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R. title: Are point‐of‐care (POC) virological tests what is needed? date: 2007-06-05 journal: Clin Microbiol Infect DOI: 10.1111/j.1469-0691.2007.01738.x sha: doc_id: 9675 cord_uid: utz0iazs file: cache/cord-009295-4c0zwhdh.json key: cord-009295-4c0zwhdh authors: Bal, A.; Destras, G.; Gaymard, A.; Bouscambert-Duchamp, M.; Valette, M.; Escuret, V.; Frobert, E.; Billaud, G.; Trouillet-Assant, S.; Cheynet, V.; Brengel-Pesce, K.; Morfin, F.; Lina, B.; Josset, L. title: Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino acid deletion in nsp2 (Asp268del) date: 2020-03-28 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.03.020 sha: doc_id: 9295 cord_uid: 4c0zwhdh file: cache/cord-275556-798oed8n.json key: cord-275556-798oed8n authors: Piubelli, Chiara; Deiana, Michela; Pomari, Elena; Silva, Ronaldo; Bisoffi, Zeno; Formenti, Fabio; Perandin, Francesca; Gobbi, Federico; Buonfrate, Dora title: Overall decrease of SARS-CoV-2 viral load and reduction of clinical burden: the experience of a Northern Italy hospital date: 2020-10-12 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.10.006 sha: doc_id: 275556 cord_uid: 798oed8n file: cache/cord-288425-po35m6d9.json key: cord-288425-po35m6d9 authors: Albert, Eliseo; 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Allerberger, F.; Cevik, M.; Huttner, A.; Paul, M.; Rodríguez-Baño, J.; Scudeller, L. title: Submissions and publications in Corona times date: 2020-05-15 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.05.008 sha: doc_id: 314288 cord_uid: 6vh7dvad file: cache/cord-331002-7uojryqz.json key: cord-331002-7uojryqz authors: Valent, Francesca; Di Chiara, Antonio title: Detection of SARS-CoV-2 in nasopharynx according to clinical phenotype of affected patients date: 2020-09-06 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.08.041 sha: doc_id: 331002 cord_uid: 7uojryqz file: cache/cord-334835-j6u8t8j2.json key: cord-334835-j6u8t8j2 authors: Berenguer, Juan; Ryan, Pablo; Rodríguez-Baño, Jesús; Jarrín, Inmaculada; Carratalà, Jordi; Pachón, Jerónimo; Yllescas, María; Arribas, José Ramón title: Characteristics and predictors of death among 4,035 consecutively hospitalized patients with COVID-19 in Spain date: 2020-08-04 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.07.024 sha: doc_id: 334835 cord_uid: j6u8t8j2 file: cache/cord-325186-nq6ay4eo.json key: cord-325186-nq6ay4eo authors: Sieswerda, Elske; 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Jakob, W.; Faes Hesse, M.; Kuster, S.P.; Meier, A.H.; Schreiber, P.W.; Clack, L.; Sax, H. title: Development and validation of a semi-automated surveillance system—lowering the fruit for non-ventilator-associated hospital-acquired pneumonia (nvHAP) prevention() date: 2019-03-25 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2019.03.019 sha: doc_id: 318021 cord_uid: 4qrf5m8s file: cache/cord-279125-w6sh7xpn.json key: cord-279125-w6sh7xpn authors: Egli, Adrian; Schrenzel, Jacques; Greub, Gilbert title: Digital microbiology date: 2020-06-27 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.06.023 sha: doc_id: 279125 cord_uid: w6sh7xpn file: cache/cord-294546-0otd1heg.json key: cord-294546-0otd1heg authors: Prendki, V.; Huttner, B.; Marti, C.; Mamin, A.; Fubini, P.E.; Meynet, M.P.; Scheffler, M.; Montet, X.; Janssens, J.P.; Reny, J.L.; Kaiser, L.; Garin, N.; Stirnemann, J. 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 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2018.12.037 sha: doc_id: 294546 cord_uid: 0otd1heg file: cache/cord-283411-40ojqv1y.json key: cord-283411-40ojqv1y authors: Ben-Shmuel, Amir; 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Seng, C.W.; Yip, C.C.Y.; Cheng, V.C.C.; Hung, I.F.N.; Yuen, K.-Y. title: Respiratory virus infection among hospitalized adult patients with or without clinically apparent respiratory infection: a prospective cohort study date: 2019-04-18 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2019.04.012 sha: doc_id: 276399 cord_uid: omjfyog0 file: cache/cord-276212-ys5njiw0.json key: cord-276212-ys5njiw0 authors: Wei, L.; Chan, K.-H.; Ip, D.K.M.; Fang, V.J.; Fung, R.O.P.; Leung, G.M.; Peiris, M.J.S.; Cowling, B.J. title: Burden, seasonal pattern and symptomatology of acute respiratory illnesses with different viral aetiologies in children presenting at outpatient clinics in Hong Kong date: 2015-05-30 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2015.05.027 sha: doc_id: 276212 cord_uid: ys5njiw0 file: cache/cord-304710-gjb6zo81.json key: cord-304710-gjb6zo81 authors: Khan, S.; Nabi, G.; Han, G.; Siddique, R.; Lian, S.; Shi, H.; Bashir, N.; Ali, A.; Shereen, M. Adnan title: Novel coronavirus: how things are in Wuhan date: 2020-02-11 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.02.005 sha: doc_id: 304710 cord_uid: gjb6zo81 file: cache/cord-283818-4m9p717r.json key: cord-283818-4m9p717r authors: Yan, Chao; Cui, Jinghua; Huang, Lei; Du, Bing; Chen, Lu; Xue, Guanhua; Li, Shaoli; Zhang, Weiwei; Zhao, Linqing; Sun, Yu; Yao, Hailan; Li, Nannan; Zhao, Hanqing; Feng, Yanling; Liu, Shiyu; Zhang, Qun; Liu, Di; Yuan, Jing title: Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal amplification assay date: 2020-04-08 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.04.001 sha: doc_id: 283818 cord_uid: 4m9p717r file: cache/cord-031493-w8agvg9g.json key: cord-031493-w8agvg9g authors: Davido, Benjamin; Seang, Sophie; Barizien, Nicolas; Tubiana, Roland; de Truchis, Pierre title: Possible therapies of Post-COVID-19 chronic symptoms() date: 2020-09-06 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.09.001 sha: doc_id: 31493 cord_uid: w8agvg9g file: cache/cord-326703-akn92p1r.json key: cord-326703-akn92p1r authors: Bartoletti, Michele; Giannella, Maddalena; Scudeller, Luigia; Tedeschi, Sara; Rinaldi, Matteo; Bussini, Linda; Fornaro, Giacomo; Pascale, Renato; Pancaldi, Livia; Pasquini, Zeno; Trapani, Filippo; Badia, Lorenzo; Campoli, Caterina; Tadolini, Marina; Attard, Luciano; Puoti, Massimo; Merli, Marco; Mussini, Cristina; Menozzi, Marianna; Meschiari, Marianna; Codeluppi, Mauro; Barchiesi, Francesco; Cristini, Francesco; Saracino, Annalisa; Licci, Alberto; Rapuano, Silvia; Tonetti, Tommaso; Gaibani, Paolo; Ranieri, Vito Marco; Viale, Pierluigi title: Development and validation of a prediction model for severe respiratory failure in hospitalized patients with SARS-Cov-2 infection: a multicenter cohort study (PREDI-CO study) date: 2020-08-08 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.08.003 sha: doc_id: 326703 cord_uid: akn92p1r file: cache/cord-294392-a8s66g96.json key: cord-294392-a8s66g96 authors: Zhang, Shuai; Guo, Mengfei; Wu, Feng; Xiong, Nian; Ma, Yanling; Wang, Zhihui; Duan, Limin; Chen, Lan; Ouyang, Haixia; Jin, Yang title: Factors associated with asymptomatic infection in health-care workers with SARS-CoV-2 infection in Wuhan, China: a multi-center retrospective cohort study date: 2020-09-07 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.08.038 sha: doc_id: 294392 cord_uid: a8s66g96 file: cache/cord-293542-o0zspgrk.json key: cord-293542-o0zspgrk authors: Ippolito, G.; Fusco, F.M.; Caro, A. Di; Nisii, C.; Pompa, M.G.; Thinus, G.; Pletschette, M.; Capobianchi, M.R. title: Facing the threat of highly infectious diseases in Europe: the need for a networking approach date: 2014-12-12 journal: Clin Microbiol Infect DOI: 10.1111/j.1469-0691.2009.02876.x sha: doc_id: 293542 cord_uid: o0zspgrk file: cache/cord-297625-eby014gm.json key: cord-297625-eby014gm authors: L'Huillier, A.G.; Tapparel, C.; Turin, L.; Boquete-Suter, P.; Thomas, Y.; Kaiser, L. title: Survival of rhinoviruses on human fingers date: 2014-12-11 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2014.12.002 sha: doc_id: 297625 cord_uid: eby014gm file: cache/cord-286544-ipmcqz8n.json key: cord-286544-ipmcqz8n authors: Cheng, Biao; Hu, Jiahao; Zuo, Xiuran; Chen, Jian; Li, Xiaochao; Chen, Yuchen; Yang, Guoliang; Shi, Xiaowu; Deng, Aiping title: Predictors of progression from moderate to severe COVID-19: a retrospective cohort date: 2020-07-02 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.06.033 sha: doc_id: 286544 cord_uid: ipmcqz8n file: cache/cord-252569-9rv1p3qh.json key: cord-252569-9rv1p3qh authors: Zanella, M.-C.; Lenggenhager, L.; Schrenzel, J.; Cordey, S.; Kaiser, L. title: High-throughput sequencing for the aetiologic identification of viral encephalitis, meningoencephalitis, and meningitis. A narrative review and clinical appraisal date: 2019-01-11 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2018.12.022 sha: doc_id: 252569 cord_uid: 9rv1p3qh file: cache/cord-009664-kb9fnbgy.json key: cord-009664-kb9fnbgy authors: nan title: Oral presentations date: 2014-12-24 journal: Clin Microbiol Infect DOI: 10.1111/j.1469-0691.2009.02857.x sha: doc_id: 9664 cord_uid: kb9fnbgy file: cache/cord-307273-pplky6g4.json key: cord-307273-pplky6g4 authors: Schrooyen, Loïc; Delforge, Marc; Lebout, Faustine; Vanbaelen, Thibaut; Lecompte, Amaryl; Dauby, Nicolas title: Homeless people hospitalized with COVID-19 in Brussels date: 2020-08-07 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.08.002 sha: doc_id: 307273 cord_uid: pplky6g4 file: cache/cord-295479-mcfqs7vf.json key: cord-295479-mcfqs7vf authors: Davido, Benjamin; Seang, Sophie; Tubiana, Roland; de Truchis, Pierre title: Post-COVID-19 chronic symptoms: a post-infectious entity?() date: 2020-07-23 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.07.028 sha: doc_id: 295479 cord_uid: mcfqs7vf file: cache/cord-317918-pl625ela.json key: cord-317918-pl625ela authors: Ripa, Marco; Galli, Laura; Poli, Andrea; Oltolini, Chiara; Spagnuolo, Vincenzo; Mastrangelo, Andrea; Muccini, Camilla; Monti, Giacomo; De Luca, Giacomo; Landoni, Giovanni; Dagna, Lorenzo; Clementi, Massimo; Querini, Patrizia Rovere; Ciceri, Fabio; Tresoldi, Moreno; Lazzarin, Adriano; Zangrillo, Alberto; Scarpellini, Paolo; Castagna, Antonella title: Secondary Infections in Patients Hospitalized with COVID-19: Incidence and Predictive Factors date: 2020-10-24 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.10.021 sha: doc_id: 317918 cord_uid: pl625ela file: cache/cord-324148-bllyruh8.json key: cord-324148-bllyruh8 authors: Loubet, Paul; Mathieu, Pauline; Lenzi, Nezha; Galtier, Florence; Lainé, Fabrice; Lesieur, Zineb; Vanhems, Philippe; Duval, Xavier; Postil, Deborah; Amour, Sélilah; Rogez, Sylvie; Lagathu, Gisèle; L'Honneur, Anne-Sophie; Foulongne, Vincent; Houhou, Nadhira; Lina, Bruno; Carrat, Fabrice; Launay, Odile title: Characteristics of human metapneumovirus infection in adults hospitalized for community-acquired influenza-like illness in France, 2012-2018: a retrospective observational study date: 2020-04-10 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.04.005 sha: doc_id: 324148 cord_uid: bllyruh8 file: cache/cord-333334-90q1xkld.json key: cord-333334-90q1xkld authors: Shengchen, D.; Gu, X.; Fan, G.; Sun, R.; Wang, Y.; Yu, D.; Li, H.; Zhou, F.; Xiong, Z.; Lu, B.; Zhu, G.; Cao, B. title: Evaluation of a molecular point-of-care testing for viral and atypical pathogens on intravenous antibiotic duration in hospitalized adults with lower respiratory tract infection: a randomized clinical trial date: 2019-06-20 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2019.06.012 sha: doc_id: 333334 cord_uid: 90q1xkld file: cache/cord-291272-srt08jh8.json key: cord-291272-srt08jh8 authors: Peters, E.J.G.; Collard, D.; Van Assen, S.; Beudel, M.; Bomers, M.K.; Buijs, J.; De Haan, L.R.; De Ruijter, W.; Douma, R.A.; Elbers, P.W.G.; Goorhuis, A.; Gritters van den Oever, N.C.; Knarren, G.H.H.; Moeniralam, H.S.; Mostard, R.L.M.; Quanjel, M.J.R.; Reidinga, A.C.; Renckens, R.; Van Den Bergh, prof, J.P.W.; Vlasveld, I.N.; Sikkens, J.J. title: Outcomes of persons with COVID-19 in hospitals with and without standard treatment with (Hydroxy)chloroquine date: 2020-10-14 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.10.004 sha: doc_id: 291272 cord_uid: srt08jh8 file: cache/cord-328499-d6cvaxm9.json key: cord-328499-d6cvaxm9 authors: Matzkies, Lucie-Marie; Leitner, Eva; Stelzl, Evelyn; Assig, Karoline; Bozic, Michael; Siebenhofer, David; Mustafa, Maria E.; Steinmetz, Ivo; Kessler, Harald H. title: Lack of sensitivity of an IVD/CE-labeled kit targeting the S gene for detection of SARS-CoV-2 date: 2020-07-08 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.06.036 sha: doc_id: 328499 cord_uid: d6cvaxm9 file: cache/cord-306083-juysx6yo.json key: cord-306083-juysx6yo authors: Choe, Young June; Park, Sangshin; Michelow, Ian C. title: Co-seasonality and co-detection of respiratory viruses and bacteraemia in children: a retrospective analysis date: 2020-09-10 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.09.006 sha: doc_id: 306083 cord_uid: juysx6yo file: cache/cord-329350-qrxl5o1e.json key: cord-329350-qrxl5o1e authors: Pan, Angelo; Matteo, Giorgi-Pierfranceschi; Giancarlo, Bosio; Lorenzo, Cammelli; Laura, Romanini title: Suggestions from Cremona, Italy - two months into the pandemic at the frontline of COVID-19 in Europe date: 2020-06-09 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.05.038 sha: doc_id: 329350 cord_uid: qrxl5o1e file: cache/cord-351028-p5cq2is5.json key: cord-351028-p5cq2is5 authors: Yang, Jia-Wei; Yang, Ling; Luo, Rong-Guang; Xu, Jin-Fu title: Corticosteroid administration for viral pneumonia: COVID-19 and beyond date: 2020-06-27 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.06.020 sha: doc_id: 351028 cord_uid: p5cq2is5 file: cache/cord-307213-i8yijbiu.json key: cord-307213-i8yijbiu authors: Ip, Jonathan Daniel; Kok, Kin-Hang; Chan, Wan-Mui; Wing-Ho Chu, Allen; Wu, Wai-Lan; Chik-Yan Yip, Cyril; To, Wing-Kin; Tak-Yin Tsang, Owen; Leung, Wai-Shing; Shiu-Hong Chik, Thomas; Chan, Kwok-Hung; Fan-Ngai Hung, Ivan; Yuen, Kwok-Yung; Kai-Wang To, Kelvin title: Intrahost non-synonymous diversity at a neutralising antibody epitope of SARS-CoV-2 spike protein N-terminal domain date: 2020-11-02 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.10.030 sha: doc_id: 307213 cord_uid: i8yijbiu file: cache/cord-300023-2dg7njki.json key: cord-300023-2dg7njki authors: Pillet, S.; Berthelot, P.; Gagneux-Brunon, A.; Mory, O.; Gay, C.; Viallon, A.; Lucht, F.; Pozzetto, B.; Botelho-Nevers, E. title: Contamination of healthcare workers' mobile phones by epidemic viruses() date: 2015-12-20 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2015.12.008 sha: doc_id: 300023 cord_uid: 2dg7njki file: cache/cord-326341-egtnqlov.json key: cord-326341-egtnqlov authors: Liotti, Flora Marzia; Menchinelli, Giulia; Lalle, Eleonora; Palucci, Ivana; Marchetti, Simona; Colavita, Francesca; La Sorda, Marilena; Sberna, Giuseppe; Bordi, Licia; Sanguinetti, Maurizio; Cattani, Paola; Capobianchi, Maria Rosaria; Posteraro, Brunella title: Performance of a novel diagnostic assay for rapid SARS-CoV-2 antigen detection in nasopharynx samples date: 2020-09-23 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.09.030 sha: doc_id: 326341 cord_uid: egtnqlov file: cache/cord-019490-m1cuuehi.json key: cord-019490-m1cuuehi authors: nan title: Abstracts cont. date: 2015-12-28 journal: Clin Microbiol Infect DOI: 10.1111/j.1469-0691.2005.clm_1134_02.x sha: doc_id: 19490 cord_uid: m1cuuehi file: cache/cord-344581-h7ikjgic.json key: cord-344581-h7ikjgic authors: Ong, David S.Y.; de Man, Stijn J.; Lindeboom, Fokke A.; Koeleman, Johannes G.M. title: Comparison of diagnostic accuracies of rapid serological tests and ELISA to molecular diagnostics in patients with suspected COVID-19 presenting to the hospital date: 2020-06-02 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.05.028 sha: doc_id: 344581 cord_uid: h7ikjgic file: cache/cord-325529-pid58g2r.json key: cord-325529-pid58g2r authors: Ben-Ami, Roni; Klochendler, Agnes; Seidel, Matan; Sido, Tal; Gurel-Gurevich, Ori; Yassour, Moran; Meshorer, Eran; Benedek, Gil; Fogel, Irit; Oiknine-Djian, Esther; Gertler, Asaf; Rotstein, Zeev; Lavi, Bruno; Dor, Yuval; Wolf, Dana G.; Salton, Maayan; Drier, Yotam title: Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection date: 2020-06-23 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.06.009 sha: doc_id: 325529 cord_uid: pid58g2r file: cache/cord-287256-hgqz1bcs.json key: cord-287256-hgqz1bcs authors: Magurano, Fabio; Baggieri, Melissa; Marchi, Antonella; Rezza, Giovanni; Nicoletti, Loredana title: SARS-CoV-2 infection: the environmental endurance of the virus can be influenced by the increase of temperature date: 2020-11-05 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.10.034 sha: doc_id: 287256 cord_uid: hgqz1bcs file: cache/cord-023592-w96h4rir.json key: cord-023592-w96h4rir authors: nan title: Abstracts cont. date: 2015-12-28 journal: Clin Microbiol Infect DOI: 10.1111/j.1469-0691.2004.0902c.x sha: doc_id: 23592 cord_uid: w96h4rir file: cache/cord-022501-9wnmdvg5.json key: cord-022501-9wnmdvg5 authors: nan title: P1460 – P1884 date: 2015-12-28 journal: Clin Microbiol Infect DOI: 10.1111/j.1470-9465.2006.12_4_1431.x sha: doc_id: 22501 cord_uid: 9wnmdvg5 Reading metadata file and updating bibliogrpahics === updating bibliographic database Building study carrel named journal-clinMicrobiolInfect-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: 1557 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: 1136 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: 1057 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: 98162 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: 98149 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: 2519 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: 1659 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: 1316 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: 97262 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: 97934 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: 1217 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: 2409 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: 1317 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: 2672 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: 792 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: 97882 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: 1593 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: 1551 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: 1270 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: 1176 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: 649 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: 2204 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: 1241 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: 2039 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: 2351 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: 1172 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: 1620 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: 2352 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: 3184 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: 2244 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: 97191 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: 2335 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: 97528 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: 98245 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: 1814 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: 97707 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: 2531 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: 97752 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: 2047 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: 3173 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: 2405 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: 1519 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: 650 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: 2057 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: 1555 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: 1642 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: 3684 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-031493-w8agvg9g author: Davido, Benjamin title: Possible therapies of Post-COVID-19 chronic symptoms() date: 2020-09-06 pages: extension: .txt txt: ./txt/cord-031493-w8agvg9g.txt cache: ./cache/cord-031493-w8agvg9g.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 1 resourceName b'cord-031493-w8agvg9g.txt' === file2bib.sh === id: cord-295479-mcfqs7vf author: Davido, Benjamin title: Post-COVID-19 chronic symptoms: a post-infectious entity?() date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-295479-mcfqs7vf.txt cache: ./cache/cord-295479-mcfqs7vf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-295479-mcfqs7vf.txt' === file2bib.sh === id: cord-307273-pplky6g4 author: Schrooyen, Loïc title: Homeless people hospitalized with COVID-19 in Brussels date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-307273-pplky6g4.txt cache: ./cache/cord-307273-pplky6g4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307273-pplky6g4.txt' === file2bib.sh === id: cord-275068-yr076sl6 author: Ayoub, Fares title: Football and COVID-19 risk: correlation is not causation date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-275068-yr076sl6.txt cache: ./cache/cord-275068-yr076sl6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-275068-yr076sl6.txt' === file2bib.sh === id: cord-288425-po35m6d9 author: Albert, Eliseo title: Field evaluation of a rapid antigen test (Panbio™ COVID-19 Ag Rapid Test Device) for COVID-19 diagnosis in primary healthcare centers date: 2020-11-13 pages: extension: .txt txt: ./txt/cord-288425-po35m6d9.txt cache: ./cache/cord-288425-po35m6d9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-288425-po35m6d9.txt' === file2bib.sh === id: cord-008258-5v55vv4s author: Raoult, D. title: Is it the end of the nervous breakdown on avian influenza? date: 2015-06-21 pages: extension: .txt txt: ./txt/cord-008258-5v55vv4s.txt cache: ./cache/cord-008258-5v55vv4s.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 1 resourceName b'cord-008258-5v55vv4s.txt' === file2bib.sh === id: cord-325186-nq6ay4eo author: Sieswerda, Elske title: Recommendations for antibacterial therapy in adults with COVID-19 – An evidence based guideline date: 2020-10-01 pages: extension: .txt txt: ./txt/cord-325186-nq6ay4eo.txt cache: ./cache/cord-325186-nq6ay4eo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-325186-nq6ay4eo.txt' === file2bib.sh === id: cord-304710-gjb6zo81 author: Khan, S. title: Novel coronavirus: how things are in Wuhan date: 2020-02-11 pages: extension: .txt txt: ./txt/cord-304710-gjb6zo81.txt cache: ./cache/cord-304710-gjb6zo81.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 11 resourceName b'cord-304710-gjb6zo81.txt' === file2bib.sh === id: cord-275556-798oed8n author: Piubelli, Chiara title: Overall decrease of SARS-CoV-2 viral load and reduction of clinical burden: the experience of a Northern Italy hospital date: 2020-10-12 pages: extension: .txt txt: ./txt/cord-275556-798oed8n.txt cache: ./cache/cord-275556-798oed8n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-275556-798oed8n.txt' === file2bib.sh === id: cord-344027-qghktrm1 author: Fiolet, Thibault title: 'Effect of hydroxychloroquine with or without azithromycin on the mortality of COVID-19 patients' – Author’s reply date: 2020-10-17 pages: extension: .txt txt: ./txt/cord-344027-qghktrm1.txt cache: ./cache/cord-344027-qghktrm1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-344027-qghktrm1.txt' === file2bib.sh === id: cord-326341-egtnqlov author: Liotti, Flora Marzia title: Performance of a novel diagnostic assay for rapid SARS-CoV-2 antigen detection in nasopharynx samples date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-326341-egtnqlov.txt cache: ./cache/cord-326341-egtnqlov.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-326341-egtnqlov.txt' === file2bib.sh === id: cord-283411-40ojqv1y author: Ben-Shmuel, Amir title: Detection and infectivity potential of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) environmental contamination in isolation units and quarantine facilities date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-283411-40ojqv1y.txt cache: ./cache/cord-283411-40ojqv1y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-283411-40ojqv1y.txt' === file2bib.sh === id: cord-306083-juysx6yo author: Choe, Young June title: Co-seasonality and co-detection of respiratory viruses and bacteraemia in children: a retrospective analysis date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-306083-juysx6yo.txt cache: ./cache/cord-306083-juysx6yo.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-306083-juysx6yo.txt' === file2bib.sh === id: cord-334835-j6u8t8j2 author: Berenguer, Juan title: Characteristics and predictors of death among 4,035 consecutively hospitalized patients with COVID-19 in Spain date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-334835-j6u8t8j2.txt cache: ./cache/cord-334835-j6u8t8j2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-334835-j6u8t8j2.txt' === file2bib.sh === id: cord-327253-gge6wzly author: Villa, Simone title: Stigma at the time of the COVID-19 pandemic date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-327253-gge6wzly.txt cache: ./cache/cord-327253-gge6wzly.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 1 resourceName b'cord-327253-gge6wzly.txt' === file2bib.sh === id: cord-298441-77w86l8q author: Lombardi, Andrea title: Characteristics of 1,573 healthcare workers who underwent nasopharyngeal swab for SARS-CoV-2 in Milano, Lombardy, Italy date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-298441-77w86l8q.txt cache: ./cache/cord-298441-77w86l8q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 32 resourceName b'cord-298441-77w86l8q.txt' === file2bib.sh === id: cord-300023-2dg7njki author: Pillet, S. title: Contamination of healthcare workers' mobile phones by epidemic viruses() date: 2015-12-20 pages: extension: .txt txt: ./txt/cord-300023-2dg7njki.txt cache: ./cache/cord-300023-2dg7njki.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300023-2dg7njki.txt' === file2bib.sh === id: cord-344581-h7ikjgic author: Ong, David S.Y. title: Comparison of diagnostic accuracies of rapid serological tests and ELISA to molecular diagnostics in patients with suspected COVID-19 presenting to the hospital date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-344581-h7ikjgic.txt cache: ./cache/cord-344581-h7ikjgic.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344581-h7ikjgic.txt' === file2bib.sh === id: cord-297625-eby014gm author: L'Huillier, A.G. title: Survival of rhinoviruses on human fingers date: 2014-12-11 pages: extension: .txt txt: ./txt/cord-297625-eby014gm.txt cache: ./cache/cord-297625-eby014gm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297625-eby014gm.txt' === file2bib.sh === id: cord-318021-4qrf5m8s author: Wolfensberger, A. title: Development and validation of a semi-automated surveillance system—lowering the fruit for non-ventilator-associated hospital-acquired pneumonia (nvHAP) prevention() date: 2019-03-25 pages: extension: .txt txt: ./txt/cord-318021-4qrf5m8s.txt cache: ./cache/cord-318021-4qrf5m8s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318021-4qrf5m8s.txt' === file2bib.sh === id: cord-314808-ssiggi2z author: Pappas, G. title: Psychosocial consequences of infectious diseases date: 2014-12-12 pages: extension: .txt txt: ./txt/cord-314808-ssiggi2z.txt cache: ./cache/cord-314808-ssiggi2z.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 23 resourceName b'cord-314808-ssiggi2z.txt' === file2bib.sh === id: cord-023592-w96h4rir author: nan title: Abstracts cont. date: 2015-12-28 pages: extension: .txt txt: ./txt/cord-023592-w96h4rir.txt cache: ./cache/cord-023592-w96h4rir.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-023592-w96h4rir.txt' === file2bib.sh === id: cord-009664-kb9fnbgy author: nan title: Oral presentations date: 2014-12-24 pages: extension: .txt txt: ./txt/cord-009664-kb9fnbgy.txt cache: ./cache/cord-009664-kb9fnbgy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-009664-kb9fnbgy.txt' === file2bib.sh === id: cord-019490-m1cuuehi author: nan title: Abstracts cont. date: 2015-12-28 pages: extension: .txt txt: ./txt/cord-019490-m1cuuehi.txt cache: ./cache/cord-019490-m1cuuehi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-019490-m1cuuehi.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 21 resourceName b'cord-022501-9wnmdvg5.txt' Que is empty; done journal-clinMicrobiolInfect-cord === reduce.pl bib === === reduce.pl bib === id = cord-008258-5v55vv4s author = Raoult, D. title = Is it the end of the nervous breakdown on avian influenza? date = 2015-06-21 pages = extension = .txt mime = text/plain words = 598 sentences = 34 flesch = 61 summary = The nervous breakdown on avian influenza that has affected the WHO, the different governments and the largest journals in the world may perhaps end with two articles published in the Journal of Infectious Diseases in May 2015 [1, 2] . This prospective survey in Egypt over 3 years on 1000 people showed that when H5N1 was endemic, 2% of the exposed population had antibodies compared with 0% of controls, and when the epidemic H9N2 appeared in poultry, seroprevalence increased from 0 to 5.6% and 7.5%, all asymptomatic infections. In total the zoonotic variant of H5N1 avian flu and H9N2 is very common in people in contact with poultry; it is banal and most of the time, asymptomatic. Avian influenza A(H5N1) and A(H9N2) seroprevalence and risk factors for infection among Egyptians: a prospective, controlled seroepidemiological study cache = ./cache/cord-008258-5v55vv4s.txt txt = ./txt/cord-008258-5v55vv4s.txt === reduce.pl bib === === reduce.pl bib === id = cord-275556-798oed8n author = Piubelli, Chiara title = Overall decrease of SARS-CoV-2 viral load and reduction of clinical burden: the experience of a Northern Italy hospital date = 2020-10-12 pages = extension = .txt mime = text/plain words = 610 sentences = 49 flesch = 59 summary = OBJECTIVES: In Italy the burden of patients with Coronavirus Disease 2019 (Covid-19) gradually decreased from March to the end of May. In this work, we aimed at evaluating a possible association between the severity of clinical manifestations and viral load over time, during the epidemiological transition from high to low transmission setting. CONCLUSIONS: We observed a reduction over time of the proportion of patients with Covid-19 requiring intensive care, along with decreasing median values of viral load. The proportion of patients requiring intensive care significantly reduced from 6.7% ( We observed a reduction over time of the proportion of patients with Covid-19 requiring intensive 46 care, along with decreasing median values of viral load. As the epidemiological context changes 47 from high to low transmission setting, people are presumably exposed to a lower viral load, which 48 has been previously associated to less severe clinical manifestations. cache = ./cache/cord-275556-798oed8n.txt txt = ./txt/cord-275556-798oed8n.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-327253-gge6wzly author = Villa, Simone title = Stigma at the time of the COVID-19 pandemic date = 2020-08-07 pages = extension = .txt mime = text/plain words = 1373 sentences = 86 flesch = 53 summary = 1 Beginning in late January 2020, when the COVID-19 epidemic was still largely limited to China, verbal and physical attacks against Chinese or people of Asian descent have been documented in many countries. 10 In contrary, uninfected COVID-19 people may be facing discrimination when applying for jobs in some countries that may implement COVID-19 passport strategies, despite recommendations of the World Health Organization against such a practice. This reactive behaviour facilitates spreading of infectious pathogens especially among those with mild symptoms who avoid seeking medical attention and act J o u r n a l P r e -p r o o f as usual not to raise suspicion on their condition. The world cannot bear a parallel pandemic of stigma, which only serves to boost the spread of infectious diseases and worsen people's health conditions and social behaviours. Noteworthy, individuals with COVID-19 may develop poor health-seeking behaviours (e.g. avoiding testing) because, by anticipating and fearing stigma, they may perceive the risk of losing their job and being marginalised in the society. cache = ./cache/cord-327253-gge6wzly.txt txt = ./txt/cord-327253-gge6wzly.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-298441-77w86l8q author = Lombardi, Andrea title = Characteristics of 1,573 healthcare workers who underwent nasopharyngeal swab for SARS-CoV-2 in Milano, Lombardy, Italy date = 2020-06-20 pages = extension = .txt mime = text/plain words = 1438 sentences = 67 flesch = 52 summary = To answer this question, we reviewed all the 59 nasopharyngeal swab performed in HCWs exposed to confirmed cases of COVID-19 at the 60 Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico located in Milan, the capital 61 of Lombardy, by large the Italian region mostly affected by We assessed 62 frequency of positive tests among symptomatic and asymptomatic HCWs and evaluated the 63 association between occupation, symptoms (type and number), and presence of the infection. Therefore, in middle-and high-resource settings a mass screening for all 163 HCWs exposed to confirmed COVID-19 cases appears the best approach to limit the spread When stratified according to occupation, test-positive frequencies were clearly higher among 177 subsets with direct contact with patients (physicians including residents, nurses and 178 midwives, healthcare assistants and health technicians) than those without (clerical works and 179 technicians). cache = ./cache/cord-298441-77w86l8q.txt txt = ./txt/cord-298441-77w86l8q.txt === reduce.pl bib === === reduce.pl bib === id = cord-288425-po35m6d9 author = Albert, Eliseo title = Field evaluation of a rapid antigen test (Panbio™ COVID-19 Ag Rapid Test Device) for COVID-19 diagnosis in primary healthcare centers date = 2020-11-13 pages = extension = .txt mime = text/plain words = 979 sentences = 71 flesch = 63 summary = We 25 evaluated the Panbio™ COVID-19 Ag Rapid Test Device for COVID-19 diagnosis in 26 symptomatic patients (n=412) attended in primary healthcare centers. Sensitivity of SARS-CoV-2 RAD 135 assays has been reported to vary between 45%-97% [3-7], yet direct comparison 136 between studies is hampered by marked dissimilarities in patient clinical characteristics 137 and age, testing sites, type of specimen processed, and time to testing, among others. In line with 146 previous reports [2-4], SARS-CoV-2 RNA load was significantly higher in RT-PCR+/ 147 RAD+ specimens than in RT-PCR+/ RAD-samples. In our setting, specimens with RT-148 PCR C T >25 (equivalent to SARS-CoV-2 RNA loads < 5.9 log 10 copies/ml) returned 149 discordant RAD/RT-PCR results. An important observation of our study was that SARS-CoV-2 could not be cultured 151 from RT-PCR+ (C T >25)/RAD-specimens. Antigen-based testing but not real-time PCR correlates with SARS-CoV-2 virus 198 culture Evaluation of 216 rapid antigen test for detection of SARS-CoV-2 virus cache = ./cache/cord-288425-po35m6d9.txt txt = ./txt/cord-288425-po35m6d9.txt === reduce.pl bib === id = cord-318021-4qrf5m8s author = Wolfensberger, A. title = Development and validation of a semi-automated surveillance system—lowering the fruit for non-ventilator-associated hospital-acquired pneumonia (nvHAP) prevention() date = 2019-03-25 pages = extension = .txt mime = text/plain words = 3611 sentences = 210 flesch = 43 summary = title: Development and validation of a semi-automated surveillance system—lowering the fruit for non-ventilator-associated hospital-acquired pneumonia (nvHAP) prevention() OBJECTIVES: Conducting manual surveillance of non-ventilator-associated hospital-acquired pneumonia (nvHAP) using ECDC (European Centre for Disease Prevention and Control) surveillance criteria is very resource intensive. Sensitivity, negative predictive value, and accuracy of semi-automated surveillance versus full manual surveillance were lowest in the validation sample consisting of patients with HAP according to the International Classification of Diseases (ICD-10) discharge diagnostic codes, with 97.5% (CI: 93.7–99.3%), 99.2% (CI: 97.9–99.8%), and 99.4% (CI: 98.4–99.8%), respectively. Three authors reported nvHAP incidence rates between 0.12 and 2.28 per 1000 patient days by applying the 2013 CDC surveillance definition to patients with International Classification of Diseases (ICD-9-CM) codes for pneumonia not present on admission [8e10] . cache = ./cache/cord-318021-4qrf5m8s.txt txt = ./txt/cord-318021-4qrf5m8s.txt === reduce.pl bib === id = cord-283411-40ojqv1y author = Ben-Shmuel, Amir title = Detection and infectivity potential of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) environmental contamination in isolation units and quarantine facilities date = 2020-09-10 pages = extension = .txt mime = text/plain words = 1174 sentences = 91 flesch = 56 summary = title: Detection and infectivity potential of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) environmental contamination in isolation units and quarantine facilities This study assessed the infectivity of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) contamination on surfaces and objects in hospital isolation units and a quarantine hotel. Surfaces and air sampling was conducted at two COVID-19 isolation units and in a quarantine hotel. Viral RNA detected in 29/55 (52.7%) and 16/42 (38%) surface samples from the surrounding of symptomatic COVID-19 patients in isolation units of two hospitals and in a quarantine hotel for asymptomatic and very mild COVID-19 patients. Surface Environmental, and 263 Personal Protective Equipment Contamination by Severe Acute Respiratory Syndrome Coronavirus 2 264 (SARS-CoV-2) From a Symptomatic Patient Detection of Severe Acute 268 Respiratory Syndrome Coronavirus 2 RNA on Surfaces in Quarantine Rooms. Severe acute respiratory 294 syndrome coronavirus 2 RNA contamination of inanimate surfaces and virus viability in a health care 295 emergency unit. cache = ./cache/cord-283411-40ojqv1y.txt txt = ./txt/cord-283411-40ojqv1y.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-334835-j6u8t8j2 author = Berenguer, Juan title = Characteristics and predictors of death among 4,035 consecutively hospitalized patients with COVID-19 in Spain date = 2020-08-04 pages = extension = .txt mime = text/plain words = 1739 sentences = 110 flesch = 54 summary = title: Characteristics and predictors of death among 4,035 consecutively hospitalized patients with COVID-19 in Spain OBJECTIVES: We aimed to analyse the characteristics and predictors of death in hospitalized patients with COVID-19 in Spain. Seventeen factors were independently associated with an increased hazard of death, the strongest among them included advanced age, liver cirrhosis, low age-adjusted oxygen saturation, higher concentrations of C-reactive protein, and lower estimated glomerular filtration rate. In the 209 final adjusted analysis, we found 17 factors independently associated with an increased hazard of 210 death: male sex, older age, arterial hypertension, obesity, liver cirrhosis, chronic neurological 211 disorder, active cancer, dementia, dyspnoea, confusion, low age-adjusted SaO2 on room air, higher 212 white cell blood count (WBC), higher neutrophil-to-lymphocyte ratio, lower platelet count, 213 prolonged INR, lower eGFR, and higher concentrations of CRP (Figure 2) . cache = ./cache/cord-334835-j6u8t8j2.txt txt = ./txt/cord-334835-j6u8t8j2.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-275068-yr076sl6 author = Ayoub, Fares title = Football and COVID-19 risk: correlation is not causation date = 2020-09-03 pages = extension = .txt mime = text/plain words = 446 sentences = 30 flesch = 56 summary = A recent 8 genome wide association analysis (GWAS) has implicated that blood group A patients had a higher risk 9 of severe COVID-19 compared to other blood types,[3] while other studies have found associations 10 between vitamin D levels/latitude, and Bacille de Calmette et Guérin (BCG) vaccine and mortality to 11 COVID-19. [4] Based on the results of these studies, shall we tell our blood group A patients to stay home 12 or tell everyone to take vitamin D or get vaccinated with BCG? [5] Low vitamin D levels have often been associated with a 16 higher risk of infections, but vitamin D supplementation has not been shown to prevent respiratory 17 1 impact journals during the pandemic, but it is important to remember that correlation does not equal 2 causation. cache = ./cache/cord-275068-yr076sl6.txt txt = ./txt/cord-275068-yr076sl6.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-314808-ssiggi2z author = Pappas, G. title = Psychosocial consequences of infectious diseases date = 2014-12-12 pages = extension = .txt mime = text/plain words = 3182 sentences = 137 flesch = 44 summary = On the other hand, numerous new major threats have emerged during the last three decades; the pandemic of AIDS, the SARS outbreak, the ominous scenarios of an avian influenza pandemic, and the threat of biological weapons are just some examples explaining the concern among health authorities, the media, and the public. The psychological response of both patients and the public to the threat of infection has been evaluated with respect to numerous circumstances in recent years, not only acute outbreaks such as SARS, but also gradually evolving pandemics such as AIDS, threats with marginal risk for humans such as bovine spongiform encephalopathy (BSE; mad cow disease), and even threats that are only theoretical such as avian influenza. Mass media is another major factor that shapes the physical and psychological response of the public to an infectious disease threat, as depicted in numerous attack scenarios in the literature [32] [33] [34] . cache = ./cache/cord-314808-ssiggi2z.txt txt = ./txt/cord-314808-ssiggi2z.txt === reduce.pl bib === id = cord-325186-nq6ay4eo author = Sieswerda, Elske title = Recommendations for antibacterial therapy in adults with COVID-19 – An evidence based guideline date = 2020-10-01 pages = extension = .txt mime = text/plain words = 855 sentences = 65 flesch = 37 summary = SCOPE: The Dutch Working Party on Antibiotic Policy constituted a multidisciplinary expert committee to provide evidence-based recommendation for the use of antibacterial therapy in hospitalized adults with a respiratory infection and suspected or proven 2019 Coronavirus disease (COVID-19). QUESTIONS ADDRESSED BY THE GUIDELINE AND RECOMMENDATIONS: We assessed evidence on the risk of bacterial infections in hospitalized COVID-19 patients, the associated bacterial pathogens, how to diagnose bacterial infections and how to treat bacterial infections. For patients with secondary bacterial respiratory infection we recommend to follow other guideline recommendations on antibacterial treatment for patients with hospital-acquired and ventilator-associated pneumonia. An antibiotic treatment duration of five days in patients with COVID-19 and suspected bacterial respiratory infection is recommended upon improvement of signs, symptoms and inflammatory markers. As COVID-19 patients frequently 72 need prolonged hospitalization and respiratory support, unnecessary antibiotics upon 73 hospitalization may increase the individual risk of subsequent hospital-acquired pneumonia 74 (HAP) and other adverse events [12, 13] . cache = ./cache/cord-325186-nq6ay4eo.txt txt = ./txt/cord-325186-nq6ay4eo.txt === reduce.pl bib === === reduce.pl bib === id = cord-344027-qghktrm1 author = Fiolet, Thibault title = 'Effect of hydroxychloroquine with or without azithromycin on the mortality of COVID-19 patients' – Author’s reply date = 2020-10-17 pages = extension = .txt mime = text/plain words = 329 sentences = 28 flesch = 45 summary = title: 'Effect of hydroxychloroquine with or without azithromycin on the mortality of COVID-19 patients' – Author's reply As with all studies at risk of critical bias included in our systematic review, it was excluded 50 from the main analysis. Treatment 154 with hydroxychloroquine, azithromycin, and combination in patients hospitalized with Clinical 158 Efficacy of Chloroquine derivatives in COVID-19 Infection: Comparative meta-analysis 159 between the Big data and the real world Hydroxychloroquine in Hospitalized Patients with COVID-19: Preliminary results from a 166 multi-centre, randomized, controlled trial COVID-19 177 prevention and treatment: A critical analysis of chloroquine and hydroxychloroquine 178 clinical pharmacology Interventions 188 for treatment of COVID-19: A living systematic review with meta-analyses and trial 189 sequential analyses (The LIVING Project) Mortality outcomes with hydroxychloroquine and chloroquine in COVID-19: an 193 international collaborative meta-analysis of randomized trials Hydroxychloroquine as pre-exposure prophylaxis for COVID-19 in healthcare workers: 203 a randomized trial cache = ./cache/cord-344027-qghktrm1.txt txt = ./txt/cord-344027-qghktrm1.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-304710-gjb6zo81 author = Khan, S. title = Novel coronavirus: how things are in Wuhan date = 2020-02-11 pages = extension = .txt mime = text/plain words = 1369 sentences = 78 flesch = 54 summary = There is a great risk of medical and clinical staff (and workers) becoming infected with 2019n-CoV because of their direct interaction with infected and suspected individuals. Working for long hours, disturbed daily routines including eating and sleeping schedules and fear of being infected are key factors that increase the risks of stress and anxiety for doctors and nurses, and may lead to their working less efficiently in terms of providing better treatment and care to patients. However, the increasing number of patients every day and the expected peak in the coming days [6] may cause a further shortage of medical staff and health and logistic issues for the frontline healthcare provider. China coronavirus: Wuhan medical staff being infected at much faster pace than reported as national death toll hits 26 Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China cache = ./cache/cord-304710-gjb6zo81.txt txt = ./txt/cord-304710-gjb6zo81.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-297625-eby014gm author = L'Huillier, A.G. title = Survival of rhinoviruses on human fingers date = 2014-12-11 pages = extension = .txt mime = text/plain words = 2635 sentences = 139 flesch = 49 summary = Our study confirms that rhinovirus infectiousness is related to the viral concentration in droplets and suggests that children represent the main transmission source, which occurs only rarely via adults. We conducted a series of experiments to assess the duration of human rhinovirus infectiousness duration on fingers, as well as the impact of viral concentration on survival rates. One hour after the deposit of disrupted droplets on the fingers of the six volunteers, infectious viruses could be detected by culture in all subjects contaminated with HC droplets (6/6), in four of the six volunteers with AC droplets, and none of the six volunteers with LC droplets, which confirmed the influence of concentration on survival (Fig. 1) . Our study showed that virus survival, and therefore infectiousness, was related to the viral concentration in droplets. Potential role of hands in the spread of respiratory viral infections: studies with human parainfluenza virus 3 and rhinovirus 14 cache = ./cache/cord-297625-eby014gm.txt txt = ./txt/cord-297625-eby014gm.txt === reduce.pl bib === === reduce.pl bib === id = cord-306083-juysx6yo author = Choe, Young June title = Co-seasonality and co-detection of respiratory viruses and bacteraemia in children: a retrospective analysis date = 2020-09-10 pages = extension = .txt mime = text/plain words = 1746 sentences = 108 flesch = 44 summary = OBJECTIVES: The aim of this study was to assess the co-seasonality and co-detection of respiratory viral infections and bacteraemia in children since the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13). Analysis of linked viral-bacterial infections in individual children indicated that the rate ratio (RR) of bacteraemia associated with hMPV (RR=2.73, 95% CI 1.12-6.85, P=0.019) and influenza (RR=2.61, 95% CI 1.21-6.11, P=0.013) were more than double that of RSV. CONCLUSIONS: There is a significant association between hMPV and influenza viruses, and bacteraemia of all causes in hospitalised children at a single paediatric centre in the United States. A study conducted in children before the 9 implementation of PCV13, demonstrated significant associations between invasive 10 pneumococcal disease (IPD) and influenza viruses and respiratory syncytial virus (RSV), as well 11 as human metapneumovirus (hMPV), which was a novel observation [5] . cache = ./cache/cord-306083-juysx6yo.txt txt = ./txt/cord-306083-juysx6yo.txt === reduce.pl bib === === reduce.pl bib === id = cord-295479-mcfqs7vf author = Davido, Benjamin title = Post-COVID-19 chronic symptoms: a post-infectious entity?() date = 2020-07-23 pages = extension = .txt mime = text/plain words = 195 sentences = 24 flesch = 50 summary = key: cord-295479-mcfqs7vf authors: Davido, Benjamin; Seang, Sophie; Tubiana, Roland; de Truchis, Pierre title: Post-COVID-19 chronic symptoms: a post-infectious entity?() date: 2020-07-23 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.07.028 sha: doc_id: 295479 cord_uid: mcfqs7vf nan COVID-19 : point épidémiologique du 21 mai Assistance Publique-Hôpitaux de Paris' response to the COVID-19 88 pandemic Anosmia and Ageusia: Common Findings 90 in COVID-19 Patients Patients Recovered from COVID-19 Active Epstein-Barr virus infection in 95 post-viral fatigue syndrome serological IgG antibody response on the Abbott Architect for established SARS-CoV-99 2 infection Neurologic manifestations in hospitalized patients 102 with COVID-19: The ALBACOVID registry Cerebrovascular disease in patients with COVID-19: 106 neuroimaging, histological and clinical description Kawasaki-like multisystem inflammatory syndrome in children during the covid-19 Chikungunya-Induced Arthritis in Reunion Island: A 113 Long-Term Observational Follow-Up Study Showing Frequently Persistent Joint 114 Some Cases of Persistent Chikungunya Immunoglobulin M Positivity, and 115 No Anticyclic Citrullinated Peptide Seroconversi cache = ./cache/cord-295479-mcfqs7vf.txt txt = ./txt/cord-295479-mcfqs7vf.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-031493-w8agvg9g author = Davido, Benjamin title = Possible therapies of Post-COVID-19 chronic symptoms() date = 2020-09-06 pages = extension = .txt mime = text/plain words = 153 sentences = 17 flesch = 59 summary = key: cord-031493-w8agvg9g authors: Davido, Benjamin; Seang, Sophie; Barizien, Nicolas; Tubiana, Roland; de Truchis, Pierre title: Possible therapies of Post-COVID-19 chronic symptoms() date: 2020-09-06 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.09.001 sha: doc_id: 31493 cord_uid: w8agvg9g nan responsible for dysautonomia in patients with persistent symptoms following acute SARS-23 COV2 infection. Physicians must keep in mind that COVID-19 is not only a disease 24 responsible for lung injury and its sequel but may affect other organs as olfactory and 25 gustatory dysfunction and as such, should inform the general audience, especially young 26 individuals that are the most concerned [2] . Actually, we did not state that these symptoms of autonomic impairment do not require 28 specific treatment, but we believe it must be a case by case management depending on the breathing/hyperventilation syndrome in adults Efficacy of 68 Therapies for Postural Tachycardia Syndrome: A Systematic Review and Meta-69 analysis cache = ./cache/cord-031493-w8agvg9g.txt txt = ./txt/cord-031493-w8agvg9g.txt === reduce.pl bib === id = cord-307273-pplky6g4 author = Schrooyen, Loïc title = Homeless people hospitalized with COVID-19 in Brussels date = 2020-08-07 pages = extension = .txt mime = text/plain words = 1006 sentences = 63 flesch = 45 summary = To the editor, Compared to the general population, homeless people have higher mortality, both related to communicable and non-communicable diseases, partly explained by higher exposure to risk factors including alcoholism, illicit drug abuse and smoking(1,2). Between 3 rd March and 26 th May 2020, 14 homeless people were identified among 238 patients hospitalized for a COVID-19 pneumonia resulting in a homelessness prevalence of 5.88%. Incidences of COVID-19 among homeless and non-homeless patients were calculated using homeless census report and our hospital catchment population. For the reporting period, incidences were 650 and 194/100.000 hospitalized homeless and non-homeless patients for COVID-19, respectively. We found a high but similar proportion of comorbidities (arterial hypertension, diabetes and cardiovascular diseases) in both populations hospitalized with COVID-19. The high prevalence of comorbidities and the increased exposure to risk factors in the homeless population could increase their risk of more severe disease and mortality following SARS-CoV-2 infection. cache = ./cache/cord-307273-pplky6g4.txt txt = ./txt/cord-307273-pplky6g4.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-326341-egtnqlov author = Liotti, Flora Marzia title = Performance of a novel diagnostic assay for rapid SARS-CoV-2 antigen detection in nasopharynx samples date = 2020-09-23 pages = extension = .txt mime = text/plain words = 514 sentences = 35 flesch = 60 summary = title: Performance of a novel diagnostic assay for rapid SARS-CoV-2 antigen detection in nasopharynx samples Conversely, rapid antigen detection assays-intrinsically less laborious and requiring few minutes 29 to results-have the potential to satisfy the pressing demand for an early SARS-CoV-2 infection 30 Suwon, South Korea) assay, a fluorescent immunoassay detecting SARS-CoV-2 nucleoprotein 33 antigen, on nasopharynx swab samples. The LOD was 5 × 10 2 41 TCID 50 /mL (2 × 10 6 RNA copies/mL) at 95% detection probability ( Supplementary Fig. S1 Our study shows that the STANDARD F COVID-19 Ag FIA assay had a good specificity for 65 SARS-CoV-2 detection in nasopharynx swab samples but had a good sensitivity only for samples 66 Evaluation of a rapid diagnostic assay for detection of SARS-CoV-102 2 antigen in nasopharyngeal swabs Evaluation of rapid 104 antigen test for detection of SARS-CoV-2 virus cache = ./cache/cord-326341-egtnqlov.txt txt = ./txt/cord-326341-egtnqlov.txt === reduce.pl bib === id = cord-009664-kb9fnbgy author = nan title = Oral presentations date = 2014-12-24 pages = extension = .txt mime = text/plain words = 71112 sentences = 3948 flesch = 47 summary = Because of the conflicting reports and lack of published data from paediatric patients, we sought to assess possible MIC change over time and to compare results generated by using different methodologies including Etest, agar dilution, and broth microdilution (MicroScan) methods. Recently, in vitro and in vivo studies have shown that NO plays a key role in the eradication of the leishmania parasite Objective: To determine whether a NO donor patch (developed by electrospinning technique) is as effective as meglumine antimoniate in the treatment of CL while causing less adverse events Methods: A double-blind, randomised, placebo-controlled clinical trial was conducted with 178 patients diagnosed with CL in Santander, Colombia, South-America. To follow the development and spread of the resistance among these strains is difficult, as antibiotic susceptibility testing of clinically relevant anaerobes in different routine laboratories in Europe is less and less frequently carried out due to the fact, that clinicians treat many presumed anaerobic infections empirically. cache = ./cache/cord-009664-kb9fnbgy.txt txt = ./txt/cord-009664-kb9fnbgy.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-300023-2dg7njki author = Pillet, S. title = Contamination of healthcare workers' mobile phones by epidemic viruses() date = 2015-12-20 pages = extension = .txt mime = text/plain words = 3087 sentences = 157 flesch = 51 summary = We aimed to evaluate the presence of virus RNA from epidemic viruses including metapneumovirus, respiratory syncytial virus, influenza viruses, rotavirus (RV) and norovirus on the MPs used by healthcare workers (HCWs) and to relate it to hygiene measures. The aims of this study were (a) to evaluate the contamination of MPs by epidemic viruses including RV, NV, influenza A and B viruses, syncytial respiratory virus (RSV) and metapneumovirus (hMPV) in clinical settings, (b) to evaluate the behaviour of HCWs using their MPs in our center by using a blindly recorded questionnaire and (c) to correlate viral contamination of MPs with the behaviour of HCWs. The study took place at the University Hospital of Saint-Étienne, France, from January to March 2013, i.e. the period of circulation of epidemic viruses (influenza viruses, RSV, gastroenteritis-associated viruses) in our setting [22] (personal data). cache = ./cache/cord-300023-2dg7njki.txt txt = ./txt/cord-300023-2dg7njki.txt === reduce.pl bib === id = cord-019490-m1cuuehi author = nan title = Abstracts cont. date = 2015-12-28 pages = extension = .txt mime = text/plain words = 93588 sentences = 5683 flesch = 50 summary = Tigecycline Evaluation Surveillance Trial (TEST) -Global in vitro antibacterial activity against selected species of glucose non-fermenting organisms Objective: Despite the introduction of new antimicrobials to treat resistant gram-positive bacteria, Staphylococcus aureus continues to be a therapeutic challenge for the clinician. Two prospective studies from our centre identified common causes of CAP in India to be Mycoplasma pneumoniae [MP] and Legionella pneumophila [LP] by serology in 11% each, and SPN in 10% by culture of respiratory secretions/blood/ Conclusion: Although SPN is the most common isolate, the rising numbers of gram negative organisms (38%) and atypical pathogens associated with increasing mortality stress the need for review of initial antibiotic choice for adults with higher PORT classes. Conclusion: The spectrum of isolates among our patients were shifting towards gram positive bacteria with high resistance to different groups of antimicrobial agents limiting few choices for alternative therapies for infection control. cache = ./cache/cord-019490-m1cuuehi.txt txt = ./txt/cord-019490-m1cuuehi.txt === reduce.pl bib === id = cord-344581-h7ikjgic author = Ong, David S.Y. title = Comparison of diagnostic accuracies of rapid serological tests and ELISA to molecular diagnostics in patients with suspected COVID-19 presenting to the hospital date = 2020-06-02 pages = extension = .txt mime = text/plain words = 2071 sentences = 120 flesch = 54 summary = OBJECTIVES: To assess the diagnostic performance of rapid lateral flow immunochromatographic assays (LFAs) compared to an enzyme-linked immunosorbent assay (ELISA) and nucleic acid amplification tests (NATs) in suspected coronavirus disease 2019 (COVID-19) patients. In the total cohort, Orient Gene Biotech COVID-19 IgG/IgM Rapid Test LFA had a sensitivity of 43/99 (43%; 95% CI 34-53) and specificity of 126/129 (98%; 95% CI 95-100). CONCLUSIONS: There is large variability in diagnostic test performance between rapid LFAs, but overall limited sensitivity and high specificity in acutely admitted patients. First, in a pilot phase 20 NAT-positive and 5 NAT-negative patients were retrospectively selected for which six LFAs were performed on heparin plasma samples obtained upon hospital presentation ( Figure S1 ), which corresponded to the dates of molecular testing. This study shows that the sensitivity of LFA was low in patients suspected for COVID-19 presenting to the hospital, but it improved in patients with at least seven days of symptoms and in those with CRP levels >100 mg/L upon presentation. cache = ./cache/cord-344581-h7ikjgic.txt txt = ./txt/cord-344581-h7ikjgic.txt === reduce.pl bib === id = cord-023592-w96h4rir author = nan title = Abstracts cont. date = 2015-12-28 pages = extension = .txt mime = text/plain words = 67857 sentences = 4136 flesch = 52 summary = Conclusions: Although the risk of developing more serious gastric lesions increased as the number of virulence factor genes are accumulated in a given Hp strain, we did not find any significant differences or relationship in the cagA, vacA or babA2 status between the Hp isolates from patients with gastritis or peptic ulcer in this study. pneumophila at the serogroup level, it was used in two different outbreaks to demonstrate rapidly the identity of the sequences between strains responsible for severe human infection and those isolated in the hot water reservoir, suggesting a common origin. To determine the antimicrobial resistance in Salmonella and Shigella strains isolated from stool specimens during a 2-year period, from patients admitted to our clinics with a diagnosis of diarrhoea. In our study the susceptibility of 65 bacterial strains isolated in hospital environment (colonising or infecting patients or carried by German cockroaches) to antibiotics and chemical disinfectants was determined. cache = ./cache/cord-023592-w96h4rir.txt txt = ./txt/cord-023592-w96h4rir.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 === === reduce.pl bib === === reduce.pl bib === ===== Reducing email addresses Creating transaction Updating adr table ===== Reducing keywords cord-265363-xw56intn cord-008258-5v55vv4s cord-009675-utz0iazs cord-275556-798oed8n cord-322585-5gio6ruj cord-327253-gge6wzly cord-270947-6e5cw2q9 cord-256853-2s31fn04 cord-292296-nocmabcg cord-009295-4c0zwhdh cord-010162-hfo35gsq cord-032016-2rzszcke cord-257248-aii0tj9x cord-254278-awdqguoo cord-279111-jaa45kyc cord-256402-b5fel2d3 cord-257696-ybu772zw cord-275068-yr076sl6 cord-297470-lx3xwg92 cord-298441-77w86l8q cord-030061-55ntc4wj cord-314288-6vh7dvad cord-331002-7uojryqz cord-288425-po35m6d9 cord-269345-5tlyy8jp cord-314808-ssiggi2z cord-253250-zet48zcl cord-334835-j6u8t8j2 cord-286525-0354438s cord-291729-4l4v9jxd cord-283411-40ojqv1y cord-279125-w6sh7xpn cord-264261-98h1bmb2 cord-256429-ntx0eay0 cord-318021-4qrf5m8s cord-325186-nq6ay4eo cord-344027-qghktrm1 cord-278807-p1crrb8n cord-294546-0otd1heg cord-276212-ys5njiw0 cord-343090-dsjq98ks cord-294392-a8s66g96 cord-326703-akn92p1r cord-304710-gjb6zo81 cord-283818-4m9p717r cord-031493-w8agvg9g cord-297625-eby014gm cord-252569-9rv1p3qh cord-009664-kb9fnbgy cord-286544-ipmcqz8n cord-307273-pplky6g4 cord-317918-pl625ela cord-276399-omjfyog0 cord-295479-mcfqs7vf cord-306083-juysx6yo cord-328499-d6cvaxm9 cord-325529-pid58g2r cord-287256-hgqz1bcs cord-333334-90q1xkld cord-293542-o0zspgrk cord-307213-i8yijbiu cord-291272-srt08jh8 cord-329350-qrxl5o1e cord-255971-kamai25b cord-300023-2dg7njki cord-351028-p5cq2is5 cord-019490-m1cuuehi cord-326341-egtnqlov cord-023592-w96h4rir cord-344581-h7ikjgic cord-022501-9wnmdvg5 cord-324148-bllyruh8 Creating transaction Updating wrd table ===== Reducing urls cord-009675-utz0iazs cord-270947-6e5cw2q9 cord-257248-aii0tj9x cord-279111-jaa45kyc cord-333334-90q1xkld cord-009664-kb9fnbgy cord-022501-9wnmdvg5 cord-283818-4m9p717r cord-294546-0otd1heg cord-300023-2dg7njki cord-291729-4l4v9jxd cord-276399-omjfyog0 cord-019490-m1cuuehi cord-318021-4qrf5m8s cord-325529-pid58g2r Creating transaction Updating url table ===== Reducing named entities cord-265363-xw56intn cord-008258-5v55vv4s cord-009295-4c0zwhdh cord-275556-798oed8n cord-009675-utz0iazs cord-288425-po35m6d9 cord-010162-hfo35gsq cord-254278-awdqguoo cord-297470-lx3xwg92 cord-298441-77w86l8q cord-314808-ssiggi2z cord-322585-5gio6ruj cord-292296-nocmabcg cord-032016-2rzszcke cord-327253-gge6wzly cord-256853-2s31fn04 cord-030061-55ntc4wj cord-269345-5tlyy8jp cord-270947-6e5cw2q9 cord-286525-0354438s cord-331002-7uojryqz cord-325186-nq6ay4eo cord-256429-ntx0eay0 cord-253250-zet48zcl cord-279111-jaa45kyc cord-257696-ybu772zw cord-257248-aii0tj9x cord-314288-6vh7dvad cord-256402-b5fel2d3 cord-334835-j6u8t8j2 cord-275068-yr076sl6 cord-255971-kamai25b cord-291729-4l4v9jxd cord-264261-98h1bmb2 cord-283411-40ojqv1y cord-318021-4qrf5m8s cord-279125-w6sh7xpn cord-278807-p1crrb8n cord-294546-0otd1heg cord-343090-dsjq98ks cord-276399-omjfyog0 cord-283818-4m9p717r cord-344027-qghktrm1 cord-276212-ys5njiw0 cord-326703-akn92p1r cord-293542-o0zspgrk cord-294392-a8s66g96 cord-031493-w8agvg9g cord-286544-ipmcqz8n cord-307273-pplky6g4 cord-317918-pl625ela cord-295479-mcfqs7vf cord-328499-d6cvaxm9 cord-304710-gjb6zo81 cord-291272-srt08jh8 cord-297625-eby014gm cord-324148-bllyruh8 cord-252569-9rv1p3qh cord-306083-juysx6yo cord-333334-90q1xkld cord-329350-qrxl5o1e cord-326341-egtnqlov cord-351028-p5cq2is5 cord-300023-2dg7njki cord-325529-pid58g2r cord-307213-i8yijbiu cord-009664-kb9fnbgy cord-344581-h7ikjgic cord-287256-hgqz1bcs cord-023592-w96h4rir cord-019490-m1cuuehi cord-022501-9wnmdvg5 Creating transaction Updating ent table ===== Reducing parts of speech cord-009675-utz0iazs cord-009295-4c0zwhdh cord-008258-5v55vv4s cord-265363-xw56intn cord-288425-po35m6d9 cord-032016-2rzszcke cord-292296-nocmabcg cord-275556-798oed8n cord-255971-kamai25b cord-279111-jaa45kyc cord-010162-hfo35gsq cord-297470-lx3xwg92 cord-254278-awdqguoo cord-256402-b5fel2d3 cord-275068-yr076sl6 cord-257696-ybu772zw cord-322585-5gio6ruj cord-256853-2s31fn04 cord-257248-aii0tj9x cord-298441-77w86l8q cord-314808-ssiggi2z cord-030061-55ntc4wj cord-269345-5tlyy8jp cord-253250-zet48zcl cord-327253-gge6wzly cord-286525-0354438s cord-270947-6e5cw2q9 cord-331002-7uojryqz cord-334835-j6u8t8j2 cord-314288-6vh7dvad cord-325186-nq6ay4eo cord-291729-4l4v9jxd cord-279125-w6sh7xpn cord-294546-0otd1heg cord-318021-4qrf5m8s cord-276212-ys5njiw0 cord-304710-gjb6zo81 cord-286544-ipmcqz8n cord-297625-eby014gm cord-317918-pl625ela cord-328499-d6cvaxm9 cord-324148-bllyruh8 cord-333334-90q1xkld cord-307213-i8yijbiu cord-326341-egtnqlov cord-300023-2dg7njki cord-291272-srt08jh8 cord-344581-h7ikjgic cord-325529-pid58g2r cord-307273-pplky6g4 cord-287256-hgqz1bcs cord-306083-juysx6yo cord-343090-dsjq98ks cord-031493-w8agvg9g cord-294392-a8s66g96 cord-295479-mcfqs7vf cord-326703-akn92p1r cord-344027-qghktrm1 cord-283818-4m9p717r cord-351028-p5cq2is5 cord-329350-qrxl5o1e cord-252569-9rv1p3qh cord-278807-p1crrb8n cord-276399-omjfyog0 cord-256429-ntx0eay0 cord-283411-40ojqv1y cord-264261-98h1bmb2 cord-293542-o0zspgrk cord-023592-w96h4rir cord-009664-kb9fnbgy cord-019490-m1cuuehi cord-022501-9wnmdvg5 Creating transaction Updating pos table Building ./etc/reader.txt cord-019490-m1cuuehi cord-022501-9wnmdvg5 cord-009664-kb9fnbgy cord-022501-9wnmdvg5 cord-019490-m1cuuehi cord-009664-kb9fnbgy number of items: 72 sum of words: 389,923 average size in words: 15,596 average readability score: 51 nouns: patients; strains; results; isolates; study; resistance; methods; infection; infections; treatment; samples; cases; data; analysis; group; hospital; days; aureus; gene; virus; disease; time; detection; years; genes; test; studies; susceptibility; use; activity; therapy; conclusion; antibiotics; blood; conclusions; objectives; risk; pneumoniae; method; species; bacteria; pathogens; type; age; viruses; influenza; pneumonia; patient; control; prevalence verbs: used; shows; included; detect; found; isolate; determined; performs; identifying; associated; compared; tested; increase; reported; followed; based; evaluated; caused; obtained; treated; collect; observed; according; suggesting; received; confirmed; acquire; studied; related; considered; developed; present; assess; described; analysed; infect; produced; reduce; investigate; carrying; remaining; provides; taken; occur; given; required; knows; demonstrated; indicate; selected adjectives: clinical; positive; respiratory; resistant; different; high; antibiotic; negative; bacterial; non; viral; antimicrobial; significant; human; common; specific; first; new; acute; severe; higher; susceptible; low; molecular; diagnostic; important; similar; rapid; present; infectious; single; several; medical; available; mean; lower; major; primary; possible; effective; many; total; oral; real; novel; patient; nosocomial; overall; invasive; potential adverbs: also; respectively; well; however; significantly; frequently; especially; therefore; often; previously; commonly; recently; even; highly; still; mainly; clinically; least; rapidly; less; currently; particularly; furthermore; alone; statistically; approximately; relatively; now; moreover; usually; probably; together; finally; worldwide; prior; directly; almost; mostly; overall; regardless; potentially; first; widely; generally; critically; far; already; subsequently; much; later pronouns: we; our; it; their; they; its; them; i; he; she; his; her; us; one; you; itself; themselves; my; mg; fusb; yourself; thereof; rhli; ours; me; lmb415; kaz)objectives; himself; him; fusr; exou; ermb; arda proper nouns: S.; PCR; mg; C.; MRSA; E.; SARS; L; MIC; CoV-2; COVID-19; P.; Staphylococcus; B.; M.; RT; A.; PFGE; K.; ICU; RNA; L.; H.; ESBL; C; B; IV; NCCLS; A; imipenem; CI; S; GRN; Objectives; M; lg; MIC90; Europe; R.; CFU; CSF; II; linezolid; Enterobacteriaceae; Table; Candida; ELISA; N.; USA; RSV keywords: sars; covid-19; patient; pcr; infection; study; strain; result; mrsa; method; isolate; gram; esbl; rna; resistance; pfge; objective; mic; dna; wuhan; virus; test; staphylococcus; rsv; nccls; lrti; icu; grn; europe; elisa; disease; china; cfu; candida; transmission; tgc; table; surveillance; srf; saudi; sample; salmonella; rvi; respiratory; pvl; public; prodesse; poc; pneumoniae; pneumonia one topic; one dimension: patients file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7162335/ titles(s): Are point‐of‐care (POC) virological tests what is needed? three topics; one dimension: patients; patients; covid file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7157935/, https://www.sciencedirect.com/science/article/pii/S1198743X18308127, https://api.elsevier.com/content/article/pii/S1198743X14604614 titles(s): P1460 – P1884 | High-throughput sequencing for the aetiologic identification of viral encephalitis, meningoencephalitis, and meningitis. A narrative review and clinical appraisal | Psychosocial consequences of infectious diseases five topics; three dimensions: patients strains isolates; strains isolates results; patients respiratory study; patients respiratory covid; public diseases health file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7157935/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172567/, https://doi.org/10.1016/j.cmi.2019.06.012, https://www.sciencedirect.com/science/article/pii/S1198743X18308127, https://api.elsevier.com/content/article/pii/S1198743X14604614 titles(s): P1460 – P1884 | Abstracts cont. | Evaluation of a molecular point-of-care testing for viral and atypical pathogens on intravenous antibiotic duration in hospitalized adults with lower respiratory tract infection: a randomized clinical trial | High-throughput sequencing for the aetiologic identification of viral encephalitis, meningoencephalitis, and meningitis. A narrative review and clinical appraisal | Psychosocial consequences of infectious diseases Type: cord title: journal-clinMicrobiolInfect-cord date: 2021-05-30 time: 15:05 username: emorgan patron: Eric Morgan email: emorgan@nd.edu input: facet_journal:"Clin Microbiol Infect" ==== make-pages.sh htm files ==== make-pages.sh complex files ==== make-pages.sh named enities ==== making bibliographics id: cord-288425-po35m6d9 author: Albert, Eliseo title: Field evaluation of a rapid antigen test (Panbio™ COVID-19 Ag Rapid Test Device) for COVID-19 diagnosis in primary healthcare centers date: 2020-11-13 words: 979.0 sentences: 71.0 pages: flesch: 63.0 cache: ./cache/cord-288425-po35m6d9.txt txt: ./txt/cord-288425-po35m6d9.txt summary: We 25 evaluated the Panbio™ COVID-19 Ag Rapid Test Device for COVID-19 diagnosis in 26 symptomatic patients (n=412) attended in primary healthcare centers. Sensitivity of SARS-CoV-2 RAD 135 assays has been reported to vary between 45%-97% [3-7], yet direct comparison 136 between studies is hampered by marked dissimilarities in patient clinical characteristics 137 and age, testing sites, type of specimen processed, and time to testing, among others. In line with 146 previous reports [2-4], SARS-CoV-2 RNA load was significantly higher in RT-PCR+/ 147 RAD+ specimens than in RT-PCR+/ RAD-samples. In our setting, specimens with RT-148 PCR C T >25 (equivalent to SARS-CoV-2 RNA loads < 5.9 log 10 copies/ml) returned 149 discordant RAD/RT-PCR results. An important observation of our study was that SARS-CoV-2 could not be cultured 151 from RT-PCR+ (C T >25)/RAD-specimens. Antigen-based testing but not real-time PCR correlates with SARS-CoV-2 virus 198 culture Evaluation of 216 rapid antigen test for detection of SARS-CoV-2 virus abstract: OBJECTIVES: To our knowledge no previous study has assessed the performance of a rapid antigen diagnostic immunoassay (RAD) conducted at the point of care (POC). We evaluated the Panbio™ COVID-19 Ag Rapid Test Device for COVID-19 diagnosis in symptomatic patients (n=412) attended in primary healthcare centers. METHODS: RAD was performed immediately after sampling following the manufacturer’s instructions (reading at 15 min.). RT-PCRs were carried out within 24 h. of specimen collection. Samples displaying discordant results were processed for culture in Vero E6 cells. Presence of SARS-CoV-2 in cell cultures was confirmed by RT-PCR. RESULTS: Out of 412 patients, 43 (10.4%) tested positive by RT-PCR and RAD and 358 (86.9%) negative by both methods, showing discordant results (RT-PCR+/RAD-) in 11 patients (2.7%). Overall specificity and sensitivity of rapid antigen detection (RAD) was 100% (95% CI, 98.7-100%), and 79.6% (95% CI, 67.-88.8%), respectively, taking RT-PCR as the reference. Overall RAD negative predictive value for an estimated prevalence of 5% and 10% was 99% (95% CI, 97.4-99.6%) and 97.9% (95% CI, 95.9-98.9), respectively. SARS-CoV-2 could not be cultured from specimens yielding RT-PCR+/RAD-results (n=11). CONCLUSION: The Panbio™ COVID-19 Ag Rapid Test Device performed well as a POCT for early diagnosis of COVID-19 in primary healthcare centers. More crucially, the data suggested that patients with RT-PCR-proven COVID-19 testing negative by RAD are unlikely to be infectious. url: https://www.sciencedirect.com/science/article/pii/S1198743X20306972?v=s5 doi: 10.1016/j.cmi.2020.11.004 id: cord-278807-p1crrb8n author: Antón, A. title: Virological surveillance of influenza and other respiratory viruses during six consecutive seasons from 2006 to 2012 in Catalonia, Spain date: 2016-03-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Most attention is given to seasonal influenza and respiratory syncytial virus outbreaks, but the cumulative burden caused by other respiratory viruses (RV) is not widely considered. The aim of the present study is to describe the circulation of RV in the general population during six consecutive seasons from 2006 to 2012 in Catalonia, Spain. Cell culture, immunofluorescence and PCR-based assays were used for the RV laboratory-confirmation and influenza subtyping. Phylogenetic and molecular characterizations of viral haemagglutinin, partial neuraminidase and matrix 2 proteins were performed from a representative sampling of influenza viruses. A total of 6315 nasopharyngeal samples were collected, of which 64% were laboratory-confirmed, mainly as influenza A viruses and rhinoviruses. Results show the significant burden of viral aetiological agents in acute respiratory infection, particularly in the youngest cases. The study of influenza strains reveals their continuous evolution through either progressive mutations or by segment reassortments. Moreover, the predominant influenza B lineage was different from that included in the recommended vaccine in half of the studied seasons, supporting the formulation and use of a quadrivalent influenza vaccine. Regarding neuraminidase inhibitors resistance, with the exception of the 2007/08 H275Y seasonal A(H1N1) strains, no other circulating influenza strains carrying known resistance genetic markers were found. Moreover, all circulating A(H1N1)pdm09 and A(H3N2) strains finally became genetically resistant to adamantanes. A wide knowledge of the seasonality patterns of the RV in the general population is well-appreciated, but it is a challenge due to the unpredictable circulation of RV, highlighting the value of local and global RV surveillance. url: https://api.elsevier.com/content/article/pii/S1198743X16001154 doi: 10.1016/j.cmi.2016.02.007 id: cord-275068-yr076sl6 author: Ayoub, Fares title: Football and COVID-19 risk: correlation is not causation date: 2020-09-03 words: 446.0 sentences: 30.0 pages: flesch: 56.0 cache: ./cache/cord-275068-yr076sl6.txt txt: ./txt/cord-275068-yr076sl6.txt summary: A recent 8 genome wide association analysis (GWAS) has implicated that blood group A patients had a higher risk 9 of severe COVID-19 compared to other blood types,[3] while other studies have found associations 10 between vitamin D levels/latitude, and Bacille de Calmette et Guérin (BCG) vaccine and mortality to 11 COVID-19. [4] Based on the results of these studies, shall we tell our blood group A patients to stay home 12 or tell everyone to take vitamin D or get vaccinated with BCG? [5] Low vitamin D levels have often been associated with a 16 higher risk of infections, but vitamin D supplementation has not been shown to prevent respiratory 17 1 impact journals during the pandemic, but it is important to remember that correlation does not equal 2 causation. abstract: nan url: https://doi.org/10.1016/j.cmi.2020.08.034 doi: 10.1016/j.cmi.2020.08.034 id: cord-009295-4c0zwhdh author: Bal, A. title: Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino acid deletion in nsp2 (Asp268del) date: 2020-03-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7142683/ doi: 10.1016/j.cmi.2020.03.020 id: cord-257696-ybu772zw author: Bartoletti, Michele title: Efficacy of corticosteroid treatment for hospitalized patients with severe COVID-19: a multicenter study date: 2020-09-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: To assess the efficacy of corticosteroids in patients with coronavirus disease 2019 (COVID-19) METHODS: Multicenter observational study from February 22 through June 30, 2020. We included consecutive adult patients with severe COVID-19 defined as respiratory rate ≥30 breath per minute, oxygen saturation ≤93% on ambient air or arterial partial pressure of oxygen to fraction of inspired oxygen ≤300 mmHg. We excluded patients treated with other immunomodulant drugs, receiving low dose of corticosteroids and those receiving corticosteroids after 72h from admission. The primary endpoint was 30-day mortality form hospital admission. The main exposure variable was corticosteroid therapy at dosage of ≥0.5 mg/kg of prednisone equivalents. It was introduced as binomial covariate in a logistic regression model for primary endpoint and inverse probability of treatment weighting using the propensity score. RESULTS: Of 1717 patients with COVID-19 evaluated, 513 patients were included in the study; of these 170 (33%) were treated with corticosteroids. During the hospitalization 166 (34%) patients reached the primary outcome [60/170 (35%) in the corticosteroid group and 106/343 (31%) in the non-corticosteroid group]. At multivariable analysis corticosteroid treatment was not associated with lower 30-day mortality rate [aOR 0.59 (0.20-1.74), p=0.33]. After inverse probability of treatment weighting, corticosteroids were not associated to lower 30-day mortality [average treatment effect 0.05 (95% -0.02 to 0.09), p=0.12]. However, subgroup analysis revealed that in patients with PO(2)/FiO(2) < 200 mmHg at admission [135 patients, 52 (38%) treated with corticosteroids] corticosteroid treatment was associated to a lower risk of 30-day mortality [23/52 (44%) vs 45/83 (54%), aOR 0.20 (95%CI 0.04 to 0.90), p=0.036]. CONCLUSION: Our study shows that the effect of corticosteroid treatment on mortality might be limited to critically ill COVID-19 patients. url: https://api.elsevier.com/content/article/pii/S1198743X20305632 doi: 10.1016/j.cmi.2020.09.014 id: cord-326703-akn92p1r author: Bartoletti, Michele title: Development and validation of a prediction model for severe respiratory failure in hospitalized patients with SARS-Cov-2 infection: a multicenter cohort study (PREDI-CO study) date: 2020-08-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: We aimed to develop and validate a risk score to predict severe respiratory failure (SRF) among patients hospitalized with coronavirus disease-2019 (COVID-19). METHODS: We performed a multicentre cohort study among hospitalized (>24 hours) patients diagnosed with COVID-19 from February 22 to April 3 2020, at 11 Italian hospitals. Patients were divided into derivation and validation cohorts according to random sorting of hospitals. SRF was assessed from admission to hospital discharge and was defined as: SpO2<93% with 100% FiO2, respiratory rate (RR)>30bpm, or respiratory distress. Multivariable logistic regression models were built to identify predictors of SRF, β-coefficients were used to develop a risk score. Trial Registration NCT04316949. RESULTS: We analyzed 1113 patients (644 derivation, 469 validation cohort). Mean (±standard deviation)age was 65.7(±15) years, 704 (63.3%) were male. SRF occurred in 189/644 (29%) and 187/469 (40%) patients in derivation and validation cohort, respectively. At multivariate analysis, risk factors for SRF in the derivation cohort assessed at hospitalization were age ≥70 years [OR 2.74 (95%CI 1.66-4.50)], obesity [OR 4.62 (95%CI 2.78-7.70)], body temperature ≥38°C [OR 1.73 (95%CI 1.30-2.29)], RR ≥22bpm [OR 3.75 (95%CI 2.01-7.01)], lymphocytes ≤900/mm(3) [OR 2.69 (95%CI 1.60-4.51)], creatinine ≥1 mg/dl [OR 2.38 (95%CI 1.59-3.56)], C-reactive protein ≥10mg/dl [OR 5.91 (95%CI 4.88-7.17)], and lactate dehydrogenase ≥350IU/L[OR 2.39 (95%CI 1.11-5.11)]. Assigning points to each variable an individual risk score (PREDI-CO score) was obtained. Area under receiver-operator curve (AUROC) was 0.89 (0.86-0.92). At score of >3, sensitivity, specificity, positive and negative predictive values were 71.6%(65-79%), 89.1% (86-92%), 74%(67-80%), and 89%(85-91%), respectively;. PREDI-CO score showed similar prognostic ability in the validation cohort: AUROC 0.85 (0.81-0.88). At score of >3, sensitivity, specificity, positive and negative predictive values were 80% (73-85%), 76 (70-81%), 69%(60-74%) and 85% (80-89%), respectively. CONCLUSION: PREDI-CO score can be useful to allocate resources and prioritize treatments during COVID-19 pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32781244/ doi: 10.1016/j.cmi.2020.08.003 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: nan sentences: nan pages: flesch: nan cache: txt: summary: 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-283411-40ojqv1y author: Ben-Shmuel, Amir title: Detection and infectivity potential of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) environmental contamination in isolation units and quarantine facilities date: 2020-09-10 words: 1174.0 sentences: 91.0 pages: flesch: 56.0 cache: ./cache/cord-283411-40ojqv1y.txt txt: ./txt/cord-283411-40ojqv1y.txt summary: title: Detection and infectivity potential of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) environmental contamination in isolation units and quarantine facilities This study assessed the infectivity of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) contamination on surfaces and objects in hospital isolation units and a quarantine hotel. Surfaces and air sampling was conducted at two COVID-19 isolation units and in a quarantine hotel. Viral RNA detected in 29/55 (52.7%) and 16/42 (38%) surface samples from the surrounding of symptomatic COVID-19 patients in isolation units of two hospitals and in a quarantine hotel for asymptomatic and very mild COVID-19 patients. Surface Environmental, and 263 Personal Protective Equipment Contamination by Severe Acute Respiratory Syndrome Coronavirus 2 264 (SARS-CoV-2) From a Symptomatic Patient Detection of Severe Acute 268 Respiratory Syndrome Coronavirus 2 RNA on Surfaces in Quarantine Rooms. Severe acute respiratory 294 syndrome coronavirus 2 RNA contamination of inanimate surfaces and virus viability in a health care 295 emergency unit. abstract: OBJECTIVES: Environmental surfaces have been suggested as likely contributors to the transmission of COVID-19. This study assessed the infectivity of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) contamination on surfaces and objects in hospital isolation units and a quarantine hotel. METHODS: SARS-CoV-2 virus stability and infectivity on non-porous surfaces was tested under controlled laboratory conditions. Surfaces and air sampling was conducted at two COVID-19 isolation units and in a quarantine hotel. Viral RNA detected by RT-PCR and infectivity was assessed by VERO E6 CPE test. RESULTS: In laboratory-controlled conditions, SARS-CoV-2 gradually lost its infectivity completely at day 4 at ambient temperature and the decay rate of viral viability on surfaces directly correlated with increase in temperature. Viral RNA detected in 29/55 (52.7%) and 16/42 (38%) surface samples from the surrounding of symptomatic COVID-19 patients in isolation units of two hospitals and in a quarantine hotel for asymptomatic and very mild COVID-19 patients. None of the surface and air samples from all three sites (0/97) were found to contain infectious titers SARS-Cov-2 in tissue culture assay. CONCLUSIONS: Despite prolonged viability of SARS-CoV-2 in laboratory-controlled conditions, uncultivable viral contamination on inanimate surfaces might suggest low feasibility for indirect fomite transmission. url: https://www.sciencedirect.com/science/article/pii/S1198743X20305322?v=s5 doi: 10.1016/j.cmi.2020.09.004 id: cord-334835-j6u8t8j2 author: Berenguer, Juan title: Characteristics and predictors of death among 4,035 consecutively hospitalized patients with COVID-19 in Spain date: 2020-08-04 words: 1739.0 sentences: 110.0 pages: flesch: 54.0 cache: ./cache/cord-334835-j6u8t8j2.txt txt: ./txt/cord-334835-j6u8t8j2.txt summary: title: Characteristics and predictors of death among 4,035 consecutively hospitalized patients with COVID-19 in Spain OBJECTIVES: We aimed to analyse the characteristics and predictors of death in hospitalized patients with COVID-19 in Spain. Seventeen factors were independently associated with an increased hazard of death, the strongest among them included advanced age, liver cirrhosis, low age-adjusted oxygen saturation, higher concentrations of C-reactive protein, and lower estimated glomerular filtration rate. In the 209 final adjusted analysis, we found 17 factors independently associated with an increased hazard of 210 death: male sex, older age, arterial hypertension, obesity, liver cirrhosis, chronic neurological 211 disorder, active cancer, dementia, dyspnoea, confusion, low age-adjusted SaO2 on room air, higher 212 white cell blood count (WBC), higher neutrophil-to-lymphocyte ratio, lower platelet count, 213 prolonged INR, lower eGFR, and higher concentrations of CRP (Figure 2) . abstract: OBJECTIVES: We aimed to analyse the characteristics and predictors of death in hospitalized patients with COVID-19 in Spain. METHODS: Retrospective observational study of the first consecutive patients hospitalized with COVID-19 confirmed by real-time polymerase chain reaction (RT-PCR) assay in 127 Spanish centres until March 17, 2020. The follow-up censoring date was April 17, 2020. We collected demographic, clinical, laboratory, treatment, and complications data. The primary endpoint was all-cause mortality. Univariable and multivariable Cox regression analyses were performed to identify factors associated with death. RESULTS: Of the 4,035 patients, males accounted for 2,433/3,987 (61.0%), the median age was 70 years, and 2,539/3,439 (73.8%) had >1 comorbidity. The most common symptoms were a history of fever, cough, malaise, and dyspnoea. During hospitalization 1,255/3,979 (31.5%) patients developed acute respiratory distress syndrome, 736/3,988 (18.5%) were admitted to intensive care units, and 619/3,992 (15.5%) underwent mechanical ventilation. Viral or host-targeted medications included lopinavir/ritonavir 2,820/4,005 (70.4%), hydroxychloroquine 2,618/3,995 (65.5%), interferon-beta 1,153/3,950 (29.2%), corticosteroids 1,109/3,965 (28.0%), and tocilizumab 373/3,951 (9.4%). Overall 1,131/4,035 (28%) patients died. Mortality increased with age (85.6% occurring in older than 65 years). Seventeen factors were independently associated with an increased hazard of death, the strongest among them included advanced age, liver cirrhosis, low age-adjusted oxygen saturation, higher concentrations of C-reactive protein, and lower estimated glomerular filtration rate. CONCLUSIONS: Our findings provide comprehensive information about characteristics and complications of severe COVID-19 and may help to identify patients at a higher risk of death. url: https://doi.org/10.1016/j.cmi.2020.07.024 doi: 10.1016/j.cmi.2020.07.024 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: nan sentences: nan pages: flesch: nan cache: txt: summary: 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-286544-ipmcqz8n author: Cheng, Biao title: Predictors of progression from moderate to severe COVID-19: a retrospective cohort date: 2020-07-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVE: Most coronavirus disease 2019 (COVID-19) cases were identified as moderate, which is defined as having a fever or dry cough and lung imaging with ground-glass opacities. The risk factors and predictors of prognosis in such cohorts remain uncertain. METHODS: All adult patients with COVID-19 of moderate severity diagnosed using qRT-PCR and hospitalized at the Central Hospital of Wuhan, China, from Jan 1 to Mar 20, 2020 were enrolled in this retrospective study. The main outcomes were progression from moderate to severe or critical condition or death. RESULTS: Among the 456 enrolled patients with moderate COVID-19, 251/456 (55.0%) had poor prognosis. Multivariate logistic regression analysis identified higher NLR on admission (OR =1.032, 95%CI 1.042-1.230, P = 0.004) and higher CRP on admission (OR =3.017, 95%CI 1.941-4.690, P < 0.001) were associated with increased odds ratios of poor prognosis. The area under the receiver operating characteristic (ROC) curve (AUC) for NLR and CRP in predicting progression to critical condition was 0.77 (95% CI 0.694-0.846, P < 0.001) and 0.84 (95% CI 0.780-0.905, P < 0.001), with a cut-off value of 2.79 and 25.95 mg/l, respectively. The AUC of NLR and CRP in predicting death was 0.81 (95% CI, 0.732-0.878, P < 0.001) and 0.89 (95% CI 0.825-0.946, P < 0.001), with a cut-off value of 3.19 and 33.4 mg/l, respectively. CONCLUSIONS: Higher levels of NLR and CRP at admission were associated with poor prognosis of moderate COVID-19 patients. NLR and CRP were good predictors of progression to critical condition and death. url: https://www.ncbi.nlm.nih.gov/pubmed/32622952/ doi: 10.1016/j.cmi.2020.06.033 id: cord-306083-juysx6yo author: Choe, Young June title: Co-seasonality and co-detection of respiratory viruses and bacteraemia in children: a retrospective analysis date: 2020-09-10 words: 1746.0 sentences: 108.0 pages: flesch: 44.0 cache: ./cache/cord-306083-juysx6yo.txt txt: ./txt/cord-306083-juysx6yo.txt summary: OBJECTIVES: The aim of this study was to assess the co-seasonality and co-detection of respiratory viral infections and bacteraemia in children since the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13). Analysis of linked viral-bacterial infections in individual children indicated that the rate ratio (RR) of bacteraemia associated with hMPV (RR=2.73, 95% CI 1.12-6.85, P=0.019) and influenza (RR=2.61, 95% CI 1.21-6.11, P=0.013) were more than double that of RSV. CONCLUSIONS: There is a significant association between hMPV and influenza viruses, and bacteraemia of all causes in hospitalised children at a single paediatric centre in the United States. A study conducted in children before the 9 implementation of PCV13, demonstrated significant associations between invasive 10 pneumococcal disease (IPD) and influenza viruses and respiratory syncytial virus (RSV), as well 11 as human metapneumovirus (hMPV), which was a novel observation [5] . abstract: OBJECTIVES: The aim of this study was to assess the co-seasonality and co-detection of respiratory viral infections and bacteraemia in children since the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13). METHODS: Children <18 years were eligible for inclusion if they had a respiratory infection and a positive PCR-based assay for respiratory viruses as well as a positive blood culture from 2010 to 2018 at a single referral centre in the United States regardless of their underlying medical condition or antibiotic treatment history. Monthly incidence rates of respiratory viruses and bacteraemia were analysed with a seasonal-trend decomposition procedure based on loess (STL) and cross-correlation functions using time series regression modelling. RESULTS: We identified 7,415 unique positive respiratory virus tests, including 2,278 RSV (31%), 1,825 influenza viruses (24%), 1,036 parainfluenza viruses (14%), 1,017 hMPV (14%), 677 seasonal coronaviruses (9%), and 582 adenoviruses (8%), and a total of 11,827 episodes of bacteraemia. Significant co-seasonality was found between all-cause bacteraemia and RSV (OR=1.76, 95% CI 1.50-2.06, P<0.001), influenza viruses (OR=1.38, 95% CI 1.13-1.68, P=0.002), and seasonal coronaviruses (OR=1.18, 95% CI 1.09-1.28, P<0.001), respectively. Analysis of linked viral-bacterial infections in individual children indicated that the rate ratio (RR) of bacteraemia associated with hMPV (RR=2.73, 95% CI 1.12-6.85, P=0.019) and influenza (RR=2.61, 95% CI 1.21-6.11, P=0.013) were more than double that of RSV. Staphylococcus aureus and Streptococcus pneumoniae were the most commonly identified pathogens causing bacteraemia. CONCLUSIONS: There is a significant association between hMPV and influenza viruses, and bacteraemia of all causes in hospitalised children at a single paediatric centre in the United States. Large multicentre studies are needed to confirm these findings and to elucidate the mechanisms by which hMPV potentiates the virulence and invasive capacity of diverse bacteria. url: https://www.sciencedirect.com/science/article/pii/S1198743X20305358?v=s5 doi: 10.1016/j.cmi.2020.09.006 id: cord-031493-w8agvg9g author: Davido, Benjamin title: Possible therapies of Post-COVID-19 chronic symptoms() date: 2020-09-06 words: 153.0 sentences: 17.0 pages: flesch: 59.0 cache: ./cache/cord-031493-w8agvg9g.txt txt: ./txt/cord-031493-w8agvg9g.txt summary: key: cord-031493-w8agvg9g authors: Davido, Benjamin; Seang, Sophie; Barizien, Nicolas; Tubiana, Roland; de Truchis, Pierre title: Possible therapies of Post-COVID-19 chronic symptoms() date: 2020-09-06 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.09.001 sha: doc_id: 31493 cord_uid: w8agvg9g nan responsible for dysautonomia in patients with persistent symptoms following acute SARS-23 COV2 infection. Physicians must keep in mind that COVID-19 is not only a disease 24 responsible for lung injury and its sequel but may affect other organs as olfactory and 25 gustatory dysfunction and as such, should inform the general audience, especially young 26 individuals that are the most concerned [2] . Actually, we did not state that these symptoms of autonomic impairment do not require 28 specific treatment, but we believe it must be a case by case management depending on the breathing/hyperventilation syndrome in adults Efficacy of 68 Therapies for Postural Tachycardia Syndrome: A Systematic Review and Meta-69 analysis abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7474820/ doi: 10.1016/j.cmi.2020.09.001 id: cord-295479-mcfqs7vf author: Davido, Benjamin title: Post-COVID-19 chronic symptoms: a post-infectious entity?() date: 2020-07-23 words: 195.0 sentences: 24.0 pages: flesch: 50.0 cache: ./cache/cord-295479-mcfqs7vf.txt txt: ./txt/cord-295479-mcfqs7vf.txt summary: key: cord-295479-mcfqs7vf authors: Davido, Benjamin; Seang, Sophie; Tubiana, Roland; de Truchis, Pierre title: Post-COVID-19 chronic symptoms: a post-infectious entity?() date: 2020-07-23 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.07.028 sha: doc_id: 295479 cord_uid: mcfqs7vf nan COVID-19 : point épidémiologique du 21 mai Assistance Publique-Hôpitaux de Paris'' response to the COVID-19 88 pandemic Anosmia and Ageusia: Common Findings 90 in COVID-19 Patients Patients Recovered from COVID-19 Active Epstein-Barr virus infection in 95 post-viral fatigue syndrome serological IgG antibody response on the Abbott Architect for established SARS-CoV-99 2 infection Neurologic manifestations in hospitalized patients 102 with COVID-19: The ALBACOVID registry Cerebrovascular disease in patients with COVID-19: 106 neuroimaging, histological and clinical description Kawasaki-like multisystem inflammatory syndrome in children during the covid-19 Chikungunya-Induced Arthritis in Reunion Island: A 113 Long-Term Observational Follow-Up Study Showing Frequently Persistent Joint 114 Some Cases of Persistent Chikungunya Immunoglobulin M Positivity, and 115 No Anticyclic Citrullinated Peptide Seroconversi abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32712242/ doi: 10.1016/j.cmi.2020.07.028 id: cord-279125-w6sh7xpn author: Egli, Adrian title: Digital microbiology date: 2020-06-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Digitalisation and artificial intelligence have an important impact on the way microbiology laboratories will work in the near future. Opportunities and challenges lay ahead to digitalise the microbiological workflows. Making an efficient use of big data, machine learning, and artificial intelligence in clinical microbiology requires a profound understanding of data handling aspects. OBJECTIVE: This review article summarizes the most important concepts of digital microbiology. The article provides microbiologists, clinicians and data scientists a viewpoint and practical examples along the diagnostic process. SOURCES: We used peer-reviewed literature identified by a Pubmed search for digitalisation, machine learning, artificial intelligence and microbiology. CONTENT: We describe the opportunities and challenges of digitalisation in microbiological diagnostic process with various examples. We also provide in this context key aspects of data structure and interoperability, as well as legal aspects. Finally, we outline the way for applications in a modern microbiology laboratory. IMPLICATIONS: We predict that digitalization and the usage of machine learning will have a profound impact on the daily routine of the laboratory staff. Along the analytical process, the most important steps should be identified, where digital technologies can be applied and provide a benefit. The education of all staff involved should be adapted to prepare for the advances in digital microbiology. url: https://api.elsevier.com/content/article/pii/S1198743X20303670 doi: 10.1016/j.cmi.2020.06.023 id: cord-344027-qghktrm1 author: Fiolet, Thibault title: ''Effect of hydroxychloroquine with or without azithromycin on the mortality of COVID-19 patients'' – Author’s reply date: 2020-10-17 words: 329.0 sentences: 28.0 pages: flesch: 45.0 cache: ./cache/cord-344027-qghktrm1.txt txt: ./txt/cord-344027-qghktrm1.txt summary: title: ''Effect of hydroxychloroquine with or without azithromycin on the mortality of COVID-19 patients'' – Author''s reply As with all studies at risk of critical bias included in our systematic review, it was excluded 50 from the main analysis. Treatment 154 with hydroxychloroquine, azithromycin, and combination in patients hospitalized with Clinical 158 Efficacy of Chloroquine derivatives in COVID-19 Infection: Comparative meta-analysis 159 between the Big data and the real world Hydroxychloroquine in Hospitalized Patients with COVID-19: Preliminary results from a 166 multi-centre, randomized, controlled trial COVID-19 177 prevention and treatment: A critical analysis of chloroquine and hydroxychloroquine 178 clinical pharmacology Interventions 188 for treatment of COVID-19: A living systematic review with meta-analyses and trial 189 sequential analyses (The LIVING Project) Mortality outcomes with hydroxychloroquine and chloroquine in COVID-19: an 193 international collaborative meta-analysis of randomized trials Hydroxychloroquine as pre-exposure prophylaxis for COVID-19 in healthcare workers: 203 a randomized trial abstract: nan url: https://www.sciencedirect.com/science/article/pii/S1198743X20306133?v=s5 doi: 10.1016/j.cmi.2020.10.002 id: cord-343090-dsjq98ks author: Fragkou, Paraskevi C. title: Review of trials currently testing treatment and prevention of COVID-19 date: 2020-05-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: As COVID-19 cases continue to rise globally, evidence from large randomised controlled trials is still lacking. Currently, numerous trials testing potential treatment and preventative options are undertaken all over the world. OBJECTIVES: We summarised all registered clinical trials examining treatment and prevention options for COVID-19. Additionally, we evaluated the quality of the retrieved studies. DATA SOURCES: Clinicaltrials.gov, the Chinese Clinical Trial Registry and the European Union Clinical Trials Register were systematically searched. STUDY ELIGIBILITY CRITERIA: Registered clinical trials examining treatment and/or prevention options for COVID-19 were included. No language, country or study design restrictions were applied. We excluded withdrawn or cancelled studies and trials not reporting therapeutic or preventative strategies for COVID-19. PARTICIPANTS: and interventions: No restrictions in terms of participants’ age and medical background or type of intervention were enforced. METHODS: The registries were searched using the term “coronavirus” or “COVID-19” from their inception until 26(th) March 2020.Additional manual search of the registries was also performed. Eligible studies were summarised and tabulated. Interventional trials were methodologically analysed, excluding expanded access studies and trials testing Traditional Chinese Medicine. RESULTS: In total, 309 trials evaluating therapeutic management options, 23 studies assessing preventive strategies and 3 studies examining both were retrieved. Finally, 214 studies were methodologically reviewed. Interventional treatment studies were mostly randomised (n=150, 76%) and open-label (n=73, 37%) with a median number of planned inclusions of 90 (IQR 40-200). Major categories of interventions that are currently being investigated are discussed. CONCLUSION: Numerous clinical trials have been registered since the onset of the COVID-19 pandemic. Summarised data on these trials will assist physicians and researchers to promote patient care and guide future research efforts for COVID-19 pandemic containment. url: https://www.sciencedirect.com/science/article/pii/S1198743X20302962?v=s5 doi: 10.1016/j.cmi.2020.05.019 id: cord-265363-xw56intn author: Gautret, P. title: Incidence of Hajj-associated febrile cough episodes among French pilgrims: a prospective cohort study on the influence of statin use and risk factors date: 2014-12-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A prospective epidemiological study was conducted to evaluate the incidence of febrile cough episodes among adult Muslims travelling from Marseille to Saudi Arabia during the Hajj pilgrimage and to assess if use of statin had an influence on this incidence. In total, 580 individuals were presented with a questionnaire. A significant proportion of individuals had chronic medical disorders, e.g. diabetes mellitus (132, 22.8%) and hypertension (147, 25.3%). Pilgrims had a low level of education and a low employment rate. Sixty (10.3%) were treated with statins for hypercholesterolemia. Four hundred and fourty-seven pilgrims were presented a questionnaire on returning home. A total of 74 travellers (16.6%) experienced fever during their stay in Saudi Arabia (67 attended a doctor) and 271 (60.6%) had cough (259 attended a doctor); 70 travellers with cough were febrile (25.9%). Seventy per cent of the travellers who suffered cough episodes developed their first symptoms within 3 days, suggesting a human to human transmission of the responsible pathogen, with short incubation time as evidenced by a bimodal distribution of cough in two peaks at a 24 h interval. None of demographical and socioeconomic characteristics, underlying diseases or vaccination against influenza significantly affected the occurrence of cough. Diabetes correlated with an increased risk of febrile cough (OR = 2.02 (1.05–3.89)) as well as unemployment (OR = 2.22 (0.91–5.53)). Use of statins had no significant influence on the occurrence of cough and/or fever during the pilgrimage. This result suggests that while treatment with a statin has been demonstrated to reduce the mortality from severe sepsis associated with respiratory tract infections, it probably does not play a role in the outcome of regular febrile cough episodes as observed in the cohort studied here. url: https://doi.org/10.1111/j.1469-0691.2009.02816.x doi: 10.1111/j.1469-0691.2009.02816.x id: cord-256402-b5fel2d3 author: Gevers, S. title: Safety considerations of chloroquine and hydroxychloroquine in treatment of COVID-19 date: 2020-05-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Chloroquine and hydroxychloroquine are both used to treat COVID-19. Safety data in this specific population is largely unknown. In particular, cardiologic, gastro-intestinal and neuropsychiatric side-effects of (hydroxychloroquine) needs special attention in COVID-19 patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32422406/ doi: 10.1016/j.cmi.2020.05.006 id: cord-256429-ntx0eay0 author: Hao, W. title: First atypical case of 2019 novel coronavirus in Yan'an, China date: 2020-02-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://api.elsevier.com/content/article/pii/S1198743X20300914 doi: 10.1016/j.cmi.2020.02.011 id: cord-030061-55ntc4wj author: Helleberg, Marie title: Invasive aspergillosis in patients with severe COVID-19 pneumonia date: 2020-08-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7403849/ doi: 10.1016/j.cmi.2020.07.047 id: cord-270947-6e5cw2q9 author: Huang, H.-S. title: Multiplex PCR system for the rapid diagnosis of respiratory virus infection: systematic review and meta-analysis date: 2017-12-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: To provide a summary of evidence for the diagnostic accuracies of three multiplex PCR systems (mPCRs)—BioFire FilmArray RP (FilmArray), Nanosphere Verigene RV+ test (Verigene RV+) and Hologic Gen-Probe Prodesse assays—on the detection of viral respiratory infections. METHODS: A comprehensive search up to 1 July 2017 was conducted on Medline and Embase for studies that utilized FilmArray, Verigene RV+ and Prodesse for diagnosis of viral respiratory infections. A summary of diagnostic accuracies for the following five viruses were calculated: influenza A virus (FluA), influenza B virus, respiratory syncytial virus, human metapneumovirus and adenovirus. Hierarchical summary receiver operating curves were used for estimating the viral detection performance per assay. RESULTS: Twenty studies of 5510 patient samples were eligible for analysis. Multiplex PCRs demonstrated high diagnostic accuracy, with area under the receiver operating characteristic curve (AUROC) equal to or more than 0.98 for all the above viruses except for adenovirus (AUROC 0.89). FilmArray, Verigene RV+ and ProFlu+ (the only Prodesse assay with enough data) demonstrated a summary sensitivity for FluA of 0.911 (95% confidence interval, 0.848–0.949), 0.949 (95% confidence interval, 0.882–0.979) and 0.954 (95% confidence interval, 0.871–0.985), respectively. The three mPCRs were comparable in terms of detection of FluA. CONCLUSIONS: Point estimates calculated from eligible studies showed that the three mPCRs (FilmArray, Verigene RV+ and ProFlu+) are highly accurate and may provide important diagnostic information for early identification of respiratory virus infections. In patients with low pretest probability for FluA, these three mPCRs can predict a low possibility of infection and may justify withholding empirical antiviral treatments. url: https://www.ncbi.nlm.nih.gov/pubmed/29208560/ doi: 10.1016/j.cmi.2017.11.018 id: cord-279111-jaa45kyc author: Ieven, M. title: Aetiology of lower respiratory tract infection in adults in primary care: a prospective study in 11 European countries date: 2018-02-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: To describe the role of bacteria (including bacterial resistance), viruses (including those recently described) and mixed bacterial–viral infections in adults presenting to primary care with lower respiratory tract infection (LRTI). METHODS: In all, 3104 adults with LRTI were enrolled, of whom 141 (4.5%) had community-acquired pneumonia (CAP), and 2985 matched controls in a prospective study in 16 primary care networks in Europe, and followed patients up at 28–35 days. We detected Streptococcus pneumoniae and Haemophilus influenzae and assessed susceptibility, atypical bacteria and viruses. RESULTS: A potential pathogen was detected in 1844 (59%) (in 350 (11%) bacterial pathogens only, in 1190 (38%) viral pathogens only, and in 304 (10%) both bacterial and viral pathogens). The most common bacterial pathogens isolated were S. pneumoniae (5.5% overall, 9.2% in CAP patients) and H. influenzae (5.4% overall, 14.2% in CAP patients). Less than 1% of S. pneumoniae were highly resistant to penicillin and 12.6% of H. influenzae were β-lactamase positive. The most common viral pathogens detected were human rhinovirus (20.1%), influenza viruses (9.9%), and human coronavirus (7.4%). Influenza virus, human parainfluenza viruses and human respiratory syncytial virus as well as human rhinovirus, human coronavirus and human metapneumovirus were detected significantly more frequently in LRTI patients than in controls. CONCLUSIONS: A bacterial pathogen is identified in approximately one in five adult patients with LRTI in primary care, and a viral pathogen in just under half, with mixed infections in one in ten. Penicillin-resistant pneumococci and β-lactamase-producing H. influenzae are uncommon. These new findings support a restrictive approach to antibiotic prescribing for LRTI and the use of first-line, narrow-spectrum agents in primary care. url: https://api.elsevier.com/content/article/pii/S1198743X18301526 doi: 10.1016/j.cmi.2018.02.004 id: cord-307213-i8yijbiu author: Ip, Jonathan Daniel title: Intrahost non-synonymous diversity at a neutralising antibody epitope of SARS-CoV-2 spike protein N-terminal domain date: 2020-11-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: SARS-CoV-2 has evolved rapidly into several genetic clusters. However, data on mutations during the course of infection are scarce. This study aims to determine viral genome diversity in serial samples of COVID-19 patients. METHODS: Targeted deep sequencing of spike gene was performed on serial respiratory specimens from COVID-19 patients using nanopore and Illumina sequencing. Sanger sequencing was then performed to confirm the single nucleotide polymorphisms. RESULTS: A total of 28 serial respiratory specimens from 12 patients were successfully sequenced using nanopore and Illumina sequencing. A 75-year-old patient with severe disease had a mutation, G22017T, identified in the second specimen. The frequency of G22017T increased from ≤5% (nanopore: 3.8%; Illumina: 5%) from first respiratory tract specimen (sputum) to ≥60% (nanopore: 67.7%; Illumina: 60.4%) in the second specimen (saliva; collected 2 days after the 1(st) specimen). The difference in G22017T frequency was also confirmed by Sanger sequencing. G22017T corresponds to W152L amino acid mutation in the spike protein which was only found in <0.03% of the sequences deposited into a public database. Spike amino acid residue 152 is located within the N-terminal domain, which mediates the binding of a neutralizing antibody. CONCLUSIONS: A spike protein amino acid mutation W152L located within a neutralizing epitope has appeared naturally in a patient. Our study demonstrated that monitoring of serial specimens is important in identifying hotspots of mutations, especially those occurring at neutralizing epitopes which may affect the therapeutic efficacy of monoclonal antibodies. url: https://doi.org/10.1016/j.cmi.2020.10.030 doi: 10.1016/j.cmi.2020.10.030 id: cord-293542-o0zspgrk author: Ippolito, G. title: Facing the threat of highly infectious diseases in Europe: the need for a networking approach date: 2014-12-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In recent years emerging and re-emerging infections, as well as the risk of bioterrorist events, have attracted increasing attention from health authorities because of the epidemic potential that renders some of them a real public health challenge. These highly infectious diseases (HIDs) are occurring more and more frequently in Europe, and despite the many initiatives in place to face them, many unsolved problems remain, and coordinated efforts for dealing with HIDs appear mandatory. Whereas uncoordinated measures would lead to only partial and poor responses to these emerging threats, networking represents a valuable approach to these diseases, in order to: (i) ensure a rapid and effective response; (ii) stimulate complementarity and prevent duplication; (iii) promote international cooperation, exchange of experience, good practice and protocols; and (iv) support the less prepared countries in the European Community. url: https://www.ncbi.nlm.nih.gov/pubmed/19486072/ doi: 10.1111/j.1469-0691.2009.02876.x id: cord-256853-2s31fn04 author: Jin, Cheng Cheng title: Correlation between viral RNA shedding and serum antibodies in COVID-19 patients date: 2020-05-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://doi.org/10.1016/j.cmi.2020.05.022 doi: 10.1016/j.cmi.2020.05.022 id: cord-304710-gjb6zo81 author: Khan, S. title: Novel coronavirus: how things are in Wuhan date: 2020-02-11 words: 1369.0 sentences: 78.0 pages: flesch: 54.0 cache: ./cache/cord-304710-gjb6zo81.txt txt: ./txt/cord-304710-gjb6zo81.txt summary: There is a great risk of medical and clinical staff (and workers) becoming infected with 2019n-CoV because of their direct interaction with infected and suspected individuals. Working for long hours, disturbed daily routines including eating and sleeping schedules and fear of being infected are key factors that increase the risks of stress and anxiety for doctors and nurses, and may lead to their working less efficiently in terms of providing better treatment and care to patients. However, the increasing number of patients every day and the expected peak in the coming days [6] may cause a further shortage of medical staff and health and logistic issues for the frontline healthcare provider. China coronavirus: Wuhan medical staff being infected at much faster pace than reported as national death toll hits 26 Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China abstract: nan url: https://www.sciencedirect.com/science/article/pii/S1198743X20300847 doi: 10.1016/j.cmi.2020.02.005 id: cord-254278-awdqguoo author: Khan, Suliman title: Association of COVID-19 infection with pregnancy outcomes in healthcare workers and general women date: 2020-04-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.sciencedirect.com/science/article/pii/S1198743X20301804?v=s5 doi: 10.1016/j.cmi.2020.03.034 id: cord-032016-2rzszcke author: Kumar, Anil title: Sarcoidosis, Steroids and Strongyloides -What’s the Catch?() date: 2020-09-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7497548/ doi: 10.1016/j.cmi.2020.09.012 id: cord-297625-eby014gm author: L''Huillier, A.G. title: Survival of rhinoviruses on human fingers date: 2014-12-11 words: 2635.0 sentences: 139.0 pages: flesch: 49.0 cache: ./cache/cord-297625-eby014gm.txt txt: ./txt/cord-297625-eby014gm.txt summary: Our study confirms that rhinovirus infectiousness is related to the viral concentration in droplets and suggests that children represent the main transmission source, which occurs only rarely via adults. We conducted a series of experiments to assess the duration of human rhinovirus infectiousness duration on fingers, as well as the impact of viral concentration on survival rates. One hour after the deposit of disrupted droplets on the fingers of the six volunteers, infectious viruses could be detected by culture in all subjects contaminated with HC droplets (6/6), in four of the six volunteers with AC droplets, and none of the six volunteers with LC droplets, which confirmed the influence of concentration on survival (Fig. 1) . Our study showed that virus survival, and therefore infectiousness, was related to the viral concentration in droplets. Potential role of hands in the spread of respiratory viral infections: studies with human parainfluenza virus 3 and rhinovirus 14 abstract: Rhinovirus is the main cause of the common cold, which remains the most frequent infection worldwide among humans. Knowledge and understanding of the rhinovirus transmission route is important to reduce morbidity as only preventive measures are effective. In this study, we investigated the potential of rhinovirus to survive on fingers. Rhinovirus-B14 was deposited on fingers for 30, 60, 90 and 120 min. Survival was defined as the ability of the virus to grow after 7 days, confirmed by immunofluorescence. Rhinovirus survival was not dependent on incubation time on fingers. Droplet disruption had no influence on survival. Survival was frequent with high rhinovirus concentrations, but rare with low-concentration droplets, which corresponded to the usual rhinovirus concentrations in mucus observed in children and adults, respectively. Our study confirms that rhinovirus infectiousness is related to the viral concentration in droplets and suggests that children represent the main transmission source, which occurs only rarely via adults. It confirms also that rhinovirus hand-related transmission is possible and supports hand hygiene as a key prevention measure. url: https://www.ncbi.nlm.nih.gov/pubmed/25614158/ doi: 10.1016/j.cmi.2014.12.002 id: cord-322585-5gio6ruj author: Lanari, Marcello title: Children and SARS-CoV-2 infection: innocent bystanders…until proven otherwise date: 2020-06-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In this commentary, we focus our attention on what is known about SARS-CoV-2 infection in the pediatric population. We report literature and National data. The possible and different explanations for understanding why the infection seems to be more benign and less frequent in children are discussed. The possible role of children in the COVID-19 viral disease pandemic is also commented. Finally, our work suggests to search for future evidence and containment strategies to manage virus spread. url: https://doi.org/10.1016/j.cmi.2020.06.017 doi: 10.1016/j.cmi.2020.06.017 id: cord-286525-0354438s author: Lee, Todd C. title: Tocilizumab versus the covid19 tempest: all’s well that ends well or much ado about nothing? date: 2020-09-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/33007475/ doi: 10.1016/j.cmi.2020.09.033 id: cord-314288-6vh7dvad author: Leibovici, L. title: Submissions and publications in Corona times date: 2020-05-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32422405/ doi: 10.1016/j.cmi.2020.05.008 id: cord-326341-egtnqlov author: Liotti, Flora Marzia title: Performance of a novel diagnostic assay for rapid SARS-CoV-2 antigen detection in nasopharynx samples date: 2020-09-23 words: 514.0 sentences: 35.0 pages: flesch: 60.0 cache: ./cache/cord-326341-egtnqlov.txt txt: ./txt/cord-326341-egtnqlov.txt summary: title: Performance of a novel diagnostic assay for rapid SARS-CoV-2 antigen detection in nasopharynx samples Conversely, rapid antigen detection assays-intrinsically less laborious and requiring few minutes 29 to results-have the potential to satisfy the pressing demand for an early SARS-CoV-2 infection 30 Suwon, South Korea) assay, a fluorescent immunoassay detecting SARS-CoV-2 nucleoprotein 33 antigen, on nasopharynx swab samples. The LOD was 5 × 10 2 41 TCID 50 /mL (2 × 10 6 RNA copies/mL) at 95% detection probability ( Supplementary Fig. S1 Our study shows that the STANDARD F COVID-19 Ag FIA assay had a good specificity for 65 SARS-CoV-2 detection in nasopharynx swab samples but had a good sensitivity only for samples 66 Evaluation of a rapid diagnostic assay for detection of SARS-CoV-102 2 antigen in nasopharyngeal swabs Evaluation of rapid 104 antigen test for detection of SARS-CoV-2 virus abstract: nan url: https://api.elsevier.com/content/article/pii/S1198743X20305838 doi: 10.1016/j.cmi.2020.09.030 id: cord-298441-77w86l8q author: Lombardi, Andrea title: Characteristics of 1,573 healthcare workers who underwent nasopharyngeal swab for SARS-CoV-2 in Milano, Lombardy, Italy date: 2020-06-20 words: 1438.0 sentences: 67.0 pages: flesch: 52.0 cache: ./cache/cord-298441-77w86l8q.txt txt: ./txt/cord-298441-77w86l8q.txt summary: To answer this question, we reviewed all the 59 nasopharyngeal swab performed in HCWs exposed to confirmed cases of COVID-19 at the 60 Foundation IRCCS Ca'' Granda Ospedale Maggiore Policlinico located in Milan, the capital 61 of Lombardy, by large the Italian region mostly affected by We assessed 62 frequency of positive tests among symptomatic and asymptomatic HCWs and evaluated the 63 association between occupation, symptoms (type and number), and presence of the infection. Therefore, in middle-and high-resource settings a mass screening for all 163 HCWs exposed to confirmed COVID-19 cases appears the best approach to limit the spread When stratified according to occupation, test-positive frequencies were clearly higher among 177 subsets with direct contact with patients (physicians including residents, nurses and 178 midwives, healthcare assistants and health technicians) than those without (clerical works and 179 technicians). abstract: OBJECTIVES: The management of healthcare workers (HCWs) exposed to confirmed cases of COVID-19 is still a matter of debate. We aimed to assess in this group the attack rate of asymptomatic carriers and the symptoms most frequently associated with the infection. METHODS: Occupational and clinical characteristics of HCWs who performed a nasopharyngeal swab for the detection of SARS-CoV-2 in a University Hospital from February 24, to March 31, 2020, were collected. For those who tested positive and for the asymptomatic positives we checked laboratory and clinical data as of May 22 to calculate the time necessary to become test-negative and to verify whether symptoms developed thereafter. Frequencies of positive tests were compared according to selected variables using multivariable logistic regression models. RESULTS: Positive tests were 139 among 1,573 HCWs (8.8%, 95% confidence interval [CI]: 7.5-10.3), with a marked difference between symptomatic (122/503, 24.2%) and asymptomatic (17/1,070, 1.6%) workers (p<0.001). Physicians were the group with the highest frequency of positive tests (61/582, 10.5%), whereas clerical workers and technicians displayed the lowest frequency (5/137, 3.6%). The likelihood of being positive increased with the number of reported symptoms and the strongest predictors were taste and smell alterations (odds ratio [OR]= 76.9) and fever (OR = 9.12). The median time from first positive test to a negative test was 27 days (95% CI: 24-30). CONCLUSIONS: A relevant number of HCWs can be infected by SARS-CoV-2 without displaying any symptom. Among symptomatic workers, the key symptoms to guide diagnosis are taste and smell alterations and fever. In median, almost four weeks are necessary to achieve negativity of nasopharyngeal swab. url: https://www.ncbi.nlm.nih.gov/pubmed/32569835/ doi: 10.1016/j.cmi.2020.06.013 id: cord-324148-bllyruh8 author: Loubet, Paul title: Characteristics of human metapneumovirus infection in adults hospitalized for community-acquired influenza-like illness in France, 2012-2018: a retrospective observational study date: 2020-04-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: To describe the prevalence, clinical features and complications of human metapneumovirus (hMPV) infections in a population of adults hospitalized with influenza-like illness (ILI). METHODS: This was a retrospective, observational, multicenter cohort study using prospectively collected data from adult patients hospitalized during influenza virus circulation, for at least 24h, for community-acquired ILI (with symptom onset <7 days). Data were collected from five French teaching hospitals over six consecutive winters (2012-2018). Respiratory viruses were identified by multiplex RT-PCR on nasopharyngeal specimens. hMPV+ patients were compared to hMPV– patients, influenza+ and respiratory syncytial virus (RSV)+ patients using multivariate logistic regressions. Primary outcome was the prevalence of hMPV in patients hospitalized for ILI. RESULTS: Among the 3148 patients included (1449 (46%) women, 1988 (63%) aged 65 and over; 2508 (80%) with chronic disease), at least one respiratory virus was detected in 1604 (51%, 95%CI [49-53]), including 100 cases of hMPV (100/3148, 3% 95%CI [3, 4]), of which 10 (10%) were viral co-infection. In the hMPV+ patients, mean length of stay was 7 days, 62% (56/90) developed a complication, 21% (14/68) were admitted to intensive care unit and 4% (4/90) died during hospitalization. In comparison with influenza+ patients, hMPV+ patients were more frequently > 65 years old (aOR=3.3, 95%CI[1.9-6.3]) and presented more acute heart failure during hospitalization (aOR=1.8, 95%CI[1.0-2.9]). Compared to RSV+ patients, hMPV+ patients had less cancer (aOR=0.4, 95%CI[0.2-0.9]) and were less likely to smoke (aOR=0.5, 95%CI[0.2-0.9]) but had similar outcomes especially high rate of respiratory and cardiovascular complications. CONCLUSIONS: Adult hMPV infections mainly affect the elderly and patients with chronic conditions and are responsible for frequent cardiac and pulmonary complications similar to those of RSV infections. At-risk populations would benefit from the development of antivirals and vaccines targeting hMPV. url: https://www.sciencedirect.com/science/article/pii/S1198743X20301907?v=s5 doi: 10.1016/j.cmi.2020.04.005 id: cord-009675-utz0iazs author: Madeley, C. R. title: Are point‐of‐care (POC) virological tests what is needed? date: 2007-06-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Point‐of‐care (POC) tests are becoming more available, although the way in which they should be used is currently undecided. Any ‘laboratory’‐based diagnosis of respiratory infections has three components: the specimen taken, the test used, and the interpretation of the results. Each of these components needs to be carefully addressed when using POC tests for the diagnosis of respiratory tract infections. Given the enthusiasm with which POC tests are being developed, it is likely that they will be used more and more widely. If so, the advantages and limitations of their use should be fully discussed and the implications recognised. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7162335/ doi: 10.1111/j.1469-0691.2007.01738.x id: cord-287256-hgqz1bcs author: Magurano, Fabio title: SARS-CoV-2 infection: the environmental endurance of the virus can be influenced by the increase of temperature date: 2020-11-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Objectives The goal of the current study is to evaluate whether the increase of temperature can influence the environmental endurance of SARS-CoV-2. Methods The virus was inoculated on plastic surface and harvested at predefined time-points in parallel at 20-25°C (RT) and at 28°C (JT). Samples collections were tested by TCID50 titers on Vero cells. Samples collections were tested by TCID50 titers on Vero cells. Results Our results confirm that fomite transmission of the emerging SARS-CoV2 is possible: the virus reserved its ability to infect cells up to 84 hours at both RT and JT on plastic surface, with a TCID50 viral titre of 0,67 and 0,25 log10 respectively. At RT, an important reduction in the viral titre, from 4 log10 to 3 log10 TCID50 was observed during the first 24-36 hours. At JT the same decay was observed more rapidly (between 8 and 12 hours), The rate of viral inactivation by D-value was 24.74 at RT and 12,21 hours at JT. Conclusions This remarkable difference between the two temperatures suggests that virus vitality can be influenced by the environmental temperature and that the hot season could reduce the probability of COVID-19 transmission. url: https://www.sciencedirect.com/science/article/pii/S1198743X20306881?v=s5 doi: 10.1016/j.cmi.2020.10.034 id: cord-328499-d6cvaxm9 author: Matzkies, Lucie-Marie title: Lack of sensitivity of an IVD/CE-labeled kit targeting the S gene for detection of SARS-CoV-2 date: 2020-07-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: New molecular tests for SARS-CoV-2 are rapidly launched in response to the COVID-19 pandemic. The aim of this study was to evaluate the analytical and the clinical performance of the VIASURE SARS-CoV-2 S gene RT-PCR Kit on the BD Max™ system and to compare results with those obtained with the cobas® SARS-CoV-2 test on the cobas® 6800 system. METHODS: For testing the analytical performance, reference material was used. Clinical samples (n=101) obtained from patients with symptoms compatible to COVID-19 were studied. Oro- and nasopharyngeal swabs were collected by using either ESwab™ or UTM™ collection systems. RESULTS: When the analytical performance was evaluated, the sample containing the lowest SARS-CoV-2 concentration tested negative with the VIASURE test while results obtained with the cobas® test were found to be concordant with the results expected. Six out of the 101 clinical samples (5.9%) showed an inhibition with the VIASURE test. When analyzing the remaining 95 clinical samples, 27 were found to be negative with both assays. Of 68 samples positive with the cobas® test, the VIASURE test missed 21 (30.9 %) samples. All of those 21 samples had shown Ct values ≥ 31 with the cobas® 6800 system. None of the samples tested positive with the VIASURE test and negative with the cobas® test. CONCLUSIONS: The VIASURE test was impaired by a lack of sensitivity and a relatively high number of invalid results. When using the VIASURE test for routine testing, a significant number of COVID-19 positive samples would have been missed. url: https://doi.org/10.1016/j.cmi.2020.06.036 doi: 10.1016/j.cmi.2020.06.036 id: cord-269345-5tlyy8jp author: Minuz, Pietro title: High rate of pulmonary thromboembolism in patients with SARS-CoV-2 pneumonia date: 2020-06-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://doi.org/10.1016/j.cmi.2020.06.011 doi: 10.1016/j.cmi.2020.06.011 id: cord-257248-aii0tj9x author: O'Grady, K.F. title: Prevalence, codetection and seasonal distribution of upper airway viruses and bacteria in children with acute respiratory illnesses with cough as a symptom date: 2016-02-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Most studies exploring the role of upper airway viruses and bacteria in paediatric acute respiratory infections (ARI) focus on specific clinical diagnoses and/or do not account for virus–bacteria interactions. We aimed to describe the frequency and predictors of virus and bacteria codetection in children with ARI and cough, irrespective of clinical diagnosis. Bilateral nasal swabs, demographic, clinical and risk factor data were collected at enrollment in children aged <15 years presenting to an emergency department with an ARI and where cough was a symptom. Swabs were tested by polymerase chain reaction for 17 respiratory viruses and seven respiratory bacteria. Logistic regression was used to investigate associations between child characteristics and codetection of the organisms of interest. Between December 2011 and August 2014, swabs were collected from 817 (93.3%) of 876 enrolled children, median age 27.7 months (interquartile range 13.9–60.3 months). Overall, 740 (90.6%) of 817 specimens were positive for any organism. Both viruses and bacteria were detected in 423 specimens (51.8%). Factors associated with codetection were age (adjusted odds ratio (aOR) for age <12 months = 4.9, 95% confidence interval (CI) 3.0, 7.9; age 12 to <24 months = 6.0, 95% CI 3.7, 9.8; age 24 to <60 months = 2.4, 95% CI 1.5, 3.9), male gender (aOR 1.46; 95% CI 1.1, 2.0), child care attendance (aOR 2.0; 95% CI 1.4, 2.8) and winter enrollment (aOR 2.0; 95% CI 1.3, 3.0). Haemophilus influenzae dominated the virus–bacteria pairs. Virus–H. influenzae interactions in ARI should be investigated further, especially as the contribution of nontypeable H. influenzae to acute and chronic respiratory diseases is being increasingly recognized. url: https://api.elsevier.com/content/article/pii/S1198743X16001129 doi: 10.1016/j.cmi.2016.02.004 id: cord-344581-h7ikjgic author: Ong, David S.Y. title: Comparison of diagnostic accuracies of rapid serological tests and ELISA to molecular diagnostics in patients with suspected COVID-19 presenting to the hospital date: 2020-06-02 words: 2071.0 sentences: 120.0 pages: flesch: 54.0 cache: ./cache/cord-344581-h7ikjgic.txt txt: ./txt/cord-344581-h7ikjgic.txt summary: OBJECTIVES: To assess the diagnostic performance of rapid lateral flow immunochromatographic assays (LFAs) compared to an enzyme-linked immunosorbent assay (ELISA) and nucleic acid amplification tests (NATs) in suspected coronavirus disease 2019 (COVID-19) patients. In the total cohort, Orient Gene Biotech COVID-19 IgG/IgM Rapid Test LFA had a sensitivity of 43/99 (43%; 95% CI 34-53) and specificity of 126/129 (98%; 95% CI 95-100). CONCLUSIONS: There is large variability in diagnostic test performance between rapid LFAs, but overall limited sensitivity and high specificity in acutely admitted patients. First, in a pilot phase 20 NAT-positive and 5 NAT-negative patients were retrospectively selected for which six LFAs were performed on heparin plasma samples obtained upon hospital presentation ( Figure S1 ), which corresponded to the dates of molecular testing. This study shows that the sensitivity of LFA was low in patients suspected for COVID-19 presenting to the hospital, but it improved in patients with at least seven days of symptoms and in those with CRP levels >100 mg/L upon presentation. abstract: OBJECTIVES: To assess the diagnostic performance of rapid lateral flow immunochromatographic assays (LFAs) compared to an enzyme-linked immunosorbent assay (ELISA) and nucleic acid amplification tests (NATs) in suspected coronavirus disease 2019 (COVID-19) patients. METHODS: Patients presenting to a Dutch teaching hospital were eligible between March 17 and April 10, 2020, when they had respiratory symptoms that were suspected for COVID-19. The performances of six different LFAs were evaluated in plasma samples obtained on corresponding respiratory sample dates of NATs testing. Subsequently, the best performing LFA was evaluated in 228 patients and in 50 sera of a historical patient control group. RESULTS: In the pilot analysis sensitivity characteristics of LFA were heterogenous ranging from 2/20 (10%; 95% confidence interval (CI) 0-23) to 11/20 (55%; 95% CI 33-77). In the total cohort, Orient Gene Biotech COVID-19 IgG/IgM Rapid Test LFA had a sensitivity of 43/99 (43%; 95% CI 34-53) and specificity of 126/129 (98%; 95% CI 95-100). Sensitivity increased to 31/52 (60%; 95% CI 46-73) in patients with at least seven days of symptoms, and to 21/33 (64%; 95% CI 47-80) in patients with C-reactive protein (CRP) >100 mg/L. Sensitivity and specificity of Wantai SARS-CoV-2 Ab ELISA was 59/95 (62%; 95% CI 52-72) and 125/128 (98%; 95% CI 95-100) in all patients, respectively, but sensitivity increased to 38/48 (79%; 95% CI 68-91) in patients with at least seven days of symptoms. CONCLUSIONS: There is large variability in diagnostic test performance between rapid LFAs, but overall limited sensitivity and high specificity in acutely admitted patients. Sensitivity improved in patients with longer existing symptoms or high CRP. LFAs should only be considered as additional triage tools when these may lead to the improvement of hospital logistics. url: https://doi.org/10.1016/j.cmi.2020.05.028 doi: 10.1016/j.cmi.2020.05.028 id: cord-329350-qrxl5o1e author: Pan, Angelo title: Suggestions from Cremona, Italy - two months into the pandemic at the frontline of COVID-19 in Europe date: 2020-06-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.sciencedirect.com/science/article/pii/S1198743X20303360?v=s5 doi: 10.1016/j.cmi.2020.05.038 id: cord-297470-lx3xwg92 author: Pan, Yunbao title: Seroprevalence of SARS-CoV-2 immunoglobulin antibodies in Wuhan, China: part of the city-wide massive testing campaign date: 2020-10-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: The outbreak of 2019 coronavirus disease (COVID-19) pandemic in Wuhan, China, has subsided after a hard hit by the disease and subsequent city lockdown. Information on the number of people involved in Wuhan is still inadequate. This study aimed to describe the screening results of 61,437 community members in Wuchang District, Wuhan. METHODS: In mid-May 2020, Wuhan launched a population-scale city-wide SARS-CoV-2 testing campaign, which aimed to perform nucleic acid and viral antibody testing for citizens in Wuhan. Here we show the screening results of cluster sampled 61,437 residents in Wuchang District, Wuhan, China. RESULTS: A total of 1470 (2.39%, 95% CI: 2.27-2.52) individuals were detected positive for at least one antiviral antibody. Among the positive individuals, 324 (0.53%, 95% CI: 0.47-0.59) and 1200 (1.95%, 95% CI: 1.85-2.07) were positive for immunoglobulin IgM and IgG, respectively, and 54 (0.08%, 95% CI: 0.07-0.12) were positive for both antibodies. The positive rate of female carriers of antibodies were higher than those of male counterparts (male-to-female ratio of 0.75), especially in elderly citizens (ratio of 0.18 in 90+ age subgroup), indicating a sexual discrepancy in seroprevalence. In addition, viral nucleic acid detection using real-time PCR had showed 8 (0.013%, 95% CI: 0.006-0.026) asymptomatic virus carriers. CONCLUSIONS: The seroprevalence of SARS-CoV-2 in Wuhan was low. Most of Wuhan residents are still susceptible to this virus. Precautions, such as wearing mask, frequent hand hygiene, and proper social distance, are necessary before an effective vaccine or antiviral treatments are available. url: https://www.ncbi.nlm.nih.gov/pubmed/33035672/ doi: 10.1016/j.cmi.2020.09.044 id: cord-314808-ssiggi2z author: Pappas, G. title: Psychosocial consequences of infectious diseases date: 2014-12-12 words: 3182.0 sentences: 137.0 pages: flesch: 44.0 cache: ./cache/cord-314808-ssiggi2z.txt txt: ./txt/cord-314808-ssiggi2z.txt summary: On the other hand, numerous new major threats have emerged during the last three decades; the pandemic of AIDS, the SARS outbreak, the ominous scenarios of an avian influenza pandemic, and the threat of biological weapons are just some examples explaining the concern among health authorities, the media, and the public. The psychological response of both patients and the public to the threat of infection has been evaluated with respect to numerous circumstances in recent years, not only acute outbreaks such as SARS, but also gradually evolving pandemics such as AIDS, threats with marginal risk for humans such as bovine spongiform encephalopathy (BSE; mad cow disease), and even threats that are only theoretical such as avian influenza. Mass media is another major factor that shapes the physical and psychological response of the public to an infectious disease threat, as depicted in numerous attack scenarios in the literature [32] [33] [34] . abstract: Historically, there has been an exaggerated fear related to infection compared to other conditions. Infection possesses unique characteristics that account for this disproportionate degree of fear: it is transmitted rapidly and invisibly; historically, it has accounted for major morbidity and mortality; old forms re-emerge and new forms emerge; and both the media and society are often in awe. Because, in an outbreak, the patient is both a victim and a vector, and because there exists the potential for infringement of personal rights in order to control an outbreak, infection may be viewed (and has been depicted in popular culture) as a foreign invasion. During recent outbreaks, fear, denial, stigmatization and loss have been recorded in the implicated individuals. Stigmatization and discrimination may further involve ethical correlations, and attempts to adress these issues through activism may also have unwarranted effects. Public health initiatives can address the public's fears by increasing health literacy, which can contribute to reducing stigmatization. url: https://api.elsevier.com/content/article/pii/S1198743X14604614 doi: 10.1111/j.1469-0691.2009.02947.x id: cord-291272-srt08jh8 author: Peters, E.J.G. title: Outcomes of persons with COVID-19 in hospitals with and without standard treatment with (Hydroxy)chloroquine date: 2020-10-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVE: To compare survival of subjects with COVID-19 treated in hospitals that either did or did not routinely treat patients with hydroxychloroquine or chloroquine. METHODS: We analysed data of COVID-19 patients treated in 9 hospitals in the Netherlands. Inclusion dates ranged from February 27(th) 2020, to May 15(th), when the Dutch national guidelines no longer supported the use of (hydroxy)chloroquine. Seven hospitals routinely treated subjects with (hydroxy)chloroquine, two hospitals did not. Primary outcome was 21-day all-cause mortality. We performed a survival analysis using log-rank test and Cox-regression with adjustment for age, sex and covariates based on premorbid health, disease severity, and the use of steroids for adult respiratory distress syndrome, including dexamethasone. RESULTS: Among 1949 included subjects, 21-day mortality was 21.5% in 1596 subjects treated in hospitals that routinely prescribed (hydroxy)chloroquine, and 15.0% in 353 subjects that were treated in hospitals that did not. In the adjusted Cox-regression models this difference disappeared, with an adjusted hazard ratio of 1.09 (95%CI 0.81-1.47). When stratified by actually received treatment in individual subjects, the use of (hydroxy)chloroquine was associated with an increased 21-day mortality (HR 1.58; 95%CI 1.24-2.02) in the full model. CONCLUSIONS: After adjustment for confounders, mortality was not significantly different in hospitals that routinely treated patients with (hydroxy)chloroquine, compared with hospitals that did not. We compared outcomes of hospital strategies rather than outcomes of individual patients to reduce the chance of indication bias. This study adds evidence against the use of (hydroxy)chloroquine in hospitalised patients with COVID-19. url: https://www.sciencedirect.com/science/article/pii/S1198743X20306157?v=s5 doi: 10.1016/j.cmi.2020.10.004 id: cord-300023-2dg7njki author: Pillet, S. title: Contamination of healthcare workers'' mobile phones by epidemic viruses() date: 2015-12-20 words: 3087.0 sentences: 157.0 pages: flesch: 51.0 cache: ./cache/cord-300023-2dg7njki.txt txt: ./txt/cord-300023-2dg7njki.txt summary: We aimed to evaluate the presence of virus RNA from epidemic viruses including metapneumovirus, respiratory syncytial virus, influenza viruses, rotavirus (RV) and norovirus on the MPs used by healthcare workers (HCWs) and to relate it to hygiene measures. The aims of this study were (a) to evaluate the contamination of MPs by epidemic viruses including RV, NV, influenza A and B viruses, syncytial respiratory virus (RSV) and metapneumovirus (hMPV) in clinical settings, (b) to evaluate the behaviour of HCWs using their MPs in our center by using a blindly recorded questionnaire and (c) to correlate viral contamination of MPs with the behaviour of HCWs. The study took place at the University Hospital of Saint-Étienne, France, from January to March 2013, i.e. the period of circulation of epidemic viruses (influenza viruses, RSV, gastroenteritis-associated viruses) in our setting [22] (personal data). abstract: Mobile phones (MPs) are potential reservoirs of nosocomial bacteria, but few data are available concerning viruses. We aimed to evaluate the presence of virus RNA from epidemic viruses including metapneumovirus, respiratory syncytial virus, influenza viruses, rotavirus (RV) and norovirus on the MPs used by healthcare workers (HCWs) and to relate it to hygiene measures. An anonymous behavioural questionnaire about MP use at hospital was administered to the HCWs of four adult and paediatric departments of a university hospital. After sampling personal (PMP) and/or professional MPs (digital enhanced cordless telephone, DECT), virus RNAs were extracted and amplified by one-step real-time reverse transcription–quantitative PCR. The molecular results were analysed in a masked manner in relation to the behavioural survey. Questionnaires from 114 HCWs (35 senior physicians, 30 residents, 32 nurses, 27 nurses' assistants) working either in adult (n = 58) or paediatric (n = 56) departments were analysed. Medical personnel used their PMP more frequently than paramedical HCWs (33/65 vs. 10/59, p <0.001). MPs were used during care more frequently in adult wards than in paediatric ones (46/58 vs. 27/56, p <0.001). Virus RNA was detected on 42/109 (38.5%) collected MPs, with RV found on 39, respiratory syncytial virus on three and metapneumovirus on one. The presence of virus RNA was significantly associated with MPs from the paediatric HCWs (p <0.001). MPs routinely used in hospital, even during care, can host virus RNA, especially RV. Promotion of frequent hand hygiene before and after MP use, along with frequent cleaning of MPs, should be encouraged. url: https://www.sciencedirect.com/science/article/pii/S1198743X15010344 doi: 10.1016/j.cmi.2015.12.008 id: cord-275556-798oed8n author: Piubelli, Chiara title: Overall decrease of SARS-CoV-2 viral load and reduction of clinical burden: the experience of a Northern Italy hospital date: 2020-10-12 words: 610.0 sentences: 49.0 pages: flesch: 59.0 cache: ./cache/cord-275556-798oed8n.txt txt: ./txt/cord-275556-798oed8n.txt summary: OBJECTIVES: In Italy the burden of patients with Coronavirus Disease 2019 (Covid-19) gradually decreased from March to the end of May. In this work, we aimed at evaluating a possible association between the severity of clinical manifestations and viral load over time, during the epidemiological transition from high to low transmission setting. CONCLUSIONS: We observed a reduction over time of the proportion of patients with Covid-19 requiring intensive care, along with decreasing median values of viral load. The proportion of patients requiring intensive care significantly reduced from 6.7% ( We observed a reduction over time of the proportion of patients with Covid-19 requiring intensive 46 care, along with decreasing median values of viral load. As the epidemiological context changes 47 from high to low transmission setting, people are presumably exposed to a lower viral load, which 48 has been previously associated to less severe clinical manifestations. abstract: OBJECTIVES: In Italy the burden of patients with Coronavirus Disease 2019 (Covid-19) gradually decreased from March to the end of May. In this work, we aimed at evaluating a possible association between the severity of clinical manifestations and viral load over time, during the epidemiological transition from high to low transmission setting. METHODS: We reviewed the cases of Covid-19 diagnosed at the Emergency Room of our hospital, retrieving the proportion of patients admitted to the intensive care unit. A raw estimation of the viral load was done evaluating the Ct (cycle threshold) trend obtained from our diagnostic Reverse Transcriptase real-time PCR test. RESULTS: The proportion of patients requiring intensive care significantly reduced from 6.7% (19/281) in March, to 1.1% (1/86) in April, and to none in May (Fisher’s test p-value=0.0067). As for viral load, we observed a trend of Ct increasing from a median value of 24 (IQR 19-29) to 34 (IQR 29-37) between March and May, with a statistically significant difference between March and April (Pairwise Wilcoxon test with Stepdown Bonferroni Adjustment for multiple testing, p=0.0003). CONCLUSIONS: We observed a reduction over time of the proportion of patients with Covid-19 requiring intensive care, along with decreasing median values of viral load. As the epidemiological context changes from high to low transmission setting, people are presumably exposed to a lower viral load, which has been previously associated to less severe clinical manifestations. url: https://doi.org/10.1016/j.cmi.2020.10.006 doi: 10.1016/j.cmi.2020.10.006 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: nan sentences: nan pages: flesch: nan cache: txt: summary: 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-008258-5v55vv4s author: Raoult, D. title: Is it the end of the nervous breakdown on avian influenza? date: 2015-06-21 words: 598.0 sentences: 34.0 pages: flesch: 61.0 cache: ./cache/cord-008258-5v55vv4s.txt txt: ./txt/cord-008258-5v55vv4s.txt summary: The nervous breakdown on avian influenza that has affected the WHO, the different governments and the largest journals in the world may perhaps end with two articles published in the Journal of Infectious Diseases in May 2015 [1, 2] . This prospective survey in Egypt over 3 years on 1000 people showed that when H5N1 was endemic, 2% of the exposed population had antibodies compared with 0% of controls, and when the epidemic H9N2 appeared in poultry, seroprevalence increased from 0 to 5.6% and 7.5%, all asymptomatic infections. In total the zoonotic variant of H5N1 avian flu and H9N2 is very common in people in contact with poultry; it is banal and most of the time, asymptomatic. Avian influenza A(H5N1) and A(H9N2) seroprevalence and risk factors for infection among Egyptians: a prospective, controlled seroepidemiological study abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7130003/ doi: 10.1016/j.cmi.2015.06.011 id: cord-317918-pl625ela author: Ripa, Marco title: Secondary Infections in Patients Hospitalized with COVID-19: Incidence and Predictive Factors date: 2020-10-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: Aim of our study was to describe the incidence and predictive factors of secondary infections in patients with COVID-19. METHODS: Cohort study on patients hospitalized with COVID-19 at IRCCS San Raffaele Hospital between February 25(th) and April 6th, 2020 (NCT04318366). We considered secondary bloodstream (BSIs) or possible lower respiratory tract infections (pLRTIs) occurred after 48 hours since hospital admission until death or discharge. We calculated multivariable Fine-Gray models, to assess factors associated with risk of secondary infections. RESULTS: Among 731 patients, a secondary infection was diagnosed in 68 patients (9.3%): 58/731 patients (7.9%) had at least one BSI and 22/731 patients (3.0%) at least one pLRTI. Overall 28-day cumulative incidence was 16.4% (95% CI 12.4% - 21.0%). The majority of BSIs was due to gram-positive pathogens (76/106 isolates, 71.7%), specifically coagulase-negative staphylococci (53/76, 69.7%), while among gram-negatives (23/106, 21.7%) Acinetobacter baumanii (7/23, 30.4%) and Escherichia coli (5/23, 21.7%) predominated. pLRTIs were mainly caused by gram-negative pathogens (14/26, 53.8%). Eleven patients were diagnosed with putative invasive aspergillosis. At multivariable analysis, factors associated with secondary infections were low baseline lymphocyte count (<0.7 vs >0.7 per 10(9)/L: subdistribution hazard ratios (sdHRs) 1.93 [95% CI 1.11-3.35]), baseline PaO(2)/FiO(2) (per 100-points lower: sdHRs 1.56 [95% CI 1.21-2.04]), and intensive-care unit (ICU) admission in the first 48 hours (sdHR 2.51 [95% CI 1.04-6.05]). CONCLUSIONS: Patients hospitalized with COVID-19 had a high incidence of secondary infections. At multivariable analysis, early need for ICU, respiratory failure, and severe lymphopenia, were identified as risk factors for secondary infections. url: https://www.sciencedirect.com/science/article/pii/S1198743X20306522?v=s5 doi: 10.1016/j.cmi.2020.10.021 id: cord-010162-hfo35gsq author: Saikku, Pekka title: Atypical respiratory pathogens date: 2014-12-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The main atypical pathogens in respiratory tract infections are classified on the basis of their ability to cause atypical pneumonia. This is not a well-defined clinical entity, and it is evident that atypical pathogens can sometimes cause ‘typical’ pneumonias and vice versa. This emphasizes the need for microbiological diagnosis, since it affects the selection of proper treatment, in which β-lactam antibiotics and aminoglycosides are not effective. Moreover, mixed infections caused by atypical and typical pathogens together are common. At this moment rapid and sensitive diagnostic methods are lacking. Besides numerous viruses, the main bacterial pathogens causing atypical pneumonias are Mycoplasma pneumoniae, two chlamydial species, Chlamydia pneumoniae and C. psittaci, one rickettsia, Coxiella burnetti, and several Legionella species. The majority of these pathogens cause upper respiratory tract infections more often than overt pneumonias. An atypical agent, Chlamydia pneumoniae, has also been associated with chronic inflammatory conditions in the cardiovascular system. The most recently discovered pathogen in atypical pneumonias is a hantavirus causing hantavirus pulmonary syndrome. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172217/ doi: 10.1111/j.1469-0691.1997.tb00464.x id: cord-307273-pplky6g4 author: Schrooyen, Loïc title: Homeless people hospitalized with COVID-19 in Brussels date: 2020-08-07 words: 1006.0 sentences: 63.0 pages: flesch: 45.0 cache: ./cache/cord-307273-pplky6g4.txt txt: ./txt/cord-307273-pplky6g4.txt summary: To the editor, Compared to the general population, homeless people have higher mortality, both related to communicable and non-communicable diseases, partly explained by higher exposure to risk factors including alcoholism, illicit drug abuse and smoking(1,2). Between 3 rd March and 26 th May 2020, 14 homeless people were identified among 238 patients hospitalized for a COVID-19 pneumonia resulting in a homelessness prevalence of 5.88%. Incidences of COVID-19 among homeless and non-homeless patients were calculated using homeless census report and our hospital catchment population. For the reporting period, incidences were 650 and 194/100.000 hospitalized homeless and non-homeless patients for COVID-19, respectively. We found a high but similar proportion of comorbidities (arterial hypertension, diabetes and cardiovascular diseases) in both populations hospitalized with COVID-19. The high prevalence of comorbidities and the increased exposure to risk factors in the homeless population could increase their risk of more severe disease and mortality following SARS-CoV-2 infection. abstract: nan url: https://api.elsevier.com/content/article/pii/S1198743X2030478X doi: 10.1016/j.cmi.2020.08.002 id: cord-292296-nocmabcg author: Shang, L. title: Fangcang shelter hospitals in COVID-19 pandemic: the practice and its significance date: 2020-05-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32360781/ doi: 10.1016/j.cmi.2020.04.038 id: cord-333334-90q1xkld author: Shengchen, D. title: Evaluation of a molecular point-of-care testing for viral and atypical pathogens on intravenous antibiotic duration in hospitalized adults with lower respiratory tract infection: a randomized clinical trial date: 2019-06-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: The primary objective was to evaluate whether a molecular point-of-care test (POCT) for viral and atypical pathogens added to routine real-time PCR could reduce duration of intravenous antibiotics in hospitalized patients with lower respiratory tract infection (LRTI) compared with routine real-time PCR. METHODS: In this single-centre, open-label, randomized controlled study, we enrolled hospitalized adults diagnosed with LRTI. Patients were randomized to an intervention group (POCT FilmArray Panel for 20 viruses, atypical pathogens and bacteria plus routine real-time PCR) or a control group (routine real-time PCR for ten pathogens). The primary outcome was duration of intravenous antibiotics during hospitalization. The secondary outcomes included length of stay, cost of hospitalization and de-escalation within 72 hours and between 72 hours and 7 days. Intention-to-treat analysis was used. RESULTS: Between October 2017 and July 2018, we enrolled 800 eligible patients (398 in the intervention group and 402 in the control group). Duration of intravenous antibiotics in the intervention group was shorter than in the control (7.0 days (interquartile range (IQR) 5.0–9.0) versus 8.0 days (IQR 6.0–11.0); p <0.001). Length of hospital stay in the intervention group was significantly shorter (8.0 days (IQR 7.0–11.0) versus 9.0 days (IQR 7.0–12.0; p <0.001) and the cost of hospitalization in the intervention group was significantly lower ($1804.7 (IQR 1298.4–2633.8) versus $2042.5 (IQR 1427.4–2926.2); p 0.002) than control group. More patients in the intervention group achieved de-escalation within 72 hours (7.9%, 29/367 versus 3.2%, 12/377; p 0.005) and between 72 hours and 7 days (29.7%, 109/367 versus 22.0%, 83/377; p 0.024). CONCLUSIONS: Use of molecular POCT testing for respiratory viruses and atypical pathogens might help to reduce intravenous antibiotic use in hospitalized LRTI patients. CLINICAL TRIAL REGISTRATION: clinicaltrials.gov Identifier: NCT03391076. url: https://doi.org/10.1016/j.cmi.2019.06.012 doi: 10.1016/j.cmi.2019.06.012 id: cord-325186-nq6ay4eo author: Sieswerda, Elske title: Recommendations for antibacterial therapy in adults with COVID-19 – An evidence based guideline date: 2020-10-01 words: 855.0 sentences: 65.0 pages: flesch: 37.0 cache: ./cache/cord-325186-nq6ay4eo.txt txt: ./txt/cord-325186-nq6ay4eo.txt summary: SCOPE: The Dutch Working Party on Antibiotic Policy constituted a multidisciplinary expert committee to provide evidence-based recommendation for the use of antibacterial therapy in hospitalized adults with a respiratory infection and suspected or proven 2019 Coronavirus disease (COVID-19). QUESTIONS ADDRESSED BY THE GUIDELINE AND RECOMMENDATIONS: We assessed evidence on the risk of bacterial infections in hospitalized COVID-19 patients, the associated bacterial pathogens, how to diagnose bacterial infections and how to treat bacterial infections. For patients with secondary bacterial respiratory infection we recommend to follow other guideline recommendations on antibacterial treatment for patients with hospital-acquired and ventilator-associated pneumonia. An antibiotic treatment duration of five days in patients with COVID-19 and suspected bacterial respiratory infection is recommended upon improvement of signs, symptoms and inflammatory markers. As COVID-19 patients frequently 72 need prolonged hospitalization and respiratory support, unnecessary antibiotics upon 73 hospitalization may increase the individual risk of subsequent hospital-acquired pneumonia 74 (HAP) and other adverse events [12, 13] . abstract: SCOPE: The Dutch Working Party on Antibiotic Policy constituted a multidisciplinary expert committee to provide evidence-based recommendation for the use of antibacterial therapy in hospitalized adults with a respiratory infection and suspected or proven 2019 Coronavirus disease (COVID-19). METHODS: We performed a literature search to answer four key questions. The committee graded the evidence and developed recommendations by using Grading of Recommendations Assessment, Development, and Evaluation methodology. QUESTIONS ADDRESSED BY THE GUIDELINE AND RECOMMENDATIONS: We assessed evidence on the risk of bacterial infections in hospitalized COVID-19 patients, the associated bacterial pathogens, how to diagnose bacterial infections and how to treat bacterial infections. Bacterial co-infection upon admission was reported in 3.5% of COVID-19 patients, while bacterial secondary infections during hospitalization occurred up to 15%. No or very low quality evidence was found to answer the other key clinical questions. Although the evidence base on bacterial infections in COVID-19 is currently limited, available evidence supports restrictive antibiotic use from an antibiotic stewardship perspective, especially upon admission. To support restrictive antibiotic use, maximum efforts should be undertaken to obtain sputum and blood culture samples as well as pneumococcal urinary antigen testing. We suggest to stop antibiotics in patients who started antibiotic treatment upon admission when representative cultures as well as urinary antigen tests show no signs of involvement of bacterial pathogens after 48 hours. For patients with secondary bacterial respiratory infection we recommend to follow other guideline recommendations on antibacterial treatment for patients with hospital-acquired and ventilator-associated pneumonia. An antibiotic treatment duration of five days in patients with COVID-19 and suspected bacterial respiratory infection is recommended upon improvement of signs, symptoms and inflammatory markers. Larger, prospective studies about the epidemiology of bacterial infections in COVID-19 are urgently needed to confirm our conclusions and ultimately prevent unnecessary antibiotic use during the COVID-19 pandemic. url: https://www.sciencedirect.com/science/article/pii/S1198743X20305942?v=s5 doi: 10.1016/j.cmi.2020.09.041 id: cord-253250-zet48zcl author: Thaden, J.T. title: When two for the price of one isn’t a bargain: Estimating prevalence and microbiology of bacterial co-infections in patients with COVID-19 date: 2020-09-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.sciencedirect.com/science/article/pii/S1198743X20305292?v=s5 doi: 10.1016/j.cmi.2020.09.002 id: cord-276399-omjfyog0 author: To, K.K.W. title: Respiratory virus infection among hospitalized adult patients with or without clinically apparent respiratory infection: a prospective cohort study date: 2019-04-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: To determine the viral epidemiology and clinical characteristics of patients with and without clinically apparent respiratory tract infection. METHODS: This prospective cohort study was conducted during the 2018 winter influenza season. Adult patients with fever/respiratory symptoms (fever/RS group) were age- and sex-matched with patients without fever/RS (non-fever/RS group) in a 1:1 ratio. Respiratory viruses were tested using NxTAG™ Respiratory Pathogen Panel IVD, a commercially-available multiplex PCR panel. RESULTS: A total of 214 acutely hospitalized patients were included in the final analysis, consisting of 107 with fever/RS (fever/RS group), and 107 age- and sex-matched patients without fever/RS (non-fever/RS group). Respiratory viruses were detected in 34.1% (73/214) of patients, and co-infection occurred in 7.9% (17/214) of patients. The incidence of respiratory virus was higher in the fever/RS group than in the non-fever/RS group (44.9% (48/107) versus 23.4% (25/107), p 0.001). Influenza B virus, enterovirus/rhinovirus and coronaviruses were detected more frequently in the fever/RS group, whereas parainfluenza virus 4B and adenovirus were detected more frequently in the non-fever/RS group. Among the non-fever/RS group, chest discomfort was more common among patients tested positive for respiratory viruses than those without respiratory virus detected (44% (11/25) versus 22% (18/82), p 0.04). CONCLUSIONS: Respiratory viruses can be frequently detected among hospitalized patients without typical features of respiratory tract infection. These patients may be a source of nosocomial outbreaks. url: https://doi.org/10.1016/j.cmi.2019.04.012 doi: 10.1016/j.cmi.2019.04.012 id: cord-331002-7uojryqz author: Valent, Francesca title: Detection of SARS-CoV-2 in nasopharynx according to clinical phenotype of affected patients date: 2020-09-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: Duration of SARS-CoV-2 in upper respiratory tract is extremely variable, but its relation to disease severity is unknown. We investigated such relation in the 530,000-inhabitant North-Eastern Italian province of Udine. METHODS: We analysed real‐time reverse‐transcriptase polymerase chain reaction (RT-PCR) tests for SARS-CoV-2 on upper respiratory specimens conducted at the Virology Laboratory of the University Hospital of Udine, Italy, serving the whole province, from March 1 to April 30, 2020, on positive subjects of four groups characterized by different disease severity (critically ill patients admitted to Intensive Care Units, patients admitted to Infectious Disease Units, symptomatic patients visited at the Emergency Department and not hospitalized, and asymptomatic subjects tested during contact tracing or screening activities). Duration of viral positivity was assessed from the first positive test to the day of the first of two consecutive negative tests. Univariate and multivariate analyses were conducted to investigate differences in the four groups. RESULTS: From March 1 to April 30, 39,483 RT-PCR tests for SARS-CoV-2 were conducted on 23,778 persons. 974 subjects had a positive test result. Among those with multiple tests (N=878), mean time to negativity was 23.7 days (standard error 0.3639) (median 23, interquartile range: 16-30 days). Mean time to negativity was longer in the ICU group than in the others, whereas no difference was observed between asymptomatic patients and those with mild disease. CONCLUSIONS: Disease control measures should not be adjusted to account for differences in viral shedding according to symptomatic status. url: https://api.elsevier.com/content/article/pii/S1198743X20305255 doi: 10.1016/j.cmi.2020.08.041 id: cord-327253-gge6wzly author: Villa, Simone title: Stigma at the time of the COVID-19 pandemic date: 2020-08-07 words: 1373.0 sentences: 86.0 pages: flesch: 53.0 cache: ./cache/cord-327253-gge6wzly.txt txt: ./txt/cord-327253-gge6wzly.txt summary: 1 Beginning in late January 2020, when the COVID-19 epidemic was still largely limited to China, verbal and physical attacks against Chinese or people of Asian descent have been documented in many countries. 10 In contrary, uninfected COVID-19 people may be facing discrimination when applying for jobs in some countries that may implement COVID-19 passport strategies, despite recommendations of the World Health Organization against such a practice. This reactive behaviour facilitates spreading of infectious pathogens especially among those with mild symptoms who avoid seeking medical attention and act J o u r n a l P r e -p r o o f as usual not to raise suspicion on their condition. The world cannot bear a parallel pandemic of stigma, which only serves to boost the spread of infectious diseases and worsen people''s health conditions and social behaviours. Noteworthy, individuals with COVID-19 may develop poor health-seeking behaviours (e.g. avoiding testing) because, by anticipating and fearing stigma, they may perceive the risk of losing their job and being marginalised in the society. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32777361/ doi: 10.1016/j.cmi.2020.08.001 id: cord-255971-kamai25b author: Wee, Liang En title: Reduction in healthcare-associated respiratory viral infections during a COVID-19 outbreak date: 2020-07-03 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.sciencedirect.com/science/article/pii/S1198743X20303736?v=s5 doi: 10.1016/j.cmi.2020.06.027 id: cord-276212-ys5njiw0 author: Wei, L. title: Burden, seasonal pattern and symptomatology of acute respiratory illnesses with different viral aetiologies in children presenting at outpatient clinics in Hong Kong date: 2015-05-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Respiratory viruses cause acute respiratory diseases with a broad and overlapping spectrum of symptoms. We examined the clinical symptoms and explored the patterns of various respiratory viral infections in children in Hong Kong. Among 2090 specimens collected from outpatient care (2007–2010), 1343 (64.3%) were positive for any virus by the xTAG assay, and 81 (3.9%) were positive for co-infection. The most frequently detected viruses among children aged 6–15 years were enterovirus/rhinovirus and influenza virus A, whereas most non-influenza viruses were more frequently detected in younger children. Higher body temperature was more common for illnesses associated with influenza viruses than for those associated with non-influenza viruses, but other symptoms were largely similar across all infections. The seasonality pattern varied among different viruses, with influenza virus A being the predominant virus detected in winter, and enterovirus/rhinovirus being more commonly detected than influenza virus A in the other three seasons, except for 2009. url: https://www.ncbi.nlm.nih.gov/pubmed/26033670/ doi: 10.1016/j.cmi.2015.05.027 id: cord-318021-4qrf5m8s author: Wolfensberger, A. title: Development and validation of a semi-automated surveillance system—lowering the fruit for non-ventilator-associated hospital-acquired pneumonia (nvHAP) prevention() date: 2019-03-25 words: 3611.0 sentences: 210.0 pages: flesch: 43.0 cache: ./cache/cord-318021-4qrf5m8s.txt txt: ./txt/cord-318021-4qrf5m8s.txt summary: title: Development and validation of a semi-automated surveillance system—lowering the fruit for non-ventilator-associated hospital-acquired pneumonia (nvHAP) prevention() OBJECTIVES: Conducting manual surveillance of non-ventilator-associated hospital-acquired pneumonia (nvHAP) using ECDC (European Centre for Disease Prevention and Control) surveillance criteria is very resource intensive. Sensitivity, negative predictive value, and accuracy of semi-automated surveillance versus full manual surveillance were lowest in the validation sample consisting of patients with HAP according to the International Classification of Diseases (ICD-10) discharge diagnostic codes, with 97.5% (CI: 93.7–99.3%), 99.2% (CI: 97.9–99.8%), and 99.4% (CI: 98.4–99.8%), respectively. Three authors reported nvHAP incidence rates between 0.12 and 2.28 per 1000 patient days by applying the 2013 CDC surveillance definition to patients with International Classification of Diseases (ICD-9-CM) codes for pneumonia not present on admission [8e10] . abstract: OBJECTIVES: Conducting manual surveillance of non-ventilator-associated hospital-acquired pneumonia (nvHAP) using ECDC (European Centre for Disease Prevention and Control) surveillance criteria is very resource intensive. We developed and validated a semi-automated surveillance system for nvHAP, and describe nvHAP incidence and aetiology at our hospital. METHODS: We applied an automated classification algorithm mirroring ECDC definition criteria to distinguish patients ‘not at risk’ from patients ‘at risk’ for suffering from nvHAP. ‘At risk’-patients were manually screened for nvHAP. For validation, we applied the reference standard of full manual evaluation to three validation samples comprising 2091 patients. RESULTS: Among the 39 519 University Hospital Zurich inpatient discharges in 2017, the algorithm identified 2454 ‘at-risk’ patients, reducing the number of medical records to be manually screened by 93.8%. From this subset, nvHAP was identified in 251 patients (0.64%, 95%CI: 0.57–0.73). Sensitivity, negative predictive value, and accuracy of semi-automated surveillance versus full manual surveillance were lowest in the validation sample consisting of patients with HAP according to the International Classification of Diseases (ICD-10) discharge diagnostic codes, with 97.5% (CI: 93.7–99.3%), 99.2% (CI: 97.9–99.8%), and 99.4% (CI: 98.4–99.8%), respectively. The overall incidence rate of nvHAP was 0.83/1000 patient days (95%CI: 0.73–0.94), with highest rates in haematology/oncology, cardiac and thoracic surgery, and internal medicine including subspecialties. CONCLUSIONS: The semi-automated surveillance demonstrated a very high sensitivity, negative predictive value, and accuracy. This approach significantly reduces manual surveillance workload, thus making continuous nvHAP surveillance feasible as a pivotal element for successful prevention efforts. url: https://api.elsevier.com/content/article/pii/S1198743X19301211 doi: 10.1016/j.cmi.2019.03.019 id: cord-283818-4m9p717r author: Yan, Chao title: Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal amplification assay date: 2020-04-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVE: To evaluate a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for detection of SARS-CoV-2, and compare it with RT polymerase chain reaction (RT-PCR). METHODS: We designed primers specific to the orf1ab and S genes of SARS-CoV-2. Total viral RNA was extracted using the QIAamp Viral RNA Mini Kit. We optimized the RT-LAMP assay. And, this assay was evaluated for its sensitivity and specificity of detection using real-time turbidity monitoring and visual observation. RESULTS: The primer sets orf1ab-4 and S-123 amplified the genes in the shortest times, the mean (±SD) time was 18 ± 1.32 min and 20 ± 1.80 min, respectively, and 63°C was the optimum reaction temperature. The sensitivity was 2×10(1) copies and 2×10(2) copies per reaction with primer sets orf1ab-4 and S-123, respectively. This assay showed no cross-reactivity with other 60 respiratory pathogens. To describe the availability of this method in clinical diagnosis, we collected 130 specimens from patients with clinically suspected SARS-CoV-2 infection. Among them, 58 were confirmed to be positive and 72 were negative by RT-LAMP. The sensiticity was 100% (95% CI 92.3% - 100%), specificity 100% (95% CI 93.7% - 100%). This assay detected SARS-CoV-2 in the mean (±SD) time of 26.28 ± 4.48 min and the results can be identified with visual observation. CONCLUSION: These results demonstrate that we developed a rapid, simple, specific, and sensitive RT-LAMP assay for SARS-CoV-2 detection among clinical samples. It will be a powerful tool for SARS-CoV-2 identification, and for monitoring suspected patients, close contacts, and high-risk groups. url: https://www.ncbi.nlm.nih.gov/pubmed/32276116/ doi: 10.1016/j.cmi.2020.04.001 id: cord-351028-p5cq2is5 author: Yang, Jia-Wei title: Corticosteroid administration for viral pneumonia: COVID-19 and beyond date: 2020-06-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Corticosteroids are commonly used as adjuvant therapy for acute respiratory distress syndrome (ARDS) by many clinicians due to their perceived anti-inflammatory effects. However, for patients with severe viral pneumonia, the corticosteroid treatment is highly controversial. OBJECTIVES: The purpose of this review is to systematically evaluate the effect and potential mechanism of corticosteroid administration in pandemic viral pneumonia. SOURCES: We comprehensively searched all manuscripts on corticosteroids therapy for influenza, SARS, MERS and SARS-CoV-2 viral pneumonia from the PubMed, EMBASE, Web of Science and Cochrane Library databases. CONTENT: We systematic summarized the effects of corticosteroids therapy for pandemic viral pneumonia and the potential mechanism of corticosteroid worked in COVID-19. IMPLICATIONS: Observational studies showed that corticosteroid treatment was associated with increased mortality and nosocomial infections for influenza and delay virus clearance for SARS-CoV and MERS-CoV. Limited data on corticosteroid therapy for COVID-19 were reported. Corticosteroids were used in about a fifth of patients (670/2995, 22.4%). Although clinical observational studies reported the improvement in symptoms and oxygenation for the severe COVID-19 patients received corticosteroids therapy, case fatality rate in the corticosteroid group was significantly higher than that in the non-corticosteroid group (69/443, 15.6% vs 56/1310, 4.3%). Compared with non-severe patients, severe patients were more likely to receive corticosteroid therapy (201/382, 52.6% vs 201/1310, 15.3%). Although there is no evidence of corticosteroid therapy reduce the mortality of COVID-19 patients, some improvements in clinical symptoms and oxygenation were reported in some clinical observational studies. Excessive inflammatory response and lymphopenia might be critical factors associated with disease severity and mortality of COVID-19. Sufficiently powered randomized controlled trials with rigorous inclusion/exclusion criteria and standardized dose and duration of corticosteroids are needed to verify the effectiveness and safety of corticosteroid therapy. url: https://api.elsevier.com/content/article/pii/S1198743X20303645 doi: 10.1016/j.cmi.2020.06.020 id: cord-252569-9rv1p3qh author: Zanella, M.-C. title: High-throughput sequencing for the aetiologic identification of viral encephalitis, meningoencephalitis, and meningitis. A narrative review and clinical appraisal date: 2019-01-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Viral aetiologies are the most common cause of central nervous system (CNS) infections. Approximately one-half of CNS infections remain of undetermined origin. High-throughput sequencing (HTS) brought new perspectives to CNS infection investigations, allowing investigation of viral aetiologies with an unbiased approach. HTS use is still limited to specific clinical situations. OBJECTIVES: The aim of this review was to evaluate the contribution and pitfalls of HTS for the aetiologic identification of viral encephalitis, meningoencephalitis, and meningitis in CNS patient samples. SOURCES: PubMed was searched from 1 January 2008 to 2 August 2018 to retrieve available studies on the topic. Additional publications were included from a review of full-text sources. CONTENT: Among 366 studies retrieved, 29 used HTS as a diagnostic technique. HTS was performed in cerebrospinal fluid and brain biopsy samples of 307 patients, including immunocompromised, immunocompetent paediatric, and adult cases. HTS was performed retrospectively in 18 studies and prospectively in 11. HTS led to the identification of a potential causal virus in 41 patients, with 11 viruses known and ten not expected to cause CNS infections. Various HTS protocols were used. IMPLICATIONS: The additional value of HTS is difficult to quantify because of various biases. Nevertheless, HTS led to the identification of a viral cause in 13% of encephalitis, meningoencephalitis, and meningitis cases in which various assays failed to identify the cause. HTS should be considered early in clinical management as a complement to routine assays. Standardized strategies and systematic studies are needed for the integration of HTS in clinical management. url: https://www.sciencedirect.com/science/article/pii/S1198743X18308127 doi: 10.1016/j.cmi.2018.12.022 id: cord-294392-a8s66g96 author: Zhang, Shuai title: Factors associated with asymptomatic infection in health-care workers with SARS-CoV-2 infection in Wuhan, China: a multi-center retrospective cohort study date: 2020-09-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: We aim to describe the fraction of asymptomatic health-care workers (HCWs) in two designated hospitals for COVID-19 treatment in Wuhan and explore the factors associated with asymptomatic SARS-CoV-2 infection. METHODS: All HCWs in Wuhan Union Hospital and Wuhan Red Cross Hospital with either positive SARS-CoV-2 nucleic acid or antibody test before April 18, 2020 were included. Exposure, epidemiologic, demographic information were retrospectively collected by a structured questionnaire. Medical records were also reviewed for clinical characteristics and CT images in HCWs. RESULTS: As of April 18, 2020, a total of 424 HCWs were identified. Among them, 276 (65.1%) were symptomatic and 148 (34.9%) were asymptomatic. 55 (19.9%) families of the symptomatic HCWs and 16 (10.8%) families of the asymptomatic HCWs were infected with SARS-CoV-2. HCWs with infected family members tend to be symptomatic cases (Odds ratio [OR], 2.053 [95% confidence interval (CI), 1.130-3.730]; P=0.018). Multivariable logistic regression analysis exhibited that performing tracheal intubation or extubation (OR, 4.057 [95% CI, 1.183-13.909]; P=0.026) was associated with an increased likelihood of symptomatic SARS-CoV-2 infection, while consistent use of N95 respirators (OR, 0.369 [95% CI, 0.201-0.680]; P=0.001) and eye protection (OR, 0.217 [95% CI, 0.116-0.404]; P<0.001) were associated with an increased likelihood of asymptomatic SARS-CoV-2 infection. CONCLUSIONS: Asymptomatic SARS-CoV-2 infection in HCWs occupies a considerable proportion during the pandemic of COVID-19. Those who have performed tracheal intubation or extubation were most likely to develop related symptoms, while those taking aggressive measures including consistent use of N95 masks, and eye protection tended to be asymptomatic cases. url: https://www.sciencedirect.com/science/article/pii/S1198743X20305218?v=s5 doi: 10.1016/j.cmi.2020.08.038 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-009664-kb9fnbgy author: nan title: Oral presentations date: 2014-12-24 words: 71112.0 sentences: 3948.0 pages: flesch: 47.0 cache: ./cache/cord-009664-kb9fnbgy.txt txt: ./txt/cord-009664-kb9fnbgy.txt summary: Because of the conflicting reports and lack of published data from paediatric patients, we sought to assess possible MIC change over time and to compare results generated by using different methodologies including Etest, agar dilution, and broth microdilution (MicroScan) methods. Recently, in vitro and in vivo studies have shown that NO plays a key role in the eradication of the leishmania parasite Objective: To determine whether a NO donor patch (developed by electrospinning technique) is as effective as meglumine antimoniate in the treatment of CL while causing less adverse events Methods: A double-blind, randomised, placebo-controlled clinical trial was conducted with 178 patients diagnosed with CL in Santander, Colombia, South-America. To follow the development and spread of the resistance among these strains is difficult, as antibiotic susceptibility testing of clinically relevant anaerobes in different routine laboratories in Europe is less and less frequently carried out due to the fact, that clinicians treat many presumed anaerobic infections empirically. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7162236/ doi: 10.1111/j.1469-0691.2009.02857.x id: cord-019490-m1cuuehi author: nan title: Abstracts cont. date: 2015-12-28 words: 93588.0 sentences: 5683.0 pages: flesch: 50.0 cache: ./cache/cord-019490-m1cuuehi.txt txt: ./txt/cord-019490-m1cuuehi.txt summary: Tigecycline Evaluation Surveillance Trial (TEST) -Global in vitro antibacterial activity against selected species of glucose non-fermenting organisms Objective: Despite the introduction of new antimicrobials to treat resistant gram-positive bacteria, Staphylococcus aureus continues to be a therapeutic challenge for the clinician. Two prospective studies from our centre identified common causes of CAP in India to be Mycoplasma pneumoniae [MP] and Legionella pneumophila [LP] by serology in 11% each, and SPN in 10% by culture of respiratory secretions/blood/ Conclusion: Although SPN is the most common isolate, the rising numbers of gram negative organisms (38%) and atypical pathogens associated with increasing mortality stress the need for review of initial antibiotic choice for adults with higher PORT classes. Conclusion: The spectrum of isolates among our patients were shifting towards gram positive bacteria with high resistance to different groups of antimicrobial agents limiting few choices for alternative therapies for infection control. 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-023592-w96h4rir author: nan title: Abstracts cont. date: 2015-12-28 words: 67857.0 sentences: 4136.0 pages: flesch: 52.0 cache: ./cache/cord-023592-w96h4rir.txt txt: ./txt/cord-023592-w96h4rir.txt summary: Conclusions: Although the risk of developing more serious gastric lesions increased as the number of virulence factor genes are accumulated in a given Hp strain, we did not find any significant differences or relationship in the cagA, vacA or babA2 status between the Hp isolates from patients with gastritis or peptic ulcer in this study. pneumophila at the serogroup level, it was used in two different outbreaks to demonstrate rapidly the identity of the sequences between strains responsible for severe human infection and those isolated in the hot water reservoir, suggesting a common origin. To determine the antimicrobial resistance in Salmonella and Shigella strains isolated from stool specimens during a 2-year period, from patients admitted to our clinics with a diagnosis of diarrhoea. In our study the susceptibility of 65 bacterial strains isolated in hospital environment (colonising or infecting patients or carried by German cockroaches) to antibiotics and chemical disinfectants was determined. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172567/ doi: 10.1111/j.1469-0691.2004.0902c.x ==== 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