innate immune response and the induction of antiviral type I interferons (IFNs). However some viruses, including the group 2 coronaviruses, have evolved mechanisms to overcome or circumvent the host antiviral response. Canine respiratory coronavirus (CRCoV) has previously been shown to have a widespread international presence and has been implicated in outbreaks of canine infectious respiratory disease (CIRD). This study aimed to quantify pro-inflammatory cytokine mRNAs following infection of canine air-interface tracheal cultures with CRCoV. Within this system, immunohistochemistry identified ciliated epithelial and goblet cells as positive for CRCoV, identical to naturally infected cases, thus the data obtained would be fully transferable to the situation in vivo. An assay of ciliary function was used to assess potential effects of CRCoV on the mucociliary system. CRCoV was shown to reduce the mRNA levels of the pro-inflammatory cytokines TNF-α and IL-6 and the chemokine IL-8 during the 72 h post-inoculation. The mechanism for this is unknown, however the suppression of a key antiviral strategy during a period of physiologic and immunological stress, such as on entry to a kennel, could potentially predispose a dog to further pathogenic challenge and the development of respiratory disease. url: https://www.ncbi.nlm.nih.gov/pubmed/18977539/ doi: 10.1016/j.vetimm.2008.09.017 id: cord-000736-6f8vyziv author: Pripuzova, Natalia title: Development of Real-Time PCR Array for Simultaneous Detection of Eight Human Blood-Borne Viral Pathogens date: 2012-08-17 words: 6818.0 sentences: 328.0 pages: flesch: 54.0 cache: ./cache/cord-000736-6f8vyziv.txt txt: ./txt/cord-000736-6f8vyziv.txt summary: FINDINGS: We developed a real-time PCR array capable of simultaneously detecting eight human viral pathogens: human immunodeficiency virus types 1 and 2 (HIV-1 and -2), hepatitis B virus (HBV), hepatitis C virus (HCV), human T-cell leukemia virus-1 and -2 (HTLV-1 and -2), vaccinia virus (VACV) and West Nile virus (WNV). The analytical sensitivity of each primer set was determined in the single virus testing using FDA/CBER panels (kindly provided by Dr. Stephen Kerby, FDA/CBER) consisting of various amounts of the viruses (0-1,000 genome copies/ml) spiked into the ''''normal'''' human plasma. The results of sensitivity testing of the real-time PCR array primer sets specific for HIV-1, HIV-2, HBV, HCV, and WNV the with FDA/CBER analytical plasma panels. Tm and C(t) values obtained with primer sets specific for HIV-1, HCV, or HBV in testing of 17 human clinical samples in the format of PCR array targeting eight different viruses. abstract: BACKGROUND: Real-time PCR array for rapid detection of multiple viral pathogens should be highly useful in cases where the sample volume and the time of testing are limited, i.e. in the eligibility testing of tissue and organ donors. FINDINGS: We developed a real-time PCR array capable of simultaneously detecting eight human viral pathogens: human immunodeficiency virus types 1 and 2 (HIV-1 and -2), hepatitis B virus (HBV), hepatitis C virus (HCV), human T-cell leukemia virus-1 and -2 (HTLV-1 and -2), vaccinia virus (VACV) and West Nile virus (WNV). One hundred twenty (120) primers were designed using a combination of bioinformatics approaches, and, after experimental testing, 24 primer sets targeting eight viral pathogens were selected to set up the array with SYBR Green chemistry. The specificity and sensitivity of the virus-specific primer sets selected for the array were evaluated using analytical panels with known amounts of viruses spiked into human plasma. The array detected: 10 genome equivalents (geq)/ml of HIV-2 and HCV, 50 geq of HIV-1 (subtype B), HBV (genotype A) and WNV. It detected 100–1,000 geq/ml of plasma of HIV-1 subtypes (A – G), group N and CRF (AE and AG) isolates. Further evaluation with a panel consisting of 28 HIV-1 and HIV-2 clinical isolates revealed no cross-reactivity of HIV-1 or HIV-2 specific primers with another type of HIV. All 28 viral isolates were identified with specific primer sets targeting the most conserved genome areas. The PCR array correctly identified viral infections in a panel of 17 previously quantified clinical plasma samples positive for HIV-1, HCV or HBV at as low as several geq per PCR reaction. CONCLUSIONS: The viral array described here demonstrated adequate performance in the testing of donors’ clinical samples. Further improvement in its sensitivity for the broad spectrum of HIV-1 subtypes is under development. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3422334/ doi: 10.1371/journal.pone.0043246 id: cord-300243-5q67tnx4 author: Priya, A. Kokila title: Prevalence of enteropathogens and their antibiotic sensitivity pattern in puppies with hemorrhagic gastroenteritis date: 2017-08-04 words: 2997.0 sentences: 172.0 pages: flesch: 50.0 cache: ./cache/cord-300243-5q67tnx4.txt txt: ./txt/cord-300243-5q67tnx4.txt summary: The aim of the study was to identify the prevalence of common enteropathogens and the antibiotic sensitivity pattern in puppies reported with HGE. Fecal polymerase chain reaction (PCR) assay was employed to screen and compare the enteropathogens in puppies with hemorrhagic diarrhea and healthy control. The potential enteropathogenic bacteria associated with bacterial gastroenteritis in dogs include Clostridium difficile, Clostridium perfringens, Escherichia coli, Campylobacter jejuni, and Salmonella sp. Fecal samples collected from all the puppies during the study period were screened by polymerase chain reaction (PCR) for the common enteropathogens, including the bacteria, their toxins and viruses. The cpa (alpha toxin) and cpe (enterotoxin) genes corresponding to the Clostridium perfringens were tested to show amplification with a molecular length of 400 and 233 bp [14] . difficile toxin B, enteric CCoV and Rotavirus were found negative in 62 puppies with hemorrhagic diarrhea screened samples. abstract: AIM: Hemorrhagic gastroenteritis (HGE) ranging from mild to severe forms is commonly encountered in puppies. The aim of the study was to identify the prevalence of common enteropathogens and the antibiotic sensitivity pattern in puppies reported with HGE. MATERIALS AND METHODS: The canine HGE activity index, with little modification, was adopted to identify Grade III/severely affected puppies below 6 months of age. Fecal polymerase chain reaction (PCR) assay was employed to screen and compare the enteropathogens in puppies with hemorrhagic diarrhea and healthy control. RESULTS: Canine parvovirus 2b was identified in 90.3% of the diarrheic and 10% of the non-diarrheic healthy puppies. Clostridium difficile was identified in all the diarrheic puppies and in 80% of the healthy puppies. Among the diarrheic puppies, 17.7% were positive for Clostridium perfringens enterotoxin, 9.7% were positive for C. perfringens alpha toxin, 6.4% were positive for Escherichia coli shiga toxin, 6.4% were positive for E. coli enterotoxin (LT), and 3.2% were positive for canine distemper virus. Whereas, none of the healthy puppies were positive for these bacteria and toxins. Fecal antibiotic sensitivity test pattern revealed gentamicin to be sensitive in 95% of the cases, azithromycin in 50%, enrofloxacin in 25%, cefotaxime in 20%, and tetracycline in 5% of the cases. CONCLUSION: Parvoviral enteritis is predominant among puppies. Yet, bacteria and their toxins also play an important role in HGE. Gentamicin has higher sensitivity against the enteropathogens associated with the condition. url: https://doi.org/10.14202/vetworld.2017.859-863 doi: 10.14202/vetworld.2017.859-863 id: cord-319845-oob2ktnz author: Proença-Modena, José Luiz title: Detection of Human Bocavirus mRNA in Respiratory Secretions Correlates with High Viral Load and Concurrent Diarrhea date: 2011-06-20 words: 5857.0 sentences: 269.0 pages: flesch: 51.0 cache: ./cache/cord-319845-oob2ktnz.txt txt: ./txt/cord-319845-oob2ktnz.txt summary: Therefore, in order to test whether active viral replication of human bocavirus is associated with respiratory diseases and to understand the clinical impact of this virus in patients with these diseases, we performed a 3-year retrospective hospital-based study of HBoV in outpatients and inpatients with symptoms of Acute Respiratory Infections (ARI) in Brazil. This article reports a cross-sectional study of HBoV in ARI patients from Ribeirão Preto, Brazil, in which the shedding of VP1 mRNA in respiratory secretions was used as surrogate marker for active HBoV replication, to look for correlations with viral load, and presence of particular clinical manifestations and simultaneous detection of other respiratory viruses. The results of this cross-sectional study of HBoV in ARI patients from Ribeirão Preto, Brazil, indicate that shedding of VP1 mRNA in respiratory secretions, as a marker of HBoV replication, correlates positively with high viral load, presence of diarrhea, and lack of co-infection by other respiratory viruses. abstract: Human bocavirus (HBoV) is a parvovirus recently identified in association with acute respiratory infections (ARI). Despite its worldwide occurrence, little is known on the pathogenesis of HBoV infections. In addition, few systematic studies of HBoV in ARI have been conducted in Latin America. Therefore, in order to test whether active viral replication of human bocavirus is associated with respiratory diseases and to understand the clinical impact of this virus in patients with these diseases, we performed a 3-year retrospective hospital-based study of HBoV in outpatients and inpatients with symptoms of Acute Respiratory Infections (ARI) in Brazil. Nasopharyngeal aspirates (NPAs) from 1015 patients with respiratory symptoms were tested for HBoV DNA by PCR. All samples positive for HBoV were tested by PCR for all other respiratory viruses, had HBoV viral loads determined by quantitative real time PCR and, when possible, were tested by RT-PCR for HBoV VP1 mRNA, as evidence of active viral replication. HBoV was detected in 4.8% of patients, with annual rates of 10.0%, 3.0% and 3.0% in 2005, 2006 and 2007, respectively. The range of respiratory symptoms was similar between HBoV-positive and HBoV-negative ARI patients. However, a higher rate of diarrhea was observed in HBoV-positive patients. High HBoV viral loads (>10(8) copies/mL) and diarrhea were significantly more frequent in patients with exclusive infection by HBoV and in patients with detection of HBoV VP1 mRNA than in patients with viral co-infection, detected in 72.9% of patients with HBoV. In summary, our data demonstrated that active HBoV replication was detected in a small percentage of patients with ARI and was correlated with concurrent diarrhea and lack of other viral co-infections. url: https://www.ncbi.nlm.nih.gov/pubmed/21701591/ doi: 10.1371/journal.pone.0021083 id: cord-293234-ouykx6g5 author: Puig-Barberà, J. title: Effectiveness of the 2010–2011 seasonal influenza vaccine in preventing confirmed influenza hospitalizations in adults: A case–case comparison, case-control study date: 2012-08-24 words: 4417.0 sentences: 226.0 pages: flesch: 44.0 cache: ./cache/cord-293234-ouykx6g5.txt txt: ./txt/cord-293234-ouykx6g5.txt summary: title: Effectiveness of the 2010–2011 seasonal influenza vaccine in preventing confirmed influenza hospitalizations in adults: A case–case comparison, case-control study INTRODUCTION: We estimated influenza vaccine effectiveness (IVE) to prevent laboratory-confirmed influenza-related hospitalizations in patients 18 years old or older during the 2010–2011 influenza season. Using a prospective case-case comparison approach, we have estimated seasonal influenza vaccine effectiveness (IVE) to prevent laboratory confirmed influenza-related hospitalizations in adults. When restricting the comparison, between cases and controls, by the presence of high-risk conditions, the differences that remained significant were age, 23-valent pneumococcal vaccination, and having been vaccinated with the previous or current season influenza vaccines (Table 2) . When restricted to those 60 years old or older, age and influenza vaccination with the previous or current seasonal influenza vaccine remained as significant differences between cases and controls ( Table 2 ). abstract: INTRODUCTION: We estimated influenza vaccine effectiveness (IVE) to prevent laboratory-confirmed influenza-related hospitalizations in patients 18 years old or older during the 2010–2011 influenza season. METHODS: We conducted a prospective case-control study in five hospitals, in Valencia, Spain. Study subjects were consecutive emergency hospitalizations for predefined conditions associated with an influenza-like illness episode <8 days before admission. Patients were considered immunized if vaccinated ≥14 days before influenza-like illness onset. Cases were those with a real time reverse transcriptase polymerase chain reaction (RT-PCR) positive for influenza and controls were RT-PCR positive for other respiratory viruses. Adjusted IVE was estimated as 100 × (1 − adjusted odds ratio). To account for indication bias we computed adjusted IVE for respiratory syncytial virus related hospitalizations. RESULTS: Of 826 eligible hospitalized patients, 102 (12%) were influenza positive and considered cases, and 116 (14%) were positive for other respiratory viruses and considered controls. Adjusted IVE was 54% (95% confidence interval, 11–76%). By subgroup, adjusted IVE was 53% (4–77%) for those with high-risk conditions, 59% (16–79%) for those ≥60 years of age, and, 54% (4–79%) for those ≥60 years of age with high-risk conditions. No influenza vaccine effect was observed against respiratory syncytial virus related hospitalization. CONCLUSION: Influenza vaccination was associated with a significant reduction on the risk of confirmed influenza hospitalization, irrespective of age and high-risk conditions. url: https://api.elsevier.com/content/article/pii/S0264410X12010079 doi: 10.1016/j.vaccine.2012.07.006 id: cord-261134-zarq507s author: Pulford, David title: Amplification refractory mutation system PCR assays for the detection of variola and Orthopoxvirus date: 2004-02-13 words: 3799.0 sentences: 215.0 pages: flesch: 50.0 cache: ./cache/cord-261134-zarq507s.txt txt: ./txt/cord-261134-zarq507s.txt summary: PCR assays that can identify the presence of variola virus (VARV) sequences in an unknown DNA sample were developed using principles established for the amplification refractory mutation system (ARMS). When a variola virus specific primer was used with a consensus primer in an ARMS assay with different Orthopoxvirus genomes, a PCR product was only amplified from variola virus DNA. Incorporating a second consensus primer into the assay produced a multiplex PCR that provided Orthopoxvirus generic and variola-specific products with variola virus DNA. The variola virus specific primers did not produce amplicons with either assay format when tested with 50 other Orthopoxvirus DNA samples. These multiplex assays employ three primers; two consensus primers generate an amplicon diagnostic of an Old World Orthopoxvirus and the third primer simultaneously binds to a variola-specific polymorphism and initiates extension of a shorter PCR product to detect the presence of variola virus. abstract: PCR assays that can identify the presence of variola virus (VARV) sequences in an unknown DNA sample were developed using principles established for the amplification refractory mutation system (ARMS). The assay’s specificity utilised unique single nucleotide polymorphisms (SNP) identified among Orthopoxvirus (OPV) orthologs of the vaccinia virus Copenhagen strain A13L and A36R genes. When a variola virus specific primer was used with a consensus primer in an ARMS assay with different Orthopoxvirus genomes, a PCR product was only amplified from variola virus DNA. Incorporating a second consensus primer into the assay produced a multiplex PCR that provided Orthopoxvirus generic and variola-specific products with variola virus DNA. We tested two single nucleotide polymorphisms with a panel of 43 variola virus strains, collected over 40 years from countries across the world, and have shown that they provide reliable markers for variola virus identification. The variola virus specific primers did not produce amplicons with either assay format when tested with 50 other Orthopoxvirus DNA samples. Our analysis shows that these two polymorphisms were conserved in variola virus genomes and provide a reliable signature of Orthopoxvirus species identification. url: https://www.ncbi.nlm.nih.gov/pubmed/15019263/ doi: 10.1016/j.jviromet.2004.01.001 id: cord-325611-tu1bn4hu author: Pérez-Sautu, Unai title: Target-independent high-throughput sequencing methods provide evidence that already known human viral pathogens play a main role in respiratory infections with unexplained etiology date: 2019-07-23 words: 5285.0 sentences: 259.0 pages: flesch: 41.0 cache: ./cache/cord-325611-tu1bn4hu.txt txt: ./txt/cord-325611-tu1bn4hu.txt summary: We systematically collected samples from a prospective cohort of pediatric patients with respiratory infections, that returned negative results by validated molecular RT–PCR assays, and studied them with a target-independent, high-throughput sequencing-based approach. In this report, we performed a systematic study of respiratory specimens collected from a carefully characterized and highly representative, prospective cohort of pediatric cases suffering unexplained ARI, and we compared the rate of detection of pathogens by utilizing validated molecular assays, and a comprehensive sequence-independent, high-throughput sequencing-based analysis. In order to assess for the clinical relevance of the viral identifications made by HTS in the specimens collected from the unexplained cases of respiratory infections, a second cohort of age-matched healthy individuals from the same epidemiologic environment was also studied with the same methodology. Respiratory viral pathogens identified by target-agnostic HTS analysis and confirmed by contig-specific molecular assays in the respiratory specimens from the cases of respiratory infection and from the control group. abstract: Despite the advanced PCR-based assays available, a fraction of the pediatric respiratory infections remain unexplained every epidemic season, and there is a perception that novel viruses might be present in these specimens. We systematically collected samples from a prospective cohort of pediatric patients with respiratory infections, that returned negative results by validated molecular RT–PCR assays, and studied them with a target-independent, high-throughput sequencing-based approach. We also included a matched cohort of children with no symptoms of respiratory infection, as a contrast study population. More than fifty percent of the specimens from the group of patients with unexplained respiratory infections were resolved. However, the higher rate of detection was not due to the presence of novel viruses, but to the identification of well-known viral respiratory pathogens. Our results show that already known viral pathogens are responsible for the majority of cases that remain unexplained after the epidemic season. High-throughput sequencing approaches that use pathogen-specific probes are easier to standardize because they ensure reproducible library enrichment and sequencing. In consequence, these techniques might be desirable from a regulatory standpoint for diagnostic laboratories seeking to benefit from the many advantages of these sequencing technologies. url: https://www.ncbi.nlm.nih.gov/pubmed/31335277/ doi: 10.1080/22221751.2019.1640587 id: cord-000010-prsvv6l9 author: Qin, Jian title: Studying copy number variations using a nanofluidic platform date: 2008-08-18 words: 4986.0 sentences: 250.0 pages: flesch: 51.0 cache: ./cache/cord-000010-prsvv6l9.txt txt: ./txt/cord-000010-prsvv6l9.txt summary: Copy number variations (CNVs) in the human genome are conventionally detected using high-throughput scanning technologies, such as comparative genomic hybridization and high-density single nucleotide polymorphism (SNP) microarrays, or relatively low-throughput techniques, such as quantitative polymerase chain reaction (PCR). We have developed a new technology to study copy numbers using a platform known as the digital array, a nanofluidic biochip capable of accurately quantitating genes of interest in DNA samples. Other existing technologies, such as quantitative polymerase chain reaction (PCR), are limited because of their inability to reliably distinguish less than a twofold difference in copy number of a particular gene in DNA samples (11) (12) (13) . In this study we demonstrate the use of a unique integrated nanofluidic system, the digital array, in the study of CNVs. The digital array (14, 15) is able to accurately quantitate DNA samples based on the fact that single DNA molecules are randomly distributed in more than 9000 reaction chambers and then PCR amplified. abstract: Copy number variations (CNVs) in the human genome are conventionally detected using high-throughput scanning technologies, such as comparative genomic hybridization and high-density single nucleotide polymorphism (SNP) microarrays, or relatively low-throughput techniques, such as quantitative polymerase chain reaction (PCR). All these approaches are limited in resolution and can at best distinguish a twofold (or 50%) difference in copy number. We have developed a new technology to study copy numbers using a platform known as the digital array, a nanofluidic biochip capable of accurately quantitating genes of interest in DNA samples. We have evaluated the digital array's performance using a model system, to show that this technology is exquisitely sensitive, capable of differentiating as little as a 15% difference in gene copy number (or between 6 and 7 copies of a target gene). We have also analyzed commercial DNA samples for their CYP2D6 copy numbers and confirmed that our results were consistent with those obtained independently using conventional techniques. In a screening experiment with breast cancer and normal DNA samples, the ERBB2 gene was found to be amplified in about 35% of breast cancer samples. The use of the digital array enables accurate measurement of gene copy numbers and is of significant value in CNV studies. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2566873/ doi: 10.1093/nar/gkn518 id: cord-350016-yxf7ykva author: Qin, Le title: A predictive model and scoring system combining clinical and CT characteristics for the diagnosis of COVID-19 date: 2020-07-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: To develop a predictive model and scoring system to enhance the diagnostic efficiency for coronavirus disease 2019 (COVID-19). METHODS: From January 19 to February 6, 2020, 88 confirmed COVID-19 patients presenting with pneumonia and 80 non-COVID-19 patients suffering from pneumonia of other origins were retrospectively enrolled. Clinical data and laboratory results were collected. CT features and scores were evaluated at the segmental level according to the lesions’ position, attenuation, and form. Scores were calculated based on the size of the pneumonia lesion, which graded at the range of 1 to 4. Air bronchogram, tree-in-bud sign, crazy-paving pattern, subpleural curvilinear line, bronchiectasis, air space, pleural effusion, and mediastinal and/or hilar lymphadenopathy were also evaluated. RESULTS: Multivariate logistic regression analysis showed that history of exposure (β = 3.095, odds ratio (OR) = 22.088), leukocyte count (β = − 1.495, OR = 0.224), number of segments with peripheral lesions (β = 1.604, OR = 1.604), and crazy-paving pattern (β = 2.836, OR = 2.836) were used for establishing the predictive model to identify COVID-19-positive patients (p < 0.05). In this model, values of area under curve (AUC) in the training and testing groups were 0.910 and 0.914, respectively (p < 0.001). A predicted score for COVID-19 (PSC-19) was calculated based on the predictive model by the following formula: PSC-19 = 2 × history of exposure (0–1 point) − 1 × leukocyte count (0–2 points) + 1 × peripheral lesions (0–1 point) + 2 × crazy-paving pattern (0–1 point), with an optimal cutoff point of 1 (sensitivity, 88.5%; specificity, 91.7%). CONCLUSIONS: Our predictive model and PSC-19 can be applied for identification of COVID-19-positive cases, assisting physicians and radiologists until receiving the results of reverse transcription–polymerase chain reaction (RT-PCR) tests. KEY POINTS: • Prediction of RT-PCR positivity is crucial for fast diagnosis of patients suspected of having coronavirus disease 2019 (COVID-19). • Typical CT manifestations are advantageous for diagnosing COVID-19 and differentiation of COVID-19 from other types of pneumonia. • A predictive model and scoring system combining both clinical and CT features were herein developed to enable high diagnostic efficiency for COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32607634/ doi: 10.1007/s00330-020-07022-1 id: cord-305059-8z54lw2d author: Qu, Jie-Ming title: Chapter 4 Diagnosis of COVID-19 date: 2021-12-31 words: 5054.0 sentences: 271.0 pages: flesch: 45.0 cache: ./cache/cord-305059-8z54lw2d.txt txt: ./txt/cord-305059-8z54lw2d.txt summary: If any one of the following pathogenic or serological tests is positive, the patient is confirmed as COVID-19: (1) positive RT-PCR results for SARS-CoV-2 nucleic acid; (2) viral gene sequencing highly homologous to the known SARS-CoV-2; or (3) serum samples positive for SARS-CoV-2-specific IgM and IgG antibodies. The fifth edition of the program was specially designed for Hubei to establish the diagnostic criteria of "clinical diagnosis cases," which include clinical compliance with the characteristics of viral pneumonia, such as corresponding clinical symptoms and imaging CT findings, especially the multiple lobes exudative ground-glass shadow and intermittent consolidation, normal or decreased total count of white blood cells in laboratory examination, and reduced lymphocyte count. The methods are: (1) real-time fluorescence RT-PCR detection of SARS-CoV-2 nucleic acid positive and (2) viral gene sequencing, highly homologous with the known novel coronavirus. abstract: The diagnosis of COVID-19 is based on epidemiological history, clinical manifestations, and pathogenic confirmation. url: https://www.sciencedirect.com/science/article/pii/B9780128240038000048 doi: 10.1016/b978-0-12-824003-8.00004-8 id: cord-282968-kjvvoveq author: Qu, Renjun title: Selection of reference genes for the quantitative real-time PCR normalization of gene expression in Isatis indigotica fortune date: 2019-03-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Isatis indigotica, a traditional Chinese medicine, produces a variety of active ingredients. However, little is known about the key genes and corresponding expression profiling involved in the biosynthesis pathways of these ingredients. Quantitative real-time polymerase chain reaction (qRT-PCR) is a powerful, commonly-used method for gene expression analysis, but the accuracy of the quantitative data produced depends on the appropriate selection of reference genes. RESULTS: In this study, the systematic analysis of the reference genes was performed for quantitative real-Time PCR normalization in I. indigotica. We selected nine candidate reference genes, including six traditional housekeeping genes (ACT, α-TUB, β-TUB, UBC, CYP, and EF1-α), and three newly stable internal control genes (MUB, TIP41, and RPL) from a transcriptome dataset of I. indigotica, and evaluated their expression stabilities in different tissues (root, stem, leaf, and petiole) and leaves exposed to three abiotic treatments (low-nitrogen, ABA, and MeJA) using geNorm, NormFinder, BestKeeper, and comprehensive RefFind algorithms. The results demonstrated that MUB and EF1-α were the two most stable reference genes for all samples. TIP41 as the optimal reference gene for low-nitrogen stress and MeJA treatment, while ACT had the highest ranking for ABA treatment and CYP was the most suitable for different tissues. CONCLUSIONS: The results revealed that the selection and validation of appropriate reference genes for normalizing data is mandatory to acquire accurate quantification results. The necessity of specific internal control for specific conditions was also emphasized. Furthermore, this work will provide valuable information to enhance further research in gene function and molecular biology on I. indigotica and other related species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12867-019-0126-y) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12867-019-0126-y doi: 10.1186/s12867-019-0126-y id: cord-292031-weiwksh6 author: Ramírez-Castillo, Flor Yazmín title: Waterborne Pathogens: Detection Methods and Challenges date: 2015-05-21 words: 7358.0 sentences: 378.0 pages: flesch: 36.0 cache: ./cache/cord-292031-weiwksh6.txt txt: ./txt/cord-292031-weiwksh6.txt summary: Quantitative microbial risk assessment (QMRA) is a helpful tool to evaluate the scenarios for pathogen contamination that involve surveillance, detection methods, analysis and decision-making. Molecular techniques, such as nucleic acid amplification procedures, offer sensitive and analytical tools for detecting a variety of pathogens, including new emerging strains, present the possibility of automation, and real-time analysis to provide information for microbial risk assessment purposes [33] . Limitations of DNA based methods such as PCR include the inability to discriminate between viable from non-viable cells that both contain DNA, the low concentration of several pathogens in water such as Cryptosporidium, Giardia and viruses, and the lack of data to indicate the real infectious risk to a population. Oligonucleotide microarrays are a powerful genomic technology that is widely utilized to monitor gene expression under different cell growth conditions, detecting specific mutations in DNA sequences and characterizing microorganisms in environmental samples [76] . abstract: Waterborne pathogens and related diseases are a major public health concern worldwide, not only by the morbidity and mortality that they cause, but by the high cost that represents their prevention and treatment. These diseases are directly related to environmental deterioration and pollution. Despite the continued efforts to maintain water safety, waterborne outbreaks are still reported globally. Proper assessment of pathogens on water and water quality monitoring are key factors for decision-making regarding water distribution systems’ infrastructure, the choice of best water treatment and prevention waterborne outbreaks. Powerful, sensitive and reproducible diagnostic tools are developed to monitor pathogen contamination in water and be able to detect not only cultivable pathogens but also to detect the occurrence of viable but non-culturable microorganisms as well as the presence of pathogens on biofilms. Quantitative microbial risk assessment (QMRA) is a helpful tool to evaluate the scenarios for pathogen contamination that involve surveillance, detection methods, analysis and decision-making. This review aims to present a research outlook on waterborne outbreaks that have occurred in recent years. This review also focuses in the main molecular techniques for detection of waterborne pathogens and the use of QMRA approach to protect public health. url: https://www.ncbi.nlm.nih.gov/pubmed/26011827/ doi: 10.3390/pathogens4020307 id: cord-331557-8axi74nn author: Raoult, Didier title: What does the future hold for clinical microbiology? date: 2004 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In the past decade, clinical microbiology laboratories have undergone important changes with the introduction of molecular biology techniques and laboratory automation. In the future, there will be a need for more rapid diagnoses, increased standardization of testing and greater adaptability to cope with new threats from infectious microorganisms, such as agents of bioterrorism and emerging pathogens. The combination of the new tools that are now being developed in research laboratories, the general reorganization of clinical laboratories and improved communication between physicians and clinical microbiologists should lead to profound changes in the way that clinical microbiologists work. url: https://www.ncbi.nlm.nih.gov/pubmed/15040262/ doi: 10.1038/nrmicro820 id: cord-001455-n7quwr4s author: Rapin, Noreen title: Activation of Innate Immune-Response Genes in Little Brown Bats (Myotis lucifugus) Infected with the Fungus Pseudogymnoascus destructans date: 2014-11-12 words: 3719.0 sentences: 198.0 pages: flesch: 50.0 cache: ./cache/cord-001455-n7quwr4s.txt txt: ./txt/cord-001455-n7quwr4s.txt summary: title: Activation of Innate Immune-Response Genes in Little Brown Bats (Myotis lucifugus) Infected with the Fungus Pseudogymnoascus destructans Using tissue samples collected at the termination of an experiment to explore the pathogenesis of White Nose Syndrome in Little Brown Bats, we determined if hibernating bats infected with the fungus Pseudogymnoascus destructans could respond to infection by activating genes responsible for innate immune and stress responses. We found that bats responded to infection with a significant increase in lungs of transcripts for Cathelicidin (an anti-microbial peptide) as well as the immune modulators tumor necrosis factor alpha and interleukins 10 and 23. We used samples collected during the experiment to address the question: Can hibernating bats respond to infection by activating genes responsible for innate immune and stress responses? We determined levels of transcripts for several immune and stress response genes (Table 1) in lungs from infected and control bats. abstract: Recently bats have been associated with the emergence of diseases, both as reservoirs for several new viral diseases in humans and other animals and, in the northern Americas, as hosts for a devastating fungal disease that threatens to drive several bat species to regional extinction. However, despite these catastrophic events little Information is available on bat defences or how they interact with their pathogens. Even less is known about the response of bats to infection during torpor or long-term hibernation. Using tissue samples collected at the termination of an experiment to explore the pathogenesis of White Nose Syndrome in Little Brown Bats, we determined if hibernating bats infected with the fungus Pseudogymnoascus destructans could respond to infection by activating genes responsible for innate immune and stress responses. Lesions due to fungal infection and, in some cases, secondary bacterial infections, were restricted to the skin. However, we were unable to obtain sufficient amounts of RNA from these sites. We therefore examined lungs for response at an epithelial surface not linked to the primary site of infection. We found that bats responded to infection with a significant increase in lungs of transcripts for Cathelicidin (an anti-microbial peptide) as well as the immune modulators tumor necrosis factor alpha and interleukins 10 and 23. In conclusion, hibernating bats can respond to experimental P. destructans infection by activating expression of innate immune response genes. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4229191/ doi: 10.1371/journal.pone.0112285 id: cord-329395-4k8js9v2 author: Ratcliff, Jeremy title: Evaluation of Different PCR Assay Formats for Sensitive and Specific Detection of SARS-CoV-2 RNA date: 2020-07-01 words: 1662.0 sentences: 124.0 pages: flesch: 55.0 cache: ./cache/cord-329395-4k8js9v2.txt txt: ./txt/cord-329395-4k8js9v2.txt summary: Polymerase chain reaction (PCR)-based assays are the gold standard for detecting viral RNA in patient samples and are used extensively in clinical settings. To enable the application of PCR in resource-poor or non-specialist laboratories, we have developed and evaluated a nested PCR method for SARS-CoV-2 RNA using simple agarose gel electrophoresis for product detection. Using clinical samples tested by conventional qPCR methods and RNA transcripts of defined RNA copy number, the nested PCR based on the RdRP gene demonstrated high sensitivity and specificity for SARS-CoV-2 RNA detection in clinical samples, but showed variable and transcript length-dependent sensitivity for RNA transcripts. The sensitivity of the nested PCR and two RT-qPCR methods was compared by measuring the 118 50% endpoints (50EP) of detection for serial dilutions of the four transcripts described above 119 (Table 1, Figure 2 ). Protocol: Real-time RT-PCR assays for the detection of SARS-CoV-2 abstract: Accurate identification of individuals infected with SARS-CoV-2 is crucial for efforts to control the ongoing COVID-19 pandemic. Polymerase chain reaction (PCR)-based assays are the gold standard for detecting viral RNA in patient samples and are used extensively in clinical settings. Most currently used quantitative PCR (RT-qPCRs) rely upon real-time detection of PCR product using specialized laboratory equipment. To enable the application of PCR in resource-poor or non-specialist laboratories, we have developed and evaluated a nested PCR method for SARS-CoV-2 RNA using simple agarose gel electrophoresis for product detection. Using clinical samples tested by conventional qPCR methods and RNA transcripts of defined RNA copy number, the nested PCR based on the RdRP gene demonstrated high sensitivity and specificity for SARS-CoV-2 RNA detection in clinical samples, but showed variable and transcript length-dependent sensitivity for RNA transcripts. Samples and transcripts were further evaluated in an additional N protein real-time quantitative PCR assay. As determined by 50% endpoint detection, the sensitivities of three RT-qPCRs and nested PCR methods varied substantially depending on the transcript target with no method approaching single copy detection. Overall, these findings highlight the need for assay validation and optimization and demonstrate the inability to precisely compare viral quantification from different PCR methodologies without calibration. url: https://doi.org/10.1101/2020.06.24.168013 doi: 10.1101/2020.06.24.168013 id: cord-350807-qdq96723 author: Reckziegel, Maria title: Viruses and atypical bacteria in the respiratory tract of immunocompromised and immunocompetent patients with airway infection date: 2020-05-27 words: 4655.0 sentences: 283.0 pages: flesch: 44.0 cache: ./cache/cord-350807-qdq96723.txt txt: ./txt/cord-350807-qdq96723.txt summary: Samples were tested by PCR for the presence of herpesviruses (HSV-1/-2; VZV; CMV; HHV6; EBV), adenoviruses, bocaviruses, entero-/rhinoviruses (HRV), parechoviruses, coronaviruses, influenza viruses (IV), parainfluenza viruses as well as for pneumoviruses (HMPV and RSV), and atypical bacteria (Mycoplasma pneumoniae, M.p.; Chlamydia pneumoniae, C.p.). Furthermore, particularly transplant patients are at risk for reactivation of diverse herpesviruses (herpes simplex virus-1/-2, HSV-1/-2; varicella zoster virus, VZV; cytomegalovirus, CMV; human herpesvirus 6, HHV-6; Epstein-Barr virus, EBV) [12, 15, [17] [18] [19] [20] . In this monocentric study, genome equivalents of viruses and M.p. were frequently detected in immunocompromised (66.7%) and immunocompetent (69.2%) patients with respiratory symptoms (Table 1) . Same authors indicated a mean age of 1.8 years Table 2 Detection of multiple pathogens in the respiratory tract of the overall study population (a) as well as of immunocompromised (b) and immunocompetent (c) patients. abstract: Respiratory tract infections (RTI) can take a serious course under immunosuppression. Data on the impact of the underlying pathogens are still controversial. Samples from the upper (n = 322) and lower RT (n = 169) were collected from 136 children and 355 adults; 225 among them have been immunocompromised patients. Exclusion criteria were presence of relevant cultivable microorganisms, C-reactive protein > 20 mg/dl, or procalcitonin > 2.0 ng/ml. Samples were tested by PCR for the presence of herpesviruses (HSV-1/-2; VZV; CMV; HHV6; EBV), adenoviruses, bocaviruses, entero-/rhinoviruses (HRV), parechoviruses, coronaviruses, influenza viruses (IV), parainfluenza viruses as well as for pneumoviruses (HMPV and RSV), and atypical bacteria (Mycoplasma pneumoniae, M.p.; Chlamydia pneumoniae, C.p.). Viral/bacterial genome equivalents were detected in more than two-thirds of specimens. Under immunosuppression, herpesviruses (EBV 30.9%/14.6%, p < 0.001; CMV 19.6%/7.9%, p < 0.001; HSV-1: 14.2%/7.1%, p = 0.012) were frequently observed, mainly through their reactivation in adults. Immunocompromised adults tended to present a higher RSV prevalence (6.4%/2.4%, p = 0.078). Immunocompetent patients were more frequently tested positive for IV (15.0%/5.8%, p = 0.001) and M.p. (6.4%/0.4%, p < 0.001), probably biased due to the influenza pandemic of 2009 and an M.p. epidemic in 2011. About 41.8% of samples were positive for a single pathogen, and among them EBV (19.9%) was most prevalent followed by HRV (18.2%) and IV (16.6%). HSV-2 and C.p. were not found. Marked seasonal effects were observed for HRV, IV, and RSV. Differences in pathogen prevalence were demonstrated between immunocompetent and immunocompromised patients. The exact contribution of some herpesviruses to the development of RTI remains unclear. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10096-020-03878-9) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/32462500/ doi: 10.1007/s10096-020-03878-9 id: cord-346325-grt67p73 author: Reilev, M. title: Characteristics and predictors of hospitalization and death in the first 9,519 cases with a positive RT-PCR test for SARS-CoV-2 in Denmark: A nationwide cohort date: 2020-05-26 words: 4655.0 sentences: 258.0 pages: flesch: 48.0 cache: ./cache/cord-346325-grt67p73.txt txt: ./txt/cord-346325-grt67p73.txt summary: Design, Setting, and Participants Nationwide population-based cohort of all 228.677 consecutive Danish individuals tested (positive or negative) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA from the identification of the first COVID-19 case on February 27th, 2020 until April 30th, 2020. In this population-based study of a Danish COVID-19 cohort capturing all individuals with a positive PCR test for SARS-CoV-2 in Denmark, we provide nationwide data on clinical characteristics and predictors of hospitalization and death for all SARS-CoV-2 PCR-positive cases identified from February 27 th , 2020 to April 30 th , 2020. In this nationwide cohort of SARS-CoV-2 PCR positive cases and test-negative individuals from the general population in Denmark, we found that older age (e.g., >70 years), male sex, and number of comorbidities were risk factors for hospitalization and death. In this first nationwide population-based study, increasing age, sex, and number and type of comorbidities were closely associated with hospitalization requirement and death in SARS-CoV-2 PCR positive cases. abstract: Objective To provide population-level knowledge on individuals at high risk of severe and fatal coronavirus disease 2019 (COVID-19) in order to inform targeted protection strategies in the general population and appropriate triage of hospital contacts. Design, Setting, and Participants Nationwide population-based cohort of all 228.677 consecutive Danish individuals tested (positive or negative) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA from the identification of the first COVID-19 case on February 27th, 2020 until April 30th, 2020. Main Outcomes and Measures We examined characteristics and predictors of inpatient hospitalization versus community-management, and death versus survival, adjusted for age-, sex- and number of comorbidities. Results We identified 9,519 SARS-CoV-2 PCR-positive cases of whom 78% were community-managed, 22% were hospitalized (3.2% at an intensive care unit) and 5.5% had died within 30 days. Median age varied from 45 years (interquartile range (IQR) 31-57) among community-managed cases to 82 years (IQR 75-89) among those who died. Age was a strong predictor of fatal disease (odds ratio (OR) 14 for 70-79-year old, OR 26 for 80-89-year old, and OR 82 for cases older than 90 years, when compared to 50-59-year old and adjusted for sex and number of comorbidities). Similarly, the number of comorbidities was strongly associated with fatal disease (OR 5.2, for cases with [≥]4 comorbidities versus no comorbidities), and 82% of fatal cases had at least 2 comorbidities. A wide range of major chronic diseases were associated with hospitalization with ORs ranging from 1.3-1.4 (e.g. stroke, ischemic heart disease) to 2.2-2.7 (e.g. heart failure, hospital-diagnosed kidney disease, chronic liver disease). Similarly, chronic diseases were associated with mortality with ORs ranging from 1.2-1.3 (e.g. ischemic heart disease, hypertension) to 2.4-2.7 (e.g. major psychiatric disorder, organ transplantation). In the absence of comorbidities, mortality was relatively low (5% or less) in persons aged up to 80 years. Conclusions and Relevance In this first nationwide population-based study, increasing age and number of comorbidities were strongly associated with hospitalization requirement and death in COVID-19. In the absence of comorbidities, the mortality was, however, lowest until the age of 80 years. These results may help in accurate identification, triage and protection of high-risk groups in general populations, i.e. when reopening societies. url: https://doi.org/10.1101/2020.05.24.20111823 doi: 10.1101/2020.05.24.20111823 id: cord-021402-wq770ik9 author: Relford, Roberta L. title: New Diagnostic Tools for Infectious Disease date: 2009-05-15 words: 3166.0 sentences: 157.0 pages: flesch: 36.0 cache: ./cache/cord-021402-wq770ik9.txt txt: ./txt/cord-021402-wq770ik9.txt summary: The most common laboratory methodologies used to identify an infectious agent include visualization of the organism via cytology/biopsy, isolation of the agent in microbiological culture, immunodiagnostics/serology, and nucleic acid technology. Fluorescent antibody and immunoblot assays are performed in commercial laboratories, whereas numerous patient-side rapid ELISA and latex agglutination kits are available for antigen detection. Until the introduction of nucleic acid amplification by the PCR, detection of an organism''s DNA or RNA often was impossible because of the small amount of antigen present in a sample. In the ELISA and IFA antibody assays, a specific antigen from the infectious agent in question is fixed to a solid surface (microtiter plate or glass slide, respectively) and the patient''s serum is added. The SVN assay evaluates the ability of antibodies in a patient''s serum to prevent the infection of culture cells or embryonated eggs with a known specific virus. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149580/ doi: 10.1016/b0-72-160423-4/50009-3 id: cord-020954-mt8mm7y4 author: Relich, Ryan F. title: Syndromic and Point-of-Care Molecular Testing date: 2018-10-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7148647/ doi: 10.1016/j.yamp.2018.07.007 id: cord-007047-7ty9mxa9 author: Reller, L. Barth title: Implications of New Technology for Infectious Diseases Practice date: 2006-11-15 words: 4095.0 sentences: 190.0 pages: flesch: 38.0 cache: ./cache/cord-007047-7ty9mxa9.txt txt: ./txt/cord-007047-7ty9mxa9.txt summary: Problems with currently available molecular assays include a lack of knowledge about the extent of microbial nucleic acid in "normal" hosts, concentration of agent material in small volume samples, lack of microbiologist expertise, lack of adequate reimbursement, and difficulty with validation based on conventional methods. Infectious diseases clinicians have relied on these expert workers, and Reliable molecular diagnostic tests are not readily available for many infectious agents Commercial tests should only be used for validated specimen types Transportation problems, low concentrations of infectious agent, primer binding site genetic changes, final assay volume, inhibition, contamination, nonspecific amplification, and operator error lead to false-negative and false-positive amplification results Genomic bacterial sequencing is subject to error because of sequence homology among different bacteria, database problems, and mutations A number of nucleic acid hybridization and amplification methods are now in use, including direct probe hybridization (AdvanDx FISH for Staphylococcus aureus [AdvanDx] and GenProbe for group A streptococci [GenProbe]), hybrid capture (Digene for human papillomavirus; Digene), PCR, branched-chain DNA (bDNA; Bayer Diagnostics), and transcription-mediated amplification (Probe-Tec for Chlamydia and N. abstract: New assays for the diagnosis of infectious diseases—particularly those that use molecular technologies—will revolutionize infectious diseases practices, but the fulfillment of the promise is several years away. Problems with currently available molecular assays include a lack of knowledge about the extent of microbial nucleic acid in “normal” hosts, concentration of agent material in small volume samples, lack of microbiologist expertise, lack of adequate reimbursement, and difficulty with validation based on conventional methods. Clinicians must appreciate the shortcomings of new technology to use it effectively and appropriately. However, we are realizing tangible progress in our ability to detect new etiological agents; the availability of rapid, accurate diagnostic tests for previously difficult infections; and advances into new, human response—based paradigms for diagnostic testing. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107913/ doi: 10.1086/508536 id: cord-259747-sl9q63oc author: Remmelink, Myriam title: Unspecific post-mortem findings despite multiorgan viral spread in COVID-19 patients date: 2020-08-12 words: 4541.0 sentences: 244.0 pages: flesch: 48.0 cache: ./cache/cord-259747-sl9q63oc.txt txt: ./txt/cord-259747-sl9q63oc.txt summary: BACKGROUND: Post-mortem studies can provide important information for understanding new diseases and small autopsy case series have already reported different findings in COVID-19 patients. IHC revealed positive cells with a heterogeneous distribution in the lungs of 11 of the 17 (65%) patients; RT-PCR yielded a wide distribution of SARS-CoV-2 in different tissues, with 8 patients showing viral presence in all tested organs (i.e., lung, heart, spleen, liver, colon, kidney, and brain). In this post-mortem study, we included the first 17 adult patients (> 18 years) who died in our hospital (either in a COVID-19 unit or an intensive care unit) from March 13, 2020, with confirmed SARS-CoV-2 infection (i.e., positive RT-PCR assay on nasopharyngeal swab and/or bronchoalveolar lavage specimen). This post-mortem study showed several histopathological abnormalities in COVID-19 non-survivors; however, none of the findings was specific for direct viral injury, even though SARS-CoV-2 was detected in all examined organs using RT-PCR. abstract: BACKGROUND: Post-mortem studies can provide important information for understanding new diseases and small autopsy case series have already reported different findings in COVID-19 patients. METHODS: We evaluated whether some specific post-mortem features are observed in these patients and if these changes are related to the presence of the virus in different organs. Complete macroscopic and microscopic autopsies were performed on different organs in 17 COVID-19 non-survivors. Presence of SARS-CoV-2 was evaluated with immunohistochemistry (IHC) in lung samples and with real-time reverse-transcription polymerase chain reaction (RT-PCR) test in the lung and other organs. RESULTS: Pulmonary findings revealed early-stage diffuse alveolar damage (DAD) in 15 out of 17 patients and microthrombi in small lung arteries in 11 patients. Late-stage DAD, atypical pneumocytes, and/or acute pneumonia were also observed. Four lung infarcts, two acute myocardial infarctions, and one ischemic enteritis were observed. There was no evidence of myocarditis, hepatitis, or encephalitis. Kidney evaluation revealed the presence of hemosiderin in tubules or pigmented casts in most patients. Spongiosis and vascular congestion were the most frequently encountered brain lesions. No specific SARS-CoV-2 lesions were observed in any organ. IHC revealed positive cells with a heterogeneous distribution in the lungs of 11 of the 17 (65%) patients; RT-PCR yielded a wide distribution of SARS-CoV-2 in different tissues, with 8 patients showing viral presence in all tested organs (i.e., lung, heart, spleen, liver, colon, kidney, and brain). CONCLUSIONS: In conclusion, autopsies revealed a great heterogeneity of COVID-19-associated organ injury and the remarkable absence of any specific viral lesions, even when RT-PCR identified the presence of the virus in many organs. url: https://www.ncbi.nlm.nih.gov/pubmed/32787909/ doi: 10.1186/s13054-020-03218-5 id: cord-293849-p3j2keyo author: Renaud, Christian title: Comparison of FilmArray Respiratory Panel and laboratory-developed real-time reverse transcription–polymerase chain reaction assays for respiratory virus detection date: 2012-12-31 words: 3288.0 sentences: 153.0 pages: flesch: 47.0 cache: ./cache/cord-293849-p3j2keyo.txt txt: ./txt/cord-293849-p3j2keyo.txt summary: Eighty-four respiratory viruses identified by laboratory-developed real-time reverse transcription–PCR assays (LDA) or by viral cultures were mixed and tested by FilmArray to assess its performance. The cost of each reagent pouch was approximately 6-fold higher than the cost per sample of the reagents needed to perform the laboratory-developed multiplexed real-time RT-PCR assays for detection of 12 respiratory viruses. The sensitivity of the FilmArray Respiratory Panel assay was comparable to our LDA for detection of 12 respiratory viruses in clinical samples and in dilutions of positive control mixes. In the analysis of 34 positive mixed clinical specimens, the FilmArray had results similar to those in another study comparing FilmArray with real-time PCR assays, identifying 90% of the 80 viruses detected by our LDA (Pierce et al., 2012) . In other situations, use of multiplexed Table 4 Results of laboratory-developed real-time RT-PCR assays and FilmArray Respiratory Panel assay for dilutions of the influenza positive mix control. abstract: Abstract The FilmArray Respiratory Panel (Idaho Technology) is a highly multiplexed respiratory virus real-time polymerase chain reaction (PCR) assay. Eighty-four respiratory viruses identified by laboratory-developed real-time reverse transcription–PCR assays (LDA) or by viral cultures were mixed and tested by FilmArray to assess its performance. FilmArray identified 72 (90%) of 80 viruses also detected by LDA. Six of the 8 viruses not detected by FilmArray had PCR cycle threshold values >35. Compared to LDA, FilmArray showed comparable sensitivity when used to test serial dilutions of virus mixtures and good agreement with negative samples. With the use of 1 FilmArray instrument, 7 clinical samples could be analyzed and reported in an 8-h shift compared to 20 using LDA and 1 real-time detection instrument. While the FilmArray was rapid and easy to use, its low throughput and qualitative results may be a disadvantage in some clinical settings. url: https://api.elsevier.com/content/article/pii/S073288931200332X doi: 10.1016/j.diagmicrobio.2012.08.003 id: cord-007234-hcpa8ej5 author: Renwick, Neil title: A Recently Identified Rhinovirus Genotype Is Associated with Severe Respiratory-Tract Infection in Children in Germany date: 2007-12-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Acute respiratory infection is a significant cause of morbidity and mortality in children worldwide. Accurate identification of causative agents is critical to case management and to prioritization in vaccine development. Sensitive multiplex diagnostics provide us with an opportunity to investigate the relative contributions of individual agents andmayalso facilitate the discovery of new pathogens. Recently, application of MassTag polymerase chain reaction (PCR) to undiagnosed infuenza-like illness in New York State led to the discovery of a novel rhinovirus genotype. Here we report the investigation, by MassTag PCR, of pediatric respiratory-tract infections in Germany, studying 97 cases for which no pathogen was identified through routine laboratory evaluation. Respiratory viruses were identified in 49 cases (51%); of the 55 identified viruses, 41 (75%) were rhinoviruses. The novel genotype represented 73% of rhinoviruses and 55% of all identified viruses. Infections with the novel genotype were associated with upper-respiratory-tract symptoms but, more frequently, with bronchitis, bronchiolitis, and pneumonia. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7109967/ doi: 10.1086/524312 id: cord-254115-hwy962a4 author: Reslova, Nikol title: xMAP Technology: Applications in Detection of Pathogens date: 2017-01-25 words: 11354.0 sentences: 530.0 pages: flesch: 40.0 cache: ./cache/cord-254115-hwy962a4.txt txt: ./txt/cord-254115-hwy962a4.txt summary: xMAP multiplex assays are currently available in various nucleic acid and immunoassay formats, enabling simultaneous detection and typing of pathogenic viruses, bacteria, parasites and fungi and also antigen or antibody interception. High-throughput multiplex detection techniques are designed for the rapid, sensitive and specific testing of large numbers of analytes (nucleic acid assays, immunoassays, enzyme assays, or receptor-ligands) in a single biological sample. Although PCR allows multiplex amplification of several targets in a single run xMAP as a methodology represents a significant step forward, and was designed with the aim of creating a high-throughput bioassay platform, enabling rapid, cost-effective, and simultaneous analysis of multiple analytes within a single biological sample. In direct DNA hybridization (DDH), allele-specific primer extension (ASPE), single base chain extension (SBCE), and Oligonucleotide ligation assay (OLA) all the target DNA sequences are amplified in multiplex PCR prior to hybridization to microspheres. abstract: xMAP technology is applicable for high-throughput, multiplex and simultaneous detection of different analytes within a single complex sample. xMAP multiplex assays are currently available in various nucleic acid and immunoassay formats, enabling simultaneous detection and typing of pathogenic viruses, bacteria, parasites and fungi and also antigen or antibody interception. As an open architecture platform, the xMAP technology is beneficial to end users and therefore it is used in various pharmaceutical, clinical and research laboratories. The main aim of this review is to summarize the latest findings and applications in the field of pathogen detection using microsphere-based multiplex assays. url: https://www.ncbi.nlm.nih.gov/pubmed/28179899/ doi: 10.3389/fmicb.2017.00055 id: cord-330800-s91zfzfi author: Reta, Daniel Hussien title: Molecular and Immunological Diagnostic Techniques of Medical Viruses date: 2020-09-04 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Viral infections are causing serious problems in human population worldwide. The recent outbreak of coronavirus disease 2019 caused by SARS-CoV-2 is a perfect example how viral infection could pose a great threat to global public health and economic sectors. Therefore, the first step in combating viral pathogens is to get a timely and accurate diagnosis. Early and accurate detection of the viral presence in patient sample is crucial for appropriate treatment, control, and prevention of epidemics. Here, we summarize some of the molecular and immunological diagnostic approaches available for the detection of viral infections of humans. Molecular diagnostic techniques provide rapid viral detection in patient sample. They are also relatively inexpensive and highly sensitive and specific diagnostic methods. Immunological-based techniques have been extensively utilized for the detection and epidemiological studies of human viral infections. They can detect antiviral antibodies or viral antigens in clinical samples. There are several commercially available molecular and immunological diagnostic kits that facilitate the use of these methods in the majority of clinical laboratories worldwide. In developing countries including Ethiopia where most of viral infections are endemic, exposure to improved or new methods is highly limited as these methods are very costly to use and also require technical skills. Since researchers and clinicians in all corners of the globe are working hard, it is hoped that in the near future, they will develop good quality tests that can be accessible in low-income countries. url: https://www.ncbi.nlm.nih.gov/pubmed/32908530/ doi: 10.1155/2020/8832728 id: cord-005048-9fs1ienf author: Retief, E. title: Potential Inoculum Sources of Phaeomoniellachlamydospora in South African Grapevine Nurseries date: 2006-06-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Petri disease of grapevine is primarily caused by Phaeomoniella chlamydospora. This pathogen affects mostly young grapevines, but is also implicated in esca disease of older grapevines. Little is known about the disease cycle of this fungus. Infected propagation material was identified as a major means of dissemination of the pathogen. Recently, the pathogen was also detected from soil in South Africa and airborne conidia have been found in vineyards. The aim of this study was to use a molecular detection technique to test different samples collected from nurseries in South Africa at different nursery stages for the presence of P. chlamydospora. A one-tube nested-PCR technique was optimised for detecting P. chlamydospora in DNA extracted from soil, water, callusing medium and grapevine wood. The one-tube nested-PCR was sensitive enough to detect as little as 1 fg of P. chlamydospora genomic DNA from water and 10 fg from wood, callusing medium and soil. PCR analyses of the different nursery samples revealed the presence of several putative 360 bp P. chlamydospora specific bands. Subsequent sequence analyses and/or restriction enzyme digestions of all 360 bp PCR bands confirmed that all bands were P. chlamydospora specific, except for five bands obtained from callusing media and one from water. Phaeomoniella chlamydospora was positively detected in 25% of rootstock cane sections collected from mother blocks, 42% of rootstock cuttings and 16% of scion cuttings collected during grafting, 40% of water samples collected after pre-storage hydration, 67% of water samples collected during grafting, 8% of callusing medium samples and 17% of soil samples collected from mother blocks. These media can therefore be considered as possible inoculum sources of the pathogen during the nursery stages. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7088137/ doi: 10.1007/s10658-006-9025-4 id: cord-310771-tnwfp1je author: Revilla-Fernández, Sandra title: The use of endogenous and exogenous reference RNAs for qualitative and quantitative detection of PRRSV in porcine semen date: 2005-02-23 words: 5933.0 sentences: 297.0 pages: flesch: 51.0 cache: ./cache/cord-310771-tnwfp1je.txt txt: ./txt/cord-310771-tnwfp1je.txt summary: A method was developed for qualitative and quantitative detection of the seminal cell-associated PRRSV RNA in relation to endogenous and exogenous reference RNAs. As endogenous control for one-step real-time reverse transcription (RT)-PCR UBE2D2 mRNA was selected. Particularly for the analysis of persistent infections associated with low copy numbers of PRRSV RNA, UBE2D2 mRNA is an ideal control due to its low expression in seminal cells and its detection in all samples analysed (n = 36). For the development of one-step real-time RT-PCR for four endogenous reference RNAs (HPRT, UBE2D2, PPIA, and HMBS) appropriate target regions were selected and the assay conditions were optimised for amplification efficiency. One-step real-time RT-PCR assays for PRRSV-1 and -2 RNA allowed quantitation with optimal efficiency (Fig. 1a ; standard curves for two additional viremic pigs infected with PRRSV-1 (data not shown)) as achieved for endogenous and Fig. 1 . abstract: Semen is known to be a route of porcine reproductive and respiratory syndrome virus (PRRSV) transmission. A method was developed for qualitative and quantitative detection of the seminal cell-associated PRRSV RNA in relation to endogenous and exogenous reference RNAs. As endogenous control for one-step real-time reverse transcription (RT)-PCR UBE2D2 mRNA was selected. Particularly for the analysis of persistent infections associated with low copy numbers of PRRSV RNA, UBE2D2 mRNA is an ideal control due to its low expression in seminal cells and its detection in all samples analysed (n = 36). However, the amount of UBE2D2 mRNA in porcine semen varied (up to 106-fold), thus its use is limited to qualitative detection of PRRSV RNA. For quantitation, a synthetic, non-metazoan RNA was added to the RNA isolation reaction at an exact copy number. The photosynthesis gene ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) from Arabidopsis thaliana was used as an exogenous spike. Unexpectedly, PRRSV RNA was detected in a herd of specific pathogen-free (SPF) boars which were tested ELISA-negative for anti-PRRSV antibodies. Therefore, RT-PCR for seminal cell-associated PRRSV is a powerful tool for managing the SPF status during quarantine programs and for routine outbreak investigations. url: https://www.ncbi.nlm.nih.gov/pubmed/15847915/ doi: 10.1016/j.jviromet.2005.01.018 id: cord-016882-c9ts2g7w author: Ribeiro, Edna title: Viruses Present Indoors and Analyses Approaches date: 2017-06-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Through human history viruses have shown enormous epidemiological and pandemic potential as the occurrence and spread of viruses in pandemic dimensions poses a threat to the health and lives of seven billion people worldwide. Scientific evidence has associated harmful health effects to indoor air hazards recognizing the existence of a vital concern in public health sector. Thus the assessment of human exposure to biological aerosols and droplets indoor became an imperative requirement of investigation. Environmental bioburden assessment of viruses relies in both culture-dependent approaches that comprise classical methodologies, still prominent and vital in the field of modern biotechnology, and culture-independent approaches based on nucleic acid amplification techniques, which are considered the gold standard in clinical virology. The main factor influencing indoor microbiology is the human being and their activities. Indoor environments to be considered are those regularly occupied by humans: residences, offices, schools, industrial buildings, health care facilities, farming activities and other settings occupied all the time, or in which occupant density is high. It’s well known that approximately 60% of total human respiratory and gastrointestinal infections are acquired indoor, since viruses have a rapid spread in the community and can be transmitted easily, especially in crowded and poorly ventilated environments, causing high morbidity and decline in quality of life and productivity. Studies have shown that respiratory syncytial virus, rhinovirus, metapneumovirus, influenza and parainfluenza virus, and human enterovirus infections may be associated with virus-induced asthma, leading to diseases such as pneumonia. Gastroenteritis infectious (about 30±40% of cases) is attributable to viruses. Rotavirus, Astrovirus, Norwalk-like viruses and other caliciviruses are responsible for 48% of all reported outbreaks of infectious intestinal disease. Safe working conditions are essential for healthy living, that’s why the programmes conceived as a result of strategic and preventive policy maintenance, in refrigeration and ventilation systems, are the determining factor for the control of biological pollutants. Moreover, the development of highly sensitive and specific detection and identification methodologies with capacity to be used in diverse applications, such as diagnosis, public health risk assessment, research and for the implementation of preventive measures and protocols are imperative. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121309/ doi: 10.1007/978-3-319-61688-9_7 id: cord-302871-x3mjov5l author: Ribeiro, Juliane title: Extra-intestinal detection of canine kobuvirus in a puppy from Southern Brazil date: 2016-11-25 words: 2586.0 sentences: 129.0 pages: flesch: 45.0 cache: ./cache/cord-302871-x3mjov5l.txt txt: ./txt/cord-302871-x3mjov5l.txt summary: This study presents the pathological, immunohistochemical, and molecular findings associated with the extra-intestinal detection of canine kobuvirus (CaKV) in a 5-month-old Chihuahua puppy, that had a clinical history of bloody-tinged feces. There are few descriptions of coinfection due to CaKV and other viral agents: a recent study identified CaKV in association with a several agents including canine herpesvirus type 1 (CaHV-1), canine distemper virus (CDV), canine parvovirus (CPV), and canine adenovirus A types 1 (CAdV-1) and 2 (CAdV-2) in diarrheic and non-diarrheic dogs from Korea [19] . Furthermore, widespread viral dissemination was demonstrated in multiple tissues as CaKV nucleic acids were detected in the liver, lung, brain, and tonsils of this Fig. 2 Phylogenetic analysis of a partial nucleotide sequence (nt 201) of the RdRp gene (a) and partial region of the VP1 protein (nt 303) of canine kobuvirus (CaKV) (b). abstract: This study presents the pathological, immunohistochemical, and molecular findings associated with the extra-intestinal detection of canine kobuvirus (CaKV) in a 5-month-old Chihuahua puppy, that had a clinical history of bloody-tinged feces. Principal pathological findings were interstitial pneumonia, necrotizing bronchitis, and parvovirus-induced enteritis. Molecular diagnostic methods identified CaKV within the cerebellum, cerebrum, lung, tonsil, and liver. CaKV and rotavirus were not identified within the feces and intestine. Immunohistochemistry (IHC) assays detected antigens of CDV and CAdV-1 in the lungs. These results confirmed the extra-intestinal detection of CaKV in this puppy and represent the first extra-intestinal detection of CaKV in a dog. url: https://www.ncbi.nlm.nih.gov/pubmed/27888408/ doi: 10.1007/s00705-016-3164-5 id: cord-281887-b511bjdy author: Ribeiro, Reitan title: Perioperative Cancer Care in the Context of Limited Resources during the COVID-19 Pandemic: Brazilian Society of Surgical Oncology Recommendations date: 2020-09-26 words: 4739.0 sentences: 234.0 pages: flesch: 45.0 cache: ./cache/cord-281887-b511bjdy.txt txt: ./txt/cord-281887-b511bjdy.txt summary: DISCUSSION: The rational use of resources to reduce the risk of surgical cancer patients being operated on during the incubation period of a corona virus infection is important in this context. CONCLUSIONS: We present a protocol, focused on the patients'' outcomes, for safe and rational use of resources to reduce the risk of surgical cancer patients being operated on during the virus incubation period, in the context of areas with limited resources. Our objective was to present the Brazilian Society of Surgical Oncology (BSSO) protocol for rational use of resources and for reducing the risk of surgical cancer patients being operated on during the coronavirus incubation period, in the context of areas with limited resources, and focused on patient outcomes. In light of all the previous considerations, Table 3 presents our suggested protocol for the rational use of resources to reduce the risk of surgical cancer patients from being operated on during the COVID-19 incubation period, in the context of areas with limited resources. abstract: BACKGROUND: As the COVID-19 pandemic moves from rich to poor nations, the healthcare systems of developing countries have to deal with this extra burden. As cancer care cannot stop and surgery is the main mechanism for cure and palliation, it is important to provide safe and rational access to cancer surgery during the COVID-19 pandemic. METHODS: From April 1st to May 1st, the committee of the Brazilian Society of Surgical Oncology (BSSO) was responsible for reviewing the literature and writing recommendations for perioperative cancer care in the context of limited resources during the pandemic. The recommendations were submitted to the BSSO board of directors. The orientations that were not consensual were removed and the suggestions were added to the text. From May 15 to 30th, the committee revised the recommendations, aligned them with the objectives of the work and standardize the text. DISCUSSION: The rational use of resources to reduce the risk of surgical cancer patients being operated on during the incubation period of a corona virus infection is important in this context. Prevalence of corona virus in the region, the need for surgery, surgical complexity, patient age and comorbidities, and availability of corona virus testing are central aspects in this matter and are discussed. CONCLUSIONS: We present a protocol, focused on the patients’ outcomes, for safe and rational use of resources to reduce the risk of surgical cancer patients being operated on during the virus incubation period, in the context of areas with limited resources. url: https://doi.org/10.1245/s10434-020-09098-x doi: 10.1245/s10434-020-09098-x id: cord-305475-lhi0hcki author: Risku, Minna title: Human bocavirus types 1, 2 and 3 in acute gastroenteritis of childhood date: 2012-05-24 words: 3575.0 sentences: 195.0 pages: flesch: 59.0 cache: ./cache/cord-305475-lhi0hcki.txt txt: ./txt/cord-305475-lhi0hcki.txt summary: We studied 878 stool specimens from children with acute gastroenteritis and 112 controls (43 children with unspecified fever, 33 with respiratory tract infection and 36 healthy children) for known HBoVs. The same specimens were previously studied for rotaviruses, noroviruses, sapoviruses, adenoviruses, coronaviruses and aichivirus. As in the case of the respiratory tract, simultaneous presence of HBoV1 with other, previously established gastroenteritis viruses is common in faecal specimens (10, 12, 13) , and no clear connection between HBoV1 and AGE of children has been established (11, 13, 14) . We did a thorough work-up of most of the established gastroenteritis viruses including rotaviruses, noroviruses, sapoviruses, enteric adenoviruses, coronaviruses and aichivirus (astroviruses or bacterial pathogens were not studied) and found co-infections in 81.2% of all bocavirus-positive AGE cases. Human bocavirus in children hospitalized for acute gastroenteritis: a case-control study abstract: Aim: Recently identified human bocavirus (HBoV) types 2 and 3 have been associated with acute gastroenteritis in children. We studied 878 stool specimens from children with acute gastroenteritis and 112 controls (43 children with unspecified fever, 33 with respiratory tract infection and 36 healthy children) for known HBoVs. The same specimens were previously studied for rotaviruses, noroviruses, sapoviruses, adenoviruses, coronaviruses and aichivirus. Methods: HBoVs were detected by PCR and positive amplicons were sequenced to identify HBoV1, HBoV2, HBoV3 and HBoV4. Results: HBoV of any type was found in 85 (9.7%) cases of acute gastroenteritis and in 6 (5.4%) controls. HBoV1 was detected in 49 (5.6%) cases and 2 (1.8%) controls, HBoV2 in 29 (3.3%) cases and 2 (1.8%) controls and HBoV3 in 8 (0.9%) cases and 2 (1.8%) controls. No HBoV4 was found. HBoV as a single infection was found in 16 (1.8%) cases and in 6 (5.4%) controls; in the remaining cases, a known gastroenteritis virus was also found. Among the single HBoV infections, HBoV2 was the most common type with 8 (50%) cases. Conclusion: HBoVs are rarely found alone in children with acute gastroenteritis. Further studies are warranted to confirm a possible specific association of HBoV2 with gastroenteritis. url: https://www.ncbi.nlm.nih.gov/pubmed/22568605/ doi: 10.1111/j.1651-2227.2012.02727.x id: cord-322389-rd93y7hu author: Ritzi-Lehnert, Marion title: On-chip analysis of respiratory viruses from nasopharyngeal samples date: 2011-05-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Point-of-care (PoC) testing followed by personalized efficient therapy of infectious diseases may result in a considerable reduction of associated health care costs. Lab-on-a-chip (LoC) systems represent a potentially high efficient class of PoC tools. Here, we present a LoC system for automated pathogen analysis of respiratory viruses from nasopharyngeal specimens. The device prepares total nucleic acids from extracted swab samples using magnetic silica beads. After reverse transcription the co-purified viral RNA is amplified in accordance with the QIAplex multiplex PCR technology. Hybridized to corresponding QIAGEN LiquiChip beads and labelled with streptavidin R-phycoerythrin, the amplified target sequences are finally detected using a QIAGEN LiquiChip200 workstation. All chemicals needed are either stored freeze-dried on the disposable chip or are provided in liquid form in a reagent cartridge for up to 24 runs. Magnetic stir bars for mixing as well as turning valves with metering structures are integrated into the injection-moulded disposable chip. The core of the controlling instrument is a rotating heating bar construction providing fixed temperatures for fast cycling. PCR times of about half an hour (for 30 cycles) could be achieved for 120 μl reactions, making this system the fastest currently available high-volume PCR chip. The functionality of the system was shown by comparing automatically processed nasopharyngeal samples to ones processed manually according to the QIAGEN “ResPlex™ II Panel v2.0” respiratory virus detection kit. A prototype of the present instrument revealed slightly weaker signal intensities with a similar sensitivity in comparison to the commercially available kit and automated nucleic acid preparation devices, even without protocol optimization. url: https://doi.org/10.1007/s10544-011-9552-4 doi: 10.1007/s10544-011-9552-4 id: cord-304720-0lgup7yj author: Robbins, R.C. title: Swine Diseases and Disorders date: 2014-08-21 words: 12872.0 sentences: 837.0 pages: flesch: 44.0 cache: ./cache/cord-304720-0lgup7yj.txt txt: ./txt/cord-304720-0lgup7yj.txt summary: The industry significance, etiology, epidemiology, pathogenesis, clinical signs, postmortem and histpathologic lesions, diagnostic testing, and generic treatment, control, and prevention are described. Important history to understand from caretakers includes: age of pigs affected, duration of clinical signs, morbidity rate, mortality rate, treatments administered, response to treatments, and any other important information regarding previous diagnoses or disease in the affected group of animals. Records include but are not limited to: where the animals originated from; number in the herd; age; daily mortality; number treated; name of treatment, route of delivery and dose; feed and water usage; high-low temperatures; and vaccinations received or administered. Postweaning infections result in a high morbidity but low mortality; most significant economic losses at this time are caused by reduced average daily gain, market weights, and overall system efficiency. Postweaning infections result in a high morbidity but low mortality; most significant economic losses at this time are caused by reduced average daily gain, market weights, and overall system efficiency. abstract: Swine diseases and disorders that are significant in modern, commercial swine production systems are organized by body system; the reader will need to know basic anatomy and physiology. The industry significance, etiology, epidemiology, pathogenesis, clinical signs, postmortem and histpathologic lesions, diagnostic testing, and generic treatment, control, and prevention are described. Diseases of a particular system are summarized in a differential diagnosis table. url: https://api.elsevier.com/content/article/pii/B9780444525123001340 doi: 10.1016/b978-0-444-52512-3.00134-0 id: cord-261735-03hvi4el author: Rodrigues, R. title: Development of a one step real time RT-PCR assay to detect and quantify Dugbe virus date: 2011-06-14 words: 2637.0 sentences: 159.0 pages: flesch: 60.0 cache: ./cache/cord-261735-03hvi4el.txt txt: ./txt/cord-261735-03hvi4el.txt summary: A one-step real time quantitative RT-PCR (qRT-PCR) assay was developed to detect all published Dugbe virus (DUGV) genomes of the Nairovirus genus. Frequently detected in tick-borne virus surveys in Africa (Guilherme et al., 1996) , DUGV is a tri-segmented single-stranded negative RNA enveloped virus and is considered endemic in arid regions (Burt et al., 1996) . The aim of this study was to develop a sensitive, specific and rapid one-step quantitative real time RT-PCR assay (qRT-PCR) to detect DUGV in infected cell supernatants, ticks or serum samples. The specificity was evaluated by using RNA extracted from supernatants from CCHFV, Hazara virus, Coronavirus and Influenza A virus infected cells. Among the 498 captured ticks, one Dugbe virus RNA was detected in one tick using the qRT-PCR assay (0.2%). In conclusion, a sensitive and specific qRT-PCR assay was developed to detect and quantify DUGV RNAs in infected cell supernatants, extracts from ticks and potentially sera. abstract: A one-step real time quantitative RT-PCR (qRT-PCR) assay was developed to detect all published Dugbe virus (DUGV) genomes of the Nairovirus genus. Primers and probes were designed to detect specific sequences on the most conserved regions of the S segment. The limit of detection of the assay was 10 copies per reaction which is an improvement of 3 log(10) FFU/mL over the sensitivity of conventional RT-PCR. The specificity of the primers and probe was confirmed with the closely related Nairoviruses CCHFV and Hazara virus, and on the non-related viruses Coronavirus and Influenza A virus. This qRT-PCR assay was used to screen nucleic acids extracted from 498 ticks collected in the Republic of Chad. One sample was found positive suggesting that DUGV is present in this part of the world. The molecular assay developed in this study is sensitive, specific and rapid and can be used for research and epidemiological studies. url: https://www.ncbi.nlm.nih.gov/pubmed/21703306/ doi: 10.1016/j.jviromet.2011.06.003 id: cord-293421-0ksn0fc7 author: Rodriguez, J. M. title: Detection of animal pathogens by using the polymerasechain reaction (PCR) date: 1997-05-31 words: 9106.0 sentences: 559.0 pages: flesch: 49.0 cache: ./cache/cord-293421-0ksn0fc7.txt txt: ./txt/cord-293421-0ksn0fc7.txt summary: Summary The polymerase chain reaction (PCR) is a nucleic acid-based technique that enables the rapid and sensitive detection of specific micro-organisms. Althougla PCR has some shortcomings, such as the problems caused by contaminants and inhibitors or the lack of suitable sequences for designing specific primers, the outstanding research effort focused on tiffs technique, together with the remarkable development of molecular biology have minimized the deficiencies and allowed its increased general use as a diagnostic tool. Sensitive studies using reference strains of BVDV fi-om persistently infected carriers have shown that reverse transo-iption (RT)-PCR has greater sensitivity than other tests, including enzyme-linked immunosorbent assay (ELISA) (Horner el aL, 1995) ; unfortunately, cost currently makes this technique unsuitahle for large-scale testing but it should be valuahle as a coniirmatm T test in cases where ELISA resuhs are in the ''suspicious range'' or where the viral titre is low, such as in batches of foetal bovine serum. Comparison of polymerase chain reaction and virus isolation for detection of epizootic hemorrhagic disease in clinical samples from naturally infected deer abstract: Summary The polymerase chain reaction (PCR) is a nucleic acid-based technique that enables the rapid and sensitive detection of specific micro-organisms. Although this technique is widely used in veterinary research, it has not yet found applications in routine microbiological analysis of veterinary clinical samples. However, advances in sample preparation together with the increasing availability of specific gene sequences will probably lead to the more widespread diagnostic use of PCR in the future. PCR is likely to have a strong impact in the epidemiology, treatment and prevention of animal infectious diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/9232118/ doi: 10.1016/s1090-0233(97)80063-9 id: cord-333805-xmqs2ax7 author: Romoli, Michele title: A systematic review of neurological manifestations of SARS‐CoV‐2 infection: the devil is hidden in the details date: 2020-06-05 words: 4025.0 sentences: 257.0 pages: flesch: 44.0 cache: ./cache/cord-333805-xmqs2ax7.txt txt: ./txt/cord-333805-xmqs2ax7.txt summary: BACKGROUND: We systematically reviewed available evidence for reports of neurological signs and symptoms in Coronavirus disease (COVID)‐19 patients to identify cases with severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) infection or immune‐mediated reaction in the nervous system. This study therefore aimed to identify clinical cases of confirmed nervous system invasion or postinfectious neurological disease in the available COVID-19 literature on the basis of a systematic review. A systematic review was carried out to study all cases reporting nervous system involvement in patients with proven SARS-CoV2 infection. There were just 2 cases with positive SARS-CoV-2 PCR in CSF among 27 patients with potential neurologic symptoms and proven COVID-19. In this regard, we see a clear need for the use of precise case definitions and focused diagnostic work-up to distinguish nonspecific complications of severe disease and focused reporting of neurological involvement in association with SARS-CoV-2 infection. abstract: BACKGROUND: We systematically reviewed available evidence for reports of neurological signs and symptoms in Coronavirus disease (COVID)‐19 patients to identify cases with severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) infection or immune‐mediated reaction in the nervous system. METHODS: We followed PRISMA guidelines and used the MEDLINE, EMBASE, Google Scholar, MedRxiv and ChinaXiv databases to search for papers on COVID‐19 and nervous system involvement which were published from January 1(st) to April 24(th) 2020. Data on design, sample size, neurologic assessment and related work‐up were extracted. Biases were assessed with the Newcastle‐Ottawa scale. RESULTS: We analysed 27 publications on potential neuroinvasive or parainfectious neurological complications of COVID‐19. The reports focused on smell and taste (n=5) and evaluation of neurological symptoms and signs in cohorts (n=5). There were cases of Guillain‐Barré syndrome/Miller‐Fisher syndrome/cranial neuropathy (7 cases), meningitis/encephalitis (9 cases) and various other conditions (5 cases). Patients with cerebrospinal fluid (CSF) examination and in particular SARS‐CoV‐2 PCR was negligible. Amongst, two had a positive SARS‐CoV‐2 PCR exam of CSF specimen. The study of potential parenchymal involvement with magnetic resonance imaging was rare. Only 4 reports received a rating for the highest quality standards. CONCLUSION: This systematic review failed to establish comprehensive insights to nervous system manifestations of COVID‐19 beyond immune‐mediated complications as aftermath of respiratory symptoms. The authors therefore provide guidance for more careful clinical, diagnostic and epidemiological studies to characterize the manifestations and burden of neurological disease caused by SARS‐CoV‐2 on behalf of the Infectious Disease Panel of the European Academy of Neurology. url: https://doi.org/10.1111/ene.14382 doi: 10.1111/ene.14382 id: cord-316295-x636ux34 author: Roth, Bernhard title: Isolation of influenza viruses in MDCK 33016PF cells and clearance of contaminating respiratory viruses date: 2012-01-11 words: 4140.0 sentences: 190.0 pages: flesch: 44.0 cache: ./cache/cord-316295-x636ux34.txt txt: ./txt/cord-316295-x636ux34.txt summary: Abstract This paper summarizes results obtained by multiplex PCR screening of human clinical samples for respiratory viruses and corresponding data obtained after passaging of virus-positive samples in MDCK 33016PF cells. Using lower inoculum dilutions than those normally applied for preparations containing influenza virus (total dilution of the original sample of ∼104), the positive results for the different viruses turned negative already after 2 or 3 passages in MDCK 33016PF cells. In a similar way, samples with positive and questionable multiplex PCR results only for viruses other than influenza virus were also cultivated for 2 or 3 passages in MDCK 33016PF cells. Considering the selection of specimens, the high percentage of influenza-positive results is not surprising, but a significant number of samples (66/370 or 17.8%) also tested positive for other viruses, such as adenovirus, bocavirus, coronavirus, enterovirus, metapneumovirus (HMPV), parainfluenza virus (PIV), rhinovirus, and respiratory syncytial virus (RSV). abstract: Abstract This paper summarizes results obtained by multiplex PCR screening of human clinical samples for respiratory viruses and corresponding data obtained after passaging of virus-positive samples in MDCK 33016PF cells. Using the ResPlexII v2.0 (Qiagen) multiplex PCR, 393 positive results were obtained in 468 clinical samples collected during an influenza season in Germany. The overall distribution of positive results was influenza A 42.0%, influenza B 38.7%, adenovirus 1.5%, bocavirus 0.5%, coronavirus 3.3%, enterovirus 5.6%, metapneumovirus 1.0%, parainfluenza virus 0.8%, rhinovirus 4.1%, and respiratory syncytial virus (RSV) 2.5%. Double infections of influenza virus together with another virus were found for adenovirus B and E, bocavirus, coronavirus, enterovirus and for rhinovirus. These other viruses were rapidly lost upon passages in MDCK 33016PF cells and under conditions as applied to influenza virus passaging. Clinical samples, in which no influenza virus but other viruses were found, were also subject to passages in MDCK 33016PF cells. Using lower inoculum dilutions than those normally applied for preparations containing influenza virus (total dilution of the original sample of ∼104), the positive results for the different viruses turned negative already after 2 or 3 passages in MDCK 33016PF cells. These results demonstrate that, under practical conditions as applied to grow influenza viruses, contaminating viruses can be effectively removed by passages in MDCK cells. In combination with their superior isolation efficiency, MDCK cells appear highly suitable to be used as an alternative to embryonated eggs to isolate and propagate influenza vaccine candidate viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/22119922/ doi: 10.1016/j.vaccine.2011.11.063 id: cord-290540-r0d6oaez author: Rottier, Peter J.M. title: The molecular dynamics of feline coronaviruses date: 1999-09-01 words: 3820.0 sentences: 200.0 pages: flesch: 56.0 cache: ./cache/cord-290540-r0d6oaez.txt txt: ./txt/cord-290540-r0d6oaez.txt summary: Special attention is given to the genetic dynamics of the viruses as these now allow us to begin to understand the origin of the different phenotypes, in particular the genesis of virulence during persistent infection. The conclusion from these experiments is that feline coronaviruses may persist in the lower intestinal tract where the virus continues to replicate at low levels. Conceivably, the persisting virus confers to its host resistance against superinfection by the closely related feline coronaviruses, which were infecting the other cats. The idea was that''feline enteric coronaviruses'' are indeed restricted in tropism, while''FIP viruses'' would cross the epithelium, infect macrophages and go systemically. The result of all these studies is that generally there is no protection when an antibody response to the spike protein is induced there is rather an enhancement of the infection, with an''early death'' phenomenon. Detection of feline coronavirus RNA in feces, tissues and body fluids of naturally infected cats by reverse transcriptase PCR abstract: Feline coronaviruses are widespread and come in different flavors. There are two main serotypes both of which occur in two pathotypes, the avirulent enteric viruses and the virulent, usually fatal peritonitis viruses, the latter in turn occurring either in a ‘wet’ or exudative form or in a ‘dry’ or proliferative form. In this paper a concise overview is given of the molecular features of these viruses. Special attention is given to the genetic dynamics of the viruses as these now allow us to begin to understand the origin of the different phenotypes, in particular the genesis of virulence during persistent infection. As discussed, the surprising new insights obtained over the last few years call for a critical reevaluation of strategies for protection. url: https://www.sciencedirect.com/science/article/pii/S0378113599000991 doi: 10.1016/s0378-1135(99)00099-1 id: cord-275275-wy8d6cw3 author: Rovida, Francesca title: Molecular detection of gastrointestinal viral infections in hospitalized patients date: 2013-09-12 words: 2595.0 sentences: 143.0 pages: flesch: 50.0 cache: ./cache/cord-275275-wy8d6cw3.txt txt: ./txt/cord-275275-wy8d6cw3.txt summary: During the period April 2011 to April 2012, 689 stool samples from as many patients hospitalized at the Fondazione IRCCS Policlinico San Matteo of Pavia exhibiting gastrointestinal syndromes were examined for the presence of rotavirus, norovirus, astrovirus, adenovirus, rhinovirus, enterovirus, parechovirus, bocavirus, coronavirus, sapovirus, cosavirus, and aichi virus using polymerase chain reaction assays. Viral pathogens causing acute gastroenteritis include Rotavirus (RV), members of the Caliciviridae family such as Norovirus (NoV) and Sapovirus (SaV), Adenovirus (HAdV) and Astrovirus (HAstV) (Eckardt and Baumgart, 2011) . Overall, 689 stool samples stored in the period April 2011 to April 2012 from as many patients (356 pediatrics and 333 adults) with gastrointestinal syndromes hospitalized at the Fondazione IRCCS Policlinico San Matteo of Pavia (a teaching and university hospital with 50,000 admissions, 2,500,000 outpatients visits, and 94,000 emergency consultations per year) were systematically examined for the presence of gastroenteric viruses. abstract: Gastrointestinal viral syndromes are a common cause of morbidity and mortality in humans worldwide. Etiological agents include a large number of viruses encompassing several orders, families, and genera. During the period April 2011 to April 2012, 689 stool samples from as many patients hospitalized at the Fondazione IRCCS Policlinico San Matteo of Pavia exhibiting gastrointestinal syndromes were examined for the presence of rotavirus, norovirus, astrovirus, adenovirus, rhinovirus, enterovirus, parechovirus, bocavirus, coronavirus, sapovirus, cosavirus, and aichi virus using polymerase chain reaction assays. Gastrointestinal viral agents were detected in 246 (36%) patients of the 689 analyzed. Adenovirus and norovirus were the most common viruses in this cohort, while aichi virus was the only gastrointestinal agent not detected. Surprisingly, rhinovirus was one of the most frequently detected viruses. However, a potential association with gastroenteritis remains to be confirmed. url: https://www.ncbi.nlm.nih.gov/pubmed/24035383/ doi: 10.1016/j.diagmicrobio.2013.07.020 id: cord-261160-g92zhv19 author: Rowland, Raymond R.R title: Lymphoid tissue tropism of porcine reproductive and respiratory syndrome virus replication during persistent infection of pigs originally exposed to virus in utero date: 2003-10-30 words: 6383.0 sentences: 322.0 pages: flesch: 48.0 cache: ./cache/cord-261160-g92zhv19.txt txt: ./txt/cord-261160-g92zhv19.txt summary: title: Lymphoid tissue tropism of porcine reproductive and respiratory syndrome virus replication during persistent infection of pigs originally exposed to virus in utero Even though PRRSV-specific antibody appears as early as 5 days post-infection and is followed by serum neutralizing activity and cell-mediated immunity Molitor, 1997, 1999; Rowland et al., 1999 Rowland et al., , 2001 persistently infected pigs can continue to shed virus. The purpose of this study was to further understand persistent infection in congenitally infected pigs by characterizing the course of clinical disease, sites of virus replication and the capacity to transmit virus in a group of pigs exposed to PRRSV in utero. Analysis of virus and antibody in blood and/or umbilical cords from the 28 live neonates showed that at least 20 or 74% were virus isolation (VI) or RT-PCR positive for PRRSV at the time of farrowing indicating that in utero infection was successful. abstract: The ability of porcine reproductive and respiratory syndrome virus (PRRSV) to establish a persistent infection is the principal contributing factor to the world-wide spread of the disease. Several studies have documented the course of viral infection in postnatally infected pigs; however, very little is known regarding sites of virus replication during persistent infection of pigs exposed to PRRSV in utero. In this study, virus replication and PRRSV-specific antibody were followed for several hundred days in a group of pigs derived from three sows infected at 90 days of gestation with PRRSV isolate VR-2332. Eighty-four percent of pigs were born viremic with a mortality of 54% within 21 days after birth. At approximately 60 days sera from pigs were negative for virus by virus isolation. Analysis of virus replication in the tissues of pigs randomly sacrificed between 63 and 132 days showed no evidence of virus in lung and other non-lymphoid organs. However, virus was easily recovered from tonsil and lymph nodes and in situ hybridization identified these tissues as sites of virus replication. Even though replication was at a low level, virus was easily transmitted to sentinel pigs. By 260 days pigs became seronegative and did not transmit virus to sentinel pigs. Sacrifice of remaining pigs after 300 days showed no evidence of virus in blood and tissues. This study shows that congenital PRRSV-infected pigs can support virus replication for an extended period during which virus replication is primarily restricted to tonsil and lymph nodes. url: https://www.ncbi.nlm.nih.gov/pubmed/14559170/ doi: 10.1016/j.vetmic.2003.07.006 id: cord-275413-e2rhioty author: Rowland, Raymond R.R. title: The interaction between PRRSV and the late gestation pig fetus date: 2010-09-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Porcine reproductive and respiratory syndrome virus (PRRSV) crosses the placenta during late gestation and productively infects the fetus. Virus replication and cytokine responses were measured in tissues of fetuses recovered at 109–112 days of gestation, just prior to parturition. At the time of recovery, gross anatomical abnormalities were evident in both infected and non-infected fetuses from the infected dams. Virus isolation and immunohistochemistry identified the thymus as the primary site of virus replication. Steady state RT-PCR amplification of inflammatory, Th1 and Th2 cytokines, showed elevated IFN-γ and TNF-α mRNAs in tissues from infected fetuses, which corresponded to elevated cytokine proteins in serum but not amniotic fluid. Further evidence for induction of immunity was found in the hyperplastic response of lymph nodes, which included the development of germinal centers occupied CDw75+ B cells. Collectively, these data support the notion that the immunocompetent fetus is capable of initiating an antiviral response, which is compartmentalized within the infected fetus. Furthermore, fetal pathology may not be a direct result of virus replication in the fetus. url: https://www.ncbi.nlm.nih.gov/pubmed/20832434/ doi: 10.1016/j.virusres.2010.09.001 id: cord-030028-s6sxi8uj author: Rubio, Luis title: Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution date: 2020-07-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Plant viruses cause considerable economic losses and are a threat for sustainable agriculture. The frequent emergence of new viral diseases is mainly due to international trade, climate change, and the ability of viruses for rapid evolution. Disease control is based on two strategies: i) immunization (genetic resistance obtained by plant breeding, plant transformation, cross-protection, or others), and ii) prophylaxis to restrain virus dispersion (using quarantine, certification, removal of infected plants, control of natural vectors, or other procedures). Disease management relies strongly on a fast and accurate identification of the causal agent. For known viruses, diagnosis consists in assigning a virus infecting a plant sample to a group of viruses sharing common characteristics, which is usually referred to as species. However, the specificity of diagnosis can also reach higher taxonomic levels, as genus or family, or lower levels, as strain or variant. Diagnostic procedures must be optimized for accuracy by detecting the maximum number of members within the group (sensitivity as the true positive rate) and distinguishing them from outgroup viruses (specificity as the true negative rate). This requires information on the genetic relationships within-group and with members of other groups. The influence of the genetic diversity of virus populations in diagnosis and disease management is well documented, but information on how to integrate the genetic diversity in the detection methods is still scarce. Here we review the techniques used for plant virus diagnosis and disease control, including characteristics such as accuracy, detection level, multiplexing, quantification, portability, and designability. The effect of genetic diversity and evolution of plant viruses in the design and performance of some detection and disease control techniques are also discussed. High-throughput or next-generation sequencing provides broad-spectrum and accurate identification of viruses enabling multiplex detection, quantification, and the discovery of new viruses. Likely, this technique will be the future standard in diagnostics as its cost will be dropping and becoming more affordable. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7380168/ doi: 10.3389/fpls.2020.01092 id: cord-278833-wlhmcdcn author: Rutschke, Nils title: Hot start reverse transcriptase: an approach for improved real-time RT-PCR performance date: 2015-06-21 words: 2280.0 sentences: 134.0 pages: flesch: 59.0 cache: ./cache/cord-278833-wlhmcdcn.txt txt: ./txt/cord-278833-wlhmcdcn.txt summary: FINDINGS: The hot start effect was investigated in a one-step real-time RT-PCR assay for the detection of Middle East respiratory syndrome coronavirus (MERS-CoV). CONCLUSIONS: The study demonstrates the potential of aptamer-dependent hot start RT for the improvement of diagnostic real-time RT-PCR assays. In the present study, the aptamer was analyzed in a one-step real-time RT-PCR assay for the detection of Middle East respiratory syndrome coronavirus (MERS-CoV) to investigate the potential of a hot start RT for improved real-time RT-PCR performance. The one-step real-time RT-PCR was performed in a 25-μL reaction mix containing 10 μL of RNA template, 1x PCR reaction buffer (altona Diagnostics GmbH), 2.4 mM MgCl 2 (Sigma-Aldrich), 240 μg/μL BSA (Roche), 1 U of Platinum® Taq DNA Polymerase high fidelity (Invitrogen), 156 U of SuperScript® III Reverse Transcriptase (Invitrogen). The analytic sensitivity was determined by analyzing a half-logarithmic serial dilution Table 1 Hit rate of 25 μM aptamer and without aptamer in real-time RT-PCR MERS-CoV assay. abstract: BACKGROUND: Reverse transcriptase is an indispensable enzyme for real-time reverse transcriptase (RT)-PCR, a standard method in molecular diagnostics for detection and quantification of defined RNA molecules. The prevention of non-specific products due to elongation of misprimed oligonucleotides by the enzyme at temperatures beneath the specific annealing temperature is one of the biggest challenges in real-time RT-PCR. In the present study, an aptamer directed against the reverse transcriptase was analyzed for its potential to attain a temperature-dependent reverse transcriptase (“hot start” RT). FINDINGS: The hot start effect was investigated in a one-step real-time RT-PCR assay for the detection of Middle East respiratory syndrome coronavirus (MERS-CoV). Results with aptamer revealed a reduced RT activity at low temperatures while achieving full activity at the specific annealing temperature of 55 °C. Sensitivity (limit of detection (LoD) 95 %) of the MERS-CoV assay was increased by about two times in the presence of aptamer. CONCLUSIONS: The study demonstrates the potential of aptamer-dependent hot start RT for the improvement of diagnostic real-time RT-PCR assays. url: https://www.ncbi.nlm.nih.gov/pubmed/32226638/ doi: 10.1186/s40543-015-0063-4 id: cord-269407-6i66zf0e author: Rutvisuttinunt, Wiriya title: Retrospective use of next-generation sequencing reveals the presence of Enteroviruses in acute influenza-like illness respiratory samples collected in South/South-East Asia during 2010–2013 date: 2017-07-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Emerging and re-emerging respiratory pathogens represent an increasing threat to public health. Etiological determination during outbreaks generally relies on clinical information, occasionally accompanied by traditional laboratory molecular or serological testing. Often, this limited testing leads to inconclusive findings. The Armed Forces Research Institute of Medical Sciences (AFRIMS) collected 12,865 nasopharyngeal specimens from acute influenza-like illness (ILI) patients in five countries in South/South East Asia during 2010–2013. Three hundred and twenty-four samples which were found to be negative for influenza virus after screening with real-time RT-PCR and cell-based culture techniques demonstrated the potential for viral infection with evident cytopathic effect (CPE) in several cell lines. OBJECTIVE: To assess whether whole genome next-generation sequencing (WG-NGS) together with conventional molecular assays can be used to reveal the etiology of influenza negative, but CPE positive specimens. STUDY DESIGN: The supernatant of these CPE positive cell cultures were grouped in 32 pools containing 2–26 supernatants per pool. Three WG-NGS runs were performed on these supernatant pools. Sequence reads were used to identify positive pools containing viral pathogens. Individual samples in the positive pools were confirmed by qRT-PCR, RT-PCR, PCR and Sanger sequencing from the CPE culture and original clinical specimens. RESULTS: WG-NGS was an effective way to expand pathogen identification in surveillance studies. This enabled the identification of a viral agent in 71.3% (231/324) of unidentified surveillance samples, including common respiratory pathogens (100/324; 30.9%): enterovirus (16/100; 16.0%), coxsackievirus (31/100; 31.0%), echovirus (22/100; 22.0%), human rhinovirus (3/100; 3%), enterovirus genus (2/100; 2.0%), influenza A (9/100; 9.0%), influenza B, (5/100; 5.0%), human parainfluenza (4/100; 4.0%), human adenovirus (3/100; 3.0%), human coronavirus (1/100; 1.0%), human metapneumovirus (2/100; 2.0%), and mumps virus (2/100; 2.0%), in addition to the non-respiratory pathogen herpes simplex virus type 1 (HSV-1) (172/324; 53.1%) and HSV-1 co-infection with respiratory viruses (41/324; 12.7%). url: https://api.elsevier.com/content/article/pii/S1386653217302007 doi: 10.1016/j.jcv.2017.07.004 id: cord-355988-4eldkteb author: SAMPATH, RANGARAJAN title: Rapid Identification of Emerging Infectious Agents Using PCR and Electrospray Ionization Mass Spectrometry date: 2007-04-23 words: 3430.0 sentences: 168.0 pages: flesch: 41.0 cache: ./cache/cord-355988-4eldkteb.txt txt: ./txt/cord-355988-4eldkteb.txt summary: Here we describe a powerful new approach for infectious disease surveillance that is based on polymerase chain reaction (PCR) to amplify nucleic acid targets from large groupings of organisms, electrospray ionization mass spectrometry (ESI‐MS) for accurate mass measurements of the PCR products, and base composition signature analysis to identify organisms in a sample. Most of the new technologies being developed for detection of infectious agents incorporate a version of quantitative polymerase chain reaction (PCR), based upon the use of highly specific primers and probes and designed to selectively identify specific pathogenic organisms. The process uses electrospray ionization mass spectrometry (ESI-MS) and base composition analysis of PCR amplification products from highly conserved genomic regions to identify and determine the relative quantity of pathogenic bacteria, FIGURE 1. Importantly, the base composition data for some of the isolates represented new measurements from regions that have not been sequenced, showing the potential of this strategy to identify previously unknown or newly emerging viruses. abstract: abstract: Newly emergent infectious diseases are a global public health problem. The population dense regions of Southeast Asia are the epicenter of many emerging diseases, as evidenced by the outbreak of Nipah, SARS, avian influenza (H5N1), Dengue, and enterovirus 71 in this region in the past decade. Rapid identification, epidemiologic surveillance, and mitigation of transmission are major challenges in ensuring public health safety. Here we describe a powerful new approach for infectious disease surveillance that is based on polymerase chain reaction (PCR) to amplify nucleic acid targets from large groupings of organisms, electrospray ionization mass spectrometry (ESI‐MS) for accurate mass measurements of the PCR products, and base composition signature analysis to identify organisms in a sample. This approach is capable of automated analysis of more than 1,500 PCR reactions a day. It is applicable to the surveillance of bacterial, viral, fungal, or protozoal pathogens and will facilitate rapid characterization of known and emerging pathogens. url: https://www.ncbi.nlm.nih.gov/pubmed/17470915/ doi: 10.1196/annals.1408.008 id: cord-312206-0pkbbb99 author: SUNAGA, Fujiko title: Development of a one-run real-time PCR detection system for pathogens associated with porcine respiratory diseases date: 2019-12-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The etiology of Porcine respiratory disease complex is complicated by infections with multiple pathogens, and multiple infections increase the difficulty in identifying the causal pathogen. In this present study, we developed a detection system of microbes from porcine respiratory by using TaqMan real-time PCR (referred to as Dempo-PCR) to screen a broad range of pathogens associated with porcine respiratory diseases in a single run. We selected 17 porcine respiratory pathogens (Actinobacillus pleuropneumoniae, Boldetella bronchiseptica, Haemophilus parasuis, Pasteurella multocida, Pasteurella multocida toxin, Streptococcus suis, Mycoplasma hyopneumoniae, Mycoplasma hyorhinis, Mycoplasma hyosynovie, porcine circovirus 2, pseudorabies virus, porcine cytomegalovirus, swine influenza A virus, porcine reproductive and respiratory virus US strain, EU strain, porcine respiratory coronavirus and porcine hemagglutinating encephalomyelitis virus) as detection targets and designed novel specific primer-probe sets for seven of them. In sensitivity test by using standard curves from synthesized DNA, all primer-probe sets showed high sensitivity. However, porcine reproductive and respiratory virus is known to have a high frequency of genetic mutations, and the primer and probe sequences will need to be checked at a considerable frequency when performing Dempo-PCR from field samples. A total of 30 lung samples from swine showing respiratory symptoms on six farms were tested by the Dempo-PCR to validate the assay’s clinical performance. As the results, 12 pathogens (5 virus and 7 bacteria) were detected and porcine reproductive and respiratory virus US strain, Mycoplasma hyorhinis, Haemophilus parasuis, and porcine cytomegalovirus were detected at high frequency. These results suggest that Dempo-PCR assay can be applied as a screening system with wide detection targets. url: https://doi.org/10.1292/jvms.19-0063 doi: 10.1292/jvms.19-0063 id: cord-301720-majpfxqn author: Saadat, Yousef title: Molecular characterization of infectious bronchitis viruses isolated from broiler flocks in Bushehr province, Iran: 2014 - 2015 date: 2017-09-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The aim of this study was to provide information on the molecular characteristic and the phylogenic relationship of infectious bronchitis viruses (IBV) strains in Bushehr province in comparison to other strains reported in the Middle East. Samples were collected from broiler flocks in Bushehr province during 2014 - 2015. These flocks had respiratory problems such as gasping, sneezing and bronchial rales. A number of 135 tracheal swabs were taken from fifteen flocks (nine swabs per flock). Each three swabs collected from each flock were pooled in one tube (finally, we had three tubes for each flock). The samples were subjected to reverse transcription polymerase chain reaction (RT-PCR). The PCR products of positive samples were analyzed by sequencing of a (392 bp) segment of the spike gene and the related results were compared with the other IBV sequences in GenBank database. Samples from twelve farms (80.0%) were found to be positive. The viruses from seven farms (46.6%) were identified as field viruses closely related to variant 2. The viruses from three farms (20.0%) were characterized as Mass type and were related to vaccine strains. Two different IB viruses (variant 2 and Mass) were detected in samples from two farms (13.3%). The variant 2 genotype detected in Bushehr had high similarity to variant 2 reported from the Middle East. These variants displayed homologies ranging from 72.9% to 76.5%, and 78.8% to 80.0% with H120 and 4/91, respectively. It is necessary to design vaccination program of poultry farms using IBV strains circulating in the region. url: https://www.ncbi.nlm.nih.gov/pubmed/29085606/ doi: nan id: cord-336975-28mtmw2z author: Sadeghi, Christine D title: Twelve years'' detection of respiratory viruses by immunofluorescence in hospitalised children: impact of the introduction of a new respiratory picornavirus assay date: 2011-02-07 words: 3032.0 sentences: 161.0 pages: flesch: 41.0 cache: ./cache/cord-336975-28mtmw2z.txt txt: ./txt/cord-336975-28mtmw2z.txt summary: PCR-based studies have suggested the important role of respiratory picornaviruses (rhinovirus and enterovirus) as a leading cause of lower respiratory tract infections in children [5] , in particular wheezing illnesses such as bronchiolitis [6, 7] , wheezy bronchitis [8] and asthma exacerbations [9] , but also pneumonia [2] . In addition, PCR has allowed for the detection of new respiratory viruses, such as hMPV [10] , which has been implicated in upper and lower respiratory tract infections in children [11] [12] [13] . A significant proportion of asymptomatic children test positive by PCR to respiratory viruses [14] [15] [16] , and picornavirus RNA can be detected by PCR up to 5 weeks after an acute infection [17] . In order to determine the value of DFA in conducting epidemiological studies on respiratory viruses now that assays for respiratory picornaviruses and hMPV are available, we retrospectively analysed the results of 12 years of DFA screening of viral pathogens in hospitalized children with respiratory disease. abstract: BACKGROUND: Direct immunofluorescence assays (DFA) are a rapid and inexpensive method for the detection of respiratory viruses and may therefore be used for surveillance. Few epidemiological studies have been published based solely on DFA and none included respiratory picornaviruses and human metapneumovirus (hMPV). We wished to evaluate the use of DFA for epidemiological studies with a long-term observation of respiratory viruses that includes both respiratory picornaviruses and hMPV. METHODS: Since 1998 all children hospitalized with respiratory illness at the University Hospital Bern have been screened with DFA for common respiratory viruses including adenovirus, respiratory syncytial virus (RSV), influenza A and B, and parainfluenza virus 1-3. In 2006 assays for respiratory picornaviruses and hMPV were added. Here we describe the epidemiological pattern for these respiratory viruses detected by DFA in 10'629 nasopharyngeal aspirates collected from 8'285 patients during a 12-year period (1998-2010). RESULTS: Addition of assays for respiratory picornaviruses and hMPV raised the proportion of positive DFA results from 35% to 58% (p < 0.0001). Respiratory picornaviruses were the most common viruses detected among patients ≥1 year old. The seasonal patterns and age distribution for the studied viruses agreed well with those reported in the literature. In 2010, an hMPV epidemic of unexpected size was observed. CONCLUSIONS: DFA is a valid, rapid, flexible and inexpensive method. The addition of assays for respiratory picornaviruses and hMPV broadens its range of viral detection. DFA is, even in the "PCR era", a particularly adapted method for the long term surveillance of respiratory viruses in a pediatric population. url: https://www.ncbi.nlm.nih.gov/pubmed/21299840/ doi: 10.1186/1471-2334-11-41 id: cord-356370-jjl1hbeb author: Sahajpal, Nikhil Shri title: Role of clinical laboratories in response to the COVID-19 pandemic date: 2020-06-19 words: 1602.0 sentences: 77.0 pages: flesch: 41.0 cache: ./cache/cord-356370-jjl1hbeb.txt txt: ./txt/cord-356370-jjl1hbeb.txt summary: In response to the outbreak, several state authorities and commercial companies have developed diagnostic assays to test individuals for the SARS-CoV-2 infection. In the US, clinical laboratories are required to perform ''bridging studies'' on FDA approved SARS-CoV-2 diagnostic assays to implement testing under the EUA regulation. Although, the reverse transcription-polymerase chain reaction (RT-PCR) based assays for the detection of SARS-CoV-2 nucleic acid regions might be the most practical approach at present, qualitative assays are far from providing insights into the evolution of the virus and the varied immune response in different populations. In addition, the RT-PCR based assays provide a unique opportunity to implement pooling sample strategy for wide-scale population screening for SARS-CoV-2. Several studies, including from our laboratory (under review) have demonstrated that pooling sample strategy is a practical and feasible method for screening populations for SARS-CoV-2 [2] . Laboratories should therefore prime for serologic testing by validating assays using RT-PCR confirmed COVID-19 samples. abstract: nan url: https://doi.org/10.4155/fmc-2020-0129 doi: 10.4155/fmc-2020-0129 id: cord-331475-mmcu18c8 author: Sahu, Amit Ranjan title: Selection and validation of suitable reference genes for qPCR gene expression analysis in goats and sheep under Peste des petits ruminants virus (PPRV), lineage IV infection date: 2018-10-29 words: 4735.0 sentences: 257.0 pages: flesch: 49.0 cache: ./cache/cord-331475-mmcu18c8.txt txt: ./txt/cord-331475-mmcu18c8.txt summary: title: Selection and validation of suitable reference genes for qPCR gene expression analysis in goats and sheep under Peste des petits ruminants virus (PPRV), lineage IV infection In this study, we evaluated the expression stability of ten most commonly used reference genes (GAPDH, ACTB, HSP90, HMBS, 18S rRNA, B2M, POLR2A, HPRT1, ACAC, YWHAZ) in fourteen different Peste des petits ruminants virus (PPRV) infected tissues of goats and sheep. GAPDH (Glyceraldehyde-3-phosphate dehydrogenase), 18S rRNA (18S ribosomal RNA), B2M (β 2 microglobulin), HSP 90 (heat shock protein 90), ACAC-alpha (Acetyl coenzyme carboxylase alpha), HMBS (Hydroxymethylbilane synthase), YWHAZ (Tyrosine 3-monooxygenase activation protein zeta polypeptide), POLR2A (Polymerase 32 II (DNA directed) polypeptide A), ACTB (beta actin) and HPRT1 (Hypoxanthin Phosphoribosyl transferase 1) in fourteen different tissues obtained from healthy and PPRV infected goats and sheep to identify the best possible reference gene(s) for qRT-PCR normalization. abstract: Identification of suitable candidate reference genes is an important prerequisite for validating the gene expression data obtained from downstream analysis of RNA sequencing using quantitative real time PCR (qRT-PCR). Though existence of a universal reference gene is myth, commonly used reference genes can be assessed for expression stability to confer their suitability to be used as candidate reference genes in gene expression studies. In this study, we evaluated the expression stability of ten most commonly used reference genes (GAPDH, ACTB, HSP90, HMBS, 18S rRNA, B2M, POLR2A, HPRT1, ACAC, YWHAZ) in fourteen different Peste des petits ruminants virus (PPRV) infected tissues of goats and sheep. RefFinder and RankAggreg software were used to deduce comprehensive ranking of reference genes. Our results suggested HMBS and B2M in goats and HMBS and HPRT1 in sheep can be used as suitable endogenous controls in gene expression studies of PPRV infection irrespective of tissues and condition as a whole, thus eliminating the use of tissue specific/ condition specific endogenous controls. We report for the first time suitable reference genes for gene expression studies in PPRV infected tissues. The reference genes determined here can be useful for future studies on gene expression in sheep and goat infected with PPRV, thus saving extra efforts and time of repeating the reference gene determination and validation. url: https://doi.org/10.1038/s41598-018-34236-7 doi: 10.1038/s41598-018-34236-7 id: cord-016000-le22pknc author: Saikumar, G. title: Porcine Circovirus date: 2019-06-06 words: 9651.0 sentences: 527.0 pages: flesch: 45.0 cache: ./cache/cord-016000-le22pknc.txt txt: ./txt/cord-016000-le22pknc.txt summary: Porcine circovirus (PCV) infections associated with post-weaning multisystemic wasting syndrome (PMWS) are characterized by weight loss, respiratory distress, jaundice, etc. Later on in 1991, a novel PCV associated with a sporadic disease called as post-weaning multisystemic wasting syndrome (PMWS), characterized by weight loss, respiratory distress, jaundice, etc., was reported from Saskatchewan, Canada (Harding 1996; Clark 1997) . Genetic characterization of type 2 porcine circovirus (PCV-2) from pigs with postweaning multisystemic wasting syndrome in different geographic regions of North America and development of a differential PCR-restriction fragment length polymorphism assay to detect and differentiate between infections with PCV-1 and PCV-2 Mycoplasma hyopneumoniae bacterins and porcine circovirus type 2 (PCV2) infection: induction of postweaning multisystemic wasting syndrome (PMWS) in the gnotobiotic swine model of PCV2-associated disease Porcine circovirus type 2 (PCV2) distribution and replication in tissues and immune cells in early infected pigs abstract: Porcine circovirus (PCV) infections associated with post-weaning multisystemic wasting syndrome (PMWS) are characterized by weight loss, respiratory distress, jaundice, etc. Although PCV2 infection is ubiquitous, the prevalence of clinical disease is lower and the most common form is PCV2 subclinical infection. Recently, a novel porcine circovirus (PCV3) has been identified in pigs in the USA that is associated with porcine dermatitis nephropathy syndrome, acute myocarditis and multisystemic inflammation, etc. Genetic heterogeneity of PCV2 has been studied in Indian pig population. Different genotypes like PCV2a-2D, PCV2b-1C, PCV2d and recombinant strain between PCV2a-2C and PCV2b-1C are reported from different studies. PCV2 has been discovered in human faeces, human vaccines and beef. But its pathogenicity in humans is not clear. PCV detection is based on common golden standard techniques including nucleic acid and antigen detection in the tissues, in situ hybridization (ISH) and immunohistochemistry (IHC) using monoclonal or polyclonal antibody against PCV2, respectively. The commercial vaccines available are effective in reducing the severity of clinical diseases and improving production parameters. Recently, antiviral compounds have also shown promising results against PCV2. This chapter summarizes aetiology, epidemiology, transmission, immunopathobiology, diagnosis, prevention and control of porcine circovirus. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120144/ doi: 10.1007/978-981-13-9073-9_10 id: cord-277057-ww41t4k2 author: Sakthivel, Senthilkumar K. title: Comparison of fast-track diagnostics respiratory pathogens multiplex real-time RT-PCR assay with in-house singleplex assays for comprehensive detection of human respiratory viruses() date: 2012-07-11 words: 4952.0 sentences: 226.0 pages: flesch: 49.0 cache: ./cache/cord-277057-ww41t4k2.txt txt: ./txt/cord-277057-ww41t4k2.txt summary: title: Comparison of fast-track diagnostics respiratory pathogens multiplex real-time RT-PCR assay with in-house singleplex assays for comprehensive detection of human respiratory viruses() Individual FTDRP assays for adenovirus, respiratory syncytial virus and rhinovirus showed the lowest comparative sensitivities with in-house assays, with most discrepancies occurring with specimens containing low virus loads and failed to detect some rhinovirus strains, even when abundant. This study reports the results of a comparison of the FTDRP multiplex assay with a panel of validated in-house singleplex real-time RT-PCR assays developed at the Centers for Disease Control and Prevention (CDC). These included 26 laboratory reference virus strains and field isolates and 265 geographically (U.S., Central and South America and Africa) and compositionally diverse specimens [nasopharyngeal and oropharyngeal swabs (223), nasal washes and aspirates (21), sputum (1), lung autopsy tissue (1) and unidentified (19)] collected from children and adults with acute respiratory illnesses (ARIs) acquired between 2008 and 2011 and previously testing positive for respiratory viruses by the in-house singleplex assays. abstract: Fast-track Diagnostics respiratory pathogens (FTDRP) multiplex real-time RT-PCR assay was compared with in-house singleplex real-time RT-PCR assays for detection of 16 common respiratory viruses. The FTDRP assay correctly identified 26 diverse respiratory virus strains, 35 of 41 (85%) external quality assessment samples spiked with cultured virus and 232 of 263 (88%) archived respiratory specimens that tested positive for respiratory viruses by in-house assays. Of 308 prospectively tested respiratory specimens selected from children hospitalized with acute respiratory illness, 270 (87.7%) and 265 (86%) were positive by FTDRP and in-house assays for one or more viruses, respectively, with combined test results showing good concordance (K = 0.812, 95% CI = 0.786–0.838). Individual FTDRP assays for adenovirus, respiratory syncytial virus and rhinovirus showed the lowest comparative sensitivities with in-house assays, with most discrepancies occurring with specimens containing low virus loads and failed to detect some rhinovirus strains, even when abundant. The FTDRP enterovirus and human bocavirus assays appeared to be more sensitive than the in-house assays with some specimens. With the exceptions noted above, most FTDRP assays performed comparably with in-house assays for most viruses while offering enhanced throughput and easy integration by laboratories using conventional real-time PCR instrumentation. url: https://www.ncbi.nlm.nih.gov/pubmed/22796035/ doi: 10.1016/j.jviromet.2012.07.010 id: cord-291954-wormplcu author: Sakulkonkij, Parichart title: A family cluster of diagnosed coronavirus disease 2019 (COVID‐19) kidney transplant recipient in Thailand date: 2020-08-08 words: 4424.0 sentences: 304.0 pages: flesch: 48.0 cache: ./cache/cord-291954-wormplcu.txt txt: ./txt/cord-291954-wormplcu.txt summary: A novel betacoronavirus, the seventh member of coronaviruses, which is shown to infect humans and lately named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes an ongoing outbreak of respiratory illness that began in December 2019 in China called coronavirus disease 2019 . On admission, a nasopharyngeal and throat swabs for SARS-CoV-2 reverse transcription-polymerase chain reaction (RT-PCR) revealed a positive result, other laboratory findings included white blood cell count (WBC) 2480 cells/mm 3 , lymphocyte (L) 18%, neutrophil (N) 78%, and C-reactive protein (CRP) 62.7 mg/L. Although acute hypoxemic respiratory failure from COVID-19 in elderly and KT recipients in our cohort seemed to be prominent, early investigation in high-risk populations, prompt initiation of potential therapy, and intensive supportive care are important to prevent adverse consequences and mortality. Case report of COVID-19 in a kidney transplant recipient: Does immunosuppression alter the clinical presentation? abstract: INTRODUCTION: Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) causes an ongoing outbreak of respiratory illness called coronavirus disease 2019 (COVID‐19). The clinical course could be ranging from mild to severe illness especially the individuals with an immunocompromised condition such as solid organ transplant recipients. METHOD: We described a family cluster of COVID‐19 patients who were admitted during 3rd April 2020 to 30th April 2020. COVID‐19 was confirmed by a presence of SARS‐CoV‐2 ribonucleic acid in the respiratory specimens detected by a qualitative, real‐time reverse transcription‐polymerase chain reaction. The study focused on the clinical course and management of our cases. RESULTS: A family cluster of four laboratory‐confirmed COVID‐19 patients, one of those carried an underlying kidney transplant (KT) receiving immunosuppressants. Clinical presentation and severity of our case series are variable depending on each individual immune status. By far, a KT recipient seems to develop more severity despite antiviral therapy, cessation of immunosuppressant, and aggressive intensive care support. CONCLUSION: Our case series plausibly affirmed a person‐to‐person transmission and potentially severe disease in the transplant population. Clinicians who are encountering with transplant recipients should be aware of possible transmission among family members. url: https://www.ncbi.nlm.nih.gov/pubmed/32770646/ doi: 10.1002/iid3.337 id: cord-276739-84vf5bts author: Sakurai, Akira title: Rapid typing of influenza viruses using super high-speed quantitative real-time PCR date: 2011-08-22 words: 3311.0 sentences: 182.0 pages: flesch: 54.0 cache: ./cache/cord-276739-84vf5bts.txt txt: ./txt/cord-276739-84vf5bts.txt summary: Using SHRT-PCR, 86 strains of influenza viruses isolated by the Tokyo Metropolitan Institute of Public Health were tested; the results showed 100% sensitivity and specificity for each influenza A and B virus, and swine-origin influenza virus. This method offers high sensitivity and selectivity, but generally requires approximately 2 h per run; therefore, qRT-PCR is not appropriate for rapid virus detection or subtyping in outbreaks of fast-spreading and/or highly pathogenic viruses at public health centers, hospitals, airports, and other public transportation hubs. The commercial reaction mixture was from the qRT-PCR kit, RNA-Direct TM SYBR ® Green Real-time PCR Master Mix (Toyobo, Osaka, Japan; http://www.toyobo.co.jp/e/). The SHRT-PCR system detects the highly conserved sequence of the corresponding viral genome, and the newly designed primer sets targeted for typing MP segments do not exhibit any cross reactions among other influenza viruses (Table 5 ). abstract: The development of a rapid and sensitive system for detecting influenza viruses is a high priority for controlling future epidemics and pandemics. Quantitative real-time PCR is often used for detecting various kinds of viruses; however, it requires more than 2 h per run. Detection assays were performed with super high-speed RT-PCR (SHRT-PCR) developed according to a newly designed heating system. The new method uses a high-speed reaction (18 s/cycle; 40 cycles in less than 20 min) for typing influenza viruses. The detection limit of SHRT-PCR was 1 copy/reaction and 10(−1) plaque-forming unit/reaction for viruses in culture supernatants during 20 min. Using SHRT-PCR, 86 strains of influenza viruses isolated by the Tokyo Metropolitan Institute of Public Health were tested; the results showed 100% sensitivity and specificity for each influenza A and B virus, and swine-origin influenza virus. Twenty-seven swabs collected from the pharyngeal mucosa of outpatients were also tested, showing positive signs for influenza virus on an immunochromatographic assay; the results between SHRT-PCR and immunochromatography exhibited 100% agreement for both positive and negative results. The rapid reaction time and high sensitivity of SHRT-PCR makes this technique well suited for monitoring epidemics and pre-pandemic influenza outbreaks. url: https://api.elsevier.com/content/article/pii/S0166093411003491 doi: 10.1016/j.jviromet.2011.08.015 id: cord-327675-uo839gvc author: Salamatian, Iman title: In vitro Acquisition and Retention of Low-Pathogenic Avian Influenza H9N2 by Musca domestica (Diptera: Muscidae) date: 2019-10-11 words: 3648.0 sentences: 220.0 pages: flesch: 60.0 cache: ./cache/cord-327675-uo839gvc.txt txt: ./txt/cord-327675-uo839gvc.txt summary: (2011) showed that infective H5N1 virus could be detected at least 72 h PE from house flies while viral RNA was still found by real-time reverse-transcription polymerase chain reaction (RRT-PCR) 96 h PE. The aim of this study was to investigate the acquisition of H9N2 AIV by the house fly under laboratory conditions and to determine virus persistence in external surface and within house fly using quantitative reverse-transcription PCR. The potential of house fly, Musca Domestica (L.) in the mechanical transmission of influenza A subtype H1N1 virus under laboratory conditions Persistence of low-pathogenic avian influenza H5N7 and H7N1 subtypes in house flies (Diptera: Muscidae) Detection and isolation of highly pathogenic H5N1 avian influenza A viruses from blow flies collected in the vicinity of an infected poultry farm in Kyoto Avian influenza virus H5N1 remained exist in gastrointestinal tracts of house flies 24 hours post-infection abstract: Avian influenza virus (AIV) H9N2 emerged in the 1990s as an economically important disease in poultry and occasionally infects humans and other mammals. The aim of this study was to evaluate the acquisition and retention of H9N2 AIV on and within the house fly, Musca domestica (Linnaeus 1758), under laboratory conditions. In first experiment, 100 adult house flies were divided into control and treatment groups equally. Treatment group was fed with a meal containing H9N2 virus, while control group was supplied with an identical meal without virus. Fifteen minutes after exposure in each group, flies were washed twice to remove surface particles, disinfected and then homogenized for testing. The two external body surface washes and the homogenate samples were tested for H9N2 to distinguish exterior from interior viral load. Second experiment was performed likewise but five flies from each group were taken at 0, 6, 24, 48, 72, 96, and 120 h post-exposure. All samples were subjected to real-time reverse-transcription polymerase chain reaction (RRT-PCR) for detecting H9-Specific viral RNA. Results of the first experiment showed that viral RNA was detectable in both of external surface and homogenates samples. Second experiment revealed that persistence of H9N2 AIVs on external body surface and within the body of M. domestica were 24 and 96 h, respectively. Moreover, viral RNAs concentration declined during the time after exposure to AIV H9N2 either outside or within house flies. Overall, house fly was able to acquire and preserve H9N2 AIV experimentally, which may contribute the spread of virus among poultry farms. url: https://www.ncbi.nlm.nih.gov/pubmed/31603474/ doi: 10.1093/jme/tjz175 id: cord-292312-cwrqorn1 author: Sales, M. J. T. title: Fernando de Noronha: how an island controlled the community transmission of COVID-19 in Brazil date: 2020-10-27 words: 4329.0 sentences: 250.0 pages: flesch: 56.0 cache: ./cache/cord-292312-cwrqorn1.txt txt: ./txt/cord-292312-cwrqorn1.txt summary: Conclusion: Despite high levels of COVID-19 in Pernambuco, continued exposure through the provision of essential services from the mainland, and lack of direction from national authorities, FNA was able to implement a series of prevention measures unique in Brazil that contained the epidemic on the island. These included imposing a lockdown, promoting physical distancing and providing emergency assistance to the neediest families; enhancing testing for Sars-Cov-2, including monitoring of arriving travelers, restricting access to the island and the initiation of the cohort study described here to estimate the incidence and prevalence of Covid-19. First we reviewed data extracted from the following sources: 1) demographic and socioeconomic data from the Brazilian Institute of Geography and Statistics 8 ; 2) state and district decrees and 4 ordinances; 3) number of cases and deaths from COVID-19 reported by the Pernambuco State Health Department; 4) flights and passengers from the National Aviation Agency 5 ; and 5) information provided by local authorities and residents. abstract: Introduction: Fernando Noronha (FNA) is a small Brazilian archipelago in the Atlantic, part of the state of Pernambuco that COVID-19 has decimated. Anticipating the worst from the pandemic, Island and state authorities implemented a series of public health actions to contain the epidemic. This paper, reporting the results of the first wave of a cohort study, documents the measures and their effects through a cohort study. Methods: Measures were documented at the time of implementation. A random sample of 904 residents were selected from the health register, interviewed and tested for COVID-19 (RT-PCR and serology). The survey explored socioeconomic variables and adherence to prevention behaviors. Results: Flights were reduced from 38 to once a week, FNA was closed to tourism, schools were closed, and testing and tracing contacts was mandated along with social distancing and use of masks. A household lockdown was briefly imposed for residents. A prevalence of 5.1% was found, and a total of 158 cases of COVID-19 was estimated, although only 28 had been reported in routine surveillance. Half of the population reported food insecurity and applied for government COVID-19 benefits. Adherence to control measures was high, except for intrahousehold mask use with family and friends. Conclusion: Despite high levels of COVID-19 in Pernambuco, continued exposure through the provision of essential services from the mainland, and lack of direction from national authorities, FNA was able to implement a series of prevention measures unique in Brazil that contained the epidemic on the island. url: http://medrxiv.org/cgi/content/short/2020.10.22.20216010v1?rss=1 doi: 10.1101/2020.10.22.20216010 id: cord-268567-2xoubkxb author: Samannodi, Mohammed title: Compliance with international guidelines in adults with encephalitis date: 2020-04-14 words: 3278.0 sentences: 192.0 pages: flesch: 43.0 cache: ./cache/cord-268567-2xoubkxb.txt txt: ./txt/cord-268567-2xoubkxb.txt summary: In this study, we are evaluating the work up, management and outcome of 241 adults with encephalitis based on the majority of current guidelines recommendations in literature [11] [12] [13] [14] . As summarized in (Supplemental Digital Content Table 1 ), all guidelines of encephalitis management have major parts in evaluating and managing patients with encephalitis; exposure evaluation, appropriate utilization of diagnostic and neurodiagnostic studies, and proportion and timing of empirical antibiotic and antiviral therapy [11] [12] [13] [14] [15] . The Infectious Disease Society of America (IDSA), British, Australian, International consortium, and French guidelines recommend that clinicians evaluate for potential exposures and risk factors and to perform appropriate utilization of diagnostic studies in patients with suspected encephalitis. Also, most of the guidelines recommends to repeat CSF HSV PCR in 3-7 days in undiagnosed cases of encephalitis in which patients have clinical features or neuroimaging findings of HSV encephalitis [11] [12] [13] [14] . abstract: BACKGROUND: Encephalitis is associated with significant neurological disability and mortality. Many guidelines are published for encephalitis management but compliance with them is unknown. OBJECTIVES: To evaluate the appropriate management and compliance to the current guidelines in adults with encephalitis. STUDY DESIGN: A retrospective multicenter study at 17 hospitals in the Greater Houston area from August 1, 2008 through September 30, 2017. All cases met the definition for possible or probable encephalitis as per the international encephalitis consortium guidelines. RESULTS: A total of 241 adults (age >17 years) with encephalitis were enrolled. The most common etiologies were unknown (41.9 %), viral (27.8 %) and autoimmune (21.2 %). An adverse clinical outcome was seen in 49 % with 12.4 % in hospital mortality. A high compliance with guidelines (>90 %) was only seen in obtaining a brain computerized tomography (CT) scan, blood cultures and cerebrospinal fluid (CSF) gram stain and culture. A CSF herpes virus simplex (HSV) polymerase chain reaction (PCR) was done in 84 % and only repeated in 14.2 % of patients with an initial negative result. Furthermore, only two-thirds of patients were started empirically on intravenous acyclovir and antibiotics. Evaluation for other etiologies were not uniformly performed: arboviral serologies (57.3 %), CSF anti-N-Methyl-d-Aspartate Receptor (NMDA) receptor antibody (35.7 %), and CSF varicella zoster virus (VZV) PCR (32 %). The highest yield for the tests were arboviral serologies (42 %), anti-NMDA antibodies (41.2 %) and VZV PCR (16.4 %). CONCLUSION: The management of encephalitis as per current guidelines is suboptimal leading to underutilization of currently available diagnostic tests and empirical therapy. url: https://www.ncbi.nlm.nih.gov/pubmed/32315818/ doi: 10.1016/j.jcv.2020.104369 id: cord-017331-ru7mvfc0 author: Samanta, Indranil title: Infectious Diseases date: 2017-02-25 words: 37735.0 sentences: 2273.0 pages: flesch: 45.0 cache: ./cache/cord-017331-ru7mvfc0.txt txt: ./txt/cord-017331-ru7mvfc0.txt summary: The chapter includes history, etiology, susceptible hosts, transmission, pathogenesis, clinical symptoms, lesion, diagnosis, zoonosis, Treatment and control strategy of Tuberculosis, Salmonellosis, Chlamydiosis, Campylobacteriosis, Lyme disease, other bacterial infection, Newcastle disease, Avian Influenza infection, West Nile Virus infection, Usutu virus infection, Avian Borna Virus infection, Beak and feather disease, other viral infection, Toxoplasmosis, Giardiasis, Cryptosporidiosis, other parasitic infection, Cryptococcosis, Aspergillosis, Other fungal infections. Clinical samples include faeces or cloacal swabs, blood/serum of live birds and affected tissues, such as liver, spleen, heart, intestine/caeca, lung, esophagus/crop, brain and kidney in 10% buffered formalin. Non-specific clinical symptoms such as neurological signs (head between legs), depression, ruffled feathers, and standing at the bottom of the cage are observed in pet birds with AIV infection (Fig. 2.13) . The virus is detected in brain, heart, liver, kidney, lungs, and intestinal tissues of laboratory mice and naturally infected birds. abstract: The chapter describes bacerial, viral, parasitic and fungal infections commonly detected in pet birds. The chapter includes history, etiology, susceptible hosts, transmission, pathogenesis, clinical symptoms, lesion, diagnosis, zoonosis, Treatment and control strategy of Tuberculosis, Salmonellosis, Chlamydiosis, Campylobacteriosis, Lyme disease, other bacterial infection, Newcastle disease, Avian Influenza infection, West Nile Virus infection, Usutu virus infection, Avian Borna Virus infection, Beak and feather disease, other viral infection, Toxoplasmosis, Giardiasis, Cryptosporidiosis, other parasitic infection, Cryptococcosis, Aspergillosis, Other fungal infections. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121861/ doi: 10.1007/978-981-10-3674-3_2 id: cord-296819-gztmidn2 author: Sambri, Vittorio title: Diagnosis of West Nile Virus Human Infections: Overview and Proposal of Diagnostic Protocols Considering the Results of External Quality Assessment Studies date: 2013-09-25 words: 6732.0 sentences: 304.0 pages: flesch: 42.0 cache: ./cache/cord-296819-gztmidn2.txt txt: ./txt/cord-296819-gztmidn2.txt summary: title: Diagnosis of West Nile Virus Human Infections: Overview and Proposal of Diagnostic Protocols Considering the Results of External Quality Assessment Studies This paper reviews the presently available methods to achieve the laboratory diagnosis of West Nile virus infections in humans, discussing the most prominent advantages and disadvantages of each in light of the results obtained during four different External Quality Assessment studies carried out by the European Network for ''Imported'' Viral Diseases (ENIVD). For the routine detection of WNV RNA using molecular techniques there are two distinct diagnostic settings: the first involves blood and organ donation screening from subjects living in an area where WNV circulation is known to be occurring, and the second involves the identification of viral genomes in serum, plasma and CSF samples from patients presenting with a clinical picture typical of WNV infection [21] . abstract: West Nile virus, genus Flavivirus, is transmitted between birds and occasionally other animals by ornithophilic mosquitoes. This virus also infects humans causing asymptomatic infections in about 85% of cases and <1% of clinical cases progress to severe neuroinvasive disease. The virus also presents a threat since most infections remain unapparent. However, the virus contained in blood and organs from asymptomatically infected donors can be transmitted to recipients of these infectious tissues. This paper reviews the presently available methods to achieve the laboratory diagnosis of West Nile virus infections in humans, discussing the most prominent advantages and disadvantages of each in light of the results obtained during four different External Quality Assessment studies carried out by the European Network for ‘Imported’ Viral Diseases (ENIVD). url: https://www.ncbi.nlm.nih.gov/pubmed/24072061/ doi: 10.3390/v5102329 id: cord-350398-w75flrwv author: Sampath, Rangarajan title: Comprehensive Biothreat Cluster Identification by PCR/Electrospray-Ionization Mass Spectrometry date: 2012-06-29 words: 11138.0 sentences: 581.0 pages: flesch: 50.0 cache: ./cache/cord-350398-w75flrwv.txt txt: ./txt/cord-350398-w75flrwv.txt summary: Coupling biothreat cluster-specific PCR to electrospray ionization mass spectrometry simultaneously provides the breadth of coverage, discrimination of near neighbors, and an extremely low false positive rate due to the requirement that an amplicon with a precise base composition of a biothreat agent be detected by mass spectrometry. In addition to detecting the threat organisms, the biothreat assay described here also detects virulence factors associated with three of the agents: Bacillus anthracis (pXO1 and pXO2), Yersinia pestis (pla and caf), and Vibrio cholera (ctx1). PCR primers were designed to conserved regions within the selected target genes such that the targeted threat agent was clearly identified and differentiated from its near-neighbor species ( Table 1) . In the biothreat assay, the Francisella biocluster is identified by two genus-specific primer pairs targeting the asd (BCT2328) and galE (BCT2332) genes ( Table 1) . abstract: Technology for comprehensive identification of biothreats in environmental and clinical specimens is needed to protect citizens in the case of a biological attack. This is a challenge because there are dozens of bacterial and viral species that might be used in a biological attack and many have closely related near-neighbor organisms that are harmless. The biothreat agent, along with its near neighbors, can be thought of as a biothreat cluster or a biocluster for short. The ability to comprehensively detect the important biothreat clusters with resolution sufficient to distinguish the near neighbors with an extremely low false positive rate is required. A technological solution to this problem can be achieved by coupling biothreat group-specific PCR with electrospray ionization mass spectrometry (PCR/ESI-MS). The biothreat assay described here detects ten bacterial and four viral biothreat clusters on the NIAID priority pathogen and HHS/USDA select agent lists. Detection of each of the biothreat clusters was validated by analysis of a broad collection of biothreat organisms and near neighbors prepared by spiking biothreat nucleic acids into nucleic acids extracted from filtered environmental air. Analytical experiments were carried out to determine breadth of coverage, limits of detection, linearity, sensitivity, and specificity. Further, the assay breadth was demonstrated by testing a diverse collection of organisms from each biothreat cluster. The biothreat assay as configured was able to detect all the target organism clusters and did not misidentify any of the near-neighbor organisms as threats. Coupling biothreat cluster-specific PCR to electrospray ionization mass spectrometry simultaneously provides the breadth of coverage, discrimination of near neighbors, and an extremely low false positive rate due to the requirement that an amplicon with a precise base composition of a biothreat agent be detected by mass spectrometry. url: https://www.ncbi.nlm.nih.gov/pubmed/22768032/ doi: 10.1371/journal.pone.0036528 id: cord-012430-3uvhoca9 author: Sanchis, Joaquin title: Improved PCR method for the creation of saturation mutagenesis libraries in directed evolution: application to difficult-to-amplify templates date: 2008-11-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Saturation mutagenesis constitutes a powerful method in the directed evolution of enzymes. Traditional protocols of whole plasmid amplification such as Stratagene’s QuikChange™ sometimes fail when the templates are difficult to amplify. In order to overcome such restrictions, we have devised a simple two-primer, two-stage polymerase chain reaction (PCR) method which constitutes an improvement over existing protocols. In the first stage of the PCR, both the mutagenic primer and the antiprimer that are not complementary anneal to the template. In the second stage, the amplified sequence is used as a megaprimer. Sites composed of one or more residues can be randomized in a single PCR reaction, irrespective of their location in the gene sequence.The method has been applied to several enzymes successfully, including P450-BM3 from Bacillus megaterium, the lipases from Pseudomonas aeruginosa and Candida antarctica and the epoxide hydrolase from Aspergillus niger. Here, we show that megaprimer size as well as the direction and design of the antiprimer are determining factors in the amplification of the plasmid. Comparison of the results with the performances of previous protocols reveals the efficiency of the improved method. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7419347/ doi: 10.1007/s00253-008-1678-9 id: cord-313506-6bb4q7nv author: Sano, Akiko title: Physiological Level Production of Antigen-Specific Human Immunoglobulin in Cloned Transchromosomic Cattle date: 2013-10-24 words: 6695.0 sentences: 313.0 pages: flesch: 54.0 cache: ./cache/cord-313506-6bb4q7nv.txt txt: ./txt/cord-313506-6bb4q7nv.txt summary: We previously showed that transchromosomic (Tc) cattle carrying a human artificial chromosome (HAC) comprising the entire unrearranged human immunoglobulin heavy-chain (hIGH) and kappa-chain (hIGK) germline loci (named as κHAC) are capable of producing functional hpAbs when both of the bovine immunoglobulin mu heavy-chains, bIGHM and bIGHML1, are homozygously inactivated (double knockouts or DKO). Therefore, in an effort to improve B cell development and hIgG production in Tc cattle, we sought to enhance pre-BCR function by engineering a new HAC into which, in addition to the hIGH, hIGK and hIGL chromosome loci that carry the entire human immunoglobulin gene repertoire, the human VpreB (hVPREB1) and λ5 (hIGLL1) genomic loci from human chromosome 22 (hChr22) was incorporated, and part of CH and TM domains, CH2-TM, of hIGHM gene, was replaced by the corresponding bovine gene sequence (bovinization of the CH2-TM domains of hIGHM). doi: 10.1371/journal.pone.0078119.g002 DT40 colonies were screened with genomic PCR (data not shown) for the correctly modified hChr2, and clone K53 was identified and selected for the final HAC construction ( Figure 5 ). abstract: Therapeutic human polyclonal antibodies (hpAbs) derived from pooled plasma from human donors are Food and Drug Administration approved biologics used in the treatment of a variety of human diseases. Powered by the natural diversity of immune response, hpAbs are effective in treating diseases caused by complex or quickly-evolving antigens such as viruses. We previously showed that transchromosomic (Tc) cattle carrying a human artificial chromosome (HAC) comprising the entire unrearranged human immunoglobulin heavy-chain (hIGH) and kappa-chain (hIGK) germline loci (named as κHAC) are capable of producing functional hpAbs when both of the bovine immunoglobulin mu heavy-chains, bIGHM and bIGHML1, are homozygously inactivated (double knockouts or DKO). However, B lymphocyte development in these Tc cattle is compromised, and the overall production of hpAbs is low. Here, we report the construction of an improved HAC, designated as cKSL-HACΔ, by incorporating all of the human immunoglobulin germline loci into the HAC. Furthermore, for avoiding the possible human-bovine interspecies incompatibility between the human immunoglobulin mu chain protein (hIgM) and bovine transmembrane α and β immunoglobulins (bIgα and bIgβ) in the pre-B cell receptor (pre-BCR) complex, we partially replaced (bovinized) the hIgM constant domain with the counterpart of bovine IgM (bIgM) that is involved in the interaction between bIgM and bIgα/Igβ; human IgM bovinization would also improve the functionality of hIgM in supporting B cell activation and proliferation. We also report the successful production of DKO Tc cattle carrying the cKSL-HACΔ (cKSL-HACΔ/DKO), the dramatic improvement of B cell development in these cattle and the high level production of hpAbs (as measured for the human IgG isotype) in the plasma. We further demonstrate that, upon immunization by tumor immunogens, high titer tumor immunogen-specific human IgG (hIgG) can be produced from such Tc cattle. url: https://doi.org/10.1371/journal.pone.0078119 doi: 10.1371/journal.pone.0078119 id: cord-299943-wzkh04dv author: Santhanam, Manikandan title: DNA/RNA Electrochemical Biosensing Devices a Future Replacement of PCR Methods for a Fast Epidemic Containment date: 2020-08-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Pandemics require a fast and immediate response to contain potential infectious carriers. In the recent 2020 Covid-19 worldwide pandemic, authorities all around the world have failed to identify potential carriers and contain it on time. Hence, a rapid and very sensitive testing method is required. Current diagnostic tools, reverse transcription PCR (RT-PCR) and real-time PCR (qPCR), have its pitfalls for quick pandemic containment such as the requirement for specialized professionals and instrumentation. Versatile electrochemical DNA/RNA sensors are a promising technological alternative for PCR based diagnosis. In an electrochemical DNA sensor, a nucleic acid hybridization event is converted into a quantifiable electrochemical signal. A critical challenge of electrochemical DNA sensors is sensitive detection of a low copy number of DNA/RNA in samples such as is the case for early onset of a disease. Signal amplification approaches are an important tool to overcome this sensitivity issue. In this review, the authors discuss the most recent signal amplification strategies employed in the electrochemical DNA/RNA diagnosis of pathogens. url: https://www.ncbi.nlm.nih.gov/pubmed/32824787/ doi: 10.3390/s20164648 id: cord-327682-i3uim0zi author: Santti, Juhana title: Molecular detection and typing of human picornaviruses date: 1999-08-25 words: 2438.0 sentences: 131.0 pages: flesch: 43.0 cache: ./cache/cord-327682-i3uim0zi.txt txt: ./txt/cord-327682-i3uim0zi.txt summary: It has been shown in a number of studies that virtually all the enterovirus serotypes and most of the HRV isolates can be detected using these primer sequences (Hyypiä et , 1989; Horsnell et al., 1995; Pulli et al., 1995; Arola et al., 1996; Huttunen et al., 1996; Pitkäranta et al., 1997; Hyypiä et al., 1998; Oberste et al., 1998) The authors became convinced of the usefulness of this technique during a recent outbreak of aseptic meningitis in Finland. Partial sequence analysis of virtually all enterovirus serotypes has shown that they belong to these four clusters (Pulli et al., 1995; Huttunen et al., 1996) and that the VP4/VP2 region sequence can be used for molecular typing of clinical isolates (Arola et al., 1996) . In hepatitis A virus infections, the molecular epidemiology has been investigated by many reseach groups and an extensive analysis of partial sequences from different geographic locations has been used to establish a useful database for further studies (Robertson et al., 1992) . abstract: Picornaviruses include several important clinical pathogens which cause diseases varying from common cold to poliomyelitis and hepatitis. Introduction of RT-PCR methods for the detection of these viruses has significantly facilitated the diagnosis of picornavirus infections and elucidated their etiological role in clinical illnesses. Partial sequence analysis of the genomes has been used for typing of the viruses and in studies of molecular epidemiology of picornaviruses. These molecular approaches are likely to become the most predominant techniques for the diagnosis and epidemiological analysis, particularly in the enterovirus infections. url: https://www.sciencedirect.com/science/article/pii/S0168170299000362 doi: 10.1016/s0168-1702(99)00036-2 id: cord-296392-2u9mz6d3 author: Sarıgül, Figen title: Investigation of compatibility of severe acute respiratory syndrome coronavirus 2 reverse transcriptase-PCR kits containing different gene targets during coronavirus disease 2019 pandemic date: 2020-08-26 words: 3891.0 sentences: 209.0 pages: flesch: 51.0 cache: ./cache/cord-296392-2u9mz6d3.txt txt: ./txt/cord-296392-2u9mz6d3.txt summary: title: Investigation of compatibility of severe acute respiratory syndrome coronavirus 2 reverse transcriptase-PCR kits containing different gene targets during coronavirus disease 2019 pandemic This value being higher than 0.73 coefficient obtained through comparison of RdRps of the two kits only, showed that inclusion of a secondary biomarker by Diagnovital improved the correlation of different kits. In this study, we investigated the compatibility between the two different SARS-CoV-2 PCR kits produced in Turkey during the COVID-19 pandemic. Nevertheless, the strong correlation of the two kit results suggested that two different RNA targeting gene assays were appropriate as suggested by WHO in the diagnosis of COVID-19 disease [20] . showed that similar results were found; the PCR kit with two different genes of the SARS-CoV-2 had a higher yield than the other two kits performing one gene analysis [21] . abstract: AIM: In the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), reverse transcriptase-PCR (RT-PCR) technique is often used. We evaluated the compatibility of SARS-CoV-2 RT-PCR kits containing different gene targets during the pandemic. MATERIALS & METHODS: Samples were tested by Bio-Speddy(®) (RdRp gene) and Diagnovital(®) (RdRp + E genes). The correlation between two assays were determined by Deming regression analysis and chi-square analyses. RESULTS: Diagnovital PCR kit showed amplification in a narrow Ct range and conveniently sharper exponential amplification curves than Bio-Speedy PCR kit. While the correlation between the findings of the two kits was apparent even with single gene target, this correlation increased when a secondary biomarker was added to the correlation calculations. CONCLUSION: We have observed high correlation between different PCR kits, however, using different PCR kits during the pandemic may provide a more accurate diagnosis of SARS-CoV-2, since despite correlation there are a number of patients showing contradicting diagnosis. url: https://www.ncbi.nlm.nih.gov/pubmed/33005213/ doi: 10.2217/fvl-2020-0169 id: cord-279229-2226jnfl author: Savan, R title: Loop‐mediated isothermal amplification: an emerging technology for detection of fish and shellfish pathogens date: 2005-11-22 words: 4188.0 sentences: 230.0 pages: flesch: 45.0 cache: ./cache/cord-279229-2226jnfl.txt txt: ./txt/cord-279229-2226jnfl.txt summary: In this paper, we review a novel method of DNA amplification known as loop-mediated isothermal amplification (LAMP) of a target nucleic acid. Screening for KHV has become very important as trade of fancy carp is an easy route for geographical spread of the virus and a rapid and efficient system like LAMP is very Figure 2 Loop-mediated isothermal amplification reaction amplifying the haemolysin gene from Edwardsiella tarda isolates. Rapid detection of a fish iridovirus using loop-mediated isothermal amplification (LAMP) Rapid diagnosis of Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease (PKD) in salmonid fish by a novel DNA amplification method, loop-mediated isothermal amplification (LAMP) Rapid diagnosis of herpes simplex virus infection by a loop-mediated isothermal amplification method A loop mediated isothermal amplification (LAMP) method for detection of infectious hematopoietic necrosis virus (IHNV) in rainbow trout (Oncorhynchus mykiss) Rapid diagnosis of human herpesvirus 6 infection by a novel DNA amplification method, loop-mediated isothermal amplification abstract: Fish and shellfish diseases are a constant threat to the sustainability and economic viability of aquaculture. Early diagnosis plays a vital role in management of fish and shellfish diseases. Traditionally, various biochemical and serological tests have been used for fish disease diagnosis. However, the time and expertise required for such diagnoses makes it difficult for aquaculturists to easily adopt them under production conditions. Polymerase chain reaction and probe‐based nucleic acid detection have become increasingly popular in fish and shellfish diagnostics. Recently, a novel technique called loop‐mediated isothermal amplification (LAMP) has been developed, which is highly sensitive and rapid. LAMP has been used for the detection of bacterial, viral, fungal and parasitic diseases in both animal and plants. In aquaculture, LAMP‐based detection of pathogens like Edwardsiella tarda, E. ictaluri, Nocardia seriolae, Tetracapsuloides bryosalmonae, white spot syndrome virus and infectious haematopoietic necrosis virus have been reported. In this review, the application of LAMP for the detection of aquaculture‐associated pathogens is discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/16302951/ doi: 10.1111/j.1365-2761.2005.00670.x id: cord-326497-458mnekj author: Schaible, Jan title: Sharp margin and geographic shape: systematic evaluation of two novel CT features in COVID-19 pneumonia date: 2020-07-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVE: CT is important in the care of patients with COVID-19 pneumonia. However, specificity might be poor in the absence of a clinical and epidemiological context. The goal of this work was to systematically evaluate two novel CT features (sharp margin and geographic shape) of COVID-19 pneumonia. METHODS: All patients with reverse transcription polymerase chain reaction proven COVID-19 pneumonia and chest CT between March first and April 15, 2020 were retrospectively identified from two tertiary care hospitals in Germany. The CTs were evaluated regarding the presence of typical CT signs (e.g. ground glass opacitiy, consolidation, crazy paving). Moreover, the shape of the opacifications (round, geographic, curvilinear) and their margin (unsharp, sharp) was determined. RESULTS: The study population comprised 108 patients (64 male) with a mean age of 59.6 years. Ground glass opacities (96%) and consolidation (75%) were the most prevalent CT signs. Crazy paving was seen in 17%, bronchial dilatation in 21%, air bronchogram in 29%, vessel enlargement in 47%, cavitation in 0%, lymphadenopathy in 32%, pleural effusion in 16%. Round configuration of densities was present in 41% of CTs, geographic shape in 27% and curvilinear opacities in 44%. 79% of opacifications were at least partially sharply marginated. In almost all cases, the lung was affected bilaterally (94%). CONCLUSION: The CT pattern of COVID-19 pneumonia in a cohort from Germany was in accordance with prior studies. However, we identified two novel CT signs of COVID-19 pneumonia which have so far not been systematically evaluated. A sharp border and geographic shape of opacifications were frequently observed. ADVANCES IN KNOWLEDGE: The newly described CT features “sharp margin” and “geographic shape” of opacifications in patients with COVID-19 pneumonia might help to increase specificity of CT. url: https://doi.org/10.1259/bjro.20200026 doi: 10.1259/bjro.20200026 id: cord-312240-0k8y86pf author: Schlaberg, Robert title: Viral Pathogen Detection by Metagenomics and Pan-Viral Group Polymerase Chain Reaction in Children With Pneumonia Lacking Identifiable Etiology date: 2017-05-01 words: 4837.0 sentences: 239.0 pages: flesch: 46.0 cache: ./cache/cord-312240-0k8y86pf.txt txt: ./txt/cord-312240-0k8y86pf.txt summary: Nasopharyngeal/oropharyngeal (NP/OP) swabs from 70 children <5 years with CAP of unknown etiology and 90 asymptomatic controls were tested by next-generation sequencing (RNA-seq) and pan viral group (PVG) PCR for 19 viral families. We first assessed the ability of RNA-seq and PVG PCR to detect known respiratory pathogens using specimens from children with CAP (n = 63) and asymptomatic control (n = 52) subjects in whom viral or atypical bacterial pathogens had been detected using the EPIC study protocol. We validated RNA-seq and PVG PCR methods to detect known respiratory pathogens by testing specimens using both methods from children with CAP (n = 63) and asymptomatic control subjects (n = 52) in whom viral or atypical bacterial pathogens had been detected using the EPIC study protocol. Using RNA-seq and PVG PCR, we identified additional viruses from upper respiratory tract specimens in >30% children hospitalized with clinical and radiographic pneumonia but in whom no pathogen was identified despite extensive testing by culture, molecular, and serologic methods. abstract: BACKGROUND. Community-acquired pneumonia (CAP) is a leading cause of pediatric hospitalization. Pathogen identification fails in approximately 20% of children but is critical for optimal treatment and prevention of hospital-acquired infections. We used two broad-spectrum detection strategies to identify pathogens in test-negative children with CAP and asymptomatic controls. METHODS. Nasopharyngeal/oropharyngeal (NP/OP) swabs from 70 children <5 years with CAP of unknown etiology and 90 asymptomatic controls were tested by next-generation sequencing (RNA-seq) and pan viral group (PVG) PCR for 19 viral families. Association of viruses with CAP was assessed by adjusted odds ratios (aOR) and 95% confidence intervals controlling for season and age group. RESULTS. RNA-seq/PVG PCR detected previously missed, putative pathogens in 34% of patients. Putative viral pathogens included human parainfluenza virus 4 (aOR 9.3, P = .12), human bocavirus (aOR 9.1, P < .01), Coxsackieviruses (aOR 5.1, P = .09), rhinovirus A (aOR 3.5, P = .34), and rhinovirus C (aOR 2.9, P = .57). RNA-seq was more sensitive for RNA viruses whereas PVG PCR detected more DNA viruses. CONCLUSIONS. RNA-seq and PVG PCR identified additional viruses, some known to be pathogenic, in NP/OP specimens from one-third of children hospitalized with CAP without a previously identified etiology. Both broad-range methods could be useful tools in future epidemiologic and diagnostic studies. url: https://academic.oup.com/jid/article-pdf/215/9/1407/24262313/jix148.pdf doi: 10.1093/infdis/jix148 id: cord-274438-tgslabi2 author: Schnee, Sarah Valerie title: Performance of the Alere i RSV assay for point-of-care detection of respiratory syncytial virus in children date: 2017-12-13 words: 3123.0 sentences: 210.0 pages: flesch: 56.0 cache: ./cache/cord-274438-tgslabi2.txt txt: ./txt/cord-274438-tgslabi2.txt summary: title: Performance of the Alere i RSV assay for point-of-care detection of respiratory syncytial virus in children False negative Alere i RSV test results mostly occurred in samples with low viral load (mean CT value 31.1; CI(95) 29.6 – 32.6). Mann-Whitney-U-test was applied to compare C T values in samples with true positive versus false negative Alere i RSV result. In comparison to the RT-PCR reference standard, the Alere i RSV test result was true positive in 213 and true negative in 278 samples, respectively. The Alere i RSV performed well in the point-of-care setting, and sensitive test results were obtained across all pediatric age groups within 13 min. Evaluation of Alere i RSV for rapid detection of respiratory syncytial virus in children hospitalized with acute respiratory tract infection Host and viral factors affecting clinical performance of a rapid diagnostic test for respiratory Syncytial virus in hospitalized children abstract: BACKGROUND: Respiratory syncytial virus (RSV) is the most important cause of severe acute respiratory tract infection in young children. Alere i RSV is a novel molecular rapid test which identifies respiratory syncytial virus in less than 13 min. METHODS: We evaluated the clinical performance of the Alere i RSV assay in a pediatric point-of-care setting during winter season 2016 / 2017. Test results from 518 nasopharyngeal swab samples were compared to a real-time reverse transcription PCR reference standard. RESULTS: The overall sensitivity and specificity of the Alere i RSV test assay was 93% (CI(95) 89% – 96%) and 96% (CI(95) 93% – 98%), respectively. Alere i RSV performed well in children of all age groups. An optimal sensitivity of 98% (CI(95) 94% - 100%) and specificity of 96% (CI(95) 90% - 99%) was obtained in children < 6 months. In children ≥ 2 years, sensitivity and specificity remained at 87% (CI(95) 73% – 96%) and 98% (CI(95) 92% – 100%), respectively. False negative Alere i RSV test results mostly occurred in samples with low viral load (mean CT value 31.1; CI(95) 29.6 – 32.6). The Alere i RSV assay is easy to use and can be operated after minimal initial training. Test results are available within 13 min, with most RSV positive samples being identified after approximately 5 min. CONCLUSION: The Alere i RSV assay has the potential to facilitate the detection of RSV in pediatric point-of-care settings. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-017-2855-1) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12879-017-2855-1 doi: 10.1186/s12879-017-2855-1 id: cord-255545-nycdhdsd author: Schoenike, Barry title: Quantitative sense-specific determination of murine coronavirus RNA by reverse transcription polymerase chain reaction date: 1999-03-10 words: 6170.0 sentences: 265.0 pages: flesch: 48.0 cache: ./cache/cord-255545-nycdhdsd.txt txt: ./txt/cord-255545-nycdhdsd.txt summary: In theory, sense-specific measurement of viral RNAs may be achieved by reverse transcription polymerase chain reaction (RT-PCR) assays which utilize primers of defined polarity during the RT step. Key RT-PCR parameters which were optimized include the design of tagged primers, DNase treatment of in vitro transcribed RNA standards, specification of temperature differences between RT and PCR annealing steps, and use of competitive RNA templates for quantitative assays. In fact, several studies have demonstrated that RT-PCR assays based on specific RNA template recognition by RT primers of defined polarity will not reliably distinguish between viral RNAs of positive or negative sense. Despite the findings above, many published research reports are based on conventional RT-PCR assays, relying on the polarity of primers added to the RT step in putative sense-specific measurements of viral RNAs; rarely are control reactions performed to rigorously show that this method is in fact sense-specific. abstract: In many applications, it is useful to know the sense and amount of viral RNAs present in a sample. In theory, sense-specific measurement of viral RNAs may be achieved by reverse transcription polymerase chain reaction (RT-PCR) assays which utilize primers of defined polarity during the RT step. However, in practice, it has been shown that such assays are prone to artifacts, such as non-specific priming, which drastically diminish their reliability. Using murine coronavirus MHV-4 as a model, we describe and validate several modifications of the RT-PCR procedure which eliminate these artifacts. Key RT-PCR parameters which were optimized include the design of tagged primers, DNase treatment of in vitro transcribed RNA standards, specification of temperature differences between RT and PCR annealing steps, and use of competitive RNA templates for quantitative assays. The assays described may be used to determine the sense and abundance of any viral or host RNA of interest in complex biological specimens. url: https://www.ncbi.nlm.nih.gov/pubmed/10204695/ doi: 10.1016/s0166-0934(98)00167-0 id: cord-018721-othar2uv author: Schwab, Stefan title: Infektionen date: 2012-03-17 words: 13415.0 sentences: 1662.0 pages: flesch: 40.0 cache: ./cache/cord-018721-othar2uv.txt txt: ./txt/cord-018721-othar2uv.txt summary: Zusammenfassend kann aufgrund der zur Verfügung stehenden Daten die Gabe von Dexamethason bei erwachsenen Patienten mit Verdacht auf eine bakterielle Meningitis (d. Für Entwicklungsländer mit eingeschränkter medizinischer Versorgung und einem hohen Anteil HIV-positiver Patienten konnte keine Wirksamkeit für Dexamethason bei der bakteriellen Meningitis nachgewiesen werden [32] , [33] , [34] . HIV-positive Patienten mit intrakraniellen Tuberkulomen können im Rahmen des "immune reconstitution syndrome" (IRIS) eine durchaus dramatische klinisch neurologische Verschlechterung erfahren, mit Zunahme der neurologi-z Diagnostik Die Untersuchung des Liquor cerebrospinalis ist für die Diagnose einer chronischen Meningitis unverzichtbar, der Liquor ist typischerweise klar, bei deutlich erhöhtem Eiweiß auch xanthochrom wirkend. Da bei der Pathogenese dieser Enzephalitis auch Autoimmunmechanismen eine wichtige Rolle spielen, scheint unter einer kombinierten Th erapie mit Aciclovir und Dexamethason die Rate von Patienten mit schlechtem Outcome geringer zu sein als unter alleiniger Th erapie mit Aciclovir [158] . abstract: Trotz Weiterentwicklung moderner Antibiotika in den letzten Jahren sind die Letalitätszahlen der bakteriellen (eitrigen) Meningitis weiterhin hoch; Überlebende haben häufig neurologische Residuen. Die ungünstigen klinischen Verläufe der bakteriellen Meningitis sind meist Folge intrakranieller Komplikationen, wie z. B. eines generalisierten Hirnödems, einer zerebrovaskulären arteriellen oder venösen Beteiligung oder eines Hydrozephalus. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123678/ doi: 10.1007/978-3-642-16911-3_32 id: cord-291029-oldket3n author: Sefers, Susan E. title: QIAamp MinElute Virus kit effectively extracts viral nucleic acids from cerebrospinal fluids and nasopharyngeal swabs() date: 2005-07-21 words: 3532.0 sentences: 182.0 pages: flesch: 53.0 cache: ./cache/cord-291029-oldket3n.txt txt: ./txt/cord-291029-oldket3n.txt summary: The QIAamp MinElute Virus kit (Qiagen Inc., Valencia, CA) was compared to the two existing methods currently used in our laboratory, IsoQuick (Orca Research Inc., Bothell, WA) for DNA extraction and RNAzol B (Leedo Laboratories Inc., Houston, TX) for RNA extraction, of viral nucleic acids. In this study, we have chosen both nasopharyngeal swab (NPS) and cerebrospinal fluid (CSF) specimens submitted for influenza A virus, enterovirus and herpesvirus testing to validate the MinElute nucleic acid extraction system. Nucleic acid recovery rates between the MinElute and RNAzol B were further determined by quantitating HIV-1 or CMV viral loads in extracted RNA or DNA specimens using a real-time TaqMan PCR. The MinElute kits possessed an equivalent sensitivity in nucleic acid recovery and detection, in comparison to the IsoQuick and RNAzol B, for both DNA and RNA extraction. abstract: BACKGROUND: Nucleic acid preparation from a variety of clinical specimens requires efficient target recovery and amplification inhibitor removal and is critical for successful molecular diagnosis. The QIAamp MinElute Virus kit (Qiagen Inc., Valencia, CA) was compared to the two existing methods currently used in our laboratory, IsoQuick (Orca Research Inc., Bothell, WA) for DNA extraction and RNAzol B (Leedo Laboratories Inc., Houston, TX) for RNA extraction, of viral nucleic acids. STUDY DESIGN: A total of 150 clinical specimens, including cerebrospinal fluid (CSF) and nasopharyngeal swabs (NPS), were used to determine the extraction efficiency of the MinElute compared to the other two methods. Nucleic acid recovery, hands-on time, turn-around-time and cost were compared across all kits. RESULTS: There was complete concordance between the MinElute and IsoQuick/RNAzol kits when herpes simplex virus (HSV), Epstein–Barr virus (EBV), varicella-zoster virus (VZV), influenza A virus or enteroviruses were detected using a colorimetric microtiter plate PCR system. The kits were equivalent in their ability to detect either DNA or RNA with superior ability to recover a high quality and quantity of RNA. With the potential to process larger specimen volumes, the MinElute kit can significantly shorten processing time from 2 h to 50–55 min. CONCLUSIONS: Although relatively high test kit costs were noted, the MinElute kit provides another rapid and user-friendly specimen processing tool in the diagnostic molecular microbiology laboratory. url: https://www.sciencedirect.com/science/article/pii/S1386653205001526 doi: 10.1016/j.jcv.2005.05.011 id: cord-334090-66d8c75g author: Seger, Waleed title: Genotyping of infectious bronchitis viruses from broiler farms in Iraq during 2014-2015 date: 2016-02-18 words: 3613.0 sentences: 178.0 pages: flesch: 54.0 cache: ./cache/cord-334090-66d8c75g.txt txt: ./txt/cord-334090-66d8c75g.txt summary: Thus, the spread of viral respiratory diseases has become the most commonly reported condition in commercial broiler flocks in Iraq; however, there have been no studies on the detection and genotyping of these viruses using molecular techniques and sequencing. Phylogenetic analysis of the 32 strains (Fig. 2) revealed that Iraqi IBV strains could be classified into four genetic groups or genotypes: group I, variant 2 IS/1494-like viruses, including 15 field isolates (46.87 %); group II, 793/Blike viruses, including 13 field strains (40.62 %); group III, QX-like viruses, including three field strains (9.37); and caused by bacteria and mycoplasmas have already been detected on broiler farms located in the central and southern parts of Iraq. Our result were in line with those of Mahmood et al., who conducted the first study of identification and genotyping of IBV isolates and indicated that the 4/91-like virus is circulating on vaccinated broiler farms of the Kurdistan region of Iraq [21] . abstract: Infectious bronchitis virus (IBV) is one of the most critical pathogens in the poultry industry, causing serious economic losses in all countries including Iraq. IBV has many genotypes that do not confer any cross-protection. This virus has been genotyped by sequence analysis of the S1 glycoprotein gene. A total of 100 tracheal and kidney tissue specimens from different commercial broiler flocks in the middle and south of Iraq were collected from September 2013 to September 2014. Thirty-two IBV-positive samples were selected from among the total and were further characterized by nested PCR. Phylogenetic analysis revealed that isolates belong to four groups (group I, variant 2 [IS/1494-like]; group II, 793/B-like; group III, QX-like; group IV, DY12-2-like). Sequence analysis revealed nucleotide sequence identities within groups I, II, and III of 99.68 %-100 %, 99.36 %-100 %, and 96.42 %-100 %, respectively. Group I (variant 2) was the dominant IBV genotype. One Chinese-like recombinant virus (DY12-2-like) that had not been reported in the Middle East was detected. In addition, the presence of QX on broiler chicken farms in the area studied was confirmed. This is the first comprehensive study on the genotyping of IBV in Iraq with useful information regarding the molecular epidemiology of IBV. The phylogenetic relationship of the strains with respect to different time sequences and geographical regions displayed complexity and diversity. Further studies are needed and should include the isolation and full-length molecular characterization of IBV in this region. url: https://www.ncbi.nlm.nih.gov/pubmed/26887967/ doi: 10.1007/s00705-016-2790-2 id: cord-292958-k5d5fo3i author: Sekhon, Simranjeet Singh title: Porcine epidemic diarrhea (PED) infection, diagnosis and vaccination: A mini review date: 2017-01-04 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Porcine epidemic diarrhea virus (PEDV) is a main etiology causing severe enteric disease in piglets with clinical signs of anorexia, vomiting, diarrhea and dehydration resulting in loss of condition and death within a few days. Historically, PED is one of major causes of loss in swine and remains prevalent in some parts of the world. Even with increase in the available tests for PED diagnosis, which include histological diagnosis; virological diagnosis and serological diagnosis, there is no vaccine or specific treatment for this disease yet. In this mini review, the overview and current situation of PED is described with updated techniques, in an effort to comprehensively discuss and understand the disease characteristics. url: https://www.ncbi.nlm.nih.gov/pubmed/32226596/ doi: 10.1007/s13530-016-0287-8 id: cord-004808-6w9n03fy author: Sekiguchi, K. title: Detection of equine arteritis virus (EAV) by polymerase chain reaction (PCR) and differentiation of EAV strains by restriction enzyme analysis of PCR products date: 1995 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A polymerase chain reaction (PCR) based assay capable of detecting and differentiating seven strains of equine arteritis virus (EAV) from around the world was developed. The primers for the PCR were chosen from the ORF 6 gene encoding the unglycosylated membrane protein (M). Viral RNA from cell culture fluids infected with each of the seven EAV strains and RNA from the live vaccine, Arvac, was detected by PCR using four sets of primers. The sensitivity of detection was increased from 100 to 1000 times by performing nested PCR enabling the detection of RNA at a level of 0.5–5 PFU. Differentiation among the virus strains and the live vaccine was achieved by cutting the PCR-amplified products from three sets of primers with six restriction endonucleases. Using this procedure it was possible to distinguish among the seven EAV strains used. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087138/ doi: 10.1007/bf01322675 id: cord-344745-sgkq1l93 author: Selim, Karim title: Molecular characterization of infectious bronchitis viruses isolated from broiler and layer chicken farms in Egypt during 2012 date: 2013-11-18 words: 2757.0 sentences: 172.0 pages: flesch: 56.0 cache: ./cache/cord-344745-sgkq1l93.txt txt: ./txt/cord-344745-sgkq1l93.txt summary: title: Molecular characterization of infectious bronchitis viruses isolated from broiler and layer chicken farms in Egypt during 2012 The aim of this study aimed to survey the Egyptian chicken field for infectious bronchitis virus and study the genomic differentiation between isolated field samples seeking the new variant strain emerged in the Egyptian field. For virus isolation, the supernatants of IBV-positive selected 13 samples determined by RT-PCR were inoculated into five specific pathogen free embryonated chicken eggs (KoumOshiem SPF chicken farm, Fayoum, Egypt) 10-day-old for each sample. The genetic analysis of 100 amino acids sequence from position 263-362 of SP1 gene for the selected 13 Egyptian viruses was done and the hypervariable region of SP1 gene showed multiple mutations as shown in Table 4 in comparison with variant-2 strain. S1 gene sequence analysis of a nephro-pathogenic strain of avian infectious bronchitis virus in Egypt abstract: One of the major problems of avian infectious bronchitis virus (IBV) is the frequent emergence of new variants. In the present study 205 tracheal swabs and organs were collected from broilers and layers chicken farms during January to August 2012 from 19 governorates all over Egypt. The chickens demonstrated respiratory signs and mortality. Out of the examined samples, 130 of which (about 64%) of suspected farms were positive for IBV with real time RT-PCR. 13 IBV-positive samples were selected for further isolation and characterization. Isolation in specific pathogen free (SPF) embryos was carried out after studies three blind successive passages and the hypervariable region of spike protein1 (SP1) was amplified by RT-PCR and sequenced to study the genetic diversity between the isolated viruses. Phylogenetic analysis of the obtained sequences of 13 isolates compared with other IBV strains from the Middle East and worldwide reveled that 11 out of the 13 isolates had close relationship the Israeli variants (IS/885 and IS/1494/06) with nucleotide homology reached up to 89.9% and 82.3%, respectively. Only two isolates had close relationship with CR/88121 and 4/91 viruses with identities of 95% and 96%, respectively. This study indicates existence of two variant groups of IBV circulating in Egypt during 2012. Group I was similar but distinguishable from Israeli variant IS/885 and group II was related to 4/91 and CR/88121 vaccine strains. There was no geographical link between the 2 groups as they were distributed all over the country. These findings necessitate the need to revise the vaccination programs and control measures for IBV. url: https://www.ncbi.nlm.nih.gov/pubmed/32289036/ doi: 10.1016/j.ijvsm.2013.10.002 id: cord-005309-147erliy author: Senanayake, Savithra D. title: Precise large deletions by the PCR-based overlap extension method date: 1995 words: 859.0 sentences: 44.0 pages: flesch: 59.0 cache: ./cache/cord-005309-147erliy.txt txt: ./txt/cord-005309-147erliy.txt summary: The authors describe an efficient method for generating large deletions (>200 nts) of precise length using the PCR-based method of gene splicing by overlap extension (1). Gene splicing by overlap extension or gene SOEing (1) is a powerful PCR-based technique for generating recombinant DNA molecules. A cloned 2231 nt subgenomic defective-interfering RNA of the bovine coronavirus in the pGEM3Zf(-) vector (Promega), containing an in-frame reporter sequence and called pDrepl (4) ( Fig. 1 ) was used for large deletion mutagenesis. GT3'', the "universal" primer for pGEM vectors, and primer B, 5''CTTACCAGGAGTAAAAGA CATTGTGACCTATGGGTGGGCC3'', which anneals to bases 192-213 and 502-519 in the genome-sense (plus) strand of pDrepl and forms the deletion, were used in the first round of PCR. Oligonucleotidedirected mutagenesis: A simple method using two oligonucleotide primers and a single-stranded DNA template abstract: The authors describe an efficient method for generating large deletions (>200 nts) of precise length using the PCR-based method of gene splicing by overlap extension (1). This method is technically simple and less time consuming than conventional loop-out mutagenesis techniques requiring preparation of a single-stranded DNA template. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7090436/ doi: 10.1007/bf02907467 id: cord-315949-7id5mitl author: Sentilhes, Anne‐Charlotte title: Respiratory virus infections in hospitalized children and adults in Lao PDR date: 2013-06-25 words: 4098.0 sentences: 246.0 pages: flesch: 49.0 cache: ./cache/cord-315949-7id5mitl.txt txt: ./txt/cord-315949-7id5mitl.txt summary: 8, 9 The purpose of this study was to describe during a limited period of time the viral etiology of acute lower respiratory infections (ALRI) in patients hospitalized in two Lao hospitals by using a set of five multiplex RT-PCR/PCR targeting 18 common respiratory viruses. In this study, we report for the first time in Lao PDR the viral etiologies in patients hospitalized for ALRIs. We identified 186 respiratory viruses in 162 (55%) patients of all ages using 5 multiplex PCR/RT-PCR. Human respiratory syncytial virus is frequently defined as the predominant virus associated with hospitalizations for ALRI in children aged ≤5 years. Respiratory virus coinfections being frequent, 5, 19, 44 it demonstrates the usefulness of the multiplex RT-PCR approach, which allows the detection of the most important viruses in only few reactions while multiple infections are often undetected in viral culture or by direct immunofluorescence. abstract: BACKGROUND: Acute respiratory infections are an important cause of morbidity and mortality worldwide, with a major burden of disease in developing countries. The relative contribution of viruses in acute lower respiratory infections (ALRI) is, however, poorly documented in Lao PDR. OBJECTIVE: The objective of this study is to investigate the etiology of ALRI in patients of all ages in two hospitals of Laos. METHODS: Multiplex PCR/RT‐PCR methods were used to target 18 major common respiratory viruses. Between August 2009 and October 2010, samples from 292 patients presenting with ALRI were collected. RESULTS AND CONCLUSION: Viruses were detected in 162 (55%) samples. In 48% (140/292) of the total ALRI cases, a single virus was detected while coinfections were observed in 8% (22/292) of the samples. The most frequent viruses were rhinovirus/enterovirus (35%), human respiratory syncytial virus (26%), and influenza viruses (13%). Parainfluenza viruses were detected in 9%, adenovirus in 6%, human metapneumovirus in 4%, coronaviruses (229E, NL63, OC43, HKU1) in 4%, and bocavirus in 3% of ALRI specimens. Most viral infections occurred in patients below 5 years of age. The distribution of viruses varied according to age‐groups. No significant correlation was observed between the severity of the disease and the age of patients or the virus species. This study provides the description of viral etiology among patients presenting with ALRI in Lao PDR. Additional investigations are required to better understand the clinical role of the different viruses and their seasonality in Laos. url: https://doi.org/10.1111/irv.12135 doi: 10.1111/irv.12135 id: cord-312223-qgwzgazd author: Shafagati, Nazly title: The Use of NanoTrap Particles as a Sample Enrichment Method to Enhance the Detection of Rift Valley Fever Virus date: 2013-07-04 words: 8834.0 sentences: 495.0 pages: flesch: 57.0 cache: ./cache/cord-312223-qgwzgazd.txt txt: ./txt/cord-312223-qgwzgazd.txt summary: RESULTS: Screening of NanoTrap particles indicated that one particle, NT53, was the most efficient at RVFV capture as demonstrated by both qRT-PCR and plaque assays. RVFV that was inactivated through either detergent or heat treatment was still found bound to NT53, indicating the ability to use NanoTrap particles for viral capture prior to transport to a BSL-2 environment. Our study demonstrates that NanoTrap particles are capable of capturing whole virus, and can be assayed with both qRT-PCR and plaque assays. A) Seven different types of NanoTrap particles were incubated with viral supernatants containing RVFV (1E+7 pfu/ml) for 30 minutes at room temperature and washed 4 times with water. In order to determine if the amplification observed in the qRT-PCR assay was due to the NanoTrap particle capturing intact viral particles or association of viral RNA (presumably due to lysed virus) with the particles, plaque assays were performed. abstract: BACKGROUND: Rift Valley Fever Virus (RVFV) is a zoonotic virus that is not only an emerging pathogen but is also considered a biodefense pathogen due to the threat it may cause to public health and national security. The current state of diagnosis has led to misdiagnosis early on in infection. Here we describe the use of a novel sample preparation technology, NanoTrap particles, to enhance the detection of RVFV. Previous studies demonstrated that NanoTrap particles lead to both 100 percent capture of protein analytes as well as an improvement of more than 100-fold in sensitivity compared to existing methods. Here we extend these findings by demonstrating the capture and enrichment of viruses. RESULTS: Screening of NanoTrap particles indicated that one particle, NT53, was the most efficient at RVFV capture as demonstrated by both qRT-PCR and plaque assays. Importantly, NT53 capture of RVFV resulted in greater than 100-fold enrichment from low viral titers when other diagnostics assays may produce false negatives. NT53 was also capable of capturing and enhancing RVFV detection from serum samples. RVFV that was inactivated through either detergent or heat treatment was still found bound to NT53, indicating the ability to use NanoTrap particles for viral capture prior to transport to a BSL-2 environment. Furthermore, both NP-40-lysed virus and purified RVFV RNA were bound by NT53. Importantly, NT53 protected viral RNA from RNase A degradation, which was not observed with other commercially available beads. Incubation of RVFV samples with NT53 also resulted in increased viral stability as demonstrated through preservation of infectivity at elevated temperatures. Finally, NanoTrap particles were capable of capturing VEEV and HIV, demonstrating the broad applicability of NanoTrap particles for viral diagnostics. CONCLUSION: This study demonstrates NanoTrap particles are capable of capturing, enriching, and protecting RVFV virions. Furthermore, the use of NanoTrap particles can be extended to a variety of viruses, including VEEV and HIV. url: https://www.ncbi.nlm.nih.gov/pubmed/23861988/ doi: 10.1371/journal.pntd.0002296 id: cord-331455-dfnn9mrf author: Shah, Aditya S. title: The utility of chest computed tomography (CT) and RT-PCR screening of asymptomatic patients for SARS-CoV-2 prior to semiurgent or urgent hospital procedures date: 2020-07-16 words: 2376.0 sentences: 130.0 pages: flesch: 48.0 cache: ./cache/cord-331455-dfnn9mrf.txt txt: ./txt/cord-331455-dfnn9mrf.txt summary: title: The utility of chest computed tomography (CT) and RT-PCR screening of asymptomatic patients for SARS-CoV-2 prior to semiurgent or urgent hospital procedures Here, we describe our experience and the results of implementing this safety project of screening and testing patients for SARS-CoV-2 (COVID-19) prior to semiurgent or urgent hospital procedures using both CT chest imaging and RT-PCR testing. If the phone-screening questionnaire was entirely negative, the patient would undergo a SARS-CoV-2 nasopharyngeal swab PCR 48 hours prior to the elective hospital procedure as well as CT imaging of the chest the day before the procedure. 17 Among asymptomatic patients on the Diamond Princess cruise ship who tested positive for SARS-CoV-2 by RT-PCR, CTs scan were negative for pulmonary opacities in 46% of cases, 18 although the prevalence of disease was relatively high in this cohort (~26%). abstract: OBJECTIVE: Presently, evidence guiding clinicians on the optimal approach to safely screen patients for coronavirus disease 2019 (COVID-19) to a nonemergent hospital procedure is scarce. In this report, we describe our experience in screening for SARS-CoV-2 prior to semiurgent and urgent hospital procedures. DESIGN: Retrospective case series. SETTING: A single tertiary-care medical center. PARTICIPANTS: Our study cohort included patients ≥18 years of age who had semiurgent or urgent hospital procedures or surgeries. METHODS: Overall, 625 patients were screened for SARS-CoV-2 using a combination of phone questionnaire (7 days prior to the anticipated procedure), RT-PCR and chest computed tomography (CT) between March 1, 2020, and April 30, 2020. RESULTS: Of the 625 patients, 520 scans (83.2%) were interpreted as normal; 1 (0.16%) had typical features of COVID-19; 18 scans (2.88%) had indeterminate features of COVID-19; and 86 (13.76%) had atypical features of COVID-19. In total, 640 RT-PCRs were performed, with 1 positive result (0.15%) in a patient with a CT scan that yielded an atypical finding. Of the 18 patients with chest CTs categorized as indeterminate, 5 underwent repeat negative RT-PCR nasopharyngeal swab 1 week after their initial swab. Also, 1 patient with a chest CT categorized as typical had a follow-up repeat negative RT-PCR, indicating that the chest CT was likely a false positive. After surgery, none of the patients developed signs or symptoms suspicious of COVID-19 that would indicate the need for a repeated RT-PCR or CT scan. CONCLUSION: In our experience, chest CT scanning did not prove provide valuable information in detecting asymptomatic cases of SARS-CoV-2 (COVID-19) in our low-prevalence population. url: https://www.ncbi.nlm.nih.gov/pubmed/32669150/ doi: 10.1017/ice.2020.331 id: cord-306829-88nihy7q author: Sharif, Saeed title: Diagnostic Methods for Feline Coronavirus: A Review date: 2010-07-28 words: 3829.0 sentences: 209.0 pages: flesch: 48.0 cache: ./cache/cord-306829-88nihy7q.txt txt: ./txt/cord-306829-88nihy7q.txt summary: Infection with FCoV can result in a diverse range of signs from clinically inapparent infections to a highly fatal disease called feline infectious peritonitis (FIP). The currently available serological tests have low specificity and sensitivity for detection of active infection and cross-react with FCoV strains of low pathogenicity, the feline enteric coronaviruses (FECV). Therefore, a quantitative real-time RT-PCR assay that could determine the amount of viral mRNA in blood may be able to better differentiate FCoV-positive healthy cats from FIP cases. Detection of feline coronaviruses by culture and reverse transcriptase-polymerase chain reaction of blood samples from healthy cats and cats with clinical feline infectious peritonitis Protein electrophoresis on effusions from cats as a diagnostic test for feline infectious peritonitis Detection of feline coronavirus RNA in feces, tissues, and body fluids of naturally infected cats by reverse transcriptase PCR Detection of feline coronavirus RNA in feces, tissues, and body fluids of naturally infected cats by reverse transcriptase PCR abstract: Feline coronaviruses (FCoVs) are found throughout the world. Infection with FCoV can result in a diverse range of signs from clinically inapparent infections to a highly fatal disease called feline infectious peritonitis (FIP). FIP is one of the most serious viral diseases of cats. While there is neither an effective vaccine, nor a curative treatment for FIP, a diagnostic protocol for FCoV would greatly assist in the management and control of the virus. Clinical findings in FIP are non-specific and not helpful in making a differential diagnosis. Haematological and biochemical abnormalities in FIP cases are also non-specific. The currently available serological tests have low specificity and sensitivity for detection of active infection and cross-react with FCoV strains of low pathogenicity, the feline enteric coronaviruses (FECV). Reverse transcriptase polymerase chain reaction (RT-PCR) has been used to detect FCoV and is rapid and sensitive, but results must be interpreted in the context of clinical findings. At present, a definitive diagnosis of FIP can be established only by histopathological examination of biopsies. This paper describes and compares diagnostic methods for FCoVs and includes a brief account of the virus biology, epidemiology, and pathogenesis. url: https://doi.org/10.4061/2010/809480 doi: 10.4061/2010/809480 id: cord-305025-pqye1ebh author: Sharifi, Majid title: Rapid diagnostics of coronavirus disease 2019 in early stages using nanobiosensors: challenges and opportunities date: 2020-09-28 words: 3583.0 sentences: 226.0 pages: flesch: 44.0 cache: ./cache/cord-305025-pqye1ebh.txt txt: ./txt/cord-305025-pqye1ebh.txt summary: The rapid outbreak of coronavirus disease 2019 (COVID-19) around the world is a tragic and shocking event that demonstrates the unpreparedness of humans to develop quick diagnostic platforms for novel infectious diseases. In conclusion, it can be deduced that as rapid COVID-19 detection infection can play a vital role in disease control and treatment, this review may be of great help for controlling the COVID-19 outbreak by providing some necessary information for the development of portable, accurate, selectable and simple nanobiosensors. Detection of severe acute respiratory syndrome (SARS) coronavirus nucleocapsid 637 protein in human serum using a localized surface plasmon coupled fluorescence fiber-optic 638 RNA as a control for multiplex real-time reverse transcription-PCR detection of influenza 790 virus and severe acute respiratory syndrome coronavirus Development and evaluation of a novel loop-mediated isothermal amplification 829 method for rapid detection of severe acute respiratory syndrome coronavirus Rapid COVID-19 detection causative virus (SARS-CoV-2) in human 933 nasopharyngeal swab specimens using field-effect transistor-based biosensor abstract: The rapid outbreak of coronavirus disease 2019 (COVID-19) around the world is a tragic and shocking event that demonstrates the unpreparedness of humans to develop quick diagnostic platforms for novel infectious diseases. In fact, statistical reports of diagnostic tools show that their accuracy, specificity and sensitivity in the detection of COVID-face challenges that can be eliminated by using nanoparticles (NPs). In this study, we aimed to present an overview on the most important way to diagnose different kinds of viruses followed by the introduction of nanobiosensors. Afterward, some methods of coronavirus detection such as imaging, laboratory and kit-based diagnostic tests are surveyed. Furthermore, nucleic acids/protein- and-immunoglobulin (Ig)-based nanobiosensors for the COVID-19 detection infection are reviewed. Finally, current challenges and future perspective for the development of diagnostic or monitoring technologies in the control of COVID-19 are discussed to persuade the scientists in advancing their technologies beyond imagination. In conclusion, it can be deduced that as rapid COVID-19 detection infection can play a vital role in disease control and treatment, this review may be of great help for controlling the COVID-19 outbreak by providing some necessary information for the development of portable, accurate, selectable and simple nanobiosensors. url: https://api.elsevier.com/content/article/pii/S0039914020309954 doi: 10.1016/j.talanta.2020.121704 id: cord-284644-9k2oox64 author: Sharma, Vikrant title: Evaluation of clinical applicability of reverse transcription-loop-mediated isothermal amplification assay for detection and subtyping of Influenza A viruses date: 2017-12-15 words: 4489.0 sentences: 220.0 pages: flesch: 49.0 cache: ./cache/cord-284644-9k2oox64.txt txt: ./txt/cord-284644-9k2oox64.txt summary: Optimized RT-LAMP assays were applied on clinical samples from patients having influenza like illness and results were compared with conventional one-step RT-PCR and real-time RT-PCR. CONCLUSIONS: RT-LAMP assay is rapid, sensitive, specific and cost effective method for detection of influenza A viruses than conventional one-step RT-PCR and it can serve as a good alternate for diagnosis and surveillance studies during influenza outbreaks in resource-limited setups of developing countries. The objectives of the current study were to (1) optimize RT-LAMP assay for detection of influenza A viruses and their subtypes (H1N1, H3N2 and pdm09/H1N1); (2) determine sensitivity and specificity of RT-LAMP assay; (3) clinical evaluation of RT-LAMP assay and conventional one-step RT-PCR in comparison to WHO recommended rRT-PCR taken as standard. Development and evaluation of reverse transcription loop-mediated isothermal amplification assay for rapid and real-time detection of the swine-origin influenza A H1N1 virus abstract: BACKGROUND: Influenza A viruses (IAVs) have always remain a serious concern for the global economy and public health. A rapid, specific and sensitive detection method is always needed to control the influenza in its early stages by timely intervention of therapy and early clinical management. OBJECTIVES: To develop RT-LAMP assays for detection of influenza A viruses, their further subtyping into seasonal (H1N1, H3N2) and novel pandemic H1N1 viruses and to evaluate clinical applicability of optimized RT-LAMP assays on patients’ samples. STUDY DESIGN: In this study, we optimized RT-LAMP assay to detect IAVs by using primers against matrix gene and subtyping of IAVs was done by using primers against hemagglutinin gene. Optimized RT-LAMP assays were applied on clinical samples from patients having influenza like illness and results were compared with conventional one-step RT-PCR and real-time RT-PCR. RESULTS: RT-LAMP assays successfully detected and differentiated IAVs into H1N1, H3N2 and pdm09/H1N1 subtypes. One hundred and sixty seven clinical swab samples from influenza suspected patients were taken and tested with RT-LAMP assay, detecting 30 (17.9%) samples positive for Influenza A virus. Out of 30 samples, 21, 7 and 2 were found positive for pdm09/H1N1, H3N2 and seasonal H1 respectively. Conventional one-step RT-PCR detected a total of 27 (16.2%) samples for influenza A and further subtyping showed 20 and 7 samples positive for pdm09/H1N1 and H3N2 virus respectively whereas none was found positive for seasonal H1N1. RT-LAMP assay demonstrated higher sensitivity (93.8%) than conventional RT-PCR (84.4%) for influenza A viruses detection in clinical samples. CONCLUSIONS: RT-LAMP assay is rapid, sensitive, specific and cost effective method for detection of influenza A viruses than conventional one-step RT-PCR and it can serve as a good alternate for diagnosis and surveillance studies during influenza outbreaks in resource-limited setups of developing countries. url: https://www.ncbi.nlm.nih.gov/pubmed/29253497/ doi: 10.1016/j.jviromet.2017.12.005 id: cord-263976-b9shffb3 author: Shaukat, Shahzad title: Identification and characterization of unrecognized viruses in stool samples of non-polio acute flaccid paralysis children by simplified VIDISCA date: 2014-08-12 words: 3687.0 sentences: 183.0 pages: flesch: 44.0 cache: ./cache/cord-263976-b9shffb3.txt txt: ./txt/cord-263976-b9shffb3.txt summary: One sequence independent method, Virus Discovery based on cDNA Amplified Fragment Length Polymorphism (VIDISCA) is capable of identifying viruses that would have remained unidentified in standard diagnostics or cell cultures. Therefore, a simplified VIDISCA protocol was developed, which lacks the last amplification round, and evaluated using viruses that were cultured from stool samples of acute flaccid paralysis children, and which had remained unrecognized on both cell culture and enterovirus specific real-time PCR. On the other hand, genetic analysis in ORF2 gene (capsid protein) showed that PAK-NIH-VS908 shared 99.7% nucleotide and 100% amino acid similarities with HAstV type 3 isolate IDH2211 (AB54844), a finding which matches with the results from VIDISCA and we conclude that the astrovirus is a recombinant, with a recombination site between ORF1a and ORF2. abstract: BACKGROUND: The use of sequence independent methods combined with next generation sequencing for identification purposes in clinical samples appears promising and exciting results have been achieved to understand unexplained infections. One sequence independent method, Virus Discovery based on cDNA Amplified Fragment Length Polymorphism (VIDISCA) is capable of identifying viruses that would have remained unidentified in standard diagnostics or cell cultures. METHODS: VIDISCA is normally combined with next generation sequencing, however, we set up a simplified VIDISCA which can be used in case next generation sequencing is not possible. Stool samples of 10 patients with unexplained acute flaccid paralysis showing cytopathic effect in rhabdomyosarcoma cells and/or mouse cells were used to test the efficiency of this method. To further characterize the viruses, VIDISCA-positive samples were amplified and sequenced with gene specific primers. RESULTS: Simplified VIDISCA detected seven viruses (70%) and the proportion of eukaryotic viral sequences from each sample ranged from 8.3 to 45.8%. Human enterovirus EV-B97, EV-B100, echovirus-9 and echovirus-21, human parechovirus type-3, human astrovirus probably a type-3/5 recombinant, and tetnovirus-1 were identified. Phylogenetic analysis based on the VP1 region demonstrated that the human enteroviruses are more divergent isolates circulating in the community. CONCLUSION: Our data support that a simplified VIDISCA protocol can efficiently identify unrecognized viruses grown in cell culture with low cost, limited time without need of advanced technical expertise. Also complex data interpretation is avoided thus the method can be used as a powerful diagnostic tool in limited resources. Redesigning the routine diagnostics might lead to additional detection of previously undiagnosed viruses in clinical samples of patients. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1743-422X-11-146) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/25112200/ doi: 10.1186/1743-422x-11-146 id: cord-345338-pf4tsh3v author: Shaw, Brian title: The lingering manifestations of COVID-19 during and after convalescence: update on long-term pulmonary consequences of coronavirus disease 2019 (COVID-19) date: 2020-10-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The long-term sequelae of coronavirus disease 2019 (COVID-19) are still unknown. Lessons from past viral epidemics reveal that, after recovery, patients with viral pulmonary infections can suffer from irreversible pulmonary dysfunction and demonstrate residual imaging or functional abnormalities. Residual ground glass opacities, consolidations, reticular and linear opacities, residual crazy paving pattern, melted sugar sign, and parenchymal fibrotic bands are several features found in the late or remission stages of COVID-19. These radiologic findings have been observed weeks after symptom onset, even after hospital discharge, and they may or may not correlate with clinical manifestations. High-resolution CT may be indicated to establish new baselines and track changes in residual impairments. In our previous review, we observed significant pulmonary sequelae in some COVID-19 survivors at follow-up. In this update, we review the current literature on the clinical and radiologic manifestations of post-recovery COVID-19 toward the end of hospital admission and after discharge. url: https://doi.org/10.1007/s11547-020-01295-8 doi: 10.1007/s11547-020-01295-8 id: cord-262826-2usqmujy author: She, Rosemary C. title: Performance of diagnostic tests to detect respiratory viruses in older adults date: 2010-07-31 words: 2874.0 sentences: 147.0 pages: flesch: 45.0 cache: ./cache/cord-262826-2usqmujy.txt txt: ./txt/cord-262826-2usqmujy.txt summary: For this population, there has not been a comprehensive comparison of current modalities for detection of respiratory viruses (i.e., direct fluorescent antibody testing [DFA], culture, multiplex nucleic acid amplification, and rapid antigen assays), and test performance is likely to differ because adults are known to shed fewer virus particles than children during RTI (Hall et al., 1976) . Although many studies have examined the utility of the various methods used for diagnosis of respiratory virus infections, to our knowledge, none have systematically and concurrently examined the performance characteristics of DFA, culture, rapid antigen testing, and PCR on an older adult population (Barenfanger et al., 2000; Falsey et al., 1996 Falsey et al., , 1995 Lam et al., 2007; Templeton et al., 2004) . The data in this study indicate that multiplexed RT-PCR is highly sensitive in detecting respiratory viruses in older adults compared to DFA, culture, and rapid antigen testing. abstract: Abstract The performance of 4 laboratory methods for diagnosis of viral respiratory tract infections (RTI) in older adults was evaluated. Seventy-four nasopharyngeal (NP) swab specimens were obtained from 60 patients with RTI at a long-term care facility over 2 respiratory seasons. Sixteen specimens were positive for a respiratory virus by at least 1 method. Multiplex reverse transcriptase polymerase chain reaction (RT-PCR) by the Luminex xTAG® Respiratory Viral Panel (RVP) detected 16 (100%) of the positive specimens, RVP of 24-h culture supernatant detected 8 (50%), direct fluorescent antibody testing detected 4 (25%), rapid culture detected 2 (12.5%), and rapid antigen testing detected none. For a comparison group, RVP was performed on NP swabs from 20 outpatient children with RTI. The mean fluorescence intensity by RVP was significantly lower for positive adult patients than pediatric patients (P = 0.0373). Our data suggest that older adult patients shed lower titers of viruses, necessitating a highly sensitive assay such as RT-PCR to reliably detect respiratory viral pathogens. url: https://api.elsevier.com/content/article/pii/S0732889310000568 doi: 10.1016/j.diagmicrobio.2010.02.020 id: cord-311506-fb8c3ix0 author: Shen, C. title: Combining PCR and CT testing for COVID date: 2020-05-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: We analyze the effect of using a screening CT-scan for evaluation of potential COVID-19 infections in order to isolate and perform contact tracing based upon a viral pneumonia diagnosis. RT-PCR is then used for continued isolation based upon a COVID diagnosis. Both the low false negative rates and rapid results of CT-scans lead to dramatically reduced transmission. The reduction in cases after 60 days with widespread use of CT-scan screening compared to PCR by itself is as high as 50x, and the reduction of effective reproduction rate R(t) is 0.20. Our results imply that much more rapid extinction of COVID is possible by combining social distancing with CT-scans and contact tracing. url: https://doi.org/10.1101/2020.05.27.20114736 doi: 10.1101/2020.05.27.20114736 id: cord-017767-zj1h5ixf author: Shieh, Wun-Ju title: Advanced Pathology Techniques for Detecting Emerging Infectious Disease Pathogens date: 2012-04-05 words: 5249.0 sentences: 247.0 pages: flesch: 35.0 cache: ./cache/cord-017767-zj1h5ixf.txt txt: ./txt/cord-017767-zj1h5ixf.txt summary: Although general practice of pathology is largely oriented toward diagnosis of neoplastic diseases, pathologists have been increasingly called upon to make diagnoses from tissue samples collected by cytology, biopsy, and autopsy procedures in response to the challenge of emerging infections [1] [2] [3] [4] . Immunolocalization of antigens by IHC provides histomorphologic correlation between the infectious pathogen and host tissue responses, which is not only crucial for diagnosis but also important to study the pathogenesis of those emerging infections [ 19, 21, 39, 40 ] . PCR ampli fi cation undoubtedly is the most sensitive method available to detect microbial organisms in tissue specimens and has become a common practice in many pathology laboratories. These differential 16S rRNA gene PCR assays provide more speci fi c information regarding the bacteria identity and are very useful for detecting bacterial pathogens in tissue samples in conjunction with histopathologic evaluation, special stains, and IHC. abstract: Detection and surveillance for emerging and reemerging pathogens need a multidisciplinary approach. The intertwining complexity of these pathogens with their diverse tissue tropisms, direct effects on host cells, multiphasic immunological responses, and additional influence of superimposed secondary agents is beyond the expertise of a single discipline in modern medicine. A combined evaluation of patient’s history, clinical manifestations, and physical examination may suggest a list of differential diagnosis, but it is often insufficient to determine the specific infectious etiology. Laboratory methods are essential to identify an etiologic agent from testing clinical samples, such as blood, serum, nasopharyngeal swab, etc. These methods, including traditional microbiological techniques, conventional immunological assays, and modern molecular methods, remain the mainstay in today’s practice of clinical microbiology and infectious disease medicine. Nevertheless, there are technical and logistic issues associated with these methods, and the test results often lack a clinicopathologic correlation that can confound the interpretation of their clinical significance. For example, microbiological culture may fail to grow a causative organism, while the organism isolated by the laboratory in vitro may arise from contamination and does not represent the actual infective agent in vivo. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122422/ doi: 10.1007/978-1-4614-3970-7_45 id: cord-018944-du42ho11 author: Shin, Jeong Hwan title: Nucleic Acid Extraction and Enrichment date: 2018-11-10 words: 6857.0 sentences: 355.0 pages: flesch: 41.0 cache: ./cache/cord-018944-du42ho11.txt txt: ./txt/cord-018944-du42ho11.txt summary: [6, 7] as follows: (1) extraction should be simple and rapid and should show high sensitivity and specificity; (2) it is preferred that there be no requirements for specialized equipment or special knowledge and skills; (3) the final nucleic acid should be pure and easy to modify for various amplification techniques; (4) the reagents and their product should be harmless; and (5) the process of preparation should resist contamination with other specimens. Although the phenolchloroform method is relatively easy compared with the CsCl/EtBr gradient and is very useful for the extraction of nucleic acids, it also is problematic for the clinical microbiology laboratory because phenol has important limitations due to its being toxic, caustic, and flammable [5, 15, 16] . In recent years, it has become possible to extract viral nucleic acid from clinical specimens having cellular components, and there have been trials of these commercially available kits to detect various clinically important viruses [30] [31] [32] . abstract: Nucleic acid extraction is the first step of any amplification experiment no matter what kind of amplification is used to detect a specific pathogen. Efficient nucleic acid extraction is essential to obtain good results using any molecular test. The optimal extraction method should fulfill the following conditions: speed, short working time, cost-effectiveness, high sensitivity and specificity, good reproducibility, and safety. The methods can be divided into solution or column based according to differences of their principles. The automated extraction instruments have many advantages, and these have proven to be very useful. Moreover, in recent years, fully automated instruments combining NA extraction and amplification have been commercially available. However, the method itself does not provide assurance, and the DNA recovery can be different among various kits or instruments that use the similar principles. Therefore, it is important to carefully evaluate the performance of any extraction method used in the clinical microbiology laboratory even though manufacturers may have reported good validation results with specific organisms. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123959/ doi: 10.1007/978-3-319-33900-9_13 id: cord-000715-zl1s82yi author: Shulman, Lester M. title: Evaluation of Four Different Systems for Extraction of RNA from Stool Suspensions Using MS-2 Coliphage as an Exogenous Control for RT-PCR Inhibition date: 2012-07-16 words: 4786.0 sentences: 248.0 pages: flesch: 50.0 cache: ./cache/cord-000715-zl1s82yi.txt txt: ./txt/cord-000715-zl1s82yi.txt summary: These samples were selected from among archived stool samples previously tested for enterovirus and MS2 after extraction by QIAamp Viral RNA Mini Kit. A sufficient number of samples with high, intermediate, and low levels of inhibitors were chosen for re-analysis to enable comparison between extraction procedures at each of these levels of inhibition. Analysis of variance ( Fig. 3 , part 2), indicated that there was no significant difference (paired t-test, P.0.05) between the inhibition of rRT-PCR of the MS2 external control and the added enterovirus (P.0.05) for protocols A, C, and D. Stool suspensions (N = 185) prepared for routine analysis of clinical stool samples sent to the Central Virology Laboratory (CVL) at Chaim Sheba Medical Center in Israel were used to evaluate the efficiency of four different RNA extraction systems in excluding inhibitors of rRT-PCR. abstract: Knowing when, and to what extent co-extracted inhibitors interfere with molecular RNA diagnostic assays is of utmost importance. The QIAamp Viral RNA Mini Kit (A); MagNA Pure LC2.0 Automatic extractor (B); KingFisher (C); and NucliSENS EasyMag (D) RNA extraction systems were evaluated for extraction efficiency and co-purification of inhibitors from stool suspensions. Real-Time Reverse Transcriptase Polymerase Chain Reaction (rRT-PCR) of MS-2 coliphage spiked into each system’s lysis buffer served as an external control for both. Cycle thresholds (Cts) of the MS2 were determined for RNA extracted from stool suspensions containing unknown (n = 93) or varying amounts of inhibitors (n = 92). Stool suspensions from the latter group were also used to determine whether MS-2 and enterovirus rRT-PCR inhibitions were correlated. Specifically 23 RNA extracts from stool suspensions were spiked with enterovirus RNA after extraction and 13 of these stool suspension were spiked with intact enterovirus before extraction. MS2 rRT-PCR inhibition varied for RNAs extracted by the different systems. Inhibition was noted in 12 (13.0%), 26 (28.3%), 7 (7.6%), and 7 (7.6%) of the first 93 RNA extracts, and 58 (63.0%), 55 (59.8%), 37 (40.2%) and 30 (32.6%) of the second 92 extracts for A, B, C, and D, respectively. Furthermore, enterovirus rRT-PCR inhibition correlated with MS2 rRT-PCR inhibition for added enterovirus RNA or virus particles. In conclusion, rRT-PCR for MS-2 RNA is a good predictor of inhibition of enterovirus RNA extracted from stool suspensions. EasyMag performed the best, however all four extraction methods were suitable provided that external controls identified problematic samples. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3397973/ doi: 10.1371/journal.pone.0039455 id: cord-284608-ba7wq52t author: Sias, Catia title: Alpha, Beta, gamma human PapillomaViruses (HPV) detection with a different sets of primers in oropharyngeal swabs, anal and cervical samples date: 2019-03-04 words: 5645.0 sentences: 281.0 pages: flesch: 55.0 cache: ./cache/cord-284608-ba7wq52t.txt txt: ./txt/cord-284608-ba7wq52t.txt summary: title: Alpha, Beta, gamma human PapillomaViruses (HPV) detection with a different sets of primers in oropharyngeal swabs, anal and cervical samples BACKGROUND: Recent studies have shown a 13-fold increase of oropharyngeal cancer in the presence of HPV, while α-HPV detection seems to be rare in oral cavity in comparison to anal or cervical district, many novel β and γ types have been isolated in this anatomical site suggesting a wide tropism range. METHODS: We analysed the presence of HPV DNA in oropharyngeal (n = 124), anal (n = 186), cervical specimens (n = 43) from HIV positive and negative patients using FAP59/64 and MY09/11 primers. In this study, we analyzed the presence of HPV DNA in oral, anal, and cervical specimens collected from HIV positive and HIV negative individuals, living in the same geographic area (regione Lazio) by using MY09/11 [20, 21] FAP59/64 primers [22] . abstract: BACKGROUND: Recent studies have shown a 13-fold increase of oropharyngeal cancer in the presence of HPV, while α-HPV detection seems to be rare in oral cavity in comparison to anal or cervical district, many novel β and γ types have been isolated in this anatomical site suggesting a wide tropism range. Currently, there are no guidelines recommending HPV oral cavity screening as a mandatory test, and it remains unknown which HPV types should be included in HPV screening programs. Our goal was to assess HPV prevalence in oropharyngeal, anal, and cervical swabs using different sets of primers,which are able to amplify α, β, γ HPV types. METHODS: We analysed the presence of HPV DNA in oropharyngeal (n = 124), anal (n = 186), cervical specimens (n = 43) from HIV positive and negative patients using FAP59/64 and MY09/11 primers. All untyped strains were genetically characterized through PCR amplification and direct sequencing of partial L1 region, and the resulting sequences were classified through phylogenetic analysis. RESULTS: HPV prevalence was 20.9% in 124 oropharyngeal swab samples, including infections with multiple HPV types (5.6%). HPV prevalence in this anatomical site was significantly associated with serostatus: 63.3%in HIV positive and 36.3% in HIV negative patients (p < 0.05). Unclassified types were detected in 6 specimens. In our analysis, we did not observe any difference in HPV (α, β, γ) prevalence between men and women. Overall, β species were the most frequently detected 69.7%. When using anal swabs, for HIV positive patients, β genus prevalence was 1% and γ genus was 3.7% including 6 unclassified types. In cervical samples from 43 HIV positive women (18 HPV negative and 25 positive by MY09/11 PCR), only one sample was positivite for β(1) species (2.4%) using FAP primers. Six of the untyped strains clustered with sequences from species 7, 9, 10, 8,12 of γ genus. Four sequences remained unclassified. Finally, β and γ HPV prevalence was significantly lower than their respective HPV prevalence as identified by the Luminex system in all anatomical sites that were analyzed in previous studies. CONCLUSION: This study provides new information about viral isolates present in oropharyngeal site and it will contribute to improve the monitoring of HPV infection. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12985-019-1132-x) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/30832688/ doi: 10.1186/s12985-019-1132-x id: cord-291958-g4jlg9pw author: Silva, Camila S title: Human Respiratory Coronaviruses Detected In Patients with Influenza-Like Illness in Arkansas, USA date: 2014-03-26 words: 4255.0 sentences: 221.0 pages: flesch: 57.0 cache: ./cache/cord-291958-g4jlg9pw.txt txt: ./txt/cord-291958-g4jlg9pw.txt summary: Our study aim was to investigate the molecular epidemiology of human CoV strains circulating in Arkansas, their genetic variability and their association with reported influenza-like symptoms. Samples were pre-screened, using a quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) multiprobe for coronavirus, and subjected to confirmatory pancoronavirus and/or strain-specific reverse transcriptase (RT)-PCR followed by sequence analysis. RNAs positive for CoV by qRT-PCR were analyzed by one-step RT-PCR, using degenerate primers for the ORF1b [20] and specific primers (Table 1) for the spike and nucleocapsid genes of human alphacoronavirus (NL63 and 229E) and betacoronavirus (OC43 and HKU1). Among the 3 feline-like samples (based on ORF1b phylogenetic analysis), two were amplified and sequenced using primers to the S region, one was shown to share the highest identity with the OC43 strain (95.9% identity) and another shared the highest identity to feline CoV (83.8% identity) ( Figure 2 ). abstract: Acute respiratory viruses often result in significant morbidity and mortality. The potential impact of human respiratory coronavirus (CoV) infections was underestimated until the severe acute respiratory syndrome (SARS-CoV) outbreak in 2003, which showed that new, highly pathogenic coronaviruses could be introduced to humans, highlighting the importance of monitoring the circulating coronaviruses. The use of sensitive molecular methods has contributed to the differential diagnosis of viruses circulating in humans. Our study aim was to investigate the molecular epidemiology of human CoV strains circulating in Arkansas, their genetic variability and their association with reported influenza-like symptoms. We analyzed 200 nasal swab samples, collected by the Arkansas Department of Health in 2010, for influenza diagnosis. All samples were from patients showing acute respiratory symptoms while testing negative for influenza. Samples were pre-screened, using a quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) multiprobe for coronavirus, and subjected to confirmatory pancoronavirus and/or strain-specific reverse transcriptase (RT)-PCR followed by sequence analysis. Seventy-nine samples (39.5%) were positive by qRT-PCR and 35 samples (17.5%) were confirmed by conventional RT-PCR. Twenty-three of the confirmed samples (59%) were sequenced. The most frequent strain detected was HCoV-OC43-like followed by NL63-like; only one sample was positive for HCoV-229E and one for HCoV-HKU1. Feline-like CoV strains were detected in three samples, representing possible evidence of interspecies transmission or a new human strain. Seventeen percent of the coronavirus positive samples were also positive for other respiratory viruses, such as Respiratory Syncytial Virus (RSV), Parainfluenza 2 and 3, and Rhinovirus. Thus, HCoV-OC43, NL63, HKU1 and new feline-like strains were circulating in Arkansas in 2010. HCoV was the sole respiratory virus detected in 16% of the patients who showed acute respiratory symptoms with negative diagnoses for influenza virus. url: https://www.ncbi.nlm.nih.gov/pubmed/27588218/ doi: 10.4172/2161-0517.s2-004 id: cord-336639-jaue41mv author: Simons, Fermin A. title: A mRNA PCR for the diagnosis of feline infectious peritonitis date: 2004-12-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A reverse transcriptase polymerase chain reaction (RT-PCR) for the detection of feline coronavirus (FCoV) messenger RNA in peripheral blood mononuclear cells (PBMCs) is described. The assay is evaluated as a diagnostic test for feline infectious peritonitis (FIP). It is based on a well-documented key event in the development of FIP: the replication of virulent FCoV mutants in monocytes/macrophages. To detect most feline coronavirus field strains, the test was designed to amplify subgenomic mRNA of the highly conserved M gene. The test was applied to 1075 feline blood samples (424 from healthy, 651 from sick cats suspected of FIP) and returned 46% of the diseased cats as positive for feline coronavirus mRNA in their peripheral blood cells; of the healthy cats, 5% tested positive. Of a group of 81 animals in which FIP had been confirmed by post-mortem examination, 75 (93%) tested positive, whereas 17 cats with different pathologies (non-FIP cases) all tested negative. In view of the low rate of false-positive results (high specificity) the mRNA RT-PCR may be a valuable addition to the diagnostic arsenal for FIP. url: https://www.sciencedirect.com/science/article/pii/S0166093404003477 doi: 10.1016/j.jviromet.2004.11.012 id: cord-281871-3j64de2i author: Sinagra, G title: Viral presence guided immunomodulation in lymphocytic myocarditis: An update date: 2020-07-19 words: 2743.0 sentences: 143.0 pages: flesch: 32.0 cache: ./cache/cord-281871-3j64de2i.txt txt: ./txt/cord-281871-3j64de2i.txt summary: In patients with lymphocytic myocarditis and heart failure (HF) with severe left ventricular dysfunction or lifethreatening ventricular arrhythmias who do not respond to conventional treatments in the short term (i.e. 7-10 days), EMB may guide more advanced medical therapy, including immunosuppression and immunomodulation 1 state, "Immunosuppression should be started only after ruling out active infection on EMB by PCR," and, "Immunosuppression may be considered, on an individual basis, in infection-negative lymphocytic myocarditis refractory to standard therapy in patients with no contraindications to Accepted Article immunosuppression." 4 Accordingly, the latest version of the Cochrane bank analysis 5 reports, "Corticosteroids may have a role in treating myocarditis without viral evidence." The same recommendations have been reaffirmed in recent reviews 1, 6, 7 , where different international experts highlight the need for ruling out viral presence in EMB via PCR analysis before starting immunosuppression or immunomodulation in clinically suspected acute myocarditis patients presenting life-threatening scenarios. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32683758/ doi: 10.1002/ejhf.1969 id: cord-289114-ifnk41oq author: Singh, Angaraj title: Effect of pre‐existing diseases on COVID‐19 infection and role of new sensors and biomaterials for its detection and treatment date: 2020-10-28 words: 6894.0 sentences: 470.0 pages: flesch: 54.0 cache: ./cache/cord-289114-ifnk41oq.txt txt: ./txt/cord-289114-ifnk41oq.txt summary: The SARS-CoV-2 infected patients with the cardiovascular problem have a higher fatality rate as compared to general COVID-19 patients. The ACE-2 has been suggested as a medicine for the treatment of diabetes because it reduces inflammation .Therefore, the diabetes and COVID-19 patients treated with ACE-2 have higher risk of infection (Zachary, 2020) . Although, the specific drug for SARS-CoV-2 is not discovered till date, the medical observers are attempting with different antiviral drugs for the treatment of COVID-19 infection . All rights reserved patients demonstrated that the combination of a new antiviral drug remdesivir and chloroquine slowed down the growth of SARS-CoV-2 (Abdul et al., 2017) . Convalescent plasma therapy has been observed as a better alternative for the treatment of severely infected COVID-19 patients. A research report suggested that plasma treatment is more effective at the initial stage (within 14 days of symptoms) of COVID-19 infection. abstract: The entire world is suffering from a new type of viral disease, occurred by severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2). The present article briefly discussed the genome sequencing and interaction of host cells with SARS‐CoV‐2. The influence of pre‐existing diseases such as diabetes, heart disease and age of the patients on COVID‐19 infection is reviewed. The possible treatments of SARS‐CoV‐2 including antiviral drugs, Chinese traditional treatment and plasma therapy are elaborately discussed. The proper vaccine for COVID‐19 is not available till date. However, the trials of pre‐existing antiviral vaccines such as, chloroquine/hydroxychloroquine, remdesivir, ritonavir and lopinavir and their consequences are briefly presented. Further, the importance of new materials and devices for the detection and treatment of COVID‐19 has also been reviewed. The polymerase chain reaction (PCR)‐based, and non‐PCR based devices are used for the detection of COVID‐19 infection. The non‐PCR based devices provide rapid results as compared to PCR based devices. url: https://www.ncbi.nlm.nih.gov/pubmed/33173852/ doi: 10.1002/mds3.10140 id: cord-313107-6cfenpxm author: Singh, Anirudh K. title: Evaluation of pooled sample analysis strategy in expediting case detection in areas with emerging outbreaks of COVID-19: A pilot study date: 2020-09-22 words: 2889.0 sentences: 124.0 pages: flesch: 50.0 cache: ./cache/cord-313107-6cfenpxm.txt txt: ./txt/cord-313107-6cfenpxm.txt summary: In this context, a pooled sample testing strategy was evaluated in the setting of emerging disease outbreak in 3 central Indian districts to assess if the cost of the test and turn-around time could be reduced without compromising its diagnostic characteristics and thus lead to early containment of the outbreak. At the reported point prevalence of 4.8% in this study, the negative predictive value of qRT-PCR on pooled samples was around 96% suggesting that the adoption of this strategy as an effective screening tool for COVID-19 needs to be carefully evaluated. We hypothesized that testing of pooled respiratory samples, collected from potentially infected individuals, could lead to faster laboratory confirmation and quicker containment of the emerging infection in these districts and, thus, undertook this study to evaluate the diagnostic concordance between the strategies of pooled vs. abstract: Timely diagnosis of COVID-19 infected individuals and their prompt isolation are essential for controlling the transmission of SARS-CoV-2. Though quantitative reverse transcriptase PCR (qRT-PCR) is the method of choice for COVID-19 diagnostics, the resource-intensive and time-consuming nature of the technique impairs its wide applicability in resource-constrained settings and calls for novel strategies to meet the ever-growing demand for more testing. In this context, a pooled sample testing strategy was evaluated in the setting of emerging disease outbreak in 3 central Indian districts to assess if the cost of the test and turn-around time could be reduced without compromising its diagnostic characteristics and thus lead to early containment of the outbreak. From 545 nasopharyngeal and oropharyngeal samples received from the three emerging districts, a total of 109 pools were created with 5 consecutive samples in each pool. The diagnostic performance of qRT-PCR on pooled sample was compared with that of individual samples in a blinded manner. While pooling reduced the cost of diagnosis by 68% and the laboratory processing time by 66%, 5 of the 109 pools showed discordant results when compared with induvial samples. Four pools which tested negative contained 1 positive sample and 1 pool which was positive did not show any positive sample on deconvolution. Presence of a single infected sample with Ct value of 34 or higher, in a pool of 5, was likely to be missed in pooled sample analysis. At the reported point prevalence of 4.8% in this study, the negative predictive value of qRT-PCR on pooled samples was around 96% suggesting that the adoption of this strategy as an effective screening tool for COVID-19 needs to be carefully evaluated. url: https://www.ncbi.nlm.nih.gov/pubmed/32960929/ doi: 10.1371/journal.pone.0239492 id: cord-322778-a411t2wg author: Skalidis, Ioannis title: Unenhanced computed tomography (CT) utility for triage at the emergency department during COVID-19 pandemic date: 2020-07-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Unenhanced chest computed tomography (CT) can assist in the diagnosis and classification of coronavirus disease 2019 (COVID-19), complementing to the reverse-transcription polymerase chain reaction (RT-PCR) tests; the performance of which has yet to be validated in emergency department (ED) setting. The study sought to evaluate the diagnostic performance of chest CT in the diagnosis and management of COVID-19 in ED. METHODS: This retrospective single-center study included 155 patients in ED who underwent both RT-PCR and chest CT for suspected COVID-19 from March 1st to April 1st, 2020. The clinical information, CT images and laboratory reports were reviewed and the performance of CT was assessed, using the RT-PCR as standard reference. Moreover, an adjudication committee retrospectively rated the probability of COVID-19 before and after the CT calculating the net reclassification improvement (NRI). Their final diagnosis was considered as reference. The proportion of patients with negative RT-PCR test that was directed to the referent hospital based on positive CT findings was also assessed. RESULTS: Among 155 patients, 42% had positive RT-PCR results, and 46% had positive CT findings. Chest CT showed a sensitivity of 84.6%, a specificity of 80.0% and a diagnostic accuracy of 81.9% in suggesting COVID-19 with RT-PCR as reference. Concurrently, corresponding values of 89.4%, 84.3% and 86.5% were retrieved with the adjudication committee diagnosis as reference. For the subgroup of patients with age > 65, specificity and sensitivity were 50% and 80.8%, respectively. In patients with negative RT-PCR results, 20% (18/90) had positive chest CT finding and 22% (4/18) of those were eventually considered as COVID-19 positive according to the adjudication committee. After CT, the estimated probability of COVID-19 changed in 10/104 (11%) patients with available data: 4 (4%) were downgraded, 6 (6%) upgraded. The NRI was 1.92% (NRI event −2.08% + NRI non-event 5.36%). No patient with negative RT-PCR but positive CT was eventually directed to hospital. CONCLUSION: Chest CT showed promising sensitivity for diagnosing COVID-19 across all patients' subgroups. However, CT did not modify the estimated probability of COVID-19 infection in a substantial proportion of patients and its utility as an emergency department triage tool warrants further analyses. url: https://doi.org/10.1016/j.ajem.2020.07.058 doi: 10.1016/j.ajem.2020.07.058 id: cord-329643-hhk900c1 author: Skalina, K. A. title: Extended Storage of SARS-CoV2 Nasopharyngeal Swabs Does Not Negatively Impact Results of Molecular-Based Testing date: 2020-05-20 words: 1869.0 sentences: 114.0 pages: flesch: 49.0 cache: ./cache/cord-329643-hhk900c1.txt txt: ./txt/cord-329643-hhk900c1.txt summary: Here we demonstrate the long-term stability of nasopharyngeal swab specimens for SARS-CoV-2 molecular testing across three assays recently approved by the U.S. FDA under Emergency Use Authorization. This study demonstrates that nasopharyngeal swab specimens can be stored under refrigeration or even ambient conditions for 21 days without clinically impacting the results of the real-time RT-PCR testing. determined that short delays (up to 4 days) in processing influenza nasal and throat swabs did not significantly affect the ability to detect viral particles by real-time RT-PCR.(5) More recently the stability of SARS-CoV-2 detection in different types of storage media over a 14-day period was evaluated. This study utilized three different automated real-time reverse-transcriptase polymerase chain reaction (RT-PCR) in vitro diagnostic platforms (Luminex ARIES, Panther Fusion, and Abbott m2000) currently in use for clinical testing of SARS-CoV-2 at the Department of Pathology, Division of Virology, Montefiore Medical Center, Bronx, NY. abstract: With the global outbreak of the novel coronavirus disease 2019, the demand for testing rapidly increased and quickly exceeded the testing capacities for many laboratories. Clinical tests which receive CE and FDA authorizations cannot always be tested thoroughly in a real-world environment. Here we demonstrate the long-term stability of nasopharyngeal swab specimens for SARS-CoV-2 molecular testing across three assays recently approved by the U.S. FDA under Emergency Use Authorization. This study demonstrates that nasopharyngeal swab specimens can be stored under refrigeration or even ambient conditions for 21 days without clinically impacting the results of the real-time RT-PCR testing. url: https://doi.org/10.1101/2020.05.16.20104158 doi: 10.1101/2020.05.16.20104158 id: cord-307338-4nta9b6w author: Slomka, Marek J. title: Original Article: Real time reverse transcription (RRT)‐polymerase chain reaction (PCR) methods for detection of pandemic (H1N1) 2009 influenza virus and European swine influenza A virus infections in pigs date: 2010-08-17 words: 7990.0 sentences: 469.0 pages: flesch: 62.0 cache: ./cache/cord-307338-4nta9b6w.txt txt: ./txt/cord-307338-4nta9b6w.txt summary: Fifteen of these specimens (six swabs and nine tissues) were shown to be Avian influenza viruses, with highly pathogenic (HP) H5 and H7 isolates indicated positive for H1N1v by non-RRT PCR approaches (Table 3) , i.e. amplification of RNA extracted from the clinical specimen by conventional RT PCR using primers that had been designed specifically for the HA gene of current H1N1v isolates, available at: http://www.who.int/csr/resources/publications/swineflu/GenomePrimers_20090512.pdf Amplicons were electrophoresed in 2% agarose and stained with RedSafeÔ (iNtRON Biotechnology, Kyungki-Do, Korea) for visualisation, excised and purified from agarose using the QIAquick Ò Gel Extraction Kit (Qiagen, Crawley, UK). These test results with archived tissue specimens obtained from the field reinforced the observation that the ''''perfect match'''' M gene RRT PCR is the most sensitive for detecting contemporary European and UK SIVs. All 31 archived UK tissue samples from SIV-positive pigs were negative by the ''''H1-118'''' RRT PCR assay (Table 2) . abstract: Please cite this paper as: Slomka et al. (2010) Real time reverse transcription (RRT)‐polymerase chain reaction (PCR) methods for detection of pandemic (H1N1) 2009 influenza virus and European swine influenza A virus infections in pigs. Influenza and Other Respiratory Viruses 4(5), 277–293. Background There is a requirement to detect and differentiate pandemic (H1N1) 2009 (H1N1v) and established swine influenza A viruses (SIVs) by real time reverse transcription (RRT) PCR methods. Objectives First, modify an existing matrix (M) gene RRT PCR for sensitive generic detection of H1N1v and other European SIVs. Second, design an H1 RRT PCR to specifically detect H1N1v infections. Methods RRT PCR assays were used to test laboratory isolates of SIV (n = 51; 37 European and 14 North American), H1N1v (n = 5) and avian influenza virus (AIV; n = 43). Diagnostic sensitivity and specificity were calculated for swabs (n = 133) and tissues (n = 116) collected from field cases and pigs infected experimentally with SIVs and H1N1v. Results The “perfect match” M gene RRT PCR was the most sensitive variant of this test for detection of established European SIVs and H1N1v. H1 RRT PCR specifically detected H1N1v but not European SIVs. Validation with clinical specimens included comparison with virus isolation (VI) as a “gold standard”, while field infection with H1N1v in swine was independently confirmed by sequencing H1N1v amplified by conventional RT PCR. “Perfect match” M gene RRT PCR had 100% sensitivity and 95·2% specificity for swabs, 93·6% and 98·6% for tissues. H1 RRT PCR demonstrated sensitivity and specificity of 100% and 99·1%, respectively, for the swabs, and 100% and 100% for the tissues. Conclusions Two RRT PCRs for the purposes of (i) generic detection of SIV and H1N1v infection in European pigs, and for (ii) specific detection of H1N1v (pandemic influenza) infection were validated. url: https://www.ncbi.nlm.nih.gov/pubmed/20716157/ doi: 10.1111/j.1750-2659.2010.00149.x id: cord-016417-3cwwmyv9 author: Sluijter, J. P. G. title: Quantitative Real-Time PCR date: 2006 words: 3110.0 sentences: 174.0 pages: flesch: 53.0 cache: ./cache/cord-016417-3cwwmyv9.txt txt: ./txt/cord-016417-3cwwmyv9.txt summary: In this chapter, we focus on the newest advancements in reverse transcription polymerase chain reaction (rt-pcr) technology, the real-time PCR or quantitative PCR, using small amounts of RNA to determine expression levels.We discuss the technique in general and describe two different approaches. Traditional methods to quantify mRNA expression levels are Northern blotting, in situ hybridization, ribonuclease protection, cDNA arrays, and reverse transcription polymerase chain reaction (rt-pcr). PCR amplification of your target DNA will increase the number of probes that hybridize with the complementary template. Accumulation of the released reporter molecules during the amplification cycles results in an increasing fluorescent signal and is correlated to the amount of the target DNA present. When the probe binds to the target sequence this will result in a separation of the reporter and quencher molecule and the fluorescent signal can be monitored. Amplification in a real-time PCR will increase the target DNA and therefore also the observed fluorescent signal. abstract: Changes in mRNA expression levels occur during physiological and pathological processes in the cardiovascular system. An increase inDNAtranscription results in increasedmRNAlevels and will subsequently result in increased protein levels that regulate processes inside and outside the cell. To determine alterations in mRNA levels, traditional methods such as Northern blot and ribonuclease protection assay can be used; however, large amounts of RNA are necessary and the methods are very labor intensive. In this chapter, we focus on the newest advancements in reverse transcription polymerase chain reaction (rt-pcr) technology, the real-time PCR or quantitative PCR, using small amounts of RNA to determine expression levels.We discuss the technique in general and describe two different approaches. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120686/ doi: 10.1007/0-387-23329-6_4 id: cord-252604-1u14i4v1 author: Smith, Alvin W. title: Vesivirus viremia and seroprevalence in humans date: 2006-03-22 words: 5270.0 sentences: 266.0 pages: flesch: 53.0 cache: ./cache/cord-252604-1u14i4v1.txt txt: ./txt/cord-252604-1u14i4v1.txt summary: To test the possibility that sera may contain Vesivirus genomes, as suggested by the clinical evidence of viremia in cases of Vesivirus illness, including humans [Smith et al., 1998a] , three complementary methods targeting three Vesivirus genomic regions were utilized to detect Vesivirus RNA in serum ( Fig. 1 ): dot blot for the ORF1 3C protease region, reverse transcriptionpolymerase chain reaction (RT-PCR) for the 3 0 terminal region of ORF1 encoding a portion of the viral RNA polymerase or for a portion of the viral capsid protein, and nucleotide sequencing of RT-PCR amplicons. abstract: Pathogenic caliciviruses of the genus Vesivirus circulate in oceanic ecosystems and spread to and among terrestrial mammals. Isolation of Vesivirus from natural and laboratory infections in humans led to this investigation of Vesivirus seroprevalence and viremia. Sera from four groups were tested for antibodies to Vesivirus as follows: blood donors whose units were cleared for donation, blood donors whose units were not accepted for donation solely because of elevated blood liver alanine aminotransferase (ALT) concentrations, patients with clinical hepatitis of unknown but suspected infectious cause, and patients with clinical hepatitis of unknown cause but associated with blood transfusion or dialysis. Additionally, sera were tested for Vesivirus genome by three methods: dot‐blot and two reverse transcription‐polymerase chain reaction (RT‐PCR) methods. The calculated seroprevalence against Vesivirus virions within these groups (N = 765) was 12%, 21%, 29%, and 47%, respectively (P < 0.001 for group differences). Additionally, 11 (9.8%) of 112 sera tested yielded RT‐PCR amplicons that by nucleotide sequence were distinct from each other and related to known Vesivirus. These data indicate that some blood donors in the population tested have serologic evidence of previous Vesivirus infection and some also have Vesivirus viremia. These results justify further investigation of an association between Vesivirus infection and illness in humans. J. Med. Virol. 78:693–701, 2006. © 2006 Wiley‐Liss, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/16555277/ doi: 10.1002/jmv.20594 id: cord-034689-se1hdn61 author: Smith, David L. title: A Characteristic Chest Radiographic Pattern in the Setting of COVID-19 Pandemic date: 2020-09-03 words: 2913.0 sentences: 156.0 pages: flesch: 48.0 cache: ./cache/cord-034689-se1hdn61.txt txt: ./txt/cord-034689-se1hdn61.txt summary: CONCLUSION: The presence of patchy and/or confluent, bandlike ground glass opacity or consolidation in a peripheral and mid-to-lower lung zone distribution on a chest radiograph obtained in the setting of pandemic COVID-19 is highly suggestive of SARS-CoV-2 infection and should be used in conjunction with clinical judgement to make a diagnosis. The characteristic COVID-19 pattern ( Fig. 2-4) was defined in accordance with the prevailingly accepted chest imaging findings of COVID-19 in recent literature [2, 12, 20, 24, 25, [27] [28] [29] including the presence of bilateral "patchy" or "confluent, bandlike" ground glass opacity or consolidation in a peripheral and mid-to-lower lung zone distribution. The presence of bilateral "patchy" and/or "confluent, bandlike" ground glass opacity or consolidation in a peripheral and mid-to-lower lung zone distribution on a chest radiograph obtained in the setting of pandemic COVID-19 is highly suggestive of SARS-CoV-2 infection and should be used in conjunction with clinical judgement to make a diagnosis, especially when rapid and reliable serologic testing is lacking. abstract: BACKGROUND: Compared with chest CT, there is a relative paucity of data regarding the role of the chest radiograph (CXR) in the diagnosis of COVID-19. PURPOSE: To determine the utility of CXR in aiding clinical diagnosis of COVID-19, utilizing RT-PCR as the standard of comparison. MATERIALS AND METHODS: A retrospective study was performed of persons under investigation (PUIs) for COVID-19 presenting to our institution during the exponential growth phase of the COVID-19 outbreak in New Orleans, USA (March 13 – 25, 2020). 376 in-hospital CXR exams for 366 individual patients were reviewed along with concurrent RT-PCR tests. Two experienced radiologists categorized each CXR as characteristic, nonspecific, or negative in appearance for COVID-19, utilizing well-documented COVID-19 imaging patterns. CXR categorization was compared against RT-PCR results to determine the utility of CXR in diagnosing COVID-19. RESULTS: There were 178/366 male (49%) and 188/366 female (51%) patients with a mean age of 52.7 years (range 17 to 98 years). 37/376 CXR exams (10%) exhibited the characteristic COVID-19 appearance; 215/376 (57%) exhibited the nonspecific appearance; and 124/376 (33%) were considered negative for a pulmonary abnormality. Of the 376 RT-PCR tests evaluated, 200/376 (53%) were positive and 176/376 (47%) were negative. RT-PCR tests took an average of 2.5 ± 0.7 days to result. Sensitivity and specificity for correctly identifying COVID-19 with a characteristic CXR pattern were 15.5% (31/200) and 96.6% (170/176), with PPV and NPV 83.8% (31/37) and 50.1% (170/339), respectively. CONCLUSION: The presence of patchy and/or confluent, bandlike ground glass opacity or consolidation in a peripheral and mid-to-lower lung zone distribution on a chest radiograph obtained in the setting of pandemic COVID-19 is highly suggestive of SARS-CoV-2 infection and should be used in conjunction with clinical judgement to make a diagnosis. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7605076/ doi: 10.1148/ryct.2020200280 id: cord-274892-a6fscyjf author: Smith, Joseph A. title: Identification and isolation of a novel herpesvirus in a captive mob of eastern grey kangaroos (Macropus giganteus) date: 2008-06-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A novel herpesvirus was detected in a captive mob of eastern grey kangaroos (Macropus giganteus) during diagnostic workup for individuals with ulcerative cloacitis. Virus was initially detected in tissues using a consensus herpesvirus PCR. No viral inclusions or particles had been evident in routine histologic or transmission electron microscopic sections of cloacal lesions. Virus was isolated from samples and transmission electron microscopy of the resulting isolates confirmed that the virus was morphologically consistent with a herpesvirus. Nucleotide sequencing of the PCR product from tissue samples and from the isolates revealed that the virus was in the subfamily Gammaherpesvirinae and was distinct from other known herpesviruses. The correlation between the lesions and the novel virus remains unknown. Two herpesviruses, both in the subfamily Alphaherpesvirinae, have previously been described in macropods and are known to cause systemic clinical disease. This is the first reported gammaherpesvirus within the order Marsupialia, and may provide valuable information regarding the evolution and phylogeny of this virus family. Based on current herpesvirus nomenclature convention, the authors propose the novel herpesvirus be named Macropodid herpesvirus 3 (MaHV-3). url: https://api.elsevier.com/content/article/pii/S0378113507005731 doi: 10.1016/j.vetmic.2007.11.019 id: cord-103163-0rreoh4o author: Smith, Sydni Caet title: Reovirus RNA recombination is sequence directed and generates internally deleted defective genome segments during passage date: 2020-10-22 words: 8965.0 sentences: 456.0 pages: flesch: 46.0 cache: ./cache/cord-103163-0rreoh4o.txt txt: ./txt/cord-103163-0rreoh4o.txt summary: We determined the titers and RNA segment profiles of reovirus (rsT1L and rsT3D I ) and rotavirus (rsSA11) laboratory strains that had been rescued by reverse genetics then serially passaged ten times, each in triplicate lineages, in cultured cells. The two reoviruses accumulated non-canonical RNAs that retain 5′ and 3′ termini and feature one or more large internal deletions, while the rotavirus rarely accumulated such DVGs. Analyses of next-generation RNA-sequencing data sets from purified rsT1L reovirus RNA revealed many junctions, with hot spots for recombination in specific viral gene segments. Taken together, lin1 RNA profiles suggest non-canonical RNA species that differ in length but have identical termini to the parental segments accumulate variably during reovirus and rotavirus serial passage in cultured cells. abstract: For viruses with segmented genomes, genetic diversity is generated by genetic drift, reassortment, and recombination. Recombination produces RNA populations distinct from full-length gene segments and can influence viral population dynamics, persistence, and host immune responses. Viruses in the Reoviridae family, including rotavirus and mammalian orthoreovirus (reovirus), have been reported to package segments containing rearrangements or internal deletions. Rotaviruses with RNA segments containing rearrangements have been isolated from immunocompromised and immunocompetent children and in vitro following serial passage at high multiplicity. Reoviruses that package small, defective RNA segments have established chronic infections in cells and in mice. However, the mechanism and extent of Reoviridae RNA recombination are undefined. Towards filling this gap in knowledge, we determined the titers and RNA segment profiles for reovirus and rotavirus following serial passage in cultured cells. The viruses exhibited occasional titer reductions characteristic of interference. Reovirus strains frequently accumulated segments that retained 5′ and 3′ terminal sequences and featured large internal deletions, while similar segments were rarely detected in rotavirus populations. Using next-generation RNA-sequencing to analyze RNA molecules packaged in purified reovirus particles, we identified distinct recombination sites within individual viral gene segments. Recombination junction sites were frequently associated with short regions of identical sequence. Taken together, these findings suggest that reovirus accumulates defective gene segments featuring internal deletions during passage and undergoes sequence-directed recombination at distinct sites. IMPORTANCE Viruses in the Reoviridae family include important pathogens of humans and other animals and have segmented RNA genomes. Recombination in RNA virus populations can facilitate novel host exploration and increased disease severity. The extent, patterns, and mechanisms of Reoviridae recombination and the functions and effects of recombined RNA products are poorly understood. Here, we provide evidence that mammalian orthoreovirus regularly synthesizes RNA recombination products that retain terminal sequences but contain internal deletions, while rotavirus rarely synthesizes such products. Recombination occurs more frequently at specific sites in the mammalian orthoreovirus genome, and short regions of identical sequence are often detected at junction sites. These findings suggest that mammalian orthoreovirus recombination events are directed in part by RNA sequences. An improved understanding of recombined viral RNA synthesis may enhance our capacity to engineer improved vaccines and virotherapies in the future. url: https://doi.org/10.1101/2020.10.19.346031 doi: 10.1101/2020.10.19.346031 id: cord-322184-kgv9f58a author: Sohn, Yujin title: Assessing Viral Shedding and Infectivity of Asymptomatic or Mildly Symptomatic Patients with COVID-19 in a Later Phase date: 2020-09-10 words: 3476.0 sentences: 182.0 pages: flesch: 55.0 cache: ./cache/cord-322184-kgv9f58a.txt txt: ./txt/cord-322184-kgv9f58a.txt summary: Conclusions: In conclusion, our study suggests that even if viral shedding is sustained in asymptomatic or mildly symptomatic patients with later phase of COVID-19, it can be expected that the transmission risk of the virus is low. In this study, we attempted to confirm the presence of viable virus by performing RT-PCR assay and culture using salivary and nasopharyngeal swabs of asymptomatic or mildly symptomatic COVID-19 patients who had been diagnosed with the disease and admitted to a CTC at least two weeks previously. Therefore, based on the evidence that the virus is rarely detected in respiratory specimens after 10 days following the onset of symptoms, especially in mild or asymptomatic cases of SARS-CoV-2 infection, even if viral shedding is sustained in the later phase of COVID-19, it can be expected that the transmission risk of the virus is low. abstract: Background: The coronavirus disease (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a major global public health issue. SARS-CoV-2 infection is confirmed by the detection of viral RNA using reverse transcription polymerase chain reaction (RT-PCR). Prolonged viral shedding has been reported in patients with SARS-CoV-2 infection, but the presence of viral RNA does not always correlate with infectivity. Therefore, the present study aimed to confirm the presence of viable virus in asymptomatic or mildly symptomatic patients in the later phase of the disease, more than two weeks after diagnosis. Method: Asymptomatic or mildly symptomatic COVID-19 patients who had been diagnosed with the disease at least two weeks previously and admitted to a community treatment center (CTC) from 15 March to 10 April 2020 were enrolled in this study. Nasopharyngeal and salivary swab specimens were collected from each patient. Using these specimens, RT-PCR assay and viral culture were performed. Result: In total, 48 patients were enrolled in this study. There were no significant differences in baseline characteristics between the asymptomatic and mildly symptomatic patient groups. RT-PCR assay and viral culture of SARS-CoV-2 were performed using nasopharyngeal and salivary swabs. The results of RT-PCR performed using salivary swab specimens, in terms of cycle threshold (Ct) values, were similar to those of RT-PCR using nasopharyngeal swab specimens. In addition, no viable virus could be cultured from swab specimens collected from the late-phase COVID-19 patients with prolonged viral RNA shedding. Conclusions: In conclusion, our study suggests that even if viral shedding is sustained in asymptomatic or mildly symptomatic patients with later phase of COVID-19, it can be expected that the transmission risk of the virus is low. In addition, saliva can be used as a reliable specimen for the diagnosis of SARS-CoV-2 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32927798/ doi: 10.3390/jcm9092924 id: cord-309644-cujlpm4i author: Sola, Augusto title: COVID-19 perinatal en América Latina date: 2020-07-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVE. To evaluate and report the clinical characteristics and outcomes of SARS-CoV-2 infection in pregnant women and newborns in Latin America. METHODS. Descriptive study based on the prospective report of the units of the Ibero-American Society of Neonatology Network. RESULTS. Of 86 pregnant women with COVID-19 confirmed by RT-PCR in seven countries (6 from Latin America, and Equatorial Guinea) 68% (59) were asymptomatic. Of 32% of symptomatic women, 89% (24) had mild symptoms and 3.5% (3) had severe respiratory symptoms. No women died. The cesarean section rate was 38%; gestational age was < 37 weeks in 6% of cases. RT-PCR was performed on all newborns between 16 and 36 hours of age; 6 (7%) were positive. All of them presented mild and transient respiratory distress; none died. Two newborns with negative RT-PCR died from other causes. Breastfeeding was authorized in only 24% of mothers; in 13% milk was expressed and 63% of newborns were fed with formula. In 76% of cases the motherchild pair was separated, and in 95% of cases the mother could not be accompanied at delivery or during the postpartum period. CONCLUSIONS. The lack of maternal accompaniment, the low rate of breastfeeding and the frequent separation of the mother-child dyad are of concern. The health care team must reflect on the need to defend humanized and family-centered care during this pandemic. url: https://doi.org/10.26633/rpsp.2020.47 doi: 10.26633/rpsp.2020.47 id: cord-290456-cgrn5c36 author: Soliman, Mohamed A. R. title: Endoscopic endonasal skull base surgery during the COVID-19 pandemic: A developing country perspective date: 2020-09-25 words: 4102.0 sentences: 241.0 pages: flesch: 51.0 cache: ./cache/cord-290456-cgrn5c36.txt txt: ./txt/cord-290456-cgrn5c36.txt summary: [16] e aim of this study is to present the current situation from a developing country perspective in dealing with emergency endoscopic endonasal skull base surgeries at the time of the COVID-19 pandemic in terms of preoperative patients'' screening, surgical techniques, and intraoperative PPE utilization. e survey consisted of 12 questions designed to explore three domains; patients'' information (age, clinical manifestations [neurological and COVID-19 related], diagnosis, preoperative COVID-19 screening, and COVID-19 symptoms during the first 3 weeks postsurgery), surgical team information (age, chronic medical conditions, and COVID-19 symptoms during the first 3 weeks postsurgery), and operative information (PPE utilization and basal craniectomy). ere was only one surgeon who developed a high-grade fever, malaise, and bony aches in the first 3 days after surgery who had undergone two nasopharyngeal swabs with RT-PCR testing 1 week apart and both came back negative representing 2.1% of the surgical team members [ Figure 2c ]. abstract: BACKGROUND: Although primarily a respiratory disorder, the coronavirus pandemic has paralyzed almost all aspects of health-care delivery. Emergency procedures are likely continuing in most countries, however, some of them raises certain concerns to the surgeons such as the endoscopic endonasal skull base surgeries. The aim of this study is to present the current situation from a developing country perspective in dealing with such cases at the time of the COVID-19 pandemic. METHODS: A cross-sectional analytical survey was distributed among neurosurgeons who performed emergency surgeries during the COVID-19 pandemic in Cairo, Egypt, between May 8, 2020, and June 7, 2020. The survey entailed patients’ information (demographics, preoperative screening, and postoperative COVID-19 symptoms), surgical team information (demographics and postoperative COVID-19 symptoms), and operative information (personal protective equipment [PPE] utilization and basal craniectomy). RESULTS: Our survey was completed on June 7, 2020 (16 completed, 100% response rate). The patients were screened for COVID-19 preoperatively through complete blood cell (CBC) (100%), computed tomography (CT) chest (68.8%), chest examination (50%), C-reactive protein (CRP) (50%), and serological testing (6.3%). Only 18.8% of the surgical team utilized N95 mask and goggles, 12.5% utilized face shield, and none used PAPRs. Regarding the basal craniectomy, 81.3% used Kerrison Rongeur and chisel, 25% used a high-speed drill, and 6.3% used a mucosal shaver. None of the patients developed any COVID-19 symptoms during the first 3 weeks postsurgery and one of the surgeons developed high fever with negative nasopharyngeal swabs. CONCLUSION: In developing countries with limited resources, preoperative screening using chest examination, CBC, and CT chest might be sufficient to replace Reverse transcription polymerase chain reaction. Developing countries require adequate support with screening tests, PPE, and critical care equipment such as ventilators. url: https://www.ncbi.nlm.nih.gov/pubmed/33093987/ doi: 10.25259/sni_547_2020 id: cord-312456-6lxc2rj2 author: Soltan, Mohamed A. title: Comparison of electron microscopy, ELISA, real time RT-PCR and insulated isothermal RT-PCR for the detection of Rotavirus group A (RVA) in feces of different animal species date: 2016-05-11 words: 4209.0 sentences: 218.0 pages: flesch: 53.0 cache: ./cache/cord-312456-6lxc2rj2.txt txt: ./txt/cord-312456-6lxc2rj2.txt summary: title: Comparison of electron microscopy, ELISA, real time RT-PCR and insulated isothermal RT-PCR for the detection of Rotavirus group A (RVA) in feces of different animal species The aim of this investigation was to evaluate a commercially available RT-iiPCR assay for RVA detection in feces from different animal species. Therefore, the aim of our investigation was to evaluate a recently available insulated isothermal RT-PCR (RT-iiPCR) reagent set (POCKIT TM Rotavirus A Reagent Set, GeneReach USA, Lexington, MA, USA) with use of a portable PCR machine, which could potentially be used for point-of-need detection for RVA in the feces of different animal species. Additionally, the sensitivity of the rotavirus RT-iiPCR reagent set was evaluated by comparison with the commercially available rtRT-PCR assay using 10-fold serial dilutions of nucleic acid extracted from a positive bovine clinical sample. There was a significant difference in the number of positive samples detected with the in-house rtRT-PCR assay versus the other two molecular tests. abstract: There is no gold standard for detection of Rotavirus Group A (RVA), one of the main causes of diarrhea in neonatal animals. Sensitive and specific real-time RT-PCR (rtRT-PCR) assays are available for RVA but require submission of the clinical samples to diagnostic laboratories. Patient-side immunoassays for RVA protein detection have shown variable results, particularly with samples from unintended species. A sensitive and specific test for detection of RVA on the farm would facilitate rapid management decisions. The insulated isothermal RT-PCR (RT-iiPCR) assay works in a portable machine to allow sensitive and specific on-site testing. The aim of this investigation was to evaluate a commercially available RT-iiPCR assay for RVA detection in feces from different animal species. This assay was compared to an in-house rtRT-PCR assay and a commercially available rtRT-PCR kit, as well as an ELISA and EM for RVA detection. All three PCR assays targeted the well-conserved NSP5 gene. Clinical fecal samples from 108 diarrheic animals (mainly cattle and horses) were tested. The percentage of positive samples by ELISA, EM, in-house rtRT-PCR, commercial rtRT-PCR, and RT-iiPCR was 29.4%, 31%, 36.7%, 51.4%, 56.9%, respectively. The agreement between different assays was high (81.3–100%) in samples containing high viral loads. The sensitivity of the RT-iiPCR assay appeared to be higher than the commercially available rtRT-PCR assay, with a limit of detection (95% confidence index) of 3–4 copies of in vitro transcribed dsRNA. In conclusion, the user-friendly, field-deployable RT-iiPCR system holds substantial promise for on-site detection of RVA. url: https://www.ncbi.nlm.nih.gov/pubmed/27180038/ doi: 10.1016/j.jviromet.2016.05.006 id: cord-256702-lwxt4587 author: Song, Lingjie title: A case of SARS-CoV-2 carrier for 32 days with several times false negative nucleic acid tests date: 2020-04-06 words: 2037.0 sentences: 144.0 pages: flesch: 57.0 cache: ./cache/cord-256702-lwxt4587.txt txt: ./txt/cord-256702-lwxt4587.txt summary: title: A case of SARS-CoV-2 carrier for 32 days with several times false negative nucleic acid tests After the onset of clinical symptoms, chest CT results showed patchy ground-glass opacity (GGO) in her lungs, but it took a total of nine nucleic acid tests to confirm the diagnosis, among which the first eight RT-PCR results were negative or single-target positive. Although the nucleic acid test was negative or single-target positive, the low number of white blood cells and lymphocytes in laboratory tests, and GGO in the lungs by CT examination indicated SARS-CoV-2 infection. https://doi.org/10.1101/2020.03.31.20045401 doi: medRxiv preprint pathogenic nucleic acid genomes from samples of asymptomatic and occult infected patients is also conducive to studying the virus mutations in the pathogenic genes providing a basis for subsequent virus tracing and epidemiological investigations. We report the epidemiological history and clinical information of a patient with negative (or single-target positive) SARS-CoV-2 infection with multiple RT-PCR tests. abstract: In 2019, a novel coronavirus (SARS-CoV-2) was first discovered in Wuhan, Hubei, China, causing severe respiratory disease in humans, and has been identified as a public health emergency of international concern. With the spread of the virus, there are more and more false negative cases of RT-PCR nucleic acid detection in the early stage of potential infection. In this paper, we collected the epidemiological history, clinical manifestations, outcomes, laboratory results and images of a SARS-CoV-2 carrier with no significant past medical history. The patient was quarantined because of her colleague had been diagnosed. After the onset of clinical symptoms, chest CT results showed patchy ground-glass opacity (GGO) in her lungs, but it took a total of nine nucleic acid tests to confirm the diagnosis, among which the first eight RT-PCR results were negative or single-target positive. In addition to coughing up phlegm during her stay in the hospital, she did not develop chills, fever, abdominal pain, diarrhea and other clinical symptoms. Since initial antiviral treatment, the lung lesions were absorbed. But the sputum nucleic acid test was still positive. In combination with antiviral and immune therapy, the patient tested negative for the virus. Notably, SARS-CoV-2 was detected only in the lower respiratory tract samples (sputum) throughout the diagnosis and treatment period. This is a confirmed case of SARS-CoV-2 infection with common symptoms, and her diagnosis has undergone multiple false negatives ,suggesting that it is difficult to identify certain carriers of the virus and that such patients may also increase the spread of the SARS-CoV-2. url: https://doi.org/10.1101/2020.03.31.20045401 doi: 10.1101/2020.03.31.20045401 id: cord-296593-ox6x53vj author: Sonoo, M. title: Correlation between PCR Examination Rate among the Population and the Containment of Pandemic of COVID-19 date: 2020-05-16 words: 1081.0 sentences: 81.0 pages: flesch: 58.0 cache: ./cache/cord-296593-ox6x53vj.txt txt: ./txt/cord-296593-ox6x53vj.txt summary: We investigated the relation between PCR examination rate among population and the success of containment of COVID-19. We investigated the relation between PCR examination rate among population and the success of containment of COVID-19. Close inspection of individual countries suggested that the social distancing is the largest factor to achieve containment, and the contribution of broad PCR tests is smaller. Close inspection of individual countries suggested that the social distancing is the largest factor to achieve containment, and the contribution of broad PCR tests is smaller. . https://doi.org/10.1101/2020.05.13.20100982 doi: medRxiv preprint Coronavirus disease 2019 (COVID-19) pandemic is now a worldwide peril and its control is an emergent issue. Trajectory analysis of new coronavirus COVID-19 cases and deaths by country No reuse allowed without permission.(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. abstract: We investigated the relation between PCR examination rate among population and the success of containment of COVID-19. Although there was moderate negative correlation, the effect cannot be separated from that of Gross Domestic Product per capita (GDP), which may well be related to the strict compliance to social distancing. Close inspection of individual countries suggested that the social distancing is the largest factor to achieve containment, and the contribution of broad PCR tests is smaller. url: https://doi.org/10.1101/2020.05.13.20100982 doi: 10.1101/2020.05.13.20100982 id: cord-305008-8gl9d79i author: Sousa, T. C. M. d. title: Socioeconomic Vulnerabilities and the Intensity of RT-PCR SARS-CoV-2 Testing Efforts in the Public Health System in Sao Paulo State date: 2020-11-03 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Background The testing of infected persons with SARS-CoV-2 is one of the cornerstones to deploy pandemic control strategies. The public diagnostic effort is particularly important among the most vulnerable socioeconomic districts where the state is the sole health provider, such as Sao Paulo state, the Brazilian epicenter of the COVID-19 pandemic. Methods We developed an RT-PCR testing intensity effort index (RT-PCR TIEI) composed of seven indicators to assess the intensity testing efforts in the state of Sao Paulo. Each Regional Health Department (RHD) was scored using anonymized public data. We used dynamic time-series cross-sectional models to analyze the association between the RT-PCR TIEI in Sao Paulo state and its 17 RHDs from epidemiological weeks 10 to 35, and the proportion of the population living under a high level of socioeconomic vulnerability, dependent on public health service (SUS), per capita income, and population density. The regression models included an intercept and the lag of the RT-PCR TIEI, and standard errors were clustered by RHD. Findings On average, the RT-PCR TIEI score was 23.50. The maximum (47.06) was reached in week 11 and declined in subsequent weeks. The lowest score (17.65) was reached in week 25. In the long-run, socioeconomic vulnerability is negatively associated with RT-PCR TIEI (p-value=0.000, 95% CI -0.896, -0.816), with a higher proportion of the population dependent on SUS (p-value= 0.000, 95% CI -0.877, 0.808) and with population density (p-value=0.000, 95% CI -0.857; -0.806). Conclusion There was a decline in the state's testing intensity as the pandemic advanced, and the most socioeconomic vulnerable RHDs showed the lowest values where local public laboratory presence is a predictor of a higher RT-PCR TIEI score. Thus, the low RT-PCR TIEI and local laboratory capacity inequality may affect surveillance capability, especially for the most socioeconomic vulnerable population. url: https://doi.org/10.1101/2020.10.29.20221960 doi: 10.1101/2020.10.29.20221960 id: cord-336636-xgfw21hk author: Spezia, Pietro Giorgio title: Redondovirus DNA in human respiratory samples date: 2020-08-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract Background Redondovirus (ReDoV) is a recently discovered circular, Rep-encoding single-stranded DNA (CRESS-DNA) virus in humans. Its pathogenesis and clinical associations are still completely unknown. Methods The presence of ReDoV DNA was investigated in biological specimens of 543 Italian subjects by in-house developed PCR assays. Results The overall ReDoV prevalence was about 4% (23 of 543 samples). The virus was detected in 22 of 209 (11 %) respiratory samples. One stool sample was also ReDoV positive. Viral DNA was not found in blood samples from immunocompetent and immunosuppressed subjects and cerebrospinal fluids from patients with neurological diseases. Genomic nucleotide differences were detected among the ReDoV isolates by sequencing a 582-nucleotide fragment of the capsid gene of the viral genome. Conclusions The results demonstrate that ReDoV is mainly present in the respiratory tract of infected people. Further investigations are needed to reveal possible clinical implications of this new CRESS-DNA virus in humans. url: https://www.ncbi.nlm.nih.gov/pubmed/32841923/ doi: 10.1016/j.jcv.2020.104586 id: cord-301823-fbeb1nw1 author: Sridhar, Sushmita title: A blueprint for the implementation of a validated approach for the detection of SARS-Cov2 in clinical samples in academic facilities date: 2020-10-21 words: 6118.0 sentences: 309.0 pages: flesch: 51.0 cache: ./cache/cord-301823-fbeb1nw1.txt txt: ./txt/cord-301823-fbeb1nw1.txt summary: Here we describe our experience in establishing a COVID-19 diagnostics laboratory in an academic containment level 2 (CL2) research facility (UK) in which we validated and established a real-time PCR workflow to detect SARS-CoV2 in nose and throat swabs from HCWs. We developed an assay and workflow over eight working days (set-up to validation to screening) that can produce a quantitative diagnostic result ~4 hours after swabbing. Establishing and validating the workflow in our setting Establishing a workflow for SARS-Cov2 qRT-PCR Upon the decision to rapidly establish the qRT-PCR assay we identified several challenges, and these included: a) establishment and validation of a method suitable for diagnostic reporting, b) safe extraction of nucleic acid from a highly transmissible virus, c) accessing reagents required for performing extractions and amplifications, d) establishing a "clean" diagnostic workflow to minimise the risk of contamination, and e) creating a system in which HCWs could be swabbed and the data reported confidentially within a specified timeframe. abstract: The COVID-19 pandemic is expanding at an unprecedented rate. As a result, diagnostic services are stretched to their limit, and there is a clear need for the provision of additional diagnostic capacity. Academic laboratories, many of which are closed due to governmental lockdowns, may be in a position to support local screening capacity by adapting their current laboratory practices. Here, we describe the process of developing a SARS-Cov2 diagnostic workflow in a conventional academic Containment Level 2 laboratory. Our outline includes simple SARS-Cov2 deactivation upon contact, the method for a quantitative real-time reverse transcriptase PCR detecting SARS-Cov2, a description of process establishment and validation, and some considerations for establishing a similar workflow elsewhere. This was achieved under challenging circumstances through the collaborative efforts of scientists, clinical staff, and diagnostic staff to mitigate to the ongoing crisis. Within 14 days, we created a validated COVID-19 diagnostics service for healthcare workers in our local hospital. The described methods are not exhaustive, but we hope may offer support to other academic groups aiming to set up something comparable in a short time frame. url: https://www.ncbi.nlm.nih.gov/pubmed/33134554/ doi: 10.12688/wellcomeopenres.15937.2 id: cord-001655-uqw74ra0 author: Stenglein, Mark D. title: Widespread Recombination, Reassortment, and Transmission of Unbalanced Compound Viral Genotypes in Natural Arenavirus Infections date: 2015-05-20 words: 8100.0 sentences: 479.0 pages: flesch: 48.0 cache: ./cache/cord-001655-uqw74ra0.txt txt: ./txt/cord-001655-uqw74ra0.txt summary: The sets of viral genotypes ranged from that which would be expected for a straightforward co-infection by 2 virus strains in snake #45, to more complex combinations such as that in snake #33, which contained the sequences of 1 S and 10 distinct L segments. We applied homogenates from samples to cultures of boa constrictor-derived JK cells and monitored levels of virus RNA by qRT-PCR using genotype-discriminating primers. Thus, sequences of multiple viral genotypes Recombinant genome segments with unusual organizations. Virus populations replicate as stable ensembles in culture: (A) Liver homogenate from snake #38 was applied to cultures of JK cells and replication was monitored by measuring supernatant viral RNA levels using qRT-PCR and genotype-specific primers. Although we detected many instances of snake tissues containing multiple viral genotypes, our results do not prove that individual cells in these animals were multiply infected. abstract: Arenaviruses are one of the largest families of human hemorrhagic fever viruses and are known to infect both mammals and snakes. Arenaviruses package a large (L) and small (S) genome segment in their virions. For segmented RNA viruses like these, novel genotypes can be generated through mutation, recombination, and reassortment. Although it is believed that an ancient recombination event led to the emergence of a new lineage of mammalian arenaviruses, neither recombination nor reassortment has been definitively documented in natural arenavirus infections. Here, we used metagenomic sequencing to survey the viral diversity present in captive arenavirus-infected snakes. From 48 infected animals, we determined the complete or near complete sequence of 210 genome segments that grouped into 23 L and 11 S genotypes. The majority of snakes were multiply infected, with up to 4 distinct S and 11 distinct L segment genotypes in individual animals. This S/L imbalance was typical: in all cases intrahost L segment genotypes outnumbered S genotypes, and a particular S segment genotype dominated in individual animals and at a population level. We corroborated sequencing results by qRT-PCR and virus isolation, and isolates replicated as ensembles in culture. Numerous instances of recombination and reassortment were detected, including recombinant segments with unusual organizations featuring 2 intergenic regions and superfluous content, which were capable of stable replication and transmission despite their atypical structures. Overall, this represents intrahost diversity of an extent and form that goes well beyond what has been observed for arenaviruses or for viruses in general. This diversity can be plausibly attributed to the captive intermingling of sub-clinically infected wild-caught snakes. Thus, beyond providing a unique opportunity to study arenavirus evolution and adaptation, these findings allow the investigation of unintended anthropogenic impacts on viral ecology, diversity, and disease potential. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4438980/ doi: 10.1371/journal.ppat.1004900 id: cord-290513-ygqin14x author: Stevens, Barry J. title: Reporting radiographers’ interpretation and use of the British Society of Thoracic Imaging’s coding system when reporting COVID-19 chest x-rays date: 2020-06-18 words: 2443.0 sentences: 139.0 pages: flesch: 51.0 cache: ./cache/cord-290513-ygqin14x.txt txt: ./txt/cord-290513-ygqin14x.txt summary: title: Reporting radiographers'' interpretation and use of the British Society of Thoracic Imaging''s coding system when reporting COVID-19 chest x-rays Methodology Retrospective review of CXR reports by radiographers for suspected COVID-19 patients attending the Emergency Department (ED) of a hospital in the UK. The criteria for inclusion were; adult patients attending the ED with the diagnostic question querying COVID-19, with a BSTI code in the report and an initial RT-PCR swab result. The fact that the reporting team and Radiologist arbiter reached agreement that the 18 false negative reports with code CVCX0 all had normal appearances, despite returning a positive RT-PCR result, corroborates findings from previous work suggesting that there may be no radiographic features in early or mild disease 7,10,21 . Correlation of Chest CT and RT-PCR Testing in Coronavirus Disease 2019 (COVID-19) in China: A Report of 1014 Cases abstract: Abstract Introduction The United Kingdom (UK) has experienced one of the worst initial waves of the COVID-19 pandemic. Clinical signs help guide initial diagnosis, though definitive diagnosis is made using the laboratory technique reverse transcription polymerase chain reaction (RT-PCR). The chest x-ray (CXR) is used as the primary imaging investigation in the United Kingdom (UK) for patients with suspected COVID-19. In some hospitals these CXRs may be reported by a radiographer. Methodology Retrospective review of CXR reports by radiographers for suspected COVID-19 patients attending the Emergency Department (ED) of a hospital in the UK. Interpretation and use of the British Society of Thoracic Imaging (BSTI) coding system was assessed. Report description and code use were cross-checked. Report and code usage were checked against the RT-PCR result to determine accuracy. Report availability was checked against the availability of the RT-PCR result. A confusion matrix was utilised to determine performance. The data were analysed manually using Excel. Results Sample size was 320 patients; 54.1% male patients (n = 173), 45.9% female patients (n = 147). The correct code matched report descriptions in 316 of the 320 cases (98.8%). In 299 of the 320 cases (93.4%), the reports were available before the RT-PCR swab result. CXR sensitivity for detecting COVID-19 was 85% compared to 93% for the initial RT-PCR. Conclusion Reporting radiographers can adequately utilise and apply the BSTI classification system when reporting COVID-19 CXRs. They can recognise the classic CXR appearances of COVID-19 and those with normal appearances. Future best practice includes checking laboratory results when reporting CXRs with ambiguous appearances. Implications for practice Utilisation of reporting radiographers to report CXRs in any future respiratory pandemic should be considered a service-enabling development. url: https://doi.org/10.1016/j.radi.2020.06.010 doi: 10.1016/j.radi.2020.06.010 id: cord-018848-6kemhsyu author: Stürenburg, Enno title: Mikrobiologische Schnelltests und molekularbiologische Analytik date: 2011-12-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Die meisten der derzeit am Markt verfügbaren mikrobiologischen Schnelltests basieren auf immunologischen Nachweisverfahren. Charakteristisch für alle immunologischen Verfahren ist, dass sie auf einer hochspezifischen Antigen-Antikörper-Reaktion beruhen. Mittels dieses immunologischen Prinzips ist sowohl der qualitative Nachweis eines Analyten als auch die quantitative Bestimmung seiner Konzentration möglich. Der Testaufbau eines immunchemischen Tests kann besonders hinsichtlich der Entstehung und Auswertung der Testsignale erheblich variieren. Bewährte und für mikrobiologische Schnelltests häufig benutzte Formate sind die Partikelagglutination und die Immunchromatographie sowie die daraus hervorgegangenen Weiterentwicklungen, beispielsweise der optische Immunoassay. Auf Basis von Nukleinsäure-Amplifikationstechniken (vor allem der Polymerase- Kettenreaktion, PCR) sind bislang nur wenige POC-Tests verfügbar; ihre Praktikabilität und Bewährung in der Praxis wird sich erst in den nächsten Jahren zeigen. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123834/ doi: 10.1007/978-3-642-20172-1_11 id: cord-309083-ew9cwiw0 author: Su, Hang title: Cyprinid viral diseases and vaccine development date: 2018-09-07 words: 11167.0 sentences: 585.0 pages: flesch: 43.0 cache: ./cache/cord-309083-ew9cwiw0.txt txt: ./txt/cord-309083-ew9cwiw0.txt summary: In this review, authors summarized six major cyprinid viral diseases, including koi herpesvirus disease (KHVD), spring viraemia of carp (SVC), grass carp hemorrhagic disease (GCHD), koi sleepy disease (KSD), carp pox disease (CPD) and herpesviral haematopoietic necrosis (HPHN). Challenge experiment reveals that the oral recombinant subunit vaccine can protect 50%-60% grass carp from infection and generate immunity against GCRV [199] . Oral vaccination is an effective way to induce mucosal immunity [215] and this strategy has shown a successful induction of the antiviral responses against viral diseases in different fish species [165] . Gene expression analysis of common carp (Cyprinus carpio L.) lines during cyprinid herpesvirus 3 infection yields insights into differential immune responses Recombinant lactobacillus expressing G protein of spring viremia of carp virus (SVCV) combined with ORF81 protein of koi herpesvirus (KHV): a promising way to induce protective immunity against SVCV and KHV infection in cyprinid fish via oral vaccination abstract: In the past decades, global freshwater fish production has been rapidly growing, while cyprinid takes the largest portion. Along with the rapid rise of novel forms of intensive aquaculture, increased global aquatic animal movement and various anthropogenic stress to aquatic ecosystems during the past century, freshwater fish farming industry encounter the emergence and breakout of many diseases, especially viral diseases. Because of the ability to safely and effectively prevent aquaculture diseases, vaccines have become the mainstream technology for prevention and control of aquatic diseases in the world. In this review, authors summarized six major cyprinid viral diseases, including koi herpesvirus disease (KHVD), spring viraemia of carp (SVC), grass carp hemorrhagic disease (GCHD), koi sleepy disease (KSD), carp pox disease (CPD) and herpesviral haematopoietic necrosis (HPHN). The present review described the characteristics of these diseases from epidemiology, pathology, etiology and diagnostics. Furthermore, the development of specific vaccines respective to these diseases is stated according to preparation methods and immunization approaches. It is hoped that the review could contribute to aquaculture in prevention and controlling of cyprinid viral diseases, and serve the healthy and sustainable development of aquaculture industry. url: https://api.elsevier.com/content/article/pii/S1050464818305394 doi: 10.1016/j.fsi.2018.09.003 id: cord-030191-tekgcthp author: Suchá, Dominika title: Suboptimal Quality and High Risk of Bias in Diagnostic Test Accuracy Studies on Chest Radiography and Computed Tomography in the Acute Setting of the COVID-19 Pandemic: A Systematic Review date: 2020-07-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: PURPOSE: Chest imaging techniques have been implemented for screening and diagnosis of COVID-19 patients, based on experience with other viral pneumonias and a handful of COVID-19 diagnostic test accuracy (DTA) studies. We performed a systematic review to synthesize the literature on DTA of chest radiography (CXR), computed tomography (CT) and ultrasound for diagnosis of COVID-19 in suspected patients in hospital setting and evaluated the extent of suboptimal reporting and risk-of-bias. METHODS: A systematic search was performed (April 26, 2020) in Embase, Pubmed and Cochrane to identify CXR, CT or ultrasound studies in adult patients with suspected COVID-19, using RT-PCR or clinical consensus as reference standard. 2x2 contingency tables were reconstructed and test sensitivity, specificity, positive predictive values (PPV) and negative predictive values (NPV) re-calculated. Reporting quality was evaluated by adherence to STARD and risk-of-bias by QUADAS-2. RESULTS: Thirteen studies were eligible (CT=12, CXR=1, US=0). Re-calculated CT sensitivity and specificity ranged between 0.57-0.97 and 0.37-0.94, respectively, PPV and NPV between 0.59-0.92 and 0.57-0.96, respectively. On average studies complied with only 35% of the STARD-guideline items. No study scored low risk-of-bias for all QUADAS-2 domains (patient selection, index test, reference test, flow and timing). High risk-of-bias in ≥one domain was scored in 10/13 studies (77%). CONCLUSION: Reported CT test accuracy for COVID-19 diagnosis varies substantially. Validity and generalizability of these findings is complicated by poor adherence to reporting guidelines and high risk-of-bias, which are most likely due to the need for urgent publication of findings in the first months of the COVID-19 pandemic. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7393956/ doi: 10.1148/ryct.2020200342 id: cord-330602-g0xaonxv author: Sugiura, Hiroaki title: Prescription Surveillance and Polymerase Chain Reaction Testing to Identify Pathogens during Outbreaks of Infection date: 2013-02-07 words: 3231.0 sentences: 150.0 pages: flesch: 34.0 cache: ./cache/cord-330602-g0xaonxv.txt txt: ./txt/cord-330602-g0xaonxv.txt summary: Japanese traditional surveillance is based on definitive diagnosis and is enforced by the infection control laws in Japan for the early detection of agents of bioterrorism and outbreaks of emerging infectious diseases. The purpose of the present study was to evaluate whether the PCR method triggered by the results of the prescription surveillance system can rapidly and accurately identify causative pathogens of local outbreaks of infection. Between October 4 and 28, 2011, 50 patients were included in the present study who either presented at a single clinic with a chief complaint of respiratory symptoms or fever or were suspected of having respiratory tract infections after being identified through the syndromic prescription surveillance system. Here, we examined a combination of syndromic surveillance and PCR testing and showed the potential to identify pathogens during the early stage of an outbreak of respiratory infections. abstract: Syndromic surveillance, including prescription surveillance, offers a rapid method for the early detection of agents of bioterrorism and emerging infectious diseases. However, it has the disadvantage of not considering definitive diagnoses. Here, we attempted to definitively diagnose pathogens using polymerase chain reaction (PCR) immediately after the prescription surveillance system detected an outbreak. Specimens were collected from 50 patients with respiratory infections. PCR was used to identify the pathogens, which included 14 types of common respiratory viruses and Mycoplasma pneumoniae. Infectious agents including M. pneumoniae, respiratory syncytial virus (RSV), rhinovirus, enterovirus, and parainfluenza virus were detected in 54% of patients. For the rapid RSV diagnosis kit, sensitivity was 80% and specificity was 85%. For the rapid adenovirus diagnosis kit, no positive results were obtained; therefore, sensitivity could not be calculated and specificity was 100%. Many patients were found to be treated for upper respiratory tract infections without the diagnosis of a specific pathogen. In Japan, an outbreak of M. pneumoniae infection began in 2011, and our results suggested that this outbreak may have included false-positive cases. By combining syndromic surveillance and PCR, we were able to rapidly and accurately identify causative pathogens during a recent respiratory infection outbreak. url: https://doi.org/10.1155/2013/746053 doi: 10.1155/2013/746053 id: cord-002757-upwe0cpj author: Sullivan, Kathleen E. title: Emerging Infections and Pertinent Infections Related to Travel for Patients with Primary Immunodeficiencies date: 2017-08-07 words: 24212.0 sentences: 1364.0 pages: flesch: 40.0 cache: ./cache/cord-002757-upwe0cpj.txt txt: ./txt/cord-002757-upwe0cpj.txt summary: The first section addresses general considerations, the second section profiles specific infections organized according to mechanism of transmission, and the third section focuses on unique phenotypes and unique susceptibilities in patients with PIDDs. This review does not address most parasitic diseases. In developing countries where polio is still endemic and oral polio vaccine is essential for eradicating the disease, it is of utmost importance that all PIDD patients and family members should not receive live oral polio (OPV) because of the reported prolonged excretion of the virus for months and even years [24] . As for host factors, although severe and fatal cases have been described in healthy immunocompetent hosts [129, 130] , there is evidence to suggest that children under the age of 10 [130] and immunocompromised hosts either secondary to hematologic malignancies, immunosuppressant treatment for organ transplantation, or HIV infection are at a greater risk to develop more severe disease with higher case fatality rates [131, 132] . abstract: In today’s global economy and affordable vacation travel, it is increasingly important that visitors to another country and their physician be familiar with emerging infections, infections unique to a specific geographic region, and risks related to the process of travel. This is never more important than for patients with primary immunodeficiency disorders (PIDD). A recent review addressing common causes of fever in travelers provides important information for the general population Thwaites and Day (N Engl J Med 376:548-560, 2017). This review covers critical infectious and management concerns specifically related to travel for patients with PIDD. This review will discuss the context of the changing landscape of infections, highlight specific infections of concern, and profile distinct infection phenotypes in patients who are immune compromised. The organization of this review will address the environment driving emerging infections and several concerns unique to patients with PIDD. The first section addresses general considerations, the second section profiles specific infections organized according to mechanism of transmission, and the third section focuses on unique phenotypes and unique susceptibilities in patients with PIDDs. This review does not address most parasitic diseases. Reference tables provide easily accessible information on a broader range of infections than is described in the text. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5693703/ doi: 10.1007/s10875-017-0426-2 id: cord-308979-qhlvd2mt author: Sumino, Kaharu C. title: Detection of Severe Human Metapneumovirus Infection by Real-Time Polymerase Chain Reaction and Histopathological Assessment date: 2005-09-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BackgroundInfections with common respiratory tract viruses can cause high mortality, especially in immunocompromised hosts, but the impact of human metapneumovirus (hMPV) in this setting was previously unknown MethodsWe evaluated consecutive bronchoalveolar lavage and bronchial wash fluid samples from 688 patients—72% were immunocompromised and were predominantly lung transplant recipients—for hMPV by use of quantitative real-time polymerase chain reaction (PCR), and positive results were correlated with clinical outcome and results of viral cultures, in situ hybridization, and lung histopathological assessment ResultsSix cases of hMPV infection were identified, and they had a similar frequency and occurred in a similar age range as other paramyxoviral infections. Four of 6 infections occurred in immunocompromised patients. Infection was confirmed by in situ hybridization for the viral nucleocapsid gene. Histopathological assessment of lung tissue samples showed acute and organizing injury, and smudge cell formation was distinct from findings in infections with other paramyxoviruses. Each patient with high titers of hMPV exhibited a complicated clinical course requiring prolonged hospitalization ConclusionsOur results provide in situ evidence of hMPV infection in humans and suggest that hMPV is a cause of clinically severe lower respiratory tract infection that can be detected during bronchoscopy by use of real-time PCR and routine histopathological assessment url: https://www.ncbi.nlm.nih.gov/pubmed/16107959/ doi: 10.1086/432728 id: cord-331558-6rqd3fmj author: Sun, Chuan-bin title: Role of the Eye in Transmitting Human Coronavirus: What We Know and What We Do Not Know date: 2020-04-24 words: 5459.0 sentences: 234.0 pages: flesch: 48.0 cache: ./cache/cord-331558-6rqd3fmj.txt txt: ./txt/cord-331558-6rqd3fmj.txt summary: Although the conjunctiva is directly exposed to extraocular pathogens, and the mucosa of the ocular surface and upper respiratory tract are connected by the nasolacrimal duct and share the same entry receptors for some respiratory viruses, the eye is rarely involved in human CoV infection, conjunctivitis is quite rare in patients with 2019-nCoV infection, and the CoV RNA positive rate by RT-PCR test in tears and conjunctival secretions from patients with 2019-nCoV and SARS-CoV infection is also extremely low. Considering that close doctor-patient contact is quite common in ophthalmic practice and is apt to transmit human CoVs via droplets and fomites, strict hand hygiene and proper personal protection are highly recommended for health care workers to avoid hospital-related viral transmission during ophthalmic practice. Considering that close doctor-patient contact is quite common in ophthalmic practice and is apt to transmit human CoVs via droplets and fomites, strict hand hygiene and proper personal protection are highly recommended for health care workers to avoid hospital-related viral transmission during ophthalmic practice. abstract: The outbreak of the current 2019 novel coronavirus (2019-nCoV, now named SARS-CoV-2) infection has become a worldwide health threat. Currently, more information is needed so as to further understand the transmission and clinical characteristics of 2019-nCoV infection and the infection control procedures required. Recently, the role of the eye in transmitting 2019-nCoV has been intensively discussed. Previous investigations of other highly infectious human CoVs, that is, severe acute respiratory syndrome coronavirus (SARS-CoV) and the Middle East respiratory syndrome coronavirus (MERS-CoV), may provide useful information. In this review, we describe the genomics and morphology of human CoVs, the epidemiology, systemic and ophthalmic manifestations, and mechanisms of human CoV infection, and recommendations for infection control procedures. The role of the eye in the transmission of 2019-nCoV is discussed in detail. Although the conjunctiva is directly exposed to extraocular pathogens, and the mucosa of the ocular surface and upper respiratory tract are connected by the nasolacrimal duct and share the same entry receptors for some respiratory viruses, the eye is rarely involved in human CoV infection, conjunctivitis is quite rare in patients with 2019-nCoV infection, and the CoV RNA positive rate by RT-PCR test in tears and conjunctival secretions from patients with 2019-nCoV and SARS-CoV infection is also extremely low. This suggests that the eye is neither a preferred organ of human CoV infection nor a preferred gateway of entry for human CoVs for infecting the respiratory tract. However, pathogens that the ocular surface is exposed to might be transported to nasal and nasopharyngeal mucosa by constant tear rinsing through the lacrimal duct system and then cause respiratory tract infection. Considering that close doctor-patient contact is quite common in ophthalmic practice and is apt to transmit human CoVs by droplets and fomites, strict hand hygiene and proper personal protection are highly recommended for health care workers to avoid hospital-related viral transmission during ophthalmic practice. url: https://doi.org/10.3389/fpubh.2020.00155 doi: 10.3389/fpubh.2020.00155 id: cord-260431-eksl7pp8 author: Sun, Heting title: Isolation and Identification of Feline Herpesvirus Type 1 from a South China Tiger in China date: 2014-02-28 words: 2523.0 sentences: 140.0 pages: flesch: 55.0 cache: ./cache/cord-260431-eksl7pp8.txt txt: ./txt/cord-260431-eksl7pp8.txt summary: In the present study, we used molecular methods, virus isolation, TEM examination and an animal challenge experiment to diagnose the cause of death of the South China tiger, and for the first time, we confirmed the infection with FHV-1 in the captive tiger population in China. The phylogenetic tree based on the TK gene sequences showed that the isolate investigated in this study, was closely related to the ten isolates of FHV-1 ( Figure 2 ), a result consistent with the alignment analysis. By PCR/RT-PCR, the only virus detected in the trachea homogenates was FHV-1, which was confirmed afterwards by virus isolation, the TEM examination of cell cultures showing CPE, and a challenge experiment in cats. In this study, the authors described the first occurrence of feline herpesvirus type 1 (FHV-1) in a South China tiger in China. abstract: In 2012, an FHV-1-like virus was isolated from a tiger that presented with clinical signs of sialorrhea, sneezing and purulent rhinorrhea. Isolation was performed with the FK81 cell line, and the virus was identified by PCR, transmission electron microscopy (TEM), and the phylogenetic analysis of the partial thymidine kinase (TK) and glycoprotein B (gB) genes. A total of 253 bp of the TK gene and 566 bp of the gB gene were amplified from the trachea of the tiger by PCR/RT-PCR method. Phylogenetic analysis showed that the isolate belonged to the same cluster with other FHV-1 strains obtained from GenBank. Herpes-like viruses with an envelope and diameters of approximately 200 nm were observed in the culture supernatants of FK81 cells inoculated with samples from the tiger. The FHV-1 infection was confirmed by an animal challenge experiment in a cat model. Our finding extends the host range of FHV-1 and has implications for FHV-1 infection and South China tiger conservation. url: https://www.ncbi.nlm.nih.gov/pubmed/24590411/ doi: 10.3390/v6031004 id: cord-284777-z7bd3a91 author: Sun, Ning title: Reverse transcription recombinase polymerase amplification with lateral flow dipsticks for detection of influenza A virus and subtyping of H1 and H3 date: 2018-10-27 words: 4298.0 sentences: 234.0 pages: flesch: 54.0 cache: ./cache/cord-284777-z7bd3a91.txt txt: ./txt/cord-284777-z7bd3a91.txt summary: Three reverse transcription recombinase polymerase amplification assays with lateral flow dipsticks (RT-RPA-LFD) were developed for identification of the matrix and hemagglutinin (HA) genes to detect influenza A virus and distinguish subtypes H1 and H3. More recently, nucleic acid amplification tests (NAATs), such as reverse transcription polymerase chain reaction (RT-PCR) [12] [13] [14] [15] , real-time RT-PCR [16, 17] , and reverse transcription loop-mediated isothermal amplification (RT-LAMP) [18, 19] , have been used for rapid and sensitive diagnosis or subtyping of IAVs. Nevertheless, these methods require expensive equipment and/or skilled technicians, making them inappropriate for use in developing countries. In order to comprehensively evaluate the performance of RT-RPA-LFD, 28 positive throat swab specimens by matrix real-time RT-PCR were tested by RIDTs (Rapid influenza A virus antigen test kits, Guangzhou Wondfo Biotechnology Co., Ltd, China). abstract: Three reverse transcription recombinase polymerase amplification assays with lateral flow dipsticks (RT-RPA-LFD) were developed for identification of the matrix and hemagglutinin (HA) genes to detect influenza A virus and distinguish subtypes H1 and H3. Assessment of the assays’ specificity showed that there was no cross-reactivity with other targets. Their limits of detection were 123.6 copies per reaction for the matrix gene, 677.1 copies per reaction for the H1 HA gene, and 112.2 copies/reaction for the H3 HA gene. Of 111 samples tested by RT-RPA-LFD assays, 27 were positive for influenza A virus, 14 were positive for H1, and 10 were positive for H3. Compared to the results obtained from real-time RT-PCR assays, the sensitivity of RT-RPA-LFD assays was 75%, 93.33% and 71.43% for the matrix, H1, and H3, with 100% specificity. The sensitivity of RT-RPA-LFD assays is lower than that of real-time RT-PCR, comparable or better than that of conventional RT-PCR, and much better than that of RIDTs. In conclusion, these assays offer an efficient and reliable tool for identification and subtyping of influenza A virus (subtype H1 and H3) in the resource-limited setting. url: https://www.ncbi.nlm.nih.gov/pubmed/30394299/ doi: 10.1016/j.mcp.2018.10.004 id: cord-354773-u86bdmvf author: Suo, Tao title: ddPCR: a more accurate tool for SARS-CoV-2 detection in low viral load specimens date: 2020-06-07 words: 4490.0 sentences: 242.0 pages: flesch: 57.0 cache: ./cache/cord-354773-u86bdmvf.txt txt: ./txt/cord-354773-u86bdmvf.txt summary: To improve the diagnostic accuracy of nucleic acid detection of SARS-Cov-2 in low viral load samples using droplet digital PCR, we compared the dynamic range and the limit of detection (LoD) with a 95% repeatable probability between ddPCR and RT-PCR in laboratory, and tested the clinical samples from 77 patients by both ddPCR and RT-PCR for head to head comparison. Throat swab samples of each patient were firstly collected for official approved RT-PCR diagnosis in hospitals and blinding laboratory RT-PCR and ddPCR tests simultaneously with the same primers/probe sets approved by Chinese CDC. As shown in Figure 3 , throat swab samples of each suspected outpatient were firstly collected for laboratory RT-PCR, ddPCR tests and official approved RT-PCR diagnosis in hospitals simultaneously with the same primers/probe sets approved by Chinese CDC (Table 1) . In this study, two throat swab samples of each supposed convalescent were collected for laboratory RT-PCR, ddPCR and official approved RT-PCR tests simultaneously with the same primers/probe sets (Table 2) . abstract: Quantitative real time PCR (RT-PCR) is widely used as the gold standard for clinical detection of SARS-CoV-2. However, due to the low viral load specimens and the limitations of RT-PCR, significant numbers of false negative reports are inevitable, which results in failure to timely diagnose, cut off transmission, and assess discharge criteria. To improve this situation, an optimized droplet digital PCR (ddPCR) was used for detection of SARS-CoV-2, which showed that the limit of detection of ddPCR is significantly lower than that of RT-PCR. We further explored the feasibility of ddPCR to detect SARS-CoV-2 RNA from 77 patients, and compared with RT-PCR in terms of the diagnostic accuracy based on the results of follow-up survey. 26 patients of COVID-19 with negative RT-PCR reports were reported as positive by ddPCR. The sensitivity, specificity, PPV, NPV, negative likelihood ratio (NLR) and accuracy were improved from 40% (95% CI: 27–55%), 100% (95% CI: 54–100%), 100%, 16% (95% CI: 13–19%), 0.6 (95% CI: 0.48–0.75) and 47% (95% CI: 33–60%) for RT-PCR to 94% (95% CI: 83–99%), 100% (95% CI: 48–100%), 100%, 63% (95% CI: 36–83%), 0.06 (95% CI: 0.02–0.18), and 95% (95% CI: 84–99%) for ddPCR, respectively. Moreover, 6/14 (42.9%) convalescents were detected as positive by ddPCR at 5–12 days post discharge. Overall, ddPCR shows superiority for clinical diagnosis of SARS-CoV-2 to reduce the false negative reports, which could be a powerful complement to the RT-PCR. url: https://www.ncbi.nlm.nih.gov/pubmed/32438868/ doi: 10.1080/22221751.2020.1772678 id: cord-255096-27dfbhsl author: Sweet, Michael J. title: Reprint of ‘Diseases in marine invertebrates associated with mariculture and commercial fisheries’ date: 2016-06-19 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Diseases in marine invertebrates are increasing in both frequency and intensity around the globe. Diseases in individuals which offer some commercial value are often well documented and subsequently well studied in comparison to those wild groups offering little commercial gain. This is particularly the case with those associated with mariculture or the commercial fisheries. Specifically, these include many Holothuroidea, and numerous crustacea and mollusca species. Pathogens/parasites consisting of both prokaryotes and eukaryotes from all groups have been associated with diseases from such organisms, including bacteria, viruses, fungi and protozoa. Viral pathogens in particular, appear to be an increasingly important group and research into this group will likely highlight a larger number of diseases and pathogens being described in the near future. Interestingly, although there are countless examples of the spread of disease usually associated with transportation of specific infected hosts for development of aquaculture practices, this process appears to be continuing with no real sign of effective management and mitigation strategies being implicated. Notably, even in well developed countries such as the UK and the US, even though live animal trade may be well managed, the transport of frozen food appears to be less well so and as evidence suggests, even these to have the potential to transmit pathogens when used as a food source for example. url: https://doi.org/10.1016/j.seares.2016.06.001 doi: 10.1016/j.seares.2016.06.001 id: cord-003505-qr6ukfti author: Tabraue-Chávez, Mavys title: A colorimetric strategy based on dynamic chemistry for direct detection of Trypanosomatid species date: 2019-03-06 words: 5655.0 sentences: 331.0 pages: flesch: 50.0 cache: ./cache/cord-003505-qr6ukfti.txt txt: ./txt/cord-003505-qr6ukfti.txt summary: In this work, we have developed a novel colorimetric molecular assay that integrates nucleic acid analysis by dynamic chemistry (ChemNAT) with reverse dot-blot hybridization in an array format for a rapid and easy discrimination of Leishmania major and Trypanosoma cruzi. Once the abasic PNA probes hybridize with target sequences, the SMART-C-Biotin dynamic incorporation takes place, enabling the unequivocal identification of the parasite present in the amplicon sample, because of the unique colorimetric pattern that each Trypanosomatid amplicon generates. DNA amplicon products were denatured and then together with the dynamic chemistry reaction reagents added directly into the internal column of the Spin-Tube that supports the nylon membrane for the color-development assay (Fig. 4) . 20 ng of human gDNA were used as PCR template for its amplification with the set of primers described in our study and neither colorimetric signals nor bands were detected using the Spin-Tube and capillary electrophoresis analysis respectively (Fig. 5 , column 2: 2A and 2B), hence probing the specificity when human gDNA is present. abstract: Leishmaniasis and Chagas disease are endemic in many countries, and re-emerging in the developed countries. A rapid and accurate diagnosis is important for early treatment for reducing the duration of infection as well as for preventing further potential health complications. In this work, we have developed a novel colorimetric molecular assay that integrates nucleic acid analysis by dynamic chemistry (ChemNAT) with reverse dot-blot hybridization in an array format for a rapid and easy discrimination of Leishmania major and Trypanosoma cruzi. The assay consists of a singleplex PCR step that amplifies a highly homologous DNA sequence which encodes for the RNA component of the large ribosome subunit. The amplicons of the two different parasites differ between them by single nucleotide variations, known as “Single Nucleotide Fingerprint” (SNF) markers. The SNF markers can be easily identified by naked eye using a novel micro Spin-Tube device "Spin-Tube", as each of them creates a specific spot pattern. Moreover, the direct use of ribosomal RNA without requiring the PCR pre-amplification step is also feasible, further increasing the simplicity of the assay. The molecular assay delivers sensitivity capable of identifying up to 8.7 copies per µL with single mismatch specificity. The Spin-Tube thus represents an innovative solution providing benefits in terms of time, cost, and simplicity, all of which are crucial for the diagnosis of infectious disease in developing countries. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6403333/ doi: 10.1038/s41598-019-39946-0 id: cord-048470-33mqfj2t author: Takano, T title: Quantitative measurement of thyroglobulin mRNA in peripheral blood of patients after total thyroidectomy date: 2001-07-17 words: 3040.0 sentences: 146.0 pages: flesch: 54.0 cache: ./cache/cord-048470-33mqfj2t.txt txt: ./txt/cord-048470-33mqfj2t.txt summary: Previous studies have reported the clinical usefulness of reverse transcription-polymerase chain reaction (RT-PCR) detection of thyroglobulin (TG) mRNA in the peripheral blood of patients with differentiated thyroid carcinoma. To evaluate this usefulness, we measured TG mRNA in the peripheral blood of patients diagnosed with thyroid carcinoma after total thyroidectomy by real-time quantitative RT-PCR using glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA as an internal control. Recent reports have demonstrated that the reverse transcription-polymerase chain reaction (RT-PCR) can be used to detect circulating cancer cells in the peripheral blood of patients with malignancies such as prostate cancer (Ghossein et al, 1995) and neuroblastoma (Mattano et al, 1992) . As such, we measured TG mRNA in the peripheral blood of patients after total thyroidectomy and determined the expression levels of TG mRNA by real time-quantitative RT-PCR using GAPDH mRNA as an internal control. abstract: Previous studies have reported the clinical usefulness of reverse transcription-polymerase chain reaction (RT-PCR) detection of thyroglobulin (TG) mRNA in the peripheral blood of patients with differentiated thyroid carcinoma. To evaluate this usefulness, we measured TG mRNA in the peripheral blood of patients diagnosed with thyroid carcinoma after total thyroidectomy by real-time quantitative RT-PCR using glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA as an internal control. Surprisingly, we detected TG mRNA in all samples obtained after total thyroidectomy, including those from 4 medullary carcinomas. Further, there was no statistical difference in expression levels of TG mRNA in the patients with or without metastasis, and no significant correlation was found between serum TG concentrations and the expression levels of TG mRNA. These results give rise to a question regarding the clinical applications of not only RT-PCR detection but also quantitative measurement of TG mRNA in peripheral blood. © 2001 Cancer Research Campaign http://www.bjcancer.com url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2363919/ doi: 10.1054/bjoc.2001.1904 id: cord-312024-qdgqif5j author: Talbot, H. Keipp title: The Diagnosis of Viral Respiratory Disease in Older Adults date: 2010-02-01 words: 3423.0 sentences: 175.0 pages: flesch: 39.0 cache: ./cache/cord-312024-qdgqif5j.txt txt: ./txt/cord-312024-qdgqif5j.txt summary: The increasing availability of new rapid and sensitive molecular diagnostics such as polymerase chain reaction testing, should provide more accurate and timely diagnoses of viral respiratory infections in older adults in the near future. This article summarizes what is known about the diagnosis of viral respiratory diseases in elderly adults, with the hope of increasing understanding of the utility and limitations of the currently available diagnostic tests for viral respiratory pathogens, such as culture, rapid antigen testing, polymerase chain reaction (PCR) testing, and serologic analysis. Compared with previous studies that have used viral culture for diagnosis, studies using PCR have more accurately detected the presence of viruses (including influenza virus, RSV, hMPV, parainfluenza virus, rhinoviruses, and coronaviruses) in the lower respiratory tract illness in older adults [5, 13, 31, 36, 40, 42] . abstract: Viral respiratory disease in older adults has been increasingly recognized as a significant cause of hospitalizations and death. Unfortunately, the recognition and diagnosis of infection due to many viral respiratory pathogens in older adults can be elusive due to atypical clinical presentations and the insensitivity of current laboratory diagnostic tests in this population. For influenza diagnosis, rapid antigen tests followed by viral culture if negative, can be useful in older adults as long as clinicians are mindful of test limitations. Although specific, rapid antigen tests are insensitive in this population. Erroneous negative results may lead to delays in timely administration of antiviral treatment and institution of appropriate isolation precautions. The increasing availability of new rapid and sensitive molecular diagnostics such as polymerase chain reaction testing, should provide more accurate and timely diagnoses of viral respiratory infections in older adults in the near future. url: https://www.ncbi.nlm.nih.gov/pubmed/20121411/ doi: 10.1086/650486 id: cord-353810-mf753ae9 author: Tan, Cedric Chih Shen title: A novel method for the capture-based purification of whole viral native RNA genomes date: 2019-04-08 words: 5929.0 sentences: 352.0 pages: flesch: 54.0 cache: ./cache/cord-353810-mf753ae9.txt txt: ./txt/cord-353810-mf753ae9.txt summary: This report also describes a successful application of capture-based purification as a direct RNA sequencing strategy that addresses certain limitations of current strategies in sequencing RNA viral genomes. Based on the mapping rates to human and DENV1 reference genomes for pre and post-capture groups, shown in Table 2 , purification factor was calculated to be 272-fold. The minimum coverage required for variant calling was, as described above, benchmarked to that of Illumina reads so that the effectiveness of our capture-based purification method could be more accurately evaluated based on the higher error read rates of direct RNA sequencing technology. Indeed, after comparison of the postcapture and concentrated post-capture sequencing runs (Table 2) , the 2.5-fold increase in the percentage of reads mapping to DENV1 suggests that scaling our method greatly improved the signal-to-noise ratio of this particular downstream RNA assay. abstract: Current technologies for targeted characterization and manipulation of viral RNA primarily involve amplification or ultracentrifugation with isopycnic gradients of viral particles to decrease host RNA background. The former strategy is non-compatible for characterizing properties innate to RNA strands such as secondary structure, RNA–RNA interactions, and also for nanopore direct RNA sequencing involving the sequencing of native RNA strands. The latter strategy, ultracentrifugation, causes loss in genomic information due to its inability to retrieve unassembled viral RNA. To address this, we developed a novel application of current nucleic acid hybridization technologies for direct characterization of RNA. In particular, we modified a current enrichment protocol to capture whole viral native RNA genomes for downstream RNA assays to circumvent the abovementioned problems. This technique involves hybridization of biotinylated baits at 500 nucleotides (nt) intervals, stringent washes and release of free native RNA strands using DNase I treatment, with a turnaround time of about 6 h 15 min. RT-qPCR was used as the primary proof of concept that capture-based purification indeed removes host background. Subsequently, capture-based purification was applied to direct RNA sequencing as proof of concept that capture-based purification can be coupled with downstream RNA assays. We report that this protocol was able to successfully purify viral RNA by 561- to 791-fold. We also report that application of this protocol to direct RNA sequencing yielded a reduction in human host RNA background by 1580-fold, a 99.91% recovery of viral genome with at least 15× coverage, and a mean coverage across the genome of 120×. This report is, to the best of our knowledge, the first description of a capture-based purification method for assays that involve direct manipulation or characterisation of native RNA. This report also describes a successful application of capture-based purification as a direct RNA sequencing strategy that addresses certain limitations of current strategies in sequencing RNA viral genomes. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13568-019-0772-y) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/30963294/ doi: 10.1186/s13568-019-0772-y id: cord-272696-1jg46veg author: Tang, An title: Detection of Novel Coronavirus by RT-PCR in Stool Specimen from Asymptomatic Child, China date: 2020-06-17 words: 1724.0 sentences: 93.0 pages: flesch: 55.0 cache: ./cache/cord-272696-1jg46veg.txt txt: ./txt/cord-272696-1jg46veg.txt summary: We collected nasopharyngeal swab and sputum samples from the boy 15 days after the last close contact and tested these specimens for SARS-CoV-2 by using RT-PCRs targeting the open reading frame lab (ORF1ab) and nucleoprotein gene regions (4) . The boy we report had close contact with confirmed COVID-19 case-patients on several occasions before he showed an equivocal RT-PCR result for respiratory specimens and subsequently positive results for stool specimens. We report an asymptomatic child who was positive for a coronavirus by reverse transcription PCR in a stool specimen 17 days after the last virus exposure. We report an asymptomatic child who was positive for a coronavirus by reverse transcription PCR in a stool specimen 17 days after the last virus exposure. Timeline for detection of novel coronavirus by RT-PCR in stool specimen from asymptomatic child, China abstract: We report an asymptomatic child who was positive for a coronavirus by reverse transcription PCR in a stool specimen 17 days after the last virus exposure. The child was virus positive in stool specimens for at least an additional 9 days. Respiratory tract specimens were negative by reverse transcription PCR. url: https://doi.org/10.3201/eid2606.200301 doi: 10.3201/eid2606.200301 id: cord-266025-bkm486jd author: Tao, Ying title: Genomic characterization of seven distinct bat coronaviruses in Kenya() date: 2012-04-26 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: To better understand the genetic diversity and genomic features of 41 coronaviruses (CoVs) identified from Kenya bats in 2006, seven CoVs as representatives of seven different phylogenetic groups identified from partial polymerase gene sequences, were subjected to extensive genomic sequencing. As a result, 15–16 kb nucleotide sequences encoding complete RNA dependent RNA polymerase, spike, envelope, membrane, and nucleocapsid proteins plus other open reading frames (ORFs) were generated. Sequences analysis confirmed that the CoVs from Kenya bats are divergent members of Alphacoronavirus and Betacoronavirus genera. Furthermore, the CoVs BtKY22, BtKY41, and BtKY43 in Alphacoronavirus genus and BtKY24 in Betacoronavirus genus are likely representatives of 4 novel CoV species. BtKY27 and BtKY33 are members of the established bat CoV species in Alphacoronavirus genus and BtKY06 is a member of the established bat CoV species in Betacoronavirus genus. The genome organization of these seven CoVs is similar to other known CoVs from the same groups except for differences in the number of putative ORFs following the N gene. The present results confirm a significant diversity of CoVs circulating in Kenya bats. These Kenya bat CoVs are phylogenetically distant from any previously described human and animal CoVs. However, because of the examples of host switching among CoVs after relatively minor sequence changes in S1 domain of spike protein, a further surveillance in animal reservoirs and understanding the interface between host susceptibility is critical for predicting and preventing the potential threat of bat CoVs to public health. url: https://www.ncbi.nlm.nih.gov/pubmed/22561208/ doi: 10.1016/j.virusres.2012.04.007 id: cord-310140-h7uwl0pb author: Templeton, K.E. title: A multi-centre pilot proficiency programme to assess the quality of molecular detection of respiratory viruses date: 2005-07-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: To assess the quality of molecular detection of respiratory viruses in clinical diagnostic laboratories. STUDY DESIGN: Respiratory virus proficiency panels were produced from diluted stocks of respiratory viruses provided and tested by four reference laboratories. The panels consisted of strong positive, positive, low positive and negative samples for influenza viruses A and B, respiratory syncytial virus, parainfluenza viruses 1 and 3, adenovirus serotypes 4 and 7, human rhinovirus serotypes 16, 72 and 90, human coronaviruses OC43 and 229E. The panels were sent to 17 participants; results and information on methodology was collected. RESULTS: All laboratories returned results, of which five submitted complete data sets. So, for analysis all results were combined. Samples were correctly identified by participants in 93.75%, 76.75% and 47.03% for the high positive, positive and low positive samples, respectively. One false positive was reported for all data sets (1.1%). The overall score for all assays using different methodologies was 78.8%. Laboratory performance was not dependant on methodology as all in-house methodologies could achieve optimal results, but dependant on careful optimisation and procedures specific to the laboratory. CONCLUSIONS: The first proficiency panel showed that in general all participants performed well. Although, it also highlights areas for improvement for all participants in order to generate robust results for use in clinical diagnostics. url: https://www.ncbi.nlm.nih.gov/pubmed/16019258/ doi: 10.1016/j.jcv.2005.05.005 id: cord-269948-zfbu9646 author: Teo, Jeanette title: VereFlu™: an integrated multiplex RT-PCR and microarray assay for rapid detection and identification of human influenza A and B viruses using lab-on-chip technology date: 2011-04-19 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Threatening sporadic outbreaks of avian influenza and the H1N1 pandemic of 2009 highlight the need for rapid and accurate detection and typing of influenza viruses. In this paper, we describe the validation of the VereFlu™ Lab-on-Chip Influenza Assay, which is based on the integration of two technologies: multiplex reverse transcription (RT)-PCR followed by microarray amplicon detection. This assay simultaneously detects five influenza virus subtypes, including the 2009 pandemic influenza A (H1N1), seasonal H1N1, H3N2, H5N1 and influenza B virus. The VereFlu™ assay was clinically validated in Singapore and compared against reference methods of real-time PCR, virus detection by immunofluorescence of cell cultures and sequencing. A sensitivity and specificity of 96.8% and 92.8%, respectively, was demonstrated for pandemic H1N1; 95.7% and 100%, respectively, for seasonal H1N1; 91.2% and 97.6%, respectively, for seasonal H3N2; 95.2% and 100%, respectively, for influenza B. Additional evaluations carried out at the World Health Organization (WHO) Collaborating Centre, Melbourne, Australia, confirmed that the test was able to reliably detect H5N1. This portable, fast time-to-answer (3 hours) device is particularly suited for diagnostic applications of detection, differentiation and identification of human influenza virus subtypes. url: https://doi.org/10.1007/s00705-011-0999-7 doi: 10.1007/s00705-011-0999-7 id: cord-294155-94skyx5f author: Terrosi, Chiara title: Human bocavirus detection in an atopic child affected by pneumonia associated with wheezing date: 2007-08-07 words: 1360.0 sentences: 82.0 pages: flesch: 52.0 cache: ./cache/cord-294155-94skyx5f.txt txt: ./txt/cord-294155-94skyx5f.txt summary: HBoV was detected in respiratory samples by PCR, but its aetiologic role in the pathogenesis of acute respiratory infectious diseases is still unclear. CONCLUSIONS: Detection of HboV, as the only microbial agent, in samples from children with wheezing and acute respiratory diseases supports the assumption that this emerging virus could have an aetiologic role in the pathogenesis of respiratory diseases. A new parvovirus, the human bocavirus (HBoV), has recently been discovered by the application of random PCR/cloning technique on respiratory samples (Allender et al., 2005) . In this report, we describe a case of pneumonia and severe wheezing associated with HBoV DNA in the pharyngeal swab sample from a child. The detection of HBoV in the nasopharyngeal swab in a child with a clinical picture of pneumonia supports the assumption that this virus has a causative role in respiratory diseases. Human bocavirus DNA detected by quantitative real-time PCR in two children hospitalized for lower respiratory tract infection abstract: BACKGROUND: Human bocavirus (HBoV) is a newly discovered human parvovirus. HBoV was detected in respiratory samples by PCR, but its aetiologic role in the pathogenesis of acute respiratory infectious diseases is still unclear. RESULTS: In this report, we describe an atopic child affected by pneumonia, with a past history of wheezing. A panel of bacteria and respiratory viruses were searched in the nasopharyngeal swab, only human bocavirus was detected by PCR. CONCLUSIONS: Detection of HboV, as the only microbial agent, in samples from children with wheezing and acute respiratory diseases supports the assumption that this emerging virus could have an aetiologic role in the pathogenesis of respiratory diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/17686654/ doi: 10.1016/j.jcv.2007.06.011 id: cord-015763-5lx179pa author: Thellier, D. title: Quels prélèvements aux urgences pour le diagnostic microbiologique d’une infection pulmonaire communautaire grave du sujet immunocompétent ? date: 2014-09-23 words: 5181.0 sentences: 450.0 pages: flesch: 51.0 cache: ./cache/cord-015763-5lx179pa.txt txt: ./txt/cord-015763-5lx179pa.txt summary: Keywords Severe community acquired pneumonia · Microbial diagnosis La pneumonie communautaire grave (PCG) est la première cause de sepsis sévère et de choc septique rencontrée aux urgences [1] . Ainsi, puisque les pathogènes responsables et l''antibiothérapie à instaurer sont connus, l''utilité de réaliser des prélèvements microbiologiques systématiques chez tous les patients admis aux urgences pour une pneumonie communautaire peut se discuter. Toutefois, cette relation entre la gravité de l''infection et la fréquence de positivité de l''hémoculture lorsqu''elle est appréciée non plus par le lieu d''admission du patient mais par un élément objectif tel que le Pneumonia Severity Index (PSI, score de Fine) ou le CURB-65 apparaît plus difficile à établir, tant les études sur le sujet rapportent des résultats discordants. Ces données ne doivent pas toutefois faire perdre de vue que les pneumonies ayant une étiologie pluri microbienne dans plus de 10 % des cas il n''est peutêtre pas raisonnable de focaliser l''antibiothérapie uniquement sur le pneumocoque en cas de test positif. abstract: Current diagnostic methods allow microbial identification in 50% of patients admitted with severe community-acquired pneumonia (CAP). Guidelines derived from epidemiological data help physicians to start empirical antimicrobial therapy. Definitive microbial diagnosis is useful to guide further pathogen-directed therapy. Blood cultures, cultures of respiratory specimens and urine antigen tests are recommended to determine the causative bacterial pathogen. Positive blood cultures range from 15 to 25% of CAP patients according to severity. Whether sputum specimens represent or not lower respiratory secretions determines its accuracy in CAP microbial diagnosis. In intubated patients, endotracheal aspirates are often of interest. Detection of positive pneumococcal or legionella urinary antigen is often associated with CAP severity. The sensitivity of this test is not decreased in patients who have received antibiotics prior to sampling. Viral pneumonia account for 10 to 40% of severe CAP. Nasal swabs are recommended for influenza identification using polymerase chain reaction (PCR) in order to deliver oseltamivir treatment. In the emergency department, atypical pneumonia serology is less useful than respiratory specimens obtained using fiberoptic bronchoscopy. Serum PCR to diagnose bacterial CAP is not superior to the other usual methods. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7117809/ doi: 10.1007/s13546-014-0923-8 id: cord-343860-2j7nbryv author: Thiberville, S.D. title: The viral etiology of an influenza‐like illness during the 2009 pandemic date: 2012-05-14 words: 3729.0 sentences: 191.0 pages: flesch: 54.0 cache: ./cache/cord-343860-2j7nbryv.txt txt: ./txt/cord-343860-2j7nbryv.txt summary: The identification of the respiratory viruses that are responsible for influenza-like illness has been reported in many countries, and the percentage of positive swabs for at least one virus ranges from 32% to 65% [Bellei et al., 2008; Laguna-Torres et al., 2009; Ren et al., 2009; Buecher et al., 2010; Renois et al., 2010; Razanajatovo et al., 2011] . Although it is possible that some EVs remained undetected, five samples were tested positive for EVs (1.7% of tested patients), which is consistent with previous studies in patients with acute respiratory infection or influenza-like illness [Bellei et al., 2008; Laguna-Torres et al., 2009; Ren et al., 2009] . Several studies have reported the results from respiratory virus testing using respiratory samples that were obtained from patients with influenza-like illness or acute respiratory infection throughout the world and during different times. abstract: Many viruses are known to cause influenza‐like illness (ILI); however, in nearly 50% of patients, the etiologic agent remains unknown. The distribution of viruses in patients with ILI was investigated during the 2009 A/H1N1 influenza pandemic (A/H1N1p). From June 2009 to January 2010, 660 patients with suspected influenza were questioned and examined, and nasal swabs were collected. All patient samples were tested for influenza virus, and 286 negative nasal swabs were tested further for 18 other respiratory viruses using real‐time RT‐PCR. Two waves of ILI were observed in the epidemic curve (weeks 35–42 and 42–49). At least eight viruses co‐circulated during this period: human rhinovirus (HRV) (58), parainfluenza 1–4 viruses (PIV) (9), human Coronavirus (hCoV) OC43 (9), enterovirus (5), adenovirus (AdV) (4), and human metapneumovirus (hMPV) (2); however, 204 samples remained negative for all viruses tested. ILI symptoms, according to the Centers for Disease Control and Prevention criteria for ILI definition, were reported in 75% of cases. These patients had positive swabs for A/H1N1p, HRV, hCoV‐OC43, PIV, AdV, and hMPV without significant difference with non‐ILI patients. This study found that many respiratory viruses circulated during this period and that the A/H1N1p did not impact on the kinetics of other respiratory viruses. The proportion of non‐documented cases remains high. ILI could not distinguish A/H1N1p infection from that due to other respiratory viruses. However, in multivariate anlaysis, cough, chills, hyperemia, and dyspnea were associated significantly with influenza virus versus other respiratory viruses. J. Med. Virol. 84: 1071–1079, 2012. © 2012 Wiley Periodicals, Inc. url: https://doi.org/10.1002/jmv.23265 doi: 10.1002/jmv.23265 id: cord-304913-qb9zeazk author: Thibivilliers, Sandra title: Generation of Phaseolus vulgaris ESTs and investigation of their regulation upon Uromyces appendiculatus infection date: 2009-04-27 words: 6680.0 sentences: 344.0 pages: flesch: 52.0 cache: ./cache/cord-304913-qb9zeazk.txt txt: ./txt/cord-304913-qb9zeazk.txt summary: RESULTS: A subtractive bean cDNA library composed of 10,581 unisequences was constructed and enriched in sequences regulated by either bean rust race 41, a virulent strain, or race 49, an avirulent strain on cultivar Early Gallatin carrying the resistance gene Ur-4. Plant gene expression was similar for both race 41 and 49 during the first 48 hours of the infection process but varied significantly at the later time points (72–96 hours after inoculation) mainly due to the presence of the Avr4 gene in the race 49 leading to a hypersensitive response in the bean plants. The stability of the expression level of the 3 remaining genes, TC127, cons6 and cons7 was evaluated by qRT-PCR on cDNAs from bean uninfected or infected with bean rust race 41 or 49 at 6, 12, 24, 48, 72, and 96 hours after inoculation (HAI). abstract: BACKGROUND: Phaseolus vulgaris (common bean) is the second most important legume crop in the world after soybean. Consequently, yield losses due to fungal infection, like Uromyces appendiculatus (bean rust), have strong consequences. Several resistant genes were identified that confer resistance to bean rust infection. However, the downstream genes and mechanisms involved in bean resistance to infection are poorly characterized. RESULTS: A subtractive bean cDNA library composed of 10,581 unisequences was constructed and enriched in sequences regulated by either bean rust race 41, a virulent strain, or race 49, an avirulent strain on cultivar Early Gallatin carrying the resistance gene Ur-4. The construction of this library allowed the identification of 6,202 new bean ESTs, significantly adding to the available sequences for this plant. Regulation of selected bean genes in response to bean rust infection was confirmed by qRT-PCR. Plant gene expression was similar for both race 41 and 49 during the first 48 hours of the infection process but varied significantly at the later time points (72–96 hours after inoculation) mainly due to the presence of the Avr4 gene in the race 49 leading to a hypersensitive response in the bean plants. A biphasic pattern of gene expression was observed for several genes regulated in response to fungal infection. CONCLUSION: The enrichment of the public database with over 6,000 bean ESTs significantly adds to the genomic resources available for this important crop plant. The analysis of these genes in response to bean rust infection provides a foundation for further studies of the mechanism of fungal disease resistance. The expression pattern of 90 bean genes upon rust infection shares several features with other legumes infected by biotrophic fungi. This finding suggests that the P. vulgaris-U. appendiculatus pathosystem could serve as a model to explore legume-rust interaction. url: https://www.ncbi.nlm.nih.gov/pubmed/19397807/ doi: 10.1186/1471-2229-9-46 id: cord-325349-57n1878d author: Thieux, M. title: Assessment of a Diagnostic Strategy Based on Chest Computed Tomography in Patients Hospitalized for COVID-19 Pneumonia: an observational study date: 2020-06-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Objectives: To assess the relevance of a diagnostic strategy for COVID-19 based on chest computed tomography (CT) in patients with hospitalization criteria. Setting: Observational study with retrospective analysis in a French emergency department (ED). Participants and intervention: From March 3 to April 2, 2020, 385 adult patients presenting to the ED for suspected COVID-19 underwent an evaluation that included history, physical examination, blood tests, real-time reverse transcription-polymerase chain reaction (RT-PCR) and chest CT. When the time-interval between chest CT and RT-PCR assays was longer than 7 days, patients were excluded from the study. Only patients with hospitalization criteria were included. Diagnosis accuracy was assessed using the sensitivity and specificity of RT-PCR. Outcomes: Sensitivity and specificity of RT-PCR, chest CT (also accompanied by lymphopenia) were measured and were also analyzed by subgroups of age and sex. Results: Among 377 included subjects, RT-PCR was positive in 36%, while chest CT was compatible with a COVID-19 diagnosis in 59%. In the population with positive RT-PCR, there were more men (55% vs 37%, p=0.015), a higher frequency of reticular and, or, interlobular septal thickening (53% vs 31%, p=0.02) as well as a higher frequency of bilateral lesion distribution (98% vs 86%, p=0.01) compared to the population with negative RT-PCR. The proportion of lymphopenia was higher in men vs women (47% vs 39%, p=0.03) and varies between patients >80 versus 50-80 and p<0.001). Using CT as reference, RT-PCR obtained a sensitivity of 61%, specificity of 93%. There was a significant difference between CT and RT-PCR diagnosis performance (p<0.001). When CT was accompanied by lymphopenia, sensitivity and specificity of RT-PCR were respectively 71% and 94%. CT abnormalities and lymphopenia provided diagnosis in 29% of patients with negative PCR. Conclusions: Chest CT had a superior yield than RT-PCR in COVID-19 hospitalized patients, especially when accompanied by lymphopenia. url: http://medrxiv.org/cgi/content/short/2020.06.29.20140129v1?rss=1 doi: 10.1101/2020.06.29.20140129 id: cord-269627-mx1mjdqc author: Thiry, Etienne title: Feline herpesvirus infection. ABCD guidelines on prevention and management date: 2009-07-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract Overview Feline viral rhinotracheitis, caused by feline herpesvirus (FHV), is an upper respiratory tract disease that is often associated with feline calicivirus and bacteria. In most cats, FHV remains latent after recovery, and they become lifelong virus carriers. Stress or corticosteroid treatment may lead to virus reactivation and shedding in oronasal and conjunctival secretions. Infection Sick cats shed FHV in oral, nasal and conjunctival secretions; shedding may last for 3 weeks. Infection requires direct contact with a shedding cat. Disease signs Feline herpesvirus infections cause acute rhinitis and conjunctivitis, usually accompanied by fever, depression and anorexia. Affected cats may also develop typical ulcerative, dendritic keratitis. Diagnosis Samples consist of conjunctival, corneal or oropharyngeal swabs, corneal scrapings or biopsies. It is not recommended that cats recently vaccinated with a modified-live virus vaccine are sampled. Positive PCR results should be interpreted with caution, as they may be produced by low-level shedding or viral latency. Disease management ‘Tender loving care’ from the owner, supportive therapy and good nursing are essential. Anorexic cats should be fed blended, highly palatable food – warmed up if required. Mucolytic drugs (eg, bromhexine) or nebulisation with saline may offer relief. Broad-spectrum antibiotics should be given to prevent secondary bacterial infections. Topical antiviral drugs may be used for the treatment of acute FHV ocular disease. The virus is labile and susceptible to most disinfectants, antiseptics and detergents. Vaccination recommendations Two injections, at 9 and 12 weeks of age, are recommended, with a first booster 1 year later. Boosters should be given annually to at-risk cats. For cats in low-risk situations (eg, indoor-only cats), 3-yearly intervals suffice. Cats that have recovered from FHV-associated disease are usually not protected for life against further disease episodes; vaccination of recovered cats is therefore recommended. url: https://doi.org/10.1016/j.jfms.2009.05.003 doi: 10.1016/j.jfms.2009.05.003 id: cord-282278-q7jp224a author: Thorburn, Fiona title: The use of next generation sequencing in the diagnosis and typing of respiratory infections date: 2015-08-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract Background Molecular assays are the gold standard methods used to diagnose viral respiratory pathogens. Pitfalls associated with this technique include limits to the number of targeted pathogens, the requirement for continuous monitoring to ensure sensitivity/specificity is maintained and the need to evolve to include emerging pathogens. Introducing target independent next generation sequencing (NGS) could resolve these issues and revolutionise respiratory viral diagnostics. Objectives To compare the sensitivity and specificity of target independent NGS against the current standard diagnostic test. Study design Diagnostic RT-PCR of clinical samples was carried out in parallel with target independent NGS. NGS sequences were analyzed to determine the proportion with viral origin and consensus sequences were used to establish viral genotypes and serotypes where applicable. Results 89 nasopharyngeal swabs were tested. A viral pathogen was detected in 43% of samples by NGS and 54% by RT-PCR. All NGS viral detections were confirmed by RT-PCR. Conclusions Target independent NGS can detect viral pathogens in clinical samples. Where viruses were detected by RT-PCR alone the Ct value was higher than those detected by both assays, suggesting an NGS detection cut-off – Ct=32. The sensitivity and specificity of NGS compared with RT-PCR was 78% and 80% respectively. This is lower than current diagnostic assays but NGS provided full genome sequences in some cases, allowing determination of viral subtype and serotype. Sequencing technology is improving rapidly and it is likely that within a short period of time sequencing depth will increase in-turn improving test sensitivity. url: https://www.sciencedirect.com/science/article/pii/S138665321500267X doi: 10.1016/j.jcv.2015.06.082 id: cord-281653-zogtpm7a author: Thurman, Kathleen A. title: Detection of Mycoplasma pneumoniae, Chlamydia pneumoniae, and Legionella spp. in clinical specimens using a single-tube multiplex real-time PCR assay() date: 2011-03-11 words: 3307.0 sentences: 195.0 pages: flesch: 45.0 cache: ./cache/cord-281653-zogtpm7a.txt txt: ./txt/cord-281653-zogtpm7a.txt summary: A multiplex real-time PCR assay for the detection of Mycoplasma pneumoniae (MP181), Chlamydia (Chlamydophila) pneumoniae (CP-Arg), Legionella spp. This procedure may allow for a practical and efficient means to test respiratory clinical specimens for atypical pneumonia agents in health care settings and facilitate an appropriate public health response to outbreaks. Specific real-time PCR assays have been developed to provide a more rapid and reliable method for detecting respiratory pathogens in clinical specimens (Apfalter et al., 2003; Hayden et al., 2001; Mitchell et al., 2009; Winchell et al., 2008) . The current study reports the development and evaluation of a multiplex real-time PCR assay for simultaneous detection of 3 atypical bacterial pneumonia-causing organisms in clinical specimens. The sensitivity observed when testing clinical specimens with the multiplex assay was found to be significantly greater in 2 agent-specific assays (CP-Arg and Pan-Leg) and the RNase P. Development of a multiplex real-time quantitative PCR assay to detect Chlamydia pneumoniae, Legionella pneumophila and Mycoplasma pneumoniae in respiratory tract secretions abstract: A multiplex real-time PCR assay for the detection of Mycoplasma pneumoniae (MP181), Chlamydia (Chlamydophila) pneumoniae (CP-Arg), Legionella spp. (Pan-Leg), and the human RNase P (RNase P) gene was developed for rapid testing of atypical bacterial respiratory pathogens in clinical specimens. This method uses 4 distinct hydrolysis probes to detect 3 leading causes of community-acquired pneumonia. The assay was evaluated for specificity and sensitivity by testing against 35 related organisms, a dilution series of each specific target and 197 clinical specimens. Specificity testing demonstrated no cross-reactivity. A comparison to previously validated singleplex real-time PCR assays for each agent was also performed. The analytical sensitivity for specific pathogen targets in both the singleplex and multiplex was identical (50 fg), while efficiencies ranged from 82% to 97% for the singleplex assays and from 90% to 100% for the multiplex assay. The clinical sensitivity of the multiplex assay was improved for the Pan-Leg and CP-Arg targets when compared to the singleplex. The MP181 assay displayed equivalent performance. This multiplex assay provides an overall improvement in the diagnostic capability for these agents by demonstrating a sensitive, high-throughput and rapid method. This procedure may allow for a practical and efficient means to test respiratory clinical specimens for atypical pneumonia agents in health care settings and facilitate an appropriate public health response to outbreaks. url: https://www.ncbi.nlm.nih.gov/pubmed/21397428/ doi: 10.1016/j.diagmicrobio.2010.11.014 id: cord-017543-60q9iecq author: Tian, Wei-Chang title: Microfluidic Applications in Biodefense date: 2008-08-23 words: 16557.0 sentences: 831.0 pages: flesch: 37.0 cache: ./cache/cord-017543-60q9iecq.txt txt: ./txt/cord-017543-60q9iecq.txt summary: Sections cover microscale sample preparation methods; immunomagnetic separations and immunoassays; proteomics; polymerase chain reaction (PCR), quantitative PCR (qPCR) and other nucleic acid amplification methods; DNA microarrays, microelectrophoresis, and finally integrated Lab-on-a-Chip systems. The intent of JBAIDS Block III, Next Generation Diagnostics (NGD), is to establish a new system incorporating the capabilities of Block I and Block II capabilities (Table 10 .1) and adding immunoassay capabilities and the ability to identify up to 50 agents including toxins in 15 minutes using automated, miniaturized sample preparation integrated with analysis for nucleic acids and proteins, in a hand held or smaller format. They will need to be completely automated or simple to use; incorporate advanced technologies including sample preparation starting from primary samples (aerosols, blood, etc.), molecular detection, automation, microfluidics, and bioinformatics; reduce reagent consumption and space requirements; and provide cost and performance advantages compared to present systems. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122129/ doi: 10.1007/978-0-387-09480-9_10 id: cord-302189-3xab3yxc author: Tillmann, Ramona Liza title: Sensitive Commercial NASBA Assay for the Detection of Respiratory Syncytial Virus in Clinical Specimen date: 2007-12-26 words: 1777.0 sentences: 90.0 pages: flesch: 45.0 cache: ./cache/cord-302189-3xab3yxc.txt txt: ./txt/cord-302189-3xab3yxc.txt summary: Thereby, NASBA turned out to be the most sensitive method with a total number of 80 RSV positive samples out of a cohort of 251 nasopharyngeal washings from patients suffering from clinical symptoms, followed by the inhouse RT-PCR (62/251) and ELISA (52/251). Despite an increasing number of newly detected respiratory pathogen the human Respiratory syncytial virus (RSV) remains the single most prevalent etiologic agent in pediatric viral respiratory tract infection [1, 2, 3] . In relation to the positive test results obtained with the NucliSENSH EasyQ NASBA, the relative sensitivity of the RT-PCR was 77,5% compared to 65% obtained with the NOWH RSV ELISA. The results showed that from the three tested methods for molecular diagnosis of RSV the NucliSENSH EasyQ NASBA (bioMerieux, Nürtingen, Germany) detected the most RSV positive samples in a cohort of 251 nasopharyngeal samples of pediatric patients hospitalized with respiratory disease. abstract: The aim of the study was to evaluate the usability of three diagnostic procedures for the detection of respiratory syncytial virus in clinical samples. Therefore, the FDA cleared CE marked NOW® RSV ELISA, the NucliSENS® EasyQ RSV A+B NASBA, and a literature based inhouse RT-PCR protocol were compared for their relative sensitivities. Thereby, NASBA turned out to be the most sensitive method with a total number of 80 RSV positive samples out of a cohort of 251 nasopharyngeal washings from patients suffering from clinical symptoms, followed by the inhouse RT-PCR (62/251) and ELISA (52/251). Thus, NASBA may serve as a rapid and highly sensitive alternative for RSV diagnostics. url: https://www.ncbi.nlm.nih.gov/pubmed/18159240/ doi: 10.1371/journal.pone.0001357 id: cord-260728-4w23kwzu author: Timmermans, Ans title: Human Sentinel Surveillance of Influenza and Other Respiratory Viral Pathogens in Border Areas of Western Cambodia date: 2016-03-30 words: 7411.0 sentences: 381.0 pages: flesch: 50.0 cache: ./cache/cord-260728-4w23kwzu.txt txt: ./txt/cord-260728-4w23kwzu.txt summary: Real-time reverse transcriptase (rRT) PCR for influenza was performed on combined nasal and throat specimens followed by viral culture, antigenic analysis, antiviral susceptibility testing and full genome sequencing for phylogenetic analysis. Between May 2010 and December 2012, we collected specimens and surveillance data for influenza and other viral respiratory pathogens from a subset of outpatients presenting with influenza-like-illness (ILI) at four sentinel sites-located in five health centers and hospitals in Battambang, Oddar Meanchey, Pailin and Banteay Meanchey provinces in Cambodia (Fig 1) . A subset of 164 culture-negative specimens (collected between May 2010 and April 2012), where we found a higher proportion (5.6%) of non-polio enteroviruses in children less than 5 years old as compared with previous studies (1%) in Cambodia [2] , were tested for enterovirus and rhinovirus by two separate nested RT-PCR methods adapted from Coiras et al., 2004 and Singh et al., 2002 [29,30] , one for simultaneous detection of pan-enteroviruses and rhinoviruses, and the other specific for enterovirus 71 (EV71). abstract: Little is known about circulation of influenza and other respiratory viruses in remote populations along the Thai-Cambodia border in western Cambodia. We screened 586 outpatients (median age 5, range 1–77) presenting with influenza-like-illness (ILI) at 4 sentinel sites in western Cambodia between May 2010 and December 2012. Real-time reverse transcriptase (rRT) PCR for influenza was performed on combined nasal and throat specimens followed by viral culture, antigenic analysis, antiviral susceptibility testing and full genome sequencing for phylogenetic analysis. ILI-specimens negative for influenza were cultured, followed by rRT-PCR for enterovirus and rhinovirus (EV/RV) and EV71. Influenza was found in 168 cases (29%) and occurred almost exclusively in the rainy season from June to November. Isolated influenza strains had close antigenic and phylogenetic relationships, matching vaccine and circulating strains found elsewhere in Cambodia. Influenza vaccination coverage was low (<20%). Western Cambodian H1N1(2009) isolate genomes were more closely related to 10 earlier Cambodia isolates (94.4% genome conservation) than to 13 Thai isolates (75.9% genome conservation), despite sharing the majority of the amino acid changes with the Thai references. Most genes showed signatures of purifying selection. Viral culture detected only adenovirus (5.7%) and parainfluenza virus (3.8%), while non-polio enteroviruses (10.3%) were detected among 164 culture-negative samples including coxsackievirus A4, A6, A8, A9, A12, B3, B4 and echovirus E6 and E9 using nested RT-PCR methods. A single specimen of EV71 was found. Despite proximity to Thailand, influenza epidemiology of these western Cambodian isolates followed patterns observed elsewhere in Cambodia, continuing to support current vaccine and treatment recommendations from the Cambodian National Influenza Center. Amino acid mutations at non-epitope sites, particularly hemagglutinin genes, require further investigation in light of an increasingly important role of permissive mutations in influenza virus evolution. Further research about the burden of adenovirus and non-polio enteroviruses as etiologic agents in acute respiratory infections in Cambodia is also needed. url: https://doi.org/10.1371/journal.pone.0152529 doi: 10.1371/journal.pone.0152529 id: cord-295296-jtjx1vgd author: Tiwari, Shashi Kant title: `In-silico primer designing and PCR for detection of novel coronavirus-19 date: 2020-10-23 words: 569.0 sentences: 43.0 pages: flesch: 67.0 cache: ./cache/cord-295296-jtjx1vgd.txt txt: ./txt/cord-295296-jtjx1vgd.txt summary: title: ''In-silico primer designing and PCR for detection of novel coronavirus-19 Novel corona virus (2019-nCoV or COVID-19) pandemic has been considered as a major public health emergency in the world of this century. Novel corona virus (2019-nCoV or COVID-19) pandemic has been considered as a major public health emergency in the world of this century. qRT-PCR primer and probe were designed within conserved region from whole genome, RNA dependent RNA polymerase (RdRP) and envelope to detect SARS-CoV2 from COVID-19 virus isolated from Wuhan, China (Gene bank No: NC_045512, MT072668.1and MT111896.1 respectively). All these sets of primers of COVID-19 were highly specific and any of the primer set either syber green based or Taqman probe based may be useful for commercial one step RT-PCR based kit development for the molecular diagnosis of COVID-19 viruses. The assay based on one step qRT-PCR detection will be sensitive, rapid and specific to detect COVID-19 viruses in mouth swab, nasal swab, abstract: Novel corona virus (2019-nCoV or COVID-19) pandemic has been considered as a major public health emergency in the world of this century. We synthesised noval 12 pairs of primers from the whole genome of COVID 19 virus by using In-silico approach. We observed primers have high binding capacity and no cross reactivity. These primers and probe may be useful for commercial development of one step RTPCR based kit for diagnosis of COVID 19. url: https://www.sciencedirect.com/science/article/pii/S1876034120307085?v=s5 doi: 10.1016/j.jiph.2020.10.010 id: cord-325969-9zhmmvdg author: To, Kelvin KW title: Additional molecular testing of saliva specimens improves the detection of respiratory viruses date: 2017-06-07 words: 4543.0 sentences: 250.0 pages: flesch: 48.0 cache: ./cache/cord-325969-9zhmmvdg.txt txt: ./txt/cord-325969-9zhmmvdg.txt summary: In the first cohort of 159 patients whose nasopharyngeal aspirates (NPAs) tested positive for respiratory viruses during routine testing, the viral load was measured using quantitative reverse transcription PCR. Although NPAs have high viral loads and remain the specimen of choice for most patients with respiratory virus infections, supplementary molecular testing of saliva can improve the clinical management of these patients. The first part of the study consisted of patients whose NPA samples tested positive for respiratory viruses by DFA or the influenza A virus M gene by real-time RT-PCR during routine respiratory virus testing in our clinical microbiology laboratory ( Figure 1 ). In the first part of this study, saliva had a higher viral load than NPA in 17.0% of the patients who tested positive for respiratory viruses by DFA or influenza A virus by RT-PCR in their NPA samples. abstract: Emerging infectious diseases in humans are often caused by respiratory viruses such as pandemic or avian influenza viruses and novel coronaviruses. Microbiological testing for respiratory viruses is important for patient management, infection control and epidemiological studies. Nasopharyngeal specimens are frequently tested, but their sensitivity is suboptimal. This study evaluated the incremental benefit of testing respiratory viruses in expectorated saliva using molecular assays. A total of 258 hospitalized adult patients with suspected respiratory infections were included. Their expectorated saliva was collected without the use of any special devices. In the first cohort of 159 patients whose nasopharyngeal aspirates (NPAs) tested positive for respiratory viruses during routine testing, the viral load was measured using quantitative reverse transcription PCR. Seventeen percent of the patients (27/159) had higher viral loads in the saliva than in the NPA. The second cohort consisted of 99 patients whose NPAs tested negative for respiratory viruses using a direct immunofluorescence assay. Their NPA and saliva specimens were additionally tested using multiplex PCR. In these patients, the concordance rate by multiplex PCR between NPA and saliva was 83.8%. Multiplex PCR detected viruses in saliva samples from 16 patients, of which nine (56.3%) had at least one virus that was not detected in the NPA. Decisions on antiviral or isolation precautions would be affected by salivary testing in six patients. Although NPAs have high viral loads and remain the specimen of choice for most patients with respiratory virus infections, supplementary molecular testing of saliva can improve the clinical management of these patients. url: https://www.ncbi.nlm.nih.gov/pubmed/28588283/ doi: 10.1038/emi.2017.35 id: cord-283786-d65njv7b author: Toptan, Tuna title: Optimized qRT-PCR Approach for the Detection of Intra- and Extra-Cellular SARS-CoV-2 RNAs date: 2020-06-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The novel coronavirus SARS-CoV-2 is the causative agent of the acute respiratory disease COVID-19, which has become a global concern due to its rapid spread. Meanwhile, increased demand for testing has led to a shortage of reagents and supplies and compromised the performance of diagnostic laboratories in many countries. Both the World Health Organization (WHO) and the Center for Disease Control and Prevention (CDC) recommend multi-step RT-PCR assays using multiple primer and probe pairs, which might complicate the interpretation of the test results, especially for borderline cases. In this study, we describe an alternative RT-PCR approach for the detection of SARS-CoV-2 RNA that can be used for the probe-based detection of clinical isolates in diagnostics as well as in research labs using a low-cost SYBR green method. For the evaluation, we used samples from patients with confirmed SARS-CoV-2 infections and performed RT-PCR assays along with successive dilutions of RNA standards to determine the limit of detection. We identified an M-gene binding primer and probe pair highly suitable for the quantitative detection of SARS-CoV-2 RNA for diagnostic and research purposes. url: https://www.ncbi.nlm.nih.gov/pubmed/32575728/ doi: 10.3390/ijms21124396 id: cord-266150-wox7pnkr author: Torres, Juan Pablo title: SARS-CoV-2 antibody prevalence in blood in a large school community subject to a Covid-19 outbreak: a cross-sectional study date: 2020-07-10 words: 4202.0 sentences: 222.0 pages: flesch: 53.0 cache: ./cache/cord-266150-wox7pnkr.txt txt: ./txt/cord-266150-wox7pnkr.txt summary: Once these forms were signed, a copy was emailed to participants for their records and they were directed to a secure survey that i) asked basic demographic questions, ii) requested information on any previous RT-PCR test for SARS-CoV-2 and potential contact with any Covid-19 positive cases, and iii) asked about symptoms experienced since the outbreak (date and duration in days of each symptom). Among students, antibody positive children were younger, had a higher PCR positivity rate (in those who underwent PCR testing during the outbreak), and were more likely to self-report contact with one or more confirmed cases, as compared to seronegative children ( Table 2 ). Overall, PCR testing and contact history was significantly higher in staff compared to students, which in addition to the higher antibody positivity observed in this study, support the more significant role of adults within the outbreak, in proportion to the overall population. abstract: BACKGROUND: A SARS-CoV-2 outbreak affecting 52 people from a large school community in Santiago, Chile was identified (March 12), nine days after the first country case. We assessed the magnitude of the outbreak and the role students and staff played using a self-administered antibody detection test and survey. METHODS: The school was closed on March 13, and the entire community was placed under quarantine. We implemented a home-delivery, self-administered, IgG/IgM antibody test and survey to a classroom stratified sample of students and all staff from May 4-19. We aimed to determine overall seroprevalence rates by age group, reported symptoms, contact exposure and to explore dynamics of transmission. RESULTS: Antibody positivity rates were 9.9% (95%CI: 8.2-11.8) for 1,009 students and 16.6% (95%CI: 12.1-21.9) for 235 staff. Among students, positivity was associated with younger age (P=0.01), lower grade level (P=0.05), prior RT-PCR positivity (P=0.03), and history of contact with a confirmed case (P<0.001). Among staff, positivity was higher in teachers (P=0.01) and in those previously RT-PCR positive (P<0.001). Excluding RT-PCR positive individuals, antibody positivity was associated with fever in adults and children (P=0.02; P=0.002), abdominal pain in children (P=0.001), and chest pain in adults (P=0.02). Within antibody positive individuals, 40% of students and 18% of staff reported no symptoms (P=0.01). CONCLUSIONS: Teachers were more affected during the outbreak and younger children were at higher infection risk, likely because index case(s) were teachers and/or parents from preschool. Self-administered antibody testing, supervised remotely, proved to be a suitable and rapid tool. Our study provides useful information for school re-openings. url: https://doi.org/10.1093/cid/ciaa955 doi: 10.1093/cid/ciaa955 id: cord-031565-mos619wp author: Troedsson, Christofer title: Quantification of copepod gut content by differential length amplification quantitative PCR (dla-qPCR) date: 2009-02-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Quantification of feeding rates and selectivity of zooplankton is vital for understanding the mechanisms structuring marine ecosystems. However, methodological limitations have made many of these studies difficult. Recently, molecular based methods have demonstrated that DNA from prey species can be used to identify zooplankton gut contents, and further, quantitative gut content estimates by quantitative PCR (qPCR) assays targeted to the 18S rRNA gene have been used to estimate feeding rates in appendicularians and copepods. However, while standard single primer based qPCR assays were quantitative for the filter feeding appendicularian Oikopleura dioica, feeding rates were consistently underestimated in the copepod Calanus finmarchicus. In this study, we test the hypothesis that prey DNA is rapidly digested after ingestion by copepods and describe a qPCR-based assay, differential length amplification qPCR (dla-qPCR), to account for DNA digestion. The assay utilizes multiple primer sets that amplify different sized fragments of the prey 18S rRNA gene and, based on the differential amplification of these fragments, the degree of digestion is estimated and corrected for. Application of this approach to C. finmarchicus fed Rhodomonas marina significantly improved quantitative feeding estimates compared to standard qPCR. The development of dla-qPCR represents a significant advancement towards a quantitative method for assessing in situ copepod feeding rates without involving cultivation-based manipulation. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7477863/ doi: 10.1007/s00227-008-1079-8 id: cord-318614-518giv0m author: Tsai, Jih-Jin title: A fully automated sample-to-answer PCR system for easy and sensitive detection of dengue virus in human serum and mosquitos date: 2019-07-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: The insulated isothermal PCR (iiPCR) technology enables consistent PCR amplification and detection in a simple heating device. A pan-dengue virus (DENV) RT-iiPCR, targeting the 5’ untranslated region, was validated previously on the semi-automated POCKIT combo system (involving separate devices for nucleic acid extraction and PCR amplification/detection) to offer performance comparable to a laboratory real-time PCR. Working on the same technologies, a compact automated sample-in-answer-out system (POCKIT Central Nucleic Acid Analyser) has been available commercially for iiPCR, minimizing human error risks and allowing easy molecular bio-detection near points of need. Here, we evaluated the analytical and clinical performance of the pan-DENV RT-iiPCR on the fully automated system by comparison to those on the semi-automated system. METHODOLOGY/PRINCIPAL FINDINGS: Testing sera containing serial diluted DENV-1, -2, -3, or -4 cell culture stock, the pan-DENV RT-iiPCR system had similar 100% detection endpoints on the two systems; i.e. at 1, 10, 1 and 10 PFU/ml, respectively, on the fully automated system, and at 10, 1, 10 and 10 PFU/ml, respectively, on the semi-automated system. Furthermore, both fully automated and semi-automated PCR system can detect all four DENV serotypes in mosquitos. Clinical performance of the reagent on the two systems was evaluated by testing 60 human serum samples. Both systems detected the same 40 samples (ten DENV-1, -2, -3, and -4 positive each) and did not detect the other 20; 100% agreement (κ = 1) was found between the two systems. CONCLUSIONS/SIGNIFICANCE: With performance comparable to a previously validated system, the fully-automated PCR system allows applications of the pan-DENV reagent as a useful tool near points of need to facilitate easy, fast and effective detection of dengue virus and help mitigate versatile public health challenges in the control and management of dengue disease. url: https://doi.org/10.1371/journal.pone.0218139 doi: 10.1371/journal.pone.0218139 id: cord-289735-iw3uq2z9 author: Tsou, P. title: Association between multiple respiratory viral infections and pediatric intensive care unit admission among infants with bronchiolitis date: 2019-11-25 words: 3864.0 sentences: 193.0 pages: flesch: 37.0 cache: ./cache/cord-289735-iw3uq2z9.txt txt: ./txt/cord-289735-iw3uq2z9.txt summary: BACKGROUND: It is unclear whether multiple respiratory viral infections are associated with more severe bronchiolitis requiring pediatric intensive care unit (PICU) admission. Other viruses frequently found in children with bronchiolitis include rhinovirus, Background: It is unclear whether multiple respiratory viral infections are associated with more severe bronchiolitis requiring pediatric intensive care unit (PICU) admission. To address these issues, we conducted a case-control study and performed a multivariable regression analysis to determine the association between severe bronchiolitis resulting in PICU admission and the number of viral co-infections among previously healthy infants hospitalized for acute bronchiolitis, while accounting for confounders. As controls, the same number of neonates (<28 days; n = 20) and infants (n = 135) were randomly selected among the 890 patients (age 1 year) with bronchiolitis admitted to the general pediatric unit, and for whom PCR was performed during the same study period, using a random sampling method. abstract: BACKGROUND: It is unclear whether multiple respiratory viral infections are associated with more severe bronchiolitis requiring pediatric intensive care unit (PICU) admission. We aimed to identify the association between multiple respiratory viral infections and PICU admission among infants with bronchiolitis. METHODS: We performed a 1:1 case-control study enrolling previously healthy full-term infants (≤12 months) with bronchiolitis admitted to the PICU as cases and those to the general pediatric ward as controls from 2015 to 2017. Multiplex polymerase chain reaction (PCR) was used for detection of the respiratory viruses. We summarized the characteristics of infants admitted to the PICU and the general pediatric unit. Multivariable logistic regression analysis was used to fit the association between multiple respiratory viral infections (≥2 strains) and PICU admission. RESULTS: A total of 135 infants admitted to the PICU were compared with 135 randomly selected control infants admitted to the general pediatric unit. The PICU patients were younger (median: 2.2 months, interquartile range: 1.3–4.2) than the general ward patients (median: 3.2 months, interquartile range: 1.6–6.4). Respiratory syncytial virus (74.1%), rhinovirus (28.9%), and coronavirus (5.9%) were the most common viruses for bronchiolitis requiring PICU admission. Patients with bronchiolitis admitted to the PICU tended to have multiple viral infections compared with patients on the general ward (23.0% vs. 10.4%, P < 0.001). In the multivariable logistic regression analysis, bronchiolitis with multiple viral infections was associated with higher odds of PICU admission (adjusted odds ratio: 2.56, 95% confidence interval: 1.17–5.57, P = 0.02). CONCLUSION: Infants with multiviral bronchiolitis have higher odds of PICU admission compared with those with a single or nondetectable viral infection. url: https://www.ncbi.nlm.nih.gov/pubmed/31780096/ doi: 10.1016/j.arcped.2019.11.006 id: cord-260481-twk5kvd3 author: Täufer, Matthias title: Rapid, large-scale, and effective detection of COVID-19 via non-adaptive testing date: 2020-08-18 words: 3854.0 sentences: 226.0 pages: flesch: 64.0 cache: ./cache/cord-260481-twk5kvd3.txt txt: ./txt/cord-260481-twk5kvd3.txt summary: More precisely, assuming knowledge about the overall incidence rate, we calculate explicit error bounds on the number of false positives which scale favourably with pool size and sample multiplicity. then in any multipooling strategy with pool size n and multiplicity k, the probability of a positive test being a false positive does not exceed fp . Table 1 : Probability of a positive result being a false positive and the compression k/n compared to individual testing for pool size n = 31, incidence ρ ≤ 0.01 and different multiplicities k. If we choose k = 4 and accept fp = 1.2% as the k fp k/n 3 0.17 0.049 4 0.012 0.066 5 0.0007 0.082 Table 2 : Probability of a positive result being a false positive and the compression k/n compared to individual testing for pool size n = 31, incidence ρ ≤ 0.01 and different multiplicities k. abstract: Pooling of samples can increase lab capacity when using Polymerase chain reaction (PCR) to detect diseases such as COVID-19. However, pool testing is typically performed via an adaptive testing strategy which requires a feedback loop in the lab and at least two PCR runs to confirm positive results. This can cost precious time. We discuss a non-adaptive testing method where each sample is distributed in a prescribed manner over several pools, and which yields reliable results after one round of testing. More precisely, assuming knowledge about the overall incidence rate, we calculate explicit error bounds on the number of false positives which scale favourably with pool size and sample multiplicity. This allows for hugely streamlined PCR testing and cuts in detection times for a large-scale testing scenario. A viable consequence of this method could be real-time screening of entire communities, frontline healthcare workers and international flight passengers, for example, using the PCR machines currently in operation. url: https://doi.org/10.1101/2020.04.06.028431 doi: 10.1101/2020.04.06.028431 id: cord-263279-afdmegq0 author: Uhteg, Katharine title: Comparing the analytical performance of three SARS-CoV-2 molecular diagnostic assays date: 2020-04-26 words: 3175.0 sentences: 186.0 pages: flesch: 51.0 cache: ./cache/cord-263279-afdmegq0.txt txt: ./txt/cord-263279-afdmegq0.txt summary: Of the first assays that were available for validations were the CDC COVID-19 RT-PCR panel assay (IDT, Coralville, IA) as well as the RealStar® SARS-CoV-2 RT-PCR (Altona Diagnostics, Hamburg, Germany), and both were initially validated for clinical use at the Johns Hopkins Hospital Medical Microbiology laboratory. To compare the analytical performance of the three assays, positive and negative SARS-CoV-2 clinical specimens (using the RealStar® SARS-CoV-2 as the reference method as this assay was the first to be offered in house for clinical diagnosis) were tested by the CDC COVID-19 RT-PCR and/ or the ePlex® SARS-CoV-2 assays. Comparing the performance of the CDC COVID-19 RT-PCR to the RealStar® SARS-CoV-2 included testing 20 positive and 48 negative clinical NP specimens. In this study, we compared the analytical performance of three different molecular assays for the detection of SARS-CoV-2; the RealStar® SARS-CoV-2 RT-PCR, ePlex® SARS-CoV-2, and the CDC COVID-19 RT-PCR tests. abstract: In December 2019, a novel coronavirus (SARS-CoV-2) was first isolated from Wuhan city, China and within three months, the global community was challenged with a devastating pandemic. The rapid spread of the virus challenged diagnostic laboratories to rapidly develop molecular diagnostic methods. As SARS CoV-2 assays became available for testing on existing molecular platforms, laboratories devoted unprecedented energy and resources into evaluating the analytical performance of the new tests and in some cases developed their own diagnostic assays under FDA-EUA guidance. This study compares the validation of three different molecular assays at the Johns Hopkins Molecular Virology laboratory: the RealStar® SARS-CoV-2 RT-PCR, ePlex® SARS-CoV-2, and the CDC COVID-19 RT-PCR tests. Overall, our studies indicate a comparable analytical performance of the three assays for the detection of SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32361285/ doi: 10.1016/j.jcv.2020.104384 id: cord-321443-89o13sox author: Umazume, Takeshi title: Survey on the use of personal protective equipment and COVID‐19 testing of pregnant women in Japan date: 2020-08-10 words: 2029.0 sentences: 116.0 pages: flesch: 53.0 cache: ./cache/cord-321443-89o13sox.txt txt: ./txt/cord-321443-89o13sox.txt summary: AIM: To clarify the status of personal protective equipment (PPE) and coronavirus disease 2019 (COVID‐19) tests for pregnant women, we conducted an urgent survey. Our study also determined that around 65.0% of facilities for doctors and 73.5% of facilities for midwives used PPE beyond the "standard gown or apron, surgical mask, goggles or face shield" during labor of asymptomatic women. 3 In order to clarify the status of PPE usage during labor and delivery and COVID-19 tests for pregnant women, we conducted an urgent survey in Japan. Status of PPE use beyond "standard gown or apron, surgical mask, goggle or face shield" during labor of women without symptoms of COVID-19 Pregnant women were tested for COVID-19 not only in perinatal medical centers and university hospitals, but also other facilities, at a rate of 9-17% (Table S2) . Appropriate guidelines for PPE usage by medical providers and COVID-19 testing for pregnant women before delivery are necessary in Japan. abstract: AIM: To clarify the status of personal protective equipment (PPE) and coronavirus disease 2019 (COVID‐19) tests for pregnant women, we conducted an urgent survey. METHODS: The survey was conducted online from April 27 to May 1, 2020. Questionnaires were sent to core facilities and affiliated hospitals of the obstetrics and gynecology training program and to hospitals of the national perinatal medical liaison council. RESULTS: A total of 296 institutions participated in our survey; however, 2 institutions were excluded. Full PPE was used by doctors in 7.1% of facilities and by midwives in 6.8%. Our study also determined that around 65.0% of facilities for doctors and 73.5% of facilities for midwives used PPE beyond the “standard gown or apron, surgical mask, goggles or face shield” during labor of asymptomatic women. N95 masks were running out of stock at 6.5% of the facilities and goggles and face shields at 2.7%. Disposable N95 masks and goggles or face shields were re‐used after re‐sterilization in 12% and 14% of facilities, respectively. Polymerase chain reaction (PCR) testing of asymptomatic patients was performed for 9% of vaginal deliveries, 14% of planned cesarean sections and 17% of emergency cesarean sections. The number of PCR tests for obstetrics and gynecology per a week ranged from zero to five in 92% of facilities. CONCLUSION: The shortage of PPE in Japan is alarming. Sufficient stockpiling of PPE is necessary to prevent unnecessary disruptions in medical care. Appropriate guidelines for PPE usage and COVID‐19 testing of pregnant women at delivery are needed in Japan. url: https://www.ncbi.nlm.nih.gov/pubmed/32779285/ doi: 10.1111/jog.14382 id: cord-300338-duhyb754 author: Urashima, Mitsuyoshi title: BCG Vaccination and Mortality of COVID-19 across 173 Countries: An Ecological Study date: 2020-08-03 words: 5672.0 sentences: 250.0 pages: flesch: 44.0 cache: ./cache/cord-300338-duhyb754.txt txt: ./txt/cord-300338-duhyb754.txt summary: We therefore aimed to explore whether recent BCG vaccine coverage is associated with COVID-19 morbidity and/or mortality rates, using linear regression models to explore associations between the two continuous random variables adjusted for a variety of potential confounders, such as median age and body mass index (BMI) in individual countries through this ecological study. As a result, ''≥60 years of age'' (p < 0.001) and ''BCG vaccine coverage'' (p = 0.002) remained significant factors associated with COVID-19 mortality, even after adjustment for morbidity and PCR-tests. As a result, ''≥60 years of age'' (p < 0.001) and ''BCG vaccine coverage'' (p = 0.002) remained significant factors associated with COVID-19 mortality, even after adjustment for morbidity and PCR-tests. abstract: Ecological studies have suggested fewer COVID-19 morbidities and mortalities in Bacillus Calmette–Guérin (BCG)-vaccinated countries than BCG-non-vaccinated countries. However, these studies obtained data during the early phase of the pandemic and did not adjust for potential confounders, including PCR-test numbers per population (PCR-tests). Currently—more than four months after declaration of the pandemic—the BCG-hypothesis needs reexamining. An ecological study was conducted by obtaining data of 61 factors in 173 countries, including BCG vaccine coverage (%), using morbidity and mortality as outcomes, obtained from open resources. ‘Urban population (%)’ and ‘insufficient physical activity (%)’ in each country was positively associated with morbidity, but not mortality, after adjustment for PCR-tests. On the other hand, recent BCG vaccine coverage (%) was negatively associated with mortality, but not morbidity, even with adjustment for percentage of the population ≥ 60 years of age, morbidity, PCR-tests and other factors. The results of this study generated a hypothesis that a national BCG vaccination program seems to be associated with reduced mortality of COVID-19, although this needs to be further examined and proved by randomized clinical trials. url: https://doi.org/10.3390/ijerph17155589 doi: 10.3390/ijerph17155589 id: cord-351492-8jv7ip67 author: Urwin, S. G. title: FebriDx point-of-care test in patients with suspected COVID-19: a pooled diagnostic accuracy study date: 2020-10-20 words: 7241.0 sentences: 397.0 pages: flesch: 53.0 cache: ./cache/cord-351492-8jv7ip67.txt txt: ./txt/cord-351492-8jv7ip67.txt summary: Methods: A literature search was performed on the 1st of October 2020 to identify studies reporting diagnostic accuracy statistics of the FebriDx POC test versus real time reverse transcriptase polymerase chain reaction (RT-PCR) testing for SARS-CoV-2. Conclusions: Based on a large sample of patients from two studies during the first wave of the SARS-CoV-2 pandemic, the FebriDx POC test had reasonable diagnostic accuracy in a hospital setting with high COVID-19 prevalence, out of influenza season. In this systematic review and pooled analysis of IPD, we found that the FebriDx LFD had a pooled sensitivity of 0.920 (95% CI: 0.875-0.950) and specificity of 0.862 (0.819-0.896) for COVID-19 across two studies performed within acute hospitals in the UK when compared to RT-PCR on nose and throat swabs during the first wave of the SARS-CoV-2 pandemic. abstract: Background: Point-of-care (POC) tests for COVID-19 could relieve pressure on isolation resource, support infection prevention and control, and help commence more timely and appropriate treatment. We aimed to undertake a systematic review and pooled diagnostic test accuracy study of available individual patient data (IPD) to evaluate the diagnostic accuracy of a commercial POC test (FebriDx) in patients with suspected COVID-19. Methods: A literature search was performed on the 1st of October 2020 to identify studies reporting diagnostic accuracy statistics of the FebriDx POC test versus real time reverse transcriptase polymerase chain reaction (RT-PCR) testing for SARS-CoV-2. Studies were screened for risk of bias. IPD were sought from studies meeting the inclusion and exclusion criteria. Logistic regression was performed to investigate the study effect on the outcome of the RT-PCR test result in order to determine whether it was appropriate to pool results. Diagnostic accuracy statistics were calculated with 95% confidence intervals (CIs). Results: 15 studies were screened, and we included two published studies with 527 hospitalised patients. 523 patients had valid FebriDx results for Myxovirus resistance protein A (MxA), an antiviral host response protein. The FebriDx test produced a pooled sensitivity of 0.920 (95% CI: 0.875-0.950) and specificity of 0.862 (0.819-0.896) compared with RT-PCR, where there was an estimated true COVID-19 prevalence of 0.405 (0.364-0.448) and overall FebriDx test yield was 99.2%. Patients were tested at a median of 4 days [interquartile range: 2:9] after symptom onset. No differences were found in a sub-group analysis of time tested since the onset of symptoms. Conclusions: Based on a large sample of patients from two studies during the first wave of the SARS-CoV-2 pandemic, the FebriDx POC test had reasonable diagnostic accuracy in a hospital setting with high COVID-19 prevalence, out of influenza season. More research is required to determine how FebriDx would perform in other healthcare settings with higher or lower COVID-19 prevalence, different patient populations, or when other respiratory infections are in circulation. url: http://medrxiv.org/cgi/content/short/2020.10.15.20213108v1?rss=1 doi: 10.1101/2020.10.15.20213108 id: cord-273840-jjm7y07m author: Vabret, Astrid title: Detection of the New Human Coronavirus HKU1: A Report of 6 Cases date: 2006-03-01 words: 3057.0 sentences: 168.0 pages: flesch: 54.0 cache: ./cache/cord-273840-jjm7y07m.txt txt: ./txt/cord-273840-jjm7y07m.txt summary: The clinical presentation of these 6 patients was as follows: 3 were admitted to the hospital for acute enteric disease resulting in severe dehydration associated with upper respiratory symptoms; 1 had fever, otitis, and febrile seizure; 1 had a sample obtained to investigate failure to thrive; and 1 had a sample obtained for exploration of X-linked agammaglobulinemia and hyperleucocytosis. Our results suggest that HCoV-HKU1 could be associated with respiratory and enteric diseases, and its detection can be related to a persistent asymptomatic infection in patients with poor underlying conditions. For 2 patients with results positive for detection of HCoV-HKU1 in respiratory specimens, stool samples obtained at the same time were available and have been tested. To eliminate cell culture contamination, the N gene HCoV-HKU1 RT-PCR was performed directly on the respiratory specimens obtained from the 6 patients. Patient 6, who tested positive for HCoV-HKU1, had an influenza C virus detected in the same clinical specimen. abstract: Background. Human coronavirus HKU1 (HCoV-HKU1), a new group 2 coronavirus, was first characterized in 2005 from 2 adults with pneumonia in Hong Kong, China. To the best of our knowledge, there is no other report to date about the detection of this new virus. We report a molecular method allowing for the detection of HCoV-HKU1 and also report the clinical presentation of 6 infected patients. Methods. We screened 141 specimens (135 nasal samples and 6 stool samples) received in February and March 2005 in our laboratory and obtained from 135 hospitalized patients (61.5% of whom were <5 years old and 34.1% of whom were >20 years old) for HCoV-HKU1. Results. HCoV-HKU1 was detected in 6 (4.4%) of the 135 nasal specimens and in 2 (33.3%) of the 6 stool samples; the positive samples were obtained from 6 patients (5 children and 1 adult). The clinical presentation of these 6 patients was as follows: 3 were admitted to the hospital for acute enteric disease resulting in severe dehydration associated with upper respiratory symptoms; 1 had fever, otitis, and febrile seizure; 1 had a sample obtained to investigate failure to thrive; and 1 had a sample obtained for exploration of X-linked agammaglobulinemia and hyperleucocytosis. Conclusion. HCoV-HKU1 can be detected in respiratory and stool samples from children and adults in a part of the world other than Hong Kong. Our results suggest that HCoV-HKU1 could be associated with respiratory and enteric diseases, and its detection can be related to a persistent asymptomatic infection in patients with poor underlying conditions. url: https://www.ncbi.nlm.nih.gov/pubmed/16447108/ doi: 10.1086/500136 id: cord-283641-2u16otbf author: Vainionpää, R. title: Diagnostic Techniques: Serological and Molecular Approaches date: 2015-03-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Virus laboratory diagnostics has an increasingly important role in modern patient care. Virological methods are needed to investigate the etiology of acute viral infection or the reactivation of a latent infection, as well as to follow virus load in antiviral treatments. Serological assays are also used for screening of blood products for the risk of certain chronic infections, evaluation of the immune status, and need for prophylactic treatments in connection with organ transplantations. For diagnostic purposes the following approaches can be used: demonstration of presence of infectious virus or its structural components directly from a patient's specimens or investigation of specific antibody response in serum specimens. Amplification techniques, most commonly polymerase chain reaction (PCR) is currently the workhorse of nucleic acid testing for the detection and quantitation of virus genomes. Virus isolation is used to demonstrate infectious virus in a patient's specimens, whereas virus antigens are investigated by antigen detection assays. Serological diagnosis is based on either the demonstration of the presence of virus-specific IgM antibodies or a significant increase in the levels and/or avidity of specific IgG antibodies. Immunoassays are the most commonly used serological assays. Point-of-care tests (POC tests), for antigens, antibodies, and also nucleic acids are also becoming more and more common in diagnostic use. In order to reach the best diagnostic efficiency for each patient it is important to select the most suitable method using the right sample collected at the right time. url: https://www.sciencedirect.com/science/article/pii/B9780128012383025587 doi: 10.1016/b978-0-12-801238-3.02558-7 id: cord-326130-wm3l1849 author: Van Pelt, Amelia title: Evaluation of COVID-19 Testing Strategies for Repopulating College and University Campuses: A Decision Tree Analysis date: 2020-11-03 words: 4767.0 sentences: 246.0 pages: flesch: 55.0 cache: ./cache/cord-326130-wm3l1849.txt txt: ./txt/cord-326130-wm3l1849.txt summary: To account for individuals presenting with symptoms that mimic COVID-19 disease that would prompt testing or positive diagnosis in the absence of testing, an estimate of .0957 was used based on the prevalence of college students who develop influenza-like illness in November (the earliest month with data available for the first semester) [22] . To the best of our knowledge, this is the first study that used a formal decision tree analysis to evaluate the true positives and negatives and the number of RT-PCR tests needed for a comprehensive range of COVID-19 testing strategies for repopulating a university campus. Based on the analysis of TTP, there is no value of willingness to trade off RT-PCR tests for true positive students detected for which Strategy 3 (universal, single RT-PCR testing) was preferred. In summary, strategies that include RT-PCR testing will identify more COVID-19 cases than symptom-based screening, but all approaches will fail to detect a proportion of infected students. abstract: PURPOSE: The optimal approach to identify SARS-CoV-2 infection among college students returning to campus is unknown. Recommendations vary from no testing to two tests per student. This research determined the strategy that optimizes the number of true positives and negatives detected and reverse transcription polymerase chain reaction (RT-PCR) tests needed. METHODS: A decision tree analysis evaluated five strategies: (1) classifying students with symptoms as having COVID-19, (2) RT-PCR testing for symptomatic students, (3) RT-PCR testing for all students, (4) RT-PCR testing for all students and retesting symptomatic students with a negative first test, and (5) RT-PCR testing for all students and retesting all students with a negative first test. The number of true positives, true negatives, RT-PCR tests, and RT-PCR tests per true positive (TTP) was calculated. RESULTS: Strategy 5 detected the most true positives but also required the most tests. The percentage of correctly identified infections was 40.6%, 29.0%, 53.7%, 72.5%, and 86.9% for Strategies 1–5, respectively. All RT-PCR strategies detected more true negatives than the symptom-only strategy. Analysis of TTP demonstrated that the repeat RT-PCR strategies weakly dominated the single RT-PCR strategy and that the thresholds for more intensive RT-PCR testing decreased as the prevalence of infection increased. CONCLUSION: Based on TTP, the single RT-PCR strategy is never preferred. If the cost of RT-PCR testing is of concern, a staged approach involving initial testing of all returning students followed by a repeat testing decision based on the measured prevalence of infection might be considered. url: https://www.ncbi.nlm.nih.gov/pubmed/33153883/ doi: 10.1016/j.jadohealth.2020.09.038 id: cord-344751-i4qnrtjq author: Van Praet, Jens T. title: Comparison of four commercial SARS-CoV-2 IgG immuno-assays in RT-PCR negative patients with suspect CT findings date: 2020-09-10 words: 2399.0 sentences: 119.0 pages: flesch: 49.0 cache: ./cache/cord-344751-i4qnrtjq.txt txt: ./txt/cord-344751-i4qnrtjq.txt summary: Clinical specificity for Covid-19 of some N protein-based immuno-assays was suboptimal, as positive results were observed in control patients with recent common human coronavirus, influenza B and adenovirus infections. To evaluate the specificity of the immuno-assays, we used a set of serum samples from control patients with recent respiratory viral or atypical bacterial infections. To this end, we tested for cross-reactivity with sera of patients with other respiratory viral or atypical bacterial infections, including common coronavirus infections, since these may present with clinical and radiological findings similar to Covid-19. Our study focused on the clinical sensitivity and specificity of four commercial immuno-assays for anti-SARS-COV-2 IgG in the subset of patients presenting with negative RT-PCR and suspect CT findings. In summary, we found good clinical sensitivity of anti-SARS-Cov-2 IgG immunoassays for Covid-19 in the subset of patients with negative RT-PCR 14 days after onset of symptoms. abstract: A subset of patients with Covid-19 presents with negative RT-PCR screening but suspect CT findings. Using four commercially available anti-SARS-CoV-2 IgG immuno-assays, we found this subset constituted 9.2% of all consecutively admitted outpatients with Covid-19 in our hospital. Clinical specificity for Covid-19 of some N protein-based immuno-assays was suboptimal, as positive results were observed in control patients with recent common human coronavirus, influenza B and adenovirus infections. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s15010-020-01523-3) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s15010-020-01523-3 doi: 10.1007/s15010-020-01523-3 id: cord-296109-kco85lqn author: Vanuytsel, Kim title: Rapid Implementation of a SARS-CoV-2 Diagnostic qRT-PCR Test with Emergency Use Authorization at a Large Academic Safety-Net Hospital date: 2020-05-19 words: 2499.0 sentences: 132.0 pages: flesch: 47.0 cache: ./cache/cord-296109-kco85lqn.txt txt: ./txt/cord-296109-kco85lqn.txt summary: Furthermore, vulnerable populations such as those served by Boston Medical Center (BMC), the largest safety net hospital in New England, represent a high-risk group across multiple dimensions, including a higher prevalence of pre-existing conditions and substance use disorders, lower health maintenance, unstable housing, and a propensity for rapid community spread, highlighting the urgent need for expedient and reliable in-house testing. In the United States, significant delays in the rapid development and distribution of diagnostic testing for SARS-CoV-2 infection have prevented adequate COVID-19 patient care and public health management of the pandemic (Sharfstein et al., 2020) , impacting the timely mapping of the dynamics of viral spread in the general population, and more topically, the conservation of personal protective equipment. Subsequently, we implemented a quantitative, real-time reverse transcriptase polymerase chain reaction (qRT-PCR)-based assay to detect viral SARS-CoV-2 RNA from nasopharyngeal swabs, based on guidelines from the Centers for Disease Control and Prevention (CDC) and the FDA for use with in-house testing of BMC patient samples ( Figure 1 ) (CDC, 2020; Wang et al., 2020a). abstract: Summary The COVID-19 pandemic is a global public health crisis. Significant delays in the rapid development and distribution of diagnostic testing for SARS-CoV-2 infection have prevented adequate public health management of the disease, impacting the timely mapping of viral spread and the conservation of personal protective equipment. Furthermore, vulnerable populations such as those served by Boston Medical Center (BMC), the largest safety net hospital in New England, represent a high-risk group across multiple dimensions, including a higher prevalence of pre-existing conditions and substance use disorders, lower health maintenance, unstable housing, and a propensity for rapid community spread, highlighting the urgent need for expedient and reliable in-house testing. Here, we report the implementation of a SARS-CoV-2 diagnostic RT-PCR assay with rapid turnaround time enabling more informed decisions with personal and public health ramifications. This work provides a blueprint for academic centers and community hospitals lacking capital-intensive automated laboratory machinery to implement in-house testing. url: https://www.sciencedirect.com/science/article/pii/S2666634020300039?v=s5 doi: 10.1016/j.medj.2020.05.001 id: cord-030026-4jew57ce author: Vasala, Antti title: Modern Tools for Rapid Diagnostics of Antimicrobial Resistance date: 2020-07-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Fast, robust, and affordable antimicrobial susceptibility testing (AST) is required, as roughly 50% of antibiotic treatments are started with wrong antibiotics and without a proper diagnosis of the pathogen. Validated growth-based AST according to EUCAST or CLSI (European Committee on Antimicrobial Susceptibility Testing, Clinical Laboratory Standards Institute) recommendations is currently suggested to guide the antimicrobial therapy. Any new AST should be validated against these standard methods. Many rapid diagnostic techniques can already provide pathogen identification. Some of them can additionally detect the presence of resistance genes or resistance proteins, but usually isolated pure cultures are needed for AST. We discuss the value of the technologies applying nucleic acid amplification, whole genome sequencing, and hybridization as well as immunodiagnostic and mass spectrometry-based methods and biosensor-based AST. Additionally, we evaluate the potential of integrated systems applying microfluidics to integrate cultivation, lysis, purification, and signal reading steps. We discuss technologies and commercial products with potential for Point-of-Care Testing (POCT) and their capability to analyze polymicrobial samples without pre-purification steps. The purpose of this critical review is to present the needs and drivers for AST development, to show the benefits and limitations of AST methods, to introduce promising new POCT-compatible technologies, and to discuss AST technologies that are likely to thrive in the future. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7373752/ doi: 10.3389/fcimb.2020.00308 id: cord-298998-n5rhhzc9 author: Vashee, Sanjay title: Cloning, Assembly, and Modification of the Primary Human Cytomegalovirus Isolate Toledo by Yeast-Based Transformation-Associated Recombination date: 2017-10-04 words: 9327.0 sentences: 440.0 pages: flesch: 48.0 cache: ./cache/cord-298998-n5rhhzc9.txt txt: ./txt/cord-298998-n5rhhzc9.txt summary: Using an early passage of the human CMV isolate Toledo, we first applied transformation-associated recombination (TAR) to clone 16 overlapping fragments covering the entire Toledo genome in Saccharomyces cerevisiae. Since next-generation sequence analysis revealed that the low-passage-number isolate represented a mixture of parental and fibroblast-adapted genomes, we selectively modified individual DNA fragments of fibroblast-adapted Toledo (Toledo-F) and again used TAR assembly to recreate parental Toledo (Toledo-P). IMPORTANCE The genomes of large DNA viruses, such as human cytomegalovirus (HCMV), are difficult to manipulate using current genetic tools, and at this time, it is not possible to obtain, molecular clones of CMV without extensive tissue culture. IMPORTANCE The genomes of large DNA viruses, such as human cytomegalovirus (HCMV), are difficult to manipulate using current genetic tools, and at this time, it is not possible to obtain, molecular clones of CMV without extensive tissue culture. abstract: Genetic engineering of cytomegalovirus (CMV) currently relies on generating a bacterial artificial chromosome (BAC) by introducing a bacterial origin of replication into the viral genome using in vivo recombination in virally infected tissue culture cells. However, this process is inefficient, results in adaptive mutations, and involves deletion of viral genes to avoid oversized genomes when inserting the BAC cassette. Moreover, BAC technology does not permit the simultaneous manipulation of multiple genome loci and cannot be used to construct synthetic genomes. To overcome these limitations, we adapted synthetic biology tools to clone CMV genomes in Saccharomyces cerevisiae. Using an early passage of the human CMV isolate Toledo, we first applied transformation-associated recombination (TAR) to clone 16 overlapping fragments covering the entire Toledo genome in Saccharomyces cerevisiae. Then, we assembled these fragments by TAR in a stepwise process until the entire genome was reconstituted in yeast. Since next-generation sequence analysis revealed that the low-passage-number isolate represented a mixture of parental and fibroblast-adapted genomes, we selectively modified individual DNA fragments of fibroblast-adapted Toledo (Toledo-F) and again used TAR assembly to recreate parental Toledo (Toledo-P). Linear, full-length HCMV genomes were transfected into human fibroblasts to recover virus. Unlike Toledo-F, Toledo-P displayed characteristics of primary isolates, including broad cellular tropism in vitro and the ability to establish latency and reactivation in humanized mice. Our novel strategy thus enables de novo cloning of CMV genomes, more-efficient genome-wide engineering, and the generation of viral genomes that are partially or completely derived from synthetic DNA. IMPORTANCE The genomes of large DNA viruses, such as human cytomegalovirus (HCMV), are difficult to manipulate using current genetic tools, and at this time, it is not possible to obtain, molecular clones of CMV without extensive tissue culture. To overcome these limitations, we used synthetic biology tools to capture genomic fragments from viral DNA and assemble full-length genomes in yeast. Using an early passage of the HCMV isolate Toledo containing a mixture of wild-type and tissue culture-adapted virus. we directly cloned the majority sequence and recreated the minority sequence by simultaneous modification of multiple genomic regions. Thus, our novel approach provides a paradigm to not only efficiently engineer HCMV and other large DNA viruses on a genome-wide scale but also facilitates the cloning and genetic manipulation of primary isolates and provides a pathway to generating entirely synthetic genomes. url: https://www.ncbi.nlm.nih.gov/pubmed/28989973/ doi: 10.1128/mspheredirect.00331-17 id: cord-017363-dmb42kna author: Vemulapalli, Ramesh title: Real-Time Reverse Transcription Polymerase Chain Reaction for Rapid Detection of Transmissible Gastroenteritis Virus date: 2015-09-10 words: 1069.0 sentences: 86.0 pages: flesch: 63.0 cache: ./cache/cord-017363-dmb42kna.txt txt: ./txt/cord-017363-dmb42kna.txt summary: Transmissible gastroenteritis (TGE) is a highly contagious disease of pigs caused by the TGE virus (TGEV). Rapid detection of the virus in the affected pigs'' feces is critical for controlling the disease outbreaks. The real-time RT-PCR assay described in this chapter can quickly detect the presence of TGEV in fecal samples with high sensitivity and specificity. The assay, along with the RNA extraction method described here, can be established in any molecular diagnostic laboratory for detection of TGEV in pig fecal samples [ 6 -8 ] . It is recommended that the nucleic acid extraction, preparation of master mix, and real-time PCR amplifi cation are performed in three physically separated areas. In our experience, RNA extracted from pig fecal samples using the following method is suitable for TGEV detection using the real-time RT-PCR assay. A real-time TaqMan ® RT-PCR assay with an internal amplifi cation control for rapid detection of transmissible gastroenteritis virus in swine fecal samples abstract: Transmissible gastroenteritis (TGE) is a highly contagious disease of pigs caused by the TGE virus (TGEV). Rapid detection of the virus in the affected pigs’ feces is critical for controlling the disease outbreaks. The real-time RT-PCR assay described in this chapter can quickly detect the presence of TGEV in fecal samples with high sensitivity and specificity. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121909/ doi: 10.1007/978-1-4939-3414-0_10 id: cord-338607-22f04uqe author: Verbeek, A. title: Genomic relationship between turkey and bovine enteric coronaviruses identified by hybridization with BCV or TCV specific cDNA probes date: 1991 words: 4120.0 sentences: 192.0 pages: flesch: 47.0 cache: ./cache/cord-338607-22f04uqe.txt txt: ./txt/cord-338607-22f04uqe.txt summary: title: Genomic relationship between turkey and bovine enteric coronaviruses identified by hybridization with BCV or TCV specific cDNA probes Genomic relationships between turkey and bovine coronavirus (TCV and BCV), which are currently placed in distinct antigenic groups, were demonstrated by hybridization using specific cDNA probes. BCV-specific recombinant plasmids p 52, p 27, and p 247, which served previously for the optimization of hybridization conditions for BCV-RNA detection [33] , and probes pN 17 and pN 9, holding respectively the BCV N and M gene ( Fig. 1) , were used in the detection of several coronaviruses in order to establish the presence of potential genomic homologies. Clinical diagnosis of TCV was assayed with a pool of six 32p-labelled BCV specific recombinant plasmids (pBCV-pool), holding non-overlapping eDNA sequences, in order to amplify the detection signal. Detection signals were absent when testing spotted supernatant fluids of non-infected HRT-18 cells (Fig. 2) and when probing identical blots with 32p-labelled pUC-DNA (not shown), confirming the specificity of the hybridization signals obtained. abstract: Genomic relationships between turkey and bovine coronavirus (TCV and BCV), which are currently placed in distinct antigenic groups, were demonstrated by hybridization using specific cDNA probes. BCV-specific recombinant plasmid probes p 52, p 27, and p 247, holding inserts derived from (probably nonstructural) genes, and plasmids pN 17 and pN 9 holding the N and M gene, respectively, permitted the detection of isolates of both BCV and TCV with similar sensitivities. Similarly, probing supernatants of cell cultures infected with several isolates of TCV, using probes pN 17 and pM 78, respectively holding the N gene of BCV and TCV, resulted in equally intense detection signals. Only a slight detection of MHV-3, which is antigenically related to BCV, was observed, whereas the probes did not allow the detection of IBV, TGEV, and HCV-229E, which are placed in antigenic groups separate from those of BCV and TCV. Detection of TCV was improved by hybridization with BCV-specific single-stranded (ss) probes holding sequences of the N and M genes and synthesized by the polymerase chain reaction. Diagnosis of TCV in 134 clinical samples by hybridization was better with PCR-produced ss BCV-specific probes than with ds PCR-produced probes or a combination of six recombinant plasmid probes holding non-overlapping BCV-specific cDNA sequences. Detection signals were absent when probing clinical samples with(32)P-labelled pUC-DNA. url: https://www.ncbi.nlm.nih.gov/pubmed/1662038/ doi: 10.1007/bf01316754 id: cord-322573-1fw1ehzd author: Vicente, Diego title: Human Bocavirus, a Respiratory and Enteric Virus date: 2007-04-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In Spain, human bocavirus (HBoV) was detected in 48 (9.1%) of 527 children with gastroenteritis at similar frequency as for children with respiratory illness (40/520, 7.7%). Fecal excretion adds new concern about the transmission of HBoV. To our knowledge, this report is the first to document HBoV in human feces. url: https://www.ncbi.nlm.nih.gov/pubmed/17553287/ doi: 10.3201/eid1304.061501 id: cord-306682-01q775up author: Vijgen, Leen title: Identification of six new polymorphisms in the human coronavirus 229E receptor gene (aminopeptidase N/CD13)() date: 2004-06-22 words: 2965.0 sentences: 166.0 pages: flesch: 54.0 cache: ./cache/cord-306682-01q775up.txt txt: ./txt/cord-306682-01q775up.txt summary: In this study we examined whether polymorphisms could be detected in the HCoV-229E binding domain of APN in a Caucasian population of 100 unrelated, healthy individuals, assuming that these mutations could be of importance in HCoV-229E attachment to human cells. A total of 100 healthy unrelated Belgian individuals were screened for polymorphisms in the human aminopeptidase N domain that is essential for its HCoV-229E receptor activity. All individuals were heterozygous for these polymorphisms, which have no apparent functional consequence, as they are located in a non-coding intron region of the APN gene. In our search for polymorphisms in the APN domain that is essential for its HCoV-229E receptor function, we identified seven polymorphisms, of which four were located in the non-coding intron 3. Three polymorphisms in APN exon 4 (C956T, G978T and G987A) in association with an intron 3 variation (C389T), were identified at a relatively high allele frequency (8.5%) in our Belgian population. abstract: Objective: Human aminopeptidase N (APN/CD13/ANPEP) has been identified as the receptor for human coronavirus (HCoV) 229E. In this study, we analyzed the region of the APN gene that encodes a stretch of amino acid residues, essential for its HCoV-229E receptor function (amino acids 260–353). Methods: Full-length APN exon 3, intron 3 and exon 4, was PCR-amplified and sequenced in DNA samples from 100 unrelated Caucasian Belgian healthy volunteers. Results: We identified seven polymorphisms, including four intron 3 and three exon 4 variations. Apart from the already known C956T exon 4 mutation, the six other polymorphisms have not yet been described. The most prevalent APN variations in this population (C956T leading to an alanine to valine substitution, G978T, G987A and intron3-C389T) always occurred together at an allele frequency of 8.5%. Haploid DNA sequencing demonstrated the presence of these four variations on the same allele. Three polymorphisms in intron 3, intron3-G395C, intron3-C86T, and intron3-C429T, were identified with an allele frequency of 3.5%, 1% and 0.5% respectively. Five haplotypes were identified in the population of 100 individuals. Conclusion: These results demonstrate that there is a relatively broad spectrum of variations in the APN domain critical for coronavirus binding. The nucleotide sequence reported here has been submitted to the GenBank database with the following accession number: AF527789. url: https://www.ncbi.nlm.nih.gov/pubmed/15234325/ doi: 10.1016/j.ijid.2004.03.004 id: cord-293629-1cno01un author: Vila Estapé, Jordi title: Métodos moleculares de diagnóstico de infecciones respiratorias. ¿Ha cambiado el esquema diagnóstico? date: 2016-07-31 words: 5051.0 sentences: 363.0 pages: flesch: 41.0 cache: ./cache/cord-293629-1cno01un.txt txt: ./txt/cord-293629-1cno01un.txt summary: En este artículo se pretende hacer una revisión de las diversas técnicas de biología molecular aplicadas al diagnóstico de las infecciones respiratorias, centrándose fundamentalmente en la neumonía, y analizar el impacto que pueden tener en el manejo del paciente con infección respiratoria aguda. En este artículo se pretende hacer una revisión de las diversas técnicas de biología molecular aplicadas al diagnóstico de las infecciones respiratorias, centrándose fundamentalmente en la neumonía, y analizar el impacto que pueden tener en el manejo del paciente con infección respiratoria aguda. En los últimos años se han realizado estudios sobre el impacto de las técnicas moleculares en el manejo y pronóstico de pacientes con infecciones respiratorias, así como de coste-efectividad de su implantación en los laboratorios de microbiología clínica. Aplicación de los métodos moleculares al diagnóstico y el estudio epidemiológico de las infecciones respiratorias causadas por virus abstract: Resumen Las infecciones respiratorias bajas siguen siendo una de las causas más frecuentes de mortalidad en todo el mundo, de ahí que el diagnóstico precoz sea fundamental. Tradicionalmente, el diagnóstico microbiológico de este tipo de infecciones se ha basado en métodos convencionales que incluyen cultivos en medios artificiales para aislamiento de bacterias y hongos y cultivos celulares para virus, así como en la detección antigénica o de anticuerpos mediante reacciones antígeno-anticuerpo. El principal inconveniente de las metodologías anteriormente citadas es el tiempo necesario para obtener un diagnóstico etiológico de la infección. Las técnicas basadas en la biología molecular han irrumpido con fuerza en las últimas décadas como herramientas de diagnóstico rápido de las infecciones. Algunas de estas técnicas —sobre todo aquellas que pueden detectar diversos microorganismos en la misma reacción— acostumbran a ser caras, por lo que la cuestión que se plantea es si el gasto de tales ensayos se ve justificado por la información obtenida y por el impacto clínico que su implementación determina. En este artículo se pretende hacer una revisión de las diversas técnicas de biología molecular aplicadas al diagnóstico de las infecciones respiratorias, centrándose fundamentalmente en la neumonía, y analizar el impacto que pueden tener en el manejo del paciente con infección respiratoria aguda. Abstract Lower respiratory tract infections remain one of the most common causes of mortality worldwide, which is why early diagnosis is crucial. Traditionally the microbiological diagnosis of these infections has been based on conventional methods including culture on artificial media for isolation of bacteria and fungi and cell cultures for virus and antibody or antigen detection using antigen-antibody reactions. The main drawback of the above mentioned methods is the time needed for an etiological diagnosis of the infection. The techniques based on molecular biology have drawn much attention in recent decades as tools for rapid diagnosis of infections. Some techniques are very expensive, especially those that can detect various microorganisms in the same reaction, therefore the question that arises is whether the cost of such testing is justified by the information obtained and by the clinical impact that its implementation will determine. In this article we make a review of the various techniques of molecular biology applied to the diagnosis of pneumonia and focus primarily on analysing the impact they may have on the management of patients with acute respiratory tract infections. url: https://www.sciencedirect.com/science/article/pii/S0213005X1630218X doi: 10.1016/s0213-005x(16)30218-x id: cord-317000-bfc51e0m author: Visci, G. title: Serologic SARS-CoV-2 testing in healthcare workers with positive RT-PCR test or Covid-19 related symptoms date: 2020-10-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Background. Limited information is available on prevalence and determinants of serologic response to SARS-CoV-2 infection among healthcare workers (HCWs). Methods. We analyzed the results of serologic testing with chemiluminescence immunoassay analyzer (CLIA), lateral flow immunoassay (LFIA) and enzyme-linked immunosorbent assay (ELISA) test among 544 HCWs with at least one positive RT-PCR test and 157 HCWs with Covid-19 related symptoms without a positive RT-PCR test from public hospitals in Bologna, Northern Italy. Tests were performed between March and August 2020. We fitted multivariate logistic regression models to identify determinants of positive serology. Results. The sensitivity of SARS-CoV-2 was 75.2% (LFIA) and 90.6% (CLIA). No differences in seropositivity were observed by sex, while older HCWs had higher positivity than other groups, and nurses had higher positivity compared to physicians, but not other HCWs. An estimated 73.4% of HCWs with Covid-19 symptoms without RT-PCR test were not infected with SARS-CoV-2. Conclusions. Our study provides the best available data on sensitivity of serologic tests and on determinants of serologic response among HCWs positive for SARS-CoV-2, and provide evidence on the low specificity of Covid-19 related symptoms to identify infected HCWs. url: http://medrxiv.org/cgi/content/short/2020.10.25.20219113v1?rss=1 doi: 10.1101/2020.10.25.20219113 id: cord-279980-49yv65gm author: WANARATANA, S. title: The potential of house flies to act as a vector of avian influenza subtype H5N1 under experimental conditions date: 2010-12-01 words: 4317.0 sentences: 240.0 pages: flesch: 58.0 cache: ./cache/cord-279980-49yv65gm.txt txt: ./txt/cord-279980-49yv65gm.txt summary: The objective of the present study was to determine the potential for house flies (Musca domestica L.) (Diptera: Muscidae) to harbour the avian influenza (AI) H5N1 virus. Before initiation of all experiments the adult stage flies were randomly selected and confirmed to be free of the AI H5N1 virus by the real-time reverse transcription-polymerase chain reaction (RRT-PCR) assay using specific primers and probes to the influenza A matrix (M) gene. The BHI washing fluid (W1) was inoculated into six 10-day-old embryonated chicken eggs to evaluate the presence of the AI H5N1 virus on the external surface of the house flies. The W2 washing fluid was inoculated into six 10-dayold embryonated chicken eggs to confirm the absence of the AI H5N1 virus on the external surface of house flies. Avian influenza (AI) H5N1 virus titre between house fly homogenates and W1 of the AI H5N1 virus exposed house flies at different times of post-exposure in embryonated chicken eggs. abstract: The objective of the present study was to determine the potential for house flies (Musca domestica L.) (Diptera: Muscidae) to harbour the avian influenza (AI) H5N1 virus. Laboratory‐reared flies were experimentally fed with a mixture containing the AI virus. Exposed flies were washed with brain–heart infusion broth and followed by 70% alcohol before preparation of whole fly homogenate. The homogenate was inoculated into six 10‐day‐old embryonated chicken eggs (ECEs). Allantoic fluids were collected to determine the virus using the haemagglutination (HA) test, reverse transcription‐polymerase chain reaction (RT‐PCR) or quantitative real‐time RT‐PCR (RRT‐PCR). In the first experiment, ECEs that were inoculated with the 50 AI virus exposed fly homogenates died within 48 h and HA and RT‐PCR were positive for AI virus. In the second experiment, ECEs that were inoculated with only one fly died with positive HA test and RT‐PCR. In the last experiment, a group of exposed flies was collected at 0, 6, 12, 24, 36, 48, 72 and 96 h post‐exposure. Fly homogenates of each time point were tested by virus titration in ECEs and RRT‐PCR. Virus titres declined in relation to exposure time. Furthermore, RRT‐PCR results were positive at any time point. The present study shows that the flies may harbour the AI virus and could act as a mechanical vector of the AI virus. url: https://doi.org/10.1111/j.1365-2915.2010.00928.x doi: 10.1111/j.1365-2915.2010.00928.x id: cord-345312-i7soyabu author: Wabe, Nasir title: The impact of rapid molecular diagnostic testing for respiratory viruses on outcomes for emergency department patients date: 2019-03-05 words: 2882.0 sentences: 147.0 pages: flesch: 46.0 cache: ./cache/cord-345312-i7soyabu.txt txt: ./txt/cord-345312-i7soyabu.txt summary: OBJECTIVE: To determine whether rapid polymerase chain reaction (PCR) testing for influenza and respiratory syncytial viruses (RSV) in emergency departments (EDs) is associated with better patient and laboratory outcomes than standard multiplex PCR testing. Rapid PCR tests were expected to facilitate timely and appropriate initiation of treatment, improve outbreak prevention and infection control measures, and expedite the assessment of patients in EDs. In this study, we analysed routinely collected data to determine whether rapid PCR testing for influenza and RSV infections in EDs is associated with improved patient and laboratory outcomes. Other studies have also reported that hospital admission numbers were significantly lower when rapid influenza virus testing was used in EDs. An analysis of outcomes for more than 300 adults at a tertiary care centre in New York found that early diagnosis of respiratory infections was associated with significantly fewer hospitalisations of influenza-positive patients. abstract: OBJECTIVE: To determine whether rapid polymerase chain reaction (PCR) testing for influenza and respiratory syncytial viruses (RSV) in emergency departments (EDs) is associated with better patient and laboratory outcomes than standard multiplex PCR testing. DESIGN, SETTING: A before‐and‐after study in four metropolitan EDs in New South Wales. PARTICIPANTS: 1491 consecutive patients tested by standard multiplex PCR during July–December 2016, and 2250 tested by rapid PCR during July–December 2017. MAIN OUTCOME MEASURES: Hospital admissions; ED length of stay (LOS); test turnaround time; patient receiving test result before leaving the ED; ordering of other laboratory tests. RESULTS: Compared with those tested by standard PCR, fewer patients tested by rapid PCR were admitted to hospital (73.3% v 77.7%; P < 0.001) and more received their test results before leaving the ED (67.4% v 1.3%; P < 0.001); the median test turnaround time was also shorter (2.4 h [IQR, 1.6–3.9 h] v 26.7 h [IQR, 21.2–37.8 h]). The proportion of patients admitted to hospital was also lower in the rapid PCR group for both children under 18 (50.6% v 66.6%; P < 0.001) and patients over 60 years of age (84.3% v 91.8%; P < 0.001). Significantly fewer blood culture, blood gas, sputum culture, and respiratory bacterial and viral serology tests were ordered for patients tested by rapid PCR. ED LOS was similar for the rapid (7.4 h; IQR, 5.0–12.9 h) and standard PCR groups (6.5 h; IQR, 4.2–11.9 h; P = 0.27). CONCLUSION: Rapid PCR testing of ED patients for influenza virus and RSV was associated with better outcomes on a range of indicators, suggesting benefits for patients and the health care system. A formal cost–benefit analysis should be undertaken. url: https://doi.org/10.5694/mja2.50049 doi: 10.5694/mja2.50049 id: cord-348975-plne3xlz author: Wagner, Tyler title: Augmented curation of clinical notes from a massive EHR system reveals symptoms of impending COVID-19 diagnosis date: 2020-07-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Understanding temporal dynamics of COVID-19 symptoms could provide fine-grained resolution to guide clinical decision-making. Here, we use deep neural networks over an institution-wide platform for the augmented curation of clinical notes from 77,167 patients subjected to COVID-19 PCR testing. By contrasting Electronic Health Record (EHR)-derived symptoms of COVID-19-positive (COVID(pos); n = 2,317) versus COVID-19-negative (COVID(neg); n = 74,850) patients for the week preceding the PCR testing date, we identify anosmia/dysgeusia (27.1-fold), fever/chills (2.6-fold), respiratory difficulty (2.2-fold), cough (2.2-fold), myalgia/arthralgia (2-fold), and diarrhea (1.4-fold) as significantly amplified in COVID(pos) over COVID(neg) patients. The combination of cough and fever/chills has 4.2-fold amplification in COVID(pos) patients during the week prior to PCR testing, in addition to anosmia/dysgeusia, constitutes the earliest EHR-derived signature of COVID-19. This study introduces an Augmented Intelligence platform for the real-time synthesis of institutional biomedical knowledge. The platform holds tremendous potential for scaling up curation throughput, thus enabling EHR-powered early disease diagnosis. url: https://www.ncbi.nlm.nih.gov/pubmed/32633720/ doi: 10.7554/elife.58227 id: cord-262328-q7mt0xve author: Wajnberg, Ania title: Humoral response and PCR positivity in patients with COVID-19 in the New York City region, USA: an observational study date: 2020-09-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic. The proportion of infected individuals who seroconvert is still an open question. In addition, it has been shown in some individuals that viral genome can be detected up to 3 months after symptom resolution. We investigated both seroconversion and PCR positivity in a large cohort of convalescent serum donors in the New York City (NY, USA) region. METHODS: In this observational study, we ran an outreach programme in the New York City area. We recruited participants via the REDCap (Vanderbilt University, Nashville, TN, USA) online survey response. Individuals with confirmed or suspected SARS-CoV-2 infection were screened via PCR for presence of viral genome and via ELISA for presence of anti-SARS-CoV-2 spike antibodies. One-way ANOVA and Fisher's exact test were used to measure the association of age, gender, symptom duration, and days from symptom onset and resolution with positive antibody results. FINDINGS: Between March 26 and April 10, 2020, we measured SARS-CoV-2 antibody titres in 1343 people. Of the 624 participants with confirmed SARS-CoV-2 infection who had serologies done after 4 weeks, all but three seroconverted to the SARS-CoV-2 spike protein, whereas 269 (37%) of 719 participants with suspected SARS-CoV-2 infection seroconverted. PCR positivity was detected up to 28 days from symptom resolution. INTERPRETATION: Most patients with confirmed COVID-19 seroconvert, potentially providing immunity to reinfection. We also report that in a large proportion of individuals, viral genome can be detected via PCR in the upper respiratory tract for weeks after symptom resolution, but it is unclear whether this signal represents infectious virus. Analysis of our large cohort suggests that most patients with mild COVID-19 seroconvert 4 weeks after illness, and raises questions about the use of PCR to clear positive individuals. FUNDING: None. url: https://www.ncbi.nlm.nih.gov/pubmed/33015652/ doi: 10.1016/s2666-5247(20)30120-8 id: cord-004133-32w6g7qk author: Walker, Faye M. title: Advances in Directly Amplifying Nucleic Acids from Complex Samples date: 2019-09-30 words: 13585.0 sentences: 664.0 pages: flesch: 42.0 cache: ./cache/cord-004133-32w6g7qk.txt txt: ./txt/cord-004133-32w6g7qk.txt summary: Studies were included if they involved direct amplification and detection of genetic material from one of six representative sample types: blood, dried blood spot, serum and plasma, saliva and sputum, swabs, urine, and stool. However, it is important to note that the sensitivity does not necessarily suffer in much more concentrated samples-in Liu et al.''s highly robust two-step amplification process with direct hairpin assembly and HCR-based detection of SNP DNA sequences in 50% (v/v) serum, they achieved a very low LOD of 100 pg [119] . However, it is important to note that the sensitivity does not necessarily suffer in much more concentrated samples-in Liu et al.''s highly robust two-step amplification process with direct hairpin assembly and HCR-based detection of SNP DNA sequences in 50% (v/v) serum, they achieved a very low LOD of 100 pg [119] . abstract: Advances in nucleic acid amplification technologies have revolutionized diagnostics for systemic, inherited, and infectious diseases. Current assays and platforms, however, often require lengthy experimental procedures and multiple instruments to remove contaminants and inhibitors from clinically-relevant, complex samples. This requirement of sample preparation has been a bottleneck for using nucleic acid amplification tests (NAATs) at the point of care (POC), though advances in “lab-on-chip” platforms that integrate sample preparation and NAATs have made great strides in this space. Alternatively, direct NAATs—techniques that minimize or even bypass sample preparation—present promising strategies for developing POC diagnostic tools for analyzing real-world samples. In this review, we discuss the current status of direct NAATs. Specifically, we surveyed potential testing systems published from 1989 to 2017, and analyzed their performances in terms of robustness, sensitivity, clinical relevance, and suitability for POC diagnostics. We introduce bubble plots to facilitate our analysis, as bubble plots enable effective visualization of the performances of these direct NAATs. Through our review, we hope to initiate an in-depth examination of direct NAATs and their potential for realizing POC diagnostics, and ultimately transformative technologies that can further enhance healthcare. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6955841/ doi: 10.3390/bios9040117 id: cord-258819-4boe6t1v author: Waller, Joseph V. title: The Limited Sensitivity of Chest Computed Tomography Relative to Reverse Transcription Polymerase Chain Reaction for Severe Acute Respiratory Syndrome Coronavirus-2 Infection: A Systematic Review on COVID-19 Diagnostics date: 2020-06-16 words: 4443.0 sentences: 226.0 pages: flesch: 49.0 cache: ./cache/cord-258819-4boe6t1v.txt txt: ./txt/cord-258819-4boe6t1v.txt summary: title: The Limited Sensitivity of Chest Computed Tomography Relative to Reverse Transcription Polymerase Chain Reaction for Severe Acute Respiratory Syndrome Coronavirus-2 Infection: A Systematic Review on COVID-19 Diagnostics OBJECTIVES: Several studies suggest the sensitivity of chest computed tomography (CT) is far greater than that of reverse transcription polymerase chain reaction (RT-PCR) in diagnosing COVID-19 patients, and therefore, CT should be included as a primary diagnostic tool. The quality assessment tool QUADAS-2 was used to stratify studies according to their risk of bias, and exclusion criteria included not providing the information deemed relevant for such a stratification, such as not indicating if the patients were symptomatic or asymptomatic, or identifying the source of the specimen for the reference standard, RT-PCR (eg, nasal, oropharyngeal, etc). A recent study by Li and colleagues 18 tested a cohort of patients assumed to have SARS-CoV-2 infection owing to CT findings consistent with a viral pneumonia and reported an RT-PCR sensitivity of 27.5% (n = 610). abstract: OBJECTIVES: Several studies suggest the sensitivity of chest computed tomography (CT) is far greater than that of reverse transcription polymerase chain reaction (RT-PCR) in diagnosing COVID-19 patients, and therefore, CT should be included as a primary diagnostic tool. This systematic review aims to stratify studies as high or low risk of bias to determine the true sensitivity of CT for severe acute respiratory syndrome coronavirus-2 infection according to the unbiased (low risk) studies, a topic of particular importance given the insufficient quantity of RT-PCR kits in many countries. We focus on sensitivity as that is the chief advantage perceived of CT. MATERIALS AND METHODS: This systematic review involved searching the PubMed and Google Scholar databases for articles conducted and published between January 1 and April 15, 2020. The quality assessment tool QUADAS-2 was used to stratify studies according to their risk of bias, and exclusion criteria included not providing the information deemed relevant for such a stratification, such as not indicating if the patients were symptomatic or asymptomatic, or identifying the source of the specimen for the reference standard, RT-PCR (eg, nasal, oropharyngeal, etc). Sensitivity values were then extracted, and random effects meta-analyses were performed. RESULTS: Of 641 search results, 37 studies (n = 9610 patients) were included in the analysis. The mean sensitivity of RT-PCR for COVID-19 reported by the biased studies was 70% (n = 5409/7 studies; 95% confidence interval [CI], 43–97; I(2) = 99.1%), compared with 78% by unbiased studies (n = 534/4 studies; 95% CI, 69–87, I(2) = 89.9%). For chest CT, the mean sensitivity reported by biased studies was 94% (n = 3371 patients/24 studies; 95% CI, 92–96; I(2) = 93.1%), compared with 75% by unbiased studies (n = 957/10 studies; 95% CI, 67–83; I(2) = 89.5%). CONCLUSIONS: The difference between the sensitivities of CT and RT-PCR for severe acute respiratory syndrome coronavirus-2 infection is lower than previously thought, as after stratifying the studies, the true sensitivity for CT based on the unbiased studies is limited. url: https://doi.org/10.1097/rli.0000000000000700 doi: 10.1097/rli.0000000000000700 id: cord-339976-tg2jkss7 author: Wang, Haibin title: Detection and Monitoring of SARS Coronavirus in the Plasma and Peripheral Blood Lymphocytes of Patients with Severe Acute Respiratory Syndrome date: 2004-07-01 words: 2579.0 sentences: 120.0 pages: flesch: 50.0 cache: ./cache/cord-339976-tg2jkss7.txt txt: ./txt/cord-339976-tg2jkss7.txt summary: title: Detection and Monitoring of SARS Coronavirus in the Plasma and Peripheral Blood Lymphocytes of Patients with Severe Acute Respiratory Syndrome Reliable and sensitive determination of the SARS CoV load would aid in the early identification of infected individuals, provide guidance for treatment (especially the use of steroid hormones and antiviral agents), and aid in monitoring of a patient''s clinical course and outcome. The method could detect the CoV load during the SARS course, as demonstrated in Fig. 1B , representative data from the 44 patients tested. High frequency of point mutations clustered within the adenosine triphosphatebinding region of BCR/ABL in patients with chronic myeloid leukemia or Ph-positive acute lymphoblastic leukemia who develop imatinib (STI571) resistance Serial analysis of the plasma concentration of SARS coronavirus RNA in pediatric patients with severe acute respiratory syndrome Quantitative analysis and prognostic implication of SARS coronavirus RNA in the plasma and serum of patients with severe acute respiratory syndrome abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/15229153/ doi: 10.1373/clinchem.2004.031237 id: cord-295445-f4p00yaw author: Wang, Hao title: Differential removal of human pathogenic viruses from sewage by conventional and ozone treatments date: 2018-02-01 words: 6889.0 sentences: 284.0 pages: flesch: 48.0 cache: ./cache/cord-295445-f4p00yaw.txt txt: ./txt/cord-295445-f4p00yaw.txt summary: Previous studies conducted in wastewater treatment plants have shown that ozone disinfection might be highly efficient in inactivating bacteria and bacteriophages after conventional sewage treatments (Kim et al., 1999; Tyrrell et al., 1995) , but knowledge regarding its effect for reducing human enteric viruses is relatively scarce. The four concentrated water samples (incoming sewage, conventionally treated, ozone treated, and outlet water) from each of the three weeks were also analyzed by qPCR for 14 common enteric viruses (adenovirus, astrovirus, hepatitis A virus, hepatitis E virus, norovirus GI, norovirus GII, norovirus GIV, parechovirus, sapovirus, aichivirus, mengovirus, torovirus, enterovirus, and rotavirus). However, in this study some viruses that were undetectable in the ozone-treated samples reoccurred in the outlet water, including parvovirus, norovirus GII, human feces pecovirus, parvovirus-like virus, gokushovirus, and HAdV-F41, although the amounts were significantly lower compared with raw sewage. abstract: Sewage contains a mixed ecosystem of diverse sets of microorganisms, including human pathogenic viruses. Little is known about how conventional as well as advanced treatments of sewage, such as ozonation, reduce the environmental spread of viruses. Analyses for viruses were therefore conducted for three weeks in influent, after conventional treatment, after additional ozonation, and after passing an open dam system at a full-scale treatment plant in Knivsta, Sweden. Viruses were concentrated by adsorption to a positively charged filter, from which they were eluted and pelleted by ultracentrifugation, with a recovery of about 10%. Ion Torrent sequencing was used to analyze influent, leading to the identification of at least 327 viral species, most of which belonged to 25 families with some having unclear classification. Real-time PCR was used to test for 21 human-related viruses in inlet, conventionally treated, and ozone-treated sewage and outlet waters. The viruses identified in influent and further analyzed were adenovirus, norovirus, sapovirus, parechovirus, hepatitis E virus, astrovirus, pecovirus, picobirnavirus, parvovirus, and gokushovirus. Conventional treatment reduced viral concentrations by one to four log10, with the exception of adenovirus and parvovirus, for which the removal was less efficient. Ozone treatment led to a further reduction by one to two log10, but less for adenovirus. This study showed that the amount of all viruses was reduced by conventional sewage treatment. Further ozonation reduced the amounts of several viruses to undetectable levels, indicating that this is a promising technique for reducing the transmission of many pathogenic human viruses. url: https://api.elsevier.com/content/article/pii/S1438463917307307 doi: 10.1016/j.ijheh.2018.01.012 id: cord-284423-fzz8g3rq author: Wang, Hui-yu title: Establishment and optimization of a liquid bead array for the simultaneous detection of ten insect-borne pathogens date: 2018-07-31 words: 4665.0 sentences: 236.0 pages: flesch: 51.0 cache: ./cache/cord-284423-fzz8g3rq.txt txt: ./txt/cord-284423-fzz8g3rq.txt summary: This study aimed to establish a liquid bead array based on Luminex xMAP technology that was able to simultaneously detect multiple insect-borne pathogens. CONCLUSIONS: This optimized liquid array detection system was high-throughput and highly specific and sensitive in screening of the insect-borne pathogens. To date, multiple molecular detection methods have been established to detect insect-borne pathogens, including reverse transcriptase-polymerase chain reaction (PCR) [8] , real-time PCR [9] , a liquid bead array [10] and a microwell membrane array [11] . In this study, we established a method that was able to simultaneously detect multiple insect-borne pathogens rapidly and effectively, including bluetongue virus (BTV), epizootic hemorrhagic disease virus of deer (EHDV), Q-fever pathogen Coxiella burnetii (CB), African swine fever virus (ASFV), West Nile fever virus (WNV), Borrelia burgdorferi (BB), vesicular stomatitis virus (VSV), Rift Valley fever virus (RVFV), Ebola virus (EBV) and Schmallenberg virus (SBV). This study established a multiplexed PCR-coupled liquid array to simultaneously detect 10 types of insect-borne pathogens. abstract: BACKGROUND: Insect-borne diseases could induce severe symptoms in human and clinical signs in animals, such as febrility, erythra, arthralgia and hemorrhagic fever, and cause significant economic losses and pose public health threat all over the world. The significant advantages of Luminex xMAP technology are high-throughput, high parallel and automation. This study aimed to establish a liquid bead array based on Luminex xMAP technology that was able to simultaneously detect multiple insect-borne pathogens. METHODS: Specific probes and primers to detect the nucleic acid of 10 insect-borne pathogens were designed. Probes were coupled with fluorescent carboxylated microspheres. The parameters of the system were optimized, including ratio of forward/reverse primers (1:2), hybridization temperature (50 °C) and duration (30 min) and quantity of PCR product (2 μl). The sensitivity and specificity of the system were also evaluated. Moreover mixed nucleic acid of 10 insect-borne pathogens, including Bluetongue virus, Epizootic hemorrhagic disease virus of deer, Coxiella burnetii, African swine fever virus, West Nile fever virus, Borrelia burgdorferi, vesicular stomatitis virus, Rift Valley fever virus, Ebola virus and Schmalenberg’s disease virus, and 3000 clinical samples were tested for practicability. RESULTS: The optimized detection system showed high sensitivity, specificity and reproducibility. Each probe showed specific fluorescence signal intensity without any cross-hybridization for the other insect-borne pathogens tested, which included dengue virus, tick-borne encephalitis virus, Japanese encephalitis virus, Xinjiang hemorrhagic fever virus, spotted fever group rickettsiae, ehrlichiae and chikungunya virus. The limit of detection was 10 copies of target gene. Insect-borne pathogens were successfully detected among the 3000 clinical samples, and the results were consistent with those obtained using gold-standard assays or commercial nucleic acid detection kits. CONCLUSIONS: This optimized liquid array detection system was high-throughput and highly specific and sensitive in screening of the insect-borne pathogens. It was promising in detection of these pathogens for molecular epidemiological studies. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13071-018-2996-0) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s13071-018-2996-0 doi: 10.1186/s13071-018-2996-0 id: cord-261823-pgluidj8 author: Wang, Ji title: Novel One-Step Single-Tube Nested Quantitative Real-Time PCR Assay for Highly Sensitive Detection of SARS-CoV-2 date: 2020-05-22 words: 3581.0 sentences: 183.0 pages: flesch: 60.0 cache: ./cache/cord-261823-pgluidj8.txt txt: ./txt/cord-261823-pgluidj8.txt summary: In this study, we have developed and evaluated a novel one-step single-tube nested quantitative real-time PCR (OSN-qRT-PCR) assay for the highly sensitive detection of SARS-CoV-2 targeting the ORF1ab and N genes. 7−10 In this study, we developed and evaluated an OSN-qRT-PCR assay for the highly sensitive detection of SARS-CoV-2, targeting the ORF1ab and N genes on the basis of a commercial qRT-PCR kit for SARS-CoV-2 (Sansure, Hunan, China). Compared to this qRT-PCR kit, the OSN-qRT-PCR assay revealed higher sensitivity and specificity, showing better suitability to clinical applications for the detection of SARS-CoV-2 in patients with low viral load. Compared to this qRT-PCR kit, the OSN-qRT-PCR assay revealed higher sensitivity and specificity, showing better suitability to clinical applications for the detection of SARS-CoV-2 in patients with low viral load. Collectively, the OSN-qRT-PCR assay has advantages of high sensitivity and easy applicability for the detection of SARS-CoV-2 in clinical samples. abstract: [Image: see text] Coronavirus disease 2019 (COVID-19) has become a public health emergency. The reverse transcriptase real-time quantitative PCR (qRT-PCR) test is currently considered as the gold standard in the laboratory for the etiological detection of COVID-19. However, qRT-PCR results could be false-negative due to the inadequate sensitivity of qRT-PCR. In this study, we have developed and evaluated a novel one-step single-tube nested quantitative real-time PCR (OSN-qRT-PCR) assay for the highly sensitive detection of SARS-CoV-2 targeting the ORF1ab and N genes. The sensitivity of the OSN-qRT-PCR assay was 1 copy/reaction and 10-fold higher than that of the commercial qRT-PCR kit (10 copies/reaction). The clinical performance of the OSN-qRT-PCR assay was evaluated using 181 clinical samples. Among them, 14 qRT-PCR-negative samples (7 had no repetitive results and 7 had no cycle threshold (CT) values) were detected by OSN-qRT-PCR. Moreover, the 7 qRT-PCR-positives in the qRT-PCR gray zone (CT values of ORF1ab ranged from 37.48 to 39.07, and CT values of N ranged from 37.34 to 38.75) were out of the gray zone and thus were deemed to be positive by OSN-qRT-PCR, indicating that the positivity of these samples is confirmative. Compared to the qRT-PCR kit, the OSN-qRT-PCR assay revealed higher sensitivity and specificity, showing better suitability to clinical applications for the detection of SARS-CoV-2 in patients with low viral load. url: https://doi.org/10.1021/acs.analchem.0c01884 doi: 10.1021/acs.analchem.0c01884 id: cord-301695-zl7cjs1k author: Wang, Ji title: Identification of Histoplasma causing an unexplained disease cluster in Matthews Ridge, Guyana date: 2019-12-31 words: 3068.0 sentences: 165.0 pages: flesch: 53.0 cache: ./cache/cord-301695-zl7cjs1k.txt txt: ./txt/cord-301695-zl7cjs1k.txt summary: Though NGS had a longer turnaround time (24 hours), it worked well with different sample types (lung tissue, brain tissue and serum from deceased cases and plasma from a severe case) and was more sensitive than nanopore sequencing. The data generated by the Ion Torrent platform were aligned with the genomic database of Histoplasma, and specific reads were found in the serum and mixed brain and lung tissue from the deceased patients and in the plasma from the severe case ( Figure 5 ) [16] . In this case, NGS also identified specific fragments of Histoplasma in all tested samples (lung, brain and blood serum) from the deceased patients, which consolidated the identification of Histoplasma as the causative pathogen, indicating higher detection sensitivity by NGS than nanopore sequencing. We conclude that Histoplasma was the causative pathogen of this disease cluster based on epidemiologic, clinical, pathological and nucleic acid evidence. abstract: Abstract Here, we report the identification of Histoplasma causing an unexplained disease cluster in Matthews Ridge, Guyana. In March 2019, 14 employees of Chongqing Bosai Mining Company, China, working in a manganese mining of Guyana, had unexplained fever, and two of them died. We obtained lung and brain tissues as well as the blood samples from the two deceased cases (patient No. 1 and 2), and bronchoscopy lavages and cerebrospinal fluid samples from one severe case (patient No. 3), respectively. All samples were tested by pathological examination, high-throughput sequencing, and real-time PCR. Pathological detection showed the presence of spore-like structures in the lung tissue of patient No. 1, indicating a fungal infection in this patient. Nanopore sequencing identified the existing of H. capsulatum in the lung tissue sample within 13 h. Next-generation sequencing identified specific fragments of H. capsulatum in all of the samples tested (lung, brain and blood serum from the deceased cases, and plasma from the severe case). Real-time PCR assays did not reveal any viral infection related to transmission from bat feces. We conclude that H. capsulatum was the causative pathogen of this disease cluster based on epidemiologic, clinical, pathological and nucleic acid evidence. url: https://www.ncbi.nlm.nih.gov/pubmed/32501448/ doi: 10.1016/j.bsheal.2019.12.003 id: cord-298002-jvnwivrg author: Wang, Jian title: COVID-19 confirmed patients with negative antibodies results date: 2020-09-22 words: 1499.0 sentences: 92.0 pages: flesch: 59.0 cache: ./cache/cord-298002-jvnwivrg.txt txt: ./txt/cord-298002-jvnwivrg.txt summary: CASE PRESENTATIONS: We present two cases of confirmed COVID-19 patients and characterize their initial symptoms, chest CT results, medication, and laboratory test results in detail (including RT-PCR, IgM/ IgG, cytokine and blood cell counts). CONCLUSION: Both of patients with confirmed COVID-19 pneumonia failed to produce either IgM or IgG even 40 to 50 days after their symptoms onset. During the outbreak of coronavirus 2019 (COVID-19) [1] [2] [3] , a small proportion of confirmed COVID-19 patients fail to produce IgM or IgG antibodies against SARS-CoV-2 even 40 days or longer periods of time after onset of their initial symptoms. From January 30 to March 15, 310 of COVID-19 patients who were positive for SARS-CoV-2 real time reverse-transcription PCR (RT-PCR) testing and received IgM and IgG detection at Wuhan Union Hospital (Wuhan, China) were enrolled. In this study, two patients with confirmed COVID-19 failed to produce either IgM or IgG even 40 to 50 days after their symptoms onset. abstract: BACKGROUND: A new coronavirus disease 2019 (COVID-19) has escalated to a pandemic since its first outbreak in Wuhan, China. A small proportion of patients may have difficulty in generating IgM or IgG antibodies against SARS-CoV-2, and little attention has been paid to them. CASE PRESENTATIONS: We present two cases of confirmed COVID-19 patients and characterize their initial symptoms, chest CT results, medication, and laboratory test results in detail (including RT-PCR, IgM/ IgG, cytokine and blood cell counts). CONCLUSION: Both of patients with confirmed COVID-19 pneumonia failed to produce either IgM or IgG even 40 to 50 days after their symptoms onset. This work provides evidence demonstrating that at least a small proportion of patients may have difficulty in rapidly gaining immunity against SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32962655/ doi: 10.1186/s12879-020-05419-3 id: cord-355874-nz6eqcdb author: Wang, Le title: A GeXP-Based Assay for Simultaneous Detection of Multiple Viruses in Hospitalized Children with Community Acquired Pneumonia date: 2016-09-14 words: 3067.0 sentences: 160.0 pages: flesch: 54.0 cache: ./cache/cord-355874-nz6eqcdb.txt txt: ./txt/cord-355874-nz6eqcdb.txt summary: title: A GeXP-Based Assay for Simultaneous Detection of Multiple Viruses in Hospitalized Children with Community Acquired Pneumonia In this study, we used the GeXP-based assay for simultaneous detection of 20 types/subtypes of viruses in 1699 nasopharyngeal specimens collected from hospitalized children with CAP. To evaluate the sensitivity of the GeXP assay, nucleic acid from all 20 target viruses and the internal control pcDNA3.1 (+) DNA were mixed to make the template pool. In the present study, we applied multiplex RT-PCR together with automated capillary electrophoresis, namely the GeXP-based assay, to detect virus in 1699 nasopharyngeal specimens from hospitalized children with CAP. We showed that the GeXP-based assay had high sensitivity and specificity for simultaneous detection of multiple viruses, and about 65% of cases tested were positive for virus. The development of a GeXP-based multiplex reverse transcription-PCR assay for simultaneous detection of sixteen human respiratory virus types/ subtypes abstract: The GeXP-based assay has recently been developed for simultaneous detection of multiple pathogens. So far, the application of the GeXP assay to test larger clinical samples has hardly been reported. Community-acquired pneumonia (CAP) is the leading cause of death in children worldwide and a substantial proportion of childhood CAP is caused by viruses. Rapid and accurate diagnosis of virus infection is important for the clinical management of CAP. In this study, we explored the GeXP assay for simultaneous detection of 20 types/subtypes of viruses in hospitalized children with CAP. A total of 1699 nasopharyngeal swabs were prospectively collected and viral nucleic acid was extracted and assayed. Using viral genomic DNA or RNA as template, we showed that at the concentration of 10(4) copies of DNA or RNA of each virus/μl, all 20 target viruses were simultaneously identified by the GeXP assay. Fifteen control microorganisms, in contrast, failed to be amplified by the assay. About 65% of cases tested in this study had viral infection, with patients aged <3 years having a 70% positive rate, significantly higher than that in patients aged > 3 years (40%). The most frequently detected virus was RSV followed by PIV3, HRV, ADV and HBoV. Seasonal distribution analysis revealed that RSV was the most predominant in autumn and winter, while in spring and summer PIV3 and RSV were the most frequently identified with similar positive percentages. One hundred twenty randomly-chosen samples tested by the GeXP assay were re-evaluated by mono-RT-PCR, the results showed 97.5% diagnosis agreement between these 2 methods. Our findings suggest that the GeXP assay could be a valuable diagnostic tool for virus infection in pediatric patients with CAP. url: https://www.ncbi.nlm.nih.gov/pubmed/27627439/ doi: 10.1371/journal.pone.0162411 id: cord-299585-fkg8d6ym author: Wang, Leyi title: Development of a triplex real-time RT-PCR assay for detection and differentiation of three US genotypes of porcine hemagglutinating encephalomyelitis virus date: 2019-04-05 words: 2722.0 sentences: 132.0 pages: flesch: 55.0 cache: ./cache/cord-299585-fkg8d6ym.txt txt: ./txt/cord-299585-fkg8d6ym.txt summary: title: Development of a triplex real-time RT-PCR assay for detection and differentiation of three US genotypes of porcine hemagglutinating encephalomyelitis virus In the present study, we report the development of a triplex real-time RT-PCR assay for detection and differentiation of three PHEV genotypes, 1, 2, and 3. The triplex real-time RT-PCR provides a rapid and sensitive method to detect and differentiate all three US genotypes of PHEV from clinical samples. Porcine hemagglutinating encephalomyelitis virus (PHEV) is one of six known porcine coronaviruses (CoVs) causing diseases in pigs (Gong et al., 2017; Wang and Zhang, 2016) . The triplex rRT-PCR developed in the present study will fulfill this purpose and can be used to monitor PHEV of different genetic genotypes and differentiate between them. The detection limit of the triplex rRT-PCR assay was determined by testing 10-fold serially diluted positive PHEV RNAs (15SW1362 and 15SW25049) and plasmid DNAs (pCR 2.1-15SW1582-N, pCR 2.1-15SW1362-NS2, and pCR 2.1-15SW25049-NS2) in duplicate. abstract: Porcine hemagglutinating encephalomyelitis virus (PHEV) is a single-stranded, positive-sense RNA virus. PHEV mainly causes two types of clinical manifestations representing vomiting and wasting and encephalomyelitis in piglets. However, our recent findings provide strong evidence that PHEV can also cause respiratory disease in older pigs. Genomic analysis of new PHEV strains identified in our former study further classifies PHEV into three genotypes. Detection and differentiation of these new mutants are critical in monitoring PHEV evolution in the field. In the present study, we report the development of a triplex real-time RT-PCR assay for detection and differentiation of three PHEV genotypes, 1, 2, and 3. Three sets of primers and probes were designed; one set of primers and probe targeting the conserved regions of the 3′ end nucleocapsid for detection of all three genotypes and another two sets of primers and probes targeting the regions of NS2 with different patterns of deletions for detection of both genotypes 1 and 3, or genotype 3 only. Genotype 1 was positive when two probe dyes showed signals, genotype 2 was positive when only one probe dye showed a signal, and genotype 3 was positive when all three probes showed signals. The detection limit of the developed triplex real-time RT-PCR was as low as 8 or 9 DNA copies for three sets of primers and probes. The specificity test showed no cross reaction with other porcine viruses. Positive field-samples were correctly typed by this new assay, which was further confirmed by DNA sequencing. The triplex real-time RT-PCR provides a rapid and sensitive method to detect and differentiate all three US genotypes of PHEV from clinical samples. url: https://doi.org/10.1016/j.jviromet.2019.04.008 doi: 10.1016/j.jviromet.2019.04.008 id: cord-288306-0chcsqe7 author: Wang, Lihua title: Recent Advances in the Diagnosis of Classical Swine Fever and Future Perspectives date: 2020-08-15 words: 5833.0 sentences: 280.0 pages: flesch: 41.0 cache: ./cache/cord-288306-0chcsqe7.txt txt: ./txt/cord-288306-0chcsqe7.txt summary: The wellestablished diagnostic methods of CSF such as virus isolation, fluorescent antibody test (FAT), antigen capture antibody enzyme-linked immunosorbent assay (ELISA), reverse-transcription polymerase chain reaction (RT-PCR), virus neutralization test (VNT), and antibody ELISA (Table 1) have been widely used and well described in the OIE Terrestrial Manual [17] . The well-established diagnostic methods of CSF such as virus isolation, fluorescent antibody test (FAT), antigen capture antibody enzyme-linked immunosorbent assay (ELISA), reverse-transcription polymerase chain reaction (RT-PCR), virus neutralization test (VNT), and antibody ELISA (Table 1 ) have been widely used and well described in the OIE Terrestrial Manual [17] . Evaluation of a multiplex real-time RT-PCR for quantitative and differential detection of wild-type viruses and C-strain vaccine of Classical swine fever virus The double-antigen ELISA concept for early detection of E rns -specific classical swine fever virus antibodies and application as an accompanying test for differentiation of infected from marker vaccinated animals abstract: Classical swine fever (CSF) is a highly contagious viral disease of pigs, including wild boar. It is regarded as one of the major problems in the pig industry as it is still endemic in many regions of the world and has the potential to cause devastating epidemics, particularly in countries free of the disease. Rapid and reliable diagnosis is of utmost importance in the control of CSF. Since clinical presentations of CSF are highly variable and may be confused with other viral diseases in pigs, laboratory diagnosis is indispensable for an unambiguous diagnosis. On an international level, well-established diagnostic tests of CSF such as virus isolation, fluorescent antibody test (FAT), antigen capture antibody enzyme-linked immunosorbent assay (ELISA), reverse-transcription polymerase chain reaction (RT-PCR), virus neutralization test (VNT), and antibody ELISA have been described in detail in the OIE Terrestrial Manual. However, improved CSF diagnostic methods or alternatives based on modern technologies have been developed in recent years. This review thus presents recent advances in the diagnosis of CSF and future perspectives. url: https://doi.org/10.3390/pathogens9080658 doi: 10.3390/pathogens9080658 id: cord-311801-m2otfdjw author: Wang, Pei title: Combination of Serological Total Antibody and RT-PCR Test for Detection of SARS-CoV-2 Infections date: 2020-06-15 words: 2724.0 sentences: 184.0 pages: flesch: 62.0 cache: ./cache/cord-311801-m2otfdjw.txt txt: ./txt/cord-311801-m2otfdjw.txt summary: The purpose of this study was to investigate the feasibility of serological total antibody tests combined with RT-PCR for detection of SARS-CoV-2. Serum samples and throat swabs were collected from 375 patients for total antibody testing against SARS-CoV-2 and RT-PCR analysis, respectively. This study supported the advantage of the combined method for detection of SARS-CoV-2 with a high degree of sensitivity and specificity, as a useful tool for accurate diagnosis and timely treatment of suspected patients, epidemiological investigation, as well as monitoring ongoing outbreaks of infections with SARS-CoV-2. In this study, we presented the results of two diagnostic methods: serum total antibody assays against SARS-CoV-2 by CMIA and the RT-PCR for detection of viral RNA. In addition, the combination of the results of the total antibody test and RT-PCR was discussed for detection of SARS-CoV-2 infections. Sensitivity, specificity for detection of SARS-CoV-2 by RT-PCR, and the total antibody test method as well as the combined methods were analysed. abstract: The purpose of this study was to investigate the feasibility of serological total antibody tests combined with RT-PCR for detection of SARS-CoV-2. We conducted a retrospective study in which 375 patients were enrolled during the outbreak of SARS-CoV-2 from 25th January to 16th March 2020. Patients were divided into a COVID-19 group (n = 141) and a control group (n = 234). Serum samples and throat swabs were collected from 375 patients for total antibody testing against SARS-CoV-2 and RT-PCR analysis, respectively. The results indicated that diagnostic sensitivity and specificity were 95.7% and 98.7%, 92.2% and 100% by total antibody tests and RT-PCR, respectively. The sensitivity and specificity of total antibody tests combined with RT-PCR were 98.6% and 98.7%. The sensitivity of the combined method was significantly higher than RT-PCR (X(2) = 5.16, P < 0.05), and similar to that of total antibody tests (X(2) = 1.15, P > 0.05). This study supported the advantage of the combined method for detection of SARS-CoV-2 with a high degree of sensitivity and specificity, as a useful tool for accurate diagnosis and timely treatment of suspected patients, epidemiological investigation, as well as monitoring ongoing outbreaks of infections with SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32554043/ doi: 10.1016/j.jviromet.2020.113919 id: cord-254101-613aftc1 author: Wang, Ping title: Establishment of a transgenic mouse model with liver-specific expression of secretory immunoglobulin D date: 2012-04-14 words: 4387.0 sentences: 239.0 pages: flesch: 60.0 cache: ./cache/cord-254101-613aftc1.txt txt: ./txt/cord-254101-613aftc1.txt summary: In this study, we generated by fusion PCR a vector to express high levels of chimeric secretory IgD (csIgD) specifically in the liver. Hyperimmunoglobulinemia D syndrome (HIDS), also called receptor-associated periodic syndrome or etiocholanolone fever, is characterized by high serum levels of immunoglobulin D (IgD) and recurrent febrile attacks, and may also include arthritis, lymphadenopathy, hepatosplenomegaly, and skin rash [1-3]. The resulting plasmids, designated en-pAlb-csIgD-H and en-pAlb-cKappa, were under control of the mouse Alb regulatory sequences to direct gene expression specifically in the liver. This indicates that the inflammation in the transgenic mice is caused by increased sIgD rather than by Mvk mutation. Skin ulcers in transgenic mice with high expression of sIgD may be caused by excessive immune activation. An albumin enhancer located 10-kb upstream functions along with its promoter to direct efficient, liver-specific expression in transgenic mice High level expression of a functional human/mouse chimeric anti-CD20 monoclonal antibody in milk of transgenic mice abstract: Mutation of mevalonate kinase (MVK) is thought to account for most cases of hyperimmunoglobulinemia D syndrome (HIDS) with recurrent fever. However, its mechanism and the relationship between elevated serum immunoglobulin D (IgD) and the clinical features of HIDS are unclear. In this study, we generated by fusion PCR a vector to express high levels of chimeric secretory IgD (csIgD) specifically in the liver. We then generated seven founder lines of transgenic mice by co-microinjection, and verified them using genomic PCR and Southern blotting. We detected the expression of csIgD by reverse transcription PCR, quantitative PCR, western blotting, and enzyme-linked immunosorbent assays. We demonstrated that csIgD could be specifically and stably expressed in the liver. We used flow cytometry to show that overexpression of csIgD in the bone marrow and spleen cells had no effect on B cell development. Morphologic and anatomical observation of the transgenic mice revealed skin damage, hepatosplenomegaly, and nephromegaly in some transgenic mice; in these mice, pathological sections showed high levels of cell necrosis and protein-like sediments in the liver, spleen, and kidney. We demonstrated that the genomic insertion sites of the transgenes did not disrupt the MVK gene on mouse chromosome 5. This transgenic mouse will be useful to explore the pathogenesis of HIDS. url: https://doi.org/10.1007/s11427-012-4301-3 doi: 10.1007/s11427-012-4301-3 id: cord-354683-l07w3lc7 author: Wang, Ruyi title: One-step multiplex TaqMan probe-based method for real-time PCR detection of four canine diarrhea viruses date: 2020-06-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Viral canine diarrhea has high morbidity and mortality and is prevalent worldwide, resulting in severe economic and spiritual losses to pet owners. However, diarrhea pathogens have similar clinical symptoms and are difficult to diagnose clinically. Thus, fast and accurate diagnostic methods are of great significance for prevention and accurate treatment. In this study, we developed a one-step multiplex TaqMan probe-based real-time PCR for the differential diagnosis of four viruses causing canine diarrhea including, CPV (Canine Parvovirus 2), CCoV (Canine Coronavirus), CAstV (Canine Astrovirus), and CaKoV (Canine Kobuviruses). The limit of detection was up to 10(2)copies/μL and performed well with high sensitivity and specificity. This assay was optimized and used to identify possible antagonistic relationships between viruses. From this, artificial pre-experiments were performed for mixed infections, and a total of 82 canine diarrhea field samples were collected from different animal hospitals in Zhejiang, China to assess the method. The virus prevalence was significantly higher than what previously reported based on RT-PCR(Reverse Transcription-Polymerase Chain Reaction). Taken together, these results suggest that the method can be used as a preferred tool for monitoring laboratory epidemics, timely prevention, and effective monitoring of disease progression. url: https://doi.org/10.1016/j.mcp.2020.101618 doi: 10.1016/j.mcp.2020.101618 id: cord-299537-lbx1plqx author: Wang, Wei title: Molecular monitoring of causative viruses in child acute respiratory infection in endemo-epidemic situations in Shanghai date: 2010-09-19 words: 3998.0 sentences: 227.0 pages: flesch: 53.0 cache: ./cache/cord-299537-lbx1plqx.txt txt: ./txt/cord-299537-lbx1plqx.txt summary: METHODS: A 2-year surveillance program of children presenting with acute respiratory infections (ARIs) was carried out to characterize the viral etiology and to assess whether using gene amplification and sequencing could be a reliable approach to monitor virus introduction and spread in a population subgroup. RESULTS: Using multiplex RT-PCR, 15 different respiratory viruses were detected within the 486 nasopharyngeal positive samples collected among 817 children aged <9-year old who presented with ARI during October 2006 to September 2008. CONCLUSIONS: This study supports the usefulness of multiplex RT-PCR for virus detection and co-infection, and for implementation of a molecular monitoring system for endemic and epidemic viral respiratory infections. In the present 2-year study, we used a five-tube mRT-PCR assay we implemented in the Pasteur Institute network in the Asian region (http://www.pasteur-international.org/ip/easysite/ pasteur-international/activites-scientifiques/projets/tous-lesprojets/sisea), which covered 17 common respiratory viruses, 10 to identify viruses in nasopharyngeal specimens in 817 children with Table 1 Criteria of patient enrollment. abstract: BACKGROUND: Numerous viruses are responsible for respiratory infections; however, both their distribution and genetic diversity, in a limited area and a population subgroup, have been studied only rarely during a sustained period of time. METHODS: A 2-year surveillance program of children presenting with acute respiratory infections (ARIs) was carried out to characterize the viral etiology and to assess whether using gene amplification and sequencing could be a reliable approach to monitor virus introduction and spread in a population subgroup. RESULTS: Using multiplex RT-PCR, 15 different respiratory viruses were detected within the 486 nasopharyngeal positive samples collected among 817 children aged <9-year old who presented with ARI during October 2006 to September 2008. A single virus was detected in 373 patients (45.7%), and two to four viruses in 113 patients (13.8%). The most frequent causative viruses were respiratory syncytial virus (RSV) (24.7%), human bocavirus (24.5%), and human rhinovirus (HRV) (15%). RSV was more prevalent in winter and among young infants. Cases of seasonal influenza A and B viruses were reported mainly in January and August. An increase in adenovirus infection was observed during the spring of the second year of the study. Sequence analyses showed multiple introductions of different virus subtypes and identified a high prevalence of the newly defined HRV-C species. A higher viral incidence was observed during the winter of 2008, which was unusually cold. CONCLUSIONS: This study supports the usefulness of multiplex RT-PCR for virus detection and co-infection, and for implementation of a molecular monitoring system for endemic and epidemic viral respiratory infections. url: https://www.ncbi.nlm.nih.gov/pubmed/20855230/ doi: 10.1016/j.jcv.2010.08.005 id: cord-313004-gdnaiodj author: Wang, Yong title: Simultaneous detection of duck circovirus and novel goose parvovirus via SYBR green I-based duplex real-time polymerase chain reaction analysis date: 2020-08-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract Beak atrophy and dwarfism syndrome (BADS) is commonly caused by co-infection with duck circovirus (DuCV) and novel goose parvovirus (NGPV). Therefore, concurrent detection of both viruses is important for monitoring and limiting BADS, although such a diagnostic test has not been reported. In this study, we developed a duplex, SYBR Green I-based real-time polymerase chain reaction (PCR) assay to enable the simultaneous detection of DuCV and NGPV. The assay readily distinguished between the two viruses, based on their different melting temperatures (Tm), where the Tm for DuCV was 80 °C and that for NGPV was 84.5 °C. Other non-target duck viruses that were tested did not show melting peaks. The detection limit of the duplex assay was 101 copies/μL for both viruses. This method exhibited high repeatability and reproducibility, and both the inter-assay and intra-assay variation coefficients were <1.6%. Thirty-one fecal samples were collected for clinical testing using real-time PCR analysis, and the results were confirmed using sequencing. The rate of co-infection was 6.5%, which was consistent with the sequencing results. This duplex real-time PCR assay offers advantages over other tests, such as rapid, sensitive, specific, and reliable detection of both viruses in a single sample, which enables the quantitative detection of DuCV and NGPV in clinical samples. Using this test may be instrumental in reducing the incidence of BADS and the associated economic losses in the duck and goose industries. url: https://api.elsevier.com/content/article/pii/S0890850820304230 doi: 10.1016/j.mcp.2020.101648 id: cord-258021-xhx74vr6 author: Waterer, Grant W. title: Diagnosing Viral and Atypical Pathogens in the Setting of Community-Acquired Pneumonia date: 2016-12-21 words: 4405.0 sentences: 223.0 pages: flesch: 38.0 cache: ./cache/cord-258021-xhx74vr6.txt txt: ./txt/cord-258021-xhx74vr6.txt summary: This review focuses principally on the diagnosis of Legionella, Mycoplasma, and influenza infections, but also covers recent publications on the cutting edge of diagnostic tools likely to transform the field of infectious diseases over the coming decade. 28 Recently, there has been interest in antigen detection assays for the diagnosis of M pneumoniae because these offer the potential for point-of-care testing, but so far these have yet to enter the clinical mainstream. 73 A single study from Taiwan indicates that PCR-electrospray ionization mass spectrometry has promise for the detection of multiple viruses in the setting of respiratory tract infection but this was done retrospectively rather than in real time. Comparison of the performance of direct fluorescent antibody staining, a point-of-care rapid antigen test and virus isolation with that of RT-PCR for the detection of novel 2009 influenza A (H1N1) virus in respiratory specimens abstract: The ‘atypical’ pathogens causing pneumonia have long been problematic for physicians because we have had to rely on serologic tests to make a diagnosis. The introduction of polymerase chain reaction techniques revolutionized the diagnosis of respiratory infections and now a new wave of technologies promising faster, cheaper, and more comprehensive testing are becoming available. This review focuses principally on the diagnosis of Legionella, Mycoplasma, and influenza infections, but also covers recent publications on the cutting edge of diagnostic tools likely to transform the field of infectious diseases over the coming decade. url: https://www.ncbi.nlm.nih.gov/pubmed/28159158/ doi: 10.1016/j.ccm.2016.11.004 id: cord-265237-sxh2nqre author: Weile, Jan title: Current applications and future trends of molecular diagnostics in clinical bacteriology date: 2009-04-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Molecular diagnostics of infectious diseases, in particular, nucleic-acid-based methods, are the fastest growing field in clinical laboratory diagnostics. These applications are stepwise replacing or complementing culture-based, biochemical, and immunological assays in microbiology laboratories. The first-generation nucleic acid assays were monoparametric such as conventional tests, determining only a single parameter. Improvements and new approaches in technology now open the possibility for the development of multiparameter assays using microarrays, multiplex nucleic acid amplification techniques, or mass spectrometry, while the introduction of closed-tube systems has resulted in rapid microbial diagnostics with a subsequently reduced contamination risk. Whereas the first assays were focused on the detection and identification of microbial pathogens, these new technologies paved the way for the parallel determination of multiple antibiotic resistance determinants or to perform microbial epidemiology and surveillance on a genetic level. url: https://doi.org/10.1007/s00216-009-2779-8 doi: 10.1007/s00216-009-2779-8 id: cord-306175-p5rtp31m author: Weissbrich, Benedikt title: Frequent detection of bocavirus DNA in German children with respiratory tract infections date: 2006-07-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: In a substantial proportion of respiratory tract diseases of suspected infectious origin, the etiology is unknown. Some of these cases may be caused by the recently described human bocavirus (hBoV). The aim of this study was to investigate the frequency and the potential clinical relevance of hBoV in pediatric patients. METHODS: We tested 835 nasopharyngeal aspirates (NPA) obtained between 2002 and 2005 from pediatric in-patients with acute respiratory tract diseases at the University of Würzburg, Germany, for the presence of hBoV DNA. The specificity of positive PCR reactions was confirmed by sequencing. RESULTS: HBoV DNA was found in 87 (10.3 %) of the NPAs. The median age of the infants and children with hBoV infection was 1.8 years (mean age 2.0 years; range 18 days – 8 years). Infections with hBoV were found year-round, though most occurred in the winter months. Coinfections were found in 34 (39.1 %) of the hBoV positive samples. RSV, influenza A, and adenoviruses were most frequently detected as coinfecting agents. Sequence determination of the PCR products in the NP-1 region revealed high identity (99 %) between the nucleotide sequences obtained in different years and in comparison to the Swedish viruses ST1 and ST2. An association of hBoV with a distinct respiratory tract manifestation was not apparent. CONCLUSION: HBoV is frequently found in NPAs of hospitalized infants and children with acute respiratory tract diseases. Proving the clinical relevance of hBoV is challenging, because application of some of Koch's revised postulates is not possible. Because of the high rate of coinfections with hBoV and other respiratory tract pathogens, an association between hBoV and respiratory tract diseases remains unproven. url: https://www.ncbi.nlm.nih.gov/pubmed/16834781/ doi: 10.1186/1471-2334-6-109 id: cord-256982-t6urqus7 author: Wellinghausen, Nele title: Evaluation of the SARS-CoV-2-IgG response in outpatients by five commercial immunoassays date: 2020-09-16 words: 2514.0 sentences: 131.0 pages: flesch: 51.0 cache: ./cache/cord-256982-t6urqus7.txt txt: ./txt/cord-256982-t6urqus7.txt summary: The sensitivity in serum samples, collected at a median of 24 days after onset of symptoms, detected by the Anti-SARS-CoV-2-ELISA IgG (Euroimmun), EDI™ Novel Coronavirus COVID-19 IgG ELISA (Epitope Diagnostics), Liaison(®) SARS-CoV-2 S1/S2 IgG (Diasorin), SARS-CoV-2 IgG on the Architect™ i2000 (Abbott), and Elecsys(®) Anti-SARS-CoV-2 (IgM/IgA/IgG) on the cobas™ e801 (Roche) was 84.3%, 78.4%, 74.5%, 86.3%, and 88.2%, respectively. Our results show significant individual differences of the IgG response against SARS-CoV-2, additionally confirmed in three patients with follow-up serum samples and seven asymptomatic but PCR-positive contact persons. In conclusion, our study shows that commercially available immunoassays detect SARS-CoV-2-IgG or total antibodies in outpatients with a satisfying sensitivity, but lower than that reported for hospitalized patients. A comparison of five commercial immunoassays in serum samples taken at least ten days after onset of symptoms from 51 PCR-confirmed COVID-19 outpatients revealed an overall sensitivity of the assays from 74.5% to 88.2%. abstract: Commercially available immunoassays have been developed for sensitive and specific detection of antibodies against SARS-CoV-2. While high sensitivity has been reported in hospitalized COVID-19 patients, little is known about the performance of the assays in ambulatory patients. Therefore, we evaluated the SARS-CoV-2-IgG response in 51 SASR-CoV-2-PCR-confirmed outpatients with five commercial immunoassays. The sensitivity in serum samples, collected at a median of 24 days after onset of symptoms, detected by the Anti-SARS-CoV-2-ELISA IgG (Euroimmun), EDI™ Novel Coronavirus COVID-19 IgG ELISA (Epitope Diagnostics), Liaison(®) SARS-CoV-2 S1/S2 IgG (Diasorin), SARS-CoV-2 IgG on the Architect™ i2000 (Abbott), and Elecsys(®) Anti-SARS-CoV-2 (IgM/IgA/IgG) on the cobas™ e801 (Roche) was 84.3%, 78.4%, 74.5%, 86.3%, and 88.2%, respectively. The sensitivity in serum samples, collected >20 days after onset of symptoms, varied between 75.0% and 90.0%, and in samples, collected at least 28 days after onset of symptoms, did not increase, except in the Anti-SARS-CoV-2-ELISA IgG by Euroimmun (90.0%). There was not an obvious association between the type of the antigen (N versus S protein) and the overall sensitivity of the assays. Our results show significant individual differences of the IgG response against SARS-CoV-2, additionally confirmed in three patients with follow-up serum samples and seven asymptomatic but PCR-positive contact persons. In conclusion, our study shows that commercially available immunoassays detect SARS-CoV-2-IgG or total antibodies in outpatients with a satisfying sensitivity, but lower than that reported for hospitalized patients. In asymptomatic persons the SARS-CoV-2-IgG response may even be absent in a relevant percentage of persons. url: https://www.ncbi.nlm.nih.gov/pubmed/32983837/ doi: 10.3205/id000066 id: cord-267671-ys43n672 author: Whary, Mark T. title: Biology and Diseases of Mice date: 2015-07-10 words: 63666.0 sentences: 3678.0 pages: flesch: 40.0 cache: ./cache/cord-267671-ys43n672.txt txt: ./txt/cord-267671-ys43n672.txt summary: Clinical Signs MCMV causes subclinical infection in adult immunocompetent mice, but experimental inoculation of neonates can cause lethal disease due to multisystemic necrosis and inflammation. Diagnosis Because infected mice do not manifest signs or lesions and the virus is very difficult to propagate in cell culture, detection and diagnosis rely on serology and molecular methods. Differential Diagnosis Reovirus infection must be differentiated from other diarrheal diseases of infant mice, including those caused by mouse coronaviruses, EDIM virus, Salmonella spp., or Clostridium piliforme. Epizootiology EDIM virus appears to be infectious only for mice and occurs episodically in mouse colonies, and infection is probably widespread geographically (Livingston and Riley, 2003; Pritchett-Corning LABORATORY ANIMAL MEDICINE et al., 2009) . Sentinel mouse surveillance, using soiled bedding, is an effective strategy for detecting MNV (Manuel et al., 2008) Differential Diagnosis The mild change in fecal consistency associated with MNV in adult mice may mimic rotavirus, coronavirus, Helicobacter spp., Citrobacter rodentium, or other enteric diseases. abstract: Today’s laboratory mouse, Mus musculus, has its origins as the ‘house mouse’ of North America and Europe. Beginning with mice bred by mouse fanciers, laboratory stocks (outbred) derived from M. musculus musculus from eastern Europe and M. m. domesticus from western Europe were developed into inbred strains. Since the mid-1980s, additional strains have been developed from Asian mice (M. m. castaneus from Thailand and M. m. molossinus from Japan) and from M. spretus which originated from the western Mediterranean region. url: https://api.elsevier.com/content/article/pii/B9780124095274000031 doi: 10.1016/b978-0-12-409527-4.00003-1 id: cord-294798-ji3p0l4j author: White, Sarah K. title: Detection and phylogenetic characterization of arbovirus dual-infections among persons during a chikungunya fever outbreak, Haiti 2014 date: 2018-05-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In the context of recent arbovirus epidemics, questions about the frequency of simultaneous infection of patients with different arbovirus species have been raised. In 2014, a major Chikungunya virus (CHIKV) epidemic impacted the Caribbean and South America. As part of ongoing screening of schoolchildren presenting with acute undifferentiated febrile illness in rural Haiti, we used RT-PCR to identify CHIKV infections in 82 of 100 children with this diagnosis during May—August 2014. Among these, eight were infected with a second arbovirus: six with Zika virus (ZIKV), one with Dengue virus serotype 2, and one with Mayaro virus (MAYV). These dual infections were only detected following culture of the specimen, suggesting low viral loads of the co-infecting species. Phylogenetic analyses indicated that the ZIKV and MAYV strains differ from those detected later in 2014 and 2015, respectively. Moreover, CHIKV and ZIKV strains from co-infected patients clustered monophyletically in their respective phylogeny, and clock calibration traced back the common ancestor of each clade to an overlapping timeframe of introduction of these arboviruses onto the island. url: https://doi.org/10.1371/journal.pntd.0006505 doi: 10.1371/journal.pntd.0006505 id: cord-345820-0n1pea70 author: Wiener, Renda Soylemez title: Angiotensin converting enzyme 2 is primarily epithelial and is developmentally regulated in the mouse lung date: 2007-03-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Angiotensin converting enzyme (ACE) 2 is a carboxypeptidase that shares 42% amino acid homology with ACE. Little is known about the regulation or pattern of expression of ACE2 in the mouse lung, including its definitive cellular distribution or developmental changes. Based on Northern blot and RT‐PCR data, we report two distinct transcripts of ACE2 in the mouse lung and kidney and describe a 5′ exon 1a previously unidentified in the mouse. Western blots show multiple isoforms of ACE2, with predominance of a 75–80 kDa protein in the mouse lung versus a 120 kDa form in the mouse kidney. Immunohistochemistry localizes ACE2 protein to Clara cells, type II cells, and endothelium and smooth muscle of small and medium vessels in the mouse lung. ACE2 mRNA levels peak at embryonic day 18.5 in the mouse lung, and immunostaining demonstrates protein primarily in the bronchiolar epithelium at that developmental time point. In murine cell lines ACE2 is strongly expressed in the Clara cell line mtCC, as opposed to the low mRNA expression detected in E10 (type I‐like alveolar epithelial cell line), MLE‐15 (type II alveolar epithelial cell line), MFLM‐4 (fetal pulmonary vasculature cell line), and BUMPT‐7 (renal proximal tubule cell line). In summary, murine pulmonary ACE2 appears to be primarily epithelial, is developmentally regulated, and has two transcripts that include a previously undescribed exon. J. Cell. Biochem. 101:1278–1291, 2007. © 2007 Wiley‐Liss, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/17340620/ doi: 10.1002/jcb.21248 id: cord-279551-py2awuav author: Willi, Barbara title: Clinical and molecular investigation of a canine distemper outbreak and vector-borne infections in a group of rescue dogs imported from Hungary to Switzerland date: 2015-07-16 words: 6264.0 sentences: 315.0 pages: flesch: 53.0 cache: ./cache/cord-279551-py2awuav.txt txt: ./txt/cord-279551-py2awuav.txt summary: title: Clinical and molecular investigation of a canine distemper outbreak and vector-borne infections in a group of rescue dogs imported from Hungary to Switzerland In the present study, we describe a distemper outbreak in 15 rescue dogs that were imported from Hungary to Switzerland by an animal welfare organisation. Canine distemper virus (CDV) is one of the most important viral pathogens in domestic dogs and causes high morbidity and mortality worldwide, particularly in unvaccinated dogs or dogs with incomplete vaccination [1] . The study provides data on vaccination, medical history, clinical examinations and diagnostic imaging of the dogs and CDV testing, testing for canine parvovirus (CPV) and vector-borne infections. The vaccine-specific real-time reverse transcription (RT)quantitative (q)PCR was negative for all ten dogs that were tested, which supports the finding of infection with a wild-type CDV strain. abstract: BACKGROUND: Canine distemper virus (CDV) is a major pathogen of dogs and wild carnivores worldwide. In Switzerland, distemper in domestic dogs is rarely reported. In recent years, the import of dogs from Eastern Europe to Switzerland has steadily increased. In the present study, we describe a distemper outbreak in 15 rescue dogs that were imported from Hungary to Switzerland by an animal welfare organisation. The data on vaccination and medical history were recorded (14 dogs), and the samples were collected to investigate CDV and vector-borne infections (13 dogs) and canine parvovirus infection (12 dogs). The dogs were monitored for six months. RESULTS: One dog was euthanised directly after import. Thirteen dogs showed clinical signs after arrival, i.e., diarrhoea (57 %), coughing (43 %) and nasal and/or ocular discharge (21 %); radiographic findings that were compatible with bronchopneumonia were present in four dogs. CDV infection was diagnosed in 11 dogs (85 %); 10 dogs (91 %) tested PCR-positive in conjunctival swabs. Vector-borne infections (Babesia spp., Leishmania infantum, Dirofilaria immitis) were found in 4 dogs (31 %). Three dogs were hospitalized, and six dogs received ambulatory therapy for up to two months until recovery. None of the dogs developed neurological disease. CDV shedding was detected for a period of up to four months. Because dogs were put under strict quarantine until CDV shedding ceased, CDV did not spread to any other dogs. The CDV isolates showed 99 % sequence identity in the HA gene among each other and belonged to the Arctic-like lineage of CDV. CONCLUSIONS: The present study highlights the imminent risks of spreading contagious viral and vector-borne infections through the non-selective import of sick dogs and dogs with incomplete vaccination from Eastern Europe. CDV shedding was detected for several months after the cessation of clinical signs, which emphasised the roles of asymptomatic carriers in CDV epidemiology. A long-term follow-up using sensitive PCR and strict quarantine measures is of upmost importance in preventing the spread of infection. Dog owners and animal welfare organisations should be educated regarding the importance of complete vaccinations and the impact of dog imports on the spread of viral and vector-borne pathogens. url: https://www.ncbi.nlm.nih.gov/pubmed/26179635/ doi: 10.1186/s12917-015-0471-0 id: cord-266523-qd5asgg8 author: Wilson, N. title: Estimating the Impact of Control Measures to Prevent Outbreaks of COVID-19 Associated with Air Travel into a COVID-19-free country: A Simulation Modelling Study date: 2020-06-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Aims: We aimed to estimate the risk of COVID-19 outbreaks associated with air travel from a country with a very low prevalence of COVID-19 infection (Australia) to a COVID-19-free country (New Zealand; [NZ]), along with the likely impact of various control measures for passengers and cabin crew. Methods: A stochastic version of the SEIR model CovidSIM v1.1, designed specifically for COVID-19 was utilized. It was populated with data for both countries and parameters for SARS-CoV-2 transmission and control measures. We assumed one Australia to NZ flight per day. Results: When no interventions were in place, an outbreak of COVID-19 in NZ was estimated to occur after an average time of 1.7 years (95% uncertainty interval [UI]: 0.04-6.09). However, the combined use of exit and entry screening (symptom questionnaire and thermal camera), masks on aircraft and two PCR tests (on days 3 and 12 in NZ), combined with self-reporting of symptoms and contact tracing and mask use until the second PCR test, reduced this risk to one outbreak every 29.8 years (0.8 to 110). If no PCR testing was performed, but mask use was used by passengers up to day 15 in NZ, the risk was one outbreak every 14.1 years. However, 14 days quarantine (NZ practice in May 2020), was the most effective strategy at one outbreak every 34.1 years (0.06 to 125); albeit combined with exit screening and mask use on flights. Conclusions: Policy-makers can require multi-layered interventions to markedly reduce the risk of importing the pandemic virus into a COVID-19-free nation via air travel. There is potential to replace 14-day quarantine with PCR testing or interventions involving mask use by passengers in NZ. However, all approaches require continuous careful management and evaluation. url: https://doi.org/10.1101/2020.06.10.20127977 doi: 10.1101/2020.06.10.20127977 id: cord-270929-utn21ce1 author: Wise, Annabel G. title: Molecular characterization of a novel coronavirus associated with epizootic catarrhal enteritis (ECE) in ferrets date: 2006-05-25 words: 6092.0 sentences: 336.0 pages: flesch: 57.0 cache: ./cache/cord-270929-utn21ce1.txt txt: ./txt/cord-270929-utn21ce1.txt summary: Using consensus PCR assays for the genus Coronavirus, followed by additional genomic sequencing and phylogenetic analyses, we provide the first molecular evidence that the virus associated with ECE in ferrets is a new coronavirus, tentatively designated as "ferret enteric coronavirus" (FECV). Table 1 shows the sequence identities between the N protein of FECV-MSU1 and those of porcine transmissible gastroenteritis virus (TGEV), canine coronavirus (CCV), feline coronavirus (FCoV), porcine epidemic diarrhea virus (PEDV), human coronavirus (HCoV) 229E, bovine coronavirus (BCV), mouse hepatitis virus (MHV), HCoV OC43, SARS virus, avian infectious bronchitis virus (IBV), and turkey coronavirus (TCoV). As with the analysis of the N protein sequence, phylogenetic analyses based upon these three other regions of the genome gave similar results, further supporting the classification of FECV as a member of group 1 coronaviruses with highest similarities to CCV, FCoV, and TGEV and more distantly related to PEDV and HcoV 229E. abstract: A novel coronavirus, designated as ferret enteric coronavirus (FECV), was identified in feces of domestic ferrets clinically diagnosed with epizootic catarrhal enteritis (ECE). Initially, partial sequences of the polymerase, spike, membrane protein, and nucleocapsid genes were generated using coronavirus consensus PCR assays. Subsequently, the complete sequences of the nucleocapsid gene and the last two open reading frames at the 3′ terminus of the FECV genome were obtained. Phylogenetic analyses based on predicted partial amino acid sequences of the polymerase, spike, and membrane proteins, and full sequence of the nucleocapsid protein showed that FECV is genetically most closely related to group 1 coronaviruses. FECV is more similar to feline coronavirus, porcine transmissible gastroenteritis virus, and canine coronavirus than to porcine epidemic diarrhea virus and human coronavirus 229E. Molecular data presented in this study provide the first genetic evidence for a new coronavirus associated with clinical cases of ECE. url: https://www.ncbi.nlm.nih.gov/pubmed/16499943/ doi: 10.1016/j.virol.2006.01.031 id: cord-310946-rjwyirld author: Wiseman, Jessica title: False negative SARS-CoV-2 PCR - A case report and literature review date: 2020-07-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The first case of the novel Coronavirus Diseases (COVID-19) caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was detected in Wuhan, China in December 2019. On January 30, 2020, the World Health Organization declared a global health emergency. Countries around the world advised social distancing, businesses and schools closed, while health care workers faced a viral war. With the declaration of a global emergency, a test to rapidly detect the SARS-CoV-2 was developed to ensure swift isolation of infected persons to prevent spread of disease. Currently, the gold standard for test is Reverse Transcriptase Polymerase Chain Reaction (RT-PCR); however, patients with a high clinical suspicion for COVID-19 can sometimes have multiple negative tests. We discuss a patient under investigation (PUI) who had classic findings of COVID-19 but repeatedly tested negative from nasopharyngeal swabs until a fifth sample obtained from a deep suctioning was tested. url: https://doi.org/10.1016/j.rmcr.2020.101140 doi: 10.1016/j.rmcr.2020.101140 id: cord-326122-5m1727m1 author: Wishaupt, Jérôme O. title: PCR testing for Paediatric Acute Respiratory Tract Infections date: 2014-08-04 words: 4910.0 sentences: 259.0 pages: flesch: 41.0 cache: ./cache/cord-326122-5m1727m1.txt txt: ./txt/cord-326122-5m1727m1.txt summary: The Pediatric Infectious Disease Society (PIDS) and the Infectious Diseases Society of America (IDSA) recommend in their guideline ''Community-Acquired Pneumonia (CAP) in Infants and Children'' the use of sensitive and specific tests for the rapid diagnosis of influenza virus and other respiratory viruses in the evaluation of children older than three months of age with CAP [19] . In another recent retrospective study of 177 children with ARI in a general hospital, antibiotic management was not influenced after detecting a viral respiratory pathogen, although the authors state that routine testing of common respiratory pathogens could lead to a better understanding of their role in disease in children with respiratory symptoms [38] . Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children abstract: Acute respiratory tract infection (ARI) is a frequently occurring disease in children. It is a clinical diagnosis for which no internationally accepted diagnostic test is available. The majority of ARI is viral in origin, though diagnostic tests for viruses were rarely performed in the past. In the past 2 decades, new molecular techniques have been introduced in many hospitals. They are capable of generating a high yield of viral and bacterial diagnoses, but their impact upon clinical practices is still questionable. In this paper, we discuss the difficulties of diagnosing ARI in children, the indications for conventional and new diagnostics and their implications. url: https://api.elsevier.com/content/article/pii/S1526054214000803 doi: 10.1016/j.prrv.2014.07.002 id: cord-316719-uej7d5zf author: Witkowski, Peter T. title: Molekulare Identifikation von Hantaviren in neuen Wirten date: 2015-08-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In addition to classical virus isolation in cell culture, the molecular detection of new virus variants by PCR techniques allows broader epidemiological insights into the world of viral pathogens. For the detection of hantaviruses–zoonotic viruses leading to fever and organ failure in humans–we developed a genus-wide nested RT-PCR format, which enables the discovery of new members within this virus genus. The methodological approach allowed the demonstration of first hantaviruses from Africa and revealed new hantavirus reservoir hosts, as shrews, moles, and bats. url: https://www.ncbi.nlm.nih.gov/pubmed/32218646/ doi: 10.1007/s12268-015-0609-4 id: cord-308422-ueyaw8pd author: Wong, Christopher W title: Optimization and clinical validation of a pathogen detection microarray date: 2007-05-28 words: 6487.0 sentences: 298.0 pages: flesch: 43.0 cache: ./cache/cord-308422-ueyaw8pd.txt txt: ./txt/cord-308422-ueyaw8pd.txt summary: Here, we report the results of a systematic investigation of the complex relationships between viral amplification efficiency, hybridization signal output, target-probe annealing specificity, and reproducibility of pathogen detection using a custom designed microarray platform. The array was designed to detect up to 35 RNA viruses using 40-mer probes tiled at an average 8-base resolution across the full length of each genome (53,555 probes; Figure S1 and Table S1 in Additional data file 1). We next hypothesized that amplification efficiency scoring could be used to select an optimal tag sequence (that is, for the RT-PCR primers) for achieving uniformly high AES Table 1 Binning of probes into specific pathogen signature probe sets across viral genomes, thus globally maximizing PCR efficiency (see supplemental methods in Additional data file 1 and [25] ). abstract: DNA microarrays used as 'genomic sensors' have great potential in clinical diagnostics. Biases inherent in random PCR-amplification, cross-hybridization effects, and inadequate microarray analysis, however, limit detection sensitivity and specificity. Here, we have studied the relationships between viral amplification efficiency, hybridization signal, and target-probe annealing specificity using a customized microarray platform. Novel features of this platform include the development of a robust algorithm that accurately predicts PCR bias during DNA amplification and can be used to improve PCR primer design, as well as a powerful statistical concept for inferring pathogen identity from probe recognition signatures. Compared to real-time PCR, the microarray platform identified pathogens with 94% accuracy (76% sensitivity and 100% specificity) in a panel of 36 patient specimens. Our findings show that microarrays can be used for the robust and accurate diagnosis of pathogens, and further substantiate the use of microarray technology in clinical diagnostics. url: https://www.ncbi.nlm.nih.gov/pubmed/17531104/ doi: 10.1186/gb-2007-8-5-r93 id: cord-266670-jxgywvwx author: Wong, Mark title: Chapter 13 Recent Advances and Future Needs in Environmental Virology date: 2007-09-06 words: 5842.0 sentences: 333.0 pages: flesch: 39.0 cache: ./cache/cord-266670-jxgywvwx.txt txt: ./txt/cord-266670-jxgywvwx.txt summary: The standard method of detection of viral pathogens in environmental samples uses assays in mammalian cell culture. The standard method of detection of viral pathogens in environmental samples uses assays in mammalian cell culture. When realtime PCR quantitative results for adenoviruses in environmental samples were compared with conventional cell culture results, it was concluded that the real-time PCR method demonstrated higher quantities of adenoviruses in comparison with conventional techniques. Detection of astroviruses, enteroviruses, and adenovirus types 40 and 41 in surface waters collected and evaluated by the information collection rule and an integrated cell culture-nested PCR procedure Application of Real-Time PCR and Tissue Culture Assay for Adenovirus Detection in Two Southern California Urban Rivers Rapid and quantitative detection of human adenovirus DNA by real-time PCR Use of cell culture-PCR assay based on combination of A549 and BGMK cell lines and molecular identification as a tool to monitor infectious adenoviruses and enteroviruses in river water abstract: The detection of viruses in water and other environmental samples constitutes special challenges. The standard method of detection of viral pathogens in environmental samples uses assays in mammalian cell culture. The infected cell cultures undergo observable morphological changes called cytopathogenic effects (CPEs) that are used for the detection of viruses. Even though many viruses are culturable in several cell lines and are thus detectable by the development of CPEs in cell culture, there are several viruses, like enteric waterborne adenoviruses types 40 and 41, which are difficult to culture and do not produce clear and consistent CPE. Other viruses, like waterborne caliciviruses, have not yet been successfully grown in cell cultures. Conventional cell culture assays for the detection of viruses in environmental samples have limited sensitivity and can be labor-intensive and timeconsuming. Two advances, the PCR and microarrays, have spurred the study of viruses and should be further applied to the field of environmental virology. The ability of both DNA viruses and RNA viruses to rapidly evolve means new and emerging viral pathogens will need to be addressed. Pathogen discovery and characterization, occurrence in the environment, exposure pathways, and health outcomes via environmental exposure need to be addressed. This will likely follow a new microbial risk framework that will require focused research on some important properties of viral disease transmission. The future will require models that examine community risks and provide explicit links between the models currently under development for environmental exposure and infectious disease. url: https://api.elsevier.com/content/article/pii/S0168706907170130 doi: 10.1016/s0168-7069(07)17013-0 id: cord-318392-r9bbomvk author: Woo, Patrick CY title: Coronavirus HKU15 in respiratory tract of pigs and first discovery of coronavirus quasispecies in 5′-untranslated region date: 2017-06-21 words: 3771.0 sentences: 213.0 pages: flesch: 56.0 cache: ./cache/cord-318392-r9bbomvk.txt txt: ./txt/cord-318392-r9bbomvk.txt summary: The genomes of two Coronavirus HKU15 strains detected in the nasopharyngeal samples of two different pigs were sequenced following our previous publications 26, 27 with modifications. Divergence times for the Coronavirus HKU15 strains were calculated based on the complete genome sequence data, utilizing the Bayesian Markov chain Monte Carlo method using BEAST 1.8.0 33 with the substitution model GTR (general time-reversible model)+G (gammadistributed rate variation)+I (estimated proportion of invariable sites), a strict molecular clock, and a constant coalescent. In one (S579N) of the two Coronavirus HKU15 genomes that we sequenced in this study, variant sites were observed at four positions; two of them were due to nucleotide substitutions, and the other two were results of indels at mononucleotide polymeric regions (189th and 376th bases). abstract: Coronavirus HKU15 is a deltacoronavirus that was discovered in fecal samples of pigs in Hong Kong in 2012. Over the past three years, Coronavirus HKU15 has been widely detected in pigs in East/Southeast Asia and North America and has been associated with fatal outbreaks. In all such epidemiological studies, the virus was generally only detected in fecal/intestinal samples. In this molecular epidemiology study, we detected Coronavirus HKU15 in 9.6% of the nasopharyngeal samples obtained from 249 pigs in Hong Kong. Samples that tested positive were mostly collected during winter. Complete genome sequencing of the Coronavirus HKU15 in two nasopharyngeal samples revealed quasispecies in one of the samples. Two of the polymorphic sites involved indels, but the other two involved transition substitutions. Phylogenetic analysis showed that the two nasopharyngeal strains in the present study were most closely related to the strains PDCoV/CHJXNI2/2015 from Jiangxi, China, and CH/Sichuan/S27/2012 from Sichuan, China. The outbreak strains in the United States possessed highly similar genome sequences and were clustered monophyletically, whereas the Asian strains were more diverse and paraphyletic. The detection of Coronavirus HKU15 in respiratory tracts of pigs implies that in addition to enteric infections, Coronavirus HKU15 may be able to cause respiratory infections in pigs and that in addition to fecal-oral transmission, the virus could possibly spread through the respiratory route. The presence of the virus in respiratory samples provides an alternative clinical sample to confirm the diagnosis of Coronavirus HKU15 infection. Quasispecies were unprecedentedly observed in the 5′-untranslated region of coronavirus genomes. url: https://www.ncbi.nlm.nih.gov/pubmed/28634353/ doi: 10.1038/emi.2017.37 id: cord-284313-rg3krh7d author: Wood, Lisa G. title: Persistent Airway Obstruction After Virus Infection Is Not Associated With Airway Inflammation date: 2007-02-28 words: 3828.0 sentences: 216.0 pages: flesch: 44.0 cache: ./cache/cord-284313-rg3krh7d.txt txt: ./txt/cord-284313-rg3krh7d.txt summary: Abstract Background:This study examined the contribution of airway inflammation to the delayed lung function recovery that occurs in some people following virus-induced asthma exacerbations. In contrast, during exacerbation, subjects with persistent airway obstruction showed no differences in inflammatory cell counts compared to stable subjects with asthma, nor did cell counts change postexacerbation. Table 3 indicates that during the exacerbation the CCQ was elevated in both the airwayrecovery and the persistent-airway-obstruction groups; then, at 4 to 6 weeks postexacerbation, a similar improvement in virus symptoms was seen in both groups (percentage change in CCQ) [Fig 1] . The poor lung function (percent predicted FEV 1 ) observed during the acute episode significantly improved in the airway-recovery group, with values returning to levels of stable asthma patients postexacerbation. 11 Conversely, patients in the persistent-airway-obstruction group showed a lower airway inflammatory profile during exacerbations similar to those with stable asthma (Fig 2) , and this did not change significantly postexacerbation (Table 4 ). abstract: Abstract Background:This study examined the contribution of airway inflammation to the delayed lung function recovery that occurs in some people following virus-induced asthma exacerbations. Methods:Subjects (n = 40) were recruited at hospital admission for acute asthma exacerbation. Respiratory virus infection was diagnosed by viral nucleic acid detection and/or cell culture, using induced sputum, nasal, or throat swabs. Data collected included lung function, answers to common cold and asthma control questionnaires, and induced sputum cellular profiles. Subjects were reexamined 4 to 6 weeks postexacerbation and were compared with stable asthmatic subjects (n = 26) who had been recruited from ambulatory care clinics. Results:Persistent airway obstruction, defined as lung function improvement at follow-up (ie, change in FEV1percent predicted [Δ%FEV1]) of <15%, was observed in 10 subjects (25%). Airway recovery (Δ%FEV1, ≥ 15%) was observed in the remaining subjects (30 subjects; 75%). During the acute episode, the airway-recovery group had increased total cell count (p = 0.019), increased number of neutrophils (p = 0.005), and increased percentage of neutrophils (p = 0.0043) compared to the group of stable subjects with asthma. Postexacerbation, the airway-recovery group had reduced numbers of neutrophils and an increased percentage of eosinophils. In contrast, during exacerbation, subjects with persistent airway obstruction showed no differences in inflammatory cell counts compared to stable subjects with asthma, nor did cell counts change postexacerbation. Symptoms improved in both groups postexacerbation. However, in the persistent-airway-obstruction group, asthma remained uncontrolled. Conclusion:Persistent airway obstruction and uncontrolled asthma are observed in some people after viral asthma exacerbations. These abnormalities are not associated with inflammatory cell influx into the airway lining fluid during the exacerbation and may reflect the involvement of noncellular elements. Further work should explore other mechanisms leading to incomplete airway recovery. url: https://www.sciencedirect.com/science/article/pii/S0012369215483254 doi: 10.1378/chest.06-1062 id: cord-332522-adul9nzf author: Wu, Qingfa title: Development of Taqman RT-nested PCR system for clinical SARS-CoV detection date: 2004-04-02 words: 2810.0 sentences: 143.0 pages: flesch: 62.0 cache: ./cache/cord-332522-adul9nzf.txt txt: ./txt/cord-332522-adul9nzf.txt summary: In this study, 12 sets of nested primers covering the SARS-CoV genome have been screened and showed sufficient sensitivity to detect SARS-CoV in RNA isolated from virus cultured in Vero 6 cells. To optimize further the reaction condition of those nested primers sets, seven sets of nested primers have been chosen to compare their reverse transcribed efficiency with specific and random primers, which is useful to combine RT with the first round of PCR into a one-step RT-PCR. Through investigations on a test panel of whole blood obtained from 30 SARS patients and 9 control persons, the specificity and sensitivity of the Taqman RT-nested PCR system was found to be 100 and 83%, respectively, which suggests that the method is a promising one to diagnose SARS in early stages. To compare the sensitivities of these 12 sets of nested primers, serial 10-fold di-lution genome cDNA of BJ01 that reverse transcribed with random primer was used as the template to carry out the nested PCR. abstract: Severe acute respiratory syndrome (SARS) is an acute newly emerged infectious respiratory illness. The etiologic agent of SARS was named ‘SARS-associated coronavirus’ (SARS-CoV) that can be detected with reverse transcription-polymerase chain reaction (RT-PCR) assays. In this study, 12 sets of nested primers covering the SARS-CoV genome have been screened and showed sufficient sensitivity to detect SARS-CoV in RNA isolated from virus cultured in Vero 6 cells. To optimize further the reaction condition of those nested primers sets, seven sets of nested primers have been chosen to compare their reverse transcribed efficiency with specific and random primers, which is useful to combine RT with the first round of PCR into a one-step RT-PCR. Based on the sensitivity and simplicity of results, the no. 73 primer set was chosen as the candidate primer set for clinical diagnoses. To specify the amplicon to minimize false positive results, a Taqman RT-nested PCR system of no. 73 nested primer set was developed. Through investigations on a test panel of whole blood obtained from 30 SARS patients and 9 control persons, the specificity and sensitivity of the Taqman RT-nested PCR system was found to be 100 and 83%, respectively, which suggests that the method is a promising one to diagnose SARS in early stages. url: https://www.ncbi.nlm.nih.gov/pubmed/15109816/ doi: 10.1016/j.jviromet.2004.02.011 id: cord-337406-25285u24 author: Wu, Xiaodong title: Incidence of Respiratory Viral Infections Detected by PCR and Real-Time PCR in Adult Patients with Community-Acquired Pneumonia: A Meta-Analysis date: 2015-03-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: With the development of more rapid and sensitive detection methods based on PCR techniques, the contributions of respiratory viral infections to community-acquired pneumonia (CAP) in adult patients are being more and more recognized. Yet, up to now, there has been a lack of synthetic data that clearly demonstrates the incidence of respiratory viral infections in adult patients with CAP. OBJECTIVES: We intended to demonstrate the incidence of respiratory viral infections detected by PCR and real-time PCR in adult patients with CAP. METHODS: We searched PubMed and Embase for studies providing the incidence of respiratory viral infections in adult patients with CAP. We investigated potential sources of heterogeneity by a univariant metaregression analysis and calculated the combined incidence of viral infections, viral infections mixed with other pathogens and individual respiratory virus species. RESULTS: We eventually identified 23 eligible reports with a total number of 6,404 patients. Incidences ranged from 8.6 to 56.2% for overall respiratory viral infections. We noted significant heterogeneity in incidence estimates for the incidence of viral infections (Cochran's χ(2) = 269.9, p < 0.0001, I(2) = 91.8%). The combined incidence of viral infections was 22.4% (95% CI = 19.0-25.7). Incidences of viral coinfections with other pathogens ranged from 3 to 28%. A high level of heterogeneity was identified as well during the estimates for incidences of coinfections (χ(2) = 200.9, p < 0.0001, I(2) = 91.5%). The combined incidence of viral coinfections with other pathogens was 12.4% (95% CI = 9.7-15.0). Our heterogeneity analyses suggested that a lower respiratory tract sample was associated with higher overall viral incidence. Moreover, the influenza virus, rhinovirus and coronavirus were the 3 most frequently detected viral pathogens in adult patients with CAP according to our study. CONCLUSIONS: Respiratory viruses are probably crucial pathogens of adult patients with CAP, with the influenza virus being the most frequent viral pathogen identified. More than half of the viral infections are characterized as mixed infections with other pathogens. url: https://www.ncbi.nlm.nih.gov/pubmed/25791384/ doi: 10.1159/000369561 id: cord-280442-jtvez46y author: Wu, Xuan title: Simultaneous and visual detection of infectious bronchitis virus and Newcastle disease virus by multiple LAMP and lateral flow dipstick date: 2019-11-01 words: 5308.0 sentences: 271.0 pages: flesch: 55.0 cache: ./cache/cord-280442-jtvez46y.txt txt: ./txt/cord-280442-jtvez46y.txt summary: To evaluate this novel detection method, PCR assays (including conventional RT-PCR, qRT-PCR and nRT-PCR) and reverse-transcription LAMP (RT-LAMP) monitored by electrophoresis were also conducted and the specificity and sensitivity of the assays were compared with those of the mRT-LAMP-LFD assay. A total of 13 IBV strains, 7 NDV strains, and the PCR and LAMP target sequences of 6 NDV and 1 turkey coronavirus strains (TCoV) synthesized by Sangon Biotech (Shanghai, China) Co, as well as 6 other avian virus strains, were used for the determination of the specificities of RT-PCR and RT-LAMP assays. Statistical significance difference studies showed that the mean detection rates of mRT-LAMP-LFD were significantly higher than that of conventional RT-PCR assays when detecting IBV or NDV alone (P < 0.05). The mean IBV and NDV detection rates of different samples, detected by mRT-LAMP-LFD, were both 95%, and were significantly higher than those detected by conventional RT-PCR and qRT-PCR (P < 0.05, Figure 6B) . abstract: ABSTRACT Infectious bronchitis virus (IBV) and Newcastle disease virus (NDV) are both important viruses seriously affecting poultry industry worldwide. In this study, reverse-transcription LAMP (RT-LAMP) was combined with lateral flow dipstick (LFD) forming a novel detection tool which could simultaneously detect IBV and NDV visually. Primers targeted the 5′-untranslated region (5′-UTR) of IBV genome and the conserved region of NDV large polymerase gene (LP). The specificity and sensitivity of this multiple reverse transcription-LAMP-LFD (mRT-LAMP-LFD) assay were compared with those of conventional RT-PCR, nested RT-PCR (nRT-PCR), quantification RT-PCR (qRT-PCR), and RT-LAMP monitored by electrophoresis. No non-specific amplifications were observed when the assays were tested with unrelated viruses. According to the sensitivity study, when detecting IBV or NDV alone, the lowest detection limits of mRT-LAMP-LFD were 100.8 IBV RNA copies/reaction and 100.7 NDV RNA copies/reaction. Furthermore, when detecting IBV and NDV simultaneously, the lowest detection limit was the same as that of the single detection assays. In the clinical sample study, mRT-LAMP-LFD performed the best among these assays. When tested with IBV or NDV single infected samples, the mean detection rates were 98.65% and 97.25%, respectively. In the IBV and NDV co-infected sample study, the mean detection rates of IBV and NDV were both 95%. This study showed that mRT-LAMP-LFD was a promising qualitative detection tool suitable for field single or multiple IBV and NDV detection. url: https://www.ncbi.nlm.nih.gov/pubmed/31265112/ doi: 10.3382/ps/pez372 id: cord-304044-i1ikf96b author: Wu, Yue title: Inhibition of white spot syndrome virus in Litopenaeus vannamei shrimp by sequence-specific siRNA date: 2007-10-03 words: 4733.0 sentences: 304.0 pages: flesch: 58.0 cache: ./cache/cord-304044-i1ikf96b.txt txt: ./txt/cord-304044-i1ikf96b.txt summary: Here, we described specific silencing of five white spot syndrome virus (WSSV) genes in Litopenaeus vannamei in vivo with sequence-specific siRNAs. These genes included DNA polymerase (dnapol), ribonucleotide reductase small subunit (rr2), thymidine kinase and thymidylate kinase (tk-tmk), vp24 and vp28. control for interference action of siRNAs. Delivery of the selected sequence-specific siRNAs resulted in increase of survival rate of shrimp infected by WSSV, as compared to the virus injected controls (Fig. 1) . To examine if treatment of specific and mutant siRNAs resulted in a reduced expression level of the selected WSSV genes in shrimp in vivo, semiquantitative and highly sensitive RT-PCR analyses were used to compare the relative silencing effects. The results showed that sequence-specific siRNAs significantly inhibited replication of WSSV relative to that of positive controls and the mutant siRNA injected group at 24 h during experiment (Fig. 3) . Our data strongly indicated that sequence-specific siRNAs significantly inhibited expression of target genes and viral replication to protect shrimp from WSSV. abstract: RNA interference (RNAi) is a sequence-specific, post-transcriptional process of mRNA degradation. Here, we described specific silencing of five white spot syndrome virus (WSSV) genes in Litopenaeus vannamei in vivo with sequence-specific siRNAs. These genes included DNA polymerase (dnapol), ribonucleotide reductase small subunit (rr2), thymidine kinase and thymidylate kinase (tk-tmk), vp24 and vp28. At 6 days post-challenged, the relative survival rates of shrimp injected with siDNApol, siRR2, siTK-TMK, siVP24 and siVP28 (siRNAs for dnapol, rr2, tk-tmk, vp24 and vp28 genes) reached 50%, 50%, 66%, 33% and 33%, respectively. Specific siRNAs of the five WSSV genes could result in suppression of the target genes and a significant reduction in the viral proliferation. In negative controls, sequence-independent siRNA (mutant siRNA) could not inhibit expression of these five genes or viral replication. Consequently, injection of sequence-dependent siRNA could induce anti-WSSV activity in shrimp. These results suggest that siRNA can suppress WSSV efficiently in shrimp, and it may provide a potential approach to the therapy of aquaculture viral disease. url: https://api.elsevier.com/content/article/pii/S0044848607005200 doi: 10.1016/j.aquaculture.2007.06.029 id: cord-354035-i3sl2r0k author: Wylie, Kristine M. title: The Virome of the Human Respiratory Tract date: 2016-12-10 words: 3901.0 sentences: 215.0 pages: flesch: 46.0 cache: ./cache/cord-354035-i3sl2r0k.txt txt: ./txt/cord-354035-i3sl2r0k.txt summary: Sensitive, culture-independent molecular assays (polymerase chain reaction and high-throughput sequencing) reveal that in addition to common viruses that cause acute, symptomatic infections the virome also includes viruses that do not cause clinical symptoms, have unknown pathogenic effect, or cause symptoms but are not among the most common viral respiratory tract pathogens. However, as characterization of the respiratory tract virome using molecular methods is a relatively new area of exploration, these studies can be useful in order to determine if viruses beyond the common, known respiratory pathogens are detected. In a study of 71 patients, viruses were assessed in nasal swabs using a panel of targeted PCR assays for common respiratory pathogens. Another study tested 89 nasopharyngeal swabs from adults with upper respiratory tract infections using reverse transcription (RT)-PCR assays for a series of common viruses, including human rhinoviruses, coronaviruses, influenza viruses and others, and by RNA sequencing. abstract: The human respiratory tract virome is defined here as the viruses present in the human respiratory tract that can infect human cells. Sensitive, culture-independent molecular assays (polymerase chain reaction and high-throughput sequencing) reveal that in addition to common viruses that cause acute, symptomatic infections the virome also includes viruses that do not cause clinical symptoms, have unknown pathogenic effect, or cause symptoms but are not among the most common viral respiratory tract pathogens. These molecular tools provide means for better defining the virome and studying the effects of viral infections on the dynamics of chronic lung diseases. url: https://doi.org/10.1016/j.ccm.2016.11.001 doi: 10.1016/j.ccm.2016.11.001 id: cord-335393-4buooi2d author: Xiang, Yangxi title: Comparative transcriptome analysis reveals the role of p53 signalling pathway during red‐spotted grouper nervous necrosis virus infection in Lateolabrax japonicus brain cells date: 2019-01-18 words: 3887.0 sentences: 221.0 pages: flesch: 46.0 cache: ./cache/cord-335393-4buooi2d.txt txt: ./txt/cord-335393-4buooi2d.txt summary: title: Comparative transcriptome analysis reveals the role of p53 signalling pathway during red‐spotted grouper nervous necrosis virus infection in Lateolabrax japonicus brain cells To better comprehend the molecular immune mechanism of sea perch (Lateolabrax japonicus) against NNV infection, the comparative transcriptome analysis of red‐spotted grouper nervous necrosis virus (RGNNV)‐infected or mock‐infected L. Based on the analysis of differentially expressed genes (DEGs), we found that p53 signalling pathway might be involved in the immune response against RGNNV, and experimentally revealed the role of L. Of these genes, many well-known immune-related genes were strongly inhibited after RGNNV infecComparative transcriptome analysis showed that 79 DEGs involved in p53 signalling pathway were regulated in RGNNV-infected LJB cells compared to control cells (Supporting Information Figure S1 ). Several studies indicated that p53 functioned as a key player in innate antiviral immunity by both enforcing the type I IFN response and inducing apoptosis in virus-infected cells (Rivas, Aaronson, & Munoz-Fontela, 2010) . abstract: Nervous necrosis virus (NNV) is one of the fish pathogens that have caused mass mortalities of many marine and freshwater fishes in the world. To better comprehend the molecular immune mechanism of sea perch (Lateolabrax japonicus) against NNV infection, the comparative transcriptome analysis of red‐spotted grouper nervous necrosis virus (RGNNV)‐infected or mock‐infected L. japonicus brain (LJB) cells was performed via RNA sequencing technology. Here, 1,969 up‐regulated genes and 9,858 down‐regulated genes, which were widely implicated in immune response pathways, were identified. Furthermore, we confirmed that p53 signalling pathway was repressed at 48 hr post‐RGNNV infection, as indicated by up‐regulation of Mdm2 and down‐regulation of p53 and its downstream target genes, including Bax, Casp8 and CytC. Overexpression of L. japonicus p53 (Ljp53) significantly inhibited RGNNV replication and up‐regulated the expression of apoptosis‐related genes, whereas the down‐regulation caused by pifithrin‐α led to the opposite effect, suggesting Ljp53 might promote cell apoptosis to repress virus replication. Luciferase assay indicated that Ljp53 could enhance the promoter activities of zebrafish interferon (IFN)1, indicating that Ljp53 could exert its anti‐RGNNV activities by enforcing the type I IFN response. This study revealed the potential antiviral role of p53 during NNV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/30659619/ doi: 10.1111/jfd.12960 id: cord-317948-svgguadm author: Xiao, Ai Tang title: Profile of RT-PCR for SARS-CoV-2: a preliminary study from 56 COVID-19 patients date: 2020-04-19 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A novel coronavirus (COVID-19) pandemic threatens the world. Here, we first studied the dynamics profile of SARS-CoV-2 from 56 recovered COVID-19 patients. We found virus shedding was up to 6 weeks after onset of symptoms. Prolonged observation period is necessary for older patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32306036/ doi: 10.1093/cid/ciaa460 id: cord-001371-wf0vonkn author: Xiao, Shuqi title: Simultaneous Detection and Differentiation of Highly Virulent and Classical Chinese-Type Isolation of PRRSV by Real-Time RT-PCR date: 2014-06-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Porcine reproductive and respiratory syndrome (PRRS) is a leading disease in pig industry worldwide and can result in serious economic losses each year. The PRRS epidemic situation in China has been very complicated since the unprecedented large-scale highly pathogenic PRRS (HP-PRRS) outbreaks in 2006. And now the HP-PRRS virus (HP-PRRSV) and classical North American type PRRSV strains have coexisted in China. Rapid differential detection of the two strains of PRRSV is very important for effective PRRS control. The real-time RT-PCR for simultaneous detection and differentiation of HP-PRRSV and PRRSV by using both SYBR Green and TaqMan probes was developed and validated. Both assays can be used for rapid detection and strain-specific identification of HP-PRRSV and PRRSV. However, the TaqMan probe method had the highest detection rate whereas the conventional RT-PCR was the lowest. The real-time RT-PCR developed based on SYBR Green and TaqMan probe could be used for simultaneous detection and differentiation of HP-PRRSV and PRRSV in China, which will benefit much the PRRS control and research. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4119655/ doi: 10.1155/2014/809656 id: cord-337701-56tmg38b author: Xiao, Yan title: Comparison of three TaqMan Real-Time Reverse Transcription-PCR assays in detecting SARS-CoV-2 date: 2020-07-06 words: 2122.0 sentences: 120.0 pages: flesch: 57.0 cache: ./cache/cord-337701-56tmg38b.txt txt: ./txt/cord-337701-56tmg38b.txt summary: In the present study, we evaluated the sensitivity, specificity, amplification efficiency, and linear detection ranges of three qRT-PCR assays, including the assays developed by our group (IPBCAMS), and the assays recommended by WHO and China CDC (CCDC). No effect of the 152 co-existed other viral nucleic acids on the LOD and the linear detection range was 153 observed, although higher Ct values were generated than those of RNA transcript 154 alone as template in all of the three qRT-PCR assays. Although most of the evaluated 232 assays exhibited good sensitivity, specificity, reproducibility and wide linear detection 233 range, performance test with clinical specimens from suspected COVID-19 patients 234 suggested that the N gene assay in IPBCAMS assays and CCDC assays, and the ORF 235 1b gene assays in IPBCAMS assays were the preferred qRT-PCR assays for accurate 236 detection of SARS-CoV-2. abstract: Quick and accurate detection of SARS-CoV-2 is critical for COVID-19 control. Dozens of real-time reverse transcription PCR (qRT-PCR) assays have been developed to meet the urgent need of COVID-19 control. However, methodological comparisons among the developed qRT-PCR assays are limited. In the present study, we evaluated the sensitivity, specificity, amplification efficiency, and linear detection ranges of three qRT-PCR assays, including the assays developed by our group (IPBCAMS), and the assays recommended by WHO and China CDC (CCDC). The three qRT-PCR assays exhibited similar sensitivities, with the limit of detection (LOD) at about 10 copies per reaction (except the ORF 1b gene assay in CCDC assays with a LOD at about 100 copies per reaction). No cross reaction with other respiratory viruses were observed in all of the three qRT-PCR assays. Wide linear detection ranges from 106 to 101 copies per reaction and acceptable reproducibility were obtained. By using 25 clinical specimens, the N gene assay of IPBCAMS assays and CCDC assays performed better (with detection rates of 92% and 100%, respectively) than that of the WHO assays (with a detection rate of 60%), and the ORF 1b gene assay in IPBCAMS assays performed better (with a detection rate of 64%) than those of the WHO assays and the CCDC assays (with detection rates of 48% and 20%, respectively). In conclusion, the N gene assays of CCDC assays and IPBCAMS assays and the ORF 1b gene assay of IPBCAMS assays were recommended for qRT-PCR screening of SARS-CoV-2. url: https://doi.org/10.1101/2020.07.06.189860 doi: 10.1101/2020.07.06.189860 id: cord-300999-20c17smt author: Xiao, Yong title: Exploration of turn-positive RT-PCR results and factors related to treatment outcome in COVID-19: A retrospective cohort study date: 2020-09-13 words: 3382.0 sentences: 181.0 pages: flesch: 52.0 cache: ./cache/cord-300999-20c17smt.txt txt: ./txt/cord-300999-20c17smt.txt summary: title: Exploration of turn-positive RT-PCR results and factors related to treatment outcome in COVID-19: A retrospective cohort study In the recurrent group, white blood cell, Neutrophils, prothrombin time, activated partial thromboplastin time, CD3, CD4, CD8, ratio of CD4/CD8, IgG and C4 complement were of significant difference among the baseline, negative and turn-positive time points. Due to a lack of specific antiviral treatments and vaccines, identifying and isolating as many potential patients as possible, especially for those with earlyonset of symptoms, is of great importance for the prevention and control of COVID-19 [2] , Real-time reverse-transcriptase polymerase-chain-reaction (RT-PCR) assay is a nucleic acid detection-based approach to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which confer an advantage to rapid detection and specificity [3, 4] . As such, we attempt to review the details of 116 COVID-19 patients in Renmin Hospitals of Wuhan University and thus, perform cause analysis of RT-PCR turn-positive and the effective screening factors related to treatment outcome in COVID-19. abstract: The cause of some patients with negative RT-PCR results experienced turn-positive after treatment remains unclear. In addition, understanding the correlation between changes in clinical data in the course of COVID-19 and treatment outcomes is of great importance in determining the prognosis of COVID-19. To perform cause analysis of RT-PCR turn-positive and the effective screening factors related to treatment outcome in COVID-19. Clinical data, including clinical manifestations, laboratory tests, radiography results, treatment methods and outcomes, were retrospectively collected and analyzed from January to March 2020 in Renmin Hospitals of Wuhan University. 116 COVID-19 patients (40 in recurrent group, 29 in recovered group and 47 in unrecovered group) were recruited. In the recurrent group, white blood cell, Neutrophils, prothrombin time, activated partial thromboplastin time, CD3, CD4, CD8, ratio of CD4/CD8, IgG and C4 complement were of significant difference among the baseline, negative and turn-positive time points. CD19 and CT scan results were found notable difference between recurrent group and recovered group. Odds from CD3, CD4, CD8, CD19, IgM, C3 complement, C4 complement and CT scan results validated associations with clinical outcomes of COVID-19. The so-called recurrence in some COVID-19 patients may be due to the false-negative of nucleic acid test results from nasopharyngeal swabs. Levels of CD3, CD4, CD8, CD19, IgM, C3 complement, C4 complement and CT results were significantly correlated with the outcome of COVID-19. The cellular immunity test could be beneficial to further screen the reliability of RT-PCR test on the basis of CT images. url: https://doi.org/10.1080/21505594.2020.1816076 doi: 10.1080/21505594.2020.1816076 id: cord-003850-in7he5o4 author: Xiu, Leshan title: Simultaneous detection of eleven sexually transmitted agents using multiplexed PCR coupled with MALDI-TOF analysis date: 2019-08-28 words: 5471.0 sentences: 286.0 pages: flesch: 45.0 cache: ./cache/cord-003850-in7he5o4.txt txt: ./txt/cord-003850-in7he5o4.txt summary: Therefore, the aim of the current study was to develop a sensitive, multitarget, and high-throughput method that can detect various agents responsible for STIs. METHODS: We developed and tested a 23-plex PCR coupled with matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) assay (sexually transmitted infection-mass spectrometry, STI-MS) that simultaneously targets 11 different agents, including 8 most common clinical pathogens related to STIs (HSV-1, HSV-2, Neisseria gonorrhoeae, Chlamydia trachomatis, Treponema pallidum, Trichomonas vaginalis, Mycoplasma genitalium, and Haemophilus ducreyi) and 3 controversial microorganisms as pathogens (Mycoplasma hominis, Ureaplasma urealyticum, and Ureaplasma parvum). 3 In this study, the MassARRAY System (Agena Bioscience, Inc., San Diego, CA, USA), a detection platform combining endpoint multiplex-PCR with matrixassisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), was utilized to develop a sexually transmitted infection assay (STI-MS) that can simultaneously detect and identify common clinical pathogens implicated in STIs, including herpes simplex virus types 1 and 2 (HSV-1 and HSV-2), Neisseria gonorrhoeae, Chlamydia trachomatis, Treponema pallidum, Trichomonas vaginalis, Mycoplasma genitalium, and Haemophilus ducreyi. abstract: PURPOSE: Sexually transmitted infections (STIs), representing a major global health problem, are caused by different microbes, including bacteria, viruses, and protozoa. Unfortunately, infections of different sexually transmitted pathogens often present similar clinical symptoms, so it is almost impossible to distinguish them clinically. Therefore, the aim of the current study was to develop a sensitive, multitarget, and high-throughput method that can detect various agents responsible for STIs. METHODS: We developed and tested a 23-plex PCR coupled with matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) assay (sexually transmitted infection-mass spectrometry, STI-MS) that simultaneously targets 11 different agents, including 8 most common clinical pathogens related to STIs (HSV-1, HSV-2, Neisseria gonorrhoeae, Chlamydia trachomatis, Treponema pallidum, Trichomonas vaginalis, Mycoplasma genitalium, and Haemophilus ducreyi) and 3 controversial microorganisms as pathogens (Mycoplasma hominis, Ureaplasma urealyticum, and Ureaplasma parvum). RESULTS: The results showed that the STI-MS approach can accurately detect the expected agents, without cross-reaction with other organisms. The limit of detection of each STI-MS assay was ranged from 1.739 to 10.009 copies/reaction, using probit analyses. The verification rate for each target organism of the STI-MS ranged from a minimum of 89.3% to a maximum of 100%, using conventional assays and ultrasensitive digital PCR to confirm the STI-MS-positive results. To further evaluate the clinical performance of this assay, 241 clinical specimens (124 urethral/cervical swabs and 117 urine) were tested in parallel using the STI-MS assay and monoplex real-time PCR for each agent. The overall validation parameters of STI-MS were extremely high including sensitivity (from 85.7% to 100%), specificity (from 92.3% to 100%), PPV (from 50% to 100%), and NPV (from 99.1% to 100%) for each target. CONCLUSION: STI-MS is a useful high-throughput screening tool for detecting mixed infections of STIs and has great potential for application in large-scale epidemiological programs for specific microorganisms of STI. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6717854/ doi: 10.2147/idr.s219580 id: cord-330079-pdaowkop author: Xu, Lin title: Surveillance and Genome Analysis of Human Bocavirus in Patients with Respiratory Infection in Guangzhou, China date: 2012-09-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Human bocavirus (HBoV) is a novel parvovirus associated with respiratory tract diseases and gastrointestinal illness in adult and pediatric patients throughout the world. To investigate the epidemiological and genetic variation of HBoV in Guangzhou, South China, we screened 3460 throat swab samples from 1686 children and 1774 adults with acute respiratory infection symptoms for HBoV between March 2010 and February 2011, and analyzed the complete genome sequence of 2 HBoV strains. Specimens were screened for HBoV by real-time PCR and other 6 common respiratory viruses by RT-PCR or PCR. HBoV was detected in 58 (1.68%) out of 3460 samples, mostly from pediatric patients (52/58) and inpatient children (47/58). Six adult patients were detected as HBoV positive and 5 were emergency cases. Of these HBoV positive cases, 19 (32.76%) had co-pathogens including influenza virus (n = 5), RSV (n = 5), parainfluenza (n = 4), adenovirus (n = 1), coronavirus (n = 7). The complete genome sequences of 2 HBoVs strains (Genbank no. JN794565 and JN794566) were analyzed. Phylogenetic analysis showed that the 2 HBoV strains were HBoV1, and were most genetically close to ST2 (GenBank accession number DQ0000496). Recombination analysis confirmed that HBoV strain GZ9081 was an intra–genotype recombinant strain among HBoV1 variants. url: https://doi.org/10.1371/journal.pone.0044876 doi: 10.1371/journal.pone.0044876 id: cord-279101-c763gzq2 author: Xu, Sen title: Identification and characterization of a novel L-type lectin (MjLTL2) from kuruma shrimp (Marsupenaeus japonicus) date: 2020-01-13 words: 4797.0 sentences: 291.0 pages: flesch: 56.0 cache: ./cache/cord-279101-c763gzq2.txt txt: ./txt/cord-279101-c763gzq2.txt summary: title: Identification and characterization of a novel L-type lectin (MjLTL2) from kuruma shrimp (Marsupenaeus japonicus) MjLTL2 was upregulated following challenge of shrimp with Vibrio anguillarum and white spot syndrome virus (WSSV). A novel L-type lectin is required for the multiplication of white spot syndrome virus (WSSV) in red swamp crayfish Procambarus clakii [12] . anguillarum-challenged shrimps were also analyzed, and results indicated that MjLTL2 expression is upregulated 24-48 h after WSSV injection in hemocytes and the hepatopancreas ( Fig. 4B and C) ; by comparison, MjLTL2 is upregulated 6-24 h after V. Shrimps were injected with WSSV after MjLTL2 silencing, followed by total RNA extraction from hemocytes at 36 and 48 hpi. Our results revealed lower VP19, VP24, VP26, and VP28 mRNA expression in the hemocytes of MjLTL2 knockdown shrimps than in the control. The results of this study revealed that expression of MjLTL2 was upregulated from 24 to 48 hpi in hemocytes and hepatopancreas after WSSV injection. abstract: L-type lectins (LTLs) belong to the lectin family and are characterized by a conserved structural motif in their carbohydrate recognition domain. LTLs are homologous to leguminous lectins. In this study, we identified and functionally characterized an LTL from kuruma shrimp Marsupenaeus japonicus. We designated this LTL as MjLTL2. MjLTL2 contains a signal peptide, a Lectin_leg domain, a coiled coil, and transmembrane domain. MjLTL2 is distributed in hemocytes, heart, hepatopancreas, gill, stomach, and intestine; higher expression levels are seen in hemocytes and the hepatopancreas than in other tissues. MjLTL2 was upregulated following challenge of shrimp with Vibrio anguillarum and white spot syndrome virus (WSSV). MjLTL2 can agglutinate several bacteria without Ca(2+). In addition, MjLTL2 could bind to several Gram-positive and -negative bacteria by binding to their lipopolysaccharide and peptidoglycan. However, MjLTL2 could not enhance the clearance of V. anguillarum in vivo. In the presence of WSSV infection, MjLTL2 knockdown by RNA interference resulted in a 7-day lower cumulative mortality of M. japonicus. Moreover, less VP19, VP24, VP26, and VP28 mRNAs were extracted from the hemocytes of MjLTL2 knockdown shrimp than from the control. These results suggest that MjLTL2 is involved in immune responses in shrimp. url: https://doi.org/10.1016/j.fsi.2020.01.022 doi: 10.1016/j.fsi.2020.01.022 id: cord-303697-oj05bstn author: YOSHIMURA, Kuniko title: Detection of Sirtuin-1 protein expression in peripheral blood leukocytes in dogs date: 2018-05-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Sirtuin-1 (SIRT1) is a nicotinamide adenine dinucleotide (NAD(+))-dependent histone deacetylase with a large number of protein substrates. It has attracted a lot of attention in association with extending lifespan. The objective of this study was to enable the evaluation of SIRT1 expression in peripheral blood mononuclear cells (PBMCs) from dogs by flow cytometry. Three transcript variants were amplified from PBMCs by reverse transcription PCR and the nucleotide sequences were analyzed. On the basis of deduced amino acid sequence, a monoclonal antibody against human SIRT1, 1F3, was selected to detect canine SIRT1. Canine SIRT1 in peripheral blood mononuclear cells was successfully detected by western blotting using this antibody. Intracellular canine SIRT1 was also detected in permeabilized 293T cells transfected with a canine SIRT1 expression plasmid by flow cytometry using this antibody. SIRT1 was detected in all leukocyte subsets including lymphocytes, granulocytes and monocytes. The expression level was markedly different among individual dogs. These results indicated that the method applied in this study is useful for evaluating canine SIRT1 levels in PBMCs from dogs. url: https://doi.org/10.1292/jvms.17-0499 doi: 10.1292/jvms.17-0499 id: cord-352562-qfb478sf author: Yamamoto, Lidia title: SARS-CoV-2 infections with emphasis on pediatric patients: a narrative review date: 2020-09-04 words: 7315.0 sentences: 341.0 pages: flesch: 45.0 cache: ./cache/cord-352562-qfb478sf.txt txt: ./txt/cord-352562-qfb478sf.txt summary: In the section devoted to the specific laboratory diagnosis of COVID-19, the most used RT-PCR protocols were described and some studies on the serological diagnosis with IgA, IgM and IgG detection were detailed, including the use of rapid immunochromatographic assays and discussing the ideal period after the onset of symptoms to perform each type of test. They identified 191 cases in hospitalized patients younger than 21 years of age, reported by hospitals in the New York State with the diagnosis of Kawasaki disease, toxic shock syndrome, myocarditis, and suspected multisystem inflammatory syndrome associated with COVID-19 in children (MIS-C). The laboratory diagnosis of COVID-19 are based on the detection of viral RNA by real time amplifications (RT-PCR) 40 or the detection of antibodies (immunoglobulins) anti-SARS-CoV-2 from the classes IgM, IgA and IgG, produced by the host''s immune system. Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) infection in children and adolescents: a systematic review abstract: This narrative review summarizes the main aspects underlying the new coronavirus SARS-CoV-2, its epidemiology, pathophysiology, pointing to differences of SARS-CoV-2 main receptors ACE2, in terms of expression and the amount of soluble ACE2 in the circulation of children, men and women, and also in those with risk factors such as the smokers and pregnant women or presenting with comorbidities (diabetes, obesity, hypertension and other cardiovascular diseases, renal and CNS pre-existing diseases). Clinical manifestations in adults and children were also described, emphasizing the particularities already seen in children, regarding signs, symptoms, viral excretion time and the involvement of all organs and systems. The COVID-19 in the pediatric population was divided into two sections: one dedicated to previously healthy children and adolescents with COVID-19, and the other to those who live with comorbidities and acquired COVID-19. A few paragraphs were reserved to the recently described severe multisystemic inflammatory syndrome associated with COVID-19 (MIS-C) that shares certain characteristics with Kawasaki disease. Some studies on the infection in pregnant and postpartum women, as well as neonates were shown. This review has also covered the laboratory diagnosis of COVID-19, passing through the imaging diagnosis made by the chest tomography revealing ground glass patching opacities, and results of non-specific exams such as the total blood with lymphopenia, the coagulation tests with increased prothrombin times, as well as marked increments of the D-dimer, troponin and proinflammatory cytokines. In the section devoted to the specific laboratory diagnosis of COVID-19, the most used RT-PCR protocols were described and some studies on the serological diagnosis with IgA, IgM and IgG detection were detailed, including the use of rapid immunochromatographic assays and discussing the ideal period after the onset of symptoms to perform each type of test. In the end, the management of pediatric patients with COVID-19 based mainly on supportive measures has been briefly commented. url: https://doi.org/10.1590/s1678-9946202062065 doi: 10.1590/s1678-9946202062065 id: cord-263417-jgu8kc5k author: Yan, Yong title: A multiplex liquid-chip assay based on Luminex xMAP technology for simultaneous detection of six common respiratory viruses date: 2017-06-17 words: 4657.0 sentences: 189.0 pages: flesch: 45.0 cache: ./cache/cord-263417-jgu8kc5k.txt txt: ./txt/cord-263417-jgu8kc5k.txt summary: We utilized one-step multiplex reverse transcription-PCR (RT-PCR) and Luminex xMAP technology to develop a respiratory multiplex liquid-chip assay (rMLA) for simultaneous detection of 6 common respiratory viruses, including influenza virus type A (FluA) and type B (FluB), para-influenza virus type 3 (PIV-3), respiratory syncytial virus (RSV), human metapneumovirus (MPV) and a threatening virus to China, Middle East Respiratory Syndrome coronavirus (MERS-CoV). In this study, one-step multiplex reverse transcription-PCR(RT-PCR) and Luminex xMAP technology were utilized to develop a respiratory multiplex LiquiChip assay (rMLA) for the detection of 6 common respiratory viruses in Jiaxing, including influenza virus type A (FluA) and B (FluB), parainfluenza virus type 3 (PIV-3), respiratory syncytial virus (RSV) and human metapneumovirus (MPV), as well as a potentially threatening virus, MERS-CoV [29] . The analytical sensitivities of the Luminex-based rMLA and multiplex real-time RT-PCR assay developed in this study were assessed by testing in duplicate 10-fold serial dilutions of positive standards ranging from 10 6 to 10 1 copies/μl of viral RNA transcripts for each target. abstract: We utilized one-step multiplex reverse transcription-PCR (RT-PCR) and Luminex xMAP technology to develop a respiratory multiplex liquid-chip assay (rMLA) for simultaneous detection of 6 common respiratory viruses, including influenza virus type A (FluA) and type B (FluB), para-influenza virus type 3 (PIV-3), respiratory syncytial virus (RSV), human metapneumovirus (MPV) and a threatening virus to China, Middle East Respiratory Syndrome coronavirus (MERS-CoV). Performance of rMLA was evaluated by comparing with real-time RT-PCR. Detection data from clinical specimens showed that the rMLA had diagnostic sensitivities of 97.10% for FluA, 94.59% for FluB, 98.68% for PIV-3, 94.87% for RSV and 95.92% for MPV (No Data for MERS-CoV due to the lack of positive specimens). Data of analytical sensitivities showed that the detection limits of the rMLA assay were 5–25 viral RNA copies per μl for FluA, FluB, PIV-3 and MERS-CoV, approximate to the real-time RT-PCR assay; while the values were 8 and 22copies/μl for MPV and RSV, lower than the real-time RT-PCR(78 and 114 copies/μl respectively). The results indicated that the rMLA is a sensitive, specific detection tool and comparable to real-time RT-PCR, especially suitable for high-throughput detection of respiratory specimens. url: https://doi.org/10.18632/oncotarget.18533 doi: 10.18632/oncotarget.18533 id: cord-025232-5itrsfmk author: Yan, Yuqian title: Construction and Characterization of a Novel Recombinant Attenuated and Replication-Deficient Candidate Human Adenovirus Type 3 Vaccine: “Adenovirus Vaccine Within an Adenovirus Vector” date: 2020-05-26 words: 5669.0 sentences: 312.0 pages: flesch: 45.0 cache: ./cache/cord-025232-5itrsfmk.txt txt: ./txt/cord-025232-5itrsfmk.txt summary: The strategy of using a clinically approved and replication-defective HAdV-5 vector provides a novel approach to develop universal adenovirus vaccine candidates against all the other types of adenoviruses causing ARDs and perhaps other adenovirus-associated diseases. In this study, the commercially-available and gene therapy use approved replication-defective HAdV-5 vector was used to construct a recombinant attenuated human adenovirus type 3 vaccine (Ginn et al. The complete hexon gene of HAdV-3 GZ01 was cloned into the AdEasy TM Adenoviral Vector, and this type-specific antigen was expressed when the recombinant adenovirus vaccine was inoculated into mice. The recombinant vaccine is expected to be used in the prevention of ARD outbreaks caused by HAdV-3 infections, and to serve as a model using adenovirus vectors for the construction of other vaccines against additional important serotypes of adenoviral respiratory pathogens. Mice were either inoculated with HAdV-3 wild-type strain GZ01 or immunized with the rAd3H recombinant vaccine by either the intranasal route or intramuscular route, respectively, to assess the antibody titer. abstract: Human adenoviruses (HAdVs) are highly contagious and result in large number of acute respiratory disease (ARD) cases with severe morbidity and mortality. Human adenovirus type 3 (HAdV-3) is the most common type that causes ARD outbreaks in Asia, Europe, and the Americas. However, there is currently no vaccine approved for its general use. The hexon protein contains the main neutralizing epitopes, provoking strong and lasting immunogenicity. In this study, a novel recombinant and attenuated adenovirus vaccine candidate against HAdV-3 was constructed based on a commercially-available replication-defective HAdV-5 gene therapy and vaccine vector. The entire HAdV-3 hexon gene was integrated into the E1 region of the vector by homologous recombination using a bacterial system. The resultant recombinants expressing the HAdV-3 hexon protein were rescued in AD293 cells, identified and characterized by RT-PCR, Western blots, indirect immunofluorescence, and electron microscopy. This potential vaccine candidate had a similar replicative efficacy as the wild-type HAdV-3 strain. However, and importantly, the vaccine strain had been rendered replication-defective and was incapable of replication in A549 cells after more than twenty-generation passages in AD293 cells. This represents a significant safety feature. The mice immunized both intranasally and intramuscularly by this vaccine candidate raised significant neutralizing antibodies against HAdV-3. Therefore, this recombinant, attenuated, and safe adenovirus vaccine is a promising HAdV-3 vaccine candidate. The strategy of using a clinically approved and replication-defective HAdV-5 vector provides a novel approach to develop universal adenovirus vaccine candidates against all the other types of adenoviruses causing ARDs and perhaps other adenovirus-associated diseases. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7248191/ doi: 10.1007/s12250-020-00234-1 id: cord-316250-w0nl88jz author: Yang, Falong title: Selection of reference genes for quantitative real-time PCR analysis in chicken embryo fibroblasts infected with avian leukosis virus subgroup J date: 2013-10-07 words: 2188.0 sentences: 112.0 pages: flesch: 51.0 cache: ./cache/cord-316250-w0nl88jz.txt txt: ./txt/cord-316250-w0nl88jz.txt summary: title: Selection of reference genes for quantitative real-time PCR analysis in chicken embryo fibroblasts infected with avian leukosis virus subgroup J The objective of our study was to identify suitable reference genes for mRNA expression analysis in chicken embryonic fibroblasts (CEF) after infection with avian leukosis virus subgroup J (ALV-J). CONCLUSIONS: The RPL30 and SDHA were deemed suitable for use as reference genes for real-time PCR analysis of mRNA gene expression during ALV-J infection, whereas commonly used ACTB and GAPDH are unsuitable to be reference genes. This highlights the necessity of reference gene selection during real-time PCR analysis for virus-infected cells. Determination of suitable housekeeping genes for normalisation of quantitative real time PCR analysis of cells infected with human immunodeficiency virus and herpes viruses Selection of reference genes for quantitative real-time PCR analysis in chicken embryo fibroblasts infected with avian leukosis virus subgroup J. abstract: BACKGROUND: The selection of stably expressed reference genes is a prerequisite when evaluating gene expression, via real-time PCR, in cells in response to viral infections. The objective of our study was to identify suitable reference genes for mRNA expression analysis in chicken embryonic fibroblasts (CEF) after infection with avian leukosis virus subgroup J (ALV-J). FINDINGS: The expression levels of 11 potential reference genes in CEF infected with ALV-J were determined by real-time PCR. The expression stability of these genes were analyzed and ranked using the geNorm tool. Analysis indicated that the genes RPL30 (ribosomal protein L30) and SDHA (succinate dehydrogenase complex, subunit A) were the most stably expressed genes in the ALV-J infected CEF. CONCLUSIONS: The RPL30 and SDHA were deemed suitable for use as reference genes for real-time PCR analysis of mRNA gene expression during ALV-J infection, whereas commonly used ACTB and GAPDH are unsuitable to be reference genes. url: https://doi.org/10.1186/1756-0500-6-402 doi: 10.1186/1756-0500-6-402 id: cord-353499-os328w9o author: Yang, H. S. title: Routine laboratory blood tests predict SARS-CoV-2 infection using machine learning date: 2020-06-19 words: 2851.0 sentences: 173.0 pages: flesch: 55.0 cache: ./cache/cord-353499-os328w9o.txt txt: ./txt/cord-353499-os328w9o.txt summary: Here we present a machine learning model incorporating patient demographic features (age, sex, race) with 27 routine laboratory tests to predict an individual''s SARS-CoV-2 infection status. Overall, this model employing routine laboratory test results offers opportunities for early and rapid identification of high-risk SARS-COV-2 infected patients before their RT-PCR results are available. In this study, we hypothesized that the results of routine laboratory tests performed within a short time frame as the RT-PCR testing, in conjunction with a limited number of previously identified predictive demographic factors (age, gender, race) (16), can predict SARS-CoV-2 infection status. selected to construct the input feature vectors of the prediction model based on the following criteria: 1) a result available for at least 30% of the patients two days before a specific SARS-CoV-2 RT-PCR test, and 2) showing a significant difference (p-value, pvalue after Bonferroni correction, p-value after demographics adjustment all less than 0.05) between patients with positive and negative RT-PCR results. abstract: Accurate diagnostic strategies to rapidly identify SARS-CoV-2 positive individuals for management of patient care and protection of health care personnel are urgently needed. The predominant diagnostic test is viral RNA detection by RT-PCR from nasopharyngeal swabs specimens, however the results of this test are not promptly obtainable in all patient care locations. Routine laboratory testing, in contrast, is readily available with a turn-around time (TAT) usually within 1-2 hours. Here we present a machine learning model incorporating patient demographic features (age, sex, race) with 27 routine laboratory tests to predict an individual's SARS-CoV-2 infection status. Laboratory test results obtained within two days before the release of SARS-CoV-2-RT-PCR result were used to train a gradient boosted decision tree (GBDT) model from 3,346 SARS-CoV-2 RT-PCR tested patients (1,394 positive and 1,952 negative) evaluated at a large metropolitan hospital. The model achieved an area under the receiver operating characteristic curve (AUC) of 0.853 (95% CI: 0.829-0.878). Application of this model to an independent patient dataset from a separate hospital resulted in a comparable AUC (0.838), validating the generalization of its use. Moreover, our model predicted initial SARS-CoV-2 RT-PCR positivity in 66% individuals whose RT-PCR result changed from negative to positive within two days. Overall, this model employing routine laboratory test results offers opportunities for early and rapid identification of high-risk SARS-COV-2 infected patients before their RT-PCR results are available. This may facilitate patient care and quarantine, indicate who requires retesting, and direct personal protective equipment use while awaiting definitive RT-PCR results. url: http://medrxiv.org/cgi/content/short/2020.06.17.20133892v1?rss=1 doi: 10.1101/2020.06.17.20133892 id: cord-329069-ejdunj41 author: Yang, He S title: Routine laboratory blood tests predict SARS-CoV-2 infection using machine learning date: 2020-08-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Accurate diagnostic strategies to rapidly identify SARS-CoV-2 positive individuals for management of patient care and protection of health care personnel are urgently needed. The predominant diagnostic test is viral RNA detection by RT-PCR from nasopharyngeal swabs specimens, however the results are not promptly obtainable in all patient care locations. Routine laboratory testing, in contrast, is readily available with a turn-around time (TAT) usually within 1-2 hours. METHOD: We developed a machine learning model incorporating patient demographic features (age, sex, race) with 27 routine laboratory tests to predict an individual’s SARS-CoV-2 infection status. Laboratory test results obtained within two days before the release of SARS-CoV-2-RT-PCR result were used to train a gradient boosted decision tree (GBDT) model from 3,356 SARS-CoV-2 RT-PCR tested patients (1,402 positive and 1,954 negative) evaluated at a metropolitan hospital. RESULTS: The model achieved an area under the receiver operating characteristic curve (AUC) of 0.854 (95% CI: 0.829-0.878). Application of this model to an independent patient dataset from a separate hospital resulted in a comparable AUC (0.838), validating the generalization of its use. Moreover, our model predicted initial SARS-CoV-2 RT-PCR positivity in 66% individuals whose RT-PCR result changed from negative to positive within two days. CONCLUSION: This model employing routine laboratory test results offers opportunities for early and rapid identification of high-risk SARS-CoV-2 infected patients before their RT-PCR results are available. It may play an important role in assisting the identification of SARS-COV-2 infected patients in areas where RT-PCR testing is not accessible due to financial or supply constraints. url: https://www.ncbi.nlm.nih.gov/pubmed/32821907/ doi: 10.1093/clinchem/hvaa200 id: cord-329517-3yn80r9h author: Yang, Jin-Long title: Development of a fluorescent quantitative real-time polymerase chain reaction assay for the detection of Goose parvovirus in vivo date: 2009-09-15 words: 3564.0 sentences: 192.0 pages: flesch: 55.0 cache: ./cache/cord-329517-3yn80r9h.txt txt: ./txt/cord-329517-3yn80r9h.txt summary: title: Development of a fluorescent quantitative real-time polymerase chain reaction assay for the detection of Goose parvovirus in vivo The objective of this study was to develop a fluorescent quantitative real-time polymerase chain reaction (PCR) (FQ-PCR) assay for fast and accurate quantification of GPV DNA in infected goslings, which can aid in the understanding of the regular distribution pattern and the nosogenesis of GPV in vivo. Ten-fold dilutions of the pVP3 plasmid DNA were tested by the established FQ-PCR assay to evaluate the sensitivity of the system, and the detection limit was found to be 2.8 × 10 1 copies/reaction. Viral load quantification using the established FQ-PCR demonstrated that the GPV DNA copy number of each sample could be calculated using the cycle threshold (Ct) value determined from the standard curve. In conclusion, the established real-time PCR assay was rapid, sensitive, and specific for the detection and quantification of GPV DNA. abstract: BACKGROUND: Goose parvovirus (GPV) is a Dependovirus associated with latent infection and mortality in geese. Currently, it severely affects geese production worldwide. The objective of this study was to develop a fluorescent quantitative real-time polymerase chain reaction (PCR) (FQ-PCR) assay for fast and accurate quantification of GPV DNA in infected goslings, which can aid in the understanding of the regular distribution pattern and the nosogenesis of GPV in vivo. RESULTS: The detection limit of the assay was 2.8 × 10(1 )standard DNA copies, with a sensitivity of 3 logs higher than that of the conventional gel-based PCR assay targeting the same gene. The real-time PCR was reproducible, as shown by satisfactory low intraassay and interassay coefficients of variation. CONCLUSION: The high sensitivity, specificity, simplicity, and reproducibility of the GPV fluorogenic PCR assay, combined with a high throughput, make this method suitable for a broad spectrum of GPV etiology-related applications. url: https://doi.org/10.1186/1743-422x-6-142 doi: 10.1186/1743-422x-6-142 id: cord-002795-i1qcanti author: Yang, Jing title: Development of a Quantitative Loop-Mediated Isothermal Amplification Assay for the Rapid Detection of Novel Goose Parvovirus date: 2017-12-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: An infectious disease characterized with short bills and protruding tongues has attacked to meat ducks in China since March 2015, which has caused ducks poor growth and enormous economic losses to duck industry of China. It was eventually proved to be caused by parvovirus after pathogen isolation and identification. As the genomic sequence analysis showed, this pathogen shared 90.8–94.6% of nucleotide identity with goose parvovirus (GPV), and it was called duck-origin novel goose parvovirus (N-GPV). In this study, a quantitative loop-mediated isothermal amplification (qLAMP) assay was developed for the rapid diagnosis of N-GPV. A set of four specific primers, two inner and two outer, were designed targeting at VP3 gene, which could be completed within 60 min at 65°C in water bath or on a real-time PCR instrument for quantitative analysis. Specificity test of LAMP assay showed that there was no cross-reactivity between N-GPV and other duck pathogens, and the detection limit of qLAMP assay was 1.0 × 10(2) copies/μL. The repeatability of this method was confirmed by inter-assay and intra-assay tests with variability ranging from 0.74 to 2.25%. The results have indicated that the qLAMP assay was a simple, rapid, accurate, sensitive, and specific method for detecting N-GPV, especially on field detection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5732990/ doi: 10.3389/fmicb.2017.02472 id: cord-283309-ovx5fzsg author: Yang, Yong-Le title: Characterization of a novel bat-HKU2-like swine enteric alphacoronavirus (SeACoV) infection in cultured cells and development of a SeACoV infectious clone date: 2019-08-09 words: 5422.0 sentences: 271.0 pages: flesch: 52.0 cache: ./cache/cord-283309-ovx5fzsg.txt txt: ./txt/cord-283309-ovx5fzsg.txt summary: Six subgenomic mRNAs containing the leader-body junction sites, including a bicistronic mRNA encoding the accessory NS7a and NS7b genes, were experimentally identified in SeACoV-infected cells. Anti-Ac (Nsp3) staining also resulted in detection of perinuclear foci at four time points, indicating localization to the viral replication-transcription complexes (Fig. 1C) , which was similar to the pattern of Nsp3 antibody observed in SARS-CoV-infected Vero cells (Prentice et al., 2004) . DMVs are membrane structures where viral genomic RNA is recognized by the host cell machinery and translated into non-structural proteins (ORF1ab), assembling into viral replication-transcription complexes (Gosert et al., 2002) , whereas LVCVs are large circular organelles that are thought to originate from Golgi compartments expanding to accommodate numerous precursor virions Positions of forward (LF) and reverse primers (S1-R, sgORF3-R, sgE-R, sgM-R, sgN-R and NS7a-R/NS7-R) used for PCR amplification of distinct subgenomic mRNAs (sgRNAs) are indicated by arrows under the genome. abstract: Swine enteric alphacoronavirus (SeACoV), also known as swine acute diarrhea syndrome coronavirus (SADS-CoV), belongs to the species Rhinolophus bat coronavirus HKU2. Herein, we report on the primary characterization of SeACoV in vitro. Four antibodies against the SeACoV spike, membrane, nucleocapsid and nonstructural protein 3 capable of reacting with viral antigens in SeACoV-infected Vero cells were generated. We established a DNA-launched SeACoV infectious clone based on the cell adapted passage-10 virus and rescued the recombinant virus with a unique genetic marker in cultured cells. Six subgenomic mRNAs containing the leader-body junction sites, including a bicistronic mRNA encoding the accessory NS7a and NS7b genes, were experimentally identified in SeACoV-infected cells. Cellular ultrastructural changes induced by SeACoV infection were visualized by electron microscopy. The availability of the SeACoV infectious clone and a panel of antibodies against different viral proteins will facilitate further studies on understanding the molecular mechanisms of SeACoV replication and pathogenesis. url: https://www.sciencedirect.com/science/article/pii/S0042682219302193 doi: 10.1016/j.virol.2019.08.006 id: cord-289200-6yhz1a23 author: Yang, Ziyi title: Vertical Transmission of Severe Acute Respiratory Syndrome Coronavirus 2: A Systematic Review date: 2020-05-13 words: 1898.0 sentences: 123.0 pages: flesch: 50.0 cache: ./cache/cord-289200-6yhz1a23.txt txt: ./txt/cord-289200-6yhz1a23.txt summary: Two authors independently and systematically searched these databases using the following MeSH terms: "pregnancy," "infant, newborn," "COVID-19," and "severe acute respiratory syndrome coronavirus 2." We also performed a manual search in Google Scholar and the websites of key journals in the related field. Indeed, breastfeeding may not be safe until COVID-19 is ruled out or until both mother and neonate clear As there is no evidence to support the possibility of intrauterine vertical transmission, the timing of delivery should not be based solely on the condition that a pregnant patient is infected but should be individualized in each case; that is, obstetricians may consider maternal and fetal wellbeing, gestational age, and other concomitant conditions to determine the time of delivery. The currently available evidence does not support the possibility of intrauterine vertical transmission of SARS-CoV-2 infection during the third trimester of pregnancy. abstract: Objective The aim of this study is to summarize currently available evidence on vertical transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Study Design A systematic review was conducted following the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-analysis Statement. Results A total of 22 studies comprising 83 neonates born to mothers diagnosed with coronavirus disease 2019 were included in the present systematic review. Among these neonates, three were confirmed with SARS-CoV-2 infection at 16, 36, and 72 hours after birth, respectively, by nasopharyngeal swab real-time polymerase chain reaction (RT-PCR) tests; another six had elevated virus-specific antibody levels in serum samples collected after birth, but negative RT-PCR test results. However, without positive RT-PCR tests of amniotic fluid, placenta, or cord blood, there is a lack of virologic evidence for intrauterine vertical transmission. Conclusion There is currently no direct evidence to support intrauterine vertical transmission of SARS-CoV-2. Additional RT-PCR tests on amniotic fluid, placenta, and cord blood are needed to ascertain the possibility of intrauterine vertical transmission. For pregnant women infected during their first and second trimesters, further studies focusing on long-term outcomes are needed. Key Points: We review neonates of mothers diagnosed with coronavirus disease 2019 detected by RT-PCR. No direct virologic evidence of vertical transmission has been reported. No evidence that cesarean delivery is safer than vaginal delivery. More RT-PCR tests on amniotic fluid, placenta, and cord blood are recommended. url: https://www.ncbi.nlm.nih.gov/pubmed/32403141/ doi: 10.1055/s-0040-1712161 id: cord-271427-af71cum9 author: Yazici, Zafer title: Circulation of Indigenous Bovine Respiratory Syncytial Virus Strains in Turkish Cattle: The First Isolation and Molecular Characterization date: 2020-09-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: SIMPLE SUMMARY: Bovine respiratory syncytial virus (BRSV) is an important pathogen of both dairy and beef cattle, and causes huge economic losses annually across the world. This study reports the identification, isolation, and molecular characterization of a new BRSV (subgroup III) strain collected from respiratory distressed cattle in Turkey. The three field isolates obtained showed 100% similarity to each other at the nucleotide (nt) level and were found to be 99.49% and 99.22% identical to another Turkish strain—KY499619—at both (nt) and amino acid (aa) levels, respectively. They were also 97.43% (nt) and 98.44% (aa) similar to the American reference strain KU159366. This important information will inform Turkish BRSV diagnostic and control strategies, as well as highlight the urgent need to better understand the burden that BRSV is placing on the Turkish agricultural sector. ABSTRACT: Bovine respiratory disease (BRD) is a huge economic burden on the livestock industries of countries worldwide. Bovine respiratory syncytial virus (BRSV) is one of the most important pathogens that contributes to BRD. In this study, we report the identification and first isolation, with molecular characterization, of a new BRSV strain from lung specimens of three beef cows in Turkey that died from respiratory distress. After the screening of lung tissues for BRD-associated viruses using a multiscreen antigen-ELISA, a BRSV antigen was detected. This was then confirmed by real-time RT-PCR specific for BRSV. Following confirmation, virus isolation was conducted in MDBK cell cultures and clear CPE, including syncytia compatible with BRSV, were detected. RT-nested PCR, using F gene-specific primers, was performed on the cultured isolates, and the products were sequenced and deposited to Genbank with accession numbers MT179304, MT024766, and MT0244767. Phylogenetic analysis of these sequences indicated that the cattle were infected with BRSV from subgroup III and were closely related to previously identified American and Turkish strains, but contained some amino acid and nucleotide differences. This research paves the way for further studies on the molecular characteristics of natural BRSV isolates, including full genome analysis and disease pathogenesis, and also contributes to the development of robust national strategies against this virus. url: https://www.ncbi.nlm.nih.gov/pubmed/32962234/ doi: 10.3390/ani10091700 id: cord-321076-kont2sff author: Yeo, Wee Song title: Cohort PCR Testing: A Strategic Method for Rapid SARS-CoV-2 Screening date: 2020-05-30 words: 809.0 sentences: 47.0 pages: flesch: 55.0 cache: ./cache/cord-321076-kont2sff.txt txt: ./txt/cord-321076-kont2sff.txt summary: title: Cohort PCR Testing: A Strategic Method for Rapid SARS-CoV-2 Screening The world is currently facing an unprecedented outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes viral pneumonias and the coronavirus disease 2019 (COVID-19) in humans. 2, 3 Various diagnostic methods have been utilized in the detection of SARS-CoV-2, among which real time reverse transcription polymerase chain reaction (RT-PCR) assay is the most established and commonly utilized test method. Last, any cohort PCR reaction tubes that are positive for SARS-CoV-2 will be followed up by running RT-PCR on each of the individual RNA samples to identify the infected individual(s). Cohort PCR is applicable for rapid screening of family/living units in the community who are likely to be negative for SARS-CoV-2. If cohort PCR is used to test a family or living unit where one member has confirmed SARS-CoV-2 infection, then there would be a very high likelihood that the pool would be positive (increasing probability with pool size). abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32472673/ doi: 10.1093/ajcp/aqaa092 id: cord-275232-0sg0hv9w author: Yeung, Siu-Wai title: A DNA biochip for on-the-spot multiplexed pathogen identification date: 2006-09-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Miniaturized integrated DNA analysis systems have largely been based on a multi-chamber design with microfluidic control to process the sample sequentially from one module to another. This microchip design in connection with optics involved hinders the deployment of this technology for point-of-care applications. In this work, we demonstrate the implementation of sample preparation, DNA amplification, and electrochemical detection in a single silicon and glass-based microchamber and its application for the multiplexed detection of Escherichia coli and Bacillus subtilis cells. The microdevice has a thin-film heater and temperature sensor patterned on the silicon substrate. An array of indium tin oxide (ITO) electrodes was constructed within the microchamber as the transduction element. Oligonucleotide probes specific to the target amplicons are individually positioned at each ITO surface by electrochemical copolymerization of pyrrole and pyrrole−probe conjugate. These immobilized probes were stable to the thermal cycling process and were highly selective. The DNA-based identification of the two model pathogens involved a number of steps including a thermal lysis step, magnetic particle-based isolation of the target genomes, asymmetric PCR, and electrochemical sequence-specific detection using silver-enhanced gold nanoparticles. The microchamber platform described here offers a cost-effective and sample-to-answer technology for on-site monitoring of multiple pathogens. url: https://www.ncbi.nlm.nih.gov/pubmed/17000638/ doi: 10.1093/nar/gkl702 id: cord-319392-zg7gkf0j author: Yi, Li title: Development of a combined canine distemper virus specific RT-PCR protocol for the differentiation of infected and vaccinated animals (DIVA) and genetic characterization of the hemagglutinin gene of seven Chinese strains demonstrated in dogs date: 2011-11-18 words: 3494.0 sentences: 200.0 pages: flesch: 59.0 cache: ./cache/cord-319392-zg7gkf0j.txt txt: ./txt/cord-319392-zg7gkf0j.txt summary: title: Development of a combined canine distemper virus specific RT-PCR protocol for the differentiation of infected and vaccinated animals (DIVA) and genetic characterization of the hemagglutinin gene of seven Chinese strains demonstrated in dogs A combined reverse-transcription polymerase chain reaction (RT-PCR) method was developed for the detection and differentiation of wild-type and vaccine strains of the canine distemper virus (CDV). The phylogenetic analysis of the hemagglutinin gene of the local wild-type CDV strains revealed that the seven local isolates all belonged to the Asia-1 lineage, and were clustered closely with one another at the same location. The CDV cDNA products were further simultaneously amplified by a combined two-step RT-PCR assay using two primer sets to distinguish the vaccine and field strains. A multiplex reverse transcriptionnested polymerase chain reaction for detection and differentiation of wild-type and vaccine strains of canine distemper virus abstract: A combined reverse-transcription polymerase chain reaction (RT-PCR) method was developed for the detection and differentiation of wild-type and vaccine strains of the canine distemper virus (CDV). A pair of primers (P1/P2) was used to detect both CDV wild-type strains and vaccines. Another pair (P3/P4) was used to detect only CDV wild-type strains. A 335 bp fragment was amplified from the genomic RNA of the vaccine and wild-type strains. A 555 bp fragment was amplified specifically from the genomic RNA of the wild-type strains. No amplification was achieved for the uninfected cells, cells infected with canine parvovirus, canine coronavirus, or canine adenovirus. The combined RT-PCR method detected effectively and differentiated the CDV wild-type and vaccine strains by two separate RT-PCRs. The method can be used for clinical detection and epidemiological surveillance. The phylogenetic analysis of the hemagglutinin gene of the local wild-type CDV strains revealed that the seven local isolates all belonged to the Asia-1 lineage, and were clustered closely with one another at the same location. These results suggested that the CDV genotype Asia-1 is circulating currently in domestic dogs in China. url: https://www.ncbi.nlm.nih.gov/pubmed/22108430/ doi: 10.1016/j.jviromet.2011.11.011 id: cord-288692-v471648u author: Yip, Shea Ping title: Use of Dual TaqMan Probes to Increase the Sensitivity of 1-Step Quantitative Reverse Transcription-PCR: Application to the Detection of SARS Coronavirus date: 2005-10-01 words: 2387.0 sentences: 117.0 pages: flesch: 51.0 cache: ./cache/cord-288692-v471648u.txt txt: ./txt/cord-288692-v471648u.txt summary: title: Use of Dual TaqMan Probes to Increase the Sensitivity of 1-Step Quantitative Reverse Transcription-PCR: Application to the Detection of SARS Coronavirus We designed a 1-step real-time quantitative RT-PCR assay for SARS-CoV with the use of 2 TaqMan probes, instead of 1 probe, hybridizing to the same PCR product to further improve the sensitivity. In conclusion, we report the use of dual TaqMan probes for quantification purposes and apply it to the detection of Clinical Chemistry 51, No. 10, 2005 SARS-CoV with a detection limit of 1 copy RNA per reaction. Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays Quantitation of severe acute respiratory syndrome coronavirus genome by real-time polymerase chain reaction assay using minor groove binder DNA probe technology Sensitive and quantitative detection of severe acute respiratory syndrome coronavirus infection by real-time nested-polymerase chain reaction abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/16189379/ doi: 10.1373/clinchem.2005.054106 id: cord-310096-a242g5kg author: Yokota, I. title: Mass screening of asymptomatic persons for SARS-CoV-2 using saliva date: 2020-08-14 words: 1956.0 sentences: 131.0 pages: flesch: 49.0 cache: ./cache/cord-310096-a242g5kg.txt txt: ./txt/cord-310096-a242g5kg.txt summary: Methods We conducted a mass-screening study to compare the utility of nucleic acid amplification, such as reverse transcriptase polymerase chain reaction (RT-PCR) testing, using NPS and saliva samples from each individual in two cohorts of asymptomatic persons: the contact tracing cohort and the airport quarantine cohort. We conducted a mass-screening study to compare the utility of nucleic acid amplification, such as reverse transcriptase polymerase chain reaction (RT-PCR) testing, using NPS and saliva samples from each individual in two cohorts of asymptomatic persons: the contact tracing cohort and the airport quarantine cohort. Currently, the diagnosis of COVID-19 is made by the detection of the nucleic acids of SARS-CoV-2 typically by real-time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) testing of specimens collected by nasopharyngeal swabs (NPS) [5, 6] . We conducted a mass-screening study to determine and compare the sensitivity and specificity of nucleic acid amplification using paired samples (self-collected saliva and NPS) for the detection of SARS-CoV-2 in two cohorts of asymptomatic individuals. abstract: Background COVID-19 has rapidly evolved to become a global pandemic due largely to the transmission of its causative virus through asymptomatic carriers. Detection of SARS-CoV-2 in asymptomatic people is an urgent priority for the prevention and containment of disease outbreaks in communities. However, few data are available in asymptomatic persons regarding the accuracy of PCR testing. Additionally, although self-collected saliva has significant logistical advantages in mass screening, its utility as an alternative specimen in asymptomatic persons is yet to be determined. Methods We conducted a mass-screening study to compare the utility of nucleic acid amplification, such as reverse transcriptase polymerase chain reaction (RT-PCR) testing, using NPS and saliva samples from each individual in two cohorts of asymptomatic persons: the contact tracing cohort and the airport quarantine cohort. Results In this mass-screening study including 1,924 individuals, the sensitivity of nucleic acid amplification testing with nasopharyngeal and saliva specimens were 86% (90%CI:77-93%) and 92% (90%CI:83-97%), respectively, with specificities greater than 99.9%. The true concordance probability between the nasopharyngeal and saliva tests was estimated at 0.998 (90%CI:0.996-0.999) on the estimated airport prevalence, 0.3%. In positive individuals, viral load was highly correlated between NPS and saliva. Conclusion Both nasopharyngeal and saliva specimens had high sensitivity and specificity. Self-collected saliva is a valuable specimen to detect SARS-CoV-2 in mass screening of asymptomatic persons. url: https://doi.org/10.1101/2020.08.13.20174078 doi: 10.1101/2020.08.13.20174078 id: cord-352894-88c46evj author: Yoon, Soon‐Seek title: Comparison of the diagnostic methods on the canine adenovirus type 2 infection date: 2010-06-02 words: 2573.0 sentences: 152.0 pages: flesch: 46.0 cache: ./cache/cord-352894-88c46evj.txt txt: ./txt/cord-352894-88c46evj.txt summary: Methods: Stray dog samples were evaluated by histopathology, polymerase chain reaction (PCR), and immunohistochemistry (IHC) to investigate the status of the CAV‐2 infection on the stray dogs in Korea. Common infectious causes of respiratory disease in dogs include canine distemper virus (CDV) and canine adenovirus type 2 (CAV-2). 3 Pulmonary CAV-2 lesions are consistent with those of bronchointerstitial pneumonia, including the presence of necrosis and large basophilic intranuclear inclusion bodies (IN/IBs) in bronchiolar and alveolar epithelial cells as well as pulmonary macrophages. 5,6 Therefore, pneumonic lung tissues were examined for CAV-2 antigen by immunochemistry and CAV-2 genes by polymerase chain reaction (PCR) in the present study. 5 CAV-2 specific IC/IBs were identified in only three cases in the present study; however, seven cases were IHC positive for CAV-2 antigen detection. These results suggested that CAV-2 particles may fail to create detectable inclusions in some cases although viral antigens were present in the lung tissues. abstract: Background and aims: Canine adenovirus type 2 (CAV‐2) infection is typically diagnosed histopathologically since intranuclear inclusion bodies (IN/IBs) are demonstrable in the infected lung. However, it is sometimes difficult to identify IN/IBs, particularly in autolyzed tissues or samples from both early and late stages of infection, and other methods were presently developed. Methods: Stray dog samples were evaluated by histopathology, polymerase chain reaction (PCR), and immunohistochemistry (IHC) to investigate the status of the CAV‐2 infection on the stray dogs in Korea. Histologic tests were performed, and dogs with pneumonic lungs were further evaluated by IHC and PCR. Results: Pathognomonic IN/IBs were identified in 3 of 213 lungs; CAV‐2 PCR was positive for 27 of 213 pneumonic lungs. A total of 7 of 27 CAV‐2 PCR‐positive lungs were IHC‐positive. No PCR‐negative lung was IHC‐positive. Positive results were primarily detected in the IN/IBs of the bronchial epithelial cells, macrophages, and very rarely in the cytoplasm of bronchial epithelial cells. Conclusions: IHC was a more reliable diagnostic method than conventional pathologic methods in the present study, and suggests that IHC should be routinely used in the diagnosis of CAV‐2 infection. Further, PCR alone may not be adequate for CAV‐2 diagnosis. url: https://www.ncbi.nlm.nih.gov/pubmed/32362936/ doi: 10.1111/j.1755-9294.2010.01073.x id: cord-353573-y9jro9gt author: You, Huey-Ling title: Simultaneous detection of respiratory syncytial virus and human metapneumovirus by one-step multiplex real-time RT-PCR in patients with respiratory symptoms date: 2017-03-27 words: 3452.0 sentences: 203.0 pages: flesch: 52.0 cache: ./cache/cord-353573-y9jro9gt.txt txt: ./txt/cord-353573-y9jro9gt.txt summary: BACKGROUND: Both respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) are important viral pathogens causing respiratory tract infection (RTI) in the pediatric population. RESULTS: Our one-step triplex qRT-PCR assay showed 100% sensitivity and specificity in testing RSV and hMPV in 86 known virus culture supernatants, with excellent linearity (R(2) > 0.99) and reliable reproducibility (CV lower than 1.04%). The aim of this study is to design and assess the diagnostic performance of clinical specimens for the simultaneous identification of RSV and hMPV by using one-step triplex qRT-PCR assay with TaqMan probes. Our one-step triplex qRT-PCR results showed that the viral load of the RSV or hMPV-positive samples from clinical specimens varied over a wide range, presenting threshold between Ct 21 and 44 (21 and 44 cycles). In this study, we established a rapid and internally controlled triplex qRT-PCR assay that can identify RSV and hMPV virus in one reaction mixtures. abstract: BACKGROUND: Both respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) are important viral pathogens causing respiratory tract infection (RTI) in the pediatric population. However, the clinical manifestations of RSV and hMPV infections are similar. Therefore, a reliable and rapid diagnostic tool is needed for diagnostic performance. METHODS: In order to optimize diagnosis efficiency of RTI, the aim of this study is to establish a rapid and advanced method for simultaneous detecting RSV and hMPV in nasopharyngeal aspirates specimens from patients. We designed a one-step triplex real-time RT-PCR (qRT-PCR) protocol using TaqMan probes for detecting RSV and hMPV. The plasmid clones containing RSV nucleoprotein gene and hMPV fusion gene were established as reference standards. We used virus culture supernatants from 86 known pediatric RTI patient to test the specificity and sensitivity of our assay. Then we used total 222 nasopharyngeal aspirates specimens from pediatric patients hospitalized with respiratory symptoms to evaluate our assay. RESULTS: Our one-step triplex qRT-PCR assay showed 100% sensitivity and specificity in testing RSV and hMPV in 86 known virus culture supernatants, with excellent linearity (R(2) > 0.99) and reliable reproducibility (CV lower than 1.04%). This assay has a wide dynamic range 10(2)-10(9)copies/reaction (limit of detection; LOD = 100 copies/reaction). A total of 222 patients hospitalized with respiratory symptoms were enrolled for clinical evaluation. In these samples, our qRT-PCR assay detected 68 RSV positive and 18 hMPV positive cases. However, standard virus culture only detected 8 RSV positive cases and 0 hMPV cases. Based on this improved triplex qRT-PCR assay, we found that RSV infection was associated with severe inflammation by chest X-ray and occurrence of pneumonia which were not observed previously. CONCLUSIONS: In summary, we have developed a highly specific and sensitive one-step triplex qRT-PCR assay to detect hMPV and RSV simultaneously. This assay offers a valuable tool for routine diagnosis. url: https://www.ncbi.nlm.nih.gov/pubmed/28347279/ doi: 10.1186/s12887-017-0843-7 id: cord-296364-7rp60d2m author: Youn, Soonjeon title: In vitro assembled, recombinant infectious bronchitis viruses demonstrate that the 5a open reading frame is not essential for replication date: 2005-02-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Molecular clones of infectious bronchitis virus (IBV), derived from the Vero cell adapted Beaudette strain, were constructed, using an in vitro assembly method. In vitro transcribed RNA from a cDNA template that had been constructed from seven cDNA fragments, encompassing the entire genome of IBV, was electroporated into BHK-21 cells. The cells were overlaid onto the susceptible Vero cells and viable virus was recovered from the molecular clone. The molecularly cloned IBV (MIBV) demonstrated growth kinetics, and plaque size and morphology that resembled the parental Beaudette strain IBV. The recombinant virus was further manipulated to express enhanced green fluorescent protein (EGFP) by replacing an open reading frame (ORF) of the group-specific gene, ORF 5a, with the EGFP ORF. The rescued recombinant virus, expressing EGFP (GIBV), replicated to lower viral titers and formed smaller plaques compared to the parental virus and the MIBV. After six passages of GIBV, a minority of plaques were observed that had reverted to the larger plaque size and virus from these plaques no longer expressed EGFP. Direct sequencing of RT-PCR products derived from cells infected with the plaque-purified virus, which had lost expression of EGFP, confirmed loss of the EGFP ORF. The loss of EGFP expression (Δ5a IBV) was also accompanied by reversion to growth kinetics resembling the standard virus and intact recombinant virus. This study demonstrates that the 5a ORF is not essential for viral multiplication in Vero cells. url: https://www.sciencedirect.com/science/article/pii/S0042682204007421 doi: 10.1016/j.virol.2004.10.045 id: cord-258724-1qhen1bj author: Young, Barnaby E title: Viral dynamics and immune correlates of COVID-19 disease severity date: 2020-08-28 words: 3612.0 sentences: 253.0 pages: flesch: 52.0 cache: ./cache/cord-258724-1qhen1bj.txt txt: ./txt/cord-258724-1qhen1bj.txt summary: METHODS: We evaluated these characteristics and established their association with clinical severity in a prospective observational cohort study of 100 patients with PCR-confirmed SARS-CoV-2 infection (mean age 46 years, 56% male, 38% with comorbidities). In this multi-pronged study, we describe the serologic evolution, inflammatory response and pattern of viral shedding and viability in patients with virologically confirmed COVID-19 in Singapore, and analyse the contributions these make to severe infections. Serum collected during the acute and convalescent phases of infection were tested for SARS-CoV-2 receptor binding domain specific IgM and IgG using capture ELISA (details in Supplementary Appendix). The central role of the immune response to SARS-CoV-2 in COVID-19 was evident from the strong correlation between disease severity and levels of IgG/IgM and inflammatory immune mediators in our cohort. Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study abstract: BACKGROUND: Key knowledge gaps remain in the understanding of viral dynamics and immune response of SARS-CoV-2 infection. METHODS: We evaluated these characteristics and established their association with clinical severity in a prospective observational cohort study of 100 patients with PCR-confirmed SARS-CoV-2 infection (mean age 46 years, 56% male, 38% with comorbidities). Respiratory samples (n=74) were collected for viral culture, serum samples for measurement of IgM/IgG levels (n=30), and plasma samples for levels of inflammatory cytokines and chemokines (n=81). Disease severity was correlated with results from viral culture, serologic testing, and immune markers. RESULTS: 57 (57%) patients developed viral pneumonia, of whom 20 (20%) required supplemental oxygen including 12 (12%) invasive mechanical ventilation. Viral culture from respiratory samples was positive for 19 of 74 patients (26%). No virus was isolated when the PCR cycle threshold (Ct) value was >30 or >14 days after symptom onset. Seroconversion occurred at a median of 12.5 days (IQR 9-18) for IgM and 15.0 days (IQR 12-20) for IgG; 54/62 patients (87.1%) sampled at day 14 or later seroconverted. Severe infections were associated with earlier seroconversion and higher peak IgM and IgG levels. Levels of IP-10, HGF, IL-6, MCP-1, MIP-1α, IL-12p70, IL-18, VEGF-A, PDGF-BB and IL-1RA significantly correlated with disease severity. CONCLUSION: We found virus viability was associated with lower PCR Ct value in early illness. A stronger antibody response was associated with disease severity. The overactive proinflammatory immune signatures offers targets for host-directed immunotherapy which should be evaluated in randomised controlled trials. url: https://www.ncbi.nlm.nih.gov/pubmed/32856707/ doi: 10.1093/cid/ciaa1280 id: cord-294335-qnu19ru5 author: Yousaf, Anna R title: A prospective cohort study in non-hospitalized household contacts with SARS-CoV-2 infection: symptom profiles and symptom change over time date: 2020-07-28 words: 3221.0 sentences: 179.0 pages: flesch: 50.0 cache: ./cache/cord-294335-qnu19ru5.txt txt: ./txt/cord-294335-qnu19ru5.txt summary: We assessed symptoms reported by household contacts on the collection date of their first RT-PCRpositive NP specimen (Figure 1 , Subset A), and categorized symptoms as constitutional (fever, chills, myalgia, or fatigue), upper respiratory (runny nose, nasal congestion, or sore throat), lower respiratory (cough, difficulty breathing, shortness of breath, wheezing, or chest pain), neurologic (headache, loss of taste, or loss of smell), and gastrointestinal (nausea/vomiting, diarrhea, or abdominal pain). We identified and prospectively followed household contacts who were asymptomatic at the time they initially tested positive for SARS-CoV-2 by PCR ( Figure 1 , Subset B) to see if they developed symptoms during the study period. The symptom profiles and demographic characteristics of our cohort of SARS-CoV-2 RT-PCR positive household contacts differ from those described in inpatient populations [3] [4] [5] 12] . abstract: BACKGROUND: Improved understanding of SARS-CoV-2 spectrum of disease is essential for clinical and public health interventions. There are limited data on mild or asymptomatic infections, but recognition of these individuals is key as they contribute to viral transmission. We describe the symptom profiles from individuals with mild or asymptomatic SARS-CoV-2 infection. METHODS: From March 22 to April 22, 2020 in Wisconsin and Utah, we enrolled and prospectively observed 198 household contacts exposed to SARS-CoV-2. We collected and tested nasopharyngeal (NP) specimens by RT-PCR two or more times during a 14-day period. Contacts completed daily symptom diaries. We characterized symptom profiles on the date of first positive RT-PCR test and described progression of symptoms over time. RESULTS: We identified 47 contacts, median age 24 (3-75) years, with detectable SARS-CoV-2 by RT-PCR. The most commonly reported symptoms on the day of first positive RT-PCR test were upper respiratory (n=32, 68%) and neurologic (n=30, 64%); fever was not commonly reported (n=9, 19%). Eight (17%) individuals were asymptomatic at the date of first positive RT-PCR collection; two (4%) had preceding symptoms that resolved and six (13%) subsequently developed symptoms. Children less frequently reported lower respiratory symptoms (age <18: 21%, age 18-49: 60%, age 50+ years: 69%; p=0.03). CONCLUSIONS: Household contacts with lab-confirmed SARS-CoV-2 infection reported mild symptoms. When assessed at a single time-point, several contacts appeared to have asymptomatic infection; however, over time all developed symptoms. These findings are important to inform infection control, contact tracing, and community mitigation strategies. url: https://doi.org/10.1093/cid/ciaa1072 doi: 10.1093/cid/ciaa1072 id: cord-328206-iylw1bvw author: Yu, Daojun title: Simultaneous Detection and Differentiation of Human Papillomavirus Genotypes 6, 11, 16 and 18 by AllGlo Quadruplex Quantitative PCR date: 2012-11-09 words: 4070.0 sentences: 209.0 pages: flesch: 48.0 cache: ./cache/cord-328206-iylw1bvw.txt txt: ./txt/cord-328206-iylw1bvw.txt summary: In this study, applying novel AllGlo fluorescent probes, we established a quadruplex quantitative PCR method to simultaneously detect and differentiate HPV 6, 11, 16 and 18 in a single tube. So AllGlo quadruplex quantitative PCR has the advantages of relatively high throughput, good reproducibility, high sensitivity, high specificity, it is easy for designing the probes and primers of multiplex qPCR and can increase the detection throughput. Two aliquots were used for the detection of HPV6-11 and HPV16-18 mixed types by TaqMan uniplex probe fluorescence quantitative PCR (Guangzhou Da''an Diagnostic Co., Ltd., China). Single-tube AllGlo probe quadruplex fluorescence qPCR could simultaneously type HPV 6, 11, 16, and 18 and quantitatively detect the viral load of each HPV at the same time. Single-tube AllGlo probe quadruplex fluorescence qPCR could simultaneously type HPV 6, 11, 16, and 18 and quantitatively detect the viral load of each HPV at the same time. abstract: BACKGROUND: Human papillomaviruses (HPV) are classified into high-risk HPV and low-risk HPV. The most common high-risk HPV types in cervical cancer are HPV 16 and 18, and the most common low-risk types causing genital warts are HPV 6 and HPV 11. In this study, applying novel AllGlo fluorescent probes, we established a quadruplex quantitative PCR method to simultaneously detect and differentiate HPV 6, 11, 16 and 18 in a single tube. METHODS: The specificity, the sensitivity, the detection limit, the reproducibility and the standard curve of this method were examined. Finally, clinical samples that had been tested previously by TaqMan PCR and HPV GenoArray (GA) test were used to verify the accuracy and sensitivity of the method. RESULTS: The assay has a sensitivity of 10(1) to 10(2) copies/test and a linear detection range from 10(1) to 10(8) copies/test. The mean amplification efficiencies for HPV 6, 11, 16, and 18 were 0.97, 1.10, 0.93 and 1.20, respectively, and the mean correlation coefficient (r(2)) of each standard curve was above 0.99 for plasmid templates ranging from 10(3) to 10(7) copies/test. There was 100% agreement between the AllGlo quadruplex quantitative PCR, HPV GA test and TaqMan uniplex qPCR methods. CONCLUSIONS: AllGlo quadruplex quantitative PCR in a single tube has the advantages of relatively high throughput, good reproducibility, high sensitivity, high specificity, and a wide linear range of detection. The convenient single tube format makes this assay a powerful tool for the studies of mixed infections by multiple pathogens, viral typing and viral load quantification. url: https://www.ncbi.nlm.nih.gov/pubmed/23152833/ doi: 10.1371/journal.pone.0048972 id: cord-018865-melttpiq author: Yu, Tian-fei title: Express Transmissible Gastroenteritis Virus Spike Gene B and C Antigen Sites in Multiple Expression Systems date: 2012 words: 2186.0 sentences: 126.0 pages: flesch: 53.0 cache: ./cache/cord-018865-melttpiq.txt txt: ./txt/cord-018865-melttpiq.txt summary: In order to illuminate the antigenicity of porcine transmissible gastroenteritis virus (TGEV) spike protein B and C antigen sites, the truncated spike gene including B and C antigen sites of Chinese isolate TH-98 was expressed respectively in E.coli, baculovirus and pichia pastoris expression systems. Dot-ELISA assays based on these three recombinant proteins were developed to detect TGEV antibodies and could avoid antibody cross-reaction from PRCV theoretically. The recombinant B and C antigen sites protein expressed into the yeast culture supernatant was identified on the bases of its molecular weight. When the amount of spotting is 50ng, the recombinant B and C antigen sites protein expressed into the yeast culture supernatant show the positive reaction in contrast with the GS115 cells transformed with pPIC9K plasmids (Fig. 2. Antigenic variation among transmissible gastroenteritis virus (TGEV) and porcine respiratory coronavirus strains detected with monoclonal antibodies to the S protein of TGEV abstract: In order to illuminate the antigenicity of porcine transmissible gastroenteritis virus (TGEV) spike protein B and C antigen sites, the truncated spike gene including B and C antigen sites of Chinese isolate TH-98 was expressed respectively in E.coli, baculovirus and pichia pastoris expression systems. Dot enzyme-linked immunosorbent assays (Dot-ELISA) based on these three recombinant proteins were developed preliminarily. Ten sera obtained correspondingly from ten piglets two months old which showed up clinical symptom were used for examination. The study indicates that the assays are rapid, reliable and sensitive and it has the potential for use as serological methods for TGEV diagnosis. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123857/ doi: 10.1007/978-3-642-27537-1_7 id: cord-297646-49l6k5h2 author: Yu, Zhongjia title: Prevalence of intestinal parasites in companion dogs with diarrhea in Beijing, China, and genetic characteristics of Giardia and Cryptosporidium species date: 2017-11-18 words: 4599.0 sentences: 244.0 pages: flesch: 52.0 cache: ./cache/cord-297646-49l6k5h2.txt txt: ./txt/cord-297646-49l6k5h2.txt summary: title: Prevalence of intestinal parasites in companion dogs with diarrhea in Beijing, China, and genetic characteristics of Giardia and Cryptosporidium species In this study, we performed a survey of intestinal parasites in fecal specimens (n = 485) collected from outpatient pet dogs with diarrhea in Beijing, China, for the entire year of 2015 by microscopic examination (all parasites) and SSU rRNA-based nested PCR detection (Giardia and Cryptosporidium). Smears were examined microscopically for the presence of common parasites by observing eggs of helminthes (e.g., Toxocara canis [canine ascariasis] and Trichuris vulpis [canine whipworm]) and oocysts or trophozoites of protozoa (e.g., coccidia, Giardia duodenalis and trichomonads Tritrichomonas foetus/Pentatrichomonas hominis). We collected a total of 485 fecal specimens in year 2015 from outpatient dogs with diarrhea, in which 124 specimens were parasite-positive by wet mount microscopic examination and/ or PCR detection (i.e., an overall positive rate at 25.6%, n = 124) ( Table 1 , Fig. 1a ). abstract: Companion animals including dogs are one of the important components in One Health. Parasites may cause not only diseases in pet animals but also many zoonotic diseases infecting humans. In this study, we performed a survey of intestinal parasites in fecal specimens (n = 485) collected from outpatient pet dogs with diarrhea in Beijing, China, for the entire year of 2015 by microscopic examination (all parasites) and SSU rRNA-based nested PCR detection (Giardia and Cryptosporidium). We observed a total of 124 (25.6%) parasite-positive specimens that contained one or more parasites, including Giardia duodenalis (12.8%), Cryptosporidium spp. (4.9%), Cystoisospora spp. (4.3%), trichomonads (4.3%), Toxocara canis (3.5%), Trichuris vulpis (0.6%), and Dipylidium caninum (0.2%). Among the 55 dog breeds, infection rates were significantly higher in border collies and bulldogs, but lower in poodles (p < 0.05). Risk factor analysis suggested that age was negatively correlated with the infection rate (p < 0.00001), while vaccination and deworming in the past 12 months could significantly reduce the parasite infections (p < 0.01). Among the 62 Giardia-positive specimens, 21 were successfully assigned into assemblages using glutamate dehydrogenase (gdh) and/or beta-giardin (bg) genes, including assemblage D (n = 15), C (n = 5), and F (n = 1). Among the 24 Cryptosporidium-positive specimens by SSU rRNA PCR, 20 PCR amplicons could be sequenced and identified as Cryptosporidium canis (n = 20). Collectively, this study indicates that parasites are a significant group of pathogens in companion dogs in Beijing, and companion dogs may potentially transmit certain zoonotic parasites to humans, particularly those with weak or weakened immunity. url: https://doi.org/10.1007/s00436-017-5631-7 doi: 10.1007/s00436-017-5631-7 id: cord-261089-aul4ifso author: Yuan, Wen title: Development of a duplex real-time RT-PCR for the simultaneous detection and differentiation of Theiler’s murine encephalomyelitis virus and rat theilovirus date: 2016-07-07 words: 4522.0 sentences: 214.0 pages: flesch: 52.0 cache: ./cache/cord-261089-aul4ifso.txt txt: ./txt/cord-261089-aul4ifso.txt summary: The aim of this study is to develop a rapid, sensitive and specific duplex real-time RT-PCR assay for the simultaneous detection of TMEV and RTV, and provide a useful tool for the routine health monitoring of these two viruses in laboratory rodents and for the screening of contaminated biological materials. In addition, twenty cecum content and spleen samples collected from eight specific pathogen free (SPF) mouse strains (BALB/c, C57BL/6, DBA, FVB, 129, ICR, KM and NIH) and two rat strains (SD and Wistar) were used to evaluate specificity of the duplex real-time RT-PCR assay, these animals were reared under barrier colonies and were confirmed as serology negative for TMEV and RTV by a commercial ELISA kit (XpressBio, Maryland, USA). The specificity of the duplex real-time RT-PCR assay was determined by evaluation of RNA extracted from positive cultures of the following rodent viral pathogens: TMEV, RTV, MHV, Reo-3, RCV, Sendai, PVM, MNV and LCMV, and from twenty cecum content and spleen samples of ten SPF rodent strains. abstract: Theiler’s murine encephalomyelitis virus (TMEV) and rat theilovirus (RTV), the member of the genus Cardiovirus, are widespread in laboratory mice and rats, and are potential contaminants of biological materials. Cardioviruses infection may cause serious complications in biomedical research. To improve the efficiency of routine screening for Cardioviruses infection, a duplex real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay was developed for simultaneous detection and differentiation of TMEV and RTV. The duplex assay was specific for reference strains of TMEV and RTV, and no cross-reaction was found with seven other rodent viruses. The limits of detection of both TMEV and RTV were 4 × 10(1) copies RNA/reaction. Reproducibility was estimated using standard dilutions, with coefficients of variation <3.1%. 439 clinical samples were evaluated by both duplex real-time RT-PCR and conventional RT-PCR. For 439 clinical samples，95 samples were positive for TMEV and 72 samples were positive for RTV using duplex real-time RT-PCR approach, whereas only 77 samples were positive for TMEV and 66 samples were positive for RTV when conventional RT-PCR was applied. Mixed infections were found in 20 samples when analyzed by conventional RT-PCR whereas 30 samples were found to be mixed infection when duplex real-time RT-PCR was applied. This duplex assay provides a useful tool for routine health monitoring and screening of contaminated biological materials of these two viruses. url: https://www.sciencedirect.com/science/article/pii/S0166093416300878 doi: 10.1016/j.jviromet.2016.07.004 id: cord-277804-ujabzic4 author: Yuk, Seong-su title: Comparison between dot-immunoblotting assay and clinical sign determination method for quantifying avian infectious bronchitis virus vaccine by titration in embryonated eggs date: 2016-01-21 words: 4146.0 sentences: 202.0 pages: flesch: 53.0 cache: ./cache/cord-277804-ujabzic4.txt txt: ./txt/cord-277804-ujabzic4.txt summary: title: Comparison between dot-immunoblotting assay and clinical sign determination method for quantifying avian infectious bronchitis virus vaccine by titration in embryonated eggs In this study, we used a dot-immunoblotting assay (DIA) to measure the titers of IBV vaccines that originated from different pathogenic strains or attenuation methods in embryonated eggs, and we compared this assay to the currently used method, clinical sign evaluation. The aim of this study was to evaluate and compare the sensitivity and specificity of the DIA to the clinical sign determination method for detecting IBV in inoculated embryonated eggs during titration of IBV vaccines. Propagation of the inoculated virus was determined using real-time RT-PCR, DIA, and the EE index method, and the 50% egg infectious dose (EID 50 ) of the five vaccines was calculated based on the method of Reed and Muench (1938) . abstract: A sensitive and specific method for measuring the vaccine titer of infectious bronchitis virus (IBV) is important to commercial manufacturers for improving vaccine quality. Typically, IBV is titrated in embryonated chicken eggs, and the infectivity of the virus dilutions is determined by assessing clinical signs in the embryos as evidence of viral propagation. In this study, we used a dot-immunoblotting assay (DIA) to measure the titers of IBV vaccines that originated from different pathogenic strains or attenuation methods in embryonated eggs, and we compared this assay to the currently used method, clinical sign evaluation. To compare the two methods, we used real-time reverse transcription-PCR, which had the lowest limit of detection for propagated IBV. As a clinical sign of infection, dwarfism of the embryo was quantified using the embryo: egg (EE) index. The DIA showed 9.41% higher sensitivity and 15.5% higher specificity than the clinical sign determination method. The DIA was particularly useful for measuring the titer of IBV vaccine that did not cause apparent stunting but propagated in embryonated chicken eggs such as a heat-adapted vaccine strain. The results of this study indicate that the DIA is a rapid, sensitive, reliable method for determining IBV vaccine titer in embryonated eggs at a relatively low cost. url: https://doi.org/10.1016/j.jviromet.2016.01.008 doi: 10.1016/j.jviromet.2016.01.008 id: cord-322987-zv58s79r author: Zali, Alireza title: Correlation between Low-Dose Chest Computed Tomography and RT-PCR Results for the Diagnosis of COVID-19: A Report of 27824 Cases in Tehran, Iran date: 2020-09-21 words: 3226.0 sentences: 157.0 pages: flesch: 48.0 cache: ./cache/cord-322987-zv58s79r.txt txt: ./txt/cord-322987-zv58s79r.txt summary: In addition, our study provides further evidence for considering patients'' socioeconomic status as an important risk factor for COVIDKeywords: COVID-19; computed tomography; RT-PCR; polymerase chain reaction; socioeconomic; correlation; diagnosis In this study, we aimed to evaluate the correlation between the number of daily positive chest CT scans and number of daily PCR-confirmed cases and COVID-19-related deaths in Tehran during a three-month period. Figure 2 shows the trend of total patients who underwent chest CT due to high clinical suspicion and also the trend of cases with positive CT scan in each specific hospital during this three-month period. The results of our study, along with the findings of previous reports, provide evidence for policymakers and healthcare leaders to consider low-dose chest CT as a safe, rapid and reliable diagnostic tool to for the detection of COVID-19, particularly in high-prevalent regions with constraint of resources such as insufficient SARS-CoV-2 molecular test kits. abstract: RATIONALE AND OBJECTIVES: Real-time polymerase chain reaction (RT-PCR) remains the gold standard for confirmation of Coronavirus disease 2019 (COVID-19) despite having many disadvantages. Here, we investigated the diagnostic performance of chest computed tomography (CT) as an alternative to RT-PCR in patients with clinical suspicion of COVID-19 infection. METHODS: In this descriptive cross-sectional study, 27824 patients with clinical suspicion of COVID-19 infection who underwent unenhanced low-dose chest CT from 20 February, 2020 to 21 May, 2020 were evaluated. Patients were recruited from seven specifically designated hospitals for patients with COVID-19 infection affiliated to Shahid Beheshti University of Medical Sciences. In each hospital, images were interpreted by two independent radiologists. CT findings were considered as positive/negative for COVID-19 infection based on RSNA diagnostic criteria. Then, the correlation between the number of daily positive chest CT scans and number of daily PCR-confirmed cases and COVID-19-related deaths in Tehran province during this three-month period was assessed. The trends of admission rate and patients with positive CT scans were also evaluated. RESULTS: A strong positive correlation between the numbers of daily positive CT scans and daily PCR-confirmed COVID-19 cases (r=0.913, p < 0.001) was observed. Furthermore, in hospitals located in regions with a lower socioeconomic status, the admission rate and number of positive cases within this three-month period was higher as compared to other hospitals. CONCLUSION: Low-dose chest CT is a safe, rapid and reliable alternative to RT-PCR for the diagnosis of COVID-19 in high-prevalence regions. In addition, our study provides further evidence for considering patients’ socioeconomic status as an important risk factor for COVID-19. url: https://www.sciencedirect.com/science/article/pii/S1076633220305420?v=s5 doi: 10.1016/j.acra.2020.09.003 id: cord-328460-thx9zh11 author: Zanoli, Laura Maria title: Isothermal Amplification Methods for the Detection of Nucleic Acids in Microfluidic Devices date: 2012-12-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Diagnostic tools for biomolecular detection need to fulfill specific requirements in terms of sensitivity, selectivity and high-throughput in order to widen their applicability and to minimize the cost of the assay. The nucleic acid amplification is a key step in DNA detection assays. It contributes to improving the assay sensitivity by enabling the detection of a limited number of target molecules. The use of microfluidic devices to miniaturize amplification protocols reduces the required sample volume and the analysis times and offers new possibilities for the process automation and integration in one single device. The vast majority of miniaturized systems for nucleic acid analysis exploit the polymerase chain reaction (PCR) amplification method, which requires repeated cycles of three or two temperature-dependent steps during the amplification of the nucleic acid target sequence. In contrast, low temperature isothermal amplification methods have no need for thermal cycling thus requiring simplified microfluidic device features. Here, the use of miniaturized analysis systems using isothermal amplification reactions for the nucleic acid amplification will be discussed. url: https://doi.org/10.3390/bios3010018 doi: 10.3390/bios3010018 id: cord-339278-9luefzyo author: Zayet, Souheil title: Contribution of anosmia and dysgeusia for diagnostic of COVID-19 in outpatients date: 2020-05-14 words: 2071.0 sentences: 112.0 pages: flesch: 58.0 cache: ./cache/cord-339278-9luefzyo.txt txt: ./txt/cord-339278-9luefzyo.txt summary: Between March, 30th and April, 3rd 2020 we retrospectively collected the following data from the medical files of patients: demographic characteristics (age, sex), interval between illness onset and consultation, functional symptoms (measured fever > 38 °C, myalgia and/ or arthralgia, headache, cough, dyspnea, dysgeusia, anosmia, rhinorrhea, nausea, vomiting, diarrhea, and abdominal pain), clinical signs (crackling sounds heard on pulmonary auscultation) and result of RT-PCR SARS-CoV-2 nasopharyngeal sample. During the study period, 217 samples (nasopharyngeal swabs) were collected in our consultation: 95 patients (44%) had a positive SARS-CoV-2 RT-PCR confirming the infection by COVID-19 and 122 patients (56%) had a negative SARS-CoV-2 RT-PCR. Outpatients presenting with dysgeusia and/or anosmia may be considered as patients infected with COVID-19, until microbiological confirmation has been obtained (as they have a high pre-test probability to be positive for SARS CoV-2 RT-PCR). abstract: nan url: https://doi.org/10.1007/s15010-020-01442-3 doi: 10.1007/s15010-020-01442-3 id: cord-280865-shwxhak9 author: Zhang, Dan title: Clinical evaluation of a panel of multiplex quantitative real-time reverse transcription polymerase chain reaction assays for the detection of 16 respiratory viruses associated with community-acquired pneumonia date: 2018-06-30 words: 2547.0 sentences: 118.0 pages: flesch: 51.0 cache: ./cache/cord-280865-shwxhak9.txt txt: ./txt/cord-280865-shwxhak9.txt summary: title: Clinical evaluation of a panel of multiplex quantitative real-time reverse transcription polymerase chain reaction assays for the detection of 16 respiratory viruses associated with community-acquired pneumonia We developed a panel of multiplex quantitative real-time reverse transcription polymerase chain reaction (mqRT-PCR) assay consisting of seven internally controlled qRT-PCR assays to detect 16 different respiratory viruses. Given that the laboratories from all of the provincial and most municipal CDC laboratories in China have access to conventional real-time PCR instrumentation, in this study, we aimed to develop a multiplex quantitative real-time RT-PCR (mqRT-PCR) consisting of a panel of seven internally controlled qRT-PCR assays to detect 16 different respiratory viruses: human coronavirus (CoV) 229E, CoV NL63, CoV OC43, CoVHKU1, parainfluenza virus (PIV)1, PIV2, PIV3, PIV4, influenza virus (IV) types A and B, human respiratory syncytial virus (RSV) types A and B, human rhinovirus (HRV), human metapneumovirus (HMPV), human adenovirus (ADV), and human bocavirus (HBoV). abstract: We developed a panel of multiplex quantitative real-time reverse transcription polymerase chain reaction (mqRT-PCR) assay consisting of seven internally controlled qRT-PCR assays to detect 16 different respiratory viruses. We compared the new mqRT-PCR with a previously reported two-tube mRT-PCR assay using 363 clinical sputum specimens. The mqRT-PCR assay performed comparably with the two-tube assay for most viruses, offering the advantages of quantitative analysis, easier performance, lower susceptibility to contamination, and shorter turnaround time in laboratories equipped with conventional real-time PCR instrumentation, and it could therefore be a valuable tool for routine surveillance of respiratory virus infections in China. url: https://www.ncbi.nlm.nih.gov/pubmed/29961119/ doi: 10.1007/s00705-018-3921-8 id: cord-338942-q4neat3x author: Zhang, Haoqing title: LAMP-on-a-chip: Revising microfluidic platforms for loop-mediated DNA amplification date: 2019-01-31 words: 5757.0 sentences: 314.0 pages: flesch: 41.0 cache: ./cache/cord-338942-q4neat3x.txt txt: ./txt/cord-338942-q4neat3x.txt summary: Isothermal deoxyribonucleic acid amplification methods, such as loop-mediated isothermal amplification (LAMP), exhibit characteristics ideal for point-of-care (POC) applications, since their instrumentation is simpler in comparison with the standard method of polymerase chain reaction. Nucleic acids amplification methods are primarily required to be performed, as the original number of either DNA or ribonucleic acid (RNA) copies in the clinical sample is insufficient for their direct detection. A microfluidic disk-based LAMP chip, integrating sample preparation and detection, was developed [44] (Fig. 2B ). Loop-mediated isothermal amplification integrated on microfluidic chips for point-of-care quantitative detection of pathogens An integrated rotary microfluidic system with DNA extraction, loop-mediated isothermal amplification, and lateral flow strip based detection for point-ofcare pathogen diagnostics An integrated microfluidic loop-mediated-isothermal-amplification system for rapid sample pre-treatment and detection of viruses Development and application of a loop-mediated isothermal amplification method on rapid detection Escherichia coli O157 strains from food samples abstract: Nucleic acid amplification for the detection of infectious diseases, food pathogens, or assessment of genetic disorders require a laboratory setting with specialized equipment and technical expertise. Isothermal deoxyribonucleic acid amplification methods, such as loop-mediated isothermal amplification (LAMP), exhibit characteristics ideal for point-of-care (POC) applications, since their instrumentation is simpler in comparison with the standard method of polymerase chain reaction. Other key advantages of LAMP are robustness and the production of pyrophosphate in the presence of the target gene, enabling to detect the reaction products using the naked eye. Polymerase inhibitors, presented in clinical samples, do not affect the amplification process, making LAMP suitable for a simple sample-to-answer diagnostic systems with simplified sample preparation. In this review, we discuss the trends in miniaturized LAMP techniques, such as microfluidic, paper-based, and digital with their advantages and disadvantages, especially for POC applications alongside our opinion of the future development of miniaturized LAMP. url: https://www.ncbi.nlm.nih.gov/pubmed/32287531/ doi: 10.1016/j.trac.2019.01.015 id: cord-317129-wa1j2f6b author: Zhang, Jia title: De Novo synthesis of PCR templates for the development of SARS diagnostic assay date: 2003 words: 2319.0 sentences: 117.0 pages: flesch: 58.0 cache: ./cache/cord-317129-wa1j2f6b.txt txt: ./txt/cord-317129-wa1j2f6b.txt summary: This highly efficient and safe strategy for obtaining SARS gene fragments is useful for the development of PCR assays, as well as for the preparation of reliable positive controls for PCR testing kits. This single-step sequential primer extension was expected to yield mainly final templates with no intermediate products. As shown in Figure 1 , DNA fragments in lengths of 182 and 204 bp were obtained from primers of set A and set B, respectively, by the single-step sequential primer extension where each reaction contained four partially overlapping a The expected products were extended from reverse primers (AR or BR) to the first forward primers. De novo synthesis of the PCR template complimentary to a viral genome provides a tool for the rapid development of early diagnostic assays for any new pathogen as soon as its sequence is known. abstract: A novel coronavirus was identified as the cause for severe acute respiratory syndrome (SARS). The complete sequence of SARS genome has provided an opportunity for the development of molecular diagnostic assays. To restrain further outbreak of SARS, the World Health Organization has posted several pairs of polymerase chain reaction (PCR) primers for early diagnosis and urged more research to be done on PCR protocols. Here we report a strategy for the de novo synthesis of PCR templates complimentary to the SARS virus genome, which has the advantage of working on PCR templates without concern about viral infection and also has the advantage that it can be used by those who do not have access to the SARS virus. This highly efficient and safe strategy for obtaining SARS gene fragments is useful for the development of PCR assays, as well as for the preparation of reliable positive controls for PCR testing kits. url: https://www.ncbi.nlm.nih.gov/pubmed/14526121/ doi: 10.1385/mb:25:2:107 id: cord-344782-ond1ziu5 author: Zhang, Jing title: Identification of a novel nidovirus as a potential cause of large scale mortalities in the endangered Bellinger River snapping turtle (Myuchelys georgesi) date: 2018-10-24 words: 6003.0 sentences: 280.0 pages: flesch: 49.0 cache: ./cache/cord-344782-ond1ziu5.txt txt: ./txt/cord-344782-ond1ziu5.txt summary: Nucleic acid sequencing of the virus isolate has identified the entire genome and indicates that this is a novel nidovirus that has a low level of nucleotide similarity to recognised nidoviruses. Following the detection of the novel virus, in November 2015 (about 6 months after the cessation of the outbreak) an intensive survey of the parts of the river where affected turtles had been detected [2] was undertaken by groups of biologists and ecologists and samples collected from a wide range of aquatic species and some terrestrial animals (n = 360) to establish the size of the remaining population and whether any other animals were carrying this virus. BRV, as a novel nidovirus, was isolated from tissues of diseased animals, very high levels of viral RNA were detected in tissues with marked pathological changes and in situ hybridisation assays demonstrated the presence of specific viral RNA in lesions in kidneys and eye tissue-two of the main affected organs. abstract: In mid-February 2015, a large number of deaths were observed in the sole extant population of an endangered species of freshwater snapping turtle, Myuchelys georgesi, in a coastal river in New South Wales, Australia. Mortalities continued for approximately 7 weeks and affected mostly adult animals. More than 400 dead or dying animals were observed and population surveys conducted after the outbreak had ceased indicated that only a very small proportion of the population had survived, severely threatening the viability of the wild population. At necropsy, animals were in poor body condition, had bilateral swollen eyelids and some animals had tan foci on the skin of the ventral thighs. Histological examination revealed peri-orbital, splenic and nephric inflammation and necrosis. A virus was isolated in cell culture from a range of tissues. Nucleic acid sequencing of the virus isolate has identified the entire genome and indicates that this is a novel nidovirus that has a low level of nucleotide similarity to recognised nidoviruses. Its closest relatives are nidoviruses that have recently been described in pythons and lizards, usually in association with respiratory disease. In contrast, in the affected turtles, the most significant pathological changes were in the kidneys. Real time PCR assays developed to detect this virus demonstrated very high virus loads in affected tissues. In situ hybridisation studies confirmed the presence of viral nucleic acid in tissues in association with pathological changes. Collectively these data suggest that this virus is the likely cause of the mortalities that now threaten the survival of this species. Bellinger River Virus is the name proposed for this new virus. url: https://doi.org/10.1371/journal.pone.0205209 doi: 10.1371/journal.pone.0205209 id: cord-327024-1k5jucae author: Zhang, Qingshui title: Isolation and characterization of an astrovirus causing fatal visceral gout in domestic goslings date: 2018-04-19 words: 4167.0 sentences: 213.0 pages: flesch: 47.0 cache: ./cache/cord-327024-1k5jucae.txt txt: ./txt/cord-327024-1k5jucae.txt summary: 18 reported the detection of avian nephritis virus infection in Croatian goose flocks and provided evidence that this AstV was associated with stunting and prehatching mortality of goose embryos. To determine the potential genetic mutation(s) that might occur during the goose embryo passage, the initial virus genome was sequenced using the total RNA extracted from the clinical case tissue homogenate. When the samples were tested by RT-PCR for virus shedding evaluation, the AAstV specific RNA was sequentially detected from the cloacal swabs of infected goslings from 2 to 12 dpi (Fig. 6 ). To evaluate the potential adaptive mutation (s) of the virus that might occur during the process of goose embryo passage, we sequenced the complete genome of initial virus using the total RNA extracted from the clinical case tissue homogenate of kidney, spleen, and liver using the method described above. abstract: Astroviruses are recognized as a leading cause of gastroenteritis in humans and animals. They are also associated with extra-intestinal diseases, such as hepatitis in ducklings, nephritis in chickens, and encephalitis in cattle. In February 2017, a fatal infection of goslings characterized by visceral urate deposition was reported in the Shandong province, China. Our systematic investigation led to the isolation of an astrovirus, designated AAstV/Goose/CHN/2017/SD01, and similar disease was reproduced by experimental infection of healthy goslings, fulfilling Koch’s postulates. The isolated astrovirus replicated well and resulted in 100% mortality of goose embryos. Complete genome sequence analysis revealed that the isolate was genetically distinct from known astroviruses and closely related to members of the avastrovirus genogroup II. Experimental infection showed that the isolate was highly pathogenic in goslings, causing clinical signs, growth repression and in many cases mortality. Histopathological examination indicated that lesions occurred mainly in the kidneys of infected birds. However, virus-specific genomic RNA was detected in all representative tissues, and virus shedding was detected up to 12 days after inoculation, suggesting that the isolate was able to spread systemically and replicate efficiently in vivo. Collectively, our study demonstrates, for the first time, the etiological role of a genetically distinct astrovirus in the fatal infection of goslings. url: https://www.ncbi.nlm.nih.gov/pubmed/29674726/ doi: 10.1038/s41426-018-0074-5 id: cord-263302-z5uhrta5 author: Zhang, Xuming title: Identification of a Noncanonical Signal for Transcription of a Novel Subgenomic mRNA of Mouse Hepatitis Virus: Implication for the Mechanism of Coronavirus RNA Transcription date: 2000-12-05 words: 7944.0 sentences: 411.0 pages: flesch: 58.0 cache: ./cache/cord-263302-z5uhrta5.txt txt: ./txt/cord-263302-z5uhrta5.txt summary: Transfection of the reporter RNA into MHV-infected cells resulted in synthesis of a CAT-specific subgenomic mRNA detected by reverse transcription-polymerase chain reaction (RT-PCR). Further sequencing on cDNA clones derived from JHM2c mRNAs by reserve transcription-polymerase chain reaction (RT-PCR) has shown that the leader-body joining sites in subgenomic mRNA2-1 are more heterogeneous . When it was placed in front of the chloramphenicol acetyl-transferase (CAT) gene in the defective-interfering (DI) RNA-CAT reporter plasmid, the IG5-1, which is devoid of any known IRES sequence, can direct the synthesis of a subgenomic CAT-containing mRNA and expression of the CAT activity, thus confirming that the IG5-1 serves as a promoter for transcription of a subgenomic mRNA. To identify the minimal sequence required for subgenomic mRNA transcription, three deletions within the 140-nt sequence were made by PCR, and the deletion fragments were cloned into the DI RNA-CAT reporter vector in place of the wild-type, full-length (140-nt) se, and MHV-1 (F), respectively. abstract: Abstract Subgenomic RNA transcription of coronaviruses involves the interaction between the leader (or antileader) and the intergenic (IG) sequences. However, it is not clear how these two sequences interact with each other. In this report, a previously unrecognized minor species of subgenomic mRNA, termed mRNA5–1, was identified in cells infected with mouse hepatitis virus (MHV) strains JHM2c, JHM(2), JHM(3), A59, and MHV-1. Sequence analysis revealed that the leader-body fusion site of the mRNA is located at approximately 150 nucleotides (nt) downstream of the consensus IG sequence for mRNA 5 and did not have sequence homology with any known IG consensus sequences. To determine whether this sequence functions independently as a promoter, we cloned a 140-nt sequence (from ≈70 nt upstream to ≈70 nt downstream of the fusion site) from viral genomic RNA and placed it in front of a reporter gene in the defective-interfering (DI) RNA-chloramphenicol acetyltransferase (CAT) reporter vector. Transfection of the reporter RNA into MHV-infected cells resulted in synthesis of a CAT-specific subgenomic mRNA detected by reverse transcription-polymerase chain reaction (RT-PCR). The strength of this promoter was similar to that of the IG7 (for mRNA 7) as measured by the CAT activity. Deletion analysis showed that the sequence as few as 13 nt was sufficient to initiate mRNA transcription, while mutations within the 13-nt abolished mRNA transcription. In vitro translation study confirmed that the envelope (E) protein was translated from mRNA5–1, which encodes the open reading frame (ORF) 5b at its 5′-end, indicating that mRNA5–1 is a functional message. Furthermore, when the ORF5b was replaced with the CAT gene and placed in the DI in the context of viral mini-genome, CAT was expressed not only from the first ORF of mRNA5–1 but also from the second and third ORF of mRNA5 and genomic DI RNA, respectively, suggesting that more than one mechanism is involved in regulation of ORF5b expression. Our findings thus support the notion that base-pairing between the leader (or antileader) and the IG is not the sole mechanism in subgenomic RNA transcription. url: https://api.elsevier.com/content/article/pii/S0042682200906378 doi: 10.1006/viro.2000.0637 id: cord-258057-ti0rpt0q author: Zhao, Kai title: Establishment of a Porcine Parvovirus (PPV) LAMP Visual Rapid Detection Method date: 2020-07-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Porcine parvovirus (PPV) is one of the major causes of reproductive pig disease. Due to its serious nature, wide spread and consequent great damage to the swine industry, an effective, rapid and convenient method for its detection is needed. A loop-mediated isothermal amplification (LAMP) assay was established to detect PPV infection. Two pairs of primers were specifically designed to recognize the six different sequences of open reading frame1 (ORF1) gene. The optimized LAMP program was as follows: 50 min at 59 °C followed by 3 min at 80 °C.The amplified products were analyzed both by visual inspection after staining with SYBR Green I dye and by conventional agarose gel electrophoresis. Both methods showed the same sensitivity. The limit of detection (LOD) for PPV by LAMP was 10 copies, which is 100-fold lower than conventional PCR. Our LAMP assay did not cross-react with other viruses. We used the established LAMP system to test 1100 field samples and detected 660 positives. The LAMP detection method for PPV represents a visual, sensitive and rapid assay which can detect the virus in the field, offering an attractive alternative for the PPV detection methods currently in use. url: https://www.ncbi.nlm.nih.gov/pubmed/32621958/ doi: 10.1016/j.jviromet.2020.113924 id: cord-282155-6jp9yx47 author: Zhao, Li title: A highly sensitive 1-tube nested real-time RT-PCR assay using LNA-modified primers for detection of respiratory syncytial virus date: 2018-09-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Respiratory syncytial virus (RSV) causes serious respiratory tract infection worldwide. The relatively low RSV load makes it difficult to detect in frail, elderly, and severely immune-compromised patients. In the present study, we developed a locked nucleic acid–-based 1-tube nested real-time RT-PCR (OTNRT-PCR) assay with the advantages of extremely high sensitivity, facile operability, and less likelihood of cross-contamination. The sensitivity, specificity, and clinical performance of the OTNRT-PCR assay were compared in parallel with a conventional TaqMan probe-based real-time PCR (qRT-PCR) assay and a traditional 2-step nested RT-PCR assay. The limit of detection of the OTNRT-PCR assay was 1.02 × 10(−1) TCID50/mL, equivalent to the traditional 2-step nested RT-PCR assay and 25-fold lower than the qRT-PCR assay. Of 616 nasopharyngeal aspirates tested, 143 RSV-negative samples by qRT-PCR were confirmed as positive by sequencing the OTNRT-PCR products. We therefore conclude that OTNRT-PCR is more sensitive than qRT-PCR for detection of RSV in clinical samples. url: https://www.sciencedirect.com/science/article/pii/S073288931830333X doi: 10.1016/j.diagmicrobio.2018.09.001 id: cord-291961-usl8z6ep author: Zheng, Wen-zhi title: Human polyomavirus type six in respiratory samples from hospitalized children with respiratory tract infections in Beijing, China date: 2015-10-13 words: 2915.0 sentences: 162.0 pages: flesch: 54.0 cache: ./cache/cord-291961-usl8z6ep.txt txt: ./txt/cord-291961-usl8z6ep.txt summary: METHODS: The VP1 gene of HPyV6 was detected with an established TaqMan real-time PCR from nasopharyngeal aspirate specimens collected from hospitalized children with respiratory tract infections. All 15 HPyV6-positive patients were diagnosed with lower respiratory tract infections, and their viral loads ranged from 1.38 to 182.42 copies/μl nasopharyngeal aspirate specimen. CONCLUSIONS: The prevalence of HPyV6 was 1.7 % in nasopharyngeal aspirate specimens from hospitalized children with respiratory tract infections, as analyzed by real-time PCR. Previous studies have indicated that a number of HPyVs are associated with human diseases, such as progressive multifocal leukoencephalopathy (JCPyV), hemorrhagic cystitis (BKPyV), Merkel cell carcinoma (MCPyV), and trichodysplasia spinulosa (TSPyV) [3, 7, 9, [17] [18] [19] . Because initial infections with most HPyVs occur in infancy, the prevalence of HPyV6 in NPAs from children was detected with real-time PCR. The detection rate for HPyV6 by real-time PCR assay was 1.7 % in 887 NPA samples collected from hospitalized children with RTI. abstract: BACKGROUND: HPyV6 is a novel human polyomavirus (HPyV), and neither its natural history nor its prevalence in human disease is well known. Therefore, the epidemiology and phylogenetic status of HPyV6 must be systematically characterized. METHODS: The VP1 gene of HPyV6 was detected with an established TaqMan real-time PCR from nasopharyngeal aspirate specimens collected from hospitalized children with respiratory tract infections. The HPyV6-positive specimens were screened for other common respiratory viruses with real-time PCR assays. RESULTS: The prevalence of HPyV6 was 1.7 % (15/887), and children ≤ 5 years of age accounted for 80 % (12/15) of cases. All 15 HPyV6-positive patients were coinfected with other respiratory viruses, of which influenza virus A (IFVA) (8/15, 53.3 %) and respiratory syncytial virus (7/15, 46.7 %) were most common. All 15 HPyV6-positive patients were diagnosed with lower respiratory tract infections, and their viral loads ranged from 1.38 to 182.42 copies/μl nasopharyngeal aspirate specimen. The most common symptoms were cough (100 %) and fever (86.7 %). The complete 4926-bp genome (BJ376 strain, GenBank accession number KM387421) was amplified and showed 100 % identity to HPyV6 strain 607a. CONCLUSIONS: The prevalence of HPyV6 was 1.7 % in nasopharyngeal aspirate specimens from hospitalized children with respiratory tract infections, as analyzed by real-time PCR. Because the coinfection rate was high and the viral load low, it was not possible to establish a correlation between HPyV6 and respiratory diseases. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12985-015-0390-5) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12985-015-0390-5 doi: 10.1186/s12985-015-0390-5 id: cord-004356-r83g3n0m author: Zheng, Zaiyu title: Development and characterization of a continuous cell line (EL) from the liver of European eel Anguilla anguilla date: 2019-12-19 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In the present study, a new hepatic tissue‐origin cell line from European eel Anguilla anguilla has been developed and characterized. This cell line designated EL has been maintained in Leibovitz L‐15 supplemented with 10% fetal bovine serum over 72 months, and subcultured more than 90 times. The EL cell line consisted predominantly of fibroblast‐like cells, which could survive over 100 days in vitro, and could grow at 15–32°C. The optimum temperature for growth was 27°C. The chromosome analysis revealed a modal diploid karyotype of 2n = 38. The origin of this cell line was confirmed by the 18S recombinant (r)RNA sequencing. The susceptibility test indicated significant cytopathic effects in the EL cells with regard to the Rana grylio virus and the Herpesvirus anguillae. The viral replication was confirmed by transmission electron microscopy and polymerase chain reaction analysis. Following poly (I:C) exposure, the expression levels of the immune‐related molecules interferon regulatory factor‐7 (irf7) and transforming growth factor‐β (TGF‐β) were downregulated in EL cells, whereas the expression levels of the rf3 and the cytochrome P450 (CYP450) were upregulated. All four genes were significantly upregulated following inflammation by lipopolysaccharide (LPS). These data suggested the application of EL cell line for viral identification, as well as for immunodiagnosis and pharmacological targeting. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7028054/ doi: 10.1002/cbin.11276 id: cord-296979-8r851j4t author: Zhong, Ying title: Host genes regulate transcription of sperm-introduced hepatitis B virus genes in embryo date: 2017-10-31 words: 6753.0 sentences: 322.0 pages: flesch: 49.0 cache: ./cache/cord-296979-8r851j4t.txt txt: ./txt/cord-296979-8r851j4t.txt summary: Eighteen healthy donors were randomly divided into six groups, and their sperm samples were used to fertilize zona-free hamster oocytes in vitro and assess the effects of the silencing of five target genes (CSH2, EIF4G2, PCBD2, PSG4 and TTN) and a control gene (ESRRG) on transcription of HBV s and x genes by real-time quantitative (q)RT-PCR. Eighteen healthy donors were randomly divided into six groups, and their sperm sample were used to fertilize zona-free hamster oocytes in vitro and assess the effects of the silencing of five target genes (CSH2, EIF4G2, PCBD2, PSG4 and TTN) and a control gene (ESRRG) on transcription of HBV S and X genes in two-cell embryos using real time qRT-PCR and 2 − CT method. abstract: Abstract Hepatitis B virus (HBV) can invade the male germline, and sperm-introduced HBV genes could be transcribed in embryo. This study was to explore whether viral gene transcription is regulated by host genes. Embryos were produced by in vitro fertilization of hamster oocytes with human sperm containing the HBV genome. Total RNA extracted from test and control embryos were subjected to SMART-PCR, SSH, microarray hybridization, sequencing and BLAST analysis. Twenty-nine sequences showing significant identity to five human gene families were identified, with CSH2, EIF4G2, PCBD2, PSG4 and TTN selected to represent target genes. Using qRT-PCR, when CSH2 and PCBD2 (or EIF4G2, PSG4 and TTN) were silenced by RNAi, transcriptional levels of HBV s and x genes decreased (or increased). This is the first report that host genes participate in regulation of sperm-introduced HBV gene transcription in embryo, which is critical to prevent negative impact of HBV infection on early embryonic development. url: https://doi.org/10.1016/j.reprotox.2017.08.009 doi: 10.1016/j.reprotox.2017.08.009 id: cord-311204-fc12f845 author: Zhou, Ling title: Full-length genomic characterization and molecular evolution of canine parvovirus in China date: 2016-04-02 words: 2229.0 sentences: 138.0 pages: flesch: 65.0 cache: ./cache/cord-311204-fc12f845.txt txt: ./txt/cord-311204-fc12f845.txt summary: Canine parvovirus type 2 (CPV-2) can cause acute haemorrhagic enteritis in dogs and myocarditis in puppies. Some faecal samples were negative for the CPV-2 antigen based on a colloidal gold test strip but were positive based on PCR, and a viral strain was isolated from one such sample. Identification of CPV-2 with cell culture and IPMA Feline kidney cell line F81 was obtained from the American Type Culture Collection, USA and was used to isolate viruses from clinical samples and to observe cytopathic effects associated with viral replication. Cloning the full-length genomic sequence of CPV-2 DNA and RNA were extracted from the homogenized samples (faeces from infected dogs) with the TIANamp Virus DNA/RNA Kit (Beijing TIANGEN Biotech Company, Beijing, China) according to the manufacturer''s protocol. One viral strain was isolated from the faeces of dogs that tested negative in the colloidal gold test strip but positive with PCR. abstract: Canine parvovirus type 2 (CPV-2) can cause acute haemorrhagic enteritis in dogs and myocarditis in puppies. This disease has become one of the most serious infectious diseases of dogs. During 2014 in China, there were many cases of acute infectious diarrhoea in dogs. Some faecal samples were negative for the CPV-2 antigen based on a colloidal gold test strip but were positive based on PCR, and a viral strain was isolated from one such sample. The cytopathic effect on susceptible cells and the results of the immunoperoxidase monolayer assay, PCR, and sequencing indicated that the pathogen was CPV-2. The strain was named CPV-NY-14, and the full-length genome was sequenced and analysed. A maximum likelihood tree was constructed using the full-length genome and all available CPV-2 genomes. New strains have replaced the original strain in Taiwan and Italy, although the CPV-2a strain is still predominant there. However, CPV-2a still causes many cases of acute infectious diarrhoea in dogs in China. url: https://doi.org/10.1007/s11262-016-1309-y doi: 10.1007/s11262-016-1309-y id: cord-323973-wszo9s3d author: Zhu, Hanliang title: The vision of point-of-care PCR tests for the COVID-19 pandemic and beyond date: 2020-07-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Infectious diseases, such as the most recent case of COVID-19, have brought the prospect of point-of-care (POC) diagnostic tests into the spotlight. A rapid, accurate, low-cost, and easy-to-use test in the field could stop epidemics before they develop into full-blown pandemics. Unfortunately, despite all the advances, it still does not exist. Here, we critically review the limited number of prototypes demonstrated to date that is based on a polymerase chain reaction (PCR) and has come close to fulfilling this vision. We summarize the requirements for the POC-PCR tests and then go on to discuss the PCR product-detection methods, the integration of their functional components, the potential applications, and other practical issues related to the implementation of lab-on-a-chip technologies. We conclude our review with a discussion of the latest findings on nucleic acid-based diagnosis. url: https://api.elsevier.com/content/article/pii/S0165993620302132 doi: 10.1016/j.trac.2020.115984 id: cord-353241-ityhcak7 author: Zhu, Hanliang title: IoT PCR for pandemic disease detection and its spread monitoring date: 2020-01-15 words: 4300.0 sentences: 208.0 pages: flesch: 54.0 cache: ./cache/cord-353241-ityhcak7.txt txt: ./txt/cord-353241-ityhcak7.txt summary: Considerable effort has been invested in the development of portable, user-friendly, and cost-effective systems for point-of-care (POC) diagnostics, which could also create an Internet of Things (IoT) for healthcare via a global network. Connecting the easy to use and cost-effective POC devices providing the DENV diagnoses via a mobile network would create an Internet of Things (IoT) [15] for healthcare [16, 17] , an essential tool to tackle any infectious disease outbreak. Prior to testing on an IoT PCR device, we verified the master mix performance and its values of critical threshold (C T ) and the melting temperature (T M ) using a commercial real-time PCR system (Supplementary Section A) beginning with a hot start at 95°C for 30 s followed by 40 cycles of PCR amplification consisting of DNA denaturation at 95°C for 8 s, primer annealing at 60°C for 30 s, and DNA sequence elongation at 72°C for 10 s, then followed by melting curve analysis (MCA) from 72°C to 95°C. abstract: During infectious disease outbreaks, the centers for disease control need to monitor particular areas. Considerable effort has been invested in the development of portable, user-friendly, and cost-effective systems for point-of-care (POC) diagnostics, which could also create an Internet of Things (IoT) for healthcare via a global network. However, at present IoT based on a functional POC instrument is not available. Here we show a fast, user-friendly, and affordable IoT system based on a miniaturized polymerase chain reaction device. We demonstrated the system’s capability by amplification of complementary deoxyribonucleic acid (cDNA) of the dengue fever virus. The resulting data were then automatically uploaded via a Bluetooth interface to an Android-based smartphone and then wirelessly sent to a global network, instantly making the test results available anywhere in the world. The IoT system presented here could become an essential tool for healthcare centers to tackle infectious disease outbreaks identified either by DNA or ribonucleic acid. url: https://www.sciencedirect.com/science/article/pii/S0925400519312973 doi: 10.1016/j.snb.2019.127098 id: cord-294947-g4ntyddb author: Zhu, Yu title: Establishment of a nanoparticle-assisted RT-PCR assay to distinguish field strains and attenuated strains of porcine epidemic diarrhea virus date: 2016-06-10 words: 2849.0 sentences: 154.0 pages: flesch: 54.0 cache: ./cache/cord-294947-g4ntyddb.txt txt: ./txt/cord-294947-g4ntyddb.txt summary: title: Establishment of a nanoparticle-assisted RT-PCR assay to distinguish field strains and attenuated strains of porcine epidemic diarrhea virus In this study, a nanoparticle-assisted polymerase chain reaction (nanoparticle-assisted RT-PCR) assay targeting the ORF3 of PEDV was developed to distinguish PEDV field strains from attenuated strains by using a specific pair of primers. The nanoparticle-assisted RT-PCR assay we describe here can be used to distinguish field strains from vaccine strains of PEDV, and it shows promise for reducing economic loss due to PEDV infection. The results showed that the nanoparticle-assisted RT-PCR assay could distinguish PEDV field strains from the attenuated strain in samples from infected pigs. The present study demonstrated that an effective nanoparticle-assisted RT-PCR assay targeting the ORF3 gene of PEDV was able to distinguish field strains from attenuated vaccine strains. Development of a nanoparticle-assisted PCR assay for detection of porcine epidemic diarrhea virus abstract: Porcine epidemic diarrhea virus (PEDV) can cause serious disease and even death in neonatal piglets, resulting in serious damage to the swine industry worldwide. Open reading frame 3 (ORF3) is the only accessory gene in the PEDV genome. Previous studies have indicated that PEDV vaccine strains have a partial deletion in ORF3. In this study, a nanoparticle-assisted polymerase chain reaction (nanoparticle-assisted RT-PCR) assay targeting the ORF3 of PEDV was developed to distinguish PEDV field strains from attenuated strains by using a specific pair of primers. The PCR products of field strains and attenuated strains were 264 bp and 215 bp in length, respectively. The sensitivity and specificity of this assay were also assessed. The nanoparticle-assisted RT-PCR assay was 10-100 times more sensitive than the conventional RT-PCR assay, with no cross-reactions when amplifying porcine pseudorabies virus (PRV), porcine circovirus type 2 (PCV2), classical swine fever virus (CSFV), porcine parvovirus (PPV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine rotavirus (RV), and porcine transmissible gastroenteritis virus (TGEV). The nanoparticle-assisted RT-PCR assay we describe here can be used to distinguish field strains from vaccine strains of PEDV, and it shows promise for reducing economic loss due to PEDV infection. url: https://doi.org/10.1007/s00705-016-2918-4 doi: 10.1007/s00705-016-2918-4 id: cord-025634-31n5fvex author: Zhuge, Shurui title: The prevalence of occult HBV infection in immunized children with HBsAg-positive parents: a hospital-based analysis date: 2020-05-29 words: 3985.0 sentences: 216.0 pages: flesch: 52.0 cache: ./cache/cord-025634-31n5fvex.txt txt: ./txt/cord-025634-31n5fvex.txt summary: title: The prevalence of occult HBV infection in immunized children with HBsAg-positive parents: a hospital-based analysis BACKGROUND AND OBJECT: The risk of occult HBV infection (OBI) in children whose mothers are HBV carriers has received more widespread attention, but there were few reports to focus on the children with HBsAg-positive parents. In this study, we aimed at exploring the prevalence of OBI in hepatitis B-vaccinated children with HBV-positive mothers and/or fathers, trying to identify the risk factors of OBI. Forty-six [14.10% (95% CI 10.3-17.9%)] HBsAg-negative children were detected HBV DNA positive by nested PCR, which were confirmed through sequencing analysis. To our acknowledgement, this is the first study to explore the prevalence of OBI among hepatitis B vaccinated children with HBsAg-positive parents lived in HBV highly endemic areas. There is an equal potential risk of occult HBV infection in children with the HBsAg-positive father and mother. abstract: BACKGROUND AND OBJECT: The risk of occult HBV infection (OBI) in children whose mothers are HBV carriers has received more widespread attention, but there were few reports to focus on the children with HBsAg-positive parents. In this study, we aimed to investigate the prevalence of OBI in immunized children with HBsAg-positive parents. METHODS: HBV-vaccinated Chinese hospitalized children with HBsAg-positive parents were analyzed in our investigation. Eligible subjects were tested using a standard nested PCR for all HBV genes, and analyzed by direct sequencing. RESULTS: There were 327 HBsAg-negative children included in the study out of about 9800 involved HBV-vaccinated hospitalized children. The positive rate of OBI was 3.1% (10/327) in the eligible children and 14.1% (46/327) with HBV DNA detectable. No significant differences were found between one and at least two regions positive groups (p > 0.05). The proportions of HBV DNA detectable in children with HBV father-carriers and mother-carriers were similar. The risk factors for HBV DNA-positive children could be male, anti-HBs levels, and anti-HBc positive. CONCLUSION: There are 3.1% of OBIs and 14.1% of suspected OBI in vaccinated children with HBsAg-positive parents. The potential risk of suspected OBI in children with HBsAg-positive father should not be ignored. Anti-HBc positivity may be a useful seromarker for suspected OBI screening in vaccinated children. To prevent HBV breakthrough infection, accurate and convenient method is needed to detect OBI timely and exhaustively. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12072-020-10055-9) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7259741/ doi: 10.1007/s12072-020-10055-9 id: cord-346138-ip42zcld author: Zhurakivska, Khrystyna title: An Overview of the Temporal Shedding of SARS-CoV-2 RNA in Clinical Specimens date: 2020-08-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Coronavirus disease 2019 quickly spread in China and has, since March 2020 become a pandemic, causing hundreds of thousands of deaths worldwide. The causative agent was promptly isolated and named SARS-CoV-2. Scientific efforts are related to identifying the best clinical management of these patients, but also in understanding their infectivity in order to limit the spread of the virus. Aimed at identifying viral RNA in the various compartments of the organism of sick subjects, diagnostic tests are carried out. However, the accuracy of such tests varies depending on the type of specimen used and the time of illness at which they are performed. This review of the literature aims to summarize the preliminary findings reported in studies on Covid-19 testing. The results highlight how the pharyngeal swab is highly sensitive in the first phase of the disease, while in the advanced stages, other specimens should be considered, such as sputum, or even stool to detect SARS-CoV-2. It highlights that most patients already reach the peak of the viral load in the upper airways within the first days of displaying symptoms, which thereafter tend to decrease. This suggests that many patients may already be infectious before symptoms start to appear. url: https://www.ncbi.nlm.nih.gov/pubmed/32974267/ doi: 10.3389/fpubh.2020.00487 id: cord-340788-p02v46xu author: Zitek, Tony title: The Appropriate Use of Testing for COVID-19 date: 2020-04-13 words: 1599.0 sentences: 101.0 pages: flesch: 61.0 cache: ./cache/cord-340788-p02v46xu.txt txt: ./txt/cord-340788-p02v46xu.txt summary: With regard to the accuracy of the test, the most commonly used test for detecting SARS-CoV-2 is a nasopharyngeal swab that uses a reverse transcriptase-polymerase chain reaction (RT-PCR) to identify viral RNA. One non-peer reviewed publication reports that, based on 87 Chinese patients who were ultimately diagnosed with COVID-19, pharyngeal RT-PCR tests have a sensitivity and specificity of 78.2% and 98.8%, respectively. Along the same lines, Winichakoon et al published a letter to the editor in which they described a case of a COVID-19 patient who had a nasopharygeal/oropharyngeal RT-PCR swab that was negative for COVID-19, but RT-PCR of BAL fluid was positive. 12 Next, in a case series described by Xie et al, five patients from the Hunan province of China had ground-glass opacities on chest computed tomography (CT) that were suggestive of COVID-19, but initial pharyngeal RT-PCR tests were negative. abstract: Many public officials are calling for increased testing for the 2019 novel coronavirus disease (COVID-19), and some governments have taken extraordinary measures to increase the availability of testing. However, little has been published about the sensitivity and specificity of the reverse transcriptase-polymerase chain reaction (RT-PCR) nasopharyngeal swabs that are commonly used for testing. This narrative review evaluates the literature regarding the accuracy of these tests, and makes recommendations based on this literature. In brief, a negative RT-PCR nasopharyngeal swab test is insufficient to rule out COVID-19. Thus, over-reliance on the results of the test may be dangerous, and the push for widespread testing may be overstated. url: https://www.ncbi.nlm.nih.gov/pubmed/32302278/ doi: 10.5811/westjem.2020.4.47370 id: cord-327105-7dsgs2sd author: Zóka, András title: Distinct changes in the real-time PCR detectability of certain SARS-CoV-2 target sequences date: 2020-05-05 words: 341.0 sentences: 24.0 pages: flesch: 58.0 cache: ./cache/cord-327105-7dsgs2sd.txt txt: ./txt/cord-327105-7dsgs2sd.txt summary: title: Distinct changes in the real-time PCR detectability of certain SARS-CoV-2 target sequences [1] highlighted notable aspects of the PCR-based diagnosis of SARS-CoV-2 infection, namely that the PCR-based detectability of certain loci might differ significantly and change over time. In our practice we also observed that the SARS-CoV-2 PCR positivity in the oropharyngeal swabs of patients might persist for weeks [2] , however, the characteristics of positivity (including the target sequences detected) may change in a predictable manner. Our results might indicate that the detectability of the viral Orf1a-related RdRp sequence might fade more rapidly during convalescence, only later followed by the N gene. This phenomenon might affect the interpretation of the results, as detecting a lone N gene might suggest a later presentation within the course of the disease. Dynamic change process of target genes by RT-PCR testing of SARS-Cov-2 during the course of a Coronavirus Disease 2019 patient Profile of RT-PCR for SARS-CoV-2: a preliminary study from 56 COVID-19 patients abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32387093/ doi: 10.1016/j.cca.2020.05.002 id: cord-256338-ovj63ith author: bhattacharya, b. title: SARS-CoV-2 RT-PCR profile in 298 Indian COVID-19 patients : a retrospective observational study date: 2020-06-20 words: 2146.0 sentences: 141.0 pages: flesch: 60.0 cache: ./cache/cord-256338-ovj63ith.txt txt: ./txt/cord-256338-ovj63ith.txt summary: title: SARS-CoV-2 RT-PCR profile in 298 Indian COVID-19 patients : a retrospective observational study Currently as per the revised government of India guidelines asymptomatic or mildly symptomatic patients can be discharged 10 days after symptom onset and the strategy of repeat RT-PCR testing has been done away with. Cases with laboratory confirmed diagnosis of COVID-19, made by positive SARS-CoV-2 RT-PCR on nasopharyngeal samples, were enrolled regardless of symptomatology. The mean duration from 1st and last positive RT-PCR assays between symptomatic and asymptomatic patients were 13·01±4·63 and 13·93±5·42 days respectively; and the difference was not statistically significant with p value <0·05 (p=0·39). This study was conducted in the initial part of pandemic in India, which, to the best of our knowledge provides the largest data on SARS-CoV-2 RNA detection in naso-pharyngeal and oro-pharyngeal samples in symptomatic or asymptomatic COVID-19 cases. Profile of RT-PCR for SARS-CoV-2: a preliminary study from 56 COVID-19 patients abstract: Background: Despite being in the 5th month of pandemic, knowledge with respect to viral dynamics, infectivity and RT-PCR positivity continues to evolve. Aim: To analyse the SARS CoV-2 nucleic acid RT-PCR profiles in COVID-19 patients. Design: It was a retrospective, observational study conducted at COVID facilities under AIIMS, New Delhi. Methods : Patients admitted with laboratory confirmed COVID-19 were eligible for enrolment. Patients with incomplete details, or only single PCR tests were excluded. Data regarding demographic details, comorbidities, treatment received and results of SARS-CoV-2 RT-PCR performed on nasopharyngeal and oropharyngeal swabs, collected at different time points, was retrieved from the hospital records. Results : 298 patients were included, majority were males (75.8%) with mean age of 39.07 years (0.6-88 years). The mean duration from symptom onset to first positive RT-PCR was 4.7 days (SD 3.67), while that of symptom onset to last positive test was 17.83 days (SD 6.22). Proportions of positive RT-PCR tests were 100%, 49%, 24%, 8.7% and 20.6% in the 1st, 2nd, 3rd, 4th & >4 weeks of illness. 12 symptomatic patients had prolonged positive test results even after 3 weeks of symptom onset. Age >= 60 years was associated with prolonged RT-PCR positivity (statistically significant). Conclusion : This study showed that the average period of PCR positivity is more than 2 weeks in COVID-19 patients; elderly patients have prolonged duration of RT-PCR positivity and requires further follow up. url: https://doi.org/10.1101/2020.06.19.20135905 doi: 10.1101/2020.06.19.20135905 id: cord-310501-ro55cqxw author: de Castro, Alessandra MMG title: Detection of porcine circovirus genotypes 2a and 2b in aborted foetuses from infected swine herds in the State of São Paulo, Brazil date: 2012-05-03 words: 2212.0 sentences: 127.0 pages: flesch: 58.0 cache: ./cache/cord-310501-ro55cqxw.txt txt: ./txt/cord-310501-ro55cqxw.txt summary: title: Detection of porcine circovirus genotypes 2a and 2b in aborted foetuses from infected swine herds in the State of São Paulo, Brazil FINDINGS: Samples of 168 aborted foetuses or mummified foetuses from five farrow-to-finish swine farms known to be infected with PCV2 and located in the State of São Paulo were tested for PCV2 by polymerase chain reaction (PCR). CONCLUSIONS: The findings indicate that the frequency of PCV2 infections in aborted porcine foetuses from the State of São Paulo is rather low (10.7%) and that co-infection with other pathogens is common and may be involved in PCV2 associated reproductive failure. Given the distribution of the virus in swine populations worldwide and the impact of PCV2 associated reproductive failure on swine herd economy, the aim of this study was to identify genotypes of PCV2 involved in reproductive failure in State of São Paulo, Brazil and to investigate the level of co-infections of foetuses with other pathogens. abstract: BACKGROUND: Porcine circovirus type 2 (PCV2) has been associated with several disease complexes, including reproductive failure. The aim of this study was to identify the subtypes of PCV2 that are associated with reproductive failure in pigs from the State of São Paulo, Brazil and to investigate co-infections with other infectious organisms. FINDINGS: Samples of 168 aborted foetuses or mummified foetuses from five farrow-to-finish swine farms known to be infected with PCV2 and located in the State of São Paulo were tested for PCV2 by polymerase chain reaction (PCR). Positive samples were additionally tested for porcine parvovirus (PPV), Leptospira spp. and Brucella spp. by PCR. PCV2 was detected in 18 of the samples (10.7%). PPV, Brucella spp. and Leptospira spp were found in 2, 10 and 0 cases, respectively. Eleven PCV2 strains were sequenced and determined to be either genotype 2a (n = 1) or 2b (n = 10). CONCLUSIONS: The findings indicate that the frequency of PCV2 infections in aborted porcine foetuses from the State of São Paulo is rather low (10.7%) and that co-infection with other pathogens is common and may be involved in PCV2 associated reproductive failure. No repeatable, characteristic amino acid motifs for regions of the PCV2 capsid protein seemed to be associated with abortion in sows. url: https://doi.org/10.1186/1751-0147-54-29 doi: 10.1186/1751-0147-54-29 id: cord-339656-u0cpklsv author: de Groot-Mijnes, Jolanda D.F. title: Identification of New Pathogens in the Intraocular Fluid of Patients With Uveitis date: 2010-11-30 words: 4012.0 sentences: 243.0 pages: flesch: 44.0 cache: ./cache/cord-339656-u0cpklsv.txt txt: ./txt/cord-339656-u0cpklsv.txt summary: Methods Ocular fluids from 139 patients suspected of infectious uveitis, but negative for herpes simplex virus, varicella-zoster virus, cytomegalovirus, and Toxoplasma gondii by polymerase chain reaction and/or antibody analysis in intraocular fluids, were assessed for the presence of 18 viruses and 3 bacteria by real-time polymerase chain reaction (PCR). The remainders of ocular fluid samples from patients with PCR-and/or GWC-confirmed infectious uveitis (ocular toxoplasmosis, n ϭ 13; HSV anterior uveitis, n ϭ 10; rubella virus-associated Fuchs heterochromic uveitis syndrome (FHUS), n ϭ 14) and from patients with cataract in the absence of intraocular inflammation (n ϭ 11) served as controls. • NUCLEIC ACID ISOLATION AND REAL-TIME PCR: The ocular fluid samples were analyzed for the presence of adenovirus, EBV, HHV6, Mycoplasma pneumoniae, Chlamydia pneumoniae, and Chlamydia trachomatis DNA and of coronaviruses 229E, OC43, and NL63, enteroviruses, human metapneumovirus, influenza A and B virus, parainfluenza virus 1 to 4, HPeV, respiratory syncytial virus A and B, and rubella virus RNA. abstract: Purpose To determine infectious causes in patients with uveitis of unknown origin by intraocular fluids analysis. Design Case-control study. Methods Ocular fluids from 139 patients suspected of infectious uveitis, but negative for herpes simplex virus, varicella-zoster virus, cytomegalovirus, and Toxoplasma gondii by polymerase chain reaction and/or antibody analysis in intraocular fluids, were assessed for the presence of 18 viruses and 3 bacteria by real-time polymerase chain reaction (PCR). The ocular fluids from 48 patients with uveitis of known etiology or with cataract were included as controls. Results Positive PCR results were found for Epstein-Barr virus, for rubella virus, and for human herpesvirus 6 each in 1 patient and for human parechovirus in 4 patients. Of the human parechovirus–positive patients, 1 was immunocompromised and had panuveitis. The other 3 patients were immunocompetent and had anterior uveitis, all with corneal involvement. Conclusions Human parechovirus might be associated with infectious (kerato)uveitis. url: https://doi.org/10.1016/j.ajo.2010.05.015 doi: 10.1016/j.ajo.2010.05.015 id: cord-345475-ttrcmtu4 author: de Oliveira, Luisa Abruzzi title: Reference Genes for the Normalization of Gene Expression in Eucalyptus Species date: 2011-12-24 words: 9744.0 sentences: 595.0 pages: flesch: 54.0 cache: ./cache/cord-345475-ttrcmtu4.txt txt: ./txt/cord-345475-ttrcmtu4.txt summary: Given the increasing interest in the functional genomics of Eucalyptus and the need for validated reference genes for a broader set of species and experimental conditions, we sought to identify the most stably expressed genes in a set of 21,432 genes assayed by microarray developed to compare stem vascular (xylem) and leaf tissues of E. According to the NormFinder analysis of gene expression in leaves, xylem tissues and among species, the stability values of the 15 genes studied were <0.138, with error bars no greater than 0.044 ( Fig. 3C ; Table 3 ). When we analyzed the gene expression in all tissues/organs and species, the stability value was in the range between 0.017 and 0.106, proving again that all genes elected are good references for RT-qPCR studies in Eucalyptus. By RT-qPCR, the expression stability of eight of the 50 best candidate genes selected by SAM and SDMA was addressed in different organs (leaves and flowers) and vascular tissues (xylem) derived from six species of Eucalyptus. abstract: Gene expression analysis is increasingly important in biological research, with reverse transcription–quantitative PCR (RT–qPCR) becoming the method of choice for high-throughput and accurate expression profiling of selected genes. Considering the increased sensitivity, reproducibility and large dynamic range of this method, the requirements for proper internal reference gene(s) for relative expression normalization have become much more stringent. Given the increasing interest in the functional genomics of Eucalyptus, we sought to identify and experimentally verify suitable reference genes for the normalization of gene expression associated with the flower, leaf and xylem of six species of the genus. We selected 50 genes that exhibited the least variation in microarrays of E. grandis leaves and xylem, and E. globulus xylem. We further performed the experimental analysis using RT–qPCR for six Eucalyptus species and three different organs/tissues. Employing algorithms geNorm and NormFinder, we assessed the gene expression stability of eight candidate new reference genes. Classic housekeeping genes were also included in the analysis. The stability profiles of candidate genes were in very good agreement. PCR results proved that the expression of novel Eucons04, Eucons08 and Eucons21 genes was the most stable in all Eucalyptus organs/tissues and species studied. We showed that the combination of these genes as references when measuring the expression of a test gene results in more reliable patterns of expression than traditional housekeeping genes. Hence, novel Eucons04, Eucons08 and Eucons21 genes are the best suitable references for the normalization of expression studies in the Eucalyptus genus. url: https://doi.org/10.1093/pcp/pcr187 doi: 10.1093/pcp/pcr187 id: cord-263134-0p4zy5t2 author: de Paz, Hector David title: Molecular isothermal techniques for combating infectious diseases: towards low-cost point-of-care diagnostics date: 2014-07-23 words: 6474.0 sentences: 304.0 pages: flesch: 34.0 cache: ./cache/cord-263134-0p4zy5t2.txt txt: ./txt/cord-263134-0p4zy5t2.txt summary: This review describes the landscape of molecular isothermal diagnostic techniques for infectious diseases, their characteristics, current state of development, and available products, with a focus on new directions towards point-of-care applications. Advances in microfluidics and miniaturization of signal detectors have allowed the integration of molecular diagnostics into microscale lab-on-achip devices that perform all necessary PCR steps automatically, from sample intake to cell lysis, DNA extraction, purification and amplification. This review describes the state-ofthe-art and new directions in the development of isothermal amplification technologies for diagnosis of infectious diseases with particular focus on those susceptible to be integrated in inexpensive molecular POC tests. • Loop-mediated isothermal amplification, smart amplification process & signal mediated amplification of RNA technology, helicasedependent amplification, strand displacement amplification, recombinase polymerase amplification and nicking and extension amplification reaction are isothermal techniques with mid/high tolerance to inhibitory compounds that allow the use of raw samples without any pretreatment step, which may be an interesting feature for PCR-based point-of-care (POC) testing. abstract: Nucleic acid amplification techniques such as PCR have facilitated rapid and accurate diagnosis in central laboratories over the past years. PCR-based amplifications require high-precision instruments to perform thermal cycling reactions. Such equipment is bulky, expensive and complex to operate. Progressive advances in isothermal amplification chemistries, microfluidics and detectors miniaturisation are paving the way for the introduction and use of compact ‘sample in-results out’ diagnostic devices. However, this paradigm shift towards decentralised testing poses diverse technological, economic and organizational challenges both in industrialized and developing countries. This review describes the landscape of molecular isothermal diagnostic techniques for infectious diseases, their characteristics, current state of development, and available products, with a focus on new directions towards point-of-care applications. url: https://doi.org/10.1586/14737159.2014.940319 doi: 10.1586/14737159.2014.940319 id: cord-291729-4l4v9jxd author: de Salazar, Adolfo title: Sample pooling for SARS-COV-2 RT-PCR screening date: 2020-09-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVE: To evaluate the efficacy of sample pooling compared to the individual analysis for the diagnosis of COVID-19, by using different commercial platforms for nucleic acid extraction and amplification. METHODS: 3519 nasopharyngeal samples received at 9 Spanish clinical microbiology laboratories were processed individually and in pools (342 pools of 10 samples and 11 pools of 9 samples) according to the existing methodology in each of the centres. RESULTS: We found that 253 pools (2519 samples) were negative, and 99 pools (990 samples) were positive; with 241 positive samples (6.85%), our pooling strategy would have saved 2167 PCR tests. For 29 pools (made out of 290 samples) we found discordant results when compared to their correspondent individual samples: in 22/29 pools (28 samples), minor discordances were found; for seven pools (7 samples), we found major discordances. Sensitivity, specificity, positive and negative predictive values for pooling were 97.10% (CI95%; 94.11-98.82), 100%, 100% and 99.79% (CI95%; 99.56-99.90) respectively; accuracy was 99.80% (CI95%; 99.59-99.92) and kappa concordant coefficient was 0.984. The dilution of samples in our pooling strategy resulted into a median loss of 2.87 (CI95%; 2.46-3.28) CTs for E gene, 3.36 (CI95%; 2.89-3.85) CTs for RdRP gene and 2.99 (CI95%; 2.56-3.43) CTs for N gene. CONCLUSION: we show a high efficiency of pooling strategies for SARS-CoV-2 RNA testing, across different RNA extraction and amplification platforms, with excellent performance in terms of sensitivity, specificity, and positive and negative predictive values. url: https://api.elsevier.com/content/article/pii/S1198743X20305371 doi: 10.1016/j.cmi.2020.09.008 id: cord-268455-btuzihsy author: de Santiago, Javier title: COVID-19: gynecologic cancer surgery at a single center in Madrid date: 2020-07-07 words: 2968.0 sentences: 170.0 pages: flesch: 46.0 cache: ./cache/cord-268455-btuzihsy.txt txt: ./txt/cord-268455-btuzihsy.txt summary: The aim of this study was to evaluate surgical treatment of gynecological cancer patients during the COVID-19 outbreak in our center. During this period, the hospital was divided into two separate areas, independent of each other, assisting COVID-19 cases and at the same time allocating resources to surgical care, follow-up, or ongoing treatments of patients with cancer. Our study showed that we were able to safely manage 126 gynecological cancer surgeries in the COVID free zone during the pandemic, avoiding delays or cancellations. The number of low complexity surgeries with short hospital stays included in the study may have influenced the risk of postoperative contagion, and the fact that the PCR test before surgery was not performed in half of the patients due to low availability could have reduced the diagnosis of the infection. This study, conducted in a partial COVID-19 free hospital, showed that with adequate preventive and protective measures, cancer surgery was possible and did not significantly compromise patients or healthcare workers. abstract: OBJECTIVES: While numerous medical facilities have been forced to suspend oncological surgery due to system overload, debate has emerged on using non-surgical options on cancer cases during the pandemic. The goal of our study was to analyze, in a retrospective cohort study, the results of gynecological cancer surgery and evaluate postoperative complications in a single center in one of the most affected areas in Europe. METHODS: We retrospectively analyzed the records of patients who were referred between March 2020 and May 2020 for primary surgical treatment of breast, endometrial, ovarian, cervical, or vulvar cancer. RESULTS: The study included a total of 126 patients. Median age was 60 years (range 29–89). Patients were referred with breast (76/126, 60.3%), endometrial (29/126, 23%), ovarian (14/126, 11.1%), cervical (5/126, 4%), or vulvar cancer (2/126, 1.6%). Polymerase chain reaction (PCR) test for detection of severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) was only conducted in 50% of cases due to the low availability of tests during the first phase of our study, and was indicated only in suspected cases according to the healthcare authorities' protocol. Median hospital stay was 1 day (range 0–18). Excluding breast surgery, laparoscopy was the most used procedure (43/126, 34.1%). 15 patients had a postoperative complication (15/126, 11.9%); only in 2 patients (2/15 13.3%) were there reports of Clavien–Dindo grade 3 or 4 complications. 6 patients tested positive for COVID-19 following a PCR diagnostic test, and these surgeries were cancelled. CONCLUSIONS: Adequate protective measures in the setting of COVID-19 free institutions enabled the continuity of cancer surgery without significant compromise of the safety of patients or healthcare workers. url: https://doi.org/10.1136/ijgc-2020-001638 doi: 10.1136/ijgc-2020-001638 id: cord-000083-3p81yr4n author: nan title: Poster Exhibition date: 2009-01-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2712310/ doi: 10.1007/s12072-009-9123-4 id: cord-000718-7whai7nr author: nan title: ESP Abstracts 2012 date: 2012-08-22 words: 166497.0 sentences: 12847.0 pages: flesch: 49.0 cache: ./cache/cord-000718-7whai7nr.txt txt: ./txt/cord-000718-7whai7nr.txt summary: Method: We analyzed consecutive gastric cancer cases in terms of AMACR immunohistochemical expression and clinical/pathological characteristics and followed patients'' postoperative history. Results: Histological, immunohistochemical and molecular examination revealed non-neoplastic lymphadenopathy with atypical paracortical T-cell hyperplasia with immunoblastic reaction in the former and burnt-out histiocytic pattern in the latter, both falling into a broad spectrum of reactive lymph node changes associated with Still''s disease. Method: We have thus collected, from our two Institutions a large number (45 cases) of cancers showing the histological definition of adenosquamous carcinomas according to the WHO criteria and performed gene analysis for k-RAS (codons 12, 13) and EGFR (codons 18, 19 and 21) mutations. Objective: We previously identified amplified fibroblast growth factor 1 (FGFR1) as a therapeutic target for small molecule inhibitor (SMI) therapy in squamous cell lung cancer (L-SCC), resulting in currently running clinical trials treating patients with stage III disease. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3400751/ doi: 10.1007/s00428-012-1284-1 id: cord-001521-l36f1gp7 author: nan title: Oral and Poster Manuscripts date: 2011-04-08 words: 183363.0 sentences: 11362.0 pages: flesch: 53.0 cache: ./cache/cord-001521-l36f1gp7.txt txt: ./txt/cord-001521-l36f1gp7.txt summary: The IC 50 values determined in functional NI assays provide valuable information for detection of resistant viruses, but should not be used to draw direct correlations with drug concentrations needed to inhibit virus replication in the infected human host, as clinical data to support such inferences are inadequate. • Standardized reagents and protocols • Choice of detection technology • Simple instrumentation requirements • High sensitivity for use with low virus concentrations • Compatibility with batch-mode processing and largescale assay throughput • Broad specificity of influenza detection • Flexibility in assay format • Additional NA assay applications -cell-based viral assays, screening for new NIs, detection of NA from other organisms Functional neuraminidase inhibition assays enable detection of any resistance mutation and are extremely important in conjunction with sequence-based screening assays for global monitoring of virus isolates for NI resistance mutations, including known and new mutations. Such new assays need to include methods to measure local antibodies and virus-specific lymphocytes, especially in the case of live attenuated influenza vaccines, because of their potential to induce such broad-based immune responses. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4313891/ doi: 10.1111/j.1750-2659.2011.00209.x id: cord-004675-n8mlxe7p author: nan title: 2019 CIS Annual Meeting: Immune Deficiency & Dysregulation North American Conference date: 2019-02-26 words: 86427.0 sentences: 5050.0 pages: flesch: 46.0 cache: ./cache/cord-004675-n8mlxe7p.txt txt: ./txt/cord-004675-n8mlxe7p.txt summary: However, the mean infusion rate per site was similar between patients aged <18 years ( XMEN disease (X-linked Immunodeficency with Magnesium defect, Epstein-Barr virus infection and Neoplasia) is a primary immune deficiency caused by mutations in MAGT1 and characterized by chronic infection with Epstein-Barr virus (EBV), EBV-driven lymphoma, CD4 T-cell lymphopenia, and dysgammaglobulinemia. We present the case of a 1-year old Hispanic infant with a pathogenic variant in MAGT1 gene that clinically manifested with early Pneumocystis jirovecii and cytomegalovirus (CMV) interstitial pneumonia, and EBV chronic infection with good response to intravenous immunoglobulins supplementation without hematopoietic stem cell transplantation or gene therapy. Chief, Laboratory of Clinical Immunology and Microbiology, IDGS, DIR, NIAID, NIH, Bethesda, MD, USA Hypomorphic Recombination Activating Gene 1 (RAG1) mutations result in residual T-and B-cell development in both humans and mice and have been found in patients presenting with delayed-onset combined immune deficiency with granulomas and/or autoimmunity (CID-G/AI). abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086569/ doi: 10.1007/s10875-019-00597-5 id: cord-004879-pgyzluwp author: nan title: Programmed cell death date: 1994 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087532/ doi: 10.1007/bf02033112 id: cord-005147-mvoq9vln author: nan title: Autorenregister date: 2017-02-23 words: 86573.0 sentences: 4356.0 pages: flesch: 45.0 cache: ./cache/cord-005147-mvoq9vln.txt txt: ./txt/cord-005147-mvoq9vln.txt summary: Using whole-exome sequencing and trio-based de novo analysis, we identified a novel heterozygous de novo frameshift variant in the leukemia inhibitory factor receptor (LIFR) gene causing instability of the mRNA in a patient presenting with bilateral CAKUT and requiring kidney transplantation at one year of age. Loss of cdkl5 associated with deficient mammalian target of rapamycin (mTOR) signaling in mice and human cells We and other groups have shown that mutations in the X-linked cyclin-dependent kinase-like 5 (CDKL5) gene cause a severe neurodevelopmental disorder with clinical features including intellectual disability, early-onset intractable seizures and autism, that are closely related to those present in Rett syndrome (RTT) patients. Functional characterization of novel GNB1 mutations as a rare cause of global developmental delay Over the past years, prioritization strategies that combined the molecular predictors of sequence variants from exomes and genomes of patients with rare Mendelian disorders with computer-readable phenotype information became a highly effective method for detecting disease-causing mutations. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7088617/ doi: 10.1007/s11825-017-0126-6 id: cord-005453-4057qib7 author: nan title: The 45th Annual Meeting of the European Society for Blood and Marrow Transplantation: Physicians – Poster Session date: 2019-07-03 words: 275771.0 sentences: 16876.0 pages: flesch: 56.0 cache: ./cache/cord-005453-4057qib7.txt txt: ./txt/cord-005453-4057qib7.txt summary: To compare the safety and efficacy of prophylactic DLI for prevention of relapse after allogeneic peripheral blood stem cell transplantation from haploidentical donors (HID-SCT) and matched-sibling donors (MSD-SCT) in patients with very high-risk acute myeloid leukemia (AML), we performed a retrospective, observational cohort study enrolled in 21 HID-SCT and 13 MSD-SCT recipients. The aim of this study is to identify the prognostic impact of pre-transplant TIM3 levels on early and late transplant related complications as well as post-transplant relapse and survival Methods: A total of 177 hematopoietic stem cell transplantation (HSCT) recipients with an initial diagnosis of acute leukemia [median age: 36(16-66) years; male/ female: 111/66] were included in the study. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7091813/ doi: 10.1038/s41409-019-0559-4 id: cord-005460-ezrn8cva author: nan title: Physicians – Poster Session date: 2017-07-28 words: 287105.0 sentences: 15681.0 pages: flesch: 56.0 cache: ./cache/cord-005460-ezrn8cva.txt txt: ./txt/cord-005460-ezrn8cva.txt summary: Still the optimal combination of immunosuppressive agents with PTCy should be elucidated for different types of SCTs. We report the 2-year update of the prospective NCT02294552 single-center trial that evaluated risk-adapted graft-versushost disease (GVHD) prophylaxis with PTCy in related, unrelated and haploidentical SCTs. 200 adult patients (median age 32 y.o., range: 18-62) with hematologic malignancies, including AML (47.5%), ALL (26.5%), CML (10.5%), MDS (4%), and lymphomas (11.5%), were enrolled in the study. Long-term follow-up from the prospective randomized phase III multicenter trial comparing a standard GvHD prophylaxis with cyclosporine A and methotrexate with or without additional pretransplant ATLG (Grafalon, previously ATG-FRESENIUS S) (given 20 mg/kg/day, days − 3 to − 1) in unrelated donor hematopoietic cell transplantation after myeloablative conditioning resulted in a significant reduction of acute and chronic GvHD without compromising relapse rate and survival [1, 2, 3] . abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7091844/ doi: 10.1038/bmt.2017.134 id: cord-006230-xta38e7j author: nan title: Deutsche Gesellschaft für Experimentelle und Klinische Pharmakologie und Toxikologie e.V. date: 2012-02-22 words: 135419.0 sentences: 7042.0 pages: flesch: 43.0 cache: ./cache/cord-006230-xta38e7j.txt txt: ./txt/cord-006230-xta38e7j.txt summary: Here, we will present our analysis of Ca 2+ signaling following stimulation of the FcεRI receptor and application of secretagogues that are supposed to affect Ca 2+ -dependent mast cell activation such as adenosine, endothelin-1, substance P and compound 48/80 in BMMCs and PMCs derived from mouse lines with inactivation of TRPC1, TRPC3, TRPC4, TRPC5 or TRPC6 since specific antagonists are still lacking for these TRP channels. These data indicate that increased PP2A activity is associated with modified gene expression in TG hearts possibly affecting stress response and regulation of cell signalling. As demonstrated by qPCR and Western blot experiments, mesangial cells showed a marked time-and dose-dependent upregulation of CSE mRNA and protein levels after treatment with platelet-derived growth factor (PDGF-BB). The transcription factor cAMP response element (CRE)-binding protein (CREB) plays a critical role in regulating gene expression in response to activation of the cAMPdependent signaling pathway, which is implicated in the pathophysiology of heart failure. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7100643/ doi: 10.1007/s00210-012-0736-0 id: cord-006860-a3b8hyyr author: nan title: 40th Annual Meeting of the GTH (Gesellschaft für Thrombose- und Hämostaseforschung) date: 1996 words: 90660.0 sentences: 5152.0 pages: flesch: 50.0 cache: ./cache/cord-006860-a3b8hyyr.txt txt: ./txt/cord-006860-a3b8hyyr.txt summary: Dept of Pediatrics, University Hospitals Kiel and Mtinster, Germany Resistance to activated protein C (APCR), in the majority of cases associated with the Arg 506 Gin point mutation in the factor V gene is present in more than 50 % of patients < 60 years of age with unexplained thrombophilia. The regular APC resistance test is not applicable to plasma from Orally anticoagulated (OAC) or heparinized patients due to decreased levels of vitamin K-dependent clotting factors and to thrombin inhibition by antithrombin, respectively. On admission an extensive coagulation screen yielded the following results (n/normal, t/elevated, I/reduced, +/positive, -/negative): PT t, aPTT t, Tr n, factor II, V, VIII n, factor VII, IX, XI, XII /,, fibrinogan t, ATIII n, protein C, S *, activated protein C sensitivity ratio 1.92 ($), FV-Leidenmutation PCR -, fibrinolytic system n, TAT t, Ft÷2 t, lupus anticoagulant +, heparin induced platelet antibodies +; no diagnosis of a specific autoimmuna disorder could be made. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7103196/ doi: 10.1007/bf00641048 id: cord-007890-bie1veti author: nan title: ECC-4 Abstracts date: 2002-04-16 words: 85992.0 sentences: 5665.0 pages: flesch: 50.0 cache: ./cache/cord-007890-bie1veti.txt txt: ./txt/cord-007890-bie1veti.txt summary: Effects of Interferon alpha plus ribavirine therapy on frequencies of HCV, HIV and CMV specific CD4-T-cell responses in peripheral blood of HIV/HCV coinfected patients after 6 months of treatment SoA9.5 Methods: Two groups of patients with chronic HCV infection were studied: 26 HIV coinfected progressors with antiretroviral therapy and 13 HIV-negative controls. In order to assess the local temporal trend of antibiotic sensitivity of the most common urinary tract bacterial pathogen, all urine-cultured Escherichia coli isolates were reviewed as to susceptibility profile, and specimen source (community-versus hospital-acquired infection). Methods: A total of 87 penicillin resistant clinical strains isolated from patients at Hacettepe Children''s Hospital, Ankara, Turkey between 1999 and 2001 were tested for their in vitro susceptibility to various antibiotics that are commonly used in the treatment of respiratory tract infections. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7126403/ doi: 10.1016/s0924-8579(02)00033-x id: cord-008777-i2reanan author: nan title: ECB12: 12th European Congess on Biotechnology date: 2005-07-19 words: 151383.0 sentences: 7577.0 pages: flesch: 43.0 cache: ./cache/cord-008777-i2reanan.txt txt: ./txt/cord-008777-i2reanan.txt summary: Mollerup Department of Chemical Engineering, Building 229, DTU, 2800 Lyngby, Denmark A variety of factors that govern the properties of proteins are utilized in the development of chromatographic processes for the recovery of biological products including the binding and release of protons, the non-covalent association with non-polar groups (often hydrophobic interactions), the association of small ions (ion exchange) and the highly specific antigen-antibody interaction (affinity interactions). Such fermenters will be needed in order to meet the increasing pressure on costs for low price commodity type products such as single cell protein or food and technical grade enzymes, and to meet the demands of the new wave of white biotech, in which bio-produced chemicals must be made at prices competitive with those of the traditional chemical industry. The presentation will focus on use of the sensitive sandwich hybridization technology for the quantitative analysis of process relevant marker genes in different kind of microbial cell cultures with a focus on the production of recombinant proteins. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7134330/ doi: 10.1016/j.jbiotec.2005.06.005 id: cord-009664-kb9fnbgy author: nan title: Oral presentations date: 2014-12-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7162236/ doi: 10.1111/j.1469-0691.2009.02857.x id: cord-010027-r0tl01kq author: nan title: Dublin Pathology 2015. 8th Joint Meeting of the British Division of the International Academy of Pathology and the Pathological Society of Great Britain & Ireland date: 2015-09-15 words: 36299.0 sentences: 2004.0 pages: flesch: 47.0 cache: ./cache/cord-010027-r0tl01kq.txt txt: ./txt/cord-010027-r0tl01kq.txt summary: Further profiling of other T cell populations may help to further understand this expression which may act as a biomarker or provide a therapeutic target Biomarkers that are able to distinguish stage II and III colon cancer patients at high risk of developing disease recurrence, who may benefit from adjuvant chemotherapy, are still lacking. *AM supported by the NIHR and the Academy of Medical Sciences ABSTRACTS S·17 Assessment of HER2 Status on Needle Core Biopsy of Breast Cancer: Impact of Histopathological Concordance P M Pigera; AHS Lee; IO Ellis; EA Rakha; Z Hodi Nottingham City Hospital, Nottingham, UK One of the key recommendations introduced in the ASCO/CAP update guideline recommendation on HER2 testing is the novel concept of "histopathological concordance." It is proposed that certain tumour morphological features such as histologic type and grade should trigger repeating a molecular test in cases of "discordance". abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7168113/ doi: 10.1002/path.4631 id: cord-010092-uftc8inx author: nan title: Abstract of 29th Regional Congress of the ISBT date: 2019-06-07 words: 233304.0 sentences: 13171.0 pages: flesch: 54.0 cache: ./cache/cord-010092-uftc8inx.txt txt: ./txt/cord-010092-uftc8inx.txt summary: Prospective testing of blood donations in endemic areas of the U.S. revealed 0.38% of donors were positive for Babesia DNA or antibodies (Moritz, NEJM, 2016) Aims: -To report results of ongoing Babesia clinical trial -To explain significance of Babesia as a TT infection Methods: In cobas â Babesia for use on the cobas â 6800/8800 Systems, is a qualitative polymerase chain reaction nucleic acid amplification test, developed to detect in whole blood (WB) donor samples the 4 Babesia species that cause human disease: B. In sensitivity analyses, there were two discrepant results for HIV testing, three for HCV, and five for anti-HBc. Summary/Conclusions: Elecsys â infectious disease parameters on the cobas e 801 analyser demonstrate high specificity/sensitivity for screening first-time blood donor samples, with similar clinical performance to other commercially available assays. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169345/ doi: 10.1111/vox.12792 id: cord-010119-t1x9gknd author: nan title: Abstract Presentations from the AABB Annual Meeting San Diego, CA ctober 7‐10, 2017 date: 2017-09-04 words: 230193.0 sentences: 13234.0 pages: flesch: 55.0 cache: ./cache/cord-010119-t1x9gknd.txt txt: ./txt/cord-010119-t1x9gknd.txt summary: Conclusion: The wide distribution in the concentration of bioactive lipids among 405 stored RBC units suggests that lipid degradation is highly donor-Background/Case Studies: To ensure availability of biological products to hospitals, blood banks have developed and validated multiple storage conditions for each of their products to maximize shelf life and quality. 1 The Department of Blood Transfusion, The PLA General Hospital, 2 The Department of Blood Transfusion, Air Force General Hospital, PLA Background/Case Studies: Recently, multi researches have reported that longer term-stored red blood cells(RBCs) units were associated with increased risks of clinically adverse events, especially in critically ill patients. Weak D types 1, 2 and 3 express all the major RhD epitopes and these patients can be managed as RhD-positive, which may lead to a reduction in unnecessary Rh immunoglobulin (RhIG) administration and conservation of RhD-negative RBCs. Study Design/Method: RHD genotyping was performed on all patient samples with weaker than expected or discrepant RhD typing results, utilizing a commercially available genotyping kit manufactured by Immucor (RHD BeadChip). abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169716/ doi: 10.1111/trf.14286 id: cord-014462-11ggaqf1 author: nan title: Abstracts of the Papers Presented in the XIX National Conference of Indian Virological Society, “Recent Trends in Viral Disease Problems and Management”, on 18–20 March, 2010, at S.V. University, Tirupati, Andhra Pradesh date: 2011-04-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3639731/ doi: 10.1007/s13337-011-0027-2 id: cord-014516-r59usk02 author: nan title: Research Communications of the 24th ECVIM‐CA Congress date: 2015-01-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4858066/ doi: 10.1111/jvim.12491 id: cord-014527-nvzfpntu author: nan title: Research Communications of the 25th ECVIM‐CA Congress date: 2015-11-09 words: 89238.0 sentences: 4996.0 pages: flesch: 52.0 cache: ./cache/cord-014527-nvzfpntu.txt txt: ./txt/cord-014527-nvzfpntu.txt summary: A negative outcome was associated with higher fecal S100A12 concentrations in CE dogs, but the response to different forms of treatment and fecal S100A12 has not been reported, and this information will be important to further evaluate the utility of fecal S100A12 as a biomarker for gastrointestinal disease. Statistical analysis was performed using non-parametric 2-or multiple-group comparisons, the likelihood ratio to evaluate the association between groups of dogs and response to treatment, and a receiver operating characteristic curve to calculate sensitivity and specificity at the optimum cut-off concentration. The objectives of this study were to describe pulmonary transit time and myocardial perfusion normalized to heart rate (nPTT and nMP, respectively), evaluated by means of contrast echocardiography, in dogs with stable stage C ACVIM myxomatous mitral valve disease (MMVD), and to assess short-term effects of pimobendan on these parameters. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4913621/ doi: 10.1111/jvim.13647 id: cord-014794-yppi30a0 author: nan title: 19th European Congress of Pathology, Ljubljana, Slovenia, September 6-11, 2003 date: 2003-07-31 words: 158059.0 sentences: 9041.0 pages: flesch: 44.0 cache: ./cache/cord-014794-yppi30a0.txt txt: ./txt/cord-014794-yppi30a0.txt summary: These parts were in a high percentage associated with fibrosis and lymphocyte rich areas and showed a higher mitotic activity than usual PTCs. Discussion The differences in the occurrence of TCV and TCmorphology between the presented series and previously reported cases might result from until now not clearly defined tall cell morphology as well as from similarities to PTCs, such as the oxyphilic variant, which is extremely rare in our series, and maybe also from often described squamous changes within PTCs. Due to these data it is not clear which tumor parts have relevance for prognosis and which tumors should be treated more aggressively than others. The aims of this study were to characterize the group of patients with BSOT and evaluate the significance of various molecular markers expression versus serous papillary ovarian carcinomas (SPOC) Material and methods We analyzed a total of 102 cases including: 64 cystadenoma, 10 borderline and 28 cystadenocarcinoma. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087991/ doi: 10.1007/s00428-003-0864-5 id: cord-014965-efmozngq author: nan title: Infectious diseases other than CMV (1st Section) date: 2001-06-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7091871/ doi: 10.1038/sj.bmt.1702942 id: cord-014976-546zaoxn author: nan title: Publication only date: 2006-03-08 words: 51926.0 sentences: 2983.0 pages: flesch: 53.0 cache: ./cache/cord-014976-546zaoxn.txt txt: ./txt/cord-014976-546zaoxn.txt summary: In order to evaluate if malignant and non malignant hematological diseases quantitatively and qualitatively affect BM derived MSCs, bone marrow from children with acute lymphoblastic leukemia (ALL diagnosis n=9, different phases of treatment n=29, end of therapy n=10), idiopathic thrombocytopenic purpura (n=16), autoimmune neutropenia (n=12) and control patients (solid tumors without BM involvement, n=30) was harvested and the mononuclear cell (MNC) fraction isolated. Case: In our hospital a total of 3 patients with relapsed Hodgkin''s disease underwent reduced-intensity conditioning (RIC) allogeneic stem cell transplantation (allo-SCT) from an HLA-identical sibling. We report a case of a young male patient of 19 years old with aggressive MS who was treated with a high-dose immunosuppressive regimen (HDIS) using myeloablation followed by autologous blood stem cell transplantation (ASCT) that has induced a dramatic and long-lasting remission of the disease. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7092326/ doi: 10.1038/sj.bmt.1705327 id: cord-015147-h0o0yqv8 author: nan title: Oral Communications and Posters date: 2014-09-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095932/ doi: 10.1007/bf03353884 id: cord-015324-y44sfr0c author: nan title: Scientific Programme date: 2007-09-01 words: 197618.0 sentences: 12774.0 pages: flesch: 53.0 cache: ./cache/cord-015324-y44sfr0c.txt txt: ./txt/cord-015324-y44sfr0c.txt summary: In order to further validate this approach, we performed a prospective randomized open-label multicenter trial in 41 low-risk pediatric renal transplant recipients (12 f, 29 m; mean age 10.1 yrs; range, 3.4 to 17.8) on CsA (target trough level 100-200 ng/ml), MMF (1200 mg/m 2 per day) and methylprednisolone (3) (4) mg/m 2 per day), who were randomly assigned >1 year posttransplant to continue steroids or to withdraw over a period of 3 months. We evaluated MMF in 15 children with LN, 11 F/4 M, mean age: 12.4±3.9 yrs, proteinuria >3 g/day, decreased C3 and increased anti-dsDNA serum levels, normal renal function. Patients and methods: 91 children and adolescents (60 male, 31 female, mean age at transplantation 9.7±5.2 years) with stable renal function and observation period exceeding 6 months were included. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101932/ doi: 10.1007/s00467-007-0558-3 id: cord-015348-qt0worsl author: nan title: Abstract date: 2010-07-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102354/ doi: 10.1007/s00428-010-0947-z id: cord-015372-76xvzvdg author: nan title: National scientific medical meeting 1996 abstracts date: 1996 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7103226/ doi: 10.1007/bf02945204 id: cord-015394-uj7fe5y6 author: nan title: Scientific Abstracts date: 2008-12-23 words: 242330.0 sentences: 15267.0 pages: flesch: 52.0 cache: ./cache/cord-015394-uj7fe5y6.txt txt: ./txt/cord-015394-uj7fe5y6.txt summary: Studies involving immunohistochemical analysis of normal ovaries have shown that granulosa cells express significantly higher levels of the activator protein-1 (AP-1) transcription factor, cFos compared to theca cells, where cFos expression is virtually absent. Following acute hypoxia (0.5% O2) for one to six hours, RhoA mRNA, total protein and activation (RhoA-GTP) levels were analysed, using semi-quantitative PCRs and western blot, and compared to normoxic non-pregnant human uterine smooth muscle control cells. Since there is an urgent need for non-invasive methods for determination of fetal (F) and placental (P) function, this study was designed to evaluate the genes differently and commonly expressed in P tissue and leukocytes in maternal (M) and F circulation.Material and Methods. The current study: 1) localized IL-6 mRNA levels in preeclamptic versus normal decidual sections; 2) evaluated mechanisms regulating IL-6 synthesis by targeting intracellular signaling pathways with specific inhibitors; 3) identified potential IL-6 targets by immunolocalizing the IL-6 receptor (IL-6R) to specific cell types in placental bed biopsies. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7104449/ doi: 10.1177/19337191080150020102 id: cord-019490-m1cuuehi author: nan title: Abstracts cont. date: 2015-12-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7129916/ doi: 10.1111/j.1469-0691.2005.clm_1134_02.x id: cord-022501-9wnmdvg5 author: nan title: P1460 – P1884 date: 2015-12-28 words: 128256.0 sentences: 7808.0 pages: flesch: 51.0 cache: ./cache/cord-022501-9wnmdvg5.txt txt: ./txt/cord-022501-9wnmdvg5.txt summary: Methods: Using published data on (1) the prevalence of MRSA and other bacterial pathogens causing cSSSI in the US, (2) the in-vitro susceptibility rates of commonly used regimens in cSSSI in the US in relation to the most pervasive pathogens identified above, and (3) estimated costs of failure of initial, empiric treatment from a recent study of a large US multi-hospital database, we developed a model to predict the expected clinical and economic impact of increasing prevalence of MRSA. Small outbreaks of VEB-1 ESBL producing Acinetobacter baumannii in Belgian nursing homes and hospitals through cross-border transfer of patients from northern France Methods: From 01/04 to 03/05, all Belgian acute hospitals were invited to report cases of nosocomial infections/colonisations due to MDR Ab isolates presenting a resistance profile similar to the French epidemic strain (resistance to all agents except carbapenems and colistin) and to send such isolates to the reference laboratory for phenotypic confirmation and for genotypic characterization (PCR of VEB-1 and class 1 Integron, PFGE typing). abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7157935/ doi: 10.1111/j.1470-9465.2006.12_4_1431.x id: cord-022888-dnsdg04n author: nan title: Poster Sessions date: 2009-08-19 words: 188640.0 sentences: 9313.0 pages: flesch: 45.0 cache: ./cache/cord-022888-dnsdg04n.txt txt: ./txt/cord-022888-dnsdg04n.txt summary: Methods: Phospho-specific Western blot analyses were performed to verify the functionality of the different IFN-g pathway components, intra-and extracellular flow cytometry experiments were employed to determine the expression of antigen processing components and HLA class I cell surface antigens, quantitative real time-PCR experiments to confirm the absence of JAK2 and presence of pathway relevant molecules as well as, genomic PCR and chromosome typing technique to prove the deletion of JAK2. In order to accomplish these objectives we induced priming or tolerance of ovalbumin (OVA 323-339 peptide)-specific T cells from DO11.10 TCR transgenic mice in vitro or, following adoptive transfer of near physiologically relevant numbers of such cells into recipients, in vivo and correlated functional outcome (via proliferation and cytokine readout assays or antibody production) with E3 ubiquitin-protein ligases expression and the ubiquitination status of the TCR signalling machinery. abstract: No Abtract url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7163517/ doi: 10.1002/eji.200990224 id: cord-022940-atbjwpo5 author: nan title: Poster Sessions date: 2016-09-07 words: 241182.0 sentences: 12746.0 pages: flesch: 47.0 cache: ./cache/cord-022940-atbjwpo5.txt txt: ./txt/cord-022940-atbjwpo5.txt summary: We have studied the effect of inhibition of IRE1 (inositol requiring enzyme 1), which is a central mediator of endoplasmic reticulum stress and controls cell proliferation and tumor growth, on hypoxic regulation of the expression of different proliferation related genes in U87 glioma cells. Transient inhibition of Akt and mTOR protein kinase activation in tumor cells followed by reactivation of signaling pathway did not result in a time-dependent difference on EGFR, HER2 and HER3 expression levels. In our study we aimed to determine cytotoxic effect of RES in K562 human CML cell line and to evaluate the expressions of miRNAs that are associated with genetics of leukemia after treatment with RES; to investigate target genes of miRNAs which show significant expression alterations and molecular mechanisms of RES treatment. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7164006/ doi: 10.1111/febs.13808 id: cord-023017-k6edtg58 author: nan title: AASLD Abstracts (pp. 282A–382A) date: 2006-02-10 words: 65796.0 sentences: 3553.0 pages: flesch: 51.0 cache: ./cache/cord-023017-k6edtg58.txt txt: ./txt/cord-023017-k6edtg58.txt summary: 14/55 (25%) patients in AC who did not discontinue by week 24 received ribavirin dose reduction in comparison to 31/108 ( The clinical outcome in response to combination therapy for treatment of chronic hepatitis C virus (HCV) infection appears to be different for Caucasian versus African American patients. Over the period of combination therapy, most patients in which serum virus titers were reduced to non detectable levels had significant increases in T cell responses to HCV proteins. CHRONIC Background: Recent large prospective trials demonstrated that the combination therapy of interferon (1FN)-alphalribavirin significantly increased the ratio of a sustained virological response in patients with chronic hepatitis C in comparison with IFN monotherapy, especially in patients with high HCV-RNA titer and genotype lb. Results: Patients with chronic HCV infection showed higher MxA gene expression levels than healthy controls, indicating that hepatitis C virus induces IFN production. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7165819/ doi: 10.1002/hep.1840380505 id: cord-023026-2r84ndzv author: nan title: Posters date: 2013-06-14 words: 138458.0 sentences: 6513.0 pages: flesch: 40.0 cache: ./cache/cord-023026-2r84ndzv.txt txt: ./txt/cord-023026-2r84ndzv.txt summary: Thus, this work provides the basis to identify molecular pathways regulated by distinct niche/environmental signals and involved in the heterogeneity of adult OPCs. Multiple sclerosis (MS) is a chronic inflammatory and neurodegenerative demyelinating disease of the central nervous system (CNS) characterized by inflammation, which leads to formation of demyelinating areas due to loss of oligodendrocytes, astrogliosis and, finally, axonal degeneration. Taken together, these results demonstrate the important role of miR-200b in modulating the MAPK pathway via c-Jun which in turn affects different aspects of the inflammatory process accompanying microglia activation including cytokine response, NO production, phagocytosis and neuronal cell death. For this purpose, coronal cryostat free-floating sections from the brain of both adult transgenic mice and their corresponding wild-type (Wt) littermates, were processed for the study of astrocytes using GFAP immunohistochemistry and microglia using antibodies against Iba1 and several markers commonly related to the activated phenotype of these microglial cells, such as CD16/32 (Fc receptor), F4/80, CD11b, CD206, CD150 and MHC-II. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7165910/ doi: 10.1002/glia.22530 id: cord-023095-4dannjjm author: nan title: Research Abstract Program of the 2011 ACVIM Forum Denver, Colorado, June 15–18, 2011 date: 2011-05-03 words: 134226.0 sentences: 6834.0 pages: flesch: 51.0 cache: ./cache/cord-023095-4dannjjm.txt txt: ./txt/cord-023095-4dannjjm.txt summary: The purpose of this study was to determine the short-term effects of ivabradine on heart rate (HR), blood pressure, left ventricular (LV) systolic and diastolic function, left atrial (LA) performance, and clinical tolerance in healthy cats after repeated oral doses. The goal of this study was to investigate the relationship between heart rate and ECG time intervals to body mass in apparently healthy horses and ponies and to calculate normal ranges for different weight groups. This study aimed to investigate the prevalence of hypercoagulability in PLN dogs based on thromboelastography (TEG), and to determine whether hypercoagulability in these patients could be predicted by clinical assessments that identify systemic hypertension (systolic blood pressure 4 160 mmHg), hypoalbuminemia (serum albumin o 2.7 mg/dl), antithrombin activity (o 70%), and degree of proteinuria (urine protein:creatinine ratio [UPC] ! abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7166756/ doi: 10.1111/j.1939-1676.2011.0726.x id: cord-023134-y665agnh author: nan title: Oral Research Communications of the 22(nd) ECVIM‐CA Congress date: 2012-11-20 words: 29595.0 sentences: 1548.0 pages: flesch: 50.0 cache: ./cache/cord-023134-y665agnh.txt txt: ./txt/cord-023134-y665agnh.txt summary: Doppler echocardiographic indices of diastolic function of the right ventricle are good prognostic markers during left ventricular (LV) failure secondary to ischemic and dilated cardiomyopathy.The aims of the present study were: to assess LV and RV diastolic function by conventional Doppler and pulsed-wave tissue Doppler imaging (PW-TDI) in dogs with mitral valve disease (MVD), with or without pulmonary hypertension (PH); to test if echocardiographic parameters of LV and RV diastolic dysfunction correlate to the Doppler-estimated pulmonary artery systolic pressure (PASP).114 dogs were prospectively evaluated, including 86 dogs with MVD. The aims of the present study were to assess whether diabetic cats have pathological evidence of islet inflammation or pancreatitis and to define islet lesions in comparison to a well-matched control population.Formalin-fixed, paraffin-embedded pancreatic samples were collected from post-mortem examination performed on diabetic and control cats died due to any disease at the Clinic for Small Animal Internal Medicine, University of Zurich (Switzerland) between 1997 and 2009. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7167033/ doi: 10.1111/jvim.12000 id: cord-023211-kt5gt26t author: nan title: Poster Session Abstracts date: 2007-08-29 words: 221224.0 sentences: 11772.0 pages: flesch: 52.0 cache: ./cache/cord-023211-kt5gt26t.txt txt: ./txt/cord-023211-kt5gt26t.txt summary: Previous studies performed using fluorescence halide efflux measurements and short-circuit current voltage clamp have shown that treatment with PPARγ (peroxisome proliferator activated receptor gamma) agonists, such as pioglitazone and FLL (FMOC-L-leucine), resulted in an increased biosynthesis and trafficking of ∆F508-CFTR to the cell surface. Physiology, School of Medical Sciences, University of Bristol, Bristol, United Kingdom Recent progress in the development of small molecule correctors and potentiators capable of restoring CFTR function have increased the need for pre-clinical test models including cultured airway epithelial cells from human CF patients as well as CF mouse models. Clinical studies have linked increased sputum and peripheral blood neutrophil MPO activity with increased airflow obstruction in cystic fibrosis (CF) patients of the same age, gender, airway bacterial flora, and CFTR genotype. Because patients expressing low levels of normal CFTR mRNA (5-20%) have mild disease symptoms, these studies demonstrate that the incorporation of the ciliated cell-specific FOXJ1 promoter into gene therapy vectors may be useful for treatment of CF. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7167830/ doi: 10.1002/ppul.20700 id: cord-023288-sqr33y72 author: nan title: Paediatric SIG: Poster Session date: 2008-03-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169050/ doi: 10.1111/j.1440-1843.2008.01252_11.x id: cord-023303-fxus38mp author: nan title: Lung Cancer/Bronchology SIGs: Combined Poster Session date: 2008-03-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169102/ doi: 10.1111/j.1440-1843.2008.01252_8.x id: cord-023308-af5nihyi author: nan title: COPD SIG: Poster Session 2 date: 2008-03-12 words: 30159.0 sentences: 1761.0 pages: flesch: 53.0 cache: ./cache/cord-023308-af5nihyi.txt txt: ./txt/cord-023308-af5nihyi.txt summary: Results Data indicate splice variant expression in dendritic cells from asthmatic patients is influenced by asthma severity. Methods Randomized controlled trials (RCTs) of GORD treatment in adults or children that reported asthma health outcomes and had symptomatic GORD were included and assessed in accordance with the standard Cochrane systematic review process. Results 11 male (44%) and 14 female (56%) patients with moderate to severe persistent asthma (mean age 44 years, SD = 11) participated. Methods A comprehensive range of intracellular T-cell and monocyte proand anti-inflammatory cytokines/chemokines was investigated in peripheral blood from 5 OSA patients and 5 aged-matched control subjects (with no evidence of sleep problems) using multiparameter flow cytometry. Methods Following completion of a 12-month exercise study, which included a supervised program (Intervention, n = 18) and control group (Control, n = 17), COPD subjects [mean age (SD): 66 (8); mean FEV1 (% predicted) = 56% (19)] were asked to complete a questionnaire. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169120/ doi: 10.1111/j.1440-1843.2008.01252_6.x id: cord-023331-jrvmgnu3 author: nan title: Asthma & Allergy SIG: Poster Session 3. Physiology, Environment, Investigation and Management date: 2008-03-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169210/ doi: 10.1111/j.1440-1843.2008.01252_3.x id: cord-023346-8sqbqjm1 author: nan title: MONDAY: POSTERS date: 2005-06-08 words: 130043.0 sentences: 7330.0 pages: flesch: 54.0 cache: ./cache/cord-023346-8sqbqjm1.txt txt: ./txt/cord-023346-8sqbqjm1.txt summary: • enhancement of automation/computerisation; • process control to provide an ''error-free pathway''; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody ''combi'' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas'' disease infection (for retrieval of otherwise wasted blood); • European Union''s in vitro diagnostics directive: this has caused some problems and reduced flexibility. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169255/ doi: 10.1111/j.1423-0410.2005.00652.x id: cord-023354-f2ciho6o author: nan title: TUESDAY PLENARY SESSION 3 TUESDAY: POSTERS date: 2005-06-08 words: 130046.0 sentences: 7333.0 pages: flesch: 54.0 cache: ./cache/cord-023354-f2ciho6o.txt txt: ./txt/cord-023354-f2ciho6o.txt summary: • enhancement of automation/computerisation; • process control to provide an ''error-free pathway''; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody ''combi'' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas'' disease infection (for retrieval of otherwise wasted blood); • European Union''s in vitro diagnostics directive: this has caused some problems and reduced flexibility. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169300/ doi: 10.1111/j.1423-0410.2005.00654.x id: cord-023364-ut56gczm author: nan title: EDUCATION DAY MONDAY: PLENARY SESSION 1 MONDAY: PARALLEL SESSIONS date: 2005-06-08 words: 130049.0 sentences: 7334.0 pages: flesch: 54.0 cache: ./cache/cord-023364-ut56gczm.txt txt: ./txt/cord-023364-ut56gczm.txt summary: • enhancement of automation/computerisation; • process control to provide an ''error-free pathway''; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody ''combi'' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas'' disease infection (for retrieval of otherwise wasted blood); • European Union''s in vitro diagnostics directive: this has caused some problems and reduced flexibility. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169338/ doi: 10.1111/j.1423-0410.2005.00651.x id: cord-023592-w96h4rir author: nan title: Abstracts cont. date: 2015-12-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172567/ doi: 10.1111/j.1469-0691.2004.0902c.x id: cord-031907-ilhr3iu5 author: nan title: ISEV2020 Abstract Book date: 2020-07-15 words: 200999.0 sentences: 11528.0 pages: flesch: 44.0 cache: ./cache/cord-031907-ilhr3iu5.txt txt: ./txt/cord-031907-ilhr3iu5.txt summary: L.M., and the National Institutes of Health (R35GM119623) to T.R.G. The addition of a size exclusion chromatography step to various urinary extracellular vesicle concentrating methods reveals differences in the small RNA profile Introduction: Urinary extracellular vesicles (EVs) and their RNA cargo are a novel source of biomarkers for various diseases, however non-vesicular RNA (e.g. associated with proteins) is also present within urine. We then evaluated efficiency of heart targeting for eAAV9 or eAAV6 and standard AAV9 or AAV6 encoding for EGFP, mCherry or firefly luciferase in different human cell lines in vitro, in black mouse and in passive immunity nude mouse model in vivo using flow cytometry, confocal microscopy, Langendorff perfusion system and Methods: HLHS patients (n = 3) after Glenn procedure and swine (n = 3) after PAB were given RV injections of allogeneic/xenogeneic MSCs. Donor-specific, HLA-I+, exosomes were isolated from plasma. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7480431/ doi: 10.1080/20013078.2020.1784511 id: cord-291860-dw1sfzqx author: van Boheemen, Sander title: Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients date: 2019-12-16 words: 5398.0 sentences: 276.0 pages: flesch: 40.0 cache: ./cache/cord-291860-dw1sfzqx.txt txt: ./txt/cord-291860-dw1sfzqx.txt summary: Herein, were studied the performance of an in-house mNGS protocol for routine diagnostics of viral respiratory infections with potential for automated pan-pathogen detection. Herein, were studied the performance of an in-house mNGS protocol for routine diagnostics of viral respiratory infections with potential for automated pan-pathogen detection. Clinical sensitivity was analyzed using the optimized procedure, which in short consisted of total nucleic acid extraction, including internal controls (1:100 dilution); the adapted New England Biolabs Next library preparation protocol, including fragmentation with zinc, for combined RNA and DNA detection (see Library Preparation); and sequencing of 10 million reads (Illumina NextSeq 500). The Centrifuge default settings, with NCBI''s nucleotide database and assignment of sequence reads to a maximum of five labels per sequence, resulted in various spurious classifications ( Figure 4) [eg, Lassa virus ( Figure 5 ), evidently highly unlikely to be present in patient samples from the Netherlands with respiratory complaints]. abstract: Viruses are the main cause of respiratory tract infections. Metagenomic next-generation sequencing (mNGS) enables unbiased detection of all potential pathogens. To apply mNGS in viral diagnostics, sensitive and simultaneous detection of RNA and DNA viruses is needed. Herein, were studied the performance of an in-house mNGS protocol for routine diagnostics of viral respiratory infections with potential for automated pan-pathogen detection. The sequencing protocol and bioinformatics analysis were designed and optimized, including exogenous internal controls. Subsequently, the protocol was retrospectively validated using 25 clinical respiratory samples. The developed protocol using Illumina NextSeq 500 sequencing showed high repeatability. Use of the National Center for Biotechnology Information’s RefSeq database as opposed to the National Center for Biotechnology Information’s nucleotide database led to enhanced specificity of classification of viral pathogens. A correlation was established between read counts and PCR cycle threshold value. Sensitivity of mNGS, compared with PCR, varied up to 83%, with specificity of 94%, dependent on the cutoff for defining positive mNGS results. Viral pathogens only detected by mNGS, not present in the routine diagnostic workflow, were influenza C, KI polyomavirus, cytomegalovirus, and enterovirus. Sensitivity and analytical specificity of this mNGS protocol were comparable to PCR and higher when considering off-PCR target viral pathogens. One single test detected all potential viral pathogens and simultaneously obtained detailed information on detected viruses. url: https://www.sciencedirect.com/science/article/pii/S1525157819304325 doi: 10.1016/j.jmoldx.2019.10.007 id: cord-259004-plst2wno author: van Elden, Leontine J. R. title: Frequent Detection of Human Coronaviruses in Clinical Specimens from Patients with Respiratory Tract Infection by Use of a Novel Real-Time Reverse-Transcriptase Polymerase Chain Reaction date: 2004-02-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: During the past years, human coronaviruses (HCoVs) have been increasingly identified as pathogens associated with more-severe respiratory tract infection (RTI). Diagnostic tests for HCoVs are not frequently used in the routine setting. It is likely that, as a result, the precise role that HCoVs play in RTIs is greatly underestimated. We describe a rapid, sensitive, and highly specific quantitative real-time reverse-transcriptase polymerase chain reaction (RT-PCR) for the detection of HCoV that can easily be implemented in the routine diagnostic setting. HCoV was detected in 28 (11%) of the 261 clinical specimens obtained from patients presenting with symptoms of RTI ranging from common cold to severe pneumonia. Only 1 (0.4%) of the 243 control specimens obtained from patients without symptoms of RTI showed the presence of HCoV. We conclude that HCoVs can be frequently detected in patients presenting with RTI. Real-time RT-PCR provides a tool for large-scale epidemiological studies to further clarify the role that coronavirus infection plays in RTI in humans. url: https://www.ncbi.nlm.nih.gov/pubmed/14767819/ doi: 10.1086/381207 id: cord-349782-djzxkus2 author: van Kasteren, Puck B. title: Response to letter of concern by Oladimeji and Pickford of PrimerDesign date: 2020-06-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://doi.org/10.1016/j.jcv.2020.104526 doi: 10.1016/j.jcv.2020.104526 id: cord-270579-rf933a0y author: van Kruijssen, Alida M. title: Detection of respiratory pathogens by real-time PCR in children with clinical suspicion of pertussis date: 2006-12-20 words: 513.0 sentences: 33.0 pages: flesch: 55.0 cache: ./cache/cord-270579-rf933a0y.txt txt: ./txt/cord-270579-rf933a0y.txt summary: title: Detection of respiratory pathogens by real-time PCR in children with clinical suspicion of pertussis The use of a multiplex respiratory real-time PCR in patients clinically suspected of pertussis increases the number of pathogens detected. Pathogens were detected by PCR in 31 out of 38 (82%) cases and 10 out of 21 (48%) cases in Group I and Group II, respectively. PCR can also give falsenegative results and fewer diagnoses in those patients with pertussis could be due to the quality of the sample. Other pathogens were detected in 31 out of 38 patients with clinical diagnosis of pertussis. Other pathogens that cause a pertussis-like disease have previously been described using serological assays and Cherry et al. pertussis and other pathogens causing pertussis-like symptoms and use of this form of diagnosis might help in treatment and improve management of patients. Evaluation of real-time PCR for detection of and discrimination between Bordetella pertussis, Bordetella parapertussis, and Bordetella holmesii for clinical diagnosis abstract: The use of a multiplex respiratory real-time PCR in patients clinically suspected of pertussis increases the number of pathogens detected. url: https://www.ncbi.nlm.nih.gov/pubmed/17177069/ doi: 10.1007/s00431-006-0378-7 id: cord-342476-0rupk21u author: van Rijn, Anneloes L. title: The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease date: 2019-10-24 words: 4036.0 sentences: 220.0 pages: flesch: 44.0 cache: ./cache/cord-342476-0rupk21u.txt txt: ./txt/cord-342476-0rupk21u.txt summary: The sensitivity, specificity and predictive values of mNGS were calculated based on 24 PCR positive and 1120 PCR negative target results of 88 samples and the normalized read counts (Table 5 ). The following markers were tested for potential associations with clinical severity of exacerbation (exacerbation severity, self-reported exacerbation severity), length of exacerbation and a decrease/increase in FEV 1 (control visit compared to baseline): mNGS pathogen positive versus negative exacerbation (qPCR targets), the number of normalized reads (log, cutoff of �5normalized reads) for the different target viruses (species level). The Shannon diversity scores for bacteriophages (normalized reads, cut-off of �5normalized reads) were comparable for COPD exacerbations of viral aetiology in PCR positive versus negative patients (Fig 5) . In this study, the respiratory virome in patients with COPD exacerbations was analysed with both mNGS and qPCR, and combined with clinical data. abstract: INTRODUCTION: Exacerbations are major contributors to morbidity and mortality in patients with chronic obstructive pulmonary disease (COPD), and respiratory bacterial and viral infections are an important trigger. However, using conventional diagnostic techniques, a causative agent is not always found. Metagenomic next-generation sequencing (mNGS) allows analysis of the complete virome, but has not yet been applied in COPD exacerbations. OBJECTIVES: To study the respiratory virome in nasopharyngeal samples during COPD exacerbations using mNGS. STUDY DESIGN: 88 nasopharyngeal swabs from 63 patients from the Bergen COPD Exacerbation Study (2006–2010) were analysed by mNGS and in-house qPCR for respiratory viruses. Both DNA and RNA were sequenced simultaneously using an Illumina library preparation protocol with in-house adaptations. RESULTS: By mNGS, 24/88 samples tested positive. Sensitivity and specificity, as compared with PCR, were 96% and 98% for diagnostic targets (23/24 and 1093/1120, respectively). Additional viral pathogens detected by mNGS were herpes simplex virus type 1 and coronavirus OC43. A positive correlation was found between Cq value and mNGS viral normalized species reads (log value) (p = 0.002). Patients with viral pathogens had lower percentages of bacteriophages (p<0.001). No correlation was found between viral reads and clinical markers. CONCLUSIONS: The mNGS protocol used was highly sensitive and specific for semi-quantitative detection of respiratory viruses. Excellent negative predictive value implicates the power of mNGS to exclude any pathogenic respiratory viral infectious cause in one test, with consequences for clinical decision making. Reduced abundance of bacteriophages in COPD patients with viral pathogens implicates skewing of the virome during infection, with potential consequences for the bacterial populations, during infection. url: https://www.ncbi.nlm.nih.gov/pubmed/31647831/ doi: 10.1371/journal.pone.0223952 id: cord-256608-ajzk86rq author: van Weezep, Erik title: PCR diagnostics: In silico validation by an automated tool using freely available software programs date: 2019-05-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: PCR diagnostics are often the first line of laboratory diagnostics and are regularly designed to either differentiate between or detect all pathogen variants of a family, genus or species. The ideal PCR test detects all variants of the target pathogen, including newly discovered and emerging variants, while closely related pathogens and their variants should not be detected. This is challenging as pathogens show a high degree of genetic variation due to genetic drift, adaptation and evolution. Therefore, frequent re-evaluation of PCR diagnostics is needed to monitor its usefulness. Validation of PCR diagnostics recognizes three stages, in silico, in vitro and in vivo validation. In vitro and in vivo testing are usually costly, labour intensive and imply a risk of handling dangerous pathogens. In silico validation reduces this burden. In silico validation checks primers and probes by comparing their sequences with available nucleotide sequences. In recent years the amount of available sequences has dramatically increased by high throughput and deep sequencing projects. This makes in silico validation more informative, but also more computing intensive. To facilitate validation of PCR tests, a software tool named PCRv was developed. PCRv consists of a user friendly graphical user interface and coordinates the use of the software programs ClustalW and SSEARCH in order to perform in silico validation of PCR tests of different formats. Use of internal control sequences makes the analysis compliant to laboratory quality control systems. Finally, PCRv generates a validation report that includes an overview as well as a list of detailed results. In-house developed, published and OIE-recommended PCR tests were easily (re-) evaluated by use of PCRv. To demonstrate the power of PCRv, in silico validation of several PCR tests are shown and discussed. url: https://doi.org/10.1016/j.jviromet.2019.05.002 doi: 10.1016/j.jviromet.2019.05.002 id: cord-263763-a8wgvgz2 author: Çelik, Ersin title: Treatment Approach to Coronavirus Disease (COVID-19) Seen Early After Open Heart Surgery. Case Report date: 2020-07-02 words: 1535.0 sentences: 90.0 pages: flesch: 50.0 cache: ./cache/cord-263763-a8wgvgz2.txt txt: ./txt/cord-263763-a8wgvgz2.txt summary: Here, we present our approach to a 54-year-old male patient who had coronary artery bypass (CABG) surgery diagnosed as high probability coronavirus disease 2019 (COVID-19) in early postoperative period. We aimed to present our approach to high probability COVID-19 pneumonia which developed on early postoperative period in our patient after coronary artery bypass grafting (CABG) operation, which was not reported in the literature before. After consultations applied by chest physicians and infectious disease departments of our hospital, COVID-19 was evaluated as a high probability due to the laboratory tests, radiological findings, and clinical course. Having considered our patient as high risk, without waiting for the RT-PCR result, we started the specific treatment for COVID-19 immediately, by evaluating clinical, laboratory, and radiology findings. Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: a report of 1024 cases abstract: SARS-CoV-2 was reported for the first time in China on December 31, 2019, as the cause of some pneumonia cases characterized by fever, cough, dyspnea, myalgia, and fatigue. Here, we present our approach to a 54-year-old male patient who had coronary artery bypass (CABG) surgery diagnosed as high probability coronavirus disease 2019 (COVID-19) in early postoperative period. url: https://www.ncbi.nlm.nih.gov/pubmed/32838156/ doi: 10.1007/s42399-020-00377-y id: cord-312222-aw5849rc author: Österdahl, Marc F. title: Detecting SARS-CoV-2 at point of care: preliminary data comparing loop-mediated isothermal amplification (LAMP) to polymerase chain reaction (PCR) date: 2020-10-20 words: 3957.0 sentences: 201.0 pages: flesch: 53.0 cache: ./cache/cord-312222-aw5849rc.txt txt: ./txt/cord-312222-aw5849rc.txt summary: METHODS: This prospective service improvement project piloted an RT-LAMP method on nasal and pharyngeal swabs on 21 residents of a high dependency care home, with two index COVID-19 cases, and compared it to multiplex tandem reverse transcription polymerase chain reaction (RT-PCR). We recorded vital signs of patients to correlate clinical and laboratory information and calculated the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of a single swab using RT-LAMP compared with the current standard, RT-PCR, as per Standards for Reporting Diagnostic Accuracy Studies (STARD) guidelines. Since then, a number [13] of other groups have published high-quality studies demonstrating that RT-LAMP has the potential to replace RT-PCR as a means for detecting SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) within RNA extracted from nose -throat swabs and endotracheal secretions/bronchoalveolar lavage fluid [5, 14, 15] . abstract: BACKGROUND: A cost effective and efficient diagnostic tool for COVID-19 as near to the point of care (PoC) as possible would be a game changer in the current pandemic. We tested reverse transcription loop mediated isothermal amplification (RT-LAMP), a method which can produce results in under 30 min, alongside standard methods in a real-life clinical setting. METHODS: This prospective service improvement project piloted an RT-LAMP method on nasal and pharyngeal swabs on 21 residents of a high dependency care home, with two index COVID-19 cases, and compared it to multiplex tandem reverse transcription polymerase chain reaction (RT-PCR). We recorded vital signs of patients to correlate clinical and laboratory information and calculated the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of a single swab using RT-LAMP compared with the current standard, RT-PCR, as per Standards for Reporting Diagnostic Accuracy Studies (STARD) guidelines. RESULTS: The novel method accurately detected 8/10 RT-PCR positive cases and identified a further 3 positive cases. Eight further cases were negative using both methods. Using repeated RT-PCR as a “gold standard”, the sensitivity and specificity of a single novel test were 80 and 73% respectively. PPV was 73% and NPV was 83%. Incorporating retesting of low signal RT-LAMP positives improved the specificity to 100%. We also speculate that hypothermia may be a significant early clinical sign of COVID-19. CONCLUSIONS: RT-LAMP testing for SARS-CoV-2 was found to be promising, fast and to work equivalently to RT-PCR methods. RT-LAMP has the potential to transform COVID-19 detection, bringing rapid and accurate testing to the PoC. RT-LAMP could be deployed in mobile community testing units, care homes and hospitals to detect disease early and prevent spread. url: https://doi.org/10.1186/s12879-020-05484-8 doi: 10.1186/s12879-020-05484-8 id: cord-278635-vwdxr1bl author: Świętoń, Edyta title: Low pathogenic avian influenza virus isolates with different levels of defective genome segments vary in pathogenicity and transmission efficiency date: 2020-08-28 words: 5432.0 sentences: 295.0 pages: flesch: 48.0 cache: ./cache/cord-278635-vwdxr1bl.txt txt: ./txt/cord-278635-vwdxr1bl.txt summary: In the present study we compared the clinical outcome, mortality and transmission in chickens and turkeys infected with the same infectious doses of H7N7 low pathogenic avian influenza virus containing different levels of defective gene segments (95/95(DVG-high) and 95/95(DVG-low)). Virions containing highly deleted forms of genome segments (defective viral genes-DVGs) are able to replicate only in the presence and at the expense of fully infectious virus, hence the term "defective interfering particles" (DIPs) [4] . To evaluate the effect of DIPs on the course of infection with low pathogenic avian influenza virus (LPAIV), a comparison of pathogenicity of two virus stocks of H7N7 LPAIV with different levels of defective genomes was performed in turkeys and chickens. Infected birds received the same infectious dose of the virus but with different amount of DVGs. The semiquantitative analysis of defective particles was done by a combination of RT-PCR, real time RT-PCR and whole genome sequencing and indicated significantly higher amount of truncated gene segments in 95/95(DVG-high). abstract: Defective interfering particles (DIPs) of influenza virus are generated through incorporation of highly truncated forms of genome segments, mostly those coding polymerase complex proteins (PB2, PB1, PA). Such particles are able to replicate only in the presence of a virus with the complete genome, thus DIPs may alter the infection outcome by suppressing production of standard virus particles, but also by stimulating the immune response. In the present study we compared the clinical outcome, mortality and transmission in chickens and turkeys infected with the same infectious doses of H7N7 low pathogenic avian influenza virus containing different levels of defective gene segments (95/95(DVG-high) and 95/95(DVG-low)). No clinical signs, mortality or transmission were noted in SPF chickens inoculated with neither virus stock. Turkeys infected with 95/95(DVG-high) showed only slight clinical signs with no mortality, and the virus was transmitted only to birds in direct contact. In contrast, more severe disease, mortality and transmission to direct and indirect contact birds was observed in turkeys infected with 95/95(DVG-low). Apathy, lower water and food intake, respiratory system disorders and a total mortality of 60% were noted. Shedding patterns in contact turkeys indicated more efficient within- and between-host spread of the virus than in 95/95(DVG-high) group. Sequencing of virus genomes showed no mutations that could account for the observed differences in pathogenicity. The results suggest that the abundance of DIPs in the inoculum was the factor responsible for the mild course of infection and disrupted virus transmission. url: https://doi.org/10.1186/s13567-020-00833-6 doi: 10.1186/s13567-020-00833-6 ==== make-pages.sh questions [ERIC WAS HERE] ==== make-pages.sh search /data-disk/reader-compute/reader-cord/bin/make-pages.sh: line 77: /data-disk/reader-compute/reader-cord/tmp/search.htm: No such file or directory Traceback (most recent call last): File "/data-disk/reader-compute/reader-cord/bin/tsv2htm-search.py", line 51, in with open( TEMPLATE, 'r' ) as handle : htm = handle.read() FileNotFoundError: [Errno 2] No such file or directory: '/data-disk/reader-compute/reader-cord/tmp/search.htm' ==== make-pages.sh topic modeling corpus Zipping study carrel