Carrel name: journal-clinInfectDis-cord Creating study carrel named journal-clinInfectDis-cord Initializing database file: cache/cord-007049-02p8ug67.json key: cord-007049-02p8ug67 authors: McGeer, Allison title: Let Him Who Desires Peace Prepare for War: United States Hospitals and Severe Acute Respiratory Syndrome Preparedness date: 2004-07-15 journal: Clin Infect Dis DOI: 10.1086/421784 sha: doc_id: 7049 cord_uid: 02p8ug67 file: cache/cord-007068-vcfs41eb.json key: cord-007068-vcfs41eb authors: Moradi, Tony; Bennett, Nicholas; Shemanski, Shelby; Kennedy, Kevin; Schlachter, Andrew; Boyd, Sarah title: Use of Procalcitonin and a Respiratory Polymerase Chain Reaction Panel to Reduce Antibiotic Use via an Electronic Medical Record Alert date: 2019-10-22 journal: Clin Infect Dis DOI: 10.1093/cid/ciz1042 sha: doc_id: 7068 cord_uid: vcfs41eb file: cache/cord-002514-pp06m5xk.json key: cord-002514-pp06m5xk authors: Venkatesan, Sudhir; Myles, Puja R.; Leonardi-Bee, Jo; Muthuri, Stella G.; Al Masri, Malak; Andrews, Nick; Bantar, Carlos; Dubnov-Raz, Gal; Gérardin, Patrick; Koay, Evelyn S. C.; Loh, Tze Ping; Memish, Ziad; Miller, Elizabeth; Oliva, Maria E.; Rath, Barbara A.; Schweiger, Brunhilde; Tang, Julian W.; Tran, Dat; Vidmar, Tjasa; Waight, Pauline A.; Nguyen-Van-Tam, Jonathan S. title: Impact of Outpatient Neuraminidase Inhibitor Treatment in Patients Infected With Influenza A(H1N1)pdm09 at High Risk of Hospitalization: An Individual Participant Data Metaanalysis date: 2017-05-15 journal: Clin Infect Dis DOI: 10.1093/cid/cix127 sha: doc_id: 2514 cord_uid: pp06m5xk file: cache/cord-007064-nepgttxf.json key: cord-007064-nepgttxf authors: Chemaly, Roy F; Dadwal, Sanjeet S; Bergeron, Anne; Ljungman, Per; Kim, Yae-Jean; Cheng, Guang-Shing; Pipavath, Sudhakar N; Limaye, Ajit P; Blanchard, Elodie; Winston, Drew J; Stiff, Patrick J; Zuckerman, Tsila; Lachance, Silvy; Rahav, Galia; Small, Catherine B; Mullane, Kathleen M; Patron, Roberto L; Lee, Dong-Gun; Hirsch, Hans H; Waghmare, Alpana; McKevitt, Matt; Jordan, Robert; Guo, Ying; German, Polina; Porter, Danielle P; Gossage, David L; Watkins, Timothy R; Marty, Francisco M; Chien, Jason W; Boeckh, Michael title: A Phase II, Randomized, Double-blind, Placebo-Controlled Trial of Presatovir for the Treatment of Respiratory Syncytial Virus Upper Respiratory Tract Infection in Hematopoietic-Cell Transplant Recipients date: 2019-12-03 journal: Clin Infect Dis DOI: 10.1093/cid/ciz1166 sha: doc_id: 7064 cord_uid: nepgttxf file: cache/cord-007170-svsfu7fj.json key: cord-007170-svsfu7fj authors: Richt, J. A.; VandeWoude, S.; Zink, M. C.; Clements, J. E.; Herzog, S.; Stitz, L.; Rott, R.; Narayan, O. title: Infection with Borna Disease Virus: Molecular and Immunobiological Characterization of the Agent date: 1992-06-17 journal: Clin Infect Dis DOI: 10.1093/clinids/14.6.1240 sha: doc_id: 7170 cord_uid: svsfu7fj file: cache/cord-007047-7ty9mxa9.json key: cord-007047-7ty9mxa9 authors: Reller, L. 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date: 2004-03-15 journal: Clin Infect Dis DOI: 10.1086/382081 sha: doc_id: 266696 cord_uid: w9sb038q file: cache/cord-266775-4npowkkz.json key: cord-266775-4npowkkz authors: Xu, Jun; Zhong, Shuqing; Liu, Jinghua; Li, Li; Li, Yong; Wu, Xinwei; Li, Zhijie; Deng, Peng; Zhang, Jingqiang; Zhong, Nanshan; Ding, Yanqing; Jiang, Yong title: Detection of Severe Acute Respiratory Syndrome Coronavirus in the Brain: Potential Role of the Chemokine Mig in Pathogenesis date: 2005-10-15 journal: Clin Infect Dis DOI: 10.1086/444461 sha: doc_id: 266775 cord_uid: 4npowkkz file: cache/cord-277307-wabruzfs.json key: cord-277307-wabruzfs authors: Gu, Wei; Deng, Xianding; Reyes, Kevin; Hsu, Elaine; Wang, Candace; Sotomayor-Gonzalez, Alicia; Federman, Scot; Bushnell, Brian; Miller, Steve; Chiu, Charles title: Associations of Early COVID-19 Cases in San Francisco with Domestic and International Travel date: 2020-05-21 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa599 sha: doc_id: 277307 cord_uid: wabruzfs file: cache/cord-269973-sntnmqqd.json key: cord-269973-sntnmqqd authors: To, Kelvin Kai-Wang; Chan, Wan-Mui; Ip, Jonathan Daniel; Chu, Allen Wing-Ho; Tam, Anthony Raymond; Liu, Raymond; Wu, Alan Ka-Lun; Lung, Kwok-Cheung; Tsang, Owen Tak-Yin; Lau, Daphne Pui-Ling; To, Wing-Kin; Kwan, Mike Yat-Wah; Yau, Yat-Sun; Ng, Anthony Chin-Ki; Yip, Cyril Chik-Yan; Chan, Kwok-Hung; Tse, Herman; Hung, Ivan Fan-Ngai; Yuen, Kwok-Yung title: Unique SARS-CoV-2 clusters causing a large COVID-19 outbreak in Hong Kong date: 2020-08-05 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1119 sha: doc_id: 269973 cord_uid: sntnmqqd file: cache/cord-266150-wox7pnkr.json key: cord-266150-wox7pnkr authors: Torres, Juan Pablo; Piñera, Cecilia; De La Maza, Verónica; Lagomarcino, Anne J; Simian, Daniela; Torres, Bárbara; Urquidi, Cinthya; Valenzuela, María Teresa; O’Ryan, Miguel title: SARS-CoV-2 antibody prevalence in blood in a large school community subject to a Covid-19 outbreak: a cross-sectional study date: 2020-07-10 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa955 sha: doc_id: 266150 cord_uid: wox7pnkr file: cache/cord-281726-s1o5l7ns.json key: cord-281726-s1o5l7ns authors: Yu, Ignatius T. S.; Wong, Tze Wai; Chiu, Yuk Lan; Lee, Nelson; Li, Yuguo title: Temporal-Spatial Analysis of Severe Acute Respiratory Syndrome among Hospital Inpatients date: 2005-05-01 journal: Clin Infect Dis DOI: 10.1086/428735 sha: doc_id: 281726 cord_uid: s1o5l7ns file: cache/cord-015516-hx7ktq8j.json key: cord-015516-hx7ktq8j authors: nan title: In the Literature date: 2005-10-15 journal: Clin Infect Dis DOI: 10.1086/497097 sha: doc_id: 15516 cord_uid: hx7ktq8j file: cache/cord-252423-ojmt4k2w.json key: cord-252423-ojmt4k2w authors: Qu, Bing; Yang, Jing title: Monologue of a physician who tested persistently positive for COVID-19 date: 2020-05-11 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa551 sha: doc_id: 252423 cord_uid: ojmt4k2w file: cache/cord-252761-ro5tj0tx.json key: cord-252761-ro5tj0tx authors: Marriott, Deborah; Beresford, Rohan; Mirdad, Feras; Stark, Damien; Glanville, Allan; Chapman, Scott; Harkness, Jock; Dore, Gregory J; Andresen, David; Matthews, Gail V title: Concomitant marked decline in prevalence of SARS-CoV-2 and other respiratory viruses among symptomatic patients following public health interventions in Australia: data from St Vincent’s Hospital and associated screening clinics, Sydney, NSW. date: 2020-08-25 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1256 sha: doc_id: 252761 cord_uid: ro5tj0tx file: cache/cord-260274-c3586tp6.json key: cord-260274-c3586tp6 authors: Somers, Emily C; 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Hjalgrim, Henrik; Lillevang, Søren Thue; Ullum, Henrik title: Estimation of SARS-CoV-2 infection fatality rate by real-time antibody screening of blood donors date: 2020-06-25 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa849 sha: doc_id: 271014 cord_uid: xzpvupms file: cache/cord-273839-oasgagpc.json key: cord-273839-oasgagpc authors: Bisno, Alan L.; Gerber, Michael A.; Jack M., Gwaltney; Kaplan, Edward L.; Schwartz, Richard H. title: Diagnosis and Management of Group A Streptococcal Pharyngitis: A Practice Guideline date: 1997-09-17 journal: Clin Infect Dis DOI: 10.1086/513768 sha: doc_id: 273839 cord_uid: oasgagpc file: cache/cord-260779-riw5xs3j.json key: cord-260779-riw5xs3j authors: van Griensven, Johan; De Weiggheleire, Anja; Delamou, Alexandre; Smith, Peter G.; Edwards, Tansy; Vandekerckhove, Philippe; Bah, Elhadj Ibrahima; Colebunders, Robert; Herve, Isola; Lazaygues, Catherine; Haba, Nyankoye; Lynen, Lutgarde title: The Use of Ebola Convalescent Plasma to Treat Ebola Virus Disease in Resource-Constrained Settings: A Perspective From the Field date: 2016-01-01 journal: Clin Infect Dis DOI: 10.1093/cid/civ680 sha: doc_id: 260779 cord_uid: riw5xs3j file: cache/cord-266808-wyuodzyt.json key: cord-266808-wyuodzyt authors: Nagler, Arielle R; Goldberg, Eric R; Aguero-Rosenfeld, Maria E; Cangiarella, Joan; Kalkut, Gary; Monahan, Carolyn Rooke; Cerfolio, Robert J title: Early Results from SARS-CoV-2 PCR testing of Healthcare Workers at an Academic Medical Center in New York City date: 2020-06-28 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa867 sha: doc_id: 266808 cord_uid: wyuodzyt file: cache/cord-268233-ibxufjrv.json key: cord-268233-ibxufjrv authors: Nagappa, Bharathnag; Marimuthu, Yamini title: Seroconversion rate and diagnostic accuracy of serological tests for COVID-19 date: 2020-05-30 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa676 sha: doc_id: 268233 cord_uid: ibxufjrv file: cache/cord-010599-nwp2if8d.json key: cord-010599-nwp2if8d authors: Hayden, Frederick G.; Herrington, Darrell T.; Coats, Teresa L.; Kim, Kenneth; Cooper, Ellen C.; Villano, Stephen A.; Liu, Siyu; Hudson, Spencer; Pevear, Daniel C.; Collett, Marc; McKinlay, Mark title: Efficacy and Safety of Oral Pleconaril for Treatment of Colds Due to Picornaviruses in Adults: Results of 2 Double-Blind, Randomized, Placebo-Controlled Trials date: 2003-06-15 journal: Clin Infect Dis DOI: 10.1086/375069 sha: doc_id: 10599 cord_uid: nwp2if8d file: cache/cord-260457-m1jbpo5l.json key: cord-260457-m1jbpo5l authors: Allander, Tobias; 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M.; Lehtinen, Pasi; üsterback, Riikka; Vuorinen, Tytti; Waris, Matti; Bjerkner, Annelie; Tiveljung-Lindell, Annika; van den Hoogen, Bernadette G.; Hyypiä, Timo; Ruuskanen, Olli title: Human Bocavirus and Acute Wheezing in Children date: 2007-04-01 journal: Clin Infect Dis DOI: 10.1086/512196 sha: doc_id: 260457 cord_uid: m1jbpo5l file: cache/cord-273956-mruywa71.json key: cord-273956-mruywa71 authors: Mathers, Amy J title: The practical challenges of making clinical use of the quantitative value for SARS-CoV-2 viral load across several dynamics date: 2020-07-10 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa958 sha: doc_id: 273956 cord_uid: mruywa71 file: cache/cord-279932-bilr71ay.json key: cord-279932-bilr71ay authors: Plotkin, Stanley A title: The Value of Human Challenges in Severe Acute Respiratory Syndrome Coronavirus 2 Vaccine Development date: 2020-07-16 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1013 sha: doc_id: 279932 cord_uid: bilr71ay file: cache/cord-280763-4bnv2t3f.json key: cord-280763-4bnv2t3f authors: Piñana, José Luis; Pérez, Ariadna; Montoro, Juan; Giménez, Estela; Gómez, María Dolores; Lorenzo, Ignacio; Madrid, Silvia; González, Eva María; Vinuesa, Víctor; Hernández-Boluda, Juan Carlos; Salavert, Miguel; Sanz, Guillermo; Solano, Carlos; Sanz, Jaime; Navarro, David title: Clinical Effectiveness of Influenza Vaccination After Allogeneic Hematopoietic Stem Cell Transplantation: A Cross-sectional, Prospective, Observational Study date: 2019-06-01 journal: Clin Infect Dis DOI: 10.1093/cid/ciy792 sha: doc_id: 280763 cord_uid: 4bnv2t3f file: cache/cord-280958-36ytqapi.json key: cord-280958-36ytqapi authors: Decker, Summer J; Goldstein, Todd A; Ford, Jonathan M; Teng, Michael N; Pugliese, Robert S; Berry, Gregory J; Pettengill, Matthew; Silbert, Suzane; Hazelton, Todd R; Wilson, Jason W; Shine, Kristy; Wang, Zi-Xuan; Hutchinson, Morgan; Castagnaro, Joseph; Bloom, Ona E; Breining, Dwayne A; Goldsmith, Barbara M; Sinnott, John T; O'Donnell, Donna Gentile; Crawford, James M; Lockwood, Charles J; Kim, Kami title: 3D Printed Alternative to the Standard Synthetic Flocked Nasopharyngeal Swabs Used for COVID-19 testing date: 2020-09-10 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1366 sha: doc_id: 280958 cord_uid: 36ytqapi file: cache/cord-007296-q9rn75qb.json key: cord-007296-q9rn75qb authors: Muether, Philipp S.; Gwaltney, Jack M. title: Variant Effect of First- and Second-Generation Antihistamines as Clues to Their Mechanism of Action on the Sneeze Reflex in the Common Cold date: 2001-11-01 journal: Clin Infect Dis DOI: 10.1086/322518 sha: doc_id: 7296 cord_uid: q9rn75qb file: cache/cord-265006-m1dmgcd1.json key: cord-265006-m1dmgcd1 authors: Kow, Chia Siang; Hasan, Syed Shahzad title: Do the meta-analyses provide a clean bill of health to the use of renin-angiotensin system inhibitors in COVID-19? date: 2020-08-08 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1167 sha: doc_id: 265006 cord_uid: m1dmgcd1 file: cache/cord-278259-pbnnp9i1.json key: cord-278259-pbnnp9i1 authors: Choi, Eun Hwa; Lee, Hoan Jong; Kim, Sun Jung; Eun, Byung Wook; Kim, Nam Hee; Lee, Jin A; Lee, Jun Ho; Song, Eun Kyung; Park, So Hee Kim1 Ji Yong; Sung, Ji Yeon title: The Association of Newly Identified Respiratory Viruses with Lower Respiratory Tract Infections in Korean Children, 2000–2005 date: 2006-09-01 journal: Clin Infect Dis DOI: 10.1086/506350 sha: doc_id: 278259 cord_uid: pbnnp9i1 file: cache/cord-001381-b0tlco4t.json key: cord-001381-b0tlco4t authors: Howie, Stephen R. 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Ian; Adegbola, Richard A. title: Etiology of Severe Childhood Pneumonia in The Gambia, West Africa, Determined by Conventional and Molecular Microbiological Analyses of Lung and Pleural Aspirate Samples date: 2014-09-01 journal: Clin Infect Dis DOI: 10.1093/cid/ciu384 sha: doc_id: 1381 cord_uid: b0tlco4t file: cache/cord-279828-es498qul.json key: cord-279828-es498qul authors: Boulle, Andrew; Davies, Mary-Ann; Hussey, Hannah; Ismail, Muzzammil; Morden, Erna; Vundle, Ziyanda; Zweigenthal, Virginia; Mahomed, Hassan; Paleker, Masudah; Pienaar, David; Tembo, Yamanya; Lawrence, Charlene; Isaacs, Washiefa; Mathema, Hlengani; Allen, Derick; Allie, Taryn; Bam, Jamy-Lee; Buddiga, Kasturi; Dane, Pierre; Heekes, Alexa; Matlapeng, Boitumelo; Mutemaringa, Themba; Muzarabani, Luckmore; Phelanyane, Florence; Pienaar, Rory; Rode, Catherine; Smith, Mariette; Tiffin, Nicki; Zinyakatira, Nesbert; Cragg, Carol; Marais, Frederick; Mudaly, Vanessa; Voget, Jacqueline; Davids, Jody; Roodt, Francois; van Zyl Smit, Nellis; 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Marais, David; Marais, Suzaan; Maritz, Francois; Maughan, Deborah; Mazondwa, Simthandile; Mbanga, Luyanda; Mbatani, Nomonde; Mbena, Bulewa; Meintjes, Graeme; Mendelson, Marc; Möller, Ernst; Moore, Allison; Ndebele, Babalwa; Nortje, Marc; Ntusi, Ntobeko; Nyengane, Funeka; Ofoegbu, Chima; Papavarnavas, Nectarios; Peter, Jonny; Pickard, Henri; Pluke, Kent; Raubenheimer, Peter J; Robertson, Gordon; Rozmiarek, Julius; Sayed, A; Scriba, Matthias; Sekhukhune, Hennie; Singh, Prasun; Smith, Elsabe; Soldati, Vuyolwethu; Stek, Cari; van den berg, Robert; van der Merwe, Le Roux; Venter, Pieter; Vermooten, Barbra; Viljoen, Gerrit; Viranna, Santhuri; Vogel, Jonno; Vundla, Nokubonga; Wasserman, Sean; Zitha, Eddy; Lomas-Marais, Vanessa; Lombard, Annie; Stuve, Katrin; Viljoen, Werner; Basson, De Vries; Le Roux, Sue; Linden-Mars, Ethel; Victor, Lizanne; Wates, Mark; Zwanepoel, Elbe; Ebrahim, Nabilah; Lahri, Sa'ad; Mnguni, Ayanda; Crede, Thomas; de Man, Martin; Evans, Katya; Hendrikse, Clint; Naude, Jonathan; Parak, Moosa; Szymanski, Patrick; Van Koningsbruggen, Candice; Abrahams, Riezaah; Allwood, Brian; Botha, Christoffel; Henndrik Botha, Matthys; Broadhurst, Alistair; Claasen, Dirkie; Daniel, Che; Dawood, Riyaadh; du Preez, Marie; Du Toit, Nicolene; Erasmus, Kobie; Koegelenberg, Coenraad F N; Gabriel, Shiraaz; Hugo, Susan; Jardine, Thabiet; Johannes, Clint; Karamchand, Sumanth; Lalla, Usha; Langenegger, Eduard; Louw, Eize; Mashigo, Boitumelo; Mhlana, Nonte; Mnqwazi, Chizama; Moodley, Ashley; Moodley, Desiree; Moolla, Saadiq; Mowlana, Abdurasiet; Nortje, Andre; Olivier, Elzanne; Parker, Arifa; Paulsen, Chané; Prozesky, Hans; Rood, Jacques; Sabela, Tholakele; Schrueder, Neshaad; Sithole, Nokwanda; Sithole, Sthembiso; Taljaard, Jantjie J; Titus, Gideon; Van Der Merwe, Tian; van Schalkwyk, Marije; Vazi, Luthando; Viljoen, Abraham J; Yazied Chothia, Mogamat; Naidoo, Vanessa; Alan Wallis, Lee; Abbass, Mumtaz; Arendse, Juanita; Armien, Rizqa; Bailey, Rochelle; Bello, Muideen; Carelse, Rachel; Forgus, Sheron; Kalawe, Nosi; Kariem, Saadiq; Kotze, Mariska; Lucas, Jonathan; McClaughlin, Juanita; Murie, Kathleen; Najjaar, Leilah; Petersen, Liesel; Porter, James; Shaw, Melanie; Stapar, Dusica; Williams, Michelle; Aldum, Linda; Berkowitz, Natacha; Girran, Raakhee; Lee, Kevin; Naidoo, Lenny; Neumuller, Caroline; Anderson, Kim; Begg, Kerrin; Boerlage, Lisa; Cornell, Morna; de Waal, Renée; Dudley, Lilian; English, René; Euvrard, Jonathan; Groenewald, Pam; Jacob, Nisha; Jaspan, Heather; Kalk, Emma; Levitt, Naomi; Malaba, Thoko; Nyakato, Patience; Patten, Gabriela; Schneider, Helen; Shung King, Maylene; Tsondai, Priscilla; Van Duuren, James; van Schaik, Nienke; Blumberg, Lucille; Cohen, Cheryl; Govender, Nelesh; Jassat, Waasila; Kufa, Tendesayi; McCarthy, Kerrigan; Morris, Lynn; Hsiao, Nei-yuan; Marais, Ruan; Ambler, Jon; Ngwenya, Olina; Osei-Yeboah, Richard; Johnson, Leigh; Kassanjee, Reshma; Tamuhla, Tsaone title: Risk factors for COVID-19 death in a population cohort study from the Western Cape Province, South Africa date: 2020-08-29 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1198 sha: doc_id: 279828 cord_uid: es498qul file: cache/cord-266820-exl36jt3.json key: cord-266820-exl36jt3 authors: Rivera, Frida; Safdar, Nasia; Ledeboer, Nathan; Schaack, Grace; Chen, Derrick J; Munoz-Price, L Silvia title: Prevalence of SARS-CoV-2 asymptomatic infections in two large academic health systems in Wisconsin date: 2020-08-19 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1225 sha: doc_id: 266820 cord_uid: exl36jt3 file: cache/cord-288432-n2y9cunc.json key: cord-288432-n2y9cunc authors: Liu, Kun; Ai, Siqi; Song, Shuxuan; Zhu, Guanghu; Tian, Fei; Li, Huan; Gao, Yuan; Wu, Yinglin; Zhang, Shiyu; Shao, Zhongjun; Liu, Qiyong; Lin, Hualiang title: Population movement, city closure in Wuhan and geographical expansion of the 2019-nCoV pneumonia infection in China in January 2020 date: 2020-04-17 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa422 sha: doc_id: 288432 cord_uid: n2y9cunc file: cache/cord-289247-qc3to2xj.json key: cord-289247-qc3to2xj authors: Yamaoka, Yutaro; Jeremiah, Sundararaj S; Miyakawa, Kei; Saji, Ryo; Nishii, Mototsugu; Takeuchi, Ichiro; Ryo, Akihide title: Whole nucleocapsid protein of SARS-CoV-2 may cause false positive results in serological assays date: 2020-05-23 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa637 sha: doc_id: 289247 cord_uid: qc3to2xj file: cache/cord-280915-yk872yaz.json key: cord-280915-yk872yaz authors: Flaherman, Valerie J; Afshar, Yalda; Boscardin, John; Keller, Roberta L; Mardy, Anne; Prahl, Mary K; Phillips, Carolyn; Asiodu, Ifeyinwa V; Berghella, W Vincenzo; Chambers, Brittany D; Crear-Perry, Joia; Jamieson, Denise J; Jacoby, Vanessa L; Gaw, Stephanie L title: Infant Outcomes Following Maternal Infection with SARS-CoV-2: First Report from the PRIORITY Study date: 2020-09-18 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1411 sha: doc_id: 280915 cord_uid: yk872yaz file: cache/cord-254183-98o0dssj.json key: cord-254183-98o0dssj authors: Waggoner, Jesse J.; Soda, Elizabeth A.; Deresinski, Stan title: Rare and Emerging Viral Infections in Transplant Recipients date: 2013-10-15 journal: Clin Infect Dis DOI: 10.1093/cid/cit456 sha: doc_id: 254183 cord_uid: 98o0dssj file: cache/cord-275454-an8xvow3.json key: cord-275454-an8xvow3 authors: Clark, Andrew E; Lee, Francesca M title: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Screening With Specimen Pools: Time to Swim, or Too Deep for Comfort? date: 2020-09-28 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1145 sha: doc_id: 275454 cord_uid: an8xvow3 file: cache/cord-011745-dbdtpojs.json key: cord-011745-dbdtpojs authors: Thompson, Mark G.; Sokolow, Leslie Z.; Almendares, Olivia; Openo, Kyle; Farley, Monica M.; Meek, James; Ray, Julie; Kirley, Pamala Daily; Reingold, Arthur; Aragon, Deborah; Hancock, Emily; Baumbach, Joan; Schaffner, William; Lynfield, Ruth; Ryan, Pat; Monroe, Maya; Cheng, Po-Yung; Fry, Alicia M.; Shay, David K. title: Effectiveness of Nonadjuvanted Monovalent Influenza A(H1N1)pdm09 Vaccines for Preventing Reverse Transcription Polymerase Chain Reaction–Confirmed Pandemic Influenza Hospitalizations: Case-Control Study of Children and Adults at 10 US Influenza Surveillance Network Sites date: 2013-12-01 journal: Clin Infect Dis DOI: 10.1093/cid/cit551 sha: doc_id: 11745 cord_uid: dbdtpojs file: cache/cord-254458-bbcef8xt.json key: cord-254458-bbcef8xt authors: Ali, Farhana; Sweeney, Daniel A title: Throat Wash Testing and COVID-19 Disease: Should We Put Our Money Where Our Mouth Is? date: 2020-04-30 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa511 sha: doc_id: 254458 cord_uid: bbcef8xt file: cache/cord-256583-z3pd339v.json key: cord-256583-z3pd339v authors: Yen, Muh-Yong; 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Ware, Robert S; Lambert, Stephen B; Mhango, Lebogang P; Tozer, Sarah; Day, Rebecca; Grimwood, Keith; Bialasiewicz, Seweryn title: Parechovirus A Infections in Healthy Australian Children During the First 2 Years of Life: A Community-based Longitudinal Birth Cohort Study date: 2019-08-13 journal: Clin Infect Dis DOI: 10.1093/cid/ciz761 sha: doc_id: 7073 cord_uid: soov8q3q file: cache/cord-277611-3iynrfzq.json key: cord-277611-3iynrfzq authors: Buetti, Niccolò; Patrier, Juliette; Le Hingrat, Quentin; Loiodice, Ambre; Bouadma, Lila; Visseaux, Benoit; Timsit, Jean-François title: Risk factors for SARS-CoV-2 detection in blood of critically ill patients date: 2020-09-02 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1315 sha: doc_id: 277611 cord_uid: 3iynrfzq file: cache/cord-275349-b35pt3mo.json key: cord-275349-b35pt3mo authors: Lenz, Heinz-Josef; Richardson, Peter; Stebbing, Justin title: The Emergence of Baricitinib: A Story of Tortoises Versus Hares date: 2020-07-06 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa940 sha: doc_id: 275349 cord_uid: b35pt3mo file: cache/cord-277788-6ls21tkr.json key: cord-277788-6ls21tkr authors: Nelson, Brian C; Laracy, Justin; Shoucri, Sherif; Dietz, Donald; Zucker, Jason; Patel, Nina; Sobieszczyk, Magdalena E; Kubin, Christine J; Gomez-Simmonds, Angela title: Clinical Outcomes Associated with Methylprednisolone in Mechanically Ventilated Patients with COVID-19 date: 2020-08-09 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1163 sha: doc_id: 277788 cord_uid: 6ls21tkr file: cache/cord-291363-re45w37d.json key: cord-291363-re45w37d authors: Sanville, Bradley; Corbett, Rebecca; Pidcock, Wesley; Hardin, Kaitlyn; Sebat, Christian; Nguyen, Minh-Vu; Thompson, George R; Haczku, Angela; Schivo, Michael; Cohen, Stuart title: A Community Transmitted Case of Severe Acute Respiratory Distress Syndrome due to SARS CoV2 in the United States date: 2020-03-30 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa347 sha: doc_id: 291363 cord_uid: re45w37d file: cache/cord-280005-i9fp5rys.json key: cord-280005-i9fp5rys authors: Wang, Mengmei; Zhao, Yang; Hu, Weihua; Zhao, Dong; Zhang, Yunting; Wang, Tao; Zheng, Zhishui; Li, Xiaochen; Zeng, Shaolin; Liu, Zhenlian; Lu, Li; Wan, Zhihui; Hu, Ke title: Treatment of COVID-19 Patients with Prolonged Post-Symptomatic Viral Shedding with Leflunomide -- a Single-Center, Randomized, Controlled Clinical Trial date: 2020-09-21 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1417 sha: doc_id: 280005 cord_uid: i9fp5rys file: cache/cord-282539-skzosh6u.json key: cord-282539-skzosh6u authors: Casadevall, Arturo; Joyner, Michael J; Pirofski, Liise-anne title: Implications of Coronavirus Disease 2019 (COVID-19) Antibody Dynamics for Immunity and Convalescent Plasma Therapy date: 2020-08-17 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1213 sha: doc_id: 282539 cord_uid: skzosh6u file: cache/cord-279550-7u2hksxm.json key: cord-279550-7u2hksxm authors: Wang, Kai; Long, Quan-Xin; Deng, Hai-Jun; Hu, Jie; Gao, Qing-Zhu; Zhang, Gui-Ji; He, Chang-Long; Huang, Lu-Yi; Hu, Jie-Li; Chen, Juan; Tang, Ni; Huang, Ai-Long title: Longitudinal dynamics of the neutralizing antibody response to SARS-CoV-2 infection date: 2020-08-03 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1143 sha: doc_id: 279550 cord_uid: 7u2hksxm file: cache/cord-015493-vf4et613.json key: cord-015493-vf4et613 authors: Deresinski, Stan title: In the Literature date: 2007-10-15 journal: Clin Infect Dis DOI: 10.1086/522526 sha: doc_id: 15493 cord_uid: vf4et613 file: cache/cord-280954-wd89nka9.json key: cord-280954-wd89nka9 authors: Ackerson, Bradley; Tseng, Hung Fu; Sy, Lina S; Solano, Zendi; Slezak, Jeff; Luo, Yi; Fischetti, Christine A; Shinde, Vivek title: Severe Morbidity and Mortality Associated With Respiratory Syncytial Virus Versus Influenza Infection in Hospitalized Older Adults date: 2019-07-15 journal: Clin Infect Dis DOI: 10.1093/cid/ciy991 sha: doc_id: 280954 cord_uid: wd89nka9 file: cache/cord-283780-h4lwzpl9.json key: cord-283780-h4lwzpl9 authors: Zhang, John J Y; Lee, Keng Siang; Ang, Li Wei; Leo, Yee Sin; Young, Barnaby Edward title: Risk Factors of Severe Disease and Efficacy of Treatment in Patients Infected with COVID-19: A Systematic Review, Meta-Analysis and Meta-Regression Analysis date: 2020-05-14 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa576 sha: doc_id: 283780 cord_uid: h4lwzpl9 file: cache/cord-261270-jkm9c5yv.json key: cord-261270-jkm9c5yv authors: Annweiler, Cédric; Sacco, Guillaume; Salles, Nathalie; Aquino, Jean-Pierre; Gautier, Jennifer; Berrut, Gilles; Guérin, Olivier; Gavazzi, Gaetan title: National French survey of COVID-19 symptoms in people aged 70 and over date: 2020-06-18 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa792 sha: doc_id: 261270 cord_uid: jkm9c5yv file: cache/cord-276995-b003vcdc.json key: cord-276995-b003vcdc authors: Wiese, Andrew D; Everson, Jordan; Grijalva, Carlos G title: Social distancing measures: evidence of interruption of seasonal influenza activity and early lessons of the SARS-CoV-2 pandemic date: 2020-06-20 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa834 sha: doc_id: 276995 cord_uid: b003vcdc file: cache/cord-287676-qh7zeyyx.json key: cord-287676-qh7zeyyx authors: Angoulvant, François; Ouldali, Naïm; Yang, David Dawei; Filser, Mathilde; Gajdos, Vincent; Rybak, Alexis; Guedj, Romain; Soussan-Banini, Valérie; Basmaci, Romain; Lefevre-Utile, Alain; Brun-Ney, Dominique; Beaujouan, Laure; Skurnik, David title: COVID-19 pandemic: Impact caused by school closure and national lockdown on pediatric visits and admissions for viral and non-viral infections, a time series analysis date: 2020-06-03 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa710 sha: doc_id: 287676 cord_uid: qh7zeyyx file: cache/cord-252005-3ld5e7f5.json key: cord-252005-3ld5e7f5 authors: Lewis, Nathaniel M; Chu, Victoria T; Ye, Dongni; Conners, Erin E; 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Cerda-Contreras et.al date: 2020-08-14 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1212 sha: doc_id: 251945 cord_uid: v077hhgk file: cache/cord-258724-1qhen1bj.json key: cord-258724-1qhen1bj authors: Young, Barnaby E; Ong, Sean W X; Ng, Lisa F P; Anderson, Danielle E; Chia, Wan Ni; Chia, Po Ying; Ang, Li Wei; Mak, Tze-Minn; Kalimuddin, Shirin; Chai, Louis Yi Ann; Pada, Surinder; Tan, Seow Yen; Sun, Louisa; Parthasarathy, Purnima; Fong, Siew-Wai; Chan, Yi-Hao; Tan, Chee Wah; Lee, Bernett; Rötzschke, Olaf; Ding, Ying; Tambyah, Paul; Low, Jenny G H; Cui, Lin; Barkham, Timothy; Lin, Raymond Tzer Pin; Leo, Yee-Sin; Renia, Laurent; Wang, Lin-Fa; Lye, David Chien title: Viral dynamics and immune correlates of COVID-19 disease severity date: 2020-08-28 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1280 sha: doc_id: 258724 cord_uid: 1qhen1bj file: cache/cord-284782-51mbq7qb.json key: cord-284782-51mbq7qb authors: Huang, Jing; Liu, Fangkun; Teng, Ziwei; Chen, Jindong; Zhao, Jingping; Wang, Xiaoping; 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Rabold, Elizabeth M; Buono, Sean; Dietrich, Elizabeth A; Reses, Hannah E; Vuong, Jeni; Pawloski, Lucia; Dasu, Trivikram; Bhattacharyya, Sanjib; Pevzner, Eric; Hall, Aron J; Tate, Jacqueline E; Kirking, Hannah L title: Epidemiological Correlates of PCR Cycle Threshold Values in the Detection of SARS-CoV-2 date: 2020-09-28 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1469 sha: doc_id: 277410 cord_uid: lt19mijb file: cache/cord-007075-sl45z4i0.json key: cord-007075-sl45z4i0 authors: Marty, Francisco M; Chemaly, Roy F; Mullane, Kathleen M; Lee, Dong-Gun; Hirsch, Hans H; Small, Catherine B; Bergeron, Anne; Shoham, Shmuel; Ljungman, Per; Waghmare, Alpana; Blanchard, Elodie; Kim, Yae-Jean; McKevitt, Matt; Porter, Danielle P; Jordan, Robert; Guo, Ying; German, Polina; Boeckh, Michael; Watkins, Timothy R; Chien, Jason W; Dadwal, Sanjeet S title: A Phase 2b, Randomized, Double-blind, Placebo-Controlled Multicenter Study Evaluating Antiviral Effects, Pharmacokinetics, Safety, and Tolerability of Presatovir in Hematopoietic Cell Transplant Recipients with Respiratory Syncytial Virus (RSV) Infection of the Lower Respiratory Tract date: 2019-12-03 journal: Clin Infect Dis DOI: 10.1093/cid/ciz1167 sha: doc_id: 7075 cord_uid: sl45z4i0 file: cache/cord-265242-y8t37p0b.json key: cord-265242-y8t37p0b authors: Cui, Wei; Fan, Ying; Wu, Wei; Zhang, Feng; Wang, Jun-ying; Ni, An-ping title: Expression of Lymphocytes and Lymphocyte Subsets in Patients with Severe Acute Respiratory Syndrome date: 2003-09-15 journal: Clin Infect Dis DOI: 10.1086/378587 sha: doc_id: 265242 cord_uid: y8t37p0b file: cache/cord-272956-0yumc7em.json key: cord-272956-0yumc7em authors: Gnavi, Roberto; Demaria, Moreno; Picariello, Roberta; Dalmasso, Marco; Ricceri, Fulvio; Costa, Giuseppe title: Therapy With Agents Acting on the Renin-Angiotensin System and Risk of Severe Acute Respiratory Syndrome Coronavirus 2 Infection date: 2020-05-22 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa634 sha: doc_id: 272956 cord_uid: 0yumc7em file: cache/cord-268809-plgip4h6.json key: cord-268809-plgip4h6 authors: Bielecki, Michel; Züst, Roland; Siegrist, Denise; Meyerhofer, Daniele; Crameri, Giovanni Andrea Gerardo; Stanga, Zeno Giovanni; Stettbacher, Andreas; Buehrer, Thomas Werner; Deuel, Jeremy Werner title: Social distancing alters the clinical course of COVID-19 in young adults: A comparative cohort study date: 2020-06-29 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa889 sha: doc_id: 268809 cord_uid: plgip4h6 file: cache/cord-269455-pkjov371.json key: cord-269455-pkjov371 authors: Faust, Jeremy Samuel title: Towards a better case fatality estimate for SARS-CoV-2 during the early phase of the United States outbreak date: 2020-05-30 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa639 sha: doc_id: 269455 cord_uid: pkjov371 file: cache/cord-285403-h8ahn8fw.json key: cord-285403-h8ahn8fw authors: Zhang, Liangsheng; Shen, Fu-ming; Chen, Fei; Lin, Zhenguo title: Origin and Evolution of the 2019 Novel Coronavirus date: 2020-02-03 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa112 sha: doc_id: 285403 cord_uid: h8ahn8fw file: cache/cord-291286-diwigcy9.json key: cord-291286-diwigcy9 authors: De Schutter, Iris; De Wachter, Elke; Crokaert, Françoise; Verhaegen, Jan; Soetens, Oriane; Piérard, Denis; Malfroot, Anne title: Microbiology of Bronchoalveolar Lavage Fluid in Children With Acute Nonresponding or Recurrent Community-Acquired Pneumonia: Identification of Nontypeable Haemophilus influenzae as a Major Pathogen date: 2011-06-15 journal: Clin Infect Dis DOI: 10.1093/cid/cir235 sha: doc_id: 291286 cord_uid: diwigcy9 file: cache/cord-271269-0gimxteg.json key: cord-271269-0gimxteg authors: Gourtsoyannis, John title: COVID-19: Possible reasons for the increased prevalence of Olfactory and Gustatory dysfunction observed in European studies date: 2020-05-31 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa685 sha: doc_id: 271269 cord_uid: 0gimxteg file: cache/cord-278084-km04sz2s.json key: cord-278084-km04sz2s authors: Martino, Rodrigo; Rámila, Elena; Rabella, Núria; Muñoz, José Manuel; Peyret, Mercé; Portos, José Manuel; Laborda, Rosario; Sierra, Jorge title: Respiratory Virus Infections in Adults with Hematologic Malignancies: A Prospective Study date: 2003-01-01 journal: Clin Infect Dis DOI: 10.1086/344899 sha: doc_id: 278084 cord_uid: km04sz2s file: cache/cord-278045-hr3r17mz.json key: cord-278045-hr3r17mz authors: Yokota, Isao; Shane, Peter Y; Okada, Kazufumi; Unoki, Yoko; Yang, Yichi; Inao, Tasuku; Sakamaki, Kentaro; Iwasaki, Sumio; Hayasaka, Kasumi; Sugita, Junichi; Nishida, Mutsumi; Fujisawa, Shinichi; Teshima, Takanori title: Mass screening of asymptomatic persons for SARS-CoV-2 using saliva date: 2020-09-25 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1388 sha: doc_id: 278045 cord_uid: hr3r17mz file: cache/cord-287923-ev93r09i.json key: cord-287923-ev93r09i authors: Apisarnthanarak, Anucha; Mundy, Linda M; Tantawichien, Terapong; Leelarasamee, Amorn title: Infection Prevention and Control in Asia: Current Evidence and Future Milestones date: 2017-05-15 journal: Clin Infect Dis DOI: 10.1093/cid/cix071 sha: doc_id: 287923 cord_uid: ev93r09i file: cache/cord-279167-fj36mzm5.json key: cord-279167-fj36mzm5 authors: Gwaltney, Jack M. title: Acute Community-Acquired Sinusitis date: 1996-12-17 journal: Clin Infect Dis DOI: 10.1093/clinids/23.6.1209 sha: doc_id: 279167 cord_uid: fj36mzm5 file: cache/cord-289598-t8upoq9a.json key: cord-289598-t8upoq9a authors: Yoon, Jane C; Montgomery, Martha P; Buff, Ann M; Boyd, Andrew T; Jamison, Calla; Hernandez, Alfonso; Schmit, Kristine; Shah, Sarita; Ajoku, Sophia; Holland, David P; Prieto, Juliana; Smith, Sasha; Swancutt, Mark A; Turner, Kim; Andrews, Tom; Flowers, Kevin; Wells, Alyssa; Marchman, Cathryn; Laney, Emaline; Bixler, Danae; Cavanaugh, Sean; Flowers, Nicole; Gaffga, Nicholas; Ko, Jean Y; Paulin, Heather N; Weng, Mark K; Mosites, Emily; Morris, Sapna Bamrah title: COVID-19 Prevalence among People Experiencing Homelessness and Homelessness Service Staff during Early Community Transmission in Atlanta, Georgia, April–May 2020 date: 2020-09-08 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1340 sha: doc_id: 289598 cord_uid: t8upoq9a file: cache/cord-280571-ntgt5hy9.json key: cord-280571-ntgt5hy9 authors: Ginocchio, Christine C. title: Strengths and Weaknesses of FDA-Approved/Cleared Diagnostic Devices for the Molecular Detection of Respiratory Pathogens date: 2011-05-01 journal: Clin Infect Dis DOI: 10.1093/cid/cir046 sha: doc_id: 280571 cord_uid: ntgt5hy9 file: cache/cord-287119-eo0evoog.json key: cord-287119-eo0evoog authors: Kendall, Emily A title: When infections don’t reflect infectiousness: interpreting contact investigation data with care date: 2020-08-08 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1144 sha: doc_id: 287119 cord_uid: eo0evoog file: cache/cord-259471-lsdodl0a.json key: cord-259471-lsdodl0a authors: Pagliano, Pasquale; Piazza, Ornella; De Caro, Francesco; Ascione, Tiziana; Filippelli, Amelia title: Is Hydroxychloroquine a Possible Postexposure Prophylaxis Drug to Limit the Transmission to Healthcare Workers Exposed to Coronavirus Disease 2019? date: 2020-03-24 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa320 sha: doc_id: 259471 cord_uid: lsdodl0a file: cache/cord-291726-8670s4st.json key: cord-291726-8670s4st authors: Che, Xiao-yan; Di, Biao; Zhao, Guo-ping; Wang, Ya-di; Qiu, Li-wen; Hao, Wei; Wang, Ming; Qin, Peng-zhe; Liu, Yu-fei; Chan, Kwok-hong; Cheng, Vincent C. 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Douglas; Dean, Nathan C.; Dowell, Scott F.; File, Thomas M.; Musher, Daniel M.; Niederman, Michael S.; Torres, Antonio; Whitney, Cynthia G. title: Infectious Diseases Society of America/American Thoracic Society Consensus Guidelines on the Management of Community-Acquired Pneumonia in Adults date: 2007-03-01 journal: Clin Infect Dis DOI: 10.1086/511159 sha: doc_id: 292094 cord_uid: vmsdhccp file: cache/cord-295525-emrwcx0m.json key: cord-295525-emrwcx0m authors: To, Kelvin Kai-Wang; Tsang, Owen Tak-Yin; Yip, Cyril Chik-Yan; Chan, Kwok-Hung; Wu, Tak-Chiu; Chan, Jacky Man-Chun; Leung, Wai-Shing; Chik, Thomas Shiu-Hong; Choi, Chris Yau-Chung; Kandamby, Darshana H; Lung, David Christopher; Tam, Anthony Raymond; Poon, Rosana Wing-Shan; Fung, Agnes Yim-Fong; Hung, Ivan Fan-Ngai; Cheng, Vincent Chi-Chung; Chan, Jasper Fuk-Woo; Yuen, Kwok-Yung title: Consistent Detection of 2019 Novel Coronavirus in Saliva date: 2020-02-12 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa149 sha: doc_id: 295525 cord_uid: emrwcx0m file: cache/cord-292546-un0blb3w.json key: cord-292546-un0blb3w authors: Dandachi, Dima; Geiger, Grant; Montgomery, Mary W; Karmen-Tuohy, Savannah; Golzy, Mojgan; Antar, Annukka A R; Llibre, Josep M; Camazine, Maraya; Díaz-De Santiago, Alberto; Carlucci, Philip M; Zacharioudakis, Ioannis M; Rahimian, Joseph; Wanjalla, Celestine N; Slim, Jihad; Arinze, Folasade; Kratz, Ann Marie Porreca; Jones, Joyce L; Patel, Shital M; Kitchell, Ellen; Francis, Adero; Ray, Manoj; Koren, David E; Baddley, John W; Hill, Brannon; Sax, Paul E; Chow, Jeremy title: Characteristics, Comorbidities, and Outcomes in a Multicenter Registry of Patients with HIV and Coronavirus Disease-19 date: 2020-09-09 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1339 sha: doc_id: 292546 cord_uid: un0blb3w file: cache/cord-295270-6ptaxg74.json key: cord-295270-6ptaxg74 authors: Titanji, Boghuma K; Farley, Monica M; Schinazi, Raymond F; Marconi, Vincent C title: Response to Correspondence: Baricitinib – Impact on COVID-19 Coagulopathy? Jorgensen et. al. date: 2020-08-14 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1210 sha: doc_id: 295270 cord_uid: 6ptaxg74 file: cache/cord-297239-or6h6p9p.json key: cord-297239-or6h6p9p authors: Ridgway, Jessica P.; Bartlett, Allison H.; Garcia-Houchins, Sylvia; Cariño, Sean; Enriquez, Aurea; Marrs, Rachel; Perez, Cynthia; Shah, Mona; Guenette, Caroline; Mosakowski, Steve; Beavis, Kathleen G.; Landon, Emily title: Influenza Among Afebrile and Vaccinated Healthcare Workers date: 2015-06-01 journal: Clin Infect Dis DOI: 10.1093/cid/civ163 sha: doc_id: 297239 cord_uid: or6h6p9p file: cache/cord-292372-kn27ghlv.json key: cord-292372-kn27ghlv authors: de Chaisemartin, Clément; de Chaisemartin, Luc title: BCG vaccination in infancy does not protect against COVID-19. Evidence from a natural experiment in Sweden date: 2020-08-23 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1223 sha: doc_id: 292372 cord_uid: kn27ghlv file: cache/cord-294718-n3gx862b.json key: cord-294718-n3gx862b authors: Tam, Patrick C K; Ly, Kathleen M; Kernich, Max L; Spurrier, Nicola; Lawrence, Diana; Gordon, David L; Tucker, Emily C title: Detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breast milk of a mildly symptomatic patient with coronavirus disease 2019 (COVID-19) date: 2020-05-30 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa673 sha: doc_id: 294718 cord_uid: n3gx862b file: cache/cord-294853-8b0s5w4u.json key: cord-294853-8b0s5w4u authors: Nolen, Leisha D; Seeman, Sara; Bruden, Dana; Klejka, Joe; Desnoyers, Chris; Tiesinga, James; Singleton, Rosalyn title: Impact of Social Distancing and Travel Restrictions on non-COVID-19 Respiratory Hospital Admissions in Young Children in Rural Alaska date: 2020-09-05 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1328 sha: doc_id: 294853 cord_uid: 8b0s5w4u file: cache/cord-296588-q2716lda.json key: cord-296588-q2716lda authors: Hanson, Kimberly E; Caliendo, Angela M; Arias, Cesar A; Englund, Janet A; Lee, Mark J; Loeb, Mark; Patel, Robin; El Alayli, Abdallah; Kalot, Mohamad A; Falck-Ytter, Yngve; Lavergne, Valery; Morgan, Rebecca L; Murad, M Hassan; Sultan, Shahnaz; Bhimraj, Adarsh; Mustafa, Reem A title: Infectious Diseases Society of America Guidelines on the Diagnosis of COVID-19 date: 2020-06-16 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa760 sha: doc_id: 296588 cord_uid: q2716lda file: cache/cord-296631-43z3ee8m.json key: cord-296631-43z3ee8m authors: de Feria, Alejandro; Ortega-Legaspi, Juan M title: ACE inhibitors/ARB use and COVID-19. Time to change practice or keep gathering data? date: 2020-07-04 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa819 sha: doc_id: 296631 cord_uid: 43z3ee8m file: cache/cord-299274-gnbp7so5.json key: cord-299274-gnbp7so5 authors: Bodkin, Claire; Mokashi, Vaibhav; Beal, Kerry; Wiwcharuk, Jill; Lennox, Robin; Guenter, Dale; Smieja, Marek; O’Shea, Timothy title: Pandemic Planning in Homeless Shelters: A pilot study of a COVID-19 testing and support program to mitigate the risk of COVID-19 outbreaks in congregate settings date: 2020-06-08 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa743 sha: doc_id: 299274 cord_uid: gnbp7so5 file: cache/cord-295940-siy32dj7.json key: cord-295940-siy32dj7 authors: Saito, Makoto; Adachi, Eisuke; Yamayoshi, Seiya; Koga, Michiko; Iwatsuki-Horimoto, Kiyoko; Kawaoka, Yoshihiro; Yotsuyanagi, Hiroshi title: Gargle lavage as a safe and sensitive alternative to swab samples to diagnose COVID-19: a case report in Japan date: 2020-04-02 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa377 sha: doc_id: 295940 cord_uid: siy32dj7 file: cache/cord-300013-6m1f4q5r.json key: cord-300013-6m1f4q5r authors: Brahier, Thomas; Meuwly, Jean-Yves; Pantet, Olivier; Brochu Vez, Marie-Josée; Gerhard Donnet, Hélène; Hartley, Mary-Anne; Hugli, Olivier; Boillat-Blanco, Noémie title: Lung ultrasonography for risk stratification in patients with COVID-19: a prospective observational cohort study date: 2020-09-17 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1408 sha: doc_id: 300013 cord_uid: 6m1f4q5r file: cache/cord-299499-66qh3r75.json key: cord-299499-66qh3r75 authors: Guilamo-Ramos, Vincent; Benzekri, Adam; Thimm-Kaiser, Marco; Hidalgo, Andrew; Perlman, David C title: Reconsidering assumptions of adolescent and young adult SARS-CoV-2 transmission dynamics date: 2020-09-07 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1348 sha: doc_id: 299499 cord_uid: 66qh3r75 file: cache/cord-300411-ppcdkfxq.json key: cord-300411-ppcdkfxq authors: Xu, Xiao-Ke; Liu, Xiao-Fan; Wu, Ye; Ali, Sheikh Taslim; Du, Zhanwei; Bosetti, Paolo; Lau, Eric H Y; Cowling, Benjamin J; Wang, Lin title: Reconstruction of Transmission Pairs for novel Coronavirus Disease 2019 (COVID-19) in mainland China: Estimation of Super-spreading Events, Serial Interval, and Hazard of Infection date: 2020-06-18 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa790 sha: doc_id: 300411 cord_uid: ppcdkfxq file: cache/cord-294558-cqa58db8.json key: cord-294558-cqa58db8 authors: Wang, Yubo; Tong, Jin; Qin, Yalan; Xie, Ting; Li, Jianghua; Li, Jianrong; Xiang, Jianhua; Cui, Yong; Higgs, Elizabeth S; Xiang, Jianglin; He, Yong title: Characterization of an asymptomatic cohort of SARS-COV-2 infected individuals outside of Wuhan, China date: 2020-05-22 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa629 sha: doc_id: 294558 cord_uid: cqa58db8 file: cache/cord-309091-te15ahvw.json key: cord-309091-te15ahvw authors: Larson, Derek; Brodniak, Sterling L; Voegtly, Logan J; Cer, Regina Z; Glang, Lindsay A; Malagon, Francisco J; Long, Kyle A; Potocki, Ronald; Smith, Darci R; Lanteri, Charlotte; Burgess, Timothy; Bishop-Lilly, Kimberly A title: A Case of Early Re-infection with SARS-CoV-2 date: 2020-09-19 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1436 sha: doc_id: 309091 cord_uid: te15ahvw file: cache/cord-310476-mhm7r3qc.json key: cord-310476-mhm7r3qc authors: Yi, Huiguang title: 2019 novel coronavirus is undergoing active recombination date: 2020-03-04 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa219 sha: doc_id: 310476 cord_uid: mhm7r3qc file: cache/cord-303330-zh8wzza5.json key: cord-303330-zh8wzza5 authors: Magleby, Reed; Westblade, Lars F; Trzebucki, Alex; Simon, Matthew S; Rajan, Mangala; Park, Joel; Goyal, Parag; Safford, Monika M; Satlin, Michael J title: Impact of SARS-CoV-2 Viral Load on Risk of Intubation and Mortality Among Hospitalized Patients with Coronavirus Disease 2019 date: 2020-06-30 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa851 sha: doc_id: 303330 cord_uid: zh8wzza5 file: cache/cord-301066-62qe4fb0.json key: cord-301066-62qe4fb0 authors: Chiu, Susan S.; Hung Chan, Kwok; Wing Chu, Ka; Kwan, See Wai; Guan, Yi; Man Poon, Leo Lit; Peiris, J. S. 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Wen, Min; Zeng, Qingrun; Chen, Chengshui; Huang, Shengwei; Yang, Su; Yang, Jianjing; Wang, Jingqiang; Hu, Yuhuan; Ding, Saidan; Zhang, Ying; Zhang, Hongxia; Feng, Yuanjing; Jin, Kunlin; ZhuGe, Qichuan title: New measures for COVID-19 response: a lesson from the Wenzhou experience date: 2020-04-03 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa386 sha: doc_id: 298539 cord_uid: yncda1us file: cache/cord-303968-ikr6eeov.json key: cord-303968-ikr6eeov authors: Perinel, Sophie; Launay, Manon; Botelho-Nevers, Élisabeth; Diconne, Éric; Louf-Durier, Aurore; Lachand, Raphaël; Murgier, Martin; Page, Dominique; Vermesch, Régine; Thierry, Guillaume; Delavenne, Xavier title: Towards Optimization of Hydroxychloroquine Dosing in Intensive Care Unit COVID-19 Patients date: 2020-04-07 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa394 sha: doc_id: 303968 cord_uid: ikr6eeov file: cache/cord-299720-f0ny4ur5.json key: cord-299720-f0ny4ur5 authors: Kim, Seung Woo; Park, Jung Wan; Jung, Hee-Dong; Yang, Jeong-Sun; Park, Yong-Shik; Lee, Changhwan; Kim, Kyung Min; Lee, Keon-Joo; Kwon, Donghyok; Hur, Young Joo; Choi, BoYoul; Ki, Moran title: Risk Factors for Transmission of Middle East Respiratory Syndrome Coronavirus Infection During the 2015 Outbreak in South Korea date: 2017-03-01 journal: Clin Infect Dis DOI: 10.1093/cid/ciw768 sha: doc_id: 299720 cord_uid: f0ny4ur5 file: cache/cord-307342-3gkiukh4.json key: cord-307342-3gkiukh4 authors: Clark, Eva; Chiao, Elizabeth Y; Amirian, E Susan title: Why contact tracing efforts have failed to curb COVID-19 transmission in much of the U.S date: 2020-08-06 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1155 sha: doc_id: 307342 cord_uid: 3gkiukh4 file: cache/cord-312905-8xlt92pl.json key: cord-312905-8xlt92pl authors: Li, Guanjian; Li, Weiran; He, Xiaojin; Cao, Yunxia title: Asymptomatic and Presymptomatic Infectors: Hidden Sources of COVID-19 Disease date: 2020-04-09 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa418 sha: doc_id: 312905 cord_uid: 8xlt92pl file: cache/cord-313617-hh7lccet.json key: cord-313617-hh7lccet authors: Sigel, Keith; Swartz, Talia; Golden, Eddye; Paranjpe, Ishan; Somani, Sulaiman; Richter, Felix; De Freitas, Jessica K; Miotto, Riccardo; Zhao, Shan; Polak, Paz; Mutetwa, Tinaye; Factor, Stephanie; Mehandru, Saurabh; Mullen, Michael; Cossarini, Francesca; Bottinger, Erwin; Fayad, Zahi; Merad, Miriam; Gnjatic, Sacha; Aberg, Judith; Charney, Alexander; Nadkarni, Girish; Glicksberg, Benjamin S title: Covid-19 and People with HIV Infection: Outcomes for Hospitalized Patients in New York City date: 2020-06-28 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa880 sha: doc_id: 313617 cord_uid: hh7lccet file: cache/cord-300550-l28tadhn.json key: cord-300550-l28tadhn authors: Luers, Jan C; Rokohl, Alexander C; Loreck, Niklas; Wawer Matos, Philomena A; Augustin, Max; Dewald, Felix; Klein, Florian; Lehmann, Clara; Heindl, Ludwig M title: Olfactory and Gustatory Dysfunction in Coronavirus Disease 19 (COVID-19) date: 2020-05-01 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa525 sha: doc_id: 300550 cord_uid: l28tadhn file: cache/cord-303603-4mi64bgm.json key: cord-303603-4mi64bgm authors: Martínez-Urbistondo, Diego; 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Yang, Yan; Huang, Hanping; Li, Dong; Gu, Dongfeng; Lu, Xiangfeng; Zhang, Zheng; Liu, Lei; Liu, Ting; Liu, Yukun; He, Yunjiao; Sun, Bin; Wei, Meilan; Yang, Guangyu; Wang, Xinghuan; Zhang, Li; Zhou, Xiaoyang; Xing, Mingzhao; Wang, Peng George title: Relationship between the ABO Blood Group and the COVID-19 Susceptibility date: 2020-08-04 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1150 sha: doc_id: 330214 cord_uid: 28ah3nig file: cache/cord-332469-zegawla5.json key: cord-332469-zegawla5 authors: Li, Wei; Zhang, Bo; Lu, Jianhua; Liu, Shihua; Chang, Zhiqiang; Cao, Peng; Liu, Xinhua; Zhang, Peng; Ling, Yan; Tao, Kaixiong; Chen, Jianying title: The characteristics of household transmission of COVID-19 date: 2020-04-17 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa450 sha: doc_id: 332469 cord_uid: zegawla5 file: cache/cord-327069-vjlisnui.json key: cord-327069-vjlisnui authors: Driscoll, Amanda J.; Karron, Ruth A.; Morpeth, Susan C.; Bhat, Niranjan; Levine, Orin S.; Baggett, Henry C.; Brooks, W. 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V. S.; Parida, M. M.; Dash, P. K.; Santhosh, S. R.; Rao, P. V. 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Paltansing, Sunita; Ong, David S Y; Vaessen, Norbert; van Nielen, Gerard; Koeleman, Johannes G M title: Outbreak of COVID-19 in a nursing home associated with aerosol transmission as a result of inadequate ventilation date: 2020-08-28 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1270 sha: doc_id: 335907 cord_uid: 93gwmo0v file: cache/cord-340678-2e2s1gof.json key: cord-340678-2e2s1gof authors: Skowronski, Danuta M; Zou, Macy; Clarke, Quinten; Chambers, Catharine; Dickinson, James A; Sabaiduc, Suzana; Olsha, Romy; Gubbay, Jonathan B; Drews, Steven J; Charest, Hugues; Winter, Anne-Luise; Jassem, Agatha; Murti, Michelle; Krajden, Mel; De Serres, Gaston title: Influenza vaccine does not increase the risk of coronavirus or other non-influenza respiratory viruses: retrospective analysis from Canada, 2010-11 to 2016-17 date: 2020-05-22 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa626 sha: doc_id: 340678 cord_uid: 2e2s1gof file: cache/cord-335767-omm04fg5.json key: cord-335767-omm04fg5 authors: Raabe, Vanessa N; 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Adalja, Amesh A; Auwaerter, Paul G; Edelson, Paul J; Hansen, Gail R; Hynes, Noreen A; Jezek, Amanda; MacArthur, Rodger D; Manabe, Yukari C; McGoodwin, Colin; Duchin, Jeffrey S title: Infectious Diseases Physicians: Improving and Protecting the Public’s Health: Why Equitable Compensation Is Critical date: 2019-07-15 journal: Clin Infect Dis DOI: 10.1093/cid/ciy888 sha: doc_id: 345045 cord_uid: nlui9d6e file: cache/cord-341359-c34gyuv6.json key: cord-341359-c34gyuv6 authors: Larson, Derek T; Sherner, John H; Gallagher, Kia M; Judy, Cynthia L; Paul, Madison B; Mahoney, Alexandra M; Weina, Peter J title: Clinical Outcomes of Coronavirus Disease 2019 With Evidence-based Supportive Care date: 2020-05-30 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa678 sha: doc_id: 341359 cord_uid: c34gyuv6 file: cache/cord-348036-yub2cqz6.json key: cord-348036-yub2cqz6 authors: Lighter, Jennifer; Phillips, Michael; Hochman, Sarah; Sterling, Stephanie; Johnson, Diane; Francois, Fritz; Stachel, Anna title: Obesity in patients younger than 60 years is a risk factor for Covid-19 hospital admission date: 2020-04-09 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa415 sha: doc_id: 348036 cord_uid: yub2cqz6 file: cache/cord-341838-lkz8ro90.json key: cord-341838-lkz8ro90 authors: Gervasoni, Cristina; Meraviglia, Paola; Riva, Agostino; Giacomelli, Andrea; Oreni, Letizia; Minisci, Davide; Atzori, Chiara; Ridolfo, Annalisa; Cattaneo, Dario title: Clinical features and outcomes of HIV patients with coronavirus disease 2019 date: 2020-05-14 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa579 sha: doc_id: 341838 cord_uid: lkz8ro90 file: cache/cord-344038-20n74z3o.json key: cord-344038-20n74z3o authors: Han, Mi Seon; Seong, Moon-Woo; Heo, Eun Young; Park, Ji Hong; Kim, Namhee; Shin, Sue; Cho, Sung Im; Park, Sung Sup; Choi, Eun Hwa title: Sequential analysis of viral load in a neonate and her mother infected with SARS-CoV-2 date: 2020-04-16 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa447 sha: doc_id: 344038 cord_uid: 20n74z3o file: cache/cord-349070-bqv03u2e.json key: cord-349070-bqv03u2e authors: Jiang, Shih Sheng; Chen, Tsan-Chi; Yang, Jyh-Yuan; Hsiung, Chao A.; Su, Ih-Jen; Liu, Ying-Lan; Chen, Po-Cheng; Juang, Jyh-Lyh title: Sensitive and Quantitative Detection of Severe Acute Respiratory Syndrome Coronavirus Infection by Real-Time Nested Polymerase Chain Reaction date: 2004-01-15 journal: Clin Infect Dis DOI: 10.1086/380841 sha: doc_id: 349070 cord_uid: bqv03u2e file: cache/cord-348478-ho89o8mj.json key: cord-348478-ho89o8mj authors: Pawlotsky, Jean-Michel title: SARS-CoV-2 pandemic : Time to revive the cyclophilin inhibitor alisporivir date: 2020-05-15 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa587 sha: doc_id: 348478 cord_uid: ho89o8mj file: cache/cord-348392-e35cd9sg.json key: cord-348392-e35cd9sg authors: Moraleda, Cinta; 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Gandia, P title: Hydroxychloroquine in COVID-19 patients: what still needs to be known about the kinetics date: 2020-05-11 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa558 sha: doc_id: 348350 cord_uid: pac9ha4q file: cache/cord-348178-6bjimde4.json key: cord-348178-6bjimde4 authors: Li, Ling; Gu, Jiang; Shi, Xicheng; Gong, Encong; Li, Xingwang; Shao, Hongquan; Shi, Xueying; Jiang, Huijun; Gao, Xiaoqiang; Cheng, Daiyun; Guo, Lizhu; Wang, Hao; Shi, Xiaohong; Wang, Peizhi; Zhang, Qianying; Shen, Bing title: Biosafety Level 3 Laboratory for Autopsies of Patients with Severe Acute Respiratory Syndrome: Principles, Practices, and Prospects date: 2005-09-15 journal: Clin Infect Dis DOI: 10.1086/432720 sha: doc_id: 348178 cord_uid: 6bjimde4 file: cache/cord-348144-t0chpsuh.json key: cord-348144-t0chpsuh authors: Lucas, Alexander H.; Apicella, Michael A.; Taylor, Christopher E. title: Carbohydrate Moieties as Vaccine Candidates date: 2005-09-01 journal: Clin Infect Dis DOI: 10.1086/432582 sha: doc_id: 348144 cord_uid: t0chpsuh file: cache/cord-349556-k312qkvh.json key: cord-349556-k312qkvh authors: Roldán-Santiago, Ernesto; Benito-Berlinches, Amparo; Martínez-García, Laura; Quereda, Carmen; Rodríguez-Martín, Eulalia; Pérez-Elías, Pilar; López-Pintor, Jose María; Walo-Delgado, P E; Moreno-Zamora, Ana; Fernández-Velasco, Jose Ignacio; García-Abellás, Patricia; Ballester-González, Rubén; Villar, Luisa M; Pérez-Elías, María Jesús title: SARS-CoV-2 spreads to lymph nodes and strongly expands CD4+ T(EMRA) cells in a patient with mild COVID-19 date: 2020-09-18 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1422 sha: doc_id: 349556 cord_uid: k312qkvh file: cache/cord-350338-lcsa06gm.json key: cord-350338-lcsa06gm authors: Wang, Kun; Zuo, Peiyuan; Liu, Yuwei; Zhang, Meng; Zhao, Xiaofang; Xie, Songpu; Zhang, Hao; Chen, Xinglin; Liu, Chengyun title: Clinical and laboratory predictors of in-hospital mortality in patients with COVID-19: a cohort study in Wuhan, China date: 2020-05-03 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa538 sha: doc_id: 350338 cord_uid: lcsa06gm file: cache/cord-350686-q2bu7o4i.json key: cord-350686-q2bu7o4i authors: Bilder, Christopher R; Iwen, Peter C; Abdalhamid, Baha title: Pool size selection when testing for SARS-CoV-2 date: 2020-06-16 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa774 sha: doc_id: 350686 cord_uid: q2bu7o4i file: cache/cord-346502-x2b0ao3q.json key: cord-346502-x2b0ao3q authors: Arabi, Yaseen M; Shalhoub, Sarah; Mandourah, Yasser; Al-Hameed, Fahad; Al-Omari, Awad; Al Qasim, Eman; Jose, Jesna; Alraddadi, Basem; Almotairi, Abdullah; Al Khatib, Kasim; Abdulmomen, Ahmed; Qushmaq, Ismael; Sindi, Anees A; Mady, Ahmed; Solaiman, Othman; Al-Raddadi, Rajaa; Maghrabi, Khalid; Ragab, Ahmed; Al Mekhlafi, Ghaleb A; Balkhy, Hanan H; Al Harthy, Abdulrahman; Kharaba, Ayman; Gramish, Jawaher A; Al-Aithan, Abdulsalam M; Al-Dawood, Abdulaziz; Merson, Laura; Hayden, Frederick G; Fowler, Robert title: Ribavirin and Interferon Therapy for Critically Ill Patients With Middle East Respiratory Syndrome: A Multicenter Observational Study date: 2019-06-25 journal: Clin Infect Dis DOI: 10.1093/cid/ciz544 sha: doc_id: 346502 cord_uid: x2b0ao3q file: cache/cord-352837-a29d5dkv.json key: cord-352837-a29d5dkv authors: Hirsch, Hans H title: Spatiotemporal Virus Surveillance for Severe Acute Respiratory Infections in Resource-limited Settings: How Deep Need We Go? date: 2019-04-01 journal: Clin Infect Dis DOI: 10.1093/cid/ciy663 sha: doc_id: 352837 cord_uid: a29d5dkv file: cache/cord-351231-aoz5jbf1.json key: cord-351231-aoz5jbf1 authors: Bartlett, John G. title: Why Infectious Diseases date: 2014-09-15 journal: Clin Infect Dis DOI: 10.1093/cid/ciu441 sha: doc_id: 351231 cord_uid: aoz5jbf1 file: cache/cord-351348-lzo0dz7z.json key: cord-351348-lzo0dz7z authors: Gu, Silan; Chen, Yanfei; Wu, Zhengjie; Chen, Yunbo; Gao, Hainv; Lv, Longxian; Guo, Feifei; Zhang, Xuewu; Luo, Rui; Huang, Chenjie; Lu, Haifeng; Zheng, Beiwen; Zhang, Jiaying; Yan, Ren; Zhang, Hua; Jiang, Huiyong; Xu, Qiaomai; Guo, Jing; Gong, Yiwen; Tang, Lingling; Li, Lanjuan title: Alterations of the Gut Microbiota in Patients with COVID-19 or H1N1 Influenza date: 2020-06-04 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa709 sha: doc_id: 351348 cord_uid: lzo0dz7z file: cache/cord-351314-atsuh8e2.json key: cord-351314-atsuh8e2 authors: Bryson-Cahn, Chloe; Duchin, Jeffrey; Makarewicz, Vanessa A; Kay, Meagan; Rietberg, Krista; Napolitano, Nathanael; Kamangu, Carole; Dellit, Timothy H; Lynch, John B title: A Novel Approach for a Novel Pathogen: using a home assessment team to evaluate patients for 2019 novel coronavirus (SARS-CoV-2) date: 2020-03-12 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa256 sha: doc_id: 351314 cord_uid: atsuh8e2 file: cache/cord-349566-zx9kt144.json key: cord-349566-zx9kt144 authors: de Alencar, Julio Cesar Garcia; Moreira, Claudia de Lucena; Müller, Alicia Dudy; Chaves, Cleuber Esteves; Fukuhara, Marina Akemi; da Silva, Elizabeth Aparecida; Miyamoto, Maria de Fátima Silva; Pinto, Vanusa Barbosa; Bueno, Cauê Gasparotto; Lazar, Felippe; Gomez, Luz Marina; Menezes, Maria Clara Saad; Marchini, Julio Flavio Meirelles; Marino, Lucas Oliveira; Brandão, Rodrigo Antônio; Souza, Heraldo Possolo title: Double-blind, randomized, placebo-controlled trial with N-acetylcysteine for treatment of severe acute respiratory syndrome caused by COVID-19 date: 2020-09-23 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1443 sha: doc_id: 349566 cord_uid: zx9kt144 file: cache/cord-351589-32kd9vva.json key: cord-351589-32kd9vva authors: Mang, Sebastian; Kaddu-Mulindwa, Dominic; Metz, Carlos; Becker, André; Seiler, Frederik; Smola, Sigrun; Maßmann, Alexander; Becker, Sören L; Papan, Cihan; Bals, Robert; Lepper, Philipp M; Danziger, Guy title: Pneumocystis Jirovecii Pneumonia and SARS-CoV-2 Co-Infection in newly diagnosed HIV-1 infection date: 2020-07-01 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa906 sha: doc_id: 351589 cord_uid: 32kd9vva file: cache/cord-352899-bt2xg0ha.json key: cord-352899-bt2xg0ha authors: Van Kerkhove, Maria D.; Peiris, Malik J. S.; Malik, Mamunur Rahman; Ben Embarek, Peter title: Interpreting Results From Environmental Contamination Studies of Middle East Respiratory Syndrome Coronavirus date: 2016-10-15 journal: Clin Infect Dis DOI: 10.1093/cid/ciw478 sha: doc_id: 352899 cord_uid: bt2xg0ha file: cache/cord-350972-0n4dumgg.json key: cord-350972-0n4dumgg authors: Sing, Chor-Wing; Tan, Kathryn C B; Wong, Ian C K; Cheung, Bernard M Y; Cheung, Ching-Lung title: Long-term outcome of short-course high-dose glucocorticoids for SARS: a 17-year follow-up in SARS survivors date: 2020-07-16 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa992 sha: doc_id: 350972 cord_uid: 0n4dumgg file: cache/cord-353103-sdij1d90.json key: cord-353103-sdij1d90 authors: Yao, Xueting; Ye, Fei; Zhang, Miao; Cui, Cheng; Huang, Baoying; Niu, Peihua; Liu, Xu; Zhao, Li; Dong, Erdan; Song, Chunli; Zhan, Siyan; Lu, Roujian; Li, Haiyan; Tan, Wenjie; Liu, Dongyang title: In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date: 2020-03-09 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa237 sha: doc_id: 353103 cord_uid: sdij1d90 file: cache/cord-353116-7t1prfkr.json key: cord-353116-7t1prfkr authors: Bhargava, Ashish; Fukushima, Elisa Akagi; Levine, Miriam; Zhao, Wei; Tanveer, Farah; Szpunar, Susanna M; Saravolatz, Louis title: Predictors for Severe COVID-19 Infection date: 2020-05-30 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa674 sha: doc_id: 353116 cord_uid: 7t1prfkr file: cache/cord-354265-udt2spoe.json key: cord-354265-udt2spoe authors: Gersh, Felice; Lavie, Carl J; O’Keefe, James H title: Menopause status and COVID-19 date: 2020-09-23 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1447 sha: doc_id: 354265 cord_uid: udt2spoe file: cache/cord-353862-7xe3fvd5.json key: cord-353862-7xe3fvd5 authors: Li, Na; Han, Lefei; Peng, Min; Lv, Yuxia; Ouyang, Yin; Liu, Kui; Yue, Linli; Li, Qiannan; Sun, Guoqiang; Chen, Lin; Yang, Lin title: Maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia: a case-control study date: 2020-03-30 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa352 sha: doc_id: 353862 cord_uid: 7xe3fvd5 file: cache/cord-354009-1ek4s8oe.json key: cord-354009-1ek4s8oe authors: Wang, Yun; Liu, Ying; Struthers, James; Lian, Min title: Spatiotemporal Characteristics of COVID-19 Epidemic in the United States date: 2020-07-08 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa934 sha: doc_id: 354009 cord_uid: 1ek4s8oe file: cache/cord-354943-wxhbwcfr.json key: cord-354943-wxhbwcfr authors: Guo, Li; Ren, Lili; Yang, Siyuan; Xiao, Meng; Chang, De; Yang, Fan; Dela Cruz, Charles S; Wang, Yingying; Wu, Chao; Xiao, Yan; Zhang, Lulu; Han, Lianlian; Dang, Shengyuan; Xu, Yan; Yang, Qi-Wen; Xu, Sheng-Yong; Zhu, Hua-Dong; Xu, Ying-Chun; Jin, Qi; Sharma, Lokesh; Wang, Linghang; Wang, Jianwei title: Profiling Early Humoral Response to Diagnose Novel Coronavirus Disease (COVID-19) date: 2020-03-21 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa310 sha: doc_id: 354943 cord_uid: wxhbwcfr file: cache/cord-353342-2n6kqyeo.json key: cord-353342-2n6kqyeo authors: Corman, Victor M.; Albarrak, Ali M.; Omrani, Ali Senosi; Albarrak, Mohammed M.; Farah, Mohamed Elamin; Almasri, Malak; Muth, Doreen; Sieberg, Andrea; Meyer, Benjamin; Assiri, Abdullah M.; Binger, Tabea; Steinhagen, Katja; Lattwein, Erik; Al-Tawfiq, Jaffar; Müller, Marcel A.; Drosten, Christian; Memish, Ziad A. title: Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection date: 2016-02-15 journal: Clin Infect Dis DOI: 10.1093/cid/civ951 sha: doc_id: 353342 cord_uid: 2n6kqyeo file: cache/cord-354011-v9t2b2ca.json key: cord-354011-v9t2b2ca authors: Benkouiten, Samir; Charrel, Rémi; Belhouchat, Khadidja; Drali, Tassadit; Salez, Nicolas; Nougairede, Antoine; Zandotti, Christine; Memish, Ziad A.; al Masri, Malak; Gaillard, Catherine; Parola, Philippe; Brouqui, Philippe; Gautret, Philippe title: Circulation of Respiratory Viruses Among Pilgrims During the 2012 Hajj Pilgrimage date: 2013-10-01 journal: Clin Infect Dis DOI: 10.1093/cid/cit446 sha: doc_id: 354011 cord_uid: v9t2b2ca file: cache/cord-354877-n5du3bqt.json key: cord-354877-n5du3bqt authors: Vasoo, Shawn; Stevens, Jane; Singh, Kamaljit title: Rapid Antigen Tests for Diagnosis of Pandemic (Swine) Influenza A/H1N1 date: 2009-10-01 journal: Clin Infect Dis DOI: 10.1086/644743 sha: doc_id: 354877 cord_uid: n5du3bqt file: cache/cord-355734-pz64534w.json key: cord-355734-pz64534w authors: Antonio-Villa, Neftali Eduardo; Bello-Chavolla, Omar Yaxmehen; Vargas-Vázquez, Arsenio; Fermín-Martínez, Carlos A; Márquez-Salinas, Alejandro; Bahena-López, Jessica Paola title: Health-care workers with COVID-19 living in Mexico City: clinical characterization and related outcomes date: 2020-09-28 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1487 sha: doc_id: 355734 cord_uid: pz64534w file: cache/cord-355618-7kfxc2w1.json key: cord-355618-7kfxc2w1 authors: McAteer, John; Yildirim, Inci; Chahroudi, Ann title: The VACCINES Act, Deciphering Vaccine Hesitancy in the Time of COVID19 date: 2020-04-13 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa433 sha: doc_id: 355618 cord_uid: 7kfxc2w1 file: cache/cord-356084-621qzpqd.json key: cord-356084-621qzpqd authors: Qu, Jiuxin; Wu, Chi; Li, Xiaoyong; Zhang, Guobin; Jiang, Zhaofang; Li, Xiaohe; zhu, Qing; Liu, Lei title: Profile of IgG and IgM antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) date: 2020-04-27 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa489 sha: doc_id: 356084 cord_uid: 621qzpqd file: cache/cord-356316-ui11jr2h.json key: cord-356316-ui11jr2h authors: Patel, Monita R; Carroll, Darin; Ussery, Emily; Whitham, Hilary; Elkins, Christopher A; Noble-Wang, Judith; Rasheed, James Kamile; Lu, Xioayan; Lindstrom, Stephen; Bowen, Virginia; Waller, Jessica; Armstrong, Gregory; Gerber, Susan; Brooks, John T title: Performance of oropharyngeal swab testing compared to nasopharyngeal swab testing for diagnosis of COVID-19 —United States, January-February 2020 date: 2020-06-16 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa759 sha: doc_id: 356316 cord_uid: ui11jr2h Reading metadata file and updating bibliogrpahics === updating bibliographic database Building study carrel named journal-clinInfectDis-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: 94248 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: 94765 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: 95300 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: 95356 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 93890 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: 94447 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: 95393 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: 94999 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: 95318 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: 95317 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: 95140 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: 96059 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: 95278 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: 95357 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: 95372 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: 95566 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: 95578 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: 95758 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: 95954 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: 95953 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: 96885 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: 96738 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: 96834 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 94077 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: 95439 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: 95116 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: 95045 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: 95222 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: 95670 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: 95855 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: 95865 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: 95982 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: 96234 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: 96657 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: 96809 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: 96860 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-032234-pfr4l1v9 author: Poloni, Chad title: Evaluating Immune Dysregulation in Patients With COVID-19 Requires a More Accurate Definition of the CD45RA(+) T-cell Phenotype date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-032234-pfr4l1v9.txt cache: ./cache/cord-032234-pfr4l1v9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-032234-pfr4l1v9.txt' === file2bib.sh === id: cord-007049-02p8ug67 author: McGeer, Allison title: Let Him Who Desires Peace Prepare for War: United States Hospitals and Severe Acute Respiratory Syndrome Preparedness date: 2004-07-15 pages: extension: .txt txt: ./txt/cord-007049-02p8ug67.txt cache: ./cache/cord-007049-02p8ug67.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007049-02p8ug67.txt' === file2bib.sh === id: cord-252423-ojmt4k2w author: Qu, Bing title: Monologue of a physician who tested persistently positive for COVID-19 date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-252423-ojmt4k2w.txt cache: ./cache/cord-252423-ojmt4k2w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-252423-ojmt4k2w.txt' === file2bib.sh === id: cord-266808-wyuodzyt author: Nagler, Arielle R title: Early Results from SARS-CoV-2 PCR testing of Healthcare Workers at an Academic Medical Center in New York City date: 2020-06-28 pages: extension: .txt txt: ./txt/cord-266808-wyuodzyt.txt cache: ./cache/cord-266808-wyuodzyt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266808-wyuodzyt.txt' === file2bib.sh === id: cord-284782-51mbq7qb author: Huang, Jing title: Care for the psychological status of frontline medical staff fighting against COVID-19 date: 2020-04-03 pages: extension: .txt txt: ./txt/cord-284782-51mbq7qb.txt cache: ./cache/cord-284782-51mbq7qb.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284782-51mbq7qb.txt' === file2bib.sh === id: cord-268233-ibxufjrv author: Nagappa, Bharathnag title: Seroconversion rate and diagnostic accuracy of serological tests for COVID-19 date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-268233-ibxufjrv.txt cache: ./cache/cord-268233-ibxufjrv.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-268233-ibxufjrv.txt' === file2bib.sh === id: cord-277307-wabruzfs author: Gu, Wei title: Associations of Early COVID-19 Cases in San Francisco with Domestic and International Travel date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-277307-wabruzfs.txt cache: ./cache/cord-277307-wabruzfs.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-277307-wabruzfs.txt' === file2bib.sh === id: cord-276995-b003vcdc author: Wiese, Andrew D title: Social distancing measures: evidence of interruption of seasonal influenza activity and early lessons of the SARS-CoV-2 pandemic date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-276995-b003vcdc.txt cache: ./cache/cord-276995-b003vcdc.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-276995-b003vcdc.txt' === file2bib.sh === id: cord-265006-m1dmgcd1 author: Kow, Chia Siang title: Do the meta-analyses provide a clean bill of health to the use of renin-angiotensin system inhibitors in COVID-19? date: 2020-08-08 pages: extension: .txt txt: ./txt/cord-265006-m1dmgcd1.txt cache: ./cache/cord-265006-m1dmgcd1.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-265006-m1dmgcd1.txt' === file2bib.sh === id: cord-289247-qc3to2xj author: Yamaoka, Yutaro title: Whole nucleocapsid protein of SARS-CoV-2 may cause false positive results in serological assays date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-289247-qc3to2xj.txt cache: ./cache/cord-289247-qc3to2xj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-289247-qc3to2xj.txt' === file2bib.sh === id: cord-279932-bilr71ay author: Plotkin, Stanley A title: The Value of Human Challenges in Severe Acute Respiratory Syndrome Coronavirus 2 Vaccine Development date: 2020-07-16 pages: extension: .txt txt: ./txt/cord-279932-bilr71ay.txt cache: ./cache/cord-279932-bilr71ay.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-279932-bilr71ay.txt' === file2bib.sh === id: cord-277611-3iynrfzq author: Buetti, Niccolò title: Risk factors for SARS-CoV-2 detection in blood of critically ill patients date: 2020-09-02 pages: extension: .txt txt: ./txt/cord-277611-3iynrfzq.txt cache: ./cache/cord-277611-3iynrfzq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-277611-3iynrfzq.txt' === file2bib.sh === id: cord-259243-1lkzcslx author: Álvarez-Aragón, Luis Miguel title: Inquiring into Benefits of Independent Activation of Non-Classical Renin-Angiotensin System in the Clinical Prognosis and Reduction of COVID-19 mortality date: 2020-04-08 pages: extension: .txt txt: ./txt/cord-259243-1lkzcslx.txt cache: ./cache/cord-259243-1lkzcslx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-259243-1lkzcslx.txt' === file2bib.sh === id: cord-269973-sntnmqqd author: To, Kelvin Kai-Wang title: Unique SARS-CoV-2 clusters causing a large COVID-19 outbreak in Hong Kong date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-269973-sntnmqqd.txt cache: ./cache/cord-269973-sntnmqqd.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269973-sntnmqqd.txt' === file2bib.sh === id: cord-275349-b35pt3mo author: Lenz, Heinz-Josef title: The Emergence of Baricitinib: A Story of Tortoises Versus Hares date: 2020-07-06 pages: extension: .txt txt: ./txt/cord-275349-b35pt3mo.txt cache: ./cache/cord-275349-b35pt3mo.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-275349-b35pt3mo.txt' === file2bib.sh === id: cord-273956-mruywa71 author: Mathers, Amy J title: The practical challenges of making clinical use of the quantitative value for SARS-CoV-2 viral load across several dynamics date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-273956-mruywa71.txt cache: ./cache/cord-273956-mruywa71.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-273956-mruywa71.txt' === file2bib.sh === id: cord-285403-h8ahn8fw author: Zhang, Liangsheng title: Origin and Evolution of the 2019 Novel Coronavirus date: 2020-02-03 pages: extension: .txt txt: ./txt/cord-285403-h8ahn8fw.txt cache: ./cache/cord-285403-h8ahn8fw.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-285403-h8ahn8fw.txt' === file2bib.sh === id: cord-266820-exl36jt3 author: Rivera, Frida title: Prevalence of SARS-CoV-2 asymptomatic infections in two large academic health systems in Wisconsin date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-266820-exl36jt3.txt cache: ./cache/cord-266820-exl36jt3.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-266820-exl36jt3.txt' === file2bib.sh === id: cord-266232-2ctfmjb8 author: Trubiano, Jason A title: Alterations in smell or taste – Classic COVID-19? date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-266232-2ctfmjb8.txt cache: ./cache/cord-266232-2ctfmjb8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 168 resourceName b'cord-266232-2ctfmjb8.txt' === file2bib.sh === id: cord-254458-bbcef8xt author: Ali, Farhana title: Throat Wash Testing and COVID-19 Disease: Should We Put Our Money Where Our Mouth Is? date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-254458-bbcef8xt.txt cache: ./cache/cord-254458-bbcef8xt.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-254458-bbcef8xt.txt' === file2bib.sh === id: cord-260630-vvpzp73r author: Mandell, Lionel A. title: Etiologies of Acute Respiratory Tract Infections date: 2005-08-15 pages: extension: .txt txt: ./txt/cord-260630-vvpzp73r.txt cache: ./cache/cord-260630-vvpzp73r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-260630-vvpzp73r.txt' === file2bib.sh === id: cord-266696-w9sb038q author: Zhou, Yi-Hua title: Is the Immune System Impaired in Patients with Severe Acute Respiratory Syndrome? date: 2004-03-15 pages: extension: .txt txt: ./txt/cord-266696-w9sb038q.txt cache: ./cache/cord-266696-w9sb038q.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-266696-w9sb038q.txt' === file2bib.sh === id: cord-261270-jkm9c5yv author: Annweiler, Cédric title: National French survey of COVID-19 symptoms in people aged 70 and over date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-261270-jkm9c5yv.txt cache: ./cache/cord-261270-jkm9c5yv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-261270-jkm9c5yv.txt' === file2bib.sh === id: cord-287923-ev93r09i author: Apisarnthanarak, Anucha title: Infection Prevention and Control in Asia: Current Evidence and Future Milestones date: 2017-05-15 pages: extension: .txt txt: ./txt/cord-287923-ev93r09i.txt cache: ./cache/cord-287923-ev93r09i.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287923-ev93r09i.txt' === file2bib.sh === id: cord-272956-0yumc7em author: Gnavi, Roberto title: Therapy With Agents Acting on the Renin-Angiotensin System and Risk of Severe Acute Respiratory Syndrome Coronavirus 2 Infection date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-272956-0yumc7em.txt cache: ./cache/cord-272956-0yumc7em.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 5 resourceName b'cord-272956-0yumc7em.txt' === file2bib.sh === id: cord-007325-g8ke9rfg author: Koskiniemi, Marjaleena title: CNS Manifestations Associated with Mycoplasma pneumoniae Infections: Summary of Cases at the University of Helsinki and Review date: 1993-08-17 pages: extension: .txt txt: ./txt/cord-007325-g8ke9rfg.txt cache: ./cache/cord-007325-g8ke9rfg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-007325-g8ke9rfg.txt' === file2bib.sh === id: cord-288432-n2y9cunc author: Liu, Kun title: Population movement, city closure in Wuhan and geographical expansion of the 2019-nCoV pneumonia infection in China in January 2020 date: 2020-04-17 pages: extension: .txt txt: ./txt/cord-288432-n2y9cunc.txt cache: ./cache/cord-288432-n2y9cunc.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288432-n2y9cunc.txt' === file2bib.sh === id: cord-280915-yk872yaz author: Flaherman, Valerie J title: Infant Outcomes Following Maternal Infection with SARS-CoV-2: First Report from the PRIORITY Study date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-280915-yk872yaz.txt cache: ./cache/cord-280915-yk872yaz.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-280915-yk872yaz.txt' === file2bib.sh === id: cord-002514-pp06m5xk author: Venkatesan, Sudhir title: Impact of Outpatient Neuraminidase Inhibitor Treatment in Patients Infected With Influenza A(H1N1)pdm09 at High Risk of Hospitalization: An Individual Participant Data Metaanalysis date: 2017-05-15 pages: extension: .txt txt: ./txt/cord-002514-pp06m5xk.txt cache: ./cache/cord-002514-pp06m5xk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-002514-pp06m5xk.txt' === file2bib.sh === id: cord-007064-nepgttxf author: Chemaly, Roy F title: A Phase II, Randomized, Double-blind, Placebo-Controlled Trial of Presatovir for the Treatment of Respiratory Syncytial Virus Upper Respiratory Tract Infection in Hematopoietic-Cell Transplant Recipients date: 2019-12-03 pages: extension: .txt txt: ./txt/cord-007064-nepgttxf.txt cache: ./cache/cord-007064-nepgttxf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007064-nepgttxf.txt' === file2bib.sh === id: cord-258304-86gqxajw author: Bahl, Prateek title: Droplets and Aerosols generated by singing and the risk of COVID-19 for choirs date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-258304-86gqxajw.txt cache: ./cache/cord-258304-86gqxajw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-258304-86gqxajw.txt' === file2bib.sh === id: cord-264660-tfktgy57 author: Creech, C Buddy title: It’s True Even in a Pandemic: Children are Not Merely Little Adults date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-264660-tfktgy57.txt cache: ./cache/cord-264660-tfktgy57.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264660-tfktgy57.txt' === file2bib.sh === id: cord-015493-vf4et613 author: Deresinski, Stan title: In the Literature date: 2007-10-15 pages: extension: .txt txt: ./txt/cord-015493-vf4et613.txt cache: ./cache/cord-015493-vf4et613.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 8 resourceName b'cord-015493-vf4et613.txt' === file2bib.sh === id: cord-291363-re45w37d author: Sanville, Bradley title: A Community Transmitted Case of Severe Acute Respiratory Distress Syndrome due to SARS CoV2 in the United States date: 2020-03-30 pages: extension: .txt txt: ./txt/cord-291363-re45w37d.txt cache: ./cache/cord-291363-re45w37d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-291363-re45w37d.txt' === file2bib.sh === id: cord-010578-uib9h1lb author: Mawle, Alison C. title: Seroepidemiology of Chronic Fatigue Syndrome: A Case-Control Study date: 1995-12-17 pages: extension: .txt txt: ./txt/cord-010578-uib9h1lb.txt cache: ./cache/cord-010578-uib9h1lb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-010578-uib9h1lb.txt' === file2bib.sh === id: cord-001800-644lf8vn author: Biggerstaff, Matthew title: Estimating the Potential Effects of a Vaccine Program Against an Emerging Influenza Pandemic—United States date: 2015-05-01 pages: extension: .txt txt: ./txt/cord-001800-644lf8vn.txt cache: ./cache/cord-001800-644lf8vn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001800-644lf8vn.txt' === file2bib.sh === id: cord-257553-479x7av6 author: Kortepeter, Mark G. title: Health Care Workers and Researchers Traveling to Developing-World Clinical Settings: Disease Transmission Risk and Mitigation date: 2010-12-01 pages: extension: .txt txt: ./txt/cord-257553-479x7av6.txt cache: ./cache/cord-257553-479x7av6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257553-479x7av6.txt' === file2bib.sh === id: cord-001381-b0tlco4t author: Howie, Stephen R. C. title: Etiology of Severe Childhood Pneumonia in The Gambia, West Africa, Determined by Conventional and Molecular Microbiological Analyses of Lung and Pleural Aspirate Samples date: 2014-09-01 pages: extension: .txt txt: ./txt/cord-001381-b0tlco4t.txt cache: ./cache/cord-001381-b0tlco4t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001381-b0tlco4t.txt' === file2bib.sh === id: cord-271014-xzpvupms author: Erikstrup, Christian title: Estimation of SARS-CoV-2 infection fatality rate by real-time antibody screening of blood donors date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-271014-xzpvupms.txt cache: ./cache/cord-271014-xzpvupms.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-271014-xzpvupms.txt' === file2bib.sh === id: cord-266775-4npowkkz author: Xu, Jun title: Detection of Severe Acute Respiratory Syndrome Coronavirus in the Brain: Potential Role of the Chemokine Mig in Pathogenesis date: 2005-10-15 pages: extension: .txt txt: ./txt/cord-266775-4npowkkz.txt cache: ./cache/cord-266775-4npowkkz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-266775-4npowkkz.txt' === file2bib.sh === id: cord-007296-q9rn75qb author: Muether, Philipp S. title: Variant Effect of First- and Second-Generation Antihistamines as Clues to Their Mechanism of Action on the Sneeze Reflex in the Common Cold date: 2001-11-01 pages: extension: .txt txt: ./txt/cord-007296-q9rn75qb.txt cache: ./cache/cord-007296-q9rn75qb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-007296-q9rn75qb.txt' === file2bib.sh === id: cord-283780-h4lwzpl9 author: Zhang, John J Y title: Risk Factors of Severe Disease and Efficacy of Treatment in Patients Infected with COVID-19: A Systematic Review, Meta-Analysis and Meta-Regression Analysis date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-283780-h4lwzpl9.txt cache: ./cache/cord-283780-h4lwzpl9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-283780-h4lwzpl9.txt' === file2bib.sh === id: cord-278084-km04sz2s author: Martino, Rodrigo title: Respiratory Virus Infections in Adults with Hematologic Malignancies: A Prospective Study date: 2003-01-01 pages: extension: .txt txt: ./txt/cord-278084-km04sz2s.txt cache: ./cache/cord-278084-km04sz2s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-278084-km04sz2s.txt' === file2bib.sh === id: cord-279828-es498qul author: Boulle, Andrew title: Risk factors for COVID-19 death in a population cohort study from the Western Cape Province, South Africa date: 2020-08-29 pages: extension: .txt txt: ./txt/cord-279828-es498qul.txt cache: ./cache/cord-279828-es498qul.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279828-es498qul.txt' === file2bib.sh === id: cord-280005-i9fp5rys author: Wang, Mengmei title: Treatment of COVID-19 Patients with Prolonged Post-Symptomatic Viral Shedding with Leflunomide -- a Single-Center, Randomized, Controlled Clinical Trial date: 2020-09-21 pages: extension: .txt txt: ./txt/cord-280005-i9fp5rys.txt cache: ./cache/cord-280005-i9fp5rys.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-280005-i9fp5rys.txt' === file2bib.sh === id: cord-007047-7ty9mxa9 author: Reller, L. Barth title: Implications of New Technology for Infectious Diseases Practice date: 2006-11-15 pages: extension: .txt txt: ./txt/cord-007047-7ty9mxa9.txt cache: ./cache/cord-007047-7ty9mxa9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007047-7ty9mxa9.txt' === file2bib.sh === id: cord-280958-36ytqapi author: Decker, Summer J title: 3D Printed Alternative to the Standard Synthetic Flocked Nasopharyngeal Swabs Used for COVID-19 testing date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-280958-36ytqapi.txt cache: ./cache/cord-280958-36ytqapi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-280958-36ytqapi.txt' === file2bib.sh === id: cord-007170-svsfu7fj author: Richt, J. A. title: Infection with Borna Disease Virus: Molecular and Immunobiological Characterization of the Agent date: 1992-06-17 pages: extension: .txt txt: ./txt/cord-007170-svsfu7fj.txt cache: ./cache/cord-007170-svsfu7fj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007170-svsfu7fj.txt' === file2bib.sh === id: cord-010599-nwp2if8d author: Hayden, Frederick G. title: Efficacy and Safety of Oral Pleconaril for Treatment of Colds Due to Picornaviruses in Adults: Results of 2 Double-Blind, Randomized, Placebo-Controlled Trials date: 2003-06-15 pages: extension: .txt txt: ./txt/cord-010599-nwp2if8d.txt cache: ./cache/cord-010599-nwp2if8d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-010599-nwp2if8d.txt' === file2bib.sh === id: cord-254183-98o0dssj author: Waggoner, Jesse J. title: Rare and Emerging Viral Infections in Transplant Recipients date: 2013-10-15 pages: extension: .txt txt: ./txt/cord-254183-98o0dssj.txt cache: ./cache/cord-254183-98o0dssj.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-254183-98o0dssj.txt' === file2bib.sh === id: cord-007068-vcfs41eb author: Moradi, Tony title: Use of Procalcitonin and a Respiratory Polymerase Chain Reaction Panel to Reduce Antibiotic Use via an Electronic Medical Record Alert date: 2019-10-22 pages: extension: .txt txt: ./txt/cord-007068-vcfs41eb.txt cache: ./cache/cord-007068-vcfs41eb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007068-vcfs41eb.txt' === file2bib.sh === id: cord-260457-m1jbpo5l author: Allander, Tobias title: Human Bocavirus and Acute Wheezing in Children date: 2007-04-01 pages: extension: .txt txt: ./txt/cord-260457-m1jbpo5l.txt cache: ./cache/cord-260457-m1jbpo5l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260457-m1jbpo5l.txt' === file2bib.sh === id: cord-280763-4bnv2t3f author: Piñana, José Luis title: Clinical Effectiveness of Influenza Vaccination After Allogeneic Hematopoietic Stem Cell Transplantation: A Cross-sectional, Prospective, Observational Study date: 2019-06-01 pages: extension: .txt txt: ./txt/cord-280763-4bnv2t3f.txt cache: ./cache/cord-280763-4bnv2t3f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-280763-4bnv2t3f.txt' === file2bib.sh === id: cord-260274-c3586tp6 author: Somers, Emily C title: Tocilizumab for treatment of mechanically ventilated patients with COVID-19 date: 2020-07-11 pages: extension: .txt txt: ./txt/cord-260274-c3586tp6.txt cache: ./cache/cord-260274-c3586tp6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-260274-c3586tp6.txt' === file2bib.sh === id: cord-266150-wox7pnkr author: Torres, Juan Pablo title: SARS-CoV-2 antibody prevalence in blood in a large school community subject to a Covid-19 outbreak: a cross-sectional study date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-266150-wox7pnkr.txt cache: ./cache/cord-266150-wox7pnkr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-266150-wox7pnkr.txt' === file2bib.sh === id: cord-260779-riw5xs3j author: van Griensven, Johan title: The Use of Ebola Convalescent Plasma to Treat Ebola Virus Disease in Resource-Constrained Settings: A Perspective From the Field date: 2016-01-01 pages: extension: .txt txt: ./txt/cord-260779-riw5xs3j.txt cache: ./cache/cord-260779-riw5xs3j.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260779-riw5xs3j.txt' === file2bib.sh === id: cord-012511-fl5llkoj author: Meltzer, Martin I. title: Standardizing Scenarios to Assess the Need to Respond to an Influenza Pandemic date: 2015-05-01 pages: extension: .txt txt: ./txt/cord-012511-fl5llkoj.txt cache: ./cache/cord-012511-fl5llkoj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-012511-fl5llkoj.txt' === file2bib.sh === id: cord-273839-oasgagpc author: Bisno, Alan L. title: Diagnosis and Management of Group A Streptococcal Pharyngitis: A Practice Guideline date: 1997-09-17 pages: extension: .txt txt: ./txt/cord-273839-oasgagpc.txt cache: ./cache/cord-273839-oasgagpc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-273839-oasgagpc.txt' === file2bib.sh === id: cord-295940-siy32dj7 author: Saito, Makoto title: Gargle lavage as a safe and sensitive alternative to swab samples to diagnose COVID-19: a case report in Japan date: 2020-04-02 pages: extension: .txt txt: ./txt/cord-295940-siy32dj7.txt cache: ./cache/cord-295940-siy32dj7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-295940-siy32dj7.txt' === file2bib.sh === id: cord-309091-te15ahvw author: Larson, Derek title: A Case of Early Re-infection with SARS-CoV-2 date: 2020-09-19 pages: extension: .txt txt: ./txt/cord-309091-te15ahvw.txt cache: ./cache/cord-309091-te15ahvw.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-309091-te15ahvw.txt' === file2bib.sh === id: cord-295525-emrwcx0m author: To, Kelvin Kai-Wang title: Consistent Detection of 2019 Novel Coronavirus in Saliva date: 2020-02-12 pages: extension: .txt txt: ./txt/cord-295525-emrwcx0m.txt cache: ./cache/cord-295525-emrwcx0m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295525-emrwcx0m.txt' === file2bib.sh === id: cord-310476-mhm7r3qc author: Yi, Huiguang title: 2019 novel coronavirus is undergoing active recombination date: 2020-03-04 pages: extension: .txt txt: ./txt/cord-310476-mhm7r3qc.txt cache: ./cache/cord-310476-mhm7r3qc.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310476-mhm7r3qc.txt' === file2bib.sh === id: cord-294853-8b0s5w4u author: Nolen, Leisha D title: Impact of Social Distancing and Travel Restrictions on non-COVID-19 Respiratory Hospital Admissions in Young Children in Rural Alaska date: 2020-09-05 pages: extension: .txt txt: ./txt/cord-294853-8b0s5w4u.txt cache: ./cache/cord-294853-8b0s5w4u.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-294853-8b0s5w4u.txt' === file2bib.sh === id: cord-312905-8xlt92pl author: Li, Guanjian title: Asymptomatic and Presymptomatic Infectors: Hidden Sources of COVID-19 Disease date: 2020-04-09 pages: extension: .txt txt: ./txt/cord-312905-8xlt92pl.txt cache: ./cache/cord-312905-8xlt92pl.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-312905-8xlt92pl.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-295270-6ptaxg74 author: Titanji, Boghuma K title: Response to Correspondence: Baricitinib – Impact on COVID-19 Coagulopathy? Jorgensen et. al. date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-295270-6ptaxg74.txt cache: ./cache/cord-295270-6ptaxg74.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-295270-6ptaxg74.txt' === file2bib.sh === id: cord-291726-8670s4st author: Che, Xiao-yan title: A Patient with Asymptomatic Severe Acute Respiratory Syndrome (SARS) and Antigenemia from the 2003–2004 Community Outbreak of SARS in Guangzhou, China date: 2006-07-01 pages: extension: .txt txt: ./txt/cord-291726-8670s4st.txt cache: ./cache/cord-291726-8670s4st.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291726-8670s4st.txt' === file2bib.sh === id: cord-297239-or6h6p9p author: Ridgway, Jessica P. title: Influenza Among Afebrile and Vaccinated Healthcare Workers date: 2015-06-01 pages: extension: .txt txt: ./txt/cord-297239-or6h6p9p.txt cache: ./cache/cord-297239-or6h6p9p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297239-or6h6p9p.txt' === file2bib.sh === id: cord-299274-gnbp7so5 author: Bodkin, Claire title: Pandemic Planning in Homeless Shelters: A pilot study of a COVID-19 testing and support program to mitigate the risk of COVID-19 outbreaks in congregate settings date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-299274-gnbp7so5.txt cache: ./cache/cord-299274-gnbp7so5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-299274-gnbp7so5.txt' === file2bib.sh === id: cord-296631-43z3ee8m author: de Feria, Alejandro title: ACE inhibitors/ARB use and COVID-19. Time to change practice or keep gathering data? date: 2020-07-04 pages: extension: .txt txt: ./txt/cord-296631-43z3ee8m.txt cache: ./cache/cord-296631-43z3ee8m.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-296631-43z3ee8m.txt' === file2bib.sh === id: cord-010570-ytv7dwr0 author: Casadevall, Arturo title: Return to the Past: The Case for Antibody-Based Therapies in Infectious Diseases date: 1995-07-17 pages: extension: .txt txt: ./txt/cord-010570-ytv7dwr0.txt cache: ./cache/cord-010570-ytv7dwr0.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-010570-ytv7dwr0.txt' === file2bib.sh === id: cord-307660-onz6vfre author: Titanji, Boghuma K title: Use of Baricitinib in Patients with Moderate and Severe COVID-19 date: 2020-06-29 pages: extension: .txt txt: ./txt/cord-307660-onz6vfre.txt cache: ./cache/cord-307660-onz6vfre.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307660-onz6vfre.txt' === file2bib.sh === id: cord-298539-yncda1us author: Ruan, Linhui title: New measures for COVID-19 response: a lesson from the Wenzhou experience date: 2020-04-03 pages: extension: .txt txt: ./txt/cord-298539-yncda1us.txt cache: ./cache/cord-298539-yncda1us.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298539-yncda1us.txt' === file2bib.sh === id: cord-294558-cqa58db8 author: Wang, Yubo title: Characterization of an asymptomatic cohort of SARS-COV-2 infected individuals outside of Wuhan, China date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-294558-cqa58db8.txt cache: ./cache/cord-294558-cqa58db8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-294558-cqa58db8.txt' === file2bib.sh === id: cord-303603-4mi64bgm author: Martínez-Urbistondo, Diego title: Early Combination of Tocilizumab and Corticosteroids: An Upgrade in Anti-inflammatory Therapy for Severe Coronavirus Disease (COVID) date: 2020-07-04 pages: extension: .txt txt: ./txt/cord-303603-4mi64bgm.txt cache: ./cache/cord-303603-4mi64bgm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-303603-4mi64bgm.txt' === file2bib.sh === id: cord-303968-ikr6eeov author: Perinel, Sophie title: Towards Optimization of Hydroxychloroquine Dosing in Intensive Care Unit COVID-19 Patients date: 2020-04-07 pages: extension: .txt txt: ./txt/cord-303968-ikr6eeov.txt cache: ./cache/cord-303968-ikr6eeov.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303968-ikr6eeov.txt' === file2bib.sh === id: cord-294718-n3gx862b author: Tam, Patrick C K title: Detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breast milk of a mildly symptomatic patient with coronavirus disease 2019 (COVID-19) date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-294718-n3gx862b.txt cache: ./cache/cord-294718-n3gx862b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294718-n3gx862b.txt' === file2bib.sh === id: cord-292372-kn27ghlv author: de Chaisemartin, Clément title: BCG vaccination in infancy does not protect against COVID-19. Evidence from a natural experiment in Sweden date: 2020-08-23 pages: extension: .txt txt: ./txt/cord-292372-kn27ghlv.txt cache: ./cache/cord-292372-kn27ghlv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-292372-kn27ghlv.txt' === file2bib.sh === id: cord-292546-un0blb3w author: Dandachi, Dima title: Characteristics, Comorbidities, and Outcomes in a Multicenter Registry of Patients with HIV and Coronavirus Disease-19 date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-292546-un0blb3w.txt cache: ./cache/cord-292546-un0blb3w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-292546-un0blb3w.txt' === file2bib.sh === id: cord-300550-l28tadhn author: Luers, Jan C title: Olfactory and Gustatory Dysfunction in Coronavirus Disease 19 (COVID-19) date: 2020-05-01 pages: extension: .txt txt: ./txt/cord-300550-l28tadhn.txt cache: ./cache/cord-300550-l28tadhn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300550-l28tadhn.txt' === file2bib.sh === id: cord-297612-swc2pitd author: Nosyk, Bohdan title: Contact tracing for COVID-19: An opportunity to reduce health disparities and End the HIV/AIDS Epidemic in the US date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-297612-swc2pitd.txt cache: ./cache/cord-297612-swc2pitd.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-297612-swc2pitd.txt' === file2bib.sh === id: cord-303330-zh8wzza5 author: Magleby, Reed title: Impact of SARS-CoV-2 Viral Load on Risk of Intubation and Mortality Among Hospitalized Patients with Coronavirus Disease 2019 date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-303330-zh8wzza5.txt cache: ./cache/cord-303330-zh8wzza5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303330-zh8wzza5.txt' === file2bib.sh === id: cord-300013-6m1f4q5r author: Brahier, Thomas title: Lung ultrasonography for risk stratification in patients with COVID-19: a prospective observational cohort study date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-300013-6m1f4q5r.txt cache: ./cache/cord-300013-6m1f4q5r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-300013-6m1f4q5r.txt' === file2bib.sh === id: cord-300411-ppcdkfxq author: Xu, Xiao-Ke title: Reconstruction of Transmission Pairs for novel Coronavirus Disease 2019 (COVID-19) in mainland China: Estimation of Super-spreading Events, Serial Interval, and Hazard of Infection date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-300411-ppcdkfxq.txt cache: ./cache/cord-300411-ppcdkfxq.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300411-ppcdkfxq.txt' === file2bib.sh === id: cord-313617-hh7lccet author: Sigel, Keith title: Covid-19 and People with HIV Infection: Outcomes for Hospitalized Patients in New York City date: 2020-06-28 pages: extension: .txt txt: ./txt/cord-313617-hh7lccet.txt cache: ./cache/cord-313617-hh7lccet.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313617-hh7lccet.txt' === file2bib.sh === id: cord-313499-8ijbesl8 author: Stowell, Sean title: Role of serology in the COVID-19 pandemic date: 2020-05-01 pages: extension: .txt txt: ./txt/cord-313499-8ijbesl8.txt cache: ./cache/cord-313499-8ijbesl8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313499-8ijbesl8.txt' === file2bib.sh === id: cord-307497-wtfvoifb author: Abu-Raya, Bahaa title: Predictors of refractory Coronavirus disease (COVID-19) pneumonia date: 2020-04-09 pages: extension: .txt txt: ./txt/cord-307497-wtfvoifb.txt cache: ./cache/cord-307497-wtfvoifb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-307497-wtfvoifb.txt' === file2bib.sh === id: cord-294335-qnu19ru5 author: Yousaf, Anna R title: A prospective cohort study in non-hospitalized household contacts with SARS-CoV-2 infection: symptom profiles and symptom change over time date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-294335-qnu19ru5.txt cache: ./cache/cord-294335-qnu19ru5.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-294335-qnu19ru5.txt' === file2bib.sh === id: cord-306495-o0ah1gj9 author: Haidar, Ghady title: COVID-19, organ transplantation, and the nuances of immunomodulation: lessons learned and what comes next date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-306495-o0ah1gj9.txt cache: ./cache/cord-306495-o0ah1gj9.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-306495-o0ah1gj9.txt' === file2bib.sh === id: cord-318358-glbr8kxh author: Naik, George O A title: COVID-19 and the RAAS date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-318358-glbr8kxh.txt cache: ./cache/cord-318358-glbr8kxh.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318358-glbr8kxh.txt' === file2bib.sh === id: cord-312928-ef8hqs4s author: Chavanet, Pascal title: Viral Upper Respiratory Tract Infection and Otitis Media Complication in Young Children date: 2008-03-15 pages: extension: .txt txt: ./txt/cord-312928-ef8hqs4s.txt cache: ./cache/cord-312928-ef8hqs4s.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-312928-ef8hqs4s.txt' === file2bib.sh === id: cord-307342-3gkiukh4 author: Clark, Eva title: Why contact tracing efforts have failed to curb COVID-19 transmission in much of the U.S date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-307342-3gkiukh4.txt cache: ./cache/cord-307342-3gkiukh4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307342-3gkiukh4.txt' === file2bib.sh === id: cord-320562-zvsf3va0 author: Dookie, Navisha title: Tuberculosis Elimination in the Era of COVID-19: A Moving Target date: 2020-09-14 pages: extension: .txt txt: ./txt/cord-320562-zvsf3va0.txt cache: ./cache/cord-320562-zvsf3va0.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320562-zvsf3va0.txt' === file2bib.sh === id: cord-325416-c0qj3yd9 author: Zachariah, Philip title: Symptomatic Infants have Higher Nasopharyngeal SARS-CoV-2 Viral Loads but Less Severe Disease than Older Children date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-325416-c0qj3yd9.txt cache: ./cache/cord-325416-c0qj3yd9.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-325416-c0qj3yd9.txt' === file2bib.sh === id: cord-324307-2zbm4iwn author: Kam, Kai-qian title: A Well Infant With Coronavirus Disease 2019 With High Viral Load date: 2020-02-28 pages: extension: .txt txt: ./txt/cord-324307-2zbm4iwn.txt cache: ./cache/cord-324307-2zbm4iwn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-324307-2zbm4iwn.txt' === file2bib.sh === id: cord-321873-9l9zp6gm author: Zhou, Bo title: The duration of viral shedding of discharged patients with severe COVID-19 date: 2020-04-17 pages: extension: .txt txt: ./txt/cord-321873-9l9zp6gm.txt cache: ./cache/cord-321873-9l9zp6gm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-321873-9l9zp6gm.txt' === file2bib.sh === id: cord-314489-e5r5s5ee author: Katsidzira, Leolin title: The SARS-CoV-2 epidemic in Zimbabwe: Quo vadis? date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-314489-e5r5s5ee.txt cache: ./cache/cord-314489-e5r5s5ee.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314489-e5r5s5ee.txt' === file2bib.sh === id: cord-301066-62qe4fb0 author: Chiu, Susan S. title: Human Coronavirus NL63 Infection and Other Coronavirus Infections in Children Hospitalized with Acute Respiratory Disease in Hong Kong, China date: 2005-06-15 pages: extension: .txt txt: ./txt/cord-301066-62qe4fb0.txt cache: ./cache/cord-301066-62qe4fb0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301066-62qe4fb0.txt' === file2bib.sh === id: cord-321603-lbbsnriv author: Rao, Mohan title: Comparing nasopharyngeal swab and early morning saliva for the identification of SARS-CoV-2 date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-321603-lbbsnriv.txt cache: ./cache/cord-321603-lbbsnriv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321603-lbbsnriv.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-299499-66qh3r75 author: Guilamo-Ramos, Vincent title: Reconsidering assumptions of adolescent and young adult SARS-CoV-2 transmission dynamics date: 2020-09-07 pages: extension: .txt txt: ./txt/cord-299499-66qh3r75.txt cache: ./cache/cord-299499-66qh3r75.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-299499-66qh3r75.txt' === file2bib.sh === id: cord-307770-1igydu3y author: Rawson, Timothy M title: Bacterial and fungal co-infection in individuals with coronavirus: A rapid review to support COVID-19 antimicrobial prescribing date: 2020-05-02 pages: extension: .txt txt: ./txt/cord-307770-1igydu3y.txt cache: ./cache/cord-307770-1igydu3y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307770-1igydu3y.txt' === file2bib.sh === id: cord-325068-j1lfq60o author: Pene, Frédéric title: Coronavirus 229E-Related Pneumonia in Immunocompromised Patients date: 2003-10-01 pages: extension: .txt txt: ./txt/cord-325068-j1lfq60o.txt cache: ./cache/cord-325068-j1lfq60o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325068-j1lfq60o.txt' === file2bib.sh === id: cord-326494-qhxlh43t author: Beckerman, Karen Palmore title: Pregnancy and Pandemic Disease date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-326494-qhxlh43t.txt cache: ./cache/cord-326494-qhxlh43t.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-326494-qhxlh43t.txt' === file2bib.sh === id: cord-327324-4c4a4bfz author: Wilkinson, Robert J title: Tuberculosis and type 2 Diabetes Mellitus: an inflammatory danger signal in the time of COVID-19 date: 2020-06-13 pages: extension: .txt txt: ./txt/cord-327324-4c4a4bfz.txt cache: ./cache/cord-327324-4c4a4bfz.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-327324-4c4a4bfz.txt' === file2bib.sh === id: cord-304487-ycvu5l5f author: Wertheim, Joel O title: A glimpse into the origins of genetic diversity in SARS-CoV-2 date: 2020-03-04 pages: extension: .txt txt: ./txt/cord-304487-ycvu5l5f.txt cache: ./cache/cord-304487-ycvu5l5f.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304487-ycvu5l5f.txt' === file2bib.sh === id: cord-316970-n2dly3oa author: Kerbaj, Jad title: COVID-19: The New Caledonia experience date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-316970-n2dly3oa.txt cache: ./cache/cord-316970-n2dly3oa.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-316970-n2dly3oa.txt' === file2bib.sh === id: cord-317940-yg91bsmm author: Chalumeau, Martin title: Transmission of Panton-Valentine Leukocidin–Producing Staphylococcus aureus to a Physician during Resuscitation of a Child date: 2005-08-01 pages: extension: .txt txt: ./txt/cord-317940-yg91bsmm.txt cache: ./cache/cord-317940-yg91bsmm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317940-yg91bsmm.txt' === file2bib.sh === id: cord-322204-kc7dy2za author: Khalil, Asma title: SARS-CoV-2-specific antibody detection in healthcare workers in a UK maternity Hospital: Correlation with SARS-CoV-2 RT-PCR results date: 2020-08-08 pages: extension: .txt txt: ./txt/cord-322204-kc7dy2za.txt cache: ./cache/cord-322204-kc7dy2za.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-322204-kc7dy2za.txt' === file2bib.sh === id: cord-305394-wwabxlgr author: Venter, W D Francois title: COVID-19: First data from Africa date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-305394-wwabxlgr.txt cache: ./cache/cord-305394-wwabxlgr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-305394-wwabxlgr.txt' === file2bib.sh === id: cord-299359-s8j78naz author: Sundaram, Maria E. title: Influenza Vaccination Is Not Associated With Detection of Noninfluenza Respiratory Viruses in Seasonal Studies of Influenza Vaccine Effectiveness date: 2013-09-15 pages: extension: .txt txt: ./txt/cord-299359-s8j78naz.txt cache: ./cache/cord-299359-s8j78naz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-299359-s8j78naz.txt' === file2bib.sh === id: cord-324007-hapzf0fl author: McGeer, Allison J. title: Diagnostic Testing or Empirical Therapy for Patients Hospitalized with Suspected Influenza: What to Do? date: 2009-01-01 pages: extension: .txt txt: ./txt/cord-324007-hapzf0fl.txt cache: ./cache/cord-324007-hapzf0fl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-324007-hapzf0fl.txt' === file2bib.sh === id: cord-329311-p68kr4ga author: Prebensen, Christian title: SARS-CoV-2 RNA in plasma is associated with ICU admission and mortality in patients hospitalized with COVID-19 date: 2020-09-05 pages: extension: .txt txt: ./txt/cord-329311-p68kr4ga.txt cache: ./cache/cord-329311-p68kr4ga.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329311-p68kr4ga.txt' === file2bib.sh === id: cord-317948-svgguadm author: Xiao, Ai Tang title: Profile of RT-PCR for SARS-CoV-2: a preliminary study from 56 COVID-19 patients date: 2020-04-19 pages: extension: .txt txt: ./txt/cord-317948-svgguadm.txt cache: ./cache/cord-317948-svgguadm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317948-svgguadm.txt' === file2bib.sh === id: cord-325455-e464idc0 author: Atchison, Christina title: Usability and acceptability of home-based self-testing for SARS-CoV-2 antibodies for population surveillance date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-325455-e464idc0.txt cache: ./cache/cord-325455-e464idc0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325455-e464idc0.txt' === file2bib.sh === id: cord-314025-h9gj814e author: Lai, Mary Y. Y. title: Survival of Severe Acute Respiratory Syndrome Coronavirus date: 2005-10-01 pages: extension: .txt txt: ./txt/cord-314025-h9gj814e.txt cache: ./cache/cord-314025-h9gj814e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-314025-h9gj814e.txt' === file2bib.sh === id: cord-303240-tv1ta3z5 author: Althoff, Keri N title: Contact tracing: Essential to the public health response and our understanding of the epidemiology of COVID-19 date: 2020-06-11 pages: extension: .txt txt: ./txt/cord-303240-tv1ta3z5.txt cache: ./cache/cord-303240-tv1ta3z5.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-303240-tv1ta3z5.txt' === file2bib.sh === id: cord-331930-w2055c42 author: Tso, Eugene Y. K. title: Persistence of Physical Symptoms in and Abnormal Laboratory Findings for Survivors of Severe Acute Respiratory Syndrome date: 2004-05-01 pages: extension: .txt txt: ./txt/cord-331930-w2055c42.txt cache: ./cache/cord-331930-w2055c42.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-331930-w2055c42.txt' === file2bib.sh === id: cord-328667-r5w09lb6 author: Schwartz, David A title: The Effects of Pregnancy on Women with COVID-19: Maternal and Infant Outcomes date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-328667-r5w09lb6.txt cache: ./cache/cord-328667-r5w09lb6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328667-r5w09lb6.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-299720-f0ny4ur5 author: Kim, Seung Woo title: Risk Factors for Transmission of Middle East Respiratory Syndrome Coronavirus Infection During the 2015 Outbreak in South Korea date: 2017-03-01 pages: extension: .txt txt: ./txt/cord-299720-f0ny4ur5.txt cache: ./cache/cord-299720-f0ny4ur5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-299720-f0ny4ur5.txt' === file2bib.sh === id: cord-326138-16kpn9db author: Weinstein, Robert A. title: Laboratory-Acquired Infections date: 2009-07-01 pages: extension: .txt txt: ./txt/cord-326138-16kpn9db.txt cache: ./cache/cord-326138-16kpn9db.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-326138-16kpn9db.txt' === file2bib.sh === id: cord-323125-qtlevnbt author: Al Hosani, Farida Ismail title: Serologic Follow-up of Middle East Respiratory Syndrome Coronavirus Cases and Contacts—Abu Dhabi, United Arab Emirates date: 2019-02-01 pages: extension: .txt txt: ./txt/cord-323125-qtlevnbt.txt cache: ./cache/cord-323125-qtlevnbt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323125-qtlevnbt.txt' === file2bib.sh === id: cord-310390-7pkbd3kg author: Han, Xiaoyu title: Novel Coronavirus Pneumonia (COVID-19) Progression Course in 17 Discharged Patients: Comparison of Clinical and Thin-Section CT Features During Recovery date: 2020-03-30 pages: extension: .txt txt: ./txt/cord-310390-7pkbd3kg.txt cache: ./cache/cord-310390-7pkbd3kg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310390-7pkbd3kg.txt' === file2bib.sh === id: cord-330214-28ah3nig author: Zhao, Jiao title: Relationship between the ABO Blood Group and the COVID-19 Susceptibility date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-330214-28ah3nig.txt cache: ./cache/cord-330214-28ah3nig.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330214-28ah3nig.txt' === file2bib.sh === id: cord-313427-6y4zvrmn author: Mani, Nandita S title: Prevalence of COVID-19 Infection and Outcomes Among Symptomatic Healthcare Workers in Seattle, Washington date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-313427-6y4zvrmn.txt cache: ./cache/cord-313427-6y4zvrmn.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313427-6y4zvrmn.txt' === file2bib.sh === id: cord-318204-t024w7h6 author: Fang, Ferric C title: The Laboratory Diagnosis of COVID-19-- Frequently-Asked Questions date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-318204-t024w7h6.txt cache: ./cache/cord-318204-t024w7h6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-318204-t024w7h6.txt' === file2bib.sh === id: cord-315356-9zf2h0xr author: Apisarnthanarak, Anucha title: Issues Relevant to the Adoption and Modification of Hospital Infection-Control Recommendations for Avian Influenza (H5N1 Infection) in Developing Countries date: 2007-11-15 pages: extension: .txt txt: ./txt/cord-315356-9zf2h0xr.txt cache: ./cache/cord-315356-9zf2h0xr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-315356-9zf2h0xr.txt' === file2bib.sh === id: cord-322650-q8inhgtr author: Fung, Yin-Wan Wendy title: Use of Clinical Criteria and Molecular Diagnosis to More Effectively Monitor Patients Recovering after Severe Acute Respiratory Syndrome Coronavirus Infection date: 2004-08-15 pages: extension: .txt txt: ./txt/cord-322650-q8inhgtr.txt cache: ./cache/cord-322650-q8inhgtr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322650-q8inhgtr.txt' === file2bib.sh === id: cord-318615-uhh3owcx author: Xiang, Fei title: Antibody Detection and Dynamic Characteristics in Patients with COVID-19 date: 2020-04-19 pages: extension: .txt txt: ./txt/cord-318615-uhh3owcx.txt cache: ./cache/cord-318615-uhh3owcx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-318615-uhh3owcx.txt' === file2bib.sh === id: cord-324607-rpwccvqi author: Rojek, Amanda M title: Core Minimal Datasets to Advance Clinical Research for Priority Epidemic Diseases date: 2020-02-15 pages: extension: .txt txt: ./txt/cord-324607-rpwccvqi.txt cache: ./cache/cord-324607-rpwccvqi.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-324607-rpwccvqi.txt' === file2bib.sh === id: cord-328267-tk0zc8il author: Liu, Qiao title: Collateral Impact of the Covid-19 Pandemic on Tuberculosis Control in Jiangsu Province, China date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-328267-tk0zc8il.txt cache: ./cache/cord-328267-tk0zc8il.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328267-tk0zc8il.txt' === file2bib.sh === id: cord-329323-1cquorhs author: Ko, Jean Y title: Risk Factors for COVID-19-associated hospitalization: COVID-19-Associated Hospitalization Surveillance Network and Behavioral Risk Factor Surveillance System date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-329323-1cquorhs.txt cache: ./cache/cord-329323-1cquorhs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329323-1cquorhs.txt' === file2bib.sh === id: cord-318458-jadk2qbm author: Jung, Chan-Young title: Association between Body Mass Index and Risk of COVID-19: A Nationwide Case-Control Study in South Korea date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-318458-jadk2qbm.txt cache: ./cache/cord-318458-jadk2qbm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318458-jadk2qbm.txt' === file2bib.sh === id: cord-317823-ztawznod author: Yehya, Nadir title: Statewide Interventions and Covid-19 Mortality in the United States: An Observational Study date: 2020-07-08 pages: extension: .txt txt: ./txt/cord-317823-ztawznod.txt cache: ./cache/cord-317823-ztawznod.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317823-ztawznod.txt' === file2bib.sh === id: cord-332469-zegawla5 author: Li, Wei title: The characteristics of household transmission of COVID-19 date: 2020-04-17 pages: extension: .txt txt: ./txt/cord-332469-zegawla5.txt cache: ./cache/cord-332469-zegawla5.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332469-zegawla5.txt' === file2bib.sh === id: cord-313693-qmkrn7pr author: Wong, Bonnie C. K. title: Possible Role of Aerosol Transmission in a Hospital Outbreak of Influenza date: 2010-11-15 pages: extension: .txt txt: ./txt/cord-313693-qmkrn7pr.txt cache: ./cache/cord-313693-qmkrn7pr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313693-qmkrn7pr.txt' === file2bib.sh === id: cord-331978-y4uo7o8g author: Maxwell, Daniel N title: “The Art of War” in the Era of Coronavirus Disease 2019 (COVID-19) date: 2020-03-04 pages: extension: .txt txt: ./txt/cord-331978-y4uo7o8g.txt cache: ./cache/cord-331978-y4uo7o8g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-331978-y4uo7o8g.txt' === file2bib.sh === id: cord-325136-oyizfh2z author: Pham, Quang Thai title: The first 100 days of SARS-CoV-2 control in Vietnam date: 2020-08-01 pages: extension: .txt txt: ./txt/cord-325136-oyizfh2z.txt cache: ./cache/cord-325136-oyizfh2z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325136-oyizfh2z.txt' === file2bib.sh === id: cord-315180-itvc86cv author: Hollingsworth, T Déirdre title: Counting Down the 2020 Goals for 9 Neglected Tropical Diseases: What Have We Learned From Quantitative Analysis and Transmission Modeling? date: 2018-06-15 pages: extension: .txt txt: ./txt/cord-315180-itvc86cv.txt cache: ./cache/cord-315180-itvc86cv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-315180-itvc86cv.txt' === file2bib.sh === id: cord-331465-humpwwk2 author: Canaday, David H title: On setting expectations for a SARS-CoV-2 Vaccine date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-331465-humpwwk2.txt cache: ./cache/cord-331465-humpwwk2.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-331465-humpwwk2.txt' === file2bib.sh === id: cord-324707-9ld73wv1 author: Mitjà, Oriol title: Hydroxychloroquine for Early Treatment of Adults with Mild Covid-19: A Randomized-Controlled Trial date: 2020-07-16 pages: extension: .txt txt: ./txt/cord-324707-9ld73wv1.txt cache: ./cache/cord-324707-9ld73wv1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-324707-9ld73wv1.txt' === file2bib.sh === id: cord-330951-k54e3lbu author: Pollett, S title: Social media and the new world of scientific communication during the COVID19 pandemic date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-330951-k54e3lbu.txt cache: ./cache/cord-330951-k54e3lbu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330951-k54e3lbu.txt' === file2bib.sh === id: cord-335038-q32ghvsv author: Huang, Jiao title: Epidemiological, virological and serological features of COVID-19 cases in people living with HIV in Wuhan City: A population-based cohort study date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-335038-q32ghvsv.txt cache: ./cache/cord-335038-q32ghvsv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-335038-q32ghvsv.txt' === file2bib.sh === id: cord-312797-hohzjx74 author: Hamelin, Marie-Ève title: Human Metapneumovirus: A New Player among Respiratory Viruses date: 2004-04-01 pages: extension: .txt txt: ./txt/cord-312797-hohzjx74.txt cache: ./cache/cord-312797-hohzjx74.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-312797-hohzjx74.txt' === file2bib.sh === id: cord-322448-s04e6po9 author: Gadsby, Naomi J. title: Comprehensive Molecular Testing for Respiratory Pathogens in Community-Acquired Pneumonia date: 2016-04-01 pages: extension: .txt txt: ./txt/cord-322448-s04e6po9.txt cache: ./cache/cord-322448-s04e6po9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-322448-s04e6po9.txt' === file2bib.sh === id: cord-329290-vqvujry3 author: Kempker, Russell R title: Loss of Smell and Taste Among Healthcare Personnel Screened for Coronavirus 2019 date: 2020-06-28 pages: extension: .txt txt: ./txt/cord-329290-vqvujry3.txt cache: ./cache/cord-329290-vqvujry3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329290-vqvujry3.txt' === file2bib.sh === id: cord-331719-uijwq8gx author: Russek-Cohen, Estelle title: FDA Perspectives on Diagnostic Device Clinical Studies for Respiratory Infections date: 2011-05-01 pages: extension: .txt txt: ./txt/cord-331719-uijwq8gx.txt cache: ./cache/cord-331719-uijwq8gx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-331719-uijwq8gx.txt' === file2bib.sh === id: cord-326297-0r9pex1o author: Hartmann, Stacy title: Coronavirus 2019 (COVID-19) Infections Among Healthcare Workers, Los Angeles County, February - May 2020 date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-326297-0r9pex1o.txt cache: ./cache/cord-326297-0r9pex1o.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-326297-0r9pex1o.txt' === file2bib.sh === id: cord-331731-c2r0kfaz author: Anugwom, Chimaobi M title: Inverse association between chronic hepatitis B infection and COVID-19: immune-exhaustion or coincidence? date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-331731-c2r0kfaz.txt cache: ./cache/cord-331731-c2r0kfaz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-331731-c2r0kfaz.txt' === file2bib.sh === id: cord-335907-93gwmo0v author: de Man, Peter title: Outbreak of COVID-19 in a nursing home associated with aerosol transmission as a result of inadequate ventilation date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-335907-93gwmo0v.txt cache: ./cache/cord-335907-93gwmo0v.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-335907-93gwmo0v.txt' === file2bib.sh === id: cord-335767-omm04fg5 author: Raabe, Vanessa N title: Importance of Pediatric Inclusion in COVID-19 Therapeutic Trials date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-335767-omm04fg5.txt cache: ./cache/cord-335767-omm04fg5.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335767-omm04fg5.txt' === file2bib.sh === id: cord-339859-anatn295 author: Paret, Michal title: SARS-CoV-2 infection (COVID-19) in febrile infants without respiratory distress date: 2020-04-17 pages: extension: .txt txt: ./txt/cord-339859-anatn295.txt cache: ./cache/cord-339859-anatn295.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339859-anatn295.txt' === file2bib.sh === id: cord-322082-80ym2rsq author: Monto, Arnold S title: Lessons From Influenza Pandemics of the Last 100 Years date: 2020-03-01 pages: extension: .txt txt: ./txt/cord-322082-80ym2rsq.txt cache: ./cache/cord-322082-80ym2rsq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322082-80ym2rsq.txt' === file2bib.sh === id: cord-337972-otfloo64 author: Kao, Shang Jyh title: Mechanism of Fulminant Pulmonary Edema Caused by Enterovirus 71 date: 2004-06-15 pages: extension: .txt txt: ./txt/cord-337972-otfloo64.txt cache: ./cache/cord-337972-otfloo64.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-337972-otfloo64.txt' === file2bib.sh === id: cord-327862-zcg3baym author: Luo, Yiqi Ruben title: Kinetics of SARS-CoV-2 Antibody Avidity Maturation and Association with Disease Severity date: 2020-09-14 pages: extension: .txt txt: ./txt/cord-327862-zcg3baym.txt cache: ./cache/cord-327862-zcg3baym.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327862-zcg3baym.txt' === file2bib.sh === id: cord-296588-q2716lda author: Hanson, Kimberly E title: Infectious Diseases Society of America Guidelines on the Diagnosis of COVID-19 date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-296588-q2716lda.txt cache: ./cache/cord-296588-q2716lda.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296588-q2716lda.txt' === file2bib.sh === id: cord-340678-2e2s1gof author: Skowronski, Danuta M title: Influenza vaccine does not increase the risk of coronavirus or other non-influenza respiratory viruses: retrospective analysis from Canada, 2010-11 to 2016-17 date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-340678-2e2s1gof.txt cache: ./cache/cord-340678-2e2s1gof.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-340678-2e2s1gof.txt' === file2bib.sh === id: cord-348036-yub2cqz6 author: Lighter, Jennifer title: Obesity in patients younger than 60 years is a risk factor for Covid-19 hospital admission date: 2020-04-09 pages: extension: .txt txt: ./txt/cord-348036-yub2cqz6.txt cache: ./cache/cord-348036-yub2cqz6.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-348036-yub2cqz6.txt' === file2bib.sh === id: cord-339004-49dkucxd author: Yu, Ignatius Tak-Sun title: Severe Acute Respiratory Syndrome Beyond Amoy Gardens: Completing the Incomplete Legacy date: 2014-03-01 pages: extension: .txt txt: ./txt/cord-339004-49dkucxd.txt cache: ./cache/cord-339004-49dkucxd.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339004-49dkucxd.txt' === file2bib.sh === id: cord-338899-qt17jhg0 author: Lakshmi, Vemu title: Clinical Features and Molecular Diagnosis of Chikungunya Fever from South India date: 2008-05-01 pages: extension: .txt txt: ./txt/cord-338899-qt17jhg0.txt cache: ./cache/cord-338899-qt17jhg0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-338899-qt17jhg0.txt' === file2bib.sh === id: cord-327069-vjlisnui author: Driscoll, Amanda J. title: Standardization of Laboratory Methods for the PERCH Study date: 2017-06-15 pages: extension: .txt txt: ./txt/cord-327069-vjlisnui.txt cache: ./cache/cord-327069-vjlisnui.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-327069-vjlisnui.txt' === file2bib.sh === id: cord-317092-5qba9jiq author: Singh, Tulika title: Lessons from COVID-19 in children: Key hypotheses to guide preventative and therapeutic strategies date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-317092-5qba9jiq.txt cache: ./cache/cord-317092-5qba9jiq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317092-5qba9jiq.txt' === file2bib.sh === id: cord-007321-7gi6xrci author: Chow, Anthony W. title: Evaluation of New Anti-Infective Drugs for the Treatment of Respiratory Tract Infections date: 1992-11-17 pages: extension: .txt txt: ./txt/cord-007321-7gi6xrci.txt cache: ./cache/cord-007321-7gi6xrci.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 139 resourceName b'cord-007321-7gi6xrci.txt' === file2bib.sh === id: cord-330742-m5xx8861 author: Qian, Jie title: Age-dependent gender differences of COVID-19 in mainland China: comparative study date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-330742-m5xx8861.txt cache: ./cache/cord-330742-m5xx8861.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-330742-m5xx8861.txt' === file2bib.sh === id: cord-340317-gwqy6u9x author: Dora, Amy V title: Using Serologic Testing to Assess the Effectiveness of Outbreak Control Efforts, Serial PCR Testing, and Cohorting of Positive SARS-CoV-2 Patients in a Skilled Nursing Facility date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-340317-gwqy6u9x.txt cache: ./cache/cord-340317-gwqy6u9x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340317-gwqy6u9x.txt' === file2bib.sh === id: cord-340579-cvze15cj author: Dudley, Joseph P title: Disparities in Age-Specific Morbidity and Mortality from SARS-CoV-2 in China and the Republic of Korea date: 2020-03-31 pages: extension: .txt txt: ./txt/cord-340579-cvze15cj.txt cache: ./cache/cord-340579-cvze15cj.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340579-cvze15cj.txt' === file2bib.sh === id: cord-335691-lsuwsm43 author: Jackson, Michael L. title: The Burden of Community-Acquired Pneumonia in Seniors: Results of a Population-Based Study date: 2004-12-01 pages: extension: .txt txt: ./txt/cord-335691-lsuwsm43.txt cache: ./cache/cord-335691-lsuwsm43.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-335691-lsuwsm43.txt' === file2bib.sh === id: cord-343827-jo61t3m0 author: Qian, Qun title: Direct evidence of active SARS-CoV-2 replication in the intestine date: 2020-07-08 pages: extension: .txt txt: ./txt/cord-343827-jo61t3m0.txt cache: ./cache/cord-343827-jo61t3m0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343827-jo61t3m0.txt' === file2bib.sh === id: cord-341435-b36h69r1 author: Dawson, Patrick title: Loss of Taste and Smell as Distinguishing Symptoms of COVID-19 date: 2020-06-21 pages: extension: .txt txt: ./txt/cord-341435-b36h69r1.txt cache: ./cache/cord-341435-b36h69r1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341435-b36h69r1.txt' === file2bib.sh === id: cord-333943-9d93na7s author: Jeong, Han Eol title: Association between NSAIDs use and adverse clinical outcomes among adults hospitalized with COVID-19 in South Korea: A nationwide study date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-333943-9d93na7s.txt cache: ./cache/cord-333943-9d93na7s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-333943-9d93na7s.txt' === file2bib.sh === id: cord-341359-c34gyuv6 author: Larson, Derek T title: Clinical Outcomes of Coronavirus Disease 2019 With Evidence-based Supportive Care date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-341359-c34gyuv6.txt cache: ./cache/cord-341359-c34gyuv6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-341359-c34gyuv6.txt' === file2bib.sh === id: cord-348350-pac9ha4q author: Martin-Blondel, G title: Hydroxychloroquine in COVID-19 patients: what still needs to be known about the kinetics date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-348350-pac9ha4q.txt cache: ./cache/cord-348350-pac9ha4q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348350-pac9ha4q.txt' === file2bib.sh === id: cord-344038-20n74z3o author: Han, Mi Seon title: Sequential analysis of viral load in a neonate and her mother infected with SARS-CoV-2 date: 2020-04-16 pages: extension: .txt txt: ./txt/cord-344038-20n74z3o.txt cache: ./cache/cord-344038-20n74z3o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344038-20n74z3o.txt' === file2bib.sh === id: cord-341838-lkz8ro90 author: Gervasoni, Cristina title: Clinical features and outcomes of HIV patients with coronavirus disease 2019 date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-341838-lkz8ro90.txt cache: ./cache/cord-341838-lkz8ro90.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-341838-lkz8ro90.txt' === file2bib.sh === id: cord-350686-q2bu7o4i author: Bilder, Christopher R title: Pool size selection when testing for SARS-CoV-2 date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-350686-q2bu7o4i.txt cache: ./cache/cord-350686-q2bu7o4i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-350686-q2bu7o4i.txt' === file2bib.sh === id: cord-348478-ho89o8mj author: Pawlotsky, Jean-Michel title: SARS-CoV-2 pandemic : Time to revive the cyclophilin inhibitor alisporivir date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-348478-ho89o8mj.txt cache: ./cache/cord-348478-ho89o8mj.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-348478-ho89o8mj.txt' === file2bib.sh === id: cord-349070-bqv03u2e author: Jiang, Shih Sheng title: Sensitive and Quantitative Detection of Severe Acute Respiratory Syndrome Coronavirus Infection by Real-Time Nested Polymerase Chain Reaction date: 2004-01-15 pages: extension: .txt txt: ./txt/cord-349070-bqv03u2e.txt cache: ./cache/cord-349070-bqv03u2e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-349070-bqv03u2e.txt' === file2bib.sh === id: cord-354265-udt2spoe author: Gersh, Felice title: Menopause status and COVID-19 date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-354265-udt2spoe.txt cache: ./cache/cord-354265-udt2spoe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354265-udt2spoe.txt' === file2bib.sh === id: cord-350338-lcsa06gm author: Wang, Kun title: Clinical and laboratory predictors of in-hospital mortality in patients with COVID-19: a cohort study in Wuhan, China date: 2020-05-03 pages: extension: .txt txt: ./txt/cord-350338-lcsa06gm.txt cache: ./cache/cord-350338-lcsa06gm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350338-lcsa06gm.txt' === file2bib.sh === id: cord-345045-nlui9d6e author: Zahn, Matthew title: Infectious Diseases Physicians: Improving and Protecting the Public’s Health: Why Equitable Compensation Is Critical date: 2019-07-15 pages: extension: .txt txt: ./txt/cord-345045-nlui9d6e.txt cache: ./cache/cord-345045-nlui9d6e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345045-nlui9d6e.txt' === file2bib.sh === id: cord-340956-1t3o24u5 author: Borkenhagen, Laura K title: High Risk of Influenza Virus Infection Among Swine Workers: Examining a Dynamic Cohort in China date: 2019-09-01 pages: extension: .txt txt: ./txt/cord-340956-1t3o24u5.txt cache: ./cache/cord-340956-1t3o24u5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340956-1t3o24u5.txt' === file2bib.sh === id: cord-351589-32kd9vva author: Mang, Sebastian title: Pneumocystis Jirovecii Pneumonia and SARS-CoV-2 Co-Infection in newly diagnosed HIV-1 infection date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-351589-32kd9vva.txt cache: ./cache/cord-351589-32kd9vva.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-351589-32kd9vva.txt' === file2bib.sh === id: cord-348392-e35cd9sg author: Moraleda, Cinta title: Multi-Inflammatory Syndrome in Children related to SARS-CoV-2 in Spain date: 2020-07-25 pages: extension: .txt txt: ./txt/cord-348392-e35cd9sg.txt cache: ./cache/cord-348392-e35cd9sg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348392-e35cd9sg.txt' === file2bib.sh === id: cord-350972-0n4dumgg author: Sing, Chor-Wing title: Long-term outcome of short-course high-dose glucocorticoids for SARS: a 17-year follow-up in SARS survivors date: 2020-07-16 pages: extension: .txt txt: ./txt/cord-350972-0n4dumgg.txt cache: ./cache/cord-350972-0n4dumgg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350972-0n4dumgg.txt' === file2bib.sh === id: cord-349556-k312qkvh author: Roldán-Santiago, Ernesto title: SARS-CoV-2 spreads to lymph nodes and strongly expands CD4+ T(EMRA) cells in a patient with mild COVID-19 date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-349556-k312qkvh.txt cache: ./cache/cord-349556-k312qkvh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349556-k312qkvh.txt' === file2bib.sh === id: cord-354877-n5du3bqt author: Vasoo, Shawn title: Rapid Antigen Tests for Diagnosis of Pandemic (Swine) Influenza A/H1N1 date: 2009-10-01 pages: extension: .txt txt: ./txt/cord-354877-n5du3bqt.txt cache: ./cache/cord-354877-n5du3bqt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-354877-n5du3bqt.txt' === file2bib.sh === id: cord-355618-7kfxc2w1 author: McAteer, John title: The VACCINES Act, Deciphering Vaccine Hesitancy in the Time of COVID19 date: 2020-04-13 pages: extension: .txt txt: ./txt/cord-355618-7kfxc2w1.txt cache: ./cache/cord-355618-7kfxc2w1.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-355618-7kfxc2w1.txt' === file2bib.sh === id: cord-352899-bt2xg0ha author: Van Kerkhove, Maria D. title: Interpreting Results From Environmental Contamination Studies of Middle East Respiratory Syndrome Coronavirus date: 2016-10-15 pages: extension: .txt txt: ./txt/cord-352899-bt2xg0ha.txt cache: ./cache/cord-352899-bt2xg0ha.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-352899-bt2xg0ha.txt' === file2bib.sh === id: cord-356084-621qzpqd author: Qu, Jiuxin title: Profile of IgG and IgM antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-356084-621qzpqd.txt cache: ./cache/cord-356084-621qzpqd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-356084-621qzpqd.txt' === file2bib.sh === id: cord-351314-atsuh8e2 author: Bryson-Cahn, Chloe title: A Novel Approach for a Novel Pathogen: using a home assessment team to evaluate patients for 2019 novel coronavirus (SARS-CoV-2) date: 2020-03-12 pages: extension: .txt txt: ./txt/cord-351314-atsuh8e2.txt cache: ./cache/cord-351314-atsuh8e2.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351314-atsuh8e2.txt' === file2bib.sh === id: cord-353116-7t1prfkr author: Bhargava, Ashish title: Predictors for Severe COVID-19 Infection date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-353116-7t1prfkr.txt cache: ./cache/cord-353116-7t1prfkr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353116-7t1prfkr.txt' === file2bib.sh === id: cord-346502-x2b0ao3q author: Arabi, Yaseen M title: Ribavirin and Interferon Therapy for Critically Ill Patients With Middle East Respiratory Syndrome: A Multicenter Observational Study date: 2019-06-25 pages: extension: .txt txt: ./txt/cord-346502-x2b0ao3q.txt cache: ./cache/cord-346502-x2b0ao3q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-346502-x2b0ao3q.txt' === file2bib.sh === id: cord-354009-1ek4s8oe author: Wang, Yun title: Spatiotemporal Characteristics of COVID-19 Epidemic in the United States date: 2020-07-08 pages: extension: .txt txt: ./txt/cord-354009-1ek4s8oe.txt cache: ./cache/cord-354009-1ek4s8oe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354009-1ek4s8oe.txt' === file2bib.sh === id: cord-352837-a29d5dkv author: Hirsch, Hans H title: Spatiotemporal Virus Surveillance for Severe Acute Respiratory Infections in Resource-limited Settings: How Deep Need We Go? date: 2019-04-01 pages: extension: .txt txt: ./txt/cord-352837-a29d5dkv.txt cache: ./cache/cord-352837-a29d5dkv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352837-a29d5dkv.txt' === file2bib.sh === id: cord-351348-lzo0dz7z author: Gu, Silan title: Alterations of the Gut Microbiota in Patients with COVID-19 or H1N1 Influenza date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-351348-lzo0dz7z.txt cache: ./cache/cord-351348-lzo0dz7z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-351348-lzo0dz7z.txt' === file2bib.sh === id: cord-336563-hwemigk7 author: Bhimraj, Adarsh title: Infectious Diseases Society of America Guidelines on the Treatment and Management of Patients with COVID-19 date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-336563-hwemigk7.txt cache: ./cache/cord-336563-hwemigk7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336563-hwemigk7.txt' === file2bib.sh === id: cord-349566-zx9kt144 author: de Alencar, Julio Cesar Garcia title: Double-blind, randomized, placebo-controlled trial with N-acetylcysteine for treatment of severe acute respiratory syndrome caused by COVID-19 date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-349566-zx9kt144.txt cache: ./cache/cord-349566-zx9kt144.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349566-zx9kt144.txt' === file2bib.sh === id: cord-356316-ui11jr2h author: Patel, Monita R title: Performance of oropharyngeal swab testing compared to nasopharyngeal swab testing for diagnosis of COVID-19 —United States, January-February 2020 date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-356316-ui11jr2h.txt cache: ./cache/cord-356316-ui11jr2h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-356316-ui11jr2h.txt' === file2bib.sh === id: cord-348178-6bjimde4 author: Li, Ling title: Biosafety Level 3 Laboratory for Autopsies of Patients with Severe Acute Respiratory Syndrome: Principles, Practices, and Prospects date: 2005-09-15 pages: extension: .txt txt: ./txt/cord-348178-6bjimde4.txt cache: ./cache/cord-348178-6bjimde4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-348178-6bjimde4.txt' === file2bib.sh === id: cord-355734-pz64534w author: Antonio-Villa, Neftali Eduardo title: Health-care workers with COVID-19 living in Mexico City: clinical characterization and related outcomes date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-355734-pz64534w.txt cache: ./cache/cord-355734-pz64534w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355734-pz64534w.txt' === file2bib.sh === id: cord-353862-7xe3fvd5 author: Li, Na title: Maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia: a case-control study date: 2020-03-30 pages: extension: .txt txt: ./txt/cord-353862-7xe3fvd5.txt cache: ./cache/cord-353862-7xe3fvd5.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-353862-7xe3fvd5.txt' === file2bib.sh === id: cord-353103-sdij1d90 author: Yao, Xueting title: In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date: 2020-03-09 pages: extension: .txt txt: ./txt/cord-353103-sdij1d90.txt cache: ./cache/cord-353103-sdij1d90.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353103-sdij1d90.txt' === file2bib.sh === id: cord-348144-t0chpsuh author: Lucas, Alexander H. title: Carbohydrate Moieties as Vaccine Candidates date: 2005-09-01 pages: extension: .txt txt: ./txt/cord-348144-t0chpsuh.txt cache: ./cache/cord-348144-t0chpsuh.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-348144-t0chpsuh.txt' === file2bib.sh === id: cord-354943-wxhbwcfr author: Guo, Li title: Profiling Early Humoral Response to Diagnose Novel Coronavirus Disease (COVID-19) date: 2020-03-21 pages: extension: .txt txt: ./txt/cord-354943-wxhbwcfr.txt cache: ./cache/cord-354943-wxhbwcfr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354943-wxhbwcfr.txt' === file2bib.sh === id: cord-353342-2n6kqyeo author: Corman, Victor M. title: Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection date: 2016-02-15 pages: extension: .txt txt: ./txt/cord-353342-2n6kqyeo.txt cache: ./cache/cord-353342-2n6kqyeo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-353342-2n6kqyeo.txt' === file2bib.sh === id: cord-351231-aoz5jbf1 author: Bartlett, John G. title: Why Infectious Diseases date: 2014-09-15 pages: extension: .txt txt: ./txt/cord-351231-aoz5jbf1.txt cache: ./cache/cord-351231-aoz5jbf1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351231-aoz5jbf1.txt' === file2bib.sh === id: cord-354011-v9t2b2ca author: Benkouiten, Samir title: Circulation of Respiratory Viruses Among Pilgrims During the 2012 Hajj Pilgrimage date: 2013-10-01 pages: extension: .txt txt: ./txt/cord-354011-v9t2b2ca.txt cache: ./cache/cord-354011-v9t2b2ca.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-354011-v9t2b2ca.txt' === file2bib.sh === id: cord-292094-vmsdhccp author: Mandell, Lionel A. title: Infectious Diseases Society of America/American Thoracic Society Consensus Guidelines on the Management of Community-Acquired Pneumonia in Adults date: 2007-03-01 pages: extension: .txt txt: ./txt/cord-292094-vmsdhccp.txt cache: ./cache/cord-292094-vmsdhccp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-292094-vmsdhccp.txt' Que is empty; done journal-clinInfectDis-cord === reduce.pl bib === id = cord-007049-02p8ug67 author = McGeer, Allison title = Let Him Who Desires Peace Prepare for War: United States Hospitals and Severe Acute Respiratory Syndrome Preparedness date = 2004-07-15 pages = extension = .txt mime = text/plain words = 1613 sentences = 92 flesch = 48 summary = In June 2003, the Centers for Disease Control and Prevention (CDC) surveyed members of the Infectious Disease Society of America Emerging Infections Network (EIN) about SARS preparedness in their hospitals. Of the 456 EIN members responding to the survey in this issue of Clinical Infectious Diseases [2] , 381 (83%) reported that patients with respiratory symptoms in their emergency department (ED) would be screened for a travel history. A careful assessment of exposures in SARS outbreaks, particularly those due to superspreading events and transmission despite compliance with isolation precautions, is needed to determine whether airborne spread occurs [10, [13] [14] [15] . At least 2 analyses of risks associated with health care worker infection despite the use of precautions now identify that 12 h of infection-control training and confidence that precautions would be protective are associated with substantial reductions in the risk of infection (Toronto SARS hospital investigation, unpublished data; Lau et al. Hospital preparedness for severe acute respiratory syndrome in the United States: views from a national survey of infectious diseases consultants cache = ./cache/cord-007049-02p8ug67.txt txt = ./txt/cord-007049-02p8ug67.txt === reduce.pl bib === id = cord-007170-svsfu7fj author = Richt, J. A. title = Infection with Borna Disease Virus: Molecular and Immunobiological Characterization of the Agent date = 1992-06-17 pages = extension = .txt mime = text/plain words = 6125 sentences = 325 flesch = 42 summary = Studies on BDV may help to illuminate several important areas of neurobiology, including the mechanisms regulating the replication of a new type of RNA virus in the nuclei of neural cells, the neuroinvasiveness and neurotropism of such viruses, their T cell-mediated immunopathology, tolerance in newborn animals to persistent viral infection of the central nervous system, and behavioral diseases and eating disorders induced by such agents. Persistently infected MDCK (Madin-Darby canine kidney) cells are widely used in indirect immunofluorescence assays for the detection of BDV-specific antibodies in serum and CSF of affected animals and humans [18, 20] . The pathological changes in the brain and retina of BDVinfected animals resemble certain types of encephalitis and Most studies on the pathogenesis of BDV infection have involved experimentally inoculated Lewis rats. Although infection of newborn rats resulted in persistent viral replication in the CNS as well as in visceral organs, these animals developed no inflammatory response or signs of Borna disease. cache = ./cache/cord-007170-svsfu7fj.txt txt = ./txt/cord-007170-svsfu7fj.txt === reduce.pl bib === id = cord-007064-nepgttxf author = Chemaly, Roy F title = A Phase II, Randomized, Double-blind, Placebo-Controlled Trial of Presatovir for the Treatment of Respiratory Syncytial Virus Upper Respiratory Tract Infection in Hematopoietic-Cell Transplant Recipients date = 2019-12-03 pages = extension = .txt mime = text/plain words = 5033 sentences = 227 flesch = 42 summary = title: A Phase II, Randomized, Double-blind, Placebo-Controlled Trial of Presatovir for the Treatment of Respiratory Syncytial Virus Upper Respiratory Tract Infection in Hematopoietic-Cell Transplant Recipients This is the largest randomized, double blind, placebo-controlled clinical trial to date for the treatment of allogeneic and autologous HCT recipients with RSV URTIs. Presatovir treatment did not meet the coprimary endpoints of a greater time-weighted average change in the RSV viral load from Day 1 to 9 and the reduced development of LRTCs through Day 28, but was well tolerated, with a comparable safety profile relative to the placebo. In a post hoc analysis of patients with lymphopenia, the proportion who developed an LRTC through Day 28 was 51% lower following treatment with presatovir, as compared to the placebo; other post hoc analyses also indicated trends toward a treatment effect on LRTCs. The results suggest lessons for the design of future clinical trials of drugs for RSV or other respiratory viruses in transplant recipients or other immunocompromised patients. cache = ./cache/cord-007064-nepgttxf.txt txt = ./txt/cord-007064-nepgttxf.txt === reduce.pl bib === id = cord-010578-uib9h1lb author = Mawle, Alison C. title = Seroepidemiology of Chronic Fatigue Syndrome: A Case-Control Study date = 1995-12-17 pages = extension = .txt mime = text/plain words = 2570 sentences = 164 flesch = 49 summary = We performed serological testing for a large number of infectious agents in 26 patients from Atlanta who had chronic fatigue syndrome (CFS) and in 50 controls matched by age, race, and sex. We performed serological testing for a large number of infectious agents in 26 patients from Atlanta who had chronic fatigue syndrome (CFS) and in 50 controls matched by age, race, and sex. We conducted serological tests for a large number of infectious agents as part of a case-control study assessing risk factors for CFS. Antibodies against human T-lymphotrophic virus types I and II were detected with an ELISA, and confirmatory testing was performed by western blotting [5] . All other agents tested were detected in ;;:::25% of CFS cases, and antibody levels were compared between cases and controls. Evidence for active Epstein-Barr virus infection in patients with persistent unexplained illness: elevated anti-early antigen antibodies cache = ./cache/cord-010578-uib9h1lb.txt txt = ./txt/cord-010578-uib9h1lb.txt === reduce.pl bib === id = cord-001800-644lf8vn author = Biggerstaff, Matthew title = Estimating the Potential Effects of a Vaccine Program Against an Emerging Influenza Pandemic—United States date = 2015-05-01 pages = extension = .txt mime = text/plain words = 4489 sentences = 175 flesch = 43 summary = For the second scenario, we clinical attack rate of the influenza pandemic is 20% and the overall case fatality ratio is 0.53% (high-severity scenario); 10 million doses (left) or 30 million doses (right) of vaccine are administered each week; the vaccination program begins 16 weeks after, 8 weeks after, the same week as, 8 weeks before, and 16 weeks before the first cases of a novel influenza virus occur in the United States; and the efficacy is "H1N1pmd09 monovalent vaccine-like." 2009 H1N1-like vaccine effectiveness: 2 doses of vaccine administered 3 weeks apart required to be fully effective (62% for persons aged <60 years and 43% for persons ≥60 years) in protecting against subclinical and clinical cases, hospitalizations, and deaths. For an influenza pandemic with a 30% overall cumulative attack rate and high-severity scenario, we estimated that a vaccination program beginning the same week as the pandemic started in the United States that administered 10 million doses of vaccine with the moderate VE per week could avert 260 000 hospitalizations and 32 000 deaths (6% reduction) (Tables 2 and 3 ; Figures 2 and 3) . cache = ./cache/cord-001800-644lf8vn.txt txt = ./txt/cord-001800-644lf8vn.txt === reduce.pl bib === id = cord-032234-pfr4l1v9 author = Poloni, Chad title = Evaluating Immune Dysregulation in Patients With COVID-19 Requires a More Accurate Definition of the CD45RA(+) T-cell Phenotype date = 2020-06-04 pages = extension = .txt mime = text/plain words = 679 sentences = 42 flesch = 49 summary = The recently published study conducted in Wuhan, China, by Qin et al indicated dysregulation of the immune response specifically related to T lymphocytes, suggesting that they are highly involved in the pathophysiology of COVID-19 [1] . T-cell dysregulation is a major contributor to age-related changes of the immune system in the elderly, where T-cell responses become defective. Qin et al sought to characterize the T-lymphocyte responses in COVID-19, with aims to differentiate between nonsevere and severe cases. The Wuhan study also identified several differences in T-cell populations between the severe and nonsevere COVID-19 cases. This terminally differentiated T-cell population has been associated with immune dysregulation in the elderly and is further characterized by low CD28 and increased CD57 expression [9] . Improved characterization of terminally differentiated CD45RA + T cells, along with screening for IRP positivity, may be beneficial in identifying those with potential for severe COVID-19. cache = ./cache/cord-032234-pfr4l1v9.txt txt = ./txt/cord-032234-pfr4l1v9.txt === reduce.pl bib === id = cord-260630-vvpzp73r author = Mandell, Lionel A. title = Etiologies of Acute Respiratory Tract Infections date = 2005-08-15 pages = extension = .txt mime = text/plain words = 2623 sentences = 120 flesch = 52 summary = In this issue of Clinical Infectious Diseases, there are 2 articles that provide us with some insight into the various etiologic agents that can cause acute respiratory tract infection (ARTI) in general practice patients in The Netherlands [1] and into the significance of the human metapneumovirus (hMPV) in patients with community-acquired pneumonia (CAP) and exacerbations of chronic obstructive pulmonary disease (COPD) in Quebec, Canada [2] . The objectives of the Dutch study were to estimate the incidence of influenza-like illnesses (ILIs) and of other ARTIs in patients visiting their general practitioners (to determine the etiologic agents) and to test the hypothesis that asymptomatic persons with subclinical infection may act as sources of transmission [1] . Nose and throat swab specimens were obtained from case patients and control subjects, and viral cultures and PCR tests were performed for detection of adenovirus, coronavirus, enterovirus, hMPV, influenza virus, parainfluenza virus, rhinovirus, and respiratory syncytial virus (RSV), as well as for Mycoplasma pneumoniae, Chlamydophila pneumoniae, and Chlamydophila psittaci. cache = ./cache/cord-260630-vvpzp73r.txt txt = ./txt/cord-260630-vvpzp73r.txt === reduce.pl bib === id = cord-257553-479x7av6 author = Kortepeter, Mark G. title = Health Care Workers and Researchers Traveling to Developing-World Clinical Settings: Disease Transmission Risk and Mitigation date = 2010-12-01 pages = extension = .txt mime = text/plain words = 3967 sentences = 217 flesch = 39 summary = title: Health Care Workers and Researchers Traveling to Developing-World Clinical Settings: Disease Transmission Risk and Mitigation This review provides practical advice for this special population of travelers, targeted to specific health care-related risks (needlestick, hemorrhagic fever viruses, severe viral respiratory disease, and tuberculosis), with suggestions for risk mitigation. Although no prophylaxis for hepatitis C virus (HCV) exposure exists, the needlestick transmission risk is lower (1.8%), and up to 20% of transmitted infections resolve spontaneously. The Centers for Disease Control and Prevention (CDC) recommends a 3-drug PEP regimen if the source patient is known to be infected with HIV and the source device is a hollow-bore needle or has visible blood contamination. During the pandemic, transmission to HCWs occurred after close, unprotected contact with symptomatic persons and was significantly mitigated once infection-control precautions were implemented; the degree of risk was related to the type and intensity of exposure (endotracheal intubation was significantly associated with contracting SARS) [27, 28] . cache = ./cache/cord-257553-479x7av6.txt txt = ./txt/cord-257553-479x7av6.txt === reduce.pl bib === id = cord-007047-7ty9mxa9 author = Reller, L. Barth title = Implications of New Technology for Infectious Diseases Practice date = 2006-11-15 pages = extension = .txt mime = text/plain words = 4095 sentences = 190 flesch = 38 summary = Problems with currently available molecular assays include a lack of knowledge about the extent of microbial nucleic acid in "normal" hosts, concentration of agent material in small volume samples, lack of microbiologist expertise, lack of adequate reimbursement, and difficulty with validation based on conventional methods. Infectious diseases clinicians have relied on these expert workers, and Reliable molecular diagnostic tests are not readily available for many infectious agents Commercial tests should only be used for validated specimen types Transportation problems, low concentrations of infectious agent, primer binding site genetic changes, final assay volume, inhibition, contamination, nonspecific amplification, and operator error lead to false-negative and false-positive amplification results Genomic bacterial sequencing is subject to error because of sequence homology among different bacteria, database problems, and mutations A number of nucleic acid hybridization and amplification methods are now in use, including direct probe hybridization (AdvanDx FISH for Staphylococcus aureus [AdvanDx] and GenProbe for group A streptococci [GenProbe]), hybrid capture (Digene for human papillomavirus; Digene), PCR, branched-chain DNA (bDNA; Bayer Diagnostics), and transcription-mediated amplification (Probe-Tec for Chlamydia and N. cache = ./cache/cord-007047-7ty9mxa9.txt txt = ./txt/cord-007047-7ty9mxa9.txt === reduce.pl bib === id = cord-266775-4npowkkz author = Xu, Jun title = Detection of Severe Acute Respiratory Syndrome Coronavirus in the Brain: Potential Role of the Chemokine Mig in Pathogenesis date = 2005-10-15 pages = extension = .txt mime = text/plain words = 3449 sentences = 167 flesch = 46 summary = In the present study, we isolated a SARS coronavirus strain from a brain tissue specimen obtained from a patient with SARS with significant central nervous symptoms. In the present study, we isolated a SARS-CoV strain from a brain tissue specimen obtained during autopsy from a patient with SARS who became severely sick and showed significant central nervous symptoms during the course of his illness. Immunohistochemistry stains for N protein of severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) in a specimen of brain tissue obtained from the patient with SARS during autopsy. With regard to the superinfection with invasive Aspergillus in the brain and other organs of the patient, we think that severe immunodepression resulting from the damage to the immune system induced by SARS-CoV infection, combined with high-dosage treatment with a corticosteroid, provided access for conditional pathogens, causing a superinfection with invasive Aspergillus in multiple organs [24] . cache = ./cache/cord-266775-4npowkkz.txt txt = ./txt/cord-266775-4npowkkz.txt === reduce.pl bib === id = cord-002514-pp06m5xk author = Venkatesan, Sudhir title = Impact of Outpatient Neuraminidase Inhibitor Treatment in Patients Infected With Influenza A(H1N1)pdm09 at High Risk of Hospitalization: An Individual Participant Data Metaanalysis date = 2017-05-15 pages = extension = .txt mime = text/plain words = 4019 sentences = 173 flesch = 40 summary = title: Impact of Outpatient Neuraminidase Inhibitor Treatment in Patients Infected With Influenza A(H1N1)pdm09 at High Risk of Hospitalization: An Individual Participant Data Metaanalysis While evidence exists to support the effectiveness of neuraminidase inhibitors (NAIs) in reducing mortality when given to hospitalized patients with A(H1N1)pdm09 virus infection, the impact of outpatient treatment on hospitalization has not been clearly established. In patients with laboratory-confirmed or clinically diagnosed A(H1N1)pdm09 influenza, after adjustment for community-based antibiotic treatment and propensity score, the likelihood of hospital admission in patients with outpatient or community-based NAI treatment was 0.24 (95% CI, 0.20-0.30) when compared to no NAI treatment in the community (Table 2) . Our main findings ( Table 2) suggest that NAI treatment in the community for patients with severe pandemic influenza substantially reduced the likelihood of hospital admission due to influenza A(H1N1)pdm09. Effectiveness of neuraminidase inhibitors in reducing mortality in patients admitted to hospital with influenza A H1N1pdm09 virus infection: a meta-analysis of individual participant data cache = ./cache/cord-002514-pp06m5xk.txt txt = ./txt/cord-002514-pp06m5xk.txt === reduce.pl bib === === reduce.pl bib === id = cord-010570-ytv7dwr0 author = Casadevall, Arturo title = Return to the Past: The Case for Antibody-Based Therapies in Infectious Diseases date = 1995-07-17 pages = extension = .txt mime = text/plain words = 7469 sentences = 454 flesch = 31 summary = In the preantibiotic era, passive antibody administration (serum therapy) was useful for the treatment of many infectious diseases. We briefly review the use of antibody-based therapy in the early 20th century and make the case for reintroducing passive antibody administration for the treatment ofinfectious diseases. Given the diminishing efficacy of existing antimicrobials because of widespread resistance and the difficulties of treating infections in immunosuppressed individuals, the reintroduction of antibody-based therapies is an option that should be given serious consideration. Thus, antibody therapy is still widely used in medicine, but its role in the treatment of infections is limited largely to viral and toxin neutralization and replacement therapy in patients with immunoglobulin deficiencies. In the past, serum therapy was effective against various pathogens despite the fact that immune sera contained only small amounts of specific antibody. Antibody-based therapies have traditionally been most effective in infections where viral and toxin neutralization modifies the course of the disease. cache = ./cache/cord-010570-ytv7dwr0.txt txt = ./txt/cord-010570-ytv7dwr0.txt === reduce.pl bib === id = cord-266696-w9sb038q author = Zhou, Yi-Hua title = Is the Immune System Impaired in Patients with Severe Acute Respiratory Syndrome? date = 2004-03-15 pages = extension = .txt mime = text/plain words = 1306 sentences = 67 flesch = 56 summary = [1] recently described pronounced lymphopenia and low counts of CD4 + cells, CD8 + cells, and B cells in patients with severe acute respiratory syndrome (SARS). Low counts of both CD4 + and CD8 + cells in the peripheral circulation do not always indicate that the immune system is impaired: redistribution of lymphocytes among peripheral and secondary lymphoid organs and migration of these cells to inflamed tissues caused by infections may also result in lymphopenia. We believe that Zhou and Chen [1] need more data to support their conclusion that the immune function of B cells in our patients appeared not to be impaired because specific anti-SARS-CoV could be detected as early as 10 days after the onset of illness. Is the immune system impaired in patients with severe acute respiratory syndrome The clinical pathology of severe acute respiratory syndrome (SARS): a report from China cache = ./cache/cord-266696-w9sb038q.txt txt = ./txt/cord-266696-w9sb038q.txt === reduce.pl bib === === reduce.pl bib === id = cord-252423-ojmt4k2w author = Qu, Bing title = Monologue of a physician who tested persistently positive for COVID-19 date = 2020-05-11 pages = extension = .txt mime = text/plain words = 1100 sentences = 95 flesch = 72 summary = The COVID-19, as other new infectious diseases, has presented us unprecedented challenges and put us into huge dilemma. As a physician on clinical frontline, I had been treating patients actively and wishing them an early recovery, but never expecting that I would be infected. As in the early stage we knew little about COVID-19 and the possibility that someone with COVID-19 can transmit the virus even if they are not showing symptoms, many healthcare professionals were infected. According to a Press Conference of the WHO-China Joint Mission on COVID-19 on February 24, 3387 medical staff have been reported to be infected, among which over 90% were from Hubei province. Exploring the reasons for healthcare workers infected with novel coronavirus disease 2019 (COVID-19) in China Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China cache = ./cache/cord-252423-ojmt4k2w.txt txt = ./txt/cord-252423-ojmt4k2w.txt === reduce.pl bib === id = cord-260274-c3586tp6 author = Somers, Emily C title = Tocilizumab for treatment of mechanically ventilated patients with COVID-19 date = 2020-07-11 pages = extension = .txt mime = text/plain words = 3645 sentences = 218 flesch = 37 summary = CONCLUSIONS: In this cohort of mechanically ventilated COVID-19 patients, tocilizumab was associated with lower mortality despite higher superinfection occurrence. At our institution, IL-6 blockade with tocilizumab is considered for patients with severe COVID-19 and suspected hyperinflammation based on rapidly worsening respiratory status and elevated inflammatory markers, with the majority of usage occurring in patients requiring mechanical ventilation. Using our COVID-19 Rapid Response Registry infrastructure, we performed an observational study of outcomes in patients with COVID-19 requiring mechanical ventilation, comparing those treated with tocilizumab with those who were not. In this observational, controlled study of patients with severe COVID-19 necessitating mechanical ventilation, receipt of tocilizumab was independently associated with improved survival. To date, the risk of superinfection in mechanically ventilated patients with severe COVID-19 remains poorly described and the incremental risk associated with a single dose of tocilizumab is not well characterized. cache = ./cache/cord-260274-c3586tp6.txt txt = ./txt/cord-260274-c3586tp6.txt === reduce.pl bib === id = cord-273839-oasgagpc author = Bisno, Alan L. title = Diagnosis and Management of Group A Streptococcal Pharyngitis: A Practice Guideline date = 1997-09-17 pages = extension = .txt mime = text/plain words = 5771 sentences = 295 flesch = 41 summary = Except under special circumstances, neither repeated bacteri-Evidence ologic testing (culture or RADT) of patients who have success-We reviewed a large number of clinical trials of diagnostic fully completed a course of antimicrobial therapy nor routine and treatment strategies for group A streptococcal pharyngitis. ple, studies of treatment were evaluated for randomization, A small percentage of patients will have recurrences of acute blinding, use of streptococcal typing to differentiate treatment pharyngitis that are associated with throat cultures (or RADTs) failures from new infections, duration and timing of follow-up positive for group A streptococci within a short period following examinations, and statistical power [1, 2] . Such tests are appropriate for streptococci in the upper respiratory tract and for the confirmation of the clinical diagnosis of acute streptococcal pharyngitis use by microbiology laboratory personnel, but most physicians who perform throat cultures would find it difficult to justify [12] (category A, grade II). cache = ./cache/cord-273839-oasgagpc.txt txt = ./txt/cord-273839-oasgagpc.txt === reduce.pl bib === id = cord-279932-bilr71ay author = Plotkin, Stanley A title = The Value of Human Challenges in Severe Acute Respiratory Syndrome Coronavirus 2 Vaccine Development date = 2020-07-16 pages = extension = .txt mime = text/plain words = 1119 sentences = 61 flesch = 52 summary = A number of people, including Nguyen et al [1] in this issue and others [2] [3] [4] [5] [6] [7] elsewhere, have proposed the use of human challenge trials as a way of confirming the protective ability of candidate vaccines, in order to allow emergency use in high-risk groups and to facilitate the way to eventual licensure and use in the general population. The idea behind human challenge trials is to recruit young, healthy volunteers who have the lowest chance of serious disease, who would be given vaccine candidates and then be challenged with SARS-CoV-2 in order to determine whether the vaccines protect. Aside from the ethical issues, the principal objection to human challenge trials with SARS-CoV-2 is the absence of a reliable rescue medication for the treatment of serious disease. Evaluating use cases for human challenge trials in accelerating SARS-CoV-2 vaccine development cache = ./cache/cord-279932-bilr71ay.txt txt = ./txt/cord-279932-bilr71ay.txt === reduce.pl bib === id = cord-266808-wyuodzyt author = Nagler, Arielle R title = Early Results from SARS-CoV-2 PCR testing of Healthcare Workers at an Academic Medical Center in New York City date = 2020-06-28 pages = extension = .txt mime = text/plain words = 1590 sentences = 117 flesch = 57 summary = title: Early Results from SARS-CoV-2 PCR testing of Healthcare Workers at an Academic Medical Center in New York City Over the following eight weeks three groups were tested: 1) symptomatic staff with fever or respiratory illness; 2) asymptomatic employees with self-reported exposure to COVID-19 which included any degree or duration of contact with an individual who had a documented COVID-19 infection in the work place or in the community; and 3) all employees who were returning to work in services that had been suspended during the epidemic's peak. Positivity rates amongst all groups of employees being tested including symptomatic employees, asymptomatic employees with self-reported exposure to COVID-19, and employees being screened for returning work declined over time ( Figure 1 ). Thus during this testing program, most NYULH employees had continued exposure to COVID patients, yet A c c e p t e d M a n u s c r i p t employees still demonstrated sharp declines in COVID infection rates. cache = ./cache/cord-266808-wyuodzyt.txt txt = ./txt/cord-266808-wyuodzyt.txt === reduce.pl bib === id = cord-260779-riw5xs3j author = van Griensven, Johan title = The Use of Ebola Convalescent Plasma to Treat Ebola Virus Disease in Resource-Constrained Settings: A Perspective From the Field date = 2016-01-01 pages = extension = .txt mime = text/plain words = 3825 sentences = 199 flesch = 46 summary = The clinical evaluation of convalescent plasma (CP) for the treatment of Ebola virus disease (EVD) in the current outbreak, predominantly affecting Guinea, Sierra Leone, and Liberia, was prioritized by the World Health Organization in September 2014. The World Health Organization (WHO) guidelines recommend both convalescent whole blood (CWB) and CP for use against Ebola virus disease (EVD) [12] . Blood transfusion is routinely done in all 3 high-transmission countries involved in the current EVD outbreak; however, plasma has numerous advantages in these settings. Use of convalescent whole blood or plasma collected from patients recovered from Ebola virus disease for transfusion, as an empirical treatment during outbreaks. Treatment of Ebola hemorrhagic fever with blood transfusions from convalescent patients. Clinical trial to evaluate the efficacy and safety of convalescent plasma for Ebola treatment (EVD001). Acute respiratory distress syndrome after convalescent plasma use: treatment of a patient with Ebola virus disease Large-scale convalescent blood and plasma transfusion therapy for Ebola virus disease cache = ./cache/cord-260779-riw5xs3j.txt txt = ./txt/cord-260779-riw5xs3j.txt === reduce.pl bib === id = cord-280763-4bnv2t3f author = Piñana, José Luis title = Clinical Effectiveness of Influenza Vaccination After Allogeneic Hematopoietic Stem Cell Transplantation: A Cross-sectional, Prospective, Observational Study date = 2019-06-01 pages = extension = .txt mime = text/plain words = 4162 sentences = 190 flesch = 35 summary = METHODS: In this prospective, cross-sectional study, we retrospectively analyzed the effect of inactivated trivalent influenza vaccination on the prevalence of influenza RVI in a consecutive cohort of 136 allo-HSCT adult recipients who developed 161 RVI over 5 flu seasons (from 2013 to 2018). The influenza virus has a significant impact on morbidity and mortality in allogeneic hematopoietic stem cell transplantation patients (allo-HSCT), leading to complications ranging from self-limited upper-respiratory tract infections to life-threatening or fatal pneumonias [1] [2] [3] [4] . We conducted a prospective, cross-sectional, observational epidemiological study of community-acquired respiratory virus (CARV) respiratory tract disease (RTD) in allo-HSCT recipients who developed upper RTD (URTD) and/or lower RTD (LRTD) symptoms after transplant. In this study, we report the prevalence of influenza RTD according to the vaccination status over 5 consecutive influenza seasons in a consecutive series of allo-HSCT recipients with virologically-documented respiratory virus infections (RVIs). cache = ./cache/cord-280763-4bnv2t3f.txt txt = ./txt/cord-280763-4bnv2t3f.txt === reduce.pl bib === === reduce.pl bib === id = cord-280958-36ytqapi author = Decker, Summer J title = 3D Printed Alternative to the Standard Synthetic Flocked Nasopharyngeal Swabs Used for COVID-19 testing date = 2020-09-10 pages = extension = .txt mime = text/plain words = 3513 sentences = 266 flesch = 63 summary = BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, can be detected in respiratory samples by Real-time Reverse Transcriptase (RT)-PCR or other molecular methods. The performance of 3DP and FLNP swabs were compared in a clinical trial of symptomatic patients at three clinical sites (n=291) using three SARS-CoV-2 EUA tests: a modified version of the CDC Real-time Reverse Transcriptase (RT)-PCR Diagnostic Panel and two commercial automated formats, Roche Cobas and NeuMoDx. RESULTS: The cycle threshold (C(t)) values from the gene targets and the RNase P gene control in the CDC assay showed no significant differences between swabs for both gene targets (p=0.152 and p=0.092), with the RNase P target performing significantly better in the 3DP swabs (p & 0.001). Given the need for widespread testing, 3DP swabs printed on-site are an alternate to FLNP that can rapidly scale in response to acute needs when supply chain disruptions affect availability of collection kits. cache = ./cache/cord-280958-36ytqapi.txt txt = ./txt/cord-280958-36ytqapi.txt === reduce.pl bib === id = cord-273956-mruywa71 author = Mathers, Amy J title = The practical challenges of making clinical use of the quantitative value for SARS-CoV-2 viral load across several dynamics date = 2020-07-10 pages = extension = .txt mime = text/plain words = 1326 sentences = 81 flesch = 61 summary = title: The practical challenges of making clinical use of the quantitative value for SARS-CoV-2 viral load across several dynamics As the numbers of patients infected with SARS-CoV-2 continues to increase in the United States so does access diagnostic molecular testing especially for hospitalized patients. However, interpreting a low Ct value at the time of hospital admission can A c c e p t e d M a n u s c r i p t only be applied for prognosis of patients in this context while learning about the natural history of a novel infection. As most laboratory reports are not context aware this may mean that additional information for interpretation of the Ct value may need to be amended to the report so that we can use this valuable data to understand how it can help us care for patients infected with SARS-CoV-2. cache = ./cache/cord-273956-mruywa71.txt txt = ./txt/cord-273956-mruywa71.txt === reduce.pl bib === id = cord-007296-q9rn75qb author = Muether, Philipp S. title = Variant Effect of First- and Second-Generation Antihistamines as Clues to Their Mechanism of Action on the Sneeze Reflex in the Common Cold date = 2001-11-01 pages = extension = .txt mime = text/plain words = 2975 sentences = 163 flesch = 46 summary = Treatment with first-generation antihistamines reduces sneezing, rhinorrhea, nasal mucus weight, and, in some instances, cough in subjects with experimental or natural colds; however, treatment with second-generation antihistamines has not been effective for these complaints in trials in subjects with natural colds. The effectiveness of first-generation antihistamines in blocking sneezing in colds may be due primarily to neuropharmacological manipulation of histaminic and muscarinic receptors in the medulla. Also, treatment with first-generation antihistamines is highly effective in reducing sneezing in subjects with experimental and natural colds [3] [4] [5] . Therefore, it would be desirable to confirm the results of the natural cold studies by testing a second-generation antihistamine in the rhinovirus challenge model, which provides more precision in the measurement of sneezing. Although the study was originally designed to determine whether loratadine by down-regulating expression of intercellular adhesion molecule-1 (ICAM-1) on nasal epithelial cells reduces rhinovirus infection rates, it provides heretoforemissing information on the results of testing a second-generation antihistamine in the virus challenge mode. cache = ./cache/cord-007296-q9rn75qb.txt txt = ./txt/cord-007296-q9rn75qb.txt === reduce.pl bib === id = cord-269973-sntnmqqd author = To, Kelvin Kai-Wang title = Unique SARS-CoV-2 clusters causing a large COVID-19 outbreak in Hong Kong date = 2020-08-05 pages = extension = .txt mime = text/plain words = 1860 sentences = 139 flesch = 63 summary = However, the number of COVID-19 cases remained relatively low due to the early implementation of stringent public health measures, including border control, voluntary community-wide wearing of face masks, hand hygiene and social distancing, prompt isolation of suspected cases, and testing and quarantine of close contacts and travelers from epidemic areas [2, 3] . Spike protein D614G mutation was not found in any genomes during the first wave, which mainly involved travelers from mainland China or other parts of Asia, or the linked local cases. The majority of genomes from locally-acquired cases (91%) during this third wave belong to a cluster HK1, a unique cluster within the GR clade, which is characterized by 4 non-synonymous mutations (nsp3 A85V, nsp15 A231V, spike protein S12F, NP A12G) and 1 synonymous mutation (NP C29144T). Two unique SARS-CoV-2 clusters have been identified during this large summer outbreak in Hong Kong shortly after the easing of social distancing policies. cache = ./cache/cord-269973-sntnmqqd.txt txt = ./txt/cord-269973-sntnmqqd.txt === reduce.pl bib === id = cord-265006-m1dmgcd1 author = Kow, Chia Siang title = Do the meta-analyses provide a clean bill of health to the use of renin-angiotensin system inhibitors in COVID-19? date = 2020-08-08 pages = extension = .txt mime = text/plain words = 842 sentences = 56 flesch = 47 summary = In fact, we are aware of the publication of few systematic reviews and metaanalyses [2] [3] [4] [5] [6] [7] [8] which included these observational studies with questionable quality to determine the association between renin-angiotensin system (RAS) inhibitors use, including angiotensin converting enzyme (ACE) inhibitors and angiotensin receptor blockers (ARBs), and mortality/severity of COVID-19. A systematic review and meta-analysis to evaluate the clinical outcomes in COVID-19 patients on angiotensin-converting enzyme inhibitors or angiotensin receptor blockers ACEI/ARB use and risk of infection or severity or mortality of COVID-19: A systematic review and meta-analysis Outcomes of renin-angiotensin-aldosterone system blockers in patients with COVID-19: a systematic review and meta-analysis The use of renin angiotensin system inhibitor on mortality in patients with coronavirus disease 2019 (COVID-19): A systematic review and meta-analysis cache = ./cache/cord-265006-m1dmgcd1.txt txt = ./txt/cord-265006-m1dmgcd1.txt === reduce.pl bib === id = cord-260457-m1jbpo5l author = Allander, Tobias title = Human Bocavirus and Acute Wheezing in Children date = 2007-04-01 pages = extension = .txt mime = text/plain words = 3713 sentences = 209 flesch = 49 summary = We investigated the presence of human bocavirus by quantitative polymerase chain reaction of nasopharyngeal aspirate specimens and selected serum samples obtained from 259 children (median age, 1.6 years) who had been hospitalized for acute expiratory wheezing. Human bocavirus DNA was frequently detected in serum specimens obtained from patients with acute wheezing, suggesting systemic infection. Results suggest a model for bocavirus infection in which high viral loads are potentially associated with respiratory symptoms and low viral loads indicate asymptomatic shedding. Of the 293 children who were randomized, 259 children (median age, 1.6 years; range, 3 months to 15 years) who had sufficient sample material available for complete virus diagnostic evaluation (nasopharyngeal aspirate specimens were used for PCR [for 16 viruses], virus culture [for 9 viruses], and antigen detection [for 7 viruses]; acute-and convalescent-phase serum samples were used for serologic testing [for 7 viruses]) were included in the present study. cache = ./cache/cord-260457-m1jbpo5l.txt txt = ./txt/cord-260457-m1jbpo5l.txt === reduce.pl bib === id = cord-001381-b0tlco4t author = Howie, Stephen R. C. title = Etiology of Severe Childhood Pneumonia in The Gambia, West Africa, Determined by Conventional and Molecular Microbiological Analyses of Lung and Pleural Aspirate Samples date = 2014-09-01 pages = extension = .txt mime = text/plain words = 2360 sentences = 123 flesch = 46 summary = title: Etiology of Severe Childhood Pneumonia in The Gambia, West Africa, Determined by Conventional and Molecular Microbiological Analyses of Lung and Pleural Aspirate Samples Molecular analyses of lung aspirates from Gambian children with severe pneumonia detected pathogens more frequently than did culture and showed a predominance of bacteria, principally Streptococcus pneumoniae, >75% being of serotypes covered by current pneumococcal conjugate vaccines. influenzae), 16S rRNA PCR, multilocus sequence typing (MLST), molecular serotyping, and multiplex fast-track 33 PCR, all using standard methods (Supplementary Appendix 2) [2, [6] [7] [8] [9] [10] [11] [12] [13] , were performed at the MRC Unit in The Gambia, and multiplex MassTag PCR [14] was performed at Columbia University. This study also confirms that molecular methods are able to detect potential pathogens far more readily than culture and have a role in defining the etiology of pneumonia. cache = ./cache/cord-001381-b0tlco4t.txt txt = ./txt/cord-001381-b0tlco4t.txt === reduce.pl bib === id = cord-288432-n2y9cunc author = Liu, Kun title = Population movement, city closure in Wuhan and geographical expansion of the 2019-nCoV pneumonia infection in China in January 2020 date = 2020-04-17 pages = extension = .txt mime = text/plain words = 2357 sentences = 144 flesch = 58 summary = BACKGROUND: The unprecedented outbreak of 2019-nCoV pneumonia infection in Wuhan City caused global concern, the outflowing population from Wuhan was believed to be a main reason for the rapid and large-scale spread of the disease, so the government implemented a city closure measure to prevent its transmission considering the large amount of travelling before the Chinese New Year. METHODS: Based on the daily reported new cases and the population movement data between January 1 and 31, we examined the effects of population outflow from Wuhan on the geographical expansion of the infection in other provinces and cities of China, as well as the impacts of the city closure in Wuhan in different scenarios of closing dates. Thus, we conducted this study with the following objectives: 1) to evaluate the impacts of the population movement on the spatial transmission of the 2019-nCoV cases at the provincial and city levels in China; 2) to estimate the potential outbreak risk at areas with the population outflowed from Wuhan; 3) to evaluate the effectiveness of the city closure measures on the epidemic control. cache = ./cache/cord-288432-n2y9cunc.txt txt = ./txt/cord-288432-n2y9cunc.txt === reduce.pl bib === id = cord-289247-qc3to2xj author = Yamaoka, Yutaro title = Whole nucleocapsid protein of SARS-CoV-2 may cause false positive results in serological assays date = 2020-05-23 pages = extension = .txt mime = text/plain words = 729 sentences = 58 flesch = 62 summary = The nucleocapsid protein (NP) of SARS-CoV-2 is one of the widely used antigens in serodiagnostics of the novel Coronavirus disease . They have generated recombinant whole nucleocapsid protein (rNP) of SARS-CoV-2 using Escherichia coli expression system and used it to develop an enzyme linked immunosorbent assay (ELISA) to detect anti-SARS-CoV-2 antibodies in plasma. Although the amino acid sequences of the entire nucleocapsid proteins (NP) of SARS-CoV and other common Coronaviruses are dissimilar to that of SARS-CoV-2 [1] , the conserved residues at the Nterminal domain of NP show a high degree of similarity (Figure-1A) . Evaluation of inapparent nosocomial severe acute respiratory syndrome coronavirus infection in Vietnam by use of highly specific recombinant truncated nucleocapsid protein-based enzyme-linked immunosorbent assay Novel Immunoglobulin M Capture Enzyme-Linked Immunosorbent Assay for Diagnosis of Severe Acute Respiratory Syndrome Coronavirus Infection Development of Monoclonal Antibody and Diagnostic Test for Middle East Respiratory Syndrome Coronavirus Using Cell-Free Synthesized Nucleocapsid Antigen cache = ./cache/cord-289247-qc3to2xj.txt txt = ./txt/cord-289247-qc3to2xj.txt === reduce.pl bib === id = cord-279828-es498qul author = Boulle, Andrew title = Risk factors for COVID-19 death in a population cohort study from the Western Cape Province, South Africa date = 2020-08-29 pages = extension = .txt mime = text/plain words = 3651 sentences = 148 flesch = 44 summary = We used Cox-proportional hazards models adjusted for age, sex, location and comorbidities to examine the association between HIV, tuberculosis and COVID-19 death from 1 March-9 June 2020 among (i) public sector "active patients" (≥1 visit in the 3 years before March 2020), (ii) laboratory-diagnosed COVID-19 cases and (iii) hospitalized COVID-19 cases. We conducted a cohort study using de-identified data from the Western Cape Provincial Health Data Centre (WCPHDC) of public sector patients aged ≥20 years with documented sex and not known to have died before March 1, 2020 (before the first diagnosed COVID-19 case in South Africa, and several weeks before the first documented COVID-19 death) and included all follow up through June 9, 2020. We used Cox-proportional hazards models adjusted for age, sex and other comorbidities to examine the association between HIV, tuberculosis and COVID-19 death among (i) all public sector patients with ≥1 health visit in the 3 years before March 1, 2020 (considered "active patients"), (ii) laboratory-diagnosed COVID-19 cases and (iii) hospitalized COVID-19 cases. cache = ./cache/cord-279828-es498qul.txt txt = ./txt/cord-279828-es498qul.txt === reduce.pl bib === === reduce.pl bib === id = cord-277307-wabruzfs author = Gu, Wei title = Associations of Early COVID-19 Cases in San Francisco with Domestic and International Travel date = 2020-05-21 pages = extension = .txt mime = text/plain words = 1096 sentences = 79 flesch = 66 summary = In San Francisco, we validated a qRT-PCR test to detect SARS-CoV-2 infection from nasopharyngeal swab samples based on the EUA (Emergency Use Authorization)approved US CDC assay 3 . Those who did not have a recent travel history, a close contact who was COVID-19 positive, or were not a frontline healthcare worker were categorized as community transmission with an unknown source of infection and comprised 39% of cases. Viruses in the G clade comprise most of the genomes sequenced from patients in Europe 8, 9 , but notably have also been identified in the vast majority of cases associated with the New York SARS-CoV-2 outbreak in March to April of 2020, which occurred after the timeline of this study 11, 12 Viruses from two additional travel-associated cases from Europe (UC43) and New York (UC41) were mapped to other clades circulating in Europe (Figure 2) . Sequencing identifies multiple, early introductions of SARS-CoV2 to New York City Region cache = ./cache/cord-277307-wabruzfs.txt txt = ./txt/cord-277307-wabruzfs.txt === reduce.pl bib === id = cord-259243-1lkzcslx author = Álvarez-Aragón, Luis Miguel title = Inquiring into Benefits of Independent Activation of Non-Classical Renin-Angiotensin System in the Clinical Prognosis and Reduction of COVID-19 mortality date = 2020-04-08 pages = extension = .txt mime = text/plain words = 755 sentences = 54 flesch = 53 summary = title: Inquiring into Benefits of Independent Activation of Non-Classical Renin-Angiotensin System in the Clinical Prognosis and Reduction of COVID-19 mortality We have read with great interest the elegant manuscript by Hanff et al [1] proposing a very interesting association between the classical renin-angiotensin system (RAS) and angiotensinconverting enzyme 2 (ACE2) dysregulation present in cardiovascular disease (CVD) and the high mortality index in patients with CVD and coronavirus disease 2019 (COVID-19). On the one hand, it will decrease the proinflammatory effect of Angiotensin II with its subsequent benefit on decreasing the risk of acute respiratory distress syndrome (ARDS) observed in these patients, and on the other hand, it will increase ACE2 expression and therefore the virulence of SARS-Cov2. In addition, in vitro studies in human renal cells treated with SLGT2 inhibitors have shown an increment in Angiotensin(1-7) due to the independent activation of the non-classical RES, leading to important anti-inflammatory and anti-M a n u s c r i p t fibrotic effects [6, 7] . cache = ./cache/cord-259243-1lkzcslx.txt txt = ./txt/cord-259243-1lkzcslx.txt === reduce.pl bib === id = cord-007325-g8ke9rfg author = Koskiniemi, Marjaleena title = CNS Manifestations Associated with Mycoplasma pneumoniae Infections: Summary of Cases at the University of Helsinki and Review date = 1993-08-17 pages = extension = .txt mime = text/plain words = 2324 sentences = 167 flesch = 33 summary = title: CNS Manifestations Associated with Mycoplasma pneumoniae Infections: Summary of Cases at the University of Helsinki and Review CNS manifestations appear in one of 1,000 patients with Mycoplasma pneumoniae-associated infections. Encephalitis is the most frequent manifestation, but cases of meningitis, myelitis, and polyradiculitis, as well as many other symptoms (e.g., coma, ataxia, psychosis, and stroke), have been reported. Besides encephalitis, adult patients had meningitis, myelitis, and polyradiculitis, two cases of each (figure 2). Central nervous system disease associated with Mycoplasma pneumoniae infection: report of five cases and review of the literature Central nervous system manifestations associated with serologically verified Mycoplasma pneumoniae infection Two fatal cases of meningoencephalitis associated with Mycoplasma pneumoniae infection Central nervous system disease associated with Mycoplasma pneumoniae infection Neurological manifestations and Mycoplasma pneumoniae infection A brainstem syndrome associated with Mycoplasma pneumoniae infection-a report of two cases Antibodies to brain and other tissues in cases of Mycoplasma pneumoniae infection cache = ./cache/cord-007325-g8ke9rfg.txt txt = ./txt/cord-007325-g8ke9rfg.txt === reduce.pl bib === id = cord-280915-yk872yaz author = Flaherman, Valerie J title = Infant Outcomes Following Maternal Infection with SARS-CoV-2: First Report from the PRIORITY Study date = 2020-09-18 pages = extension = .txt mime = text/plain words = 1528 sentences = 98 flesch = 54 summary = In a prospective U.S. registry of 263 infants born to mothers testing positive or negative for SARS-CoV-2, SARS-CoV-2 status was not associated with birth weight, difficulty breathing, apnea or upper or lower respiratory infection through 8 weeks of age. Currently, national and international guidelines for management of infants born to mothers with SARS-CoV-2 [6] [7] [8] are based on limited data without outcomes reported past the neonatal period. To address this urgent need, we report here early findings from infants born to mothers enrolled in the PRegnancy CoronavIrus Outcomes RegIsTrY (PRIORITY), an ongoing nationwide study of pregnant or recently pregnant women who have confirmed or suspected SARS-CoV-2. Among 263 initial infants enrolled in the PRIORITY study, adverse outcomes, including preterm birth, NICU admission, and respiratory disease did not differ between those born to mothers testing positive for SARS-CoV-2 and those born to mothers testing negative. cache = ./cache/cord-280915-yk872yaz.txt txt = ./txt/cord-280915-yk872yaz.txt === reduce.pl bib === id = cord-266820-exl36jt3 author = Rivera, Frida title = Prevalence of SARS-CoV-2 asymptomatic infections in two large academic health systems in Wisconsin date = 2020-08-19 pages = extension = .txt mime = text/plain words = 873 sentences = 76 flesch = 61 summary = title: Prevalence of SARS-CoV-2 asymptomatic infections in two large academic health systems in Wisconsin We aim to determine the prevalence of asymptomatic SARS-CoV-2 infection at two hospital systems in two counties in Wisconsin. This study aims to determine the prevalence of asymptomatic SARS-CoV-2 infection at two hospital systems in two counties with markedly different rates of COVID-19. From April 6, 2020 to June 04, 2020, a total of 11,654 asymptomatic patients were tested for SARS-CoV-2, and 61 (0.52%) were positive [Froedtert Health, 38; UW Health, 23]. During the study period, we observed a low prevalence of asymptomatic SARS-CoV-2 infections in these two academic health systems in South Wisconsin. This low prevalence of asymptomatic infections has been recently reported in other areas with high COVID-19 rates, such as Boston and Philadelphia [4, 5] ; however, these two studies included pregnant women and children. In contrast, two hospitals in New York City reported a prevalence of SARS-CoV-2 asymptomatic infections of 14% among women admitted for delivery. cache = ./cache/cord-266820-exl36jt3.txt txt = ./txt/cord-266820-exl36jt3.txt === reduce.pl bib === id = cord-007068-vcfs41eb author = Moradi, Tony title = Use of Procalcitonin and a Respiratory Polymerase Chain Reaction Panel to Reduce Antibiotic Use via an Electronic Medical Record Alert date = 2019-10-22 pages = extension = .txt mime = text/plain words = 3669 sentences = 197 flesch = 38 summary = We sought to determine whether an automated electronic medical record best practice alert (BPA) based on procalcitonin and respiratory polymerase chain reaction (PCR) results could help reduce inappropriate antibiotic use in patients with likely viral respiratory illness. In the study group, a BPA alerted providers of the diagnostic results suggesting viral infection and prompted them to reassess the need for antibiotics. CONCLUSIONS: The automated antimicrobial stewardship BPA effectively reduced antibiotic use and discharge prescribing rates when diagnostics suggested viral respiratory tract infection, without a higher rate for reinitiation of antibiotics after discontinuation. The aim of our study was to determine if antibiotic use could be reduced by deploying an automated antimicrobial stewardship provider alert that prompted antibiotic de-escalation if 3 criteria were met: PCT <0.25 ng/mL, virus detected on respiratory PCR, and active use of systemic antibiotics. cache = ./cache/cord-007068-vcfs41eb.txt txt = ./txt/cord-007068-vcfs41eb.txt === reduce.pl bib === id = cord-268233-ibxufjrv author = Nagappa, Bharathnag title = Seroconversion rate and diagnostic accuracy of serological tests for COVID-19 date = 2020-05-30 pages = extension = .txt mime = text/plain words = 610 sentences = 52 flesch = 69 summary = We read the recent article by Zhao J et al which studied the antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019 [1] . However in results, the authors have mentioned that only 112 out of 173 participants tested positive for RNA over complete duration of the study, which contradicts the methodology. Third, Antibody tests in this study population should be interpreted cautiously since 1) there is plausibility to have cross reaction to antibodies related to other corona virus strains and 2) also diseases caused by other corona virus present with similar symptoms as COVID-19, and symptomatic patients might have antibodies which may lead to increased false positivity rate. Therefore present study should carefully interpret the serological tests and sensitivity should be calculated only in participants tested positive for RNA. Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019 cache = ./cache/cord-268233-ibxufjrv.txt txt = ./txt/cord-268233-ibxufjrv.txt === reduce.pl bib === id = cord-271014-xzpvupms author = Erikstrup, Christian title = Estimation of SARS-CoV-2 infection fatality rate by real-time antibody screening of blood donors date = 2020-06-25 pages = extension = .txt mime = text/plain words = 2366 sentences = 177 flesch = 57 summary = title: Estimation of SARS-CoV-2 infection fatality rate by real-time antibody screening of blood donors The objective was to perform nationwide real-time seroprevalence surveying among blood donors as a tool to estimate previous SARS-CoV-2 infections and the population based IFR. We have initiated real-time nationwide anti-SARS-CoV-2 seroprevalence surveying of blood donations as a tool in monitoring the epidemic. Thus, numbers of patients tested positive for SARS-CoV-2, admitted to hospital, needing respiratory assistance or deceased from coronavirus disease 2019 (COVID-19) are updated on a daily basis. The objective of this study is to perform a seroprevalence survey among blood donors as a tool in the monitoring of the SARS-CoV-2 epidemic. In this survey of SARS-CoV-2 antibodies in Danish blood donors we found a seroprevalence of 1.9 (CI: 0.8-2.3) adjusted for the assay performance and a low IFR of 89/100,000 (CI: 72-211). The ratio between estimated antibody-positive individuals and confirmed COVID-19 cases is expected given the targeted early Danish SARS-CoV-2 testing strategy. cache = ./cache/cord-271014-xzpvupms.txt txt = ./txt/cord-271014-xzpvupms.txt === reduce.pl bib === id = cord-254183-98o0dssj author = Waggoner, Jesse J. title = Rare and Emerging Viral Infections in Transplant Recipients date = 2013-10-15 pages = extension = .txt mime = text/plain words = 3927 sentences = 236 flesch = 44 summary = In this review, we first discuss viral diagnostics and the developing field of viral discovery and then focus on rare and emerging viruses in the transplant population: human T-cell leukemia virus type 1; hepatitis E virus; bocavirus; KI and WU polyomaviruses; coronaviruses HKU1 and NL63; influenza, H1N1; measles; dengue; rabies; and lymphocytic choriomeningitis virus. Detection and reporting of such rare pathogens in transplant recipients is critical to patient care and improving our understanding of posttransplant infections. In a multicenter review of 85 cases of acute HEV infection, 65.9% of the solid organ transplant (SOT) recipients developed chronic hepatitis of whom 14.3% developed cirrhosis. Cases of lymphocytic choriomeningitis virus (LCMV) transmitted through organ transplantation (4 clusters, including 14 cases and 11 deaths) document the ability of this pathogen to cause severe disease in the immunocompromised host [10, [49] [50] [51] . Human T-cell leukemia virus type I-associated myelopathy following living-donor liver transplantation cache = ./cache/cord-254183-98o0dssj.txt txt = ./txt/cord-254183-98o0dssj.txt === reduce.pl bib === id = cord-010599-nwp2if8d author = Hayden, Frederick G. title = Efficacy and Safety of Oral Pleconaril for Treatment of Colds Due to Picornaviruses in Adults: Results of 2 Double-Blind, Randomized, Placebo-Controlled Trials date = 2003-06-15 pages = extension = .txt mime = text/plain words = 3985 sentences = 215 flesch = 45 summary = More recently, retrospective analysis of 2 phase II randomized, double-blind, placebo-controlled studies found that pleconaril treatment provided clinical benefit for colds due to picornaviruses in previously healthy adults [10] . Calculations indicated that enrollment of 1000 subjects in each study was required to detect a 25% relative difference between treatment groups in the proportion of picornavirus-infected subjects reaching the primary end point (or an estimated 2-day difference in median time) with 90% power (2-sided test at the 5% level of significance [20] ). Among the picornavirus-infected (ITT-I) population, the time to reach the primary end point of illness alleviation was significantly shorter among pleconaril-treated subjects than among placebo recipients in each study (figure 1). severity score was reduced by 19% over the duration of the study for pleconaril recipients (table 4) , who also experienced significant reductions from baseline in symptom severity scores by day 2 of treatment, compared with placebo recipients (figure 2). cache = ./cache/cord-010599-nwp2if8d.txt txt = ./txt/cord-010599-nwp2if8d.txt === reduce.pl bib === === reduce.pl bib === id = cord-266150-wox7pnkr author = Torres, Juan Pablo title = SARS-CoV-2 antibody prevalence in blood in a large school community subject to a Covid-19 outbreak: a cross-sectional study date = 2020-07-10 pages = extension = .txt mime = text/plain words = 4202 sentences = 222 flesch = 53 summary = Once these forms were signed, a copy was emailed to participants for their records and they were directed to a secure survey that i) asked basic demographic questions, ii) requested information on any previous RT-PCR test for SARS-CoV-2 and potential contact with any Covid-19 positive cases, and iii) asked about symptoms experienced since the outbreak (date and duration in days of each symptom). Among students, antibody positive children were younger, had a higher PCR positivity rate (in those who underwent PCR testing during the outbreak), and were more likely to self-report contact with one or more confirmed cases, as compared to seronegative children ( Table 2 ). Overall, PCR testing and contact history was significantly higher in staff compared to students, which in addition to the higher antibody positivity observed in this study, support the more significant role of adults within the outbreak, in proportion to the overall population. cache = ./cache/cord-266150-wox7pnkr.txt txt = ./txt/cord-266150-wox7pnkr.txt === reduce.pl bib === id = cord-258304-86gqxajw author = Bahl, Prateek title = Droplets and Aerosols generated by singing and the risk of COVID-19 for choirs date = 2020-09-18 pages = extension = .txt mime = text/plain words = 1553 sentences = 85 flesch = 58 summary = title: Droplets and Aerosols generated by singing and the risk of COVID-19 for choirs The results of detailed particle tracking (in supplementary video) reveals that the maximum velocity of droplets expelled, specifically for certain syllables such as 'do', 'fa' and 'ti', is approx. Figure 2c shows the velocity distribution of droplets that are visible while the subject was singing syllable 'sol' & 'la' and the direction in which these droplets are moving. Nevertheless, the droplets observed do not appear to be settling down rapidly and without adequate ventilation, these droplets can potentially saturate the indoor environment which can likely explain the very high attack rates of COVID-19 seen in choirs in the US and Europe (almost 87% in Skagit County, Washington) [1] . We note the present study only provides visual evidence of the droplets and aerosols expelled during singing and compare the associated velocities and directions with speaking and coughing. cache = ./cache/cord-258304-86gqxajw.txt txt = ./txt/cord-258304-86gqxajw.txt === reduce.pl bib === id = cord-254458-bbcef8xt author = Ali, Farhana title = Throat Wash Testing and COVID-19 Disease: Should We Put Our Money Where Our Mouth Is? date = 2020-04-30 pages = extension = .txt mime = text/plain words = 1107 sentences = 76 flesch = 59 summary = The tragedy that is the US aircraft carrier Theodore Roosevelt, in which 60 percent of the 600 sailors who tested positive for SARS-CoV-2 infection were asymptomatic, further highlights the need for accurate laboratory diagnostics for COVID-19 disease [2] . make the case that testing of throat wash samples may be more sensitive than testing of NP swabs for COVID-19 disease. Interestingly, there is biologic plausibility that a sample collected via the oral cavity (such as a throat wash) may yield higher results than a NP swab test based on a study by Xu et al. Finally, the authors' detection of virus late in the patients' clinical course emphasizes the uncertainty faced by policy makers as they try to determine the optimal length of isolation for an individual recovering from COVID-19 disease. Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs cache = ./cache/cord-254458-bbcef8xt.txt txt = ./txt/cord-254458-bbcef8xt.txt === reduce.pl bib === id = cord-264660-tfktgy57 author = Creech, C Buddy title = It’s True Even in a Pandemic: Children are Not Merely Little Adults date = 2020-05-30 pages = extension = .txt mime = text/plain words = 980 sentences = 64 flesch = 55 summary = In this issue of CID, Mehta et al (CID PAPER) provide a systematic review of pediatric COVID-19, evaluating the available literature to date to glean characteristics of disease and transmission. The authors report that children represent only 5% or less of diagnosed COVID cases and the data available at the time of review suggest that children are less likely to develop either severe pneumonia or the laboratory alterations commonly associated with severe disease, such as lymphopenia and elevated inflammatory markers. The authors also report that intrauterine transmission appears to be extremely uncommon and that newborns born to infected mothers are likely to experience either asymptomatic disease or mild disease. Taken together, it would appear that children experience a very different response to SARS-CoV-2 infection than adults and raises the hypothesis that dysregulated host responses may be the primary driver of disease severity. cache = ./cache/cord-264660-tfktgy57.txt txt = ./txt/cord-264660-tfktgy57.txt === reduce.pl bib === === reduce.pl bib === id = cord-275349-b35pt3mo author = Lenz, Heinz-Josef title = The Emergence of Baricitinib: A Story of Tortoises Versus Hares date = 2020-07-06 pages = extension = .txt mime = text/plain words = 1403 sentences = 63 flesch = 37 summary = The artificial intelligence algorithms predicted that baricitinib would inhibit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection of cells [2] , (an effect later confirmed in human liver spheroids) [3] , combined with its better-known anti-inflammatory properties. Consequently, the combined potential antiviral and anti-inflammatory effects of this dually acting drug could be ideal for halting the progression of the disease in hospitalized patients, when taken for a limited duration. This new paper in the journal extends the previous published reports of baricitinib treatment in mild-tomoderate COVID19 patients and provides further evidence that baricitinib could be a potential treatment for unwell hospitalized patients with this disease, independent of severity. One would be advised to remain vigilant of such signals reflecting thromboembolic or infection risk in randomized controlled trials testing a variety of immunomodulatory therapies in COVID-19 patients, either alone or in combination, especially in view of associations between clots and SARS-CoV-2 infection [10] . cache = ./cache/cord-275349-b35pt3mo.txt txt = ./txt/cord-275349-b35pt3mo.txt === reduce.pl bib === === reduce.pl bib === id = cord-015493-vf4et613 author = Deresinski, Stan title = In the Literature date = 2007-10-15 pages = extension = .txt mime = text/plain words = 1565 sentences = 67 flesch = 45 summary = Tetracyclines as an oral treatment option for patients with community-onset methicillin-resistant Staphylococcus aureus skin and soft-tissue infections. Subgroup analysis that included only the 225 episodes in which incision and drainage were performed at presentation confirmed that blactam antibiotic therapy was significantly associated with treatment failure. These results are consistent with those of several other recent studies that have found that administration of an antibiotic that inhibits the growth of MRSA improves outcomes, even in patients who have undergone incision and drainage. For example, in a similar retrospective study of 531 episodes of community-acquired MRSA SSTI, most of which were treated with incision and drainage, Ruhe et al. Although Ruhe and colleagues provide evidence of the benefit of doxycyline for the treatment of SSTI due to antibioticsusceptible MRSA, alternative antibiotic choices may be considered. Prospective randomized trial of empiric therapy with trimethoprim-sulfamethoxazole or doxycycline for outpatient skin and soft tissue infections in an area of high prevalence of methicillin-resistant Staphylococcus aureus cache = ./cache/cord-015493-vf4et613.txt txt = ./txt/cord-015493-vf4et613.txt === reduce.pl bib === id = cord-283780-h4lwzpl9 author = Zhang, John J Y title = Risk Factors of Severe Disease and Efficacy of Treatment in Patients Infected with COVID-19: A Systematic Review, Meta-Analysis and Meta-Regression Analysis date = 2020-05-14 pages = extension = .txt mime = text/plain words = 3118 sentences = 221 flesch = 50 summary = title: Risk Factors of Severe Disease and Efficacy of Treatment in Patients Infected with COVID-19: A Systematic Review, Meta-Analysis and Meta-Regression Analysis We conducted a systematic review and meta-analysis of all published studies up to March 15, 2020 which reported COVID-19 clinical features and/or treatment outcomes. To address this gap in the literature, we conducted a systematic review, meta-analysis and meta-regression to 1) investigate the predictive value of laboratory investigations for severe disease and adverse outcomes, and 2) evaluate the efficacy of antivirals and corticosteroids for COVID-19. Among the patients with antiviral use reported in our meta-analysis, overall rates of mortality, ICU admission and ARDS were 5.7%, 11.8% and 20.2%, respectively. Our meta-analysis suggested that the use of corticosteroids is associated with disease severity (ICU admission) and higher ARDS rates. To the best of our knowledge, this is the first systematic review and meta-analysis of COVID-19 to describe specific laboratory predictors of severe disease and adverse outcomes. cache = ./cache/cord-283780-h4lwzpl9.txt txt = ./txt/cord-283780-h4lwzpl9.txt === reduce.pl bib === id = cord-261270-jkm9c5yv author = Annweiler, Cédric title = National French survey of COVID-19 symptoms in people aged 70 and over date = 2020-06-18 pages = extension = .txt mime = text/plain words = 1708 sentences = 114 flesch = 57 summary = The following symptoms observed within the first 72 hours of SARS-CoV-2 infection (i.e., 72h from suspicion, possibly before diagnostic confirmation by RT-PCR test) were collected for each patient using yes/no questions: general signs (sudden deterioration of general condition, temperature, blood pressure), respiratory signs (cough, polypnea), ear nose and throat (ENT) signs (rhinorrhea, odynophagia, otalgia, conjunctivitis, dysgeusia or ageusia, anosmia), gastrointestinal signs (diarrhea, nausea or vomiting) and geriatric syndromes (falls, hypo or overactive delirium, altered consciousness). This national French survey shows that older adults with COVID-19 exhibit a paucisymptomatic clinical picture with less than 3 signs during the first 72h of the infection, generally combining general and respiratory signs (e.g. hyperthermia and cough) with peculiarities that should alert the clinician (e.g. sudden deterioration of general condition, diarrhea, lymphopenia, and/or geriatric syndromes including falls and delirium). cache = ./cache/cord-261270-jkm9c5yv.txt txt = ./txt/cord-261270-jkm9c5yv.txt === reduce.pl bib === id = cord-276995-b003vcdc author = Wiese, Andrew D title = Social distancing measures: evidence of interruption of seasonal influenza activity and early lessons of the SARS-CoV-2 pandemic date = 2020-06-20 pages = extension = .txt mime = text/plain words = 818 sentences = 54 flesch = 39 summary = And while novel surveillance systems have been implemented to monitor SARS-CoV-2 activity, pre-existing surveillance systems have the advantage of allowing comparison to trends in prior years to assess the impact of social distancing measures on the activity of influenza and other respiratory pathogens. In this issue of the journal, Hyunju Lee and colleagues describe the use of national influenza surveillance data to assess the impact of social distancing measures, implemented in response to the SARS-CoV-2 pandemic, on seasonal influenza activity in Korea. [1] [2] [3] In this study, investigators compared the A c c e p t e d M a n u s c r i p t While surveillance data are helpful to identify abnormal activity of certain diseases of public health interest, and to demonstrate the impact of major interventions, such as implementation of social distancing measures, it is important to understand the limitations and strengths of specific surveillance systems. cache = ./cache/cord-276995-b003vcdc.txt txt = ./txt/cord-276995-b003vcdc.txt === reduce.pl bib === id = cord-280005-i9fp5rys author = Wang, Mengmei title = Treatment of COVID-19 Patients with Prolonged Post-Symptomatic Viral Shedding with Leflunomide -- a Single-Center, Randomized, Controlled Clinical Trial date = 2020-09-21 pages = extension = .txt mime = text/plain words = 3185 sentences = 172 flesch = 49 summary = title: Treatment of COVID-19 Patients with Prolonged Post-Symptomatic Viral Shedding with Leflunomide -a Single-Center, Randomized, Controlled Clinical Trial CONCLUSIONS: In COVID-19 patients with prolonged PCR positivity, no benefit in terms of the duration of viral shedding was observed with the combined treatment of leflunomide and IFN α-2a beyond IFN α-2a alone. Based on that background, we conducted a prospective randomized, controlled, open-label trial, to evaluate the efficacy and safety of oral leflunomide to treat hospitalized COVID-19 patients with prolonged post-symptomatic viral shedding. Fifty eligible patients were randomly assigned to a combination treatment group that received leflunomide (50 mg, q12h, three consecutive times, orally; then 20 mg, once a day for 8 days; a total course of 10 days) plus nebulized IFN -2a (3 million IU each time, adding 2 ml of sterilized water, atomization inhalation twice daily for 10 days), or to a control group that received nebulized IFN -2a This was an open-label, prospective randomized, controlled trial, which was conducted at East Campus, Renmin Hospital of Wuhan University. cache = ./cache/cord-280005-i9fp5rys.txt txt = ./txt/cord-280005-i9fp5rys.txt === reduce.pl bib === id = cord-291363-re45w37d author = Sanville, Bradley title = A Community Transmitted Case of Severe Acute Respiratory Distress Syndrome due to SARS CoV2 in the United States date = 2020-03-30 pages = extension = .txt mime = text/plain words = 1308 sentences = 86 flesch = 53 summary = title: A Community Transmitted Case of Severe Acute Respiratory Distress Syndrome due to SARS CoV2 in the United States The current novel coronavirus (SARS CoV2) outbreak, which was identified in December 2019 in Wuhan, Hubei, China has spread rapidly causing a significant public health crisis worldwide 1 . Two healthcare workers in contact with the patient at the outside hospital have subsequently tested positive for SARS CoV2. Overall, these reviews note a case fatality rate of 1.40-3.46%, though this may be considerably lower when accounting for a likely large number of mild or asymptomatic patients that were not tested 6, 9, 10 DeWit and colleagues from the NIH, Gilead, and Columbia University successfully treated rhesus macaques against a model of MERS 13 . As noted in a recent editorial, diagnosis becomes even more difficult considering the likelihood of a large number of mild or asymptomatic patients who are not formally identified with a SARS CoV2 infection 18, 19 . cache = ./cache/cord-291363-re45w37d.txt txt = ./txt/cord-291363-re45w37d.txt === reduce.pl bib === id = cord-266232-2ctfmjb8 author = Trubiano, Jason A title = Alterations in smell or taste – Classic COVID-19? date = 2020-05-28 pages = extension = .txt mime = text/plain words = 693 sentences = 74 flesch = 66 summary = A c c e p t e d M a n u s c r i p t Dear Editor, There are increased reports of loss of smell (anosmia) and taste (ageusia) in patients with confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causing coronavirus disease 2019 , in particular in the setting of mild disease. Luers and colleagues described from a retrospective adult cohort of confirmed SARS-CoV-2 from Germany (n = 72) that 74% of patients reported anosmia and 69% ageusia [7] . prior to this also described from a retrospective cohort study of COVID-19 patients interviewed 5-6 days post diagnosis that 64.4% reported alternations in taste or smell [1] . It is important for clinicians to realize that ansomia and ageusia are likely to be commonly reported symptoms in other upper respiratory tract infections, when appropriately asked (8.9% of our COVID-19 test negative group) [3, 8] . Self-reported olfactory and taste disorders in SARS-CoV-2 patients: a cross-sectional study cache = ./cache/cord-266232-2ctfmjb8.txt txt = ./txt/cord-266232-2ctfmjb8.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-277611-3iynrfzq author = Buetti, Niccolò title = Risk factors for SARS-CoV-2 detection in blood of critically ill patients date = 2020-09-02 pages = extension = .txt mime = text/plain words = 810 sentences = 86 flesch = 68 summary = In their multivariate analysis the authors showed that SARS-CoV-2 RNAaemia was strongly associated with the clinical class, with higher level RNAaemia among critically ill patients. Therefore, we conducted a similar study using prospectively collected data at the Bichat University Hospital, France, in order to identify risk factors for SARS-CoV-2 detection in blood in critically ill intubated patients. In order to identify risk factors for SARS-CoV-2 detection in blood, we used univariable and multivariable mixed-effect logistic models for clustered data (PROC GLIMMIX of SAS) and we adjusted for the time between symptoms' onset and date of sampling. Using univariable mixed-effect models after adjusting for the time interval between onset of symptoms and date of sampling, we showed that immunosuppression (OR 12.16, 95% CI 1.74-84.93, p=0.013) and chronic renal failure (OR 5.98, A c c e p t e d M a n u s c r i p t 3 95% CI 1.14-31.35, p=0.035) increased the risk for SARS-CoV-2 detection in blood (Table) . cache = ./cache/cord-277611-3iynrfzq.txt txt = ./txt/cord-277611-3iynrfzq.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-007321-7gi6xrci author = Chow, Anthony W. title = Evaluation of New Anti-Infective Drugs for the Treatment of Respiratory Tract Infections date = 1992-11-17 pages = extension = .txt mime = text/plain words = 16053 sentences = 825 flesch = 31 summary = These guidelines for the evaluation of drugs for the treatment of respiratory tract infections include acute streptococcal pharyngitis and tonsillitis, acute otitis media, acute and chronic sinusitis, acute exacerbations of chronic bronchitis, and acute infectious pneumonia (table 1). This is often the case in otitis media, sinusitis, and pneumonia, when the use of invasive procedures such as tympanocentesis, sinus puncture, or transtracheal aspiration to confirm microbial eradication in the patient who is improving clinically generally is considered unjustified. Patients eligible for study entrance are children or adults with symptomatic pharyngitis or tonsillitis of acute onset clinically consistent with infection with group A I3-hemolytic streptococci and from whom group A (3-hemolytic streptococci have been isolated in cultures of throat -swab specimen or for whom a rapid screening test has indicated the presence of streptococci. cache = ./cache/cord-007321-7gi6xrci.txt txt = ./txt/cord-007321-7gi6xrci.txt === reduce.pl bib === === reduce.pl bib === id = cord-284782-51mbq7qb author = Huang, Jing title = Care for the psychological status of frontline medical staff fighting against COVID-19 date = 2020-04-03 pages = extension = .txt mime = text/plain words = 314 sentences = 21 flesch = 63 summary = key: cord-284782-51mbq7qb authors: Huang, Jing; Liu, Fangkun; Teng, Ziwei; Chen, Jindong; Zhao, Jingping; Wang, Xiaoping; Wu, Renrong title: Care for the psychological status of frontline medical staff fighting against COVID-19 cord_uid: 51mbq7qb Besides, a total of 6, 097 medical workers from different provinces in China were in Hubei province to assist in the COVID-19 by Jan 30, 2020 2 . For example, the emergency medical team from the Second Xiangya Hospital is able to set up field hospitals and ambulances to help and serve the With the increasing spreading of the virus worldwide, COVID-19 outbreak is now becoming a pandemic. None of the authors has any potential conflicts of interest to disclose. Timely mental health care for the 2019 novel coronavirus outbreak is urgently needed The immediate psychological and occupational impact of the 2003 SARS outbreak in a teaching hospital Protecting Health Care Workers during the COVID-19 Coronavirus Outbreak -Lessons from Taiwan's SARS response cache = ./cache/cord-284782-51mbq7qb.txt txt = ./txt/cord-284782-51mbq7qb.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-012511-fl5llkoj author = Meltzer, Martin I. title = Standardizing Scenarios to Assess the Need to Respond to an Influenza Pandemic date = 2015-05-01 pages = extension = .txt mime = text/plain words = 4122 sentences = 207 flesch = 56 summary = We were tasked to evaluate the 6 following interventions: invasive mechanical ventilators, influenza antiviral drugs for treatment (but not large-scale prophylaxis), influenza vaccines, respiratory protective devices for healthcare workers and surgical face masks for patients, school closings to reduce transmission, and airport-based screening to identify those ill with novel influenza virus entering the United States. To allow easy comparison between results (a specification), we standardized a risk space defined by using ranges of transmission and clinical severity from a previously published influenza severity assessment framework ( Figure 1 ) [5] . Standardized epidemiological curves-contact matrix: To model the 4 epidemic curves (Figure 2 ), we built a simple, nonprobabilistic (ie, deterministic) model in which we divided the population into 4 age groups (0-10, 11-20, 21-60, ≥61 years). cache = ./cache/cord-012511-fl5llkoj.txt txt = ./txt/cord-012511-fl5llkoj.txt === reduce.pl bib === === reduce.pl bib === id = cord-272956-0yumc7em author = Gnavi, Roberto title = Therapy With Agents Acting on the Renin-Angiotensin System and Risk of Severe Acute Respiratory Syndrome Coronavirus 2 Infection date = 2020-05-22 pages = extension = .txt mime = text/plain words = 1772 sentences = 90 flesch = 51 summary = Exposure to agents acting on the renin-angiotensin system was not associated with a risk increase of COVID-19 infection in 2 Italian matched case-control studies, 1 nested in hypertensive patients and the other in patients with cardiovascular diseases or diabetes. Consequently, patients treated with ACE inhibitors (ACEIs) or angiotensin II receptor blockers (ARBs), in particular those with diabetes or cardiovascular disease, should be considered at higher risk of developing severe coronavirus disease 2019 (COVID-19) infection (CVi), and of experiencing unfavorable outcomes [2, 3] . As, to the best of our knowledge, a relationship between ACEI or ARB treatments and increased risk of CVi has never been demonstrated [8] , the aim of the present study was to determine whether an association exists between therapies based on agents acting on the RAAS and CVi in 2 populations at greater risk of being diagnosed with SARS-CoV-2 infection: hypertensive patients and patients who were affected by a cardio-cerebrovascular disease. cache = ./cache/cord-272956-0yumc7em.txt txt = ./txt/cord-272956-0yumc7em.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-285403-h8ahn8fw author = Zhang, Liangsheng title = Origin and Evolution of the 2019 Novel Coronavirus date = 2020-02-03 pages = extension = .txt mime = text/plain words = 830 sentences = 48 flesch = 57 summary = To the Editor-The 2019 novel coronavirus disease (2019-nCoV or COVID-19) recently reported from Wuhan (China), which has cases in Thailand, Japan, South Korea, and the United States, has been confirmed as a new coronavirus [1] . Based on our phylogenomic analysis of the recently released genomic data of 2019-nCoV, we showed that the 2019-nCoV is most closely related to 2 severe acute respiratory syndrome (SARS)-like CoV sequences that were isolated in bats during 2015 to 2017 [2] , suggesting that the bats' CoV and the human 2019-nCoV share a recent common ancestor ( Figure 1A) . This market also sells wild animals or mammals, which were likely intermediate hosts of 2019-nCoV, which originated from bat hosts ( Figure 1B ). The 2019-nCoVs have long branches (0.09) for the 2 isolated in the phylogenomic tree ( Figure 1A) , indicating that the 2019-nCoVs likely share bat hosts. There were 3 genotypes present in samples from Guangdong province, indicating that the 6 strains were infected from different places in Wuhan. cache = ./cache/cord-285403-h8ahn8fw.txt txt = ./txt/cord-285403-h8ahn8fw.txt === reduce.pl bib === === reduce.pl bib === id = cord-278084-km04sz2s author = Martino, Rodrigo title = Respiratory Virus Infections in Adults with Hematologic Malignancies: A Prospective Study date = 2003-01-01 pages = extension = .txt mime = text/plain words = 3119 sentences = 167 flesch = 48 summary = On multivariate analysis, the only variable that predicted progression to pneumonia in patients with an upper respiratory tract infection was the presence of respiratory syncytial virus, whereas lymphocytopenia had a nonsignificant trend. We performed a prospective 2-year study to assess the role of respiratory virus infections in the pathogenesis of URTI and LRTI and risk factors for severe LRTI in an adult clinical hematology department. All adult patients with a hematologic malignancy (including HSCT recipients) who had signs and symptoms of a URTI or LRTI in the inpatient and outpatient settings underwent a detailed clinical evaluation, and samples from the upper and/or lower respiratory tracts were screened for the presence of respiratory viruses. A first episode of infection was defined as the period during which the patient had symptoms of URTI and/ or LRTI, regardless of whether a respiratory virus was isolated. cache = ./cache/cord-278084-km04sz2s.txt txt = ./txt/cord-278084-km04sz2s.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-287923-ev93r09i author = Apisarnthanarak, Anucha title = Infection Prevention and Control in Asia: Current Evidence and Future Milestones date = 2017-05-15 pages = extension = .txt mime = text/plain words = 1310 sentences = 61 flesch = 27 summary = This issue of Clinical Infectious Diseases focuses on 3 key themes of infection prevention and control in healthcare settings across the Asia-Pacific regions: (1) epidemiology and evidence to support prevention and control interventions, (2) enhancements to infection prevention and control in healthcare settings, and (3) practices associated with the containment of emerging infectious diseases and outbreaks. We thank the Infectious Diseases Association of Thailand for its partial sponsorship of this issue and share our hope that the collective experience from the study contributors reporting work in this issue will serve as a 2017 platform for improvement in the science and practice of infection prevention in the Asia-Pacific region and in other resource-limited settings. This article appears as part of the supplement "Infection Prevention in Asia Pacific, " sponsored by the Infectious Diseases Association of Thailand (IDAT) with additional author sponsorship. cache = ./cache/cord-287923-ev93r09i.txt txt = ./txt/cord-287923-ev93r09i.txt === reduce.pl bib === === reduce.pl bib === id = cord-291726-8670s4st author = Che, Xiao-yan title = A Patient with Asymptomatic Severe Acute Respiratory Syndrome (SARS) and Antigenemia from the 2003–2004 Community Outbreak of SARS in Guangzhou, China date = 2006-07-01 pages = extension = .txt mime = text/plain words = 2584 sentences = 102 flesch = 46 summary = Seventeen serum specimens were collected from 4 index case patients who exhibited recurrence of SARS with laboratory-confirmed SARS-CoV infection in Guangzhou City, China, from 22 December 2003 through 30 January 2004. The findings of these 2 assays had been validated previously with the use of serum specimens obtained from patients with serologically confirmed SARS, and the sensitivity and specificity of the N antigen-capture ELISA were documented [4] [5] [6] . Although none of the 4 index case patients showed evidence of secondary spread of the infection [1] , the direct detection of SARS-CoV N protein by the highly sensitive CIA a Serum samples in a serial 2-fold dilution (from 10-fold to 5120-fold). However, in the 2003-2004 community outbreak of SARS, none of the 4 index case patients with confirmed SARS had severe illness, and they all seemed to have acquired infection with SARS-CoV directly from animals. cache = ./cache/cord-291726-8670s4st.txt txt = ./txt/cord-291726-8670s4st.txt === reduce.pl bib === id = cord-294335-qnu19ru5 author = Yousaf, Anna R title = A prospective cohort study in non-hospitalized household contacts with SARS-CoV-2 infection: symptom profiles and symptom change over time date = 2020-07-28 pages = extension = .txt mime = text/plain words = 3221 sentences = 179 flesch = 50 summary = We assessed symptoms reported by household contacts on the collection date of their first RT-PCRpositive NP specimen (Figure 1 , Subset A), and categorized symptoms as constitutional (fever, chills, myalgia, or fatigue), upper respiratory (runny nose, nasal congestion, or sore throat), lower respiratory (cough, difficulty breathing, shortness of breath, wheezing, or chest pain), neurologic (headache, loss of taste, or loss of smell), and gastrointestinal (nausea/vomiting, diarrhea, or abdominal pain). We identified and prospectively followed household contacts who were asymptomatic at the time they initially tested positive for SARS-CoV-2 by PCR ( Figure 1 , Subset B) to see if they developed symptoms during the study period. The symptom profiles and demographic characteristics of our cohort of SARS-CoV-2 RT-PCR positive household contacts differ from those described in inpatient populations [3] [4] [5] 12] . cache = ./cache/cord-294335-qnu19ru5.txt txt = ./txt/cord-294335-qnu19ru5.txt === reduce.pl bib === id = cord-292094-vmsdhccp author = Mandell, Lionel A. title = Infectious Diseases Society of America/American Thoracic Society Consensus Guidelines on the Management of Community-Acquired Pneumonia in Adults date = 2007-03-01 pages = extension = .txt mime = text/plain words = 28389 sentences = 1424 flesch = 37 summary = Severity-of-illness scores, such as the CURB-65 criteria (confusion, uremia, respiratory rate, low blood pressure, age 65 years or greater), or prognostic models, such as the Pneumonia Severity Index (PSI), can be used to identify patients with CAP who may be candidates for outpatient treatment. A respiratory fluoroquinolone should be used for penicillin-allergic patients.) Increasing resistance rates have suggested that empirical therapy with a macrolide alone can be used only for the treat-ment of carefully selected hospitalized patients with nonsevere disease and without risk factors for infection with drug-resistant pathogens. Advantages include the high specificity, the ability of some assays to distinguish between influenza A and B, the rapidity with which the results can be obtained, the possibly reduced use of antibacterial agents, and the utility of establishing this diagnosis for epidemiologic purposes, especially in hospitalized patients who may require infection control precautions. cache = ./cache/cord-292094-vmsdhccp.txt txt = ./txt/cord-292094-vmsdhccp.txt === reduce.pl bib === id = cord-295525-emrwcx0m author = To, Kelvin Kai-Wang title = Consistent Detection of 2019 Novel Coronavirus in Saliva date = 2020-02-12 pages = extension = .txt mime = text/plain words = 1912 sentences = 110 flesch = 55 summary = The 2019 novel coronavirus (2019-nCoV) was detected in the self-collected saliva of 91.7% (11/12) of patients. The 2019 novel coronavirus (2019-nCoV) was detected in the self-collected saliva of 91.7% (11/12) of patients. We have previously demonstrated that saliva has a high concordance rate of greater than 90% with nasopharyngeal specimens in the detection of respiratory viruses, including coronaviruses [5, 6] . A patient is considered to have laboratory-confirmed infection if 2019-nCoV was detected in their nasopharyngeal or sputum specimens. For patient K, the first saliva specimen collected on the day of hospital admission tested negative. The use of saliva is preferred over nasopharyngeal or oropharyngeal specimens for serial viral load monitoring because this would reduce the discomfort to the patient and reduce the health hazards to healthcare workers during repeated sampling. Our results have demonstrated the potential for saliva to be a noninvasive specimen type for the diagnosis and viral load monitoring of 2019-nCoV. cache = ./cache/cord-295525-emrwcx0m.txt txt = ./txt/cord-295525-emrwcx0m.txt === reduce.pl bib === id = cord-292546-un0blb3w author = Dandachi, Dima title = Characteristics, Comorbidities, and Outcomes in a Multicenter Registry of Patients with HIV and Coronavirus Disease-19 date = 2020-09-09 pages = extension = .txt mime = text/plain words = 3438 sentences = 274 flesch = 57 summary = BACKGROUND: People with HIV (PWH) may have numerous risk factors for acquiring Coronavirus disease-19 (COVID-19) and developing severe outcomes, but current data are conflicting. [12] [13] [14] [15] Some of these studies reported that PWH with COVID-19 had similar clinical characteristics and comparable risk of severe disease to the general population. Study variables included patient demographics, HIV-associated variables, underlying medical problems, COVID-19 clinical presentation as reported by patients, laboratory values, treatment, and clinical outcomes. In a multivariable analysis, older age, lower CD4 count, chronic lung disease, hypertension, and high comorbidity burden were significantly associated with severe outcomes (Table 4) . As reported in multiple other studies in people without HIV, we found that age, chronic lung disease, and comorbidity burden were associated with increased rates of severe outcomes. In addition, among HIV-specific factors, we found that a lower CD4 count (< 200 cells/mm3) was associated with poor outcomes, including higher hospitalization rates, lower ICU-free survival, and overall survival. cache = ./cache/cord-292546-un0blb3w.txt txt = ./txt/cord-292546-un0blb3w.txt === reduce.pl bib === id = cord-292372-kn27ghlv author = de Chaisemartin, Clément title = BCG vaccination in infancy does not protect against COVID-19. Evidence from a natural experiment in Sweden date = 2020-08-23 pages = extension = .txt mime = text/plain words = 2819 sentences = 151 flesch = 56 summary = Instead, this paper takes advantage of a rare nationwide natural experiment that took place in Sweden in 1975, where discontinuation of newborns BCG vaccination led to a dramatic fall of the BCG coverage rate, thus allowing us to estimate the BCG's effect without the biases associated with cross-country comparisons. found that countries with universal Bacillus Calmette-Guérin (BCG) childhood vaccination policies tend to be less affected by the COVID-19 pandemic, in terms of their number of cases and deaths [7] . In this study, we took advantage of a change in vaccination policy in Sweden to investigate the link between BCG vaccination in infancy and Covid-19 cases, hospitalizations and deaths, using a regression discontinuity approach. For instance, this study estimates the effect of universal BCG vaccination for individuals born around April 1st 1975, who are in their mid-forties during the COVID-19 pandemic, and cannot be generalized to the entire population. cache = ./cache/cord-292372-kn27ghlv.txt txt = ./txt/cord-292372-kn27ghlv.txt === reduce.pl bib === id = cord-297239-or6h6p9p author = Ridgway, Jessica P. title = Influenza Among Afebrile and Vaccinated Healthcare Workers date = 2015-06-01 pages = extension = .txt mime = text/plain words = 2674 sentences = 145 flesch = 46 summary = To prevent transmission of influenza from healthcare workers (HCWs) to patients, many hospitals exclude febrile HCWs from working, but allow afebrile HCWs with respiratory symptoms to have contact with patients. During the 2013–2014 influenza season at our hospital, an influenza-positive HCW with respiratory symptoms but no fever was linked to a case of possible healthcare-associated influenza in a patient. In accordance with the CDC's guidelines, our hospital's routine sick policy at the time prohibited febrile HCWs from working, but not those with respiratory symptoms in the absence of fever. Given the risk of influenza transmission to patients from afebrile employees with influenza, we implemented a temporary mandatory influenza-testing policy for all HCWs with respiratory symptoms. To prevent healthcare-associated influenza, hospitals should consider more stringent infection control measures for HCWs with respiratory symptoms, even if no fever is present. cache = ./cache/cord-297239-or6h6p9p.txt txt = ./txt/cord-297239-or6h6p9p.txt === reduce.pl bib === id = cord-294853-8b0s5w4u author = Nolen, Leisha D title = Impact of Social Distancing and Travel Restrictions on non-COVID-19 Respiratory Hospital Admissions in Young Children in Rural Alaska date = 2020-09-05 pages = extension = .txt mime = text/plain words = 922 sentences = 52 flesch = 50 summary = title: Impact of Social Distancing and Travel Restrictions on non-COVID-19 Respiratory Hospital Admissions in Young Children in Rural Alaska Hospitalizations due to non-COVID-19 respiratory illnesses decreased dramatically after social distancing was implemented in a high-risk population in rural Alaska. People in the remote Yukon-Kuskokwim Delta (YKD) region of Alaska have a high burden of respiratory illnesses, with up to ten times the rate of infant hospitalization for pneumonia compared to the general US population [4] and the highest reported rates of infant RSV hospitalization in the United States, reaching 259 per 1,000 We compared the total, ARI, and RSV hospitalization rate in YKD children <3 years in the first 5 months of 2020 to the previous ten respiratory illness seasons. One limitation of our study is the inability to distinguish what proportion of the decline in ARI hospitalizations in YKD children is due to avoidance of care versus a decrease in circulation of respiratory pathogens secondary to the health mandates. cache = ./cache/cord-294853-8b0s5w4u.txt txt = ./txt/cord-294853-8b0s5w4u.txt === reduce.pl bib === id = cord-294718-n3gx862b author = Tam, Patrick C K title = Detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breast milk of a mildly symptomatic patient with coronavirus disease 2019 (COVID-19) date = 2020-05-30 pages = extension = .txt mime = text/plain words = 1606 sentences = 135 flesch = 61 summary = title: Detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breast milk of a mildly symptomatic patient with coronavirus disease 2019 (COVID-19) Although RNA has been detected in various clinical samples, no reports to date have documented SARS-CoV-2 in human milk. This case report describes an actively breastfeeding patient with COVID-19 infection with detectable viral RNA in human milk. The first sampling of human milk occurred five days following maternal symptom onset with no episodes of breastfeeding in those five days prior to collection of the sample. An additional six samples of human milk were collected with one further sample demonstrating detectable SARS-COV-2 RNA (Figure 1 ). These samples continued to have detectable RNA sixty-six days following infant symptom onset (Figure 1 ). To our knowledge, this is the first case of detectable SARS-CoV-2 RNA from human milk in a patient with COVID-19. cache = ./cache/cord-294718-n3gx862b.txt txt = ./txt/cord-294718-n3gx862b.txt === reduce.pl bib === id = cord-296588-q2716lda author = Hanson, Kimberly E title = Infectious Diseases Society of America Guidelines on the Diagnosis of COVID-19 date = 2020-06-16 pages = extension = .txt mime = text/plain words = 10179 sentences = 681 flesch = 47 summary = OBJECTIVE: The IDSA's goal was to develop an evidence-based diagnostic guideline to assists clinicians, clinical laboratorians, patients and policymakers in decisions related to the optimal use of SARS-CoV-2 nucleic acid amplification tests. It is important to note as well, that not all specimens were collected from the same patient at the same time, the time of collection from symptom onset was not provided in all studies and various approaches for establishing SARS-CoV-2 positivity were used to define positive results (i.e., clinical evaluation, detection different gene targets versus nucleic acid sequencing). While NP swab collection is widely used and the primary specimen type for commercial direct SARS-CoV-2 test platforms, based on current available evidence, clinical practice, and availability of testing resources, the panel believes there are comparable alternative methods for sampling the nasal passages. cache = ./cache/cord-296588-q2716lda.txt txt = ./txt/cord-296588-q2716lda.txt === reduce.pl bib === id = cord-296631-43z3ee8m author = de Feria, Alejandro title = ACE inhibitors/ARB use and COVID-19. Time to change practice or keep gathering data? date = 2020-07-04 pages = extension = .txt mime = text/plain words = 896 sentences = 70 flesch = 60 summary = This mechanism of entry, in combination with the findings of the previously mentioned risk factors, raised concerns that angiotensin-converting enzyme inhibitors (ACEi) and angiotensin receptor blockers (ARBs) could increase both the susceptibility and severity of SARS CoV-2 infection. An international, multicenter study which included electronic records from 169 hospitals in 11 countries on three continents again confirmed that advanced age (>65), heart failure, coronary disease, and hypertension (among other factors) increased risk for in hospital mortality with COVID-19, but ACEi/ARB therapy showed no harm [4] . In contrast to these findings, early studies out of China suggested that ARB therapy may improve clinical outcomes in COVID-19 infection [5, 6] . The current study is unique in that it focuses on patients with "severe COVID" disease and found that chronic ACE inhibitor and ARB use was associated with an increased risk of acute kidney injury, as well as a signal for a dosage effect. cache = ./cache/cord-296631-43z3ee8m.txt txt = ./txt/cord-296631-43z3ee8m.txt === reduce.pl bib === id = cord-299274-gnbp7so5 author = Bodkin, Claire title = Pandemic Planning in Homeless Shelters: A pilot study of a COVID-19 testing and support program to mitigate the risk of COVID-19 outbreaks in congregate settings date = 2020-06-08 pages = extension = .txt mime = text/plain words = 1643 sentences = 113 flesch = 59 summary = title: Pandemic Planning in Homeless Shelters: A pilot study of a COVID-19 testing and support program to mitigate the risk of COVID-19 outbreaks in congregate settings We tested 104 residents and 141 staff for COVID-19 who failed daily symptom screening in homeless shelters in Hamilton, Canada. The objective of this report is to describe our experience with shelter facility restructuring, daily symptom screening and rapid testing to mitigate the risk of COVID-19 in the homeless shelter setting in Hamilton, Ontario, Canada. Between March 17 and April 30, 2020, COVID-19 testing was performed on all shelter residents and staff who failed daily screening for potential COVID-19 related symptoms as well as staff and residents identified as close contacts of positive cases. We have thus far been successful in preventing large outbreaks in the shelter setting despite identifying positive cases in both staff and residents. cache = ./cache/cord-299274-gnbp7so5.txt txt = ./txt/cord-299274-gnbp7so5.txt === reduce.pl bib === id = cord-300013-6m1f4q5r author = Brahier, Thomas title = Lung ultrasonography for risk stratification in patients with COVID-19: a prospective observational cohort study date = 2020-09-17 pages = extension = .txt mime = text/plain words = 3247 sentences = 220 flesch = 54 summary = This study describes and compares LUS characteristics between patients with different clinical outcomes METHODS: Prospective observational study of PCR-confirmed COVID-19 adults with symptoms of lower respiratory tract infection in the emergency department (ED) of Lausanne University Hospital. We describe and compare early LUS findings (acquired within 24hours of presentation to the ED) between patient groups based on their outcome at 7 days after inclusion: 1) outpatients, 2) hospitalised and 3) intubated/death. Median normalized LUS score had a good level of discrimination between outpatients and others with area under the ROC of 0.80 (95% CI 0.68-0.92) CONCLUSIONS: Systematic LUS has potential as a reliable, cheap and easy-to-use triage tool for the early risk stratification in COVID-19 patients presenting in EDs Despite the potential of LUS as a cheap, portable and accessible point-of-care triage tool in acute respiratory disease (especially in low resource settings), a multinational consensus recently stated that the lack of studies limited specific recommendations for the management of COVID-19 patients (27) . cache = ./cache/cord-300013-6m1f4q5r.txt txt = ./txt/cord-300013-6m1f4q5r.txt === reduce.pl bib === id = cord-295940-siy32dj7 author = Saito, Makoto title = Gargle lavage as a safe and sensitive alternative to swab samples to diagnose COVID-19: a case report in Japan date = 2020-04-02 pages = extension = .txt mime = text/plain words = 533 sentences = 48 flesch = 66 summary = title: Gargle lavage as a safe and sensitive alternative to swab samples to diagnose COVID-19: a case report in Japan Moreover, the sensitivity for virus detection is low with these swabs; viral load is reportedly higher in sputum samples. 3 Here we report a case in which gargle lavage samples yielded a positive PCR result. Additional gargle lavage samples and oropharyngeal swabs were collected and tested on Days 8 and 9 and found to be positive, with a slightly higher amount of viral genome in the gargle lavage sample (Supplement Figure 3) . For other respiratory pathogens, gargle lavage samples have been reported to be more sensitive than throat swabs. 1 Gargle lavage thus offers a safer and possibly more sensitive alternative or additional option for diagnosing COVID-19. SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients Comparison of gargle samples and throat swab samples for the detection of respiratory pathogens cache = ./cache/cord-295940-siy32dj7.txt txt = ./txt/cord-295940-siy32dj7.txt === reduce.pl bib === id = cord-300411-ppcdkfxq author = Xu, Xiao-Ke title = Reconstruction of Transmission Pairs for novel Coronavirus Disease 2019 (COVID-19) in mainland China: Estimation of Super-spreading Events, Serial Interval, and Hazard of Infection date = 2020-06-18 pages = extension = .txt mime = text/plain words = 1957 sentences = 140 flesch = 55 summary = title: Reconstruction of Transmission Pairs for novel Coronavirus Disease 2019 (COVID-19) in mainland China: Estimation of Super-spreading Events, Serial Interval, and Hazard of Infection METHODS: A unique database with detailed demographic characteristics, travel history, social relationships, and epidemiological timelines for 1,407 transmission pairs that formed 643 transmission clusters in mainland China was reconstructed from 9,120 COVID-19 confirmed cases reported during January 15 February 29, 2020. CONCLUSIONS: Non-negligible frequency of super-spreading events, short serial intervals, and a higher risk of being infected outside of households for male people of working age indicate a significant barrier to the identification and management of COVID-19 cases, which requires enhanced non-pharmaceutical interventions to mitigate this pandemic. We have built a line-list database with detailed demographic information, travel history, epidemiological timelines, and social relationships for 1,407 transmission pairs that formed 643 transmission clusters in mainland China outside Hubei Province. cache = ./cache/cord-300411-ppcdkfxq.txt txt = ./txt/cord-300411-ppcdkfxq.txt === reduce.pl bib === id = cord-294558-cqa58db8 author = Wang, Yubo title = Characterization of an asymptomatic cohort of SARS-COV-2 infected individuals outside of Wuhan, China date = 2020-05-22 pages = extension = .txt mime = text/plain words = 2858 sentences = 214 flesch = 57 summary = BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, resulting in the coronavirus disease COVID-19) is highly transmissible among people. METHODS: We identified close contacts of confirmed COVID-19 cases in northeast Chongqing who were RT-PCR+ yet remained asymptomatic throughout their infections. In December 2019 a novel coronavirus, which was later named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), caused a large outbreak of infectious disease, designated COVID-19. Symptomatic COVID-19 patients and asymptomatic cases are both a source of infection and patients in the incubation period can transmit SARS-CoV-2 to other persons [7] [8] [9] [10] . Epidemiological data collection was achieved by interviewing each patient and their family members, including the dates and times of close contact with (working together, living or gathering) or to exposure individuals from the affected area (not only Wuhan) with confirmed or suspected SARS-CoV-2 infection. cache = ./cache/cord-294558-cqa58db8.txt txt = ./txt/cord-294558-cqa58db8.txt === reduce.pl bib === id = cord-310476-mhm7r3qc author = Yi, Huiguang title = 2019 novel coronavirus is undergoing active recombination date = 2020-03-04 pages = extension = .txt mime = text/plain words = 737 sentences = 48 flesch = 48 summary = The single origin of 2019-nCov indicates a persistent animal to human transmission is unlikely, otherwise, multiple nodes with above characteristics should be observed. To quantify the significance of recombination over recurring sequencing error/mutations, Phi [6] and Max Chi-squared tests [7] in the software PhiPack [8] were performed. It showed p-values of 0.03 and 0.005 for Phi and Max Chi-squared, respectively, indicating the presence of recombinants in 2019-nCoV population. Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event cache = ./cache/cord-310476-mhm7r3qc.txt txt = ./txt/cord-310476-mhm7r3qc.txt === reduce.pl bib === id = cord-309091-te15ahvw author = Larson, Derek title = A Case of Early Re-infection with SARS-CoV-2 date = 2020-09-19 pages = extension = .txt mime = text/plain words = 498 sentences = 57 flesch = 63 summary = A c c e p t e d M a n u s c r i p t 3 Dear Editor, It is with great interest that we read the first report of re-infection from SARS-CoV-2, which represented an important data point in the ongoing COVID-19 pandemic [1] [2] [3] . 42-year-old healthy male military healthcare provider presented with cough, subjective fever, and myalgias on 21 March following a workplace COVID-19 exposure and tested positive by SARS-CoV-2 RT-PCR ( Figure 1 ). The SARS-CoV-2 genome from the re-infection sample was deposited in NCBI GenBank under Accession The identification of specific products, scientific instrumentation, or organization is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the author, DoD, or any component agency. COVID-19 re-infection by a phylogenetically distinct SARScoronavirus-2 strain confirmed by whole genome sequencing Persistent positivity and fluctuations of SARS-CoV-2 RNA in clinically-recovered COVID-19 patients Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus cache = ./cache/cord-309091-te15ahvw.txt txt = ./txt/cord-309091-te15ahvw.txt === reduce.pl bib === id = cord-303330-zh8wzza5 author = Magleby, Reed title = Impact of SARS-CoV-2 Viral Load on Risk of Intubation and Mortality Among Hospitalized Patients with Coronavirus Disease 2019 date = 2020-06-30 pages = extension = .txt mime = text/plain words = 3557 sentences = 204 flesch = 51 summary = In two studies of hospitalized patients in China, those with severe presentations of COVID-19 had higher viral loads than those with mild presentations, but the impact of SARS-CoV-2 viral load on the risk of intubation or death was not evaluated [10, 11] . We hypothesized that assessing SARS-CoV-2 viral load by analyzing Ct values from an initial NP swab sample could be a clinically valuable tool to identify patients at highest risk of intubation and death and provide insights into the pathogenesis of COVID-19. We therefore conducted this retrospective analysis of SARS-CoV-2 viral loads on admission, clinical presentations, and outcomes at two affiliated New York City hospitals using a high-throughput RT-PCR assay. In conclusion, we found that admission SARS-CoV-2 viral loads, as determined by Ct values that are generated with standard-of-care diagnostic assays, are independently associated with intubation and death among hospitalized patients with COVID-19. cache = ./cache/cord-303330-zh8wzza5.txt txt = ./txt/cord-303330-zh8wzza5.txt === reduce.pl bib === id = cord-307660-onz6vfre author = Titanji, Boghuma K title = Use of Baricitinib in Patients with Moderate and Severe COVID-19 date = 2020-06-29 pages = extension = .txt mime = text/plain words = 1084 sentences = 75 flesch = 51 summary = Coronavirus Infectious Disease-19 (COVID-19), caused by Severe Acute Respiratory Virus Syndrome Coronavirus-2 (SARS-CoV-2) has led to over 8 million confirmed infections worldwide with an estimated global mortality of 5.6% as of June 17 th 2020 1 . Patients had laboratory confirmed COVID-19, diagnosed by quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR) testing of oropharyngeal, nasopharyngeal or tracheal aspirate samples and were treated at the discretion of the medical team with a combination of hydroxychloroquine and baricitinib if they fulfilled at least one of the following criteria: 1) evidence of pneumonia on lung imaging and requiring supplemental oxygen on admission or development of a new oxygen requirement during the course of their hospitalization 2) moderate disease requiring hospitalization (e.g., severe diarrhea requiring volume resuscitation, encephalopathy, evidence of end-A c c e p t e d M a n u s c r i p t organ damage); 3) elevated or rising inflammatory markers during hospitalization. cache = ./cache/cord-307660-onz6vfre.txt txt = ./txt/cord-307660-onz6vfre.txt === reduce.pl bib === id = cord-297612-swc2pitd author = Nosyk, Bohdan title = Contact tracing for COVID-19: An opportunity to reduce health disparities and End the HIV/AIDS Epidemic in the US date = 2020-04-27 pages = extension = .txt mime = text/plain words = 1637 sentences = 104 flesch = 57 summary = title: Contact tracing for COVID-19: An opportunity to reduce health disparities and End the HIV/AIDS Epidemic in the US We argue that COVID-19 contact tracing may provide a unique opportunity to also conduct widespread HIV testing, among other health promotion activities. M a n u s c r i p t Massive SARS-CoV2 testing and contact tracing at a scale and speed never before seen have been proposed as critical components of a COVID-19 public health strategy that could, in theory, safely allow us to relax social distancing measures and begin to bring back the world we left behind before a cure or effective vaccine is delivered. Aside from the potentially profound health benefits of a combination implementation approach, pairing COVID-19 contact tracing with testing for HIV may serve to offset the immense costs of such an approach. cache = ./cache/cord-297612-swc2pitd.txt txt = ./txt/cord-297612-swc2pitd.txt === reduce.pl bib === id = cord-301066-62qe4fb0 author = Chiu, Susan S. title = Human Coronavirus NL63 Infection and Other Coronavirus Infections in Children Hospitalized with Acute Respiratory Disease in Hong Kong, China date = 2005-06-15 pages = extension = .txt mime = text/plain words = 3944 sentences = 220 flesch = 56 summary = In 2001 and 2002, we performed prospective clinical and virological studies of children (age, р18 years) with acute respiratory tract infection who were admitted to Queen Mary Hospital (Hong Kong, China). We studied a systematic sample of children (age, р18 years) with acute respiratory infection admitted to Queen Mary Hospital during the period from August 2001 to March 2002. One child with HCoV-NL63 upper respiratory tract infection had positive results of only the consensus primer PCR, so no viral load could be measured. We documented that human coronavirus infection was a significant cause of hospitalization for children aged р18 years, accounting for 4.4% of all admissions for acute respiratory infections. A previous study showed that 8.2% of children aged !18 months who were admitted to a Chicago, Illinois, hospital with lower respiratory tract diseases had serological evidence of HCoV-229E or HCoV-OC43 infection [13] . cache = ./cache/cord-301066-62qe4fb0.txt txt = ./txt/cord-301066-62qe4fb0.txt === reduce.pl bib === id = cord-298539-yncda1us author = Ruan, Linhui title = New measures for COVID-19 response: a lesson from the Wenzhou experience date = 2020-04-03 pages = extension = .txt mime = text/plain words = 1233 sentences = 73 flesch = 53 summary = This is the result of the more than 90,000 people who return to Wenzhou from Wuhan during On January 17 when the first case of COVID-19 was confirmed, the Wenzhou New Coronavirus Pneumonia Prevention and Control Committee launched emergency epidemic prevention and control measures, which in general consisted of two phases. The main measures included (1) centralizing the confirmed and suspected patients in designated hospitals for treatment, (2) identifying and investigating all returnees from Wuhan using a big data network and persuading them to undergo 14-day home quarantine, and (3) centralizing and medically observing individuals who had been exposed to a confirmed COVID-19 patient. However, the numbers of new cases in these cities were meaningfully reduced after implementation of most aggressive social distancing and quarantining measures, which was similar to Wenzhou second-phase measures on February 10 ( Figure 1A) . cache = ./cache/cord-298539-yncda1us.txt txt = ./txt/cord-298539-yncda1us.txt === reduce.pl bib === id = cord-303968-ikr6eeov author = Perinel, Sophie title = Towards Optimization of Hydroxychloroquine Dosing in Intensive Care Unit COVID-19 Patients date = 2020-04-07 pages = extension = .txt mime = text/plain words = 1933 sentences = 125 flesch = 61 summary = Apart from the ongoing clinical evaluation of the efficacy of HCQ, little information is available concerning the modalities of administration of this drug for Intensive Care Unit (ICU) patients, especially in the context of COVID-19. M a n u s c r i p t Treatment Patients received 200 mg of oral HCQ, three times daily, as suggested by a recent study [9] . To more clearly understand HCQ PK and the effect of the dosing regimen, a simulation based on a PK population study in patients with rheumatoid arthritis was performed [2] . In this study, we demonstrated that the 200 mg three times daily dosing regimen is inappropriate to reach a supposed target blood level of 1 -2 mg/L in this population. This regimen could constitute an appropriate option, although the results of our study suggest that 800 mg once daily on the first day can more rapidly reach therapeutic levels in ICU patients. cache = ./cache/cord-303968-ikr6eeov.txt txt = ./txt/cord-303968-ikr6eeov.txt === reduce.pl bib === id = cord-295270-6ptaxg74 author = Titanji, Boghuma K title = Response to Correspondence: Baricitinib – Impact on COVID-19 Coagulopathy? Jorgensen et. al. date = 2020-08-14 pages = extension = .txt mime = text/plain words = 501 sentences = 54 flesch = 63 summary = authors: Titanji, Boghuma K; Farley, Monica M; Schinazi, Raymond F; Marconi, Vincent C Baricitinib through its immunomodulatory effects as highlighted by Jorgensen et.al may in fact be beneficial in terms of reducing coagulopathy in patients with COVID-19, which is thought to be primarily mediated by hyper-inflammation and endothelial damage. All of the cohort studies of baricitinib for COVID-19 treatment led to significant decline in inflammatory M a n u s c r i p t markers for patients who received the drug 2,3,8 . Regarding baricitinib, ACTT2 should provide clarity on the VTE issue in the near future and its role in the treatment of COVID-19 in moderate to severe patients. Ruxolitinib in treatment of severe coronavirus disease 2019 (COVID-19): A multicenter, single-blind, randomized controlled trial Use of Baricitinib in patients with moderate and severe COVID-19 Vincent Marconi and Raymond F Schinazi are partially funded by -Emory University Center for AIDS Research (AI050409). cache = ./cache/cord-295270-6ptaxg74.txt txt = ./txt/cord-295270-6ptaxg74.txt === reduce.pl bib === id = cord-313617-hh7lccet author = Sigel, Keith title = Covid-19 and People with HIV Infection: Outcomes for Hospitalized Patients in New York City date = 2020-06-28 pages = extension = .txt mime = text/plain words = 2565 sentences = 190 flesch = 56 summary = We collected data on baseline clinical characteristics, laboratory values, HIV infection status, COVID-19 treatment, and outcomes from this group and matched comparators (one PWH to up to five patients by age, sex, race/ethnicity and calendar week of infection). INTERPRETATION: We found no differences in adverse outcomes associated with HIV infection for hospitalized COVID-19 patients compared to a demographically similar patient group. We then compared differences in time to death to assess disease trajectory for hospitalized patients by HIV status by fitting unadjusted cumulative incidence function curves with hospital discharge as a competing risk. [7] To compare cumulative incidence of death by HIV status accounting for potential confounding factors we then fit a multivariable survival model using Fine-Grey competing risk methods, including demographics, COVID-19 severity, comorbid conditions and laboratory values that differed by HIV status. cache = ./cache/cord-313617-hh7lccet.txt txt = ./txt/cord-313617-hh7lccet.txt === reduce.pl bib === id = cord-307342-3gkiukh4 author = Clark, Eva title = Why contact tracing efforts have failed to curb COVID-19 transmission in much of the U.S date = 2020-08-06 pages = extension = .txt mime = text/plain words = 3272 sentences = 192 flesch = 55 summary = By late April 2020, public discourse in the U.S. had shifted toward the idea of using more targeted case-based mitigation tactics (e.g., contact tracing) to combat COVID-19 transmission while allowing for the safe "re-opening" of society, in an effort to reduce the social, economic, and political ramifications associated with stricter approaches. This viewpoint offers a discussion of why testing-tracing efforts failed to sufficiently mitigate COVID-19 across much of the nation, with the hope that such deliberation will help the U.S. public health community better plan for the future. Partly for this reason, our nation rushed to espouse the idea of targeted, case-based COVID-19 management [3] [4] [5] [6] , focusing on expanded testing and contact tracing, while disregarding several major obstacles that set us apart from countries that succeeded in mounting a timely, targeted response. cache = ./cache/cord-307342-3gkiukh4.txt txt = ./txt/cord-307342-3gkiukh4.txt === reduce.pl bib === id = cord-312905-8xlt92pl author = Li, Guanjian title = Asymptomatic and Presymptomatic Infectors: Hidden Sources of COVID-19 Disease date = 2020-04-09 pages = extension = .txt mime = text/plain words = 690 sentences = 61 flesch = 58 summary = At the time of writing this paper, the authors claimed that "evidence regarding transmission from individuals with asymptomatic infection or mild illness is limited", but that the current evidence may need an update. Recently, two epidemiological studies on COVID-19 have reported that typically asymptomatic carriers transmit the virus to close contacts, resulting in aggregated infection of symptomatic COVID-19 diseases [2, 3] . This study used a prospective design to follow up the viral load and clinical manifestations of 2147 close contacts of symptomatic and asymptomatic COVID-19 cases. The authors suggested that the transmission ability of asymptomatic individuals should not be ignored. First Mildly Ill, Non-Hospitalized Case of Coronavirus Disease 2019 (COVID-19) Without Viral Transmission in the United States Clinical characteristics of 24 asymptomatic infections with COVID-19 screened among close contacts in Nanjing The epidemiological characteristics of infection in close contacts of COVID-19 in Ningbo city cache = ./cache/cord-312905-8xlt92pl.txt txt = ./txt/cord-312905-8xlt92pl.txt === reduce.pl bib === id = cord-300550-l28tadhn author = Luers, Jan C title = Olfactory and Gustatory Dysfunction in Coronavirus Disease 19 (COVID-19) date = 2020-05-01 pages = extension = .txt mime = text/plain words = 1755 sentences = 129 flesch = 65 summary = In this cross-sectional study, two-thirds of European patients with polymerase chain reaction confirmed COVID-19 reported olfactory and gustatory dysfunction, indicating the significance of this history in the early diagnostics. First of all, patients were asked for the onset of fever, cough, sore throat, rhinitis, muscle aches, headache, diarrhea, reduced olfaction, and a reduced sense of taste during COVID-19. To investigate factors related to reduced olfaction as well as to a reduced sense of taste two general linear models were used with explanatory variables of age, gender, TNSS, fever, cough, sore throat, rhinitis, and headache, respectively. In addition, fever, cough, sore throat, rhinitis, headache, and TNSS were also not associated with reduced olfaction or reduced sense of taste (p ≥ 0.05, respectively). Our study shows for the first time that both olfactory and gustatory dysfunction is very common in COVID-19 patients, with olfactory dysfunction even leveling the symptom 'cough' at > 70%. cache = ./cache/cord-300550-l28tadhn.txt txt = ./txt/cord-300550-l28tadhn.txt === reduce.pl bib === id = cord-303603-4mi64bgm author = Martínez-Urbistondo, Diego title = Early Combination of Tocilizumab and Corticosteroids: An Upgrade in Anti-inflammatory Therapy for Severe Coronavirus Disease (COVID) date = 2020-07-04 pages = extension = .txt mime = text/plain words = 656 sentences = 40 flesch = 47 summary = title: Early Combination of Tocilizumab and Corticosteroids: An Upgrade in Anti-inflammatory Therapy for Severe Coronavirus Disease (COVID) In our experience, the early administration of corticosteroids associated to tocilizumab, according to the previously published recommendations by the Spanish Ministry of Health [6] , may solve this high failure rate. In the HM Sanchinarro Hospital, a 200 bed teaching institution, we consecutively and ambispectively collected the outcome of 136 patients who received tocilizumab plus corticosteroids to treat severe COVID, defined as a SpO2/FiO2 <325 with bilateral pneumonia and a clinical diagnosis of infection by SARS-CoV-2. Generalized linear and Cox regression models, adjusted by age, sex, interaction between age and sex, CCI, time from onset to admission, dose of corticosteroids and tocilizumab and C-reactive protein and D-dimer levels at anti-inflammatory therapy administration, showed benefit in the use of ET in COVID patients (Relative Risk, 0.18, P = .01, and Hazard Ratio, 0.13, P = .01, respectively). cache = ./cache/cord-303603-4mi64bgm.txt txt = ./txt/cord-303603-4mi64bgm.txt === reduce.pl bib === id = cord-299499-66qh3r75 author = Guilamo-Ramos, Vincent title = Reconsidering assumptions of adolescent and young adult SARS-CoV-2 transmission dynamics date = 2020-09-07 pages = extension = .txt mime = text/plain words = 4199 sentences = 218 flesch = 42 summary = In this viewpoint, we highlight evidence regarding the increased potential of AYA to transmit SARS-CoV-2 that, to date, has received little attention, discuss adolescent and young adult specific considerations for future COVID-19 control measures, and provide applied programmatic suggestions. Adolescents and young adults (AYA), who are between the ages of 10 and 24 years, account for approximately 20% of the total population in the United States (US), but the extent to which AYA contribute to forward transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not fully understood. In this viewpoint, we highlight evidence regarding the increased potential of AYA to transmit SARS-CoV-2 that, to date, has received little attention, discuss adolescent and young adultspecific considerations for future COVID-19 control measures, and provide applied programmatic suggestions. Adolescent and young adult-specific data Furthermore, behavioral factors unique to AYA may increase the risk of forward transmission of SARS-CoV-2 relative to both younger children and older adults. cache = ./cache/cord-299499-66qh3r75.txt txt = ./txt/cord-299499-66qh3r75.txt === reduce.pl bib === id = cord-306495-o0ah1gj9 author = Haidar, Ghady title = COVID-19, organ transplantation, and the nuances of immunomodulation: lessons learned and what comes next date = 2020-08-11 pages = extension = .txt mime = text/plain words = 1262 sentences = 74 flesch = 47 summary = Thus, while morbidity and mortality related to COVID-19 in SOT recipients are substantial, A c c e p t e d M a n u s c r i p t 3 they appear to be driven by age and underlying medical conditions and unaffected by immunosuppression, corroborating the results of other studies in the general population. The study included only 30 lung transplant recipients was therefore unable to assess whether mortality in these patients is greatest (as is the case with sepsis [3] ), or whether COVID-19 precipitates acute or chronic lung allograft rejection. Furthermore, since all laboratory testing was done as standard of care, the study could not evaluate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viremia or the duration of SARS-CoV-2 PCR positivity, which may be longer than that of non-transplant patients. cache = ./cache/cord-306495-o0ah1gj9.txt txt = ./txt/cord-306495-o0ah1gj9.txt === reduce.pl bib === id = cord-299720-f0ny4ur5 author = Kim, Seung Woo title = Risk Factors for Transmission of Middle East Respiratory Syndrome Coronavirus Infection During the 2015 Outbreak in South Korea date = 2017-03-01 pages = extension = .txt mime = text/plain words = 3914 sentences = 206 flesch = 47 summary = title: Risk Factors for Transmission of Middle East Respiratory Syndrome Coronavirus Infection During the 2015 Outbreak in South Korea Transmission heterogeneity was observed during the 2015 Korean outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection. Transmission heterogeneity was a significant characteristic of the 2015 South Korean outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection [1] . Epidemiological reports from the outbreak were evaluated to collect data regarding basic demographic characteristics, medical history, MERS-CoV exposure, symptoms and their onset date(s), sampling date(s), contact history, and post-exposure infection control. In the univariate analyses, transmission was associated with underlying respiratory disease, Ct value, interval from symptom onset to diagnosis, number of contacts, and pre-isolation hospitalization or ER visits. It appears that both host infectivity and the number of contacts influenced MERS-CoV transmission, whereas super-spreading events were mostly associated with a greater likelihood of encountering other people under diverse environmental conditions. cache = ./cache/cord-299720-f0ny4ur5.txt txt = ./txt/cord-299720-f0ny4ur5.txt === reduce.pl bib === id = cord-307497-wtfvoifb author = Abu-Raya, Bahaa title = Predictors of refractory Coronavirus disease (COVID-19) pneumonia date = 2020-04-09 pages = extension = .txt mime = text/plain words = 511 sentences = 30 flesch = 38 summary = In addition, refractory COVID-19 patients were more likely to receive oxygen, mechanical ventilation, expectorant, adjunctive treatment including corticosteroids, antiviral drugs and immune enhancers when compared to general COVID-19 patients. The authors have further attempted to explore predictive factors for refractory COVID-19 using a multivariate analysis showing that male sex, anorexia on admission and being afebrile are independent risk factors for the development of a refractory disease. Furthermore, out of this analysis the authors have found that patients with refractory COVID-19 were more likely to receive oxygen, expectorant, corticosteroids, lopinavir/ritonavir and immune enhancer. In their paper, the authors compared categorical and continuous variables between the two groups of patients and these variables that differed significantly between the two groups were included in the multivariate regression analysis. In their paper, the authors included the treatment introduced at the time of patient admission and/or hospitalization in the multivariate analysis aiming to identify independent risk factors for refractory COVID-19. cache = ./cache/cord-307497-wtfvoifb.txt txt = ./txt/cord-307497-wtfvoifb.txt === reduce.pl bib === id = cord-313693-qmkrn7pr author = Wong, Bonnie C. K. title = Possible Role of Aerosol Transmission in a Hospital Outbreak of Influenza date = 2010-11-15 pages = extension = .txt mime = text/plain words = 4196 sentences = 222 flesch = 46 summary = Airflow measurements were conducted, and concentrations of hypothetical virus-laden aerosols at different ward locations were estimated using computational fluid dynamics modeling. A major nosocomial outbreak of severe acute respiratory syndrome (SARS) occurred at PWH in 2003 [15, 23] ; since then, all patients hospitalized with acute febrile respiratory illnesses are put on droplet precautions; if influenza is confirmed, the patients will be isolated or cohorted in designated wards [21, 22] . Dispersion of the hypothetical virus-laden aerosols, originated from the index patient's bed through the entire ward, was analyzed by computational fluid dynamics (CFD) method. In clinical studies, virus-laden particles less than 5-6 mm (ie, within the respirable aerosol fraction) have been detected in exhaled breaths of patients with influenza and in the air sampled from an acute healthcare setting during seasonal peak [19, 35, 36] . In conclusion, our findings suggest a possible role of aerosol transmission of influenza in an acute ward setting. cache = ./cache/cord-313693-qmkrn7pr.txt txt = ./txt/cord-313693-qmkrn7pr.txt === reduce.pl bib === id = cord-314025-h9gj814e author = Lai, Mary Y. Y. title = Survival of Severe Acute Respiratory Syndrome Coronavirus date = 2005-10-01 pages = extension = .txt mime = text/plain words = 3089 sentences = 159 flesch = 58 summary = SARS-CoV GVU6109 can survive for 4 days in diarrheal stool samples with an alkaline pH, and it can remain infectious in respiratory specimens for >7 days at room temperature. Soon after the isolation of SARS-CoV in our laboratory, we were able to perform a survival study of the virus, and partial results were reported on the World Health Organization Communicable Disease Surveillance and Response Web site on SARS [6] . Here, we provide a full report of our study of the survival characteristics of SARS-CoV in different clinical sample matrices, as well as on various environmental surfaces in the laboratory and hospital. The present study demonstrates that SARS-CoV can survive in respiratory samples for 5 days at room temperature and for up to 3 weeks at 4ЊC. Our present data show that, at a high concentration of virus (10 6 TCID 50 / mL), SARS-CoV can survive for 4-5 days at room temperature in both respiratory and diarrheal stool samples. cache = ./cache/cord-314025-h9gj814e.txt txt = ./txt/cord-314025-h9gj814e.txt === reduce.pl bib === id = cord-307770-1igydu3y author = Rawson, Timothy M title = Bacterial and fungal co-infection in individuals with coronavirus: A rapid review to support COVID-19 antimicrobial prescribing date = 2020-05-02 pages = extension = .txt mime = text/plain words = 2998 sentences = 266 flesch = 45 summary = title: Bacterial and fungal co-infection in individuals with coronavirus: A rapid review to support COVID-19 antimicrobial prescribing Articles presenting clinical data for patients with coronavirus infection (defined as SARS-1, MERS, SARS-COV-2, and other coronavirus) and bacterial/fungal co-infection reported in English, Mandarin, or Italian were included. CONCLUSIONS: Despite frequent prescription of broad-spectrum empirical antimicrobials in patients with coronavirus associated respiratory infections, there is a paucity of data to support the association with respiratory bacterial/fungal co-infection. In terms of antimicrobial prescribing bacterial/fungal co-infection of the respiratory tract; some patients presenting to hospital with SARS-COV-2 infection have a clinical phenotype that is not dissimilar from atypical bacterial pneumonia. [13] We performed a review of the medical literature to explore commonly reported bacterial/fungal co-infections in patients admitted to hospital with coronavirus lower respiratory tract infections. It is not clear whether these patients were in critical or nonSelection of empiric antimicrobial therapy for respiratory bacterial/fungal co-infection and recommendations for duration of treatment require several considerations. cache = ./cache/cord-307770-1igydu3y.txt txt = ./txt/cord-307770-1igydu3y.txt === reduce.pl bib === id = cord-299359-s8j78naz author = Sundaram, Maria E. title = Influenza Vaccination Is Not Associated With Detection of Noninfluenza Respiratory Viruses in Seasonal Studies of Influenza Vaccine Effectiveness date = 2013-09-15 pages = extension = .txt mime = text/plain words = 3247 sentences = 157 flesch = 35 summary = We investigated the association between influenza infection, vaccination, and detection of other respiratory viruses among children <5 years old and adults ≥50 years old with acute respiratory illness who participated in seasonal studies of influenza vaccine effectiveness. This could theoretically contribute to overestimation of true VE (ie, bias away from the null); therefore, a key assumption of the test-negative control design of influenza vaccine effectiveness studies is that the proportion of noninfluenza viral illness does not differ by influenza vaccination status [9] . The goals of this study were to determine if influenza vaccination is associated with detection of noninfluenza respiratory viruses and to determine if vaccine effectiveness estimates differ when different control groups are used in the analysis. For participants in these age groups, multiplex reverse transcription polymerase chain reaction (RT-PCR) testing was subsequently performed to detect other respiratory viruses, providing an opportunity to investigate the relationship between influenza vaccination and infection with other viral pathogens. cache = ./cache/cord-299359-s8j78naz.txt txt = ./txt/cord-299359-s8j78naz.txt === reduce.pl bib === id = cord-313427-6y4zvrmn author = Mani, Nandita S title = Prevalence of COVID-19 Infection and Outcomes Among Symptomatic Healthcare Workers in Seattle, Washington date = 2020-06-16 pages = extension = .txt mime = text/plain words = 3433 sentences = 226 flesch = 57 summary = Using data from these testing centers, we report the prevalence of SARS-CoV-2 infection among symptomatic employees and describe the clinical characteristics and outcomes among employees with COVID-19. Multiple factors have been reported to contribute to the risk of infections in HCWs, including lack of awareness during the early weeks of the outbreak, inadequate personal protective equipment (PPE) supply and training, insufficient rapid diagnostic testing for COVID-19, long work hours in high-risk environments, and ongoing community spread and household exposures. [12] [13] [14] A c c e p t e d M a n u s c r i p t Early and high-throughput testing for SARS-CoV-2 among symptomatic employees is essential to prevent nosocomial transmission of COVID-19 to patients, minimize clusters among HCWs, and maintain staffing during the pandemic. HCWs. 16 Here we describe the approach to establishing high-throughput employee testing centers, the prevalence of infections among symptomatic frontline versus non-frontline staff, and clinical outcomes associated with COVID-19 in these employees. cache = ./cache/cord-313427-6y4zvrmn.txt txt = ./txt/cord-313427-6y4zvrmn.txt === reduce.pl bib === id = cord-321603-lbbsnriv author = Rao, Mohan title = Comparing nasopharyngeal swab and early morning saliva for the identification of SARS-CoV-2 date = 2020-08-06 pages = extension = .txt mime = text/plain words = 2186 sentences = 172 flesch = 59 summary = The aim of this study was to compare patient-performed testing based on a morning saliva sample with the current standard testing method, healthcare worker-collected sampling via a nasopharyngeal swab (NPS). METHODS: This was a prospective single center study which recruited 217 asymptomatic adult male participants in a COVID-19 quarantine center who had tested positive for SARS-CoV-2 8-10 days prior isolation. The current standard sampling techniques such as NPS and OPS used for surveillance and serial monitoring of infected patients are exposing healthcare workers to SARS-CoV-2 virus and other unknown pathogens via aerosols from swabbing and jeopardizing physical distancing. This prospective single center diagnostic study was conducted among 217 individuals who were tested positive for SARS-CoV-2 via NPS at a COVID-19 quarantine center, MAEPS. Nevertheless, we had 72 individuals with their saliva specimen tested positive for SARS-CoV-2 while they were test negative for nasopharyngeal swab. Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs. cache = ./cache/cord-321603-lbbsnriv.txt txt = ./txt/cord-321603-lbbsnriv.txt === reduce.pl bib === id = cord-315356-9zf2h0xr author = Apisarnthanarak, Anucha title = Issues Relevant to the Adoption and Modification of Hospital Infection-Control Recommendations for Avian Influenza (H5N1 Infection) in Developing Countries date = 2007-11-15 pages = extension = .txt mime = text/plain words = 3003 sentences = 156 flesch = 36 summary = In developing countries, health care worker preparedness training should address the modes of avian influenza transmission and specify how to implement appropriate infection-control strategies to prevent and control the spread of avian influenza. Pandemic influenza preparedness plans must include health care administrative support, mechanisms to rapidly create temporary isolation facilities, systems to restrict access to exposed health care workers, and plans to involve specialists to screen and identify cases early, to provide for continuous monitoring to ensure adherence to optimal infection-control practices, and to provide regular feedback to health care workers Given the experience of severe acute respiratory syndrome (SARS) outbreaks, which occurred in both designated "SARS hospitals" and "non-SARS hospitals" [40] [41] [42] , global preparedness plans should facilitate administrative, fiscal, and infrastructure support for routine occupational health and safety programs for HCWs, appropriate infection-control expertise, and infrastructure in health care settings, available PPE for HCWs, and epidemiological resources for the prevention and control of emerging infectious diseases. cache = ./cache/cord-315356-9zf2h0xr.txt txt = ./txt/cord-315356-9zf2h0xr.txt === reduce.pl bib === id = cord-318358-glbr8kxh author = Naik, George O A title = COVID-19 and the RAAS date = 2020-06-20 pages = extension = .txt mime = text/plain words = 715 sentences = 64 flesch = 54 summary = Further to Thomas Hanff et al [1] timely call for epidemiological and clinical investigations of COVID-19 infectious disease, measurements of the renin angiotensin aldosterone system (RAAS) components, as sub-studies would be insightful of this pandemic. Angiotensin-converting enzyme 2 (ACE 2) participates in the coronavirus (SARS-CoV-2) cell entry. Drugs that block RAAS also affect ACE 2 expression: it is down regulated by renin inhibition (RI) and up regulated by angiotensin-converting enzyme inhibitors (ACEIs), angiotensin receptor blockers (ARBs) (1) and mineralocorticoid receptor antagonists (MRAs) [2] . Such perturbations would also indirectly influence other RAAS components, and the coordination between circulating and local tissue expressions, as shown in Figure 1 ACE 2 is distributed throughout the body and is abundantly expressed in the lung, small intestine, and in blood vessels of many organs including the brain, heart, kidney and testis [4] . Mineralocorticoid receptor blocker increases angiotensin-converting enzyme 2 activity in congestive heart failure patients cache = ./cache/cord-318358-glbr8kxh.txt txt = ./txt/cord-318358-glbr8kxh.txt === reduce.pl bib === id = cord-325068-j1lfq60o author = Pene, Frédéric title = Coronavirus 229E-Related Pneumonia in Immunocompromised Patients date = 2003-10-01 pages = extension = .txt mime = text/plain words = 2583 sentences = 134 flesch = 35 summary = The results of inoculation tests performed with HUH7 cells were also positive, revealing corona-like particles that were subsequently identified as coronavirus 229E by RT-PCR performed on both culture supernatant and BAL fluid specimens. However, respiratory symptoms only appeared after completion of antiviral treatment and improvement of skin eruptions, and both viral culture and PCR for VZV performed on BAL fluid specimens were negative. The prevalence of coronavirus pulmonary infections among immunocompromised patients is unknown, and it is probably largely underestimated in the absence of the routine performance of sensitive cell culture, RT-PCR, or electron microscopy on BAL fluid specimens. Thus, only 1 case of coronavirus-associated pneumonia was previously described in an immunocompromised patient following autologous bone marrow transplantation, with the diagnosis based on the presence of viral particles in BAL fluid specimens [22] . cache = ./cache/cord-325068-j1lfq60o.txt txt = ./txt/cord-325068-j1lfq60o.txt === reduce.pl bib === id = cord-325416-c0qj3yd9 author = Zachariah, Philip title = Symptomatic Infants have Higher Nasopharyngeal SARS-CoV-2 Viral Loads but Less Severe Disease than Older Children date = 2020-05-20 pages = extension = .txt mime = text/plain words = 502 sentences = 59 flesch = 67 summary = title: Symptomatic Infants have Higher Nasopharyngeal SARS-CoV-2 Viral Loads but Less Severe Disease than Older Children A report published in this journal described the presence of a high nasopharyngeal (NP) viral load of severe acute respiratory coronavirus 2 (SARS-CoV-2) in a well infant [4] . While some data have suggested a higher disease severity in infants [2, 6] , how NP viral load correlates with severity across the pediatric age spectrum has not been firmly established. For each patient, we extracted age, time from reported symptom onset to the date of test, and severity of disease during hospitalization. Our report suggests symptomatic infants have higher NP viral loads at presentation but develop less severe disease as compared to older children and adolescents. A Well Infant with Coronavirus Disease 2019 (COVID-19) with High Viral Load Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China cache = ./cache/cord-325416-c0qj3yd9.txt txt = ./txt/cord-325416-c0qj3yd9.txt === reduce.pl bib === id = cord-324007-hapzf0fl author = McGeer, Allison J. title = Diagnostic Testing or Empirical Therapy for Patients Hospitalized with Suspected Influenza: What to Do? date = 2009-01-01 pages = extension = .txt mime = text/plain words = 2893 sentences = 142 flesch = 37 summary = In a retrospective study of adult patients with influenza who were admitted to the Prince of Wales Hospital in Hong Kong during the 2004-2005 influenza season with fever and respiratory and systemic symptoms, a clinically and statistically significant reduction in length of hospital stay was associated with treatment with oseltamivir [14] . The accumulating evidence suggests that, for patients with acute cardiorespiratory illness requiring hospital admission during influenza season, consideration should be given to either prompt laboratory diagnostic testing and treatment for influenza virus-infected patients or empirical antiviral therapy for influenza. The best choice is made on a case-by-case basis and depends on the severity of illness in the patient being admitted (since earlier therapy for pneumonia is more effective), the probability of influenza virus infection in the individual patient, and the sensitivity of the rapid diagnostic tests available. cache = ./cache/cord-324007-hapzf0fl.txt txt = ./txt/cord-324007-hapzf0fl.txt === reduce.pl bib === id = cord-310390-7pkbd3kg author = Han, Xiaoyu title = Novel Coronavirus Pneumonia (COVID-19) Progression Course in 17 Discharged Patients: Comparison of Clinical and Thin-Section CT Features During Recovery date = 2020-03-30 pages = extension = .txt mime = text/plain words = 3174 sentences = 196 flesch = 56 summary = title: Novel Coronavirus Pneumonia (COVID-19) Progression Course in 17 Discharged Patients: Comparison of Clinical and Thin-Section CT Features During Recovery BACKGROUND: To retrospectively analyze the evolution of clinical features and thin-section CT imaging of novel coronavirus pneumonia (COVID-19) in 17 discharged patients. Hence, this study aimed to analyze the serial thin-section CT changes of 17 discharged patients with COVID-19, and to compare the progression trend of imaging pattern and clinical parameters. The standard for survive and discharge of patients was according to the guideline of Diagnosis and Treatment of Pneumonia Caused by SARS-COV-2 (trial sixth version) published by the China Ministry of Health [22] , which include: temperature returning to normal for more than 3 days, both the clinical and chest imaging showing significant improvement, and two consecutive respiratory pathogen nucleic acid tests turning negative (the interval at least 24 hours). cache = ./cache/cord-310390-7pkbd3kg.txt txt = ./txt/cord-310390-7pkbd3kg.txt === reduce.pl bib === id = cord-314489-e5r5s5ee author = Katsidzira, Leolin title = The SARS-CoV-2 epidemic in Zimbabwe: Quo vadis? date = 2020-05-11 pages = extension = .txt mime = text/plain words = 1948 sentences = 132 flesch = 57 summary = The trajectory, and impact of the SARS-CoV-2 pandemic in sub-Saharan Africa is unclear, but it is seemingly varied between different countries, with most reporting low numbers. Using Zimbabwe as an example, we argue that the magnitude, and impact of the epidemic in most of sub-Saharan Africa is likely to be smaller than anticipated, with a reduced morbidity and mortality. This case strongly influenced the subsequent response to COVID-19 by both the government, and the private healthcare industry in Zimbabwe, and played a pivotal role in raising public awareness. There is a link between the volume of international flights, and the magnitude of the SARS-CoV-2 epidemic in sub-Saharan Africa [7, 11] . A potential source of higher than anticipated mortality from COVID-19 disease in sub-Saharan Africa is the high burden of HIV infection [5] . Moreover, considerable progress has It remains unclear whether complete lockdowns are the most ideal method to limit the spread of SARS-CoV-2 in sub-Saharan Africa [22] . cache = ./cache/cord-314489-e5r5s5ee.txt txt = ./txt/cord-314489-e5r5s5ee.txt === reduce.pl bib === id = cord-327324-4c4a4bfz author = Wilkinson, Robert J title = Tuberculosis and type 2 Diabetes Mellitus: an inflammatory danger signal in the time of COVID-19 date = 2020-06-13 pages = extension = .txt mime = text/plain words = 872 sentences = 61 flesch = 43 summary = title: Tuberculosis and type 2 Diabetes Mellitus: an inflammatory danger signal in the time of COVID-19 Active tuberculosis has a transcriptomic signature dominated by a neutrophil-driven type 1 and 2 interferoninducible gene profile. The exaggerated inflammation that characterizes HIV-tuberculosis-associated immune reconstitution inflammatory syndrome is triggered by Toll-like receptor and inflammasome signalling [14] . Male sex and diabetes have been identified in virtually every study as risk factors for severe COVID-19 infection, associated in the largest study to date with an adjusted hazard ratio for in-hospital death of 1.99 (male sex) and 1.50 for controlled (HbA1c < 58 mmol/mol) and 2.36 for uncontrolled DM [18] . Diabetes mellitus increases the risk of active tuberculosis: a systematic review of 13 observational studies HIV-tuberculosis-associated immune reconstitution inflammatory syndrome is characterized by Toll-like receptor and inflammasome signalling Complement pathway gene activation and rising circulating immune complexes characterize early disease in HIV-associated tuberculosis cache = ./cache/cord-327324-4c4a4bfz.txt txt = ./txt/cord-327324-4c4a4bfz.txt === reduce.pl bib === id = cord-324707-9ld73wv1 author = Mitjà, Oriol title = Hydroxychloroquine for Early Treatment of Adults with Mild Covid-19: A Randomized-Controlled Trial date = 2020-07-16 pages = extension = .txt mime = text/plain words = 4268 sentences = 263 flesch = 54 summary = Study outcomes were the reduction of viral RNA load in nasopharyngeal swabs up to 7 days after treatment start, patient disease progression using the WHO scale up to 28 days, and time to complete resolution of symptoms. Adult patients aged 18 years or more were eligible if they had mild symptoms of Covid-19 (i.e., fever, acute cough, shortness of breath, sudden olfactory or gustatory loss, or influenza-like-illness) for less than five days before enrollment, were non-hospitalized, and had a positive PCR test for SARS-CoV-2 in the baseline nasopharyngeal swab. We estimated that a sample size of 280 patients would provide the trial with 80% power to detect a difference of 0.5 log 10 in the mean reduction of SARS-CoV-2 viral load at a two-sided significance level of α = 0.05, assuming an expected standard deviation of 1.5 [23] . cache = ./cache/cord-324707-9ld73wv1.txt txt = ./txt/cord-324707-9ld73wv1.txt === reduce.pl bib === id = cord-324307-2zbm4iwn author = Kam, Kai-qian title = A Well Infant With Coronavirus Disease 2019 With High Viral Load date = 2020-02-28 pages = extension = .txt mime = text/plain words = 1914 sentences = 123 flesch = 62 summary = A well 6-month-old infant with coronavirus disease 2019 (COVID-19) had persistently positive nasopharyngeal swabs up to day 16 of admission. A well 6-month-old infant with coronavirus disease 2019 (COVID-19) had persistently positive nasopharyngeal swabs up to day 16 of admission. Two specific real-time reverse-transcription polymerase chain reaction (rRT-PCR) methods, targeting the N and ORF1ab genes, were designed to detect the presence of SARS-CoV-2 in clinical samples. A nasopharyngeal specimen taken on admission and tested by rRT-PCR confirmed the diagnosis of COVID-19 infection with low cycle threshold (N gene, 15.57; Orf1ab gene, 13.73), suggesting high viral load. On day 2 of admission, he was found to be viremic with detection of SARS-CoV-2 in his blood sample via rRT-PCR. Repeat testing of his urine on day 9 of admission was negative, but his stool sample became positive for SARS-CoV-2. Similar to reports of adult COVID-19, we confirm the detection of SARS-CoV-2 RNA in the stool of our infant. cache = ./cache/cord-324307-2zbm4iwn.txt txt = ./txt/cord-324307-2zbm4iwn.txt === reduce.pl bib === id = cord-326138-16kpn9db author = Weinstein, Robert A. title = Laboratory-Acquired Infections date = 2009-07-01 pages = extension = .txt mime = text/plain words = 3648 sentences = 183 flesch = 38 summary = Although the precise risk of infection after an exposure remains poorly defined, surveys of laboratory-acquired infections suggest that Brucella species, Shigella species, Salmonella species, Mycobacterium tuberculosis, and Neisseria meningitidis are the most common causes. Surveys of diagnostic laboratory workers in the United Kingdom conducted since 1971 have reported that tuberculosis and enteric infections (especially shigellosis) were the most common laboratory-acquired infections [7, 8] . Similar results were obtained from a survey of clinical microbiology laboratories in Utah from the period 1978-1992, with shigellosis reported to be the most common laboratory-acquired infection [10] . Although no controlled studies have been performed to assess the benefit of postexposure prophylaxis (PEP), it should be considered for laboratory workers who have high-risk exposure to Brucella species (e.g., because of direct manipulation of Brucella cultures outside of laminar-flow BSCs). Viral agents transmitted through blood and bodily fluids cause most of the laboratory-acquired infections in diagnostic laboratories and among health care workers [1] . cache = ./cache/cord-326138-16kpn9db.txt txt = ./txt/cord-326138-16kpn9db.txt === reduce.pl bib === id = cord-320562-zvsf3va0 author = Dookie, Navisha title = Tuberculosis Elimination in the Era of COVID-19: A Moving Target date = 2020-09-14 pages = extension = .txt mime = text/plain words = 1288 sentences = 85 flesch = 53 summary = In this issue, Liu and colleagues describe the impact of a temporary disruption in health services due to COVID-19 mitigation measures on diagnosis and treatment of TB in the Jiangsu province of China. Thus, the resulting decline in case notifications is likely an unintended consequence of limited access to health care services during the pandemic. resulting from limited access to diagnosis and treatment, could potentially escalate TB related mortality have a lasting impact on TB burden. Thus, disruption to health care services will likely result in short term escalation in TB mortality and postlockdown surge in TB case notification, followed by a sustained increase in TB incidence and mortality over the next several years, with long-term consequences on TB elimination. The potential impact of the covid-19 response on tuberculosis in high-burden countries: a modelling analysis Potential impact of the COVID-19 pandemic on HIV, tuberculosis, and malaria in low-income and middle-income countries: a modelling study cache = ./cache/cord-320562-zvsf3va0.txt txt = ./txt/cord-320562-zvsf3va0.txt === reduce.pl bib === id = cord-315180-itvc86cv author = Hollingsworth, T Déirdre title = Counting Down the 2020 Goals for 9 Neglected Tropical Diseases: What Have We Learned From Quantitative Analysis and Transmission Modeling? date = 2018-06-15 pages = extension = .txt mime = text/plain words = 4494 sentences = 193 flesch = 41 summary = In 2012, the World Health Organization set ambitious targets for eliminating many of these diseases as a public health problem by 2020, an aspiration that was supported by donations of treatments, intervention materials, and funding committed by a broad partnership of stakeholders in the London Declaration on NTDs. Alongside these efforts, there has been an increasing role for quantitative analysis and modeling to support the achievement of these goals through evaluation of the likely impact of interventions, the factors that could undermine these achievements, and the role of new diagnostics and treatments in reducing transmission. This article acts as an introduction for a special issue that aims to increase the accessibility of the results so far by summarizing insights from NTD models and identifying key themes for the control of these diseases. The modeling summarized in this issue highlights the value of vector control in reducing the infectiousness of all infected individuals, as well as the value of increasing diagnosis rates (Table 1) . cache = ./cache/cord-315180-itvc86cv.txt txt = ./txt/cord-315180-itvc86cv.txt === reduce.pl bib === id = cord-303240-tv1ta3z5 author = Althoff, Keri N title = Contact tracing: Essential to the public health response and our understanding of the epidemiology of COVID-19 date = 2020-06-11 pages = extension = .txt mime = text/plain words = 1402 sentences = 106 flesch = 61 summary = M a n u s c r i p t As the pandemic in the US continues to evolve, data from contact tracing can continue to inform our understanding about SARS-CoV-2 transmission and guide the public health response. Contact tracing that includes home-based molecular and/or serologic specimen collection to trigger isolation and quarantine may be especially critical when both testing and physical distancing are necessary to achieve the public health goals of epidemic control and mitigation of community transmission. "re-opening"), and test and trace strategies will again be deployed to facilitate epidemic control and interruption of SARS-CoV-2 transmission via isolation and quarantine. Test and trace initiatives will yield equally important information in the current phase of the epidemic as communities begins to "re-open." The contact tracers who will continue to log endless hours to protect the health of the population against COVID-19, and subsequently the stability of our healthcare systems, should be supported and commended. cache = ./cache/cord-303240-tv1ta3z5.txt txt = ./txt/cord-303240-tv1ta3z5.txt === reduce.pl bib === id = cord-325455-e464idc0 author = Atchison, Christina title = Usability and acceptability of home-based self-testing for SARS-CoV-2 antibodies for population surveillance date = 2020-08-12 pages = extension = .txt mime = text/plain words = 3279 sentences = 204 flesch = 57 summary = BACKGROUND: This study assesses acceptability and usability of home-based self-testing for SARS-CoV-2 antibodies using lateral flow immunoassays (LFIA). On a population level, by conducting seroprevalence surveys through widespread random sampling of the general public, and by adjusting for the sensitivity and specificity characteristics of the LFIA used, it is possible to estimate the levels of past infection with SARS-CoV-2 in the community (3) . Usability research on HIV selftesting has generally found good acceptability, the devices easy to use and high validity in interpretation of self-reported test results (7) (8) (9) . To mitigate against this, and given the scientific Our study is original because focusing on the acceptability and usability of LFIAs for self-testing for SARS-CoV-2 antibody in a home-based setting has not been done at such scale in the general population. Overall, our study has demonstrated that home-based self-testing LFIAs for use in large communitybased seroprevalence surveys of SARS-CoV-2 antibody are both acceptable and feasible. cache = ./cache/cord-325455-e464idc0.txt txt = ./txt/cord-325455-e464idc0.txt === reduce.pl bib === id = cord-318458-jadk2qbm author = Jung, Chan-Young title = Association between Body Mass Index and Risk of COVID-19: A Nationwide Case-Control Study in South Korea date = 2020-08-25 pages = extension = .txt mime = text/plain words = 3657 sentences = 219 flesch = 52 summary = METHODS: We examined the association between BMI level and the risk of COVID-19 infection in a nationwide case-control study comprised of 3,788 case patients confirmed with COVID-19 between January 24 and April 9, 2020 and 15,152 controls matched by age and sex, who were aged 20 years or more and underwent National Health Insurance Service (NHIS) health examinations between 2015−2017, using data from the Korean NHIS with linkage to the Korea Centers for Disease Control and Prevention data. In multivariable logistic regression models adjusted for sociodemographic, comorbidity, laboratory and medication data, there was a graded association between higher BMI levels and higher risk of COVID-19 infection; compared to normal weight individuals, the adjusted ORs in the overweight and obese individuals were 1.13 (95% CI, 1.03-1.25) and 1.26 (95% CI, 1.15-1.39), respectively. cache = ./cache/cord-318458-jadk2qbm.txt txt = ./txt/cord-318458-jadk2qbm.txt === reduce.pl bib === id = cord-313499-8ijbesl8 author = Stowell, Sean title = Role of serology in the COVID-19 pandemic date = 2020-05-01 pages = extension = .txt mime = text/plain words = 1211 sentences = 61 flesch = 39 summary = In this issue of Clinical Infections Diseases, F Xiang et al present a serologic study of 85 nucleic acid test (NAT) SARS-CoV-2 positive patients and 24 NAT negative patients who had symptoms suspicious for COVID-19 1 . Serological testing consisted of an enzyme linked immunosorbent assay designed to detect IgM and IgG antibodies against the N protein of SARS-CoV-2. In patients with suspected COVID-19 who tested NAT negative, IgM antibodies were detected in 87.5% and IgG was present in 70.8%. In the case of COVID-19, while serological analysis may be helpful in examining exposure, such approaches can be more challenging to interpret in patients with acute infection. Despite these considerations, the results of this manuscript suggest repeat serological testing may be informative in the acute setting, especially in patients who continue to follow a COVID-19-like disease course despite NAT negativity. Additional testing, such as NAT testing, may be warranted in serological positive individuals to determine potential risk for infecting others. cache = ./cache/cord-313499-8ijbesl8.txt txt = ./txt/cord-313499-8ijbesl8.txt === reduce.pl bib === id = cord-312928-ef8hqs4s author = Chavanet, Pascal title = Viral Upper Respiratory Tract Infection and Otitis Media Complication in Young Children date = 2008-03-15 pages = extension = .txt mime = text/plain words = 590 sentences = 36 flesch = 43 summary = title: Viral Upper Respiratory Tract Infection and Otitis Media Complication in Young Children [1] conducted a large, longitudinal observational study of children with upper respiratory infection and examined for otitis complicationeither acute otitis media or otitis media with effusion. Indeed, in this study, the rate of respiratory syncitial virus infection was found to be low, probably as a result of the method used (conventional assays, type of molecular technique, RT-PCR vs. In this study, children aged !1 year and those who attended day care centers had a greater risk of acquiring upper respiratory tract infection and otitis media, compared with older children and those who were cared for at home. This article is important, especially because the rate of complications of otitis in upper respiratory tract infection was longitudinally studied. Viral upper respiratory tract infection and otitis media complication in young children Rates of hospitalisation for influenza, respiratory syncytial virus and human metapneumovirus among infants and young children cache = ./cache/cord-312928-ef8hqs4s.txt txt = ./txt/cord-312928-ef8hqs4s.txt === reduce.pl bib === id = cord-317823-ztawznod author = Yehya, Nadir title = Statewide Interventions and Covid-19 Mortality in the United States: An Observational Study date = 2020-07-08 pages = extension = .txt mime = text/plain words = 3509 sentences = 228 flesch = 56 summary = Historical analysis of the 1918-1919 influenza pandemic during the second wave of infections that examined 43 cities in the United States demonstrated an association between earlier school closures and bans on public gatherings with lower mortality [5] . Therefore, we assessed the association between the timing of emergency declarations and school closures, two specific statewide distancing measures, and subsequent Covid-19 mortality. Second, because deaths per million is a common method to compare localities, we provide an analysis testing the association between deaths per million at the state level after multivariable adjustment relative to timing of emergency declarations or statewide school closures. States implementing emergency declarations or school closures later in the course of the pandemic experienced higher Covid-19 mortality, with each day of delay increasing mortality risk 5 to 6%. cache = ./cache/cord-317823-ztawznod.txt txt = ./txt/cord-317823-ztawznod.txt === reduce.pl bib === id = cord-318204-t024w7h6 author = Fang, Ferric C title = The Laboratory Diagnosis of COVID-19-- Frequently-Asked Questions date = 2020-06-08 pages = extension = .txt mime = text/plain words = 2976 sentences = 218 flesch = 51 summary = As communities attempt to re-open following periods of shutdown, the detection of both SARS-CoV-2 and specific antibodies recognizing the virus will become increasingly important as a means to assess infection and immunity in individuals and communities. In view of the less than ideal sensitivity of an NP swab to detect SARS-CoV-2 infection, it may be useful to repeat testing in a patient in whom the clinical suspicion is high (32) . Although the primary use of serologic tests is to determine prior exposure to SARS-CoV-2, the detection of specific antibodies may support the diagnosis of COVID-19 in a patient with a high clinical suspicion but negative PCR tests (57-59). Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China Early detection of SARS-CoV-2 antibodies in COVID-19 patients as a serologic marker of infection cache = ./cache/cord-318204-t024w7h6.txt txt = ./txt/cord-318204-t024w7h6.txt === reduce.pl bib === id = cord-317940-yg91bsmm author = Chalumeau, Martin title = Transmission of Panton-Valentine Leukocidin–Producing Staphylococcus aureus to a Physician during Resuscitation of a Child date = 2005-08-01 pages = extension = .txt mime = text/plain words = 1045 sentences = 60 flesch = 43 summary = title: Transmission of Panton-Valentine Leukocidin–Producing Staphylococcus aureus to a Physician during Resuscitation of a Child We report the first case of transmission of Panton-Valentine leukocidin–producing Staphylococcus aureus to a physician during the resuscitation of an infant with fatal pneumonia. We report the first case of transmission of Panton-Valentine leukocidin-producing Staphylococcus aureus to a physician during the resuscitation of an infant with fatal pneumonia. Severe respiratory diseases, in immunocompetent infants, and chronic furunculosis have been associated with Staphylococcus aureus strains producing Panton-Valentine leukocidin (PVL), a cytotoxin that causes leukocyte destruction and tissue necrosis [1] . S. aureus strains susceptible to methicillin were isolated from samples from the physician and from 5 other health care workers. aureus isolates from the infant (S1) and the physician (S2) but not from the isolates from the other health care workers. aureus strain from a patient to a health care worker during resuscitation. cache = ./cache/cord-317940-yg91bsmm.txt txt = ./txt/cord-317940-yg91bsmm.txt === reduce.pl bib === id = cord-323125-qtlevnbt author = Al Hosani, Farida Ismail title = Serologic Follow-up of Middle East Respiratory Syndrome Coronavirus Cases and Contacts—Abu Dhabi, United Arab Emirates date = 2019-02-01 pages = extension = .txt mime = text/plain words = 3706 sentences = 183 flesch = 45 summary = BACKGROUND: Although there is evidence of person-to-person transmission of Middle East respiratory syndrome coronavirus (MERS-CoV) in household and healthcare settings, more data are needed to describe and better understand the risk factors and transmission routes in both settings, as well as the extent to which disease severity affects transmission. METHODS: A seroepidemiological investigation was conducted among MERS-CoV case patients (cases) and their household contacts to investigate transmission risk in Abu Dhabi, United Arab Emirates. In this investigation, we use serological detection of MERS-CoV antibodies to evaluate if asymptomatic or mildly ill case patients had detectable MERS-CoV antibodies, estimate transmission rates from known cases to their household contacts, and identify potential risk factors. For each MERS-CoV case identified in the investigation, clinical information, including symptoms, was collected using the International Severe Acute Respiratory and Emerging Infection Consortium form, which was filled out in real time by healthcare providers and subsequently verified by retrospective chart review. cache = ./cache/cord-323125-qtlevnbt.txt txt = ./txt/cord-323125-qtlevnbt.txt === reduce.pl bib === id = cord-304487-ycvu5l5f author = Wertheim, Joel O title = A glimpse into the origins of genetic diversity in SARS-CoV-2 date = 2020-03-04 pages = extension = .txt mime = text/plain words = 1202 sentences = 74 flesch = 43 summary = Evolution tinkers with these viruses in bats, and the epidemiological consequences are seen both in pathogenic zoonotic diseases (e.g., SARS, MERS, and COVID-19) and in the less-virulent circulating coronaviruses causing common colds. Molecular epidemiology can use the genetic variation of SARS-CoV-2 to trace its history and better understand clusters of transmission. However, deep-sequencing of viral genomes from 7 patients (including this probable transmission pair), the authors detect substantial variation in the number and frequency of minority variants within different individuals. The evolutionary history of MERS-CoV in its intermediate host, camels, is littered with recombination events [6] . However, as the number of infections increases and the circulating viruses become more genetically distinct, natural selection will become more efficient, making viral adaptation more of a possibility. For now, SARS-CoV-2 genetic variation is likely evolutionarily inconsequential and will be more important for facilitating molecular epidemiology in tracing the origins of novel clusters of viral infection. cache = ./cache/cord-304487-ycvu5l5f.txt txt = ./txt/cord-304487-ycvu5l5f.txt === reduce.pl bib === id = cord-321873-9l9zp6gm author = Zhou, Bo title = The duration of viral shedding of discharged patients with severe COVID-19 date = 2020-04-17 pages = extension = .txt mime = text/plain words = 608 sentences = 49 flesch = 64 summary = title: The duration of viral shedding of discharged patients with severe COVID-19 However, little studies have focused on clinical characteristics of discharged patients with severe COVID-19, especially the duration of viral shedding. The RT-PCR tests were performed on throat swabs following a previously described method 3 Moreover, another study displayed that four patients with COVID-19 who met the criteria for hospital discharge in China had positive RT-PCR test results 5 to 13 days later 6 , suggesting that recovered patients might still be virus carriers. Based on the results, we did not observe shortening of viral shedding time in the above groups, so it implied that all patients with severe COVID-19 should complete adequate course of treatment, regardless of sex and age. Clinical features of patients infected with 2019 novel coronavirus in Wuhan Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study cache = ./cache/cord-321873-9l9zp6gm.txt txt = ./txt/cord-321873-9l9zp6gm.txt === reduce.pl bib === id = cord-312797-hohzjx74 author = Hamelin, Marie-Ève title = Human Metapneumovirus: A New Player among Respiratory Viruses date = 2004-04-01 pages = extension = .txt mime = text/plain words = 3353 sentences = 170 flesch = 41 summary = Despite the fact that prospective and case-control studies have been limited, the epidemiology and clinical manifestations associated with hMPV have been found to be reminiscent of those of the human respiratory syncytial virus, with most severe respiratory tract infections occurring in infants, elderly subjects, and immunocompromised hosts. In addition, studies have shown that hMPV is not a new pathogen, with serological evidence of human infection dating from 1958 in The Netherlands [4] and viral isolation for the past 10-20 years in Europe and Canada [4, 7] . Symptoms of both upper and lower respiratory tract infections have been associated with hMPV in young children, although most reports are biased towards description of the most severe symptomatology in hospitalized subjects. Virological features and clinical manifestations associated with human metapneumovirus: a new paramyxovirus responsible for acute respiratory-tract infections in all age groups cache = ./cache/cord-312797-hohzjx74.txt txt = ./txt/cord-312797-hohzjx74.txt === reduce.pl bib === id = cord-305394-wwabxlgr author = Venter, W D Francois title = COVID-19: First data from Africa date = 2020-08-31 pages = extension = .txt mime = text/plain words = 1469 sentences = 78 flesch = 54 summary = This data is from an ongoing surveillance cohort that has previously generated rich data on disease patterns in the Western Cape, and currently continues to provide near real-time updates on the impact of PCR-confirmed SARS-CoV-2 on factors ranging from death to oxygen consumption within hospitals. Key strengths of the paper include a dataset covering over 3 million healthcare users in the Western Cape Province, and the use of both hospitalized and nonhospitalized cases and deaths Davies' data shows similar mortality risk factors, including age, sex, diabetes (especially uncontrolled diabetes), hypertension and renal disease to other cohorts from richer countries. For South Africa, a sigh of relief at a relatively small increase in mortality in HIV and TB should be quickly tempered; diabetes was the second commonest cause of death in the country pre-COVID-19, and most patients in the country have poor glucose control, a major risk factor from Davies' data (7) . cache = ./cache/cord-305394-wwabxlgr.txt txt = ./txt/cord-305394-wwabxlgr.txt === reduce.pl bib === id = cord-326494-qhxlh43t author = Beckerman, Karen Palmore title = Pregnancy and Pandemic Disease date = 2020-06-10 pages = extension = .txt mime = text/plain words = 1199 sentences = 95 flesch = 59 summary = Globally, estimates suggest it is a disease of men (57%), however women (32%) and children < age 15 (11%) together make up close to half of those living with TB. 10 They report an unexpectedly high proportion of women (37%) living with TB, The strong implication of these pregnancy data, that exposure and transmission in the population studied is both continuous and ongoing, is striking. have provided proof of concept data that routine testing during pregnancy could be an ideal method of assessing the extent of community spread of both recognized endemic infection as well as emerging infectious diseases. Today, we continue to rely on universal HIV testing of pregnant women to estimate community HIV prevalence and to prevent vertical transmission, both in resource-rich and resource-limited regions. Tuberculosis infection in women of reproductive age -a cross-sectional study at antenatal care clinics in an Ethiopian city Control of maternal HIV-1 disease during pregnancy cache = ./cache/cord-326494-qhxlh43t.txt txt = ./txt/cord-326494-qhxlh43t.txt === reduce.pl bib === id = cord-317948-svgguadm author = Xiao, Ai Tang title = Profile of RT-PCR for SARS-CoV-2: a preliminary study from 56 COVID-19 patients date = 2020-04-19 pages = extension = .txt mime = text/plain words = 1290 sentences = 96 flesch = 58 summary = title: Profile of RT-PCR for SARS-CoV-2: a preliminary study from 56 COVID-19 patients To date, an outbreak of infectious diseases--coronavirus disease 2019 (COVID-19) associated with Severe Acute Respiratory Syndrome Coronavirus -2 (SARS-CoV-2) continues in Wuhan, China and threatens countries such as Korea, Italy, Iraq and Japan, etc. Currently no study reported the viral dynamics of SARS-CoV-2 infection in a long observation period. Therefore, we collected clinical specimens from 56 COVID-19 patients and reported the results of SARS-CoV-2 detection during the disease course. If two consecutive negative results were achieved, the period between symptoms onset and the date of first negative RT-PCR test result was defined as viral nucleic acid conversion time. In first 3 weeks after symptoms onset, majority results of RT-PCR for SARS-CoV-2 were positive. [14] [15] [16] This preliminary study has found evidence of the dynamic profile of SARS-CoV-2 in non-ICU COVID-19 patients during disease course. cache = ./cache/cord-317948-svgguadm.txt txt = ./txt/cord-317948-svgguadm.txt === reduce.pl bib === id = cord-322448-s04e6po9 author = Gadsby, Naomi J. title = Comprehensive Molecular Testing for Respiratory Pathogens in Community-Acquired Pneumonia date = 2016-04-01 pages = extension = .txt mime = text/plain words = 4371 sentences = 206 flesch = 34 summary = Sputum (96%) or endotracheal aspirate (4%) specimens were cultured as per routine practice and also tested with fast multiplex real-time polymerase-chain reaction (PCR) assays for 26 respiratory bacteria and viruses. Comprehensive molecular testing of single lower respiratory tract (LRT) specimens achieved pathogen detection in 87% of CAP patients compared with 39% with culture-based methods. Comprehensive molecular testing significantly improves pathogen detection in CAP, particularly in antimicrobial-exposed patients, and requires only a single LRT specimen. The development of multiplex real-time polymerase-chain reaction (PCR) assays currently enables a respiratory specimen to be rapidly screened for a wide range of viral and atypical bacterial pathogens in a small number of reactions [10] [11] [12] [13] [14] [15] . As our study focused on testing sputum by molecular methods, our high level of pathogen detection for typical bacteria may not be directly comparable to results from other recent studies in hospitalized adult CAP. cache = ./cache/cord-322448-s04e6po9.txt txt = ./txt/cord-322448-s04e6po9.txt === reduce.pl bib === id = cord-329311-p68kr4ga author = Prebensen, Christian title = SARS-CoV-2 RNA in plasma is associated with ICU admission and mortality in patients hospitalized with COVID-19 date = 2020-09-05 pages = extension = .txt mime = text/plain words = 1454 sentences = 111 flesch = 61 summary = title: SARS-CoV-2 RNA in plasma is associated with ICU admission and mortality in patients hospitalized with COVID-19 Routine biochemistry was taken at admission and study-specific samples of EDTA plasma and serum were taken at three time points; baseline (enrollment), day 3 (1 day) and day 9 ( 2 days) in patients who were still hospitalized (details in Supplementary Figure 1) . SARS-CoV-2 RNAemia was detected in at least one sample in 58/123 (47%) patients, and in a significantly higher proportion of patients who were admitted to the ICU or died (80% vs. RNAemia was significantly more frequent at all time points in patients who reached the primary endpoint, whereas RNA loads were significantly higher at baseline and day 3 ( Table 1 , Supplementary Figure 2A ). In this prospective study of patients hospitalized with COVID-19 we detected SARS-CoV-2 RNAemia in 47% of included patients, and a significantly higher frequency of RNAemia and higher RNA loads in and similarly found that RNAemia was associated with ICU admission and hospital mortality [3] . cache = ./cache/cord-329311-p68kr4ga.txt txt = ./txt/cord-329311-p68kr4ga.txt === reduce.pl bib === id = cord-325136-oyizfh2z author = Pham, Quang Thai title = The first 100 days of SARS-CoV-2 control in Vietnam date = 2020-08-01 pages = extension = .txt mime = text/plain words = 2655 sentences = 164 flesch = 53 summary = METHODS: Clinical and demographic data on the first 270 SARS-CoV-2 infected cases and the timing and nature of Government control measures, including numbers of tests and quarantined individuals, were analysed. Data from 270 SARS-CoV-2-confirmed cases to May 1 st 2020 included their age, gender, nationality, dates of symptom onset (if any), entry to the country and quarantine (if any), hospital admission and discharge, and the results of RT-PCR tests. The epidemic timeline for Vietnam, including the numbers quarantined and hospitalised, tests performed, cases confirmed, population movements, and the timing and nature of major Government-led control measures are summarised in Figure 1 . Entry of airline passengers into Vietnam from Wuhan city and elsewhere in China was monitored and progressively limited ( Table 1) After further measures to prevent entry of infected international travellers (Table 1) Forty-three percent (89/208) of discharged cases never developed symptoms, and this was not significantly associated with age, gender, nationality, or origin of infection (imported or domestically-acquired). cache = ./cache/cord-325136-oyizfh2z.txt txt = ./txt/cord-325136-oyizfh2z.txt === reduce.pl bib === id = cord-329323-1cquorhs author = Ko, Jean Y title = Risk Factors for COVID-19-associated hospitalization: COVID-19-Associated Hospitalization Surveillance Network and Behavioral Risk Factor Surveillance System date = 2020-09-18 pages = extension = .txt mime = text/plain words = 4184 sentences = 240 flesch = 44 summary = Generalized Poisson regression models were used to calculate adjusted rate ratios (aRR) for hospitalization RESULTS: Among 5,416 adults, hospitalization rates were higher among those with ≥3 underlying conditions (versus without)(aRR: 5.0; 95%CI: 3.9, 6.3), severe obesity (aRR:4.4; 95%CI: 3.4, 5.7), chronic kidney disease (aRR:4.0; 95%CI: 3.0, 5.2), diabetes (aRR:3.2; 95%CI: 2.5, 4.1), obesity (aRR:2.9; 95%CI: 2.3, 3.5), hypertension (aRR:2.8; 95%CI: 2.3, 3.4), and asthma (aRR:1.4; 95%CI: 1.1, 1.7), after adjusting for age, sex, and race/ethnicity. BRFSS data were used to calculate weighted population estimates of community-dwelling adults with and without individual underlying medical conditions by age, sex, and race/ethnicity strata for the COVID-NET catchment area and served as the analytic A c c e p t e d M a n u s c r i p t 7 denominators. cache = ./cache/cord-329323-1cquorhs.txt txt = ./txt/cord-329323-1cquorhs.txt === reduce.pl bib === id = cord-331719-uijwq8gx author = Russek-Cohen, Estelle title = FDA Perspectives on Diagnostic Device Clinical Studies for Respiratory Infections date = 2011-05-01 pages = extension = .txt mime = text/plain words = 4838 sentences = 205 flesch = 41 summary = In the former circumstance, a clinical reference method is considered to be the best available method for establishing the presence or absence of the target organism [1] but the reference method cannot incorporate results reported by the new device; for example, a new enzymelinked immunosorbent assay (ELISA) could not be used as one of the diagnostic criteria for the reference method in a study used to evaluate the performance of the assay. In a clinical study with only 5 specimens positive for a specific pathogen (via the reference method) and an observed sensitivity of 5/5 (100%) results in a lower confidence bound of only 55.6%, meaning diagnostic performance is very uncertain. Detailed information regarding the design of studies for a CLIA waiver application, including the minimal performance criteria acceptable for a CLIA-waived device, is described in ''FDA guidance for industry and FDA staff: recommendations for Clinical Laboratory Improvement Amendments of 1988 (CLIA) waiver applications for manufacturers of in vitro diagnostic devices'' [9] . cache = ./cache/cord-331719-uijwq8gx.txt txt = ./txt/cord-331719-uijwq8gx.txt === reduce.pl bib === id = cord-316970-n2dly3oa author = Kerbaj, Jad title = COVID-19: The New Caledonia experience date = 2020-05-16 pages = extension = .txt mime = text/plain words = 1444 sentences = 115 flesch = 68 summary = Every passenger with fever or cough was hospitalized in the Centre Hospitalier Territorial CHT (the main island's hospital, reference center in Infectious Diseases) and tested by SARS-CoV-2 reverse transcriptase Polymerase Chain Reaction (RT-PCR). On February 10, screening by SARS-CoV-2 RT-PCR started for all patients hospitalized for an Influenza like illness or a severe acute respiratory infection (SARI). All close contact to person confirmed with COVID-19 infection were isolated in a quarantine facility for 14 days. Iceland has quickly considered all travels outside the island as high risk, has done a large population screening and important tracking of SARS-A c c e p t e d M a n u s c r i p t 6 CoV-2 infections, associating these measures with quarantine, self-isolation and social distancing (8) . The surveillance, quarantine measures, the hospitalization of all detected COVID-19 positive patients and the rapid lockdown had probably an impact on stopping the spread. cache = ./cache/cord-316970-n2dly3oa.txt txt = ./txt/cord-316970-n2dly3oa.txt === reduce.pl bib === id = cord-324607-rpwccvqi author = Rojek, Amanda M title = Core Minimal Datasets to Advance Clinical Research for Priority Epidemic Diseases date = 2020-02-15 pages = extension = .txt mime = text/plain words = 1260 sentences = 63 flesch = 39 summary = Among the noteworthy successes of vaccine trials, and the commendable efforts to implement clinical treatment trials during Ebola outbreaks, we should also focus on strengthening the collection and curation of epidemiological and observational data that can improve the conception and design of clinical research. Table 1 identifies some key domains that could contribute to a core minimal dataset that informs clinical trial design for each priority pathogen. While these data have their most important benefits in improving patient management (through better recognition of disease complications and informing supportive care) and public health control, patient-based data are also used to determine key parameters for clinical trials, such as the inclusion criteria, the nature and rate of clinically relevant outcomes, and potential confounders. A systematic review and meta-analysis of patient data from the west Africa (2013-16) Ebola virus disease epidemic cache = ./cache/cord-324607-rpwccvqi.txt txt = ./txt/cord-324607-rpwccvqi.txt === reduce.pl bib === id = cord-322082-80ym2rsq author = Monto, Arnold S title = Lessons From Influenza Pandemics of the Last 100 Years date = 2020-03-01 pages = extension = .txt mime = text/plain words = 4089 sentences = 229 flesch = 46 summary = Since this was the first true pandemic since 1918, there was immediate concern about its potential impact and great relief when it was found to resemble seasonal influenza with morbidity highest in children and mortality at the extremes of age [26, 27] (Figure 3 ). However, the new A(H3N2) virus completely replaced the previous subtype, and its variants, more than 50 years later, have been responsible for the greatest proportion of mortality from influenza viruses. In the United States, there was particular attention directed to nonpharmaceutical interventions, a result of the recognition that pandemic-specific vaccines would be available relatively late and that influenza-specific antiviral drugs, while important, would be limited in quantity. " The latter issue has been made worse by the repeated recognition of the pandemic potential of different avian influenza virus variants that have infected humans [63] [64] [65] . cache = ./cache/cord-322082-80ym2rsq.txt txt = ./txt/cord-322082-80ym2rsq.txt === reduce.pl bib === id = cord-328667-r5w09lb6 author = Schwartz, David A title = The Effects of Pregnancy on Women with COVID-19: Maternal and Infant Outcomes date = 2020-05-11 pages = extension = .txt mime = text/plain words = 1518 sentences = 88 flesch = 48 summary = In contrast, some pregnant women might be asymptomatic or have only mild or nonspecific symptoms from an infectious disease, resulting in their escaping detection as having infection even when the embryo or fetus is severely affected. [9] evaluated for the first time the effects of being pregnant on COVID-19 disease and pneumonia using a case-control experimental design conducted at the Maternal and Child Health Hospital of Hubei Province, a 1900-bed tertiary medical center in Wuhan, China. To accomplish this, the authors enrolled two cohorts of pregnant women with COVID-19 and pneumonia -one consisting of 16 pregnant women with pneumonia and rt-PCR confirmed SARS-CoV-2 infection, and the other with 18 pregnant women with pneumonia who were clinically and radiologically suspected of having COVID-19 but had negative rt-PCR test results. An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: Maternal coronavirus infections and pregnancy outcomes Maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia: a case-control study cache = ./cache/cord-328667-r5w09lb6.txt txt = ./txt/cord-328667-r5w09lb6.txt === reduce.pl bib === id = cord-318615-uhh3owcx author = Xiang, Fei title = Antibody Detection and Dynamic Characteristics in Patients with COVID-19 date = 2020-04-19 pages = extension = .txt mime = text/plain words = 2365 sentences = 133 flesch = 53 summary = METHODS: The antibodies against SARS-CoV-2 were detected by an enzyme-linked immunosorbent assay (ELISA) based on the recombinant nucleocapsid protein of SARS-CoV-2 in patients with confirmed or suspected COVID-19 at 3-40 days after symptom onset. Here, we detected dynamics characteristics and magnitude of antibody response in patients with COVID-19, and evaluated serodiagnostic value of ELISA-based IgM, IgG tests for COVID-19 pneumonia. Detection of IgM and IgG Antibody on Different Periods (Table 2.) We evaluated specificity of IgM and IgG antibodies based on ELISA from 216 serum sample of 85 confirmed COVID-19 pneumonia patients. To evaluate the diagnostic potential of serological IgM and IgG antibodies detection, 66 patients with confirmed COVID-19 pneumonia were evaluated and compare to standard RT-PCR assays. * Specific IgM and IgG antibodies against SARS-CoV-2 from 216 serum samples of 85 confirmed COVID-19 pneumonia cases were tested with ELISA. cache = ./cache/cord-318615-uhh3owcx.txt txt = ./txt/cord-318615-uhh3owcx.txt === reduce.pl bib === id = cord-322204-kc7dy2za author = Khalil, Asma title = SARS-CoV-2-specific antibody detection in healthcare workers in a UK maternity Hospital: Correlation with SARS-CoV-2 RT-PCR results date = 2020-08-08 pages = extension = .txt mime = text/plain words = 448 sentences = 50 flesch = 60 summary = title: SARS-CoV-2-specific antibody detection in healthcare workers in a UK maternity Hospital: Correlation with SARS-CoV-2 RT-PCR results Universal healthcare worker (HCW) testing is potentially useful in ameliorating workforce depletion and reducing asymptomatic spread of SARS-CoV-2. Nasopharyngeal swab polymerase chain reaction (RT-PCR) can diagnose only current or recent infection; testing for antibody responses against SARS-CoV-2 could enhance the ability to expedite reinstatement of services, while ensuring patient and staff safety. Tests are now available for immunoglobulin (Ig) G against the SARS-CoV-2 nucleocapsid protein; the Abbott SARS-CoV-2 IgG ELISA is reported to have high specificity We previously reported that 32% of HCW testing positive for SARS-CoV-2 on nasopharyngeal swab were asymptomatic at the time. 2 Symptomatic and asymptomatic SARS-CoV-2 positive adults have similar viral loads and infectious virus isolation. Of those testing positive for SARS-CoV-2 IgG, 39% had an earlier negative nasopharyngeal swab. 5 Both symptomatic and asymptomatic infections were associated with SARS-COV-2 IgG antibodies, as were 10% of cache = ./cache/cord-322204-kc7dy2za.txt txt = ./txt/cord-322204-kc7dy2za.txt === reduce.pl bib === id = cord-317092-5qba9jiq author = Singh, Tulika title = Lessons from COVID-19 in children: Key hypotheses to guide preventative and therapeutic strategies date = 2020-05-08 pages = extension = .txt mime = text/plain words = 4971 sentences = 355 flesch = 49 summary = The current pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), reveals a peculiar trend of milder disease and lower case fatality in children compared to adults. Understanding differences in children's immunity, host cellular factors required for virus replication, and physiology can provide insights into the correlates of protection from SARS-CoV-2 and other CoVs. In this review, we summarize current pediatric-specific knowledge on clinical disease, transmission, risks for severe disease, protective immunity, and novel therapies and vaccines in trial. 38 For example, a regulator of lung morphogenesis that is lower in childhood, nuclear factor kappa-light-chainenhancer of activated B cells (NF-b), plays a pathologic role in inflammatory diseases and should be evaluated as a protective host factor in pediatric versus adult SARS-CoV-2 infections. In this review, we evaluated recent reports on the pathology and immunity to SARS-CoV-2 infection and offered several hypotheses for how these features may differ in children versus adults, and how they may differentially modulate disease in these populations. cache = ./cache/cord-317092-5qba9jiq.txt txt = ./txt/cord-317092-5qba9jiq.txt === reduce.pl bib === id = cord-330214-28ah3nig author = Zhao, Jiao title = Relationship between the ABO Blood Group and the COVID-19 Susceptibility date = 2020-08-04 pages = extension = .txt mime = text/plain words = 1109 sentences = 72 flesch = 64 summary = To explore any relationship between the ABO blood group and the COVID-19 susceptibility, we compared ABO blood group distributions in 2,173 COVID-19 patients with local control populations, and found that blood group A was associated with an increased risk of infection, whereas group O was associated with a decreased risk. Here, we investigated the relationship between the ABO blood type and the susceptibility to COVID-19 in patients from three hospitals in Wuhan and Shenzhen, China. These results showed associations between ABO blood groups and COVID-19 susceptibility. The COVID-19 risk significantly increased for blood group A ( Figure 1 shows the estimates of ORs of the risk of ABO blood groups for COVID-19 on the pooled data from the three hospitals by random effects models. In this study, we found that ABO blood groups displayed different association risks for the infection with SARS-CoV-2 resulting in COVID-19. In the 285 patients from Shenzhen, we also found that blood group AB had an increased risk of infection. cache = ./cache/cord-330214-28ah3nig.txt txt = ./txt/cord-330214-28ah3nig.txt === reduce.pl bib === id = cord-332469-zegawla5 author = Li, Wei title = The characteristics of household transmission of COVID-19 date = 2020-04-17 pages = extension = .txt mime = text/plain words = 2513 sentences = 164 flesch = 64 summary = Secondary attack rates of SARS-CoV-2 to the contact members were computed and the risk factors for transmission within household were estimated. The secondary attack rate to contacts who were spouses of index cases was 27.8% comparing with 17.3% to other adult members in the households. Spouse relationship was another risk factor for the infection of SARS-CoV-2 to household contacts and the secondary attack rate to individuals who were spouses of index cases was 27.8%, compared to 17.3% to other members in the households (OR 2.21, 95% CI 1.18 to 4.12, p=0.013). The gender, symptoms and the time between onset of illness of index patients and hospitalization were not related to the secondary attack rates of SARS-CoV-2 to household contacts (Table 3 The results showed no infected contacts in the households with index cases who implemented quarantine immediately after appearance of symptoms, and so the secondary attack rate was zero. cache = ./cache/cord-332469-zegawla5.txt txt = ./txt/cord-332469-zegawla5.txt === reduce.pl bib === id = cord-327069-vjlisnui author = Driscoll, Amanda J. title = Standardization of Laboratory Methods for the PERCH Study date = 2017-06-15 pages = extension = .txt mime = text/plain words = 4725 sentences = 221 flesch = 42 summary = To build capacity at the sites, and in alignment with the priorities of the Bill & Melinda Gates Foundation, all PERCH testing was done locally, with the exception of quality assurance testing and a select subset of specialized assays, which were performed at the study reference laboratory (Canterbury Health Laboratories, Christchurch, New Zealand), which also served as the study specimen and isolate biorepository. Induced sputum, pleural fluid, and lung aspirate specimens were collected in saline in universal containers and either refrigerated at 2°C-8°C for a maximum of 24 hours, or frozen at -80°C prior to nucleic acid extraction. Organism identification was done according to standard microbiological methods that were documented in SOPs and clarified at each site at the outset; antimicrobial susceptibility testing followed the Clinical and Laboratory Standards Institute (CLSI) guidelines [15] . cache = ./cache/cord-327069-vjlisnui.txt txt = ./txt/cord-327069-vjlisnui.txt === reduce.pl bib === id = cord-331978-y4uo7o8g author = Maxwell, Daniel N title = “The Art of War” in the Era of Coronavirus Disease 2019 (COVID-19) date = 2020-03-04 pages = extension = .txt mime = text/plain words = 1520 sentences = 83 flesch = 53 summary = With rapidly increasing cases and local community transmission in multiple countries outside of China, including the United States, the outbreak has entered a new phase, which requires a shift in primary battle strategy from a focus on containment in China to international mitigation. As cases of COVID-19 explode internationally, a strategic shift is required away from primarily containment, keeping the virus "out there", to home-based mitigation and public health responses. Now, the task is bearing the burden of identifying, isolating, triaging and managing the rising number of cases, necessitating total engagement of the medical community, public health sector, governments and society as a whole. As Sun Tzu noted, "If in training soldiers' commands are habitually enforced, the army will be well-disciplined." 1 The authors also highlight improvements in infection prevention and control (IPC) infrastructure, administrative controls, and public health coordination compared to their 2003 SARS experience. cache = ./cache/cord-331978-y4uo7o8g.txt txt = ./txt/cord-331978-y4uo7o8g.txt === reduce.pl bib === id = cord-331930-w2055c42 author = Tso, Eugene Y. K. title = Persistence of Physical Symptoms in and Abnormal Laboratory Findings for Survivors of Severe Acute Respiratory Syndrome date = 2004-05-01 pages = extension = .txt mime = text/plain words = 529 sentences = 34 flesch = 61 summary = title: Persistence of Physical Symptoms in and Abnormal Laboratory Findings for Survivors of Severe Acute Respiratory Syndrome Sir-We performed a cross-sectional study to assess the physical symptoms in and abnormal laboratory findings for survivors of severe acute respiratory syndrome (SARS) at their first follow-up visit after discharge from Princess Margaret Hospital (Hong Kong, China). The median interval (‫ע‬SD) between the onset of SARS symptoms and the first follow-up visit was weeks. Symptoms reported at the first followup visit included palpitation (45.1% of patients), exertional dyspnea (41.9%), malaise (40.3%), easy forgetfulness (30.6%), chest discomfort (22.5%), hand tremor (21%), dizziness (17.7%), depression (16.1%), myalgia (12.9%), headache (9.6%), diarrhoea (8.1%), cough (8.1%), insomnia (6.5%), and hair loss over the scalp (3.2%). Laboratory findings included the following mean values (‫ע‬SD): hemoglobin of patients. However, for 1 female patient, PCR of a stool sample obtained 35 days after the onset of SARS symptoms was positive for SARS-CoV RNA. cache = ./cache/cord-331930-w2055c42.txt txt = ./txt/cord-331930-w2055c42.txt === reduce.pl bib === id = cord-329290-vqvujry3 author = Kempker, Russell R title = Loss of Smell and Taste Among Healthcare Personnel Screened for Coronavirus 2019 date = 2020-06-28 pages = extension = .txt mime = text/plain words = 1907 sentences = 90 flesch = 55 summary = HCP with symptoms consistent with a viral-like illness were triaged to the employee health services staff for a virtual clinical assessment and then scheduled for SARS-CoV-2 testing. HCP with a positive SARS-CoV-2 test compared with those with a negative test had a higher mean number of symptoms and were more likely to have reported fever, chills, myalgia, and loss of smell or taste (Table 1 ). We are the first to evaluate the sensitivity of loss of smell and taste in distinguishing symptomatic HCP with and without a positive SARS-CoV-2 test and support their recent inclusion to the list of symptoms associated with COVID-19 provided by the CDC [4] . The high specificity and positive predictive value of loss of smell and/or taste for a positive SARS-CoV-2 test in our cohort highlights the utility of including these symptoms in COVID-19 screening algorithms. cache = ./cache/cord-329290-vqvujry3.txt txt = ./txt/cord-329290-vqvujry3.txt === reduce.pl bib === id = cord-335038-q32ghvsv author = Huang, Jiao title = Epidemiological, virological and serological features of COVID-19 cases in people living with HIV in Wuhan City: A population-based cohort study date = 2020-08-17 pages = extension = .txt mime = text/plain words = 3171 sentences = 231 flesch = 59 summary = title: Epidemiological, virological and serological features of COVID-19 cases in people living with HIV in Wuhan City: A population-based cohort study METHODS: This population-based cohort study identified all COVID-19 cases among the whole PLWH in Wuhan city, China, by April 16, 2020. Previous studies have found that PLWH with low CD4 cell count, high HIV viral load and not taking antiretroviral treatment have an increased risk of other respiratory infections [9] . This indicates that COVID-19 cases in PLWH may have delayed viral clearance for SARS-CoV-2 because of immunosuppression, although clinical improvement of COVID-19 in PLWH was not worse than that of individuals without HIV infection as described in the present study and other published studies [25, 32] . CD4 cell count and the risk of AIDS or death in HIV-Infected adults on combination antiretroviral therapy with a suppressed viral load: a longitudinal cohort study from COHERE cache = ./cache/cord-335038-q32ghvsv.txt txt = ./txt/cord-335038-q32ghvsv.txt === reduce.pl bib === id = cord-322650-q8inhgtr author = Fung, Yin-Wan Wendy title = Use of Clinical Criteria and Molecular Diagnosis to More Effectively Monitor Patients Recovering after Severe Acute Respiratory Syndrome Coronavirus Infection date = 2004-08-15 pages = extension = .txt mime = text/plain words = 1132 sentences = 64 flesch = 50 summary = title: Use of Clinical Criteria and Molecular Diagnosis to More Effectively Monitor Patients Recovering after Severe Acute Respiratory Syndrome Coronavirus Infection In conclusion, voriconazole is highly active against Aspergillus species, but additional studies are needed to confirm that our low drug concentrations result from the method of sampling and not from poor efficacy of this molecule in the CSF. In early 2003, a novel severe acute respiratory syndrome (SARS) coronavirus (CoV) [1] spread around the world; ultimately, more than 8000 patients in 32 countries contracted SARS, many of whom died. The ERT method clearly demonstrated the presence of SARS CoV in all samples obtained from the patient on 16 June (table 1) , which was 1 day before his transfer to WTSH. More studies will be necessary to determine the infectivity status of patients who have ERT results positive for SARS CoV. Severe acute respiratory syndrome (SARS): laboratory diagnostic tests cache = ./cache/cord-322650-q8inhgtr.txt txt = ./txt/cord-322650-q8inhgtr.txt === reduce.pl bib === id = cord-328267-tk0zc8il author = Liu, Qiao title = Collateral Impact of the Covid-19 Pandemic on Tuberculosis Control in Jiangsu Province, China date = 2020-08-28 pages = extension = .txt mime = text/plain words = 1667 sentences = 119 flesch = 50 summary = title: Collateral Impact of the Covid-19 Pandemic on Tuberculosis Control in Jiangsu Province, China We compared tuberculosis case notifications, tuberculosis treatment outcomes, and diagnostic screening for multidrug resistance (MDR) among tuberculosis patients from 2015-2020 before and after the Covid-19 pandemic began in China. We A c c e p t e d M a n u s c r i p t Discussion This is the first data from China reporting the potential indirect impact on tuberculosis control of the Covid-19 pandemic. In addition, reductions in treatment completion and MDR screening during this time period suggest that both deterred health care seeking and community disease management are likely drivers of these trends. Our analysis suggests that collateral effects of the Covid-19 pandemic on tuberculosis control are substantial, with a reduction of 36%-52% in tuberculosis notifications in 2020 compared to 2015-2019. cache = ./cache/cord-328267-tk0zc8il.txt txt = ./txt/cord-328267-tk0zc8il.txt === reduce.pl bib === id = cord-330951-k54e3lbu author = Pollett, S title = Social media and the new world of scientific communication during the COVID19 pandemic date = 2020-05-12 pages = extension = .txt mime = text/plain words = 813 sentences = 49 flesch = 51 summary = The human and social toll of the COVID19 pandemic has already spurred several major public health 'lessons learned', and the theme of effective and responsible scientific communication is among them. This discussion also serves as a succinct primer on some of the pivotal epidemiological analyses (and their communication) during the early phases of the COVID19 outbreak, as seen through the lens of a Twitterfeed. The expansion of the outbreak has demanded a rapid response from public health authorities; fundamental epidemiological and scientific evidence has been acquired at break-neck speed to support those decisions. We propose that Twitter has played a fundamental -but often precarious -role in permitting real-time global communication between scientists during the COVID19 epidemic, on a scale not seen before. This discussion also serves as a succinct primer on some of the pivotal epidemiological analyses (and their communication) during the early phases of the COVID19 outbreak, as seen through the lens of a Twitter-feed. cache = ./cache/cord-330951-k54e3lbu.txt txt = ./txt/cord-330951-k54e3lbu.txt === reduce.pl bib === id = cord-335691-lsuwsm43 author = Jackson, Michael L. title = The Burden of Community-Acquired Pneumonia in Seniors: Results of a Population-Based Study date = 2004-12-01 pages = extension = .txt mime = text/plain words = 3625 sentences = 168 flesch = 44 summary = To estimate rates of community-acquired pneumonia and to identify risk factors for this disease, we conducted a large, population-based cohort study of persons aged ⩾65 years that included both hospitalizations and outpatient visits for pneumonia. In multivariate analysis, age, male sex, current smoking, diabetes mellitus, congestive heart failure, lung cancer, serious nonlung cancer, COPD, asthma without COPD, dementia, stroke, receipt of prednisone, use of home oxygen services, greater number of outpatient visits, and hospitalization for pneumonia in the year prior to the study start date were independently associated with risk of all CAP (table 3) . A population-based study involving 4175 elderly persons in Finland found that crude CAP rates did not differ between men and women and that male sex was not significantly associated with CAP after accounting for age and certain chronic medical conditions and risk factors, including asthma, receipt of immunosuppressive therapy, and heart disease [21] . cache = ./cache/cord-335691-lsuwsm43.txt txt = ./txt/cord-335691-lsuwsm43.txt === reduce.pl bib === id = cord-331465-humpwwk2 author = Canaday, David H title = On setting expectations for a SARS-CoV-2 Vaccine date = 2020-06-04 pages = extension = .txt mime = text/plain words = 997 sentences = 67 flesch = 45 summary = Therefore, the expectation that a SARS-CoV-2 vaccine can develop this level of protection from an immune naive state, especially in the setting of immunizing elderly individuals whose naive B and T cells are substantially diminished, needs to be set with caution. Data from several influenza studies suggest that increased CMI, specifically including both CD4+ and CD8+ T cells, helps mitigate influenza severity in older adults when infected despite vaccination [6] [7] [8] . We should expect all of the existing clinical trial candidates to have incomplete effectiveness, and we need to establish whether those that ineffectively recruit CMI have inferior disease mitigation when COVID-19 develops despite vaccination. Logically, none of the current clinical trials use a live attenuated vaccine, as we simply do not know enough about SARS-CoV-2 virology to safely put forward such a candidate. mRNA vaccines against H10N8 and H7N9 influenza viruses of pandemic potential are immunogenic and well tolerated in healthy adults in phase 1 randomized clinical trials cache = ./cache/cord-331465-humpwwk2.txt txt = ./txt/cord-331465-humpwwk2.txt === reduce.pl bib === id = cord-331731-c2r0kfaz author = Anugwom, Chimaobi M title = Inverse association between chronic hepatitis B infection and COVID-19: immune-exhaustion or coincidence? date = 2020-06-05 pages = extension = .txt mime = text/plain words = 711 sentences = 64 flesch = 58 summary = M a n u s c r i p t Dear Editor, We read with great interest the report by Zhao et al, regarding a case of delayed immune response to SARS-CoV-2 in a patient with HIV and HCV co-infection [1] . It is unclear whether this is a simple epidemiological "misconnection" or if being chronically infected with HBV impacts the chances of clinically significant infection with SARS-CoV-2 leading to less hospital admissions, in a similar fashion as that reported by Zhao et al to HIV and HCV. Early virus clearance and delayed antibody response in a case of COVID-19 with a history of co-infection with HIV-1 and HCV Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series cache = ./cache/cord-331731-c2r0kfaz.txt txt = ./txt/cord-331731-c2r0kfaz.txt === reduce.pl bib === id = cord-326297-0r9pex1o author = Hartmann, Stacy title = Coronavirus 2019 (COVID-19) Infections Among Healthcare Workers, Los Angeles County, February - May 2020 date = 2020-08-17 pages = extension = .txt mime = text/plain words = 2195 sentences = 144 flesch = 62 summary = The Los Angeles County Department of Public Health (LAC DPH) set out to understand the impact of COVID-19 on healthcare facilities and HCWs by tracking and analyzing data from case-patient interviews of HCWs. As of May 31st, over three months into the pandemic, nearly 5,500 positive HCWs were reported to LAC DPH, representing 9.6% of all cases. All LAC residents who test positive for COVID-19 are interviewed by LAC DPH using a standardized form that identifies if the case-patient worked in a high-risk environment, such as a healthcare setting. From case-patient interviews and/or emailed reports, LAC DPH recorded occupational setting, occupational role, date of symptom onset, date last worked, known exposure, and if hospitalized for each HCW. At the end of April, HCWs represented 12.8% of all LAC cases, whereas only 9.6% at the end of May. When asked if they had a known exposure to COVID-19, (Table 3) , healthcare exposures within their facility accounted for nearly 44%, including contact with either a positive patient, co-worker, or both. cache = ./cache/cord-326297-0r9pex1o.txt txt = ./txt/cord-326297-0r9pex1o.txt === reduce.pl bib === id = cord-327862-zcg3baym author = Luo, Yiqi Ruben title = Kinetics of SARS-CoV-2 Antibody Avidity Maturation and Association with Disease Severity date = 2020-09-14 pages = extension = .txt mime = text/plain words = 1141 sentences = 93 flesch = 59 summary = The kinetics of IgG avidity maturation during SARS-CoV-2 infection was studied. It was found that there was a strong correlation between IgG avidity and days since symptom onset, and peak readings were significantly higher in severe than mild disease cases. 3, 4 Here we report the development of a method to characterize SARS-CoV-2 IgG avidity maturation in COVID-19 patients from initial diagnosis through convalescence. The IgG avidity assay was established on a novel label-free immunoassay platform Gator Analyzer (Gator Bio, Palo Alto, CA) to measure SARS-CoV-2 IgG avidity to the virus spike protein receptor-binding domain (RBD). The signal increase in the final step, which is proportional to the quantity of RBD-IgG-Anti-IgG immune complex on the sensing probe, was measured. As other isotypes of antibodies might bind to RBD in the second step, the measurement of the RBD-IgG-Anti-IgG immune complex enhanced the assay specificity. Magnitude and kinetics of anti-SARS-CoV-2 antibody responses and their relationship to disease severity cache = ./cache/cord-327862-zcg3baym.txt txt = ./txt/cord-327862-zcg3baym.txt === reduce.pl bib === id = cord-336563-hwemigk7 author = Bhimraj, Adarsh title = Infectious Diseases Society of America Guidelines on the Treatment and Management of Patients with COVID-19 date = 2020-04-27 pages = extension = .txt mime = text/plain words = 8308 sentences = 448 flesch = 42 summary = Given the rapidity of emerging literature, IDSA identified the need to develop living, frequently updated evidence-based guidelines to support patients, clinicians and other health-care professionals in their decisions about treatment and management of patients with COVID-19. Two RCTs of patients with confirmed COVID-19 with mild pneumonia (e.g., positive CT scan without oxygen requirement) or non-severe infection admitted to the hospital treated with hydroxychloroquine (HCQ) reported on mortality at 14 days, clinical progression (radiological progression on CT scan), clinical improvement, failure of virologic clearance (PCR), and adverse events (both) [11, 12] (Table 1 ). In addition, we identified four publications describing three trials of combination treatment with HCQ plus azithromycin (AZ) among hospitalized patients with COVID-19 reporting on the outcomes of mortality, failure of virologic clearance (assessed with PCR test), and adverse events (i.e., significant QT prolongation leading to treatment discontinuation) [13] [14] [15] [16] (Table 2) . cache = ./cache/cord-336563-hwemigk7.txt txt = ./txt/cord-336563-hwemigk7.txt === reduce.pl bib === id = cord-338899-qt17jhg0 author = Lakshmi, Vemu title = Clinical Features and Molecular Diagnosis of Chikungunya Fever from South India date = 2008-05-01 pages = extension = .txt mime = text/plain words = 3623 sentences = 178 flesch = 48 summary = Emergence or reemergence of severe arboviral hemorrhagic fevers caused by mosquitoborne viruses, such as dengue virus and Chikungunya (CHIK) virus, have been frequently reported in the Indian subcontinent in the past few years. We report clinical observations and laboratory investigations involving virus isolation methods and molecular assays performed for 296 clinically suspected cases of CHIK fever. Of particular interest was the applicability of a novel method of gene amplificatio called real-time loop-mediated isothermal amplifica tion (RT-LAMP) as a rapid, sensitive, and specifi real-time method to detect and quantify CHIK virus in the acute phase of the infection. All 132 patients who had clinically suspected CHIK virus but whose RT-PCR and RT-LAMP results were negative presented 17 days after the onset of fever; this may be the reason for the negative test results. The RT-LAMP allows rapid, realtime detection of CHIK virus in acute-phase serum samples, without requiring sophisticated equipment, and has potential usefulness for clinical diagnosis and surveillance of CHIK virus in developing countries. cache = ./cache/cord-338899-qt17jhg0.txt txt = ./txt/cord-338899-qt17jhg0.txt === reduce.pl bib === id = cord-330742-m5xx8861 author = Qian, Jie title = Age-dependent gender differences of COVID-19 in mainland China: comparative study date = 2020-05-30 pages = extension = .txt mime = text/plain words = 3535 sentences = 214 flesch = 61 summary = METHODS: We used the national surveillance database of COVID-19 in mainland China to compared gender differences in attack rate (AR), proportion of severe and critical cases (PSCC) and case fatality rate (CFR) in relation to age, affected province, and onset-to-diagnosis interval. After adjusting for age, affected province and onset-to-diagnosis interval, the female-to-male difference in AR, PSCC and CFR remained significant in multivariate logistic regression analyses. In this study, we used the surveillance data containing all confirmed cases in mainland China as of April 28, 2020 to evaluated gender-specific differences in attack rate, proportion of severe and critical cases, and case fatality in relation to age, affected province and onset-to-diagnosis interval, in order to provide evidence-based guidance for more effective and equitable interventions and treatments. cache = ./cache/cord-330742-m5xx8861.txt txt = ./txt/cord-330742-m5xx8861.txt === reduce.pl bib === id = cord-337972-otfloo64 author = Kao, Shang Jyh title = Mechanism of Fulminant Pulmonary Edema Caused by Enterovirus 71 date = 2004-06-15 pages = extension = .txt mime = text/plain words = 1949 sentences = 135 flesch = 53 summary = Destruction of the medial, ventral, and caudal medulla may lead to sympathetic overactivation, causing blood to shift to the lungs. Destruction of the medial, ventral, and caudal medulla may lead to sympathetic overactivation, causing blood to shift to the lungs. Central sympathetic activation resulting in systemic vasoconstriction and the shift of blood volume to the pulmonary region of the circulatory system, as demonstrated in earlier findings from our laboratory, was used to explain centrogenic PE [2, 3] . In the present study, we report CNS lesions in patients associated with PE due to enterovirus infection. The present study also supports the contention that hyperglycemia, leukocytosis, and elevated protein levels in CSF are risk factors for the development of ARDS due to enterovirus infection [1, 2] . In this connection, we found that endogenous and exogenous nitric oxide reduced pulmonary hypertension but increased the capillary filtration coefficient and the extent of injury in an isolated rat's lung that was subjected to ischemia and reperfusion [16] . cache = ./cache/cord-337972-otfloo64.txt txt = ./txt/cord-337972-otfloo64.txt === reduce.pl bib === id = cord-339859-anatn295 author = Paret, Michal title = SARS-CoV-2 infection (COVID-19) in febrile infants without respiratory distress date = 2020-04-17 pages = extension = .txt mime = text/plain words = 1286 sentences = 105 flesch = 59 summary = title: SARS-CoV-2 infection (COVID-19) in febrile infants without respiratory distress We report two cases of SARS-CoV-2 infection (COVID-19) in infants presenting with fever in the absence of respiratory distress who required hospitalization for evaluation of possible invasive bacterial infections. The diagnoses resulted from routine isolation and real-time RT-PCR-based testing for SARS-CoV-2 for febrile infants in an outbreak setting. [2] [3] [4] Even in the setting of asymptomatic or mildly symptomatic infection, children may represent a source of SARS-CoV-2 spread in community or hospital settings, so understanding the spectrum of COVID-19 illness in infants, particularly regarding conditions that result in hospitalization, is crucial to establishment of effective infection control interventions. Vital signs and pertinent laboratory findings appear in the A real-time RT-PCR assay performed at the New York State Department of Health detected SARS-CoV-2 RNA in the patient's NP sample. cache = ./cache/cord-339859-anatn295.txt txt = ./txt/cord-339859-anatn295.txt === reduce.pl bib === id = cord-335907-93gwmo0v author = de Man, Peter title = Outbreak of COVID-19 in a nursing home associated with aerosol transmission as a result of inadequate ventilation date = 2020-08-28 pages = extension = .txt mime = text/plain words = 564 sentences = 57 flesch = 73 summary = title: Outbreak of COVID-19 in a nursing home associated with aerosol transmission as a result of inadequate ventilation Recently, we were involved in an outbreak in a Dutch nursing home that was likely to be the result of aerosol transmission in a setting of inadequate ventilation. In total, 17 (81%) residents from one of the seven wards in a nursing home with psychogeriatric residents were diagnosed with COVID-19 as confirmed by RT-PCR ( Figure 1 ) [2] . To prevent and control COVID-19 infections all HCWs in this nursing home had been assigned to specific wards and did wear surgical masks during patient contacts since April 26, 2020 [4] . Because of the remarkable increase of COVID-19 infections in a very short time period despite the use of surgical masks, the ventilation system of the outbreak ward was investigated in addition to routine source and contact tracing. In this situation, low CO2 production by inactive nursing home patients might have limited the ventilation with outside air. cache = ./cache/cord-335907-93gwmo0v.txt txt = ./txt/cord-335907-93gwmo0v.txt === reduce.pl bib === id = cord-340678-2e2s1gof author = Skowronski, Danuta M title = Influenza vaccine does not increase the risk of coronavirus or other non-influenza respiratory viruses: retrospective analysis from Canada, 2010-11 to 2016-17 date = 2020-05-22 pages = extension = .txt mime = text/plain words = 1646 sentences = 113 flesch = 45 summary = Influenza vaccine effectiveness against influenza and non-influenza respiratory viruses (NIRV) was assessed by test-negative design using historic datasets of the community-based Canadian Sentinel Practitioner Surveillance Network (SPSN), spanning 2010-11 to 2016-17. Here, we use historic datasets of the community-based Canadian Sentinel Practitioner Surveillance Network (SPSN) to assess the association between influenza vaccine and NIRV risk, notably seasonal coronaviruses. Conversely, influenza vaccine had no effect on non-influenza causes of ILI, with the likelihood of vaccination among NIRV cases relative to test-negative controls approaching unity. In combined NIRV analysis, relative to pan-negative controls, Wolff adjusted for age and excluded specimens that tested influenza-positive. We illustrate the impact of this bias in Supplementary_Material_3, where we have re-analyzed Wolff's data as well as our own, comparing influenza vaccine effect against NIRV when influenza testpositive specimens are properly excluded (as per TND prerequisite) or improperly included (as per Wolff [4] ) within the control group. cache = ./cache/cord-340678-2e2s1gof.txt txt = ./txt/cord-340678-2e2s1gof.txt === reduce.pl bib === id = cord-335767-omm04fg5 author = Raabe, Vanessa N title = Importance of Pediatric Inclusion in COVID-19 Therapeutic Trials date = 2020-05-27 pages = extension = .txt mime = text/plain words = 1468 sentences = 57 flesch = 32 summary = Not only do children and the medical community lose out on opportunities to gain the highest level of clinical evidence for efficacy in a vulnerable population, but due to the lack of availability of pediatric trials, many children hospitalized for COVID-19 are receiving off-label use of therapeutic agents with unproven benefit against COVID-19. In addition to offering enhanced safety monitoring, enrollment of children in clinical trials ensures that parents and older children are fully informed of the potential risks and benefits associated with use of the therapeutic agent, a conversation often omitted when medications are prescribed off-label. Inclusion of children in these clinical trials is feasible under current regulations, provides direct benefit to pediatric trial participants from a safety perspective compared to off-label prescribing, and provides systematic collection of the highest quality of evidence for COVID-19 therapeutics in a vulnerable population where SARS-CoV-2 infection behaves differently from adults. cache = ./cache/cord-335767-omm04fg5.txt txt = ./txt/cord-335767-omm04fg5.txt === reduce.pl bib === id = cord-333943-9d93na7s author = Jeong, Han Eol title = Association between NSAIDs use and adverse clinical outcomes among adults hospitalized with COVID-19 in South Korea: A nationwide study date = 2020-07-27 pages = extension = .txt mime = text/plain words = 3387 sentences = 218 flesch = 47 summary = title: Association between NSAIDs use and adverse clinical outcomes among adults hospitalized with COVID-19 in South Korea: A nationwide study BACKGROUND: Non-steroidal anti-inflammatory drugs (NSAIDs) may exacerbate COVID-19 and worsen associated outcomes by upregulating the enzyme that SARS-CoV-2 binds to enter cells. [1, 2] Concerns exist that the use of nonsteroidal anti-inflammatory drugs (NSAIDs) may exacerbate COVID-19 by upregulating angiotensin-converting enzyme 2 (ACE2) expressions, [3, 4] the enzyme which SARS-CoV-2 binds to enter cells. This cohort study therefore aimed to examine the association between NSAIDs use, compared to non-use, and worsened clinical outcomes among adults hospitalized with A c c e p t e d M a n u s c r i p t page | 5 COVID-19 using South Korea's nationwide healthcare database containing all COVID-19 patients. To our knowledge, this is the first population-based study conducted using all hospitalized patients with COVID-19 to assess the association between NSAID use and COVID-19 related outcomes. cache = ./cache/cord-333943-9d93na7s.txt txt = ./txt/cord-333943-9d93na7s.txt === reduce.pl bib === id = cord-339004-49dkucxd author = Yu, Ignatius Tak-Sun title = Severe Acute Respiratory Syndrome Beyond Amoy Gardens: Completing the Incomplete Legacy date = 2014-03-01 pages = extension = .txt mime = text/plain words = 1772 sentences = 78 flesch = 55 summary = The temporal and spatial distributions of the 2003 severe acute respiratory syndrome (SARS) outbreak in Amoy Gardens of Hong Kong was reexamined using all confirmed cases. The temporal and spatial distributions of the 2003 severe acute respiratorysyndrome (SARS) outbreak in Amoy Gardens of Hong Kong was reexamined using all confirmed cases. In 2004, we analyzed the temporal and spatial distributions of the initial 187 cases in 7 blocks (A-G) of Amoy Gardens, a residential building complex with 19 buildings, where the largest community outbreak of SARS took place. Considering that cases in Telford Gardens and Tak Bo Garden with symptom onset during 24-29 March were most likely resulting from the common source originating in block E of Amoy Gardens, the distance of airborne transmission in that outbreak could be >200 m. In conclusion, the airborne spread in the largest community outbreak of SARS in 2003 actually extended beyond the Amoy Gardens and affected residential buildings >200 m from the source. cache = ./cache/cord-339004-49dkucxd.txt txt = ./txt/cord-339004-49dkucxd.txt === reduce.pl bib === id = cord-340956-1t3o24u5 author = Borkenhagen, Laura K title = High Risk of Influenza Virus Infection Among Swine Workers: Examining a Dynamic Cohort in China date = 2019-09-01 pages = extension = .txt mime = text/plain words = 4184 sentences = 179 flesch = 50 summary = Despite elevated titers, among the 187 study subjects for whom we had complete follow-up, participants working at swine CAFOs had significantly greater odds of seroconverting against both the swine H1N1 (odds ratio [OR] 19.16, 95% confidence interval [CI] 3.55–358.65) and swine H3N2 (OR 2.97, 95% CI 1.16–8.01) viruses, compared to unexposed and non-CAFO swine workers with less intense swine exposure. Conversely, higher odds of seroconversion against swine H3N2 virus were observed among the unexposed (OR 2.27, 95% CI 1.43-3.60) and CAFO-exposed (OR 1.98, 95% CI 1.11-3.42), when compared to the non-CAFO swine workers; the unexposed participants had higher geometric mean MN titers, compared to the other 2 groups, for all time points (Table 3) . In this report, we present the first 24 months of data from a 5-year prospective, cohort study of IAV among participants exposed and unexposed to swine in China. cache = ./cache/cord-340956-1t3o24u5.txt txt = ./txt/cord-340956-1t3o24u5.txt === reduce.pl bib === id = cord-340317-gwqy6u9x author = Dora, Amy V title = Using Serologic Testing to Assess the Effectiveness of Outbreak Control Efforts, Serial PCR Testing, and Cohorting of Positive SARS-CoV-2 Patients in a Skilled Nursing Facility date = 2020-08-28 pages = extension = .txt mime = text/plain words = 1598 sentences = 109 flesch = 55 summary = title: Using Serologic Testing to Assess the Effectiveness of Outbreak Control Efforts, Serial PCR Testing, and Cohorting of Positive SARS-CoV-2 Patients in a Skilled Nursing Facility Despite numerous outbreaks, the performance of serologic testing for SARS-CoV-2 in residents of skilled nursing facilities (SNF) is not well described; its utility in epidemiologic sero-surveillance studies and outbreak reporting is under evaluation. As our objective was to identify potentially missed cases of COVID-19 during serial surveillance testing, samples from residents with historically negative SARS-CoV-2 RT-PCR tests with DiaSorin IgG-positive results were re-tested on a second serologic testing platform (Abbott SARS-CoV-2 IgG Immunoassay) for IgG antibody specific to SARS-CoV-2 nucleocapsid. In a cohort of 150 nursing home residents tested for SARS-CoV-2 infection by RT-PCR, including 26 previously diagnosed with COVID-19, the sensitivity of the DiaSorin assay was 92% (24/26) and the specificity was 98% (122/124). cache = ./cache/cord-340317-gwqy6u9x.txt txt = ./txt/cord-340317-gwqy6u9x.txt === reduce.pl bib === id = cord-341435-b36h69r1 author = Dawson, Patrick title = Loss of Taste and Smell as Distinguishing Symptoms of COVID-19 date = 2020-06-21 pages = extension = .txt mime = text/plain words = 1688 sentences = 104 flesch = 56 summary = In a household study, loss of taste and/or smell was the fourth most reported symptom (26/42; 62%) among COVID-19 case-patients and had the highest positive predictive value (83%; 95% CI: 55–95%) among household contacts. This investigation provided an opportunity to identify household COVID-19 cases and describe their symptom profiles, including loss of taste and smell, prior to diagnosis. Among the 64 household members of COVID-19 index cases, loss of taste and/or smell was reported by 12 individuals, of whom 10 were positive for SARS-CoV-2. The positive predictive value (PPV) of any loss of taste and/or smell (83%, 95% CI: 55-95%) was higher than for fever (subjective or measured) and cough, two of the three classic symptoms, and equal to the third, shortness of breath (83%, 95% CI: 44-97%) ( Table 1 ). In the absence of confirmatory laboratory testing, CSTE criteria for a probable COVID-19 case now include loss of taste and/or smell in conjunction with other non-classic symptoms (3). cache = ./cache/cord-341435-b36h69r1.txt txt = ./txt/cord-341435-b36h69r1.txt === reduce.pl bib === id = cord-340579-cvze15cj author = Dudley, Joseph P title = Disparities in Age-Specific Morbidity and Mortality from SARS-CoV-2 in China and the Republic of Korea date = 2020-03-31 pages = extension = .txt mime = text/plain words = 1430 sentences = 74 flesch = 46 summary = There is a need to gain greater understanding of the highest risk populations for infection and serious disease from the SARS-CoV-2 virus to support the development and implementation of effective public health surveillance and mitigation efforts, and minimize the adverse effects of the current COVID-19 Pandemic in countries worldwide [1] . The reported data on confirmed cases and fatalities from the SARS-CoV-2 indicate highly significant The available epidemiological and observational data from the ROK suggests that reduced rates of compliance with social distancing and self-quarantine recommendations among different sectors of the population -especially the younger adult and juvenile age cohorts --may have a significant impact on the age-specific rates of morbidity and mortality within the population as a whole. Comparison of Age-Specific Morbidity and Mortality Rates Among Reported Confirmed Cases from China and Republic of Korea Figure 1 cache = ./cache/cord-340579-cvze15cj.txt txt = ./txt/cord-340579-cvze15cj.txt === reduce.pl bib === id = cord-343827-jo61t3m0 author = Qian, Qun title = Direct evidence of active SARS-CoV-2 replication in the intestine date = 2020-07-08 pages = extension = .txt mime = text/plain words = 1314 sentences = 98 flesch = 53 summary = We investigated the presence of virions and pathological changes in surgical rectal tissues of a clinically confirmed COVID-19 patient with rectal adenocarcinoma. RNA of SARS-CoV-2 was detected in surgically resected rectal specimens, but not in samples collected on 37 day after discharge. Notably, coincidence with rectal tissues of surgical specimens tested nucleic acid positive for SARS-CoV-2, typical coronavirus virions in rectal tissue were observed under electron microscopy. Notably, fecal samples remained positive for SARS-CoV-2 RNA nearly 5 weeks after the viral clearance from the upper respiratory tract in COVID-19 patients [8] . To clarify the above questions, we performed a retrospective study to detect the presence of SARS-CoV-2 virions and determine the pathological changes in rectal tissues of this patient. Samples of rectal tissues, succus entericus and intestinal mucosa of ileostomy, and rectal mucosa were tested for SARS-CoV-2 nucleic acid using qRT-PCR. cache = ./cache/cord-343827-jo61t3m0.txt txt = ./txt/cord-343827-jo61t3m0.txt === reduce.pl bib === id = cord-345045-nlui9d6e author = Zahn, Matthew title = Infectious Diseases Physicians: Improving and Protecting the Public’s Health: Why Equitable Compensation Is Critical date = 2019-07-15 pages = extension = .txt mime = text/plain words = 3570 sentences = 170 flesch = 37 summary = Unfortunately, much of this work is undercompensated despite the proven efficacy of public health interventions such as hospital acquired infection prevention, antimicrobial stewardship, disease surveillance, and outbreak response. Here, we examine compensation data for ID physicians compared to their value in population and public health settings and suggest policy recommendations to address the pay disparities that exist between cognitive and procedural specialties that prevent more medical students and residents from entering the field. In 2015, 8515 ID physicians were practicing in the United States [5] , often combining clinical care with work as educators, epidemiologists, public health leaders, antimicrobial stewardship or infection prevention and control directors, researchers, administrators, and policymakers. Further, the work of ID physicians provides broader public protection against infectious threats through community and healthcare facility-based infection control and prevention activities, surveillance, outbreak response, and other public health activities. cache = ./cache/cord-345045-nlui9d6e.txt txt = ./txt/cord-345045-nlui9d6e.txt === reduce.pl bib === id = cord-348036-yub2cqz6 author = Lighter, Jennifer title = Obesity in patients younger than 60 years is a risk factor for Covid-19 hospital admission date = 2020-04-09 pages = extension = .txt mime = text/plain words = 722 sentences = 62 flesch = 69 summary = title: Obesity in patients younger than 60 years is a risk factor for Covid-19 hospital admission Covid-19 disease, caused by SARS-CoV-2 infection includes a spectrum of illness; from asymptomatic infection [2] to severe pneumonia characterized by acute respiratory injury in about 20% of patients presenting to medical care [3] . A c c e p t e d M a n u s c r i p t years were 2.2 (95% CI 1.7-2.9, p<.0001) and 3.6 (95% CI 2.5-5.3, p=<.0001) times more likely to be admitted to acute and critical care compared to patients in the same age category who had BMI <30. Though patients aged <60 years are generally considered a lower risk group of Covid-19 disease severity, based on data from our institution, obesity appears to be a previously unrecognized risk factor for hospital admission and need for critical care. cache = ./cache/cord-348036-yub2cqz6.txt txt = ./txt/cord-348036-yub2cqz6.txt === reduce.pl bib === id = cord-341838-lkz8ro90 author = Gervasoni, Cristina title = Clinical features and outcomes of HIV patients with coronavirus disease 2019 date = 2020-05-14 pages = extension = .txt mime = text/plain words = 1794 sentences = 117 flesch = 59 summary = The aim of this retrospective study was to describe the clinical characteristics and outcomes of HIVinfected patients with a probable/proven diagnosis of SARS-CoV-2 infection who have been regularly followed up by our hospital. As in the general population, the large majority of our patients were males, but their mean age was nearly 10 years lower than that observed in HIV-negative COVID-19 patients. 16 Furthermore, the findings of this study document favourable outcomes in HIV patients treated mainly with integrase inhibitors (11% protease inhibitors), which apparently indicates that antiretroviral therapy does not play a key role, A c c e p t e d M a n u s c r i p t 8 although a potentially protective effect of tenofovir cannot be ruled out given its recently reported effect against SARS-CoV-2 RNA-dependent RNA polymerase. In conclusion, our findings suggest that HIV-positive patients with SARS-CoV-2 infection are not at greater risk of severe disease or death than HIV-negative patients. cache = ./cache/cord-341838-lkz8ro90.txt txt = ./txt/cord-341838-lkz8ro90.txt === reduce.pl bib === id = cord-341359-c34gyuv6 author = Larson, Derek T title = Clinical Outcomes of Coronavirus Disease 2019 With Evidence-based Supportive Care date = 2020-05-30 pages = extension = .txt mime = text/plain words = 1203 sentences = 62 flesch = 42 summary = This retrospective study of an institutional cohort including 135 patients with confirmed COVID-19 demonstrates positive outcomes when organizational standards of care consist of evidence-based supportive therapies. Following widespread use of therapeutic agents with limited data to support their use, calls were made to focus on the evidence-based care that has been the foundation of modern medical therapy for most acute respiratory viral infections [7, 8] . Our study is the first report of COVID-19 outcomes when institutional standards of care consist solely of known evidence-based practices of supportive care. Of those diagnosed with COVID-19, 21 (15.6%) had severe enough disease to necessitate hospitalization and 6 (4.4%) required care in the ICU. Our study demonstrates favorable outcomes for patients with mild to moderately severe COVID-19 disease when evidence-based supportive care is considered the institutional standard. cache = ./cache/cord-341359-c34gyuv6.txt txt = ./txt/cord-341359-c34gyuv6.txt === reduce.pl bib === id = cord-344038-20n74z3o author = Han, Mi Seon title = Sequential analysis of viral load in a neonate and her mother infected with SARS-CoV-2 date = 2020-04-16 pages = extension = .txt mime = text/plain words = 1548 sentences = 110 flesch = 67 summary = In this study, we described the clinical manifestation of COVID-19 in a neonate and her mother, and further analyzed the viral load kinetics of SARS-CoV-2 in clinical specimens from different sources. The neonate was febrile and SARS-CoV-2 RNA was detected in all of her clinical specimens, with high viral loads in the respiratory and stool samples. Her mother had mild symptoms with SARS-CoV-2 RNA detected in the respiratory and stool specimens at low titers. An interesting finding in this study is that SARS-CoV-2 RNA was detected in all of the neonate's clinical specimens, including blood, urine, stool, and saliva along with the upper respiratory tract specimens. In comparison, although exposed to the same infection source, only the mother's respiratory and stool specimens were positive for SARS-CoV-2 and at a much lower viral load. Recent studies have reported that SARS-CoV-2 RNA could be detected in different types of clinical specimens other than respiratory tract samples [9] . cache = ./cache/cord-344038-20n74z3o.txt txt = ./txt/cord-344038-20n74z3o.txt === reduce.pl bib === id = cord-349070-bqv03u2e author = Jiang, Shih Sheng title = Sensitive and Quantitative Detection of Severe Acute Respiratory Syndrome Coronavirus Infection by Real-Time Nested Polymerase Chain Reaction date = 2004-01-15 pages = extension = .txt mime = text/plain words = 2465 sentences = 110 flesch = 51 summary = title: Sensitive and Quantitative Detection of Severe Acute Respiratory Syndrome Coronavirus Infection by Real-Time Nested Polymerase Chain Reaction In most of the cases, we and others have found that the single-step real time RT-PCR methods (as suggested by the World Health Organization [WHO] ; available at http://www.who.int/csr/sars/diagnostic tests/en/) could specifically detect SARS-CoV but were unable to proficiently detect !10 copies of virus per test, suggesting that the conventional RT-PCR assay may actually yield falsenegative results. In contrast, the second-round amplification by nested real-time PCR proficiently generated a signal of SARS-CoV DNA without apparent background, compared with no detectable signal for the negative control samples ( figure 1A ). After 25 cycles of first-round amplification and 25 cycles of nested PCR amplification, our assay could detect a theoretical single copy of extracted viral RNA (figure 1A), suggesting its superior sensitivity for detection of SARS-CoV. cache = ./cache/cord-349070-bqv03u2e.txt txt = ./txt/cord-349070-bqv03u2e.txt === reduce.pl bib === id = cord-348478-ho89o8mj author = Pawlotsky, Jean-Michel title = SARS-CoV-2 pandemic : Time to revive the cyclophilin inhibitor alisporivir date = 2020-05-15 pages = extension = .txt mime = text/plain words = 2100 sentences = 138 flesch = 48 summary = This Viewpoint summarizes the strong scientific arguments supporting the use of alisporivir, a non-immunosuppressive analogue of cyclosporine A with potent cyclophilin inhibition properties that has reached Phase 3 clinical development, for the treatment of COVID-19. They include the strong cyclophilin dependency of the lifecycle of many coronaviruses, including SARS-CoV and MERS-CoV, and preclinical data showing strong antiviral and cytoprotective properties of alisporivir in various models of coronavirus infection, including SARS-CoV-2. It has indeed been shown that the lifecycles of human coronaviruses 229E (HCoV-229E) and NL-63 (HCoV-NL63), responsible for mild respiratory infections in humans, of feline infectious peritonitis coronavirus (FPIV), responsible for a fatal disease in cats, and of SARS-CoV were highly dependent on cyclophilin A (and possibly also cyclophilin B for FPIV) [18] [19] [20] [21] [22] . Human coronavirus NL63 replication is cyclophilin A-dependent and inhibited by non-immunosuppressive cyclosporine Aderivatives including alisporivir Inhibition of SARS-CoV-2 infection by the cyclophilin inhibitor Alisporivir (Debio 025) cache = ./cache/cord-348478-ho89o8mj.txt txt = ./txt/cord-348478-ho89o8mj.txt === reduce.pl bib === id = cord-348350-pac9ha4q author = Martin-Blondel, G title = Hydroxychloroquine in COVID-19 patients: what still needs to be known about the kinetics date = 2020-05-11 pages = extension = .txt mime = text/plain words = 1824 sentences = 136 flesch = 59 summary = Different dosage regimens of hydroxychloroquine are used to manage COVID-19 patients, without information on the pharmacokinetics in this population.Blood samples (n=101) were collected from 57 COVID-19 patients for 7 days and concentrations were compared with simulated kinetic profiles.Hydroxychloroquine exposure is low and cannot be predicted by other populations. Because of the severity of COVID-19 and the pharmacokinetics of hydroxychloroquine in SLE patients [5] , a loading dose was rapidly included in the new hospital regimens to optimize drug distribution in tissues and more precisely in the lungs. For each regimen applied at the Toulouse University Hospital, an example of the expected kinetic profiles for a body weight of 80 kg (the median weight in our population) are presented in Figure 1 with the corresponding serum concentration for each patient. cache = ./cache/cord-348350-pac9ha4q.txt txt = ./txt/cord-348350-pac9ha4q.txt === reduce.pl bib === id = cord-348392-e35cd9sg author = Moraleda, Cinta title = Multi-Inflammatory Syndrome in Children related to SARS-CoV-2 in Spain date = 2020-07-25 pages = extension = .txt mime = text/plain words = 1759 sentences = 165 flesch = 66 summary = Some clusters of children with a multisystem inflammatory syndrome associated with SARS-CoV-2 infection (MIS-C) have been reported. MIS-C is a potentially severe condition that presents in children with recent SARS-CoV-2 infection. This is a case series of children with MIS-C associated with SARS-CoV-2 enrolled in the Epidemiological Study of COVID-19 in Children of the Spanish Society of Pediatrics (EPICO-AEP), from March 1 st to June 1 st, 2020. Inclusion criteria included positivity in real-time polymerase chain reaction (RT-PCR) positive, IgM or IgG in lateral-flow rapid test, ELISA or immuno chemiluminescence serology (see Table 1 ), or severe disease suggestive of MIS-C and recent household contact with a confirmed patient with COVID-19. In this registry, entry criteria was COVID-19 disease, differently from the previous reports that include patient without SARS-CoV-2 1,3 . MIS-C is a potentially severe condition that presents in some children after SARS-CoV-2 infection. cache = ./cache/cord-348392-e35cd9sg.txt txt = ./txt/cord-348392-e35cd9sg.txt === reduce.pl bib === id = cord-348178-6bjimde4 author = Li, Ling title = Biosafety Level 3 Laboratory for Autopsies of Patients with Severe Acute Respiratory Syndrome: Principles, Practices, and Prospects date = 2005-09-15 pages = extension = .txt mime = text/plain words = 3684 sentences = 205 flesch = 52 summary = title: Biosafety Level 3 Laboratory for Autopsies of Patients with Severe Acute Respiratory Syndrome: Principles, Practices, and Prospects A specially designed biosafety level 3 (BSL-3) autopsy laboratory was constructed and divided into a clean area, a semicontaminated area, a contaminated area, and 2 buffer zones. Our experience suggests that BSL-3 laboratory operating principles should be among the special requirements for performing autopsies of contaminated bodies and that they can safeguard the clinicians and the environment involved in these procedures. According to the guidelines of World Health Organization and the Centers for Disease Control and Prevention (CDC) in the United States, SARS-CoV fulfills the criteria for a biohazard group 3 pathogen. The biosafety of our BSL-3 autopsy laboratory has been ensured in 4 ways: through the design of the facility, use of PPE, decontamination, and administrative regulation. Interim laboratory biosafety guidelines for handling and processing specimens associated with severe acute respiratory syndrome (SARS) cache = ./cache/cord-348178-6bjimde4.txt txt = ./txt/cord-348178-6bjimde4.txt === reduce.pl bib === id = cord-348144-t0chpsuh author = Lucas, Alexander H. title = Carbohydrate Moieties as Vaccine Candidates date = 2005-09-01 pages = extension = .txt mime = text/plain words = 5556 sentences = 238 flesch = 29 summary = We discuss the cellular basis of carbohydrate immunity, newly identified glycotope processing pathways and recognition capabilities, and the synthetic and microarray technologies that are being developed that will permit new experimental approaches to carbohydrate vaccine development and the exploration of the interaction of the immune system with self and nonself glycans. It has long been known that bactericidal and/or opsonic antibodies directed against capsular polysaccharide (PS) glycotopes protect against invasive diseases caused by encapsulated bacteria, and, accordingly, vaccine development has focused on the elicitation of these antibody specificities. Purified microbial PS vaccines have been in use for 140 years, but they have proven to be variably immunogenic and variably efficacious in protecting susceptible populations against invasive meningococcal, pneumococcal, and Haemophilus influenzae type b (Hib) diseases [1, 2] . Significant variation in serotype-specific immunogenicity of the sevenvalent Streptococcus pneumoniae capsular polysaccharide-CRM197 conjugate vaccine occurs despite vigorous T cell help induced by the carrier protein cache = ./cache/cord-348144-t0chpsuh.txt txt = ./txt/cord-348144-t0chpsuh.txt === reduce.pl bib === id = cord-350338-lcsa06gm author = Wang, Kun title = Clinical and laboratory predictors of in-hospital mortality in patients with COVID-19: a cohort study in Wuhan, China date = 2020-05-03 pages = extension = .txt mime = text/plain words = 2469 sentences = 157 flesch = 51 summary = title: Clinical and laboratory predictors of in-hospital mortality in patients with COVID-19: a cohort study in Wuhan, China We then validated these models by randomly collecting COVID-19 patients in the Infection department of Union Hospital in Wuhan from January 1, 2020, to February 20, 2020. The laboratory model developed with age, high-sensitivity C-reactive protein (hsCRP), peripheral capillary oxygen saturation (SpO2), neutrophil and lymphocyte count, D-dimer, aspartate aminotransferase (AST) and glomerular filtration rate (GFR) had a significantly stronger discriminatory power than the clinical model (p=0.0157), with AUC of 0.98 (95% CI, 0.92-0.99); threshold, -2.998; sensitivity, 100.00%; specificity, 92.82% and NPV, 100.00%. We developed a clinical model and laboratory model for predicting the in-hospital mortality of COVID-19 patients, the AUCs (95% CI) were 0.88 (0.80, 0.95) and 0.98 (0.92, 0.99) in training cohort, and 0.83 (0.68, 0.93) and 0.88 (0.77, 0.95) in validation cohort, respectively. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China cache = ./cache/cord-350338-lcsa06gm.txt txt = ./txt/cord-350338-lcsa06gm.txt === reduce.pl bib === id = cord-349556-k312qkvh author = Roldán-Santiago, Ernesto title = SARS-CoV-2 spreads to lymph nodes and strongly expands CD4+ T(EMRA) cells in a patient with mild COVID-19 date = 2020-09-18 pages = extension = .txt mime = text/plain words = 1831 sentences = 148 flesch = 64 summary = title: SARS-CoV-2 spreads to lymph nodes and strongly expands CD4+ T(EMRA) cells in a patient with mild COVID-19 After a FNAP we demonstrate that SARS-CoV-2 is found in lymph nodes (LNs) even in mild disease along with a strong expansion of terminally differentiated effector memory CD4+T-cells , a cell population that is practically absent in LN. Naive or central memory cells, which are the two main CD4+ subsets that are usually detected in normal or reactive LN that are or are not infected by EBV (Fig. 1B) , switched almost completely to effector memory and especially to T EMRA T-cells (Fig. 1A) . The findings strongly suggest that the enlarged LN was a consequence of EBV rather than SARS-CoV-2 infection, but this co-infection was an excellent opportunity to assess the presence of coronavirus in LNs from patients with mild symptoms. This case suggests that virus reaches LNs , regardless of disease severity.The other relevant finding of this study is an unexpected expansion of CD4+ T EMRA in the patient's cervical LN. cache = ./cache/cord-349556-k312qkvh.txt txt = ./txt/cord-349556-k312qkvh.txt === reduce.pl bib === id = cord-350686-q2bu7o4i author = Bilder, Christopher R title = Pool size selection when testing for SARS-CoV-2 date = 2020-06-16 pages = extension = .txt mime = text/plain words = 539 sentences = 55 flesch = 71 summary = title: Pool size selection when testing for SARS-CoV-2 M a n u s c r i p t Dear Editor-Pooling samples has been proposed in multiple articles as an efficient way to test for SARS-CoV-2 [1] [2] [3] [4] . They concluded that "this pooling method can be applied immediately in current clinical testing laboratories." However, this research [1] and similar research of others [2] [3] missed answering a very important question: How does one choose the most efficient pool size relative to SARS-CoV-2 prevalence in samples? The efficiencies from pooling samples occur when pools test negative. For example, the most efficient pool size is four samples when prevalence is 10% (calculation to be discussed shortly). By changing the size to 32 samples in our example, only 3% of the pools will test negative. Pooling of samples for testing for SARS-CoV-2 in asymptomatic people cache = ./cache/cord-350686-q2bu7o4i.txt txt = ./txt/cord-350686-q2bu7o4i.txt === reduce.pl bib === id = cord-346502-x2b0ao3q author = Arabi, Yaseen M title = Ribavirin and Interferon Therapy for Critically Ill Patients With Middle East Respiratory Syndrome: A Multicenter Observational Study date = 2019-06-25 pages = extension = .txt mime = text/plain words = 4076 sentences = 188 flesch = 44 summary = BACKGROUND: The objective of this study was to evaluate the effect of ribavirin and recombinant interferon (RBV/rIFN) therapy on the outcomes of critically ill patients with Middle East respiratory syndrome (MERS), accounting for time-varying confounders. We evaluated the association of RBV/rIFN with 90-day mortality and MERS coronavirus (MERS-CoV) RNA clearance using marginal structural modeling to account for baseline and time-varying confounders. After adjusting for baseline and time-varying confounders using a marginal structural model, RBV/rIFN was not associated with changes in 90-day mortality (adjusted odds ratio, 1.03 [95% confidence interval {CI}, .73–1.44]; P = .87) or with more rapid MERS-CoV RNA clearance (adjusted hazard ratio, 0.65 [95% CI, .30–1.44]; P = .29). The objective of this study was to examine the effect of RBV/ rIFN therapy in a large cohort of critically ill patients with MERS on the 90-day mortality and MERS-CoV RNA clearance by accounting for baseline and time-varying confounders. cache = ./cache/cord-346502-x2b0ao3q.txt txt = ./txt/cord-346502-x2b0ao3q.txt === reduce.pl bib === id = cord-352837-a29d5dkv author = Hirsch, Hans H title = Spatiotemporal Virus Surveillance for Severe Acute Respiratory Infections in Resource-limited Settings: How Deep Need We Go? date = 2019-04-01 pages = extension = .txt mime = text/plain words = 1993 sentences = 79 flesch = 36 summary = Given the technical and bioinformatic advances as well as the declining laboratory costs, the application of deep sequencing to identify etiologic agents in clinical samples has been approached in different pathologies, including those caused by community-acquired respiratory viruses (CARVs). With these caveats in mind, and given the significant global burden of viral respiratory tract disease in the very young and the very old [10] [11] [12] oropharyngeal (NP/OP) samples of SARI cases were identified through a national surveillance study conducted by the Uganda Virus Research Institute from 2010 through 2015. Taken together, this report from resource-limiting settings is also of relevance for resource-rich countries and raises the question about how to best expand current first-or second-line testing for respiratory viral pathogens including CMV, parvovirus B19, and measles, and how to move to more deep sequencing virome analysis and comprehensive metagenomics in the near future. cache = ./cache/cord-352837-a29d5dkv.txt txt = ./txt/cord-352837-a29d5dkv.txt === reduce.pl bib === id = cord-351231-aoz5jbf1 author = Bartlett, John G. title = Why Infectious Diseases date = 2014-09-15 pages = extension = .txt mime = text/plain words = 5505 sentences = 276 flesch = 43 summary = The value of the infectious disease practitioner is now magnified by the crisis of antibiotic resistance, the expanding consequences of international travel, the introduction of completely new pathogen diagnostics, and healthcare reform with emphasis on infection prevention and cost in dollars and lives. The point is that epidemics are the domain of infectious diseases and public health, with the expectation for management or prevention of outbreaks with requirements for detection, reporting, isolation, and case management. This began with a patient transferred from a New York City hospital with a KPC infection and became the source of an institutional outbreak that required extraordinary efforts to control, including a wall constructed to isolate cases, removal of plumbing (as a possible source), use of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) molecular diagnostics to detect cases and carriers, hydrogen peroxide room aerosols, and "whole house" surveillance cultures. The new healthcare system should value infectious disease expertise based on its important role in addressing resistance and costs associated with nosocomial infections. cache = ./cache/cord-351231-aoz5jbf1.txt txt = ./txt/cord-351231-aoz5jbf1.txt === reduce.pl bib === id = cord-351348-lzo0dz7z author = Gu, Silan title = Alterations of the Gut Microbiota in Patients with COVID-19 or H1N1 Influenza date = 2020-06-04 pages = extension = .txt mime = text/plain words = 1994 sentences = 147 flesch = 50 summary = METHODS: We conducted a cross-sectional study of 30 COVID-19 patients, 24 influenza A (H1N1) patients, and 30 matched healthy controls (HC) to identify differences in the gut microbiota by 16S ribosomal RNA (rRNA) gene V3-V4 region sequencing. Previous studies indicated that the intestinal flora was closely related to respiratory virus infection and could affect the occurrence and development of diseases through the gut-lung axis [13] . The analysis of group similarities indicated that differences in richness, diversity, A c c e p t e d M a n u s c r i p t and structure of the gut microbiota were not significantly different between general and severe COVID-19 patients (ANOSIM, p=0.426; Supplementary Figure S1 ), indicating that the experimental design was adequate. The gut microbiota signature of COVID-19 and H1N1 patients was analyzed to assess correlations between disease characteristics and the microbiome. cache = ./cache/cord-351348-lzo0dz7z.txt txt = ./txt/cord-351348-lzo0dz7z.txt === reduce.pl bib === id = cord-351314-atsuh8e2 author = Bryson-Cahn, Chloe title = A Novel Approach for a Novel Pathogen: using a home assessment team to evaluate patients for 2019 novel coronavirus (SARS-CoV-2) date = 2020-03-12 pages = extension = .txt mime = text/plain words = 1255 sentences = 67 flesch = 45 summary = Safe evaluation of persons for suspected infection with a special pathogen (including SARS-CoV-2) in the traditional healthcare environment is costly and resource intensive. It requires specialized rooms, use of personal protective equipment (PPE), monitored donning and doffing, logistically-complicated patient transportation from the community to the healthcare facility and back (typically through emergency medical services), and appropriate decontamination of transport and hospital environments. 4 The patient is evaluated by the physician, who gathers a focused history and All involved HAT members complete a daily log including temperature and respiratory and gastrointestinal symptom reporting through employee health for 14 days or until SARS-CoV-2 testing returns negative from the index visit. This model benefits both the public health and clinical healthcare systems by increasing safety and efficiency while reducing the costs and complexity of SARS-CoV-2 testing for patients who do not require emergency evaluation or hospitalization. cache = ./cache/cord-351314-atsuh8e2.txt txt = ./txt/cord-351314-atsuh8e2.txt === reduce.pl bib === id = cord-349566-zx9kt144 author = de Alencar, Julio Cesar Garcia title = Double-blind, randomized, placebo-controlled trial with N-acetylcysteine for treatment of severe acute respiratory syndrome caused by COVID-19 date = 2020-09-23 pages = extension = .txt mime = text/plain words = 2957 sentences = 213 flesch = 55 summary = title: Double-blind, randomized, placebo-controlled trial with N-acetylcysteine for treatment of severe acute respiratory syndrome caused by COVID-19 There is still no robust experimental confirmation for this fact; however, increased serum AngII levels have been reported in patients with severe Covid-19 cases [7] and enhanced expression of ACE2 in adults, compared to children, has been advocated to cause the difference of disease prevalence in these age ranges [8] . Therefore, we designed a double-blind, placebo-controlled, randomized clinical trial to determine whether NAC (in doses used to treat acute liver failure), is able to protect alveolar cells and avoid respiratory failure in patients with severe acute respiratory syndrome caused by (confirmed or suspect) Covid-19. This is a double-blind, randomized, placebo-controlled trial to assess the effectiveness and safety of intravenous NAC to prevent respiratory failure in patients with confirmed or suspect severe Covid-19. cache = ./cache/cord-349566-zx9kt144.txt txt = ./txt/cord-349566-zx9kt144.txt === reduce.pl bib === id = cord-351589-32kd9vva author = Mang, Sebastian title = Pneumocystis Jirovecii Pneumonia and SARS-CoV-2 Co-Infection in newly diagnosed HIV-1 infection date = 2020-07-01 pages = extension = .txt mime = text/plain words = 561 sentences = 58 flesch = 60 summary = title: Pneumocystis Jirovecii Pneumonia and SARS-CoV-2 Co-Infection in newly diagnosed HIV-1 infection We report the case of a 52-year-old male from our intensive care unit (ICU) who developed acute respiratory failure due to Covid-19, Pneumocystis jirovecii Pneumonia (PJP) and newly diagnosed HIV, stage 3 [2] . He deteriorated further despite escalated pressure-controlled invasive ventilation and was finally transferred to our intensive care unit on 13 th May, 2020, for possible initiation of extracorporeal membrane oxygenation (ECMO). As a potential sign for subacute manifestation, airway changes, pleural changes, fibrosis, and nodules were present (Figure 1 Over the next two weeks, his state improved significantly. Why Aren't People Living with HIV at Higher Risk for Developing Severe Coronavirus Disease 2019 (COVID-19) Radiological findings from 81 patients with COVID-19 pneumonia in Wuhan, China: a descriptive study. Coronavirus Disease 2019 (COVID-19) CT Findings: A Systematic Review and Meta-analysis cache = ./cache/cord-351589-32kd9vva.txt txt = ./txt/cord-351589-32kd9vva.txt === reduce.pl bib === id = cord-352899-bt2xg0ha author = Van Kerkhove, Maria D. title = Interpreting Results From Environmental Contamination Studies of Middle East Respiratory Syndrome Coronavirus date = 2016-10-15 pages = extension = .txt mime = text/plain words = 804 sentences = 41 flesch = 44 summary = authors: Van Kerkhove, Maria D.; Peiris, Malik J. Researchers in Korea have recently published studies [4, 5] evaluating environmental and/or air contamination by MERS-CoV and should be commended for their efforts to evaluate the hospital outbreaks in their country. To fully understand the possible role of environmental contamination, including the possible detection of MERS-CoV in the air, additional studies must be conducted to see whether these results can be replicatedfor example, in hospitals in the Middle East where patients with MERS-CoV are treated, to evaluate virus persistence in hospital environments. A more complete understanding of the results of environmental and air contamination studies will have important implications for the application of infection prevention and control measures [8] currently used in hospitals treating patients with MERS-CoV, possibly leading to more detailed recommendations. Environmental contamination and viral shedding in MERS patients during MERS-CoV outbreak in South Korea Middle East respiratory syndrome coronavirus (MERS-CoV) cache = ./cache/cord-352899-bt2xg0ha.txt txt = ./txt/cord-352899-bt2xg0ha.txt === reduce.pl bib === id = cord-350972-0n4dumgg author = Sing, Chor-Wing title = Long-term outcome of short-course high-dose glucocorticoids for SARS: a 17-year follow-up in SARS survivors date = 2020-07-16 pages = extension = .txt mime = text/plain words = 1789 sentences = 143 flesch = 59 summary = title: Long-term outcome of short-course high-dose glucocorticoids for SARS: a 17-year follow-up in SARS survivors Results showed that high-dose glucocorticoids greatly increased long-term risk of avascular necrosis, but not other major diseases. Hong Kong had an outbreak of severe acute respiratory syndrome (SARS; caused by SARS-CoV-1) in 2003, resulting in 1,755 cases and 299 deaths 3 Short course of very-high-dose (VHD) glucocorticoids was used for the treatment of SARS, especially to prevent cytokine storm. To understand the long-term consequences of VHD glucocorticoids, we studied the clinical outcomes of SARS survivors after 17 years. We identified SARS survivors using an electronic medical record database, Clinical Data Analysis and Reporting System (CDARS) of the Hong Kong Hospital Authority, the details of which have been described elsewhere. In this retrospective study of SARS survivors with 17 years of follow-up, a short-course use of VHD glucocorticoids was not associated with major diseases except AVN. cache = ./cache/cord-350972-0n4dumgg.txt txt = ./txt/cord-350972-0n4dumgg.txt === reduce.pl bib === id = cord-354265-udt2spoe author = Gersh, Felice title = Menopause status and COVID-19 date = 2020-09-23 pages = extension = .txt mime = text/plain words = 579 sentences = 45 flesch = 51 summary = A c c e p t e d M a n u s c r i p t Dear Editor, We greatly appreciate the publication of this important research article, for its exploration of the connection of estradiol levels and menopausal status with outcomes from infections with SARS-CoV-2 in women. We advocate for the use of physiologically dosed human-identical transdermal estradiol as hormone replacement, combined with human-identical cyclic progesterone, in appropriate recently menopausal women. (8) Given the potential for serious negative effects ensuing from a state of estradiol deficiency, heightened by the COVID-19 pandemic, not only should appropriate postmenopausal women be considered for hormone replacement therapy, but women being treated with aromatase inhibitors and estrogen receptor antagonists should be counseled on the risks and benefits of those drugs, personalized in each case, in light of the findings of this study. Potential influence of menstrual status and sex hormones on female SARS-CoV-2 infection: A cross-sectional study from Multicentre in Wuhan cache = ./cache/cord-354265-udt2spoe.txt txt = ./txt/cord-354265-udt2spoe.txt === reduce.pl bib === id = cord-353116-7t1prfkr author = Bhargava, Ashish title = Predictors for Severe COVID-19 Infection date = 2020-05-30 pages = extension = .txt mime = text/plain words = 2635 sentences = 188 flesch = 55 summary = BACKGROUND: COVID-19 is a pandemic disease caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In multivariable logistic regression analysis, risk factors for severe infection included pre-existing renal disease (odds ratio [OR], 7.4; 95% CI 2.5-22.0), oxygen requirement at hospitalization (OR, 2.9; 95% CI, 1.3-6.7), acute renal injury (OR, 2.7; 95% CI 1.3-5.6) and initial CRP (OR,1.006; 95% CI, 1.001-1.01). CONCLUSIONS: Acute or pre-existing renal disease, supplemental oxygen at the time of hospitalization and initial CRP were independent predictors for the development of severe COVID-19 infections. The most common symptoms at the onset of illness in the studied cohort were cough (141 including higher white blood cell counts, lower lymphocyte and platelet counts, and increased C-reactive protein (CRP) levels compared with those patients with non-severe infection. In our study we report pre-existing renal disease, supplemental oxygen requirement at admission, acute renal insufficiency, and initial CRP value as independent predictors of severe COVID-19 infections. cache = ./cache/cord-353116-7t1prfkr.txt txt = ./txt/cord-353116-7t1prfkr.txt === reduce.pl bib === id = cord-353862-7xe3fvd5 author = Li, Na title = Maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia: a case-control study date = 2020-03-30 pages = extension = .txt mime = text/plain words = 3515 sentences = 199 flesch = 52 summary = METHODS: We conducted a case-control study to compare clinical characteristics, maternal and neonatal outcomes of pregnant women with and without COVID-19 pneumonia. An earlier study by Chen et al reported nine pregnant women with COVID-19 pneumonia, who took cesarean section in a tertiary hospital of Wuhan [8] . To date, none of previous studies have investigated the adverse effects of COVID-19 infection on pregnancy, by comparing maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia to those without pneumonia. Similar to two previous reports of nine and one pregnant women with confirmed COVID-19 infection [8, 22] , we did not find any evidence to support the vertical transmission of SARS-CoV-2 from mother to fetus via placenta or during cesarean section. Second, we collected the data of sixteen pregnant women with laboratory confirmed COVID-19 pneumonia and eighteen suspected cases with typical CT imaging. cache = ./cache/cord-353862-7xe3fvd5.txt txt = ./txt/cord-353862-7xe3fvd5.txt === reduce.pl bib === id = cord-353103-sdij1d90 author = Yao, Xueting title = In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date = 2020-03-09 pages = extension = .txt mime = text/plain words = 3449 sentences = 191 flesch = 52 summary = title: In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Using the PBPK models, hydroxychloroquine concentrations in lung fluid were simulated under 5 different dosing regimens to explore the most effective regimen whilst considering the drug's safety profile. Based on PBPK models results, a loading dose of 400 mg twice daily of hydroxychloroquine sulfate given orally, followed by a maintenance dose of 200 mg given twice daily for 4 days is recommended for SARS-CoV-2 infection, as it reached three times the potency of chloroquine phosphate when given 500 mg twice daily 5 days in advance. In this study we aimed to: (i) investigate the antiviral and prophylactic activity of hydroxychloroquine and chloroquine in vitro, (ii) build a PBPK model for hydroxychloroquine and chloroquine using data from literature, and, (iii) predict drug concentrations under different dosing regimens using the developed PBPK models. cache = ./cache/cord-353103-sdij1d90.txt txt = ./txt/cord-353103-sdij1d90.txt === reduce.pl bib === id = cord-354009-1ek4s8oe author = Wang, Yun title = Spatiotemporal Characteristics of COVID-19 Epidemic in the United States date = 2020-07-08 pages = extension = .txt mime = text/plain words = 3143 sentences = 207 flesch = 59 summary = We characterized the dynamics of COVID-19 epidemic through detecting weekly hotspots of newly confirmed cases using Spatial and Space-Time Scan Statistics and quantifying the trends of incidence of COVID-19 by county characteristics using the Joinpoint analysis. The results would enhance our understanding of small area-based spatiotemporal dynamics of COVID-19 outbreak, thus help inform multilevel strategies to control the spread of coronavirus and appropriate allocations of public health and healthcare resources in the United States. To identify the characteristics of counties with a high burden of COVID-19, we examined county-level geographic and sociodemographic factors, including rural-urban context, distance to the nearest core airport, population density, percentage of non-white minority population, percentage of population 65 years or older, and percentage of population below the federal poverty line. cache = ./cache/cord-354009-1ek4s8oe.txt txt = ./txt/cord-354009-1ek4s8oe.txt === reduce.pl bib === id = cord-354943-wxhbwcfr author = Guo, Li title = Profiling Early Humoral Response to Diagnose Novel Coronavirus Disease (COVID-19) date = 2020-03-21 pages = extension = .txt mime = text/plain words = 3486 sentences = 181 flesch = 55 summary = METHODS: The host humoral response against SARS-CoV-2, including IgA, IgM, and IgG response, was examined by using an ELISA-based assay on the recombinant viral nucleocapsid protein. The positive detection rate is significantly increased (98.6%) when combining IgM ELISA assay with PCR for each patient compared with a single qPCR test (51.9%). Western blot analysis showed that there was no cross-reactivity of SARS-CoV-2 rNP with human plasma positive for IgG antibodies against NL63, 229E, OC43, and HKU1. The antibody levels were then evaluated in the plasma samples of CCs and PCs. The appearance of IgM, IgA, and IgG antibodies against SARS-CoV-2 was positive as early as day 1 after the symptom onset ( Figure 3A) . These results suggest that IgM ELISA can increase the positive detection rate when combined with the PCR method and can be used for the early diagnosis of COVID-19 infections. cache = ./cache/cord-354943-wxhbwcfr.txt txt = ./txt/cord-354943-wxhbwcfr.txt === reduce.pl bib === id = cord-353342-2n6kqyeo author = Corman, Victor M. title = Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection date = 2016-02-15 pages = extension = .txt mime = text/plain words = 4046 sentences = 223 flesch = 52 summary = title: Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection The Middle East respiratory syndrome (MERS) coronavirus causes isolated cases and outbreaks of severe respiratory disease. We studied 37 adult patients infected with MERS coronavirus for viral load in the lower and upper respiratory tracts (LRT and URT, respectively), blood, stool, and urine. Quantitative data, such as viral loads and antibody titers, could enable comparisons with related diseases, in particular, severe acute respiratory syndrome (SARS), for which studies of natural history were conducted in the aftermath of the 2002-2003 epidemic [7] . DISCUSSION We studied quantitative viral excretion and serum antibody kinetics of a substantial group of hospitalized patients infected with MERS-CoV. Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays cache = ./cache/cord-353342-2n6kqyeo.txt txt = ./txt/cord-353342-2n6kqyeo.txt === reduce.pl bib === id = cord-354011-v9t2b2ca author = Benkouiten, Samir title = Circulation of Respiratory Viruses Among Pilgrims During the 2012 Hajj Pilgrimage date = 2013-10-01 pages = extension = .txt mime = text/plain words = 3755 sentences = 172 flesch = 49 summary = We performed a prospective survey among a cohort of pilgrims departing from Marseille, France, to Mecca in the Kingdom of Saudi Arabia (KSA) for the 2012 Hajj season. This study suggests a rapid acquisition of respiratory viruses among pilgrims during their stay in the KSA, most notably rhinovirus, and highlights the potential of spreading these infections in the pilgrims' home countries upon their return. This study, including sample collection and laboratory methods, was conducted among a cohort of pilgrims departing from Marseille, France, to Mecca in the KSA for the 2012 Hajj season. Each sample was tested for the following viruses by real-time reverse transcription polymerase chain reaction (rRT-PCR): influenza A (FLUA) [11] , influenza B (FLUB) [11] , influenza C (FLUC), and A/2009/H1N1 [12] viruses; human respiratory syncytial virus A and B (RSVB) [13] ; human metapneumovirus (HMPV) [14] ; human rhinovirus (HRV) [15] ; MS2 bacteriophage; human adenovirus (HAdV) [16] ; and human enterovirus (HEV) [17] . cache = ./cache/cord-354011-v9t2b2ca.txt txt = ./txt/cord-354011-v9t2b2ca.txt === reduce.pl bib === id = cord-354877-n5du3bqt author = Vasoo, Shawn title = Rapid Antigen Tests for Diagnosis of Pandemic (Swine) Influenza A/H1N1 date = 2009-10-01 pages = extension = .txt mime = text/plain words = 1783 sentences = 96 flesch = 45 summary = During the period from 1 May 2009 through 2 June 2009, a convenience sample of 84 positive, nonduplicate nasopharyngeal specimens were tested using 3 different rapid antigen test kits: BD Directigen EZ Flu A+B test (Becton Dickinson), BinaxNOW Influenza A&B (Inverness Medical), and QuickVue Influenza A+B Test (Quidel). Patient charts were reviewed, if available, for potential factors that may have been associated with rapid antigen test result; these included patient age, duration of symptoms before presentation, inpatient or emergency department versus outpatient status, and the median number of RT-PCR fluorescence intensity (MFI) units. Because of the widespread interest regarding the clinical performance of rapid antigen tests for detection of pandemic influenza A/H1N1 virus, we used a convenience sample of positive specimens to allow for a quick yet relatively accurate assessment of these tests. cache = ./cache/cord-354877-n5du3bqt.txt txt = ./txt/cord-354877-n5du3bqt.txt === reduce.pl bib === id = cord-355734-pz64534w author = Antonio-Villa, Neftali Eduardo title = Health-care workers with COVID-19 living in Mexico City: clinical characterization and related outcomes date = 2020-09-28 pages = extension = .txt mime = text/plain words = 3261 sentences = 215 flesch = 49 summary = Physicians had higher risk for hospitalization and for severe outcomes compared with nurses and other HCWs. CONCLUSIONS: We report a high prevalence of SARS-CoV-2 infection in HCWs in Mexico City. The situation in Mexico is complex, given that SARS-CoV-2 infections coexist with a high prevalence of comorbidities associated with COVID-19 complications in a large proportion of patients, including HCWs. Furthermore, healthcare systems within Mexico are highly fragmented and quality of care and the ability to protect HCWs within each institution is highly heterogeneous due to structural inequalities, which overall could increase the disparities in risk among HCWs within marginalized communities (7) . Our results also show that comorbidities in HCWs, particularly those related to chronic noncommunicable diseases (e.g., diabetes, obesity and arterial hypertension), and the presentation of severe respiratory symptoms at the time of clinical assessment, increases the risk of adverse COVID-19 outcomes. cache = ./cache/cord-355734-pz64534w.txt txt = ./txt/cord-355734-pz64534w.txt === reduce.pl bib === id = cord-355618-7kfxc2w1 author = McAteer, John title = The VACCINES Act, Deciphering Vaccine Hesitancy in the Time of COVID19 date = 2020-04-13 pages = extension = .txt mime = text/plain words = 1893 sentences = 106 flesch = 48 summary = In his statement of support 7 , the WHO Director-General Dr. Tedros Ghebreyesus asserted that "These online efforts must be matched by tangible steps by governments and the health sector to promote trust in vaccination and respond to the needs and concerns of parents." In order to adequately respond to these needs and concerns, which differ depending on the cultural, societal, and personal beliefs of a particular region, the WHO recommends that each country take steps to develop an understanding of vaccine hesitancy at a local level on an ongoing basis 8 . In recognition of these missed opportunities and in response to declining immunization rates and increasing national skepticism on the safety of vaccines, Congress has introduced bipartisan legislation to expand research into vaccine hesitancy. The bipartisan VACCINES Act is an important step in supporting evidence-based research into vaccine hesitancy. Association between vaccine refusal and vaccine-preventable diseases in the United States: a review of measles and pertussis cache = ./cache/cord-355618-7kfxc2w1.txt txt = ./txt/cord-355618-7kfxc2w1.txt === reduce.pl bib === id = cord-356084-621qzpqd author = Qu, Jiuxin title = Profile of IgG and IgM antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) date = 2020-04-27 pages = extension = .txt mime = text/plain words = 1578 sentences = 98 flesch = 61 summary = title: Profile of IgG and IgM antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) We profiled the serological responses to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) nucleocapsid (N) protein and spike (S) glycoprotein. In this study, we investigated the humoral immunity of hospitalized patients, analyzed the profile of IgG and IgM antibodies against the SARS-CoV-2 in 41 COVID-19 patients between three and 43 days of their illness. Li et al., reported that both IgG and IgM antibody levels increased to detectable levels from the second week of illness in 20 SARS-CoV patients [5] . found that acute lung injury in Chinese macaques caused by SARS-CoV could be mediated by higher anti-spike IgG [9] , and we detected high levels of IgG antibody in critical patients. Longitudinal profile of immunoglobulin G (IgG), IgM, and IgA antibodies against the severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein in patients with pneumonia due to the SARS coronavirus cache = ./cache/cord-356084-621qzpqd.txt txt = ./txt/cord-356084-621qzpqd.txt === reduce.pl bib === id = cord-356316-ui11jr2h author = Patel, Monita R title = Performance of oropharyngeal swab testing compared to nasopharyngeal swab testing for diagnosis of COVID-19 —United States, January-February 2020 date = 2020-06-16 pages = extension = .txt mime = text/plain words = 1181 sentences = 88 flesch = 62 summary = Among 146 nasopharyngeal (NP) and oropharyngeal (OP) swab pairs collected ≤7 days since illness onset, CDC real-time RT-PCR SARS-CoV-2 assay diagnostic results were 95.2% concordant. Current US Centers for Disease Control and Prevention (CDC) guidelines identify nasopharyngeal (NP) and oropharyngeal (OP) swabs as acceptable upper respiratory specimens to test for presence of SARS-CoV-2 ribonucleic acid (RNA) (1) . Overall, among persons with specimens collected early in the illness course, SARS-CoV-2 RNA diagnostic results were highly concordant between OP and NP swabs. Current Infectious Diseases Society of America Guidelines specifically recommend collection of NP, mid-turbinate or nasal swabs rather than OP swabs alone for all symptomatic persons; our findings suggest this recommendation may be particularly relevant for persons later in the illness course and who may have lower amount of SARS-CoV-2 viral RNA (7). Together, our findings support CDC guidelines that identify NP and OP swabs as acceptable specimens for SARS-CoV-2 RNA testing; but suggest that NP swab may comparatively be a more sensitive specimen type for testing persons later in the illness course. cache = ./cache/cord-356316-ui11jr2h.txt txt = ./txt/cord-356316-ui11jr2h.txt ===== Reducing email addresses cord-261270-jkm9c5yv Creating transaction Updating adr table ===== Reducing keywords cord-002514-pp06m5xk cord-260630-vvpzp73r cord-007047-7ty9mxa9 cord-266150-wox7pnkr cord-007068-vcfs41eb cord-001800-644lf8vn cord-277307-wabruzfs cord-257553-479x7av6 cord-010570-ytv7dwr0 cord-266820-exl36jt3 cord-032234-pfr4l1v9 cord-281726-s1o5l7ns cord-277611-3iynrfzq cord-269973-sntnmqqd cord-007325-g8ke9rfg cord-252423-ojmt4k2w cord-266775-4npowkkz cord-280958-36ytqapi cord-273956-mruywa71 cord-007049-02p8ug67 cord-007296-q9rn75qb cord-007170-svsfu7fj cord-265006-m1dmgcd1 cord-261270-jkm9c5yv cord-284782-51mbq7qb cord-268233-ibxufjrv cord-260274-c3586tp6 cord-278259-pbnnp9i1 cord-291286-diwigcy9 cord-272956-0yumc7em cord-279828-es498qul cord-001381-b0tlco4t cord-266696-w9sb038q cord-280763-4bnv2t3f cord-271014-xzpvupms cord-280915-yk872yaz cord-275454-an8xvow3 cord-012511-fl5llkoj cord-256583-z3pd339v cord-291363-re45w37d cord-264660-tfktgy57 cord-277788-6ls21tkr cord-260457-m1jbpo5l cord-280005-i9fp5rys cord-265242-y8t37p0b cord-275349-b35pt3mo cord-252761-ro5tj0tx cord-007321-7gi6xrci cord-282539-skzosh6u cord-279550-7u2hksxm cord-007064-nepgttxf cord-259243-1lkzcslx cord-010599-nwp2if8d cord-015493-vf4et613 cord-279932-bilr71ay cord-011745-dbdtpojs cord-254183-98o0dssj cord-015516-hx7ktq8j cord-283780-h4lwzpl9 cord-289247-qc3to2xj cord-254458-bbcef8xt cord-287676-qh7zeyyx cord-266232-2ctfmjb8 cord-276995-b003vcdc cord-288432-n2y9cunc cord-273839-oasgagpc cord-258304-86gqxajw cord-266808-wyuodzyt cord-260779-riw5xs3j cord-281418-mvgp6qfv cord-010578-uib9h1lb cord-290133-4ou7ubb4 cord-007050-ibmr5bev cord-267152-m9m0aunk cord-251945-v077hhgk cord-273840-jjm7y07m cord-285403-h8ahn8fw cord-277410-lt19mijb cord-007075-sl45z4i0 cord-287923-ev93r09i cord-279167-fj36mzm5 cord-268809-plgip4h6 cord-278045-hr3r17mz cord-292094-vmsdhccp cord-292546-un0blb3w cord-294335-qnu19ru5 cord-291726-8670s4st cord-271269-0gimxteg cord-287119-eo0evoog cord-280571-ntgt5hy9 cord-295270-6ptaxg74 cord-292372-kn27ghlv cord-269455-pkjov371 cord-294718-n3gx862b cord-295940-siy32dj7 cord-296588-q2716lda cord-299274-gnbp7so5 cord-278084-km04sz2s cord-296631-43z3ee8m cord-259471-lsdodl0a cord-299499-66qh3r75 cord-294853-8b0s5w4u cord-294558-cqa58db8 cord-309091-te15ahvw cord-300411-ppcdkfxq cord-310476-mhm7r3qc cord-300013-6m1f4q5r cord-303330-zh8wzza5 cord-307660-onz6vfre cord-289598-t8upoq9a cord-295525-emrwcx0m cord-007073-soov8q3q cord-280954-wd89nka9 cord-258724-1qhen1bj cord-297239-or6h6p9p cord-283788-04gwxo4b cord-288558-rthnj6wd cord-252005-3ld5e7f5 cord-312905-8xlt92pl cord-301066-62qe4fb0 cord-297612-swc2pitd cord-298539-yncda1us cord-303968-ikr6eeov cord-307342-3gkiukh4 cord-313617-hh7lccet cord-300550-l28tadhn cord-299720-f0ny4ur5 cord-303603-4mi64bgm cord-306495-o0ah1gj9 cord-307497-wtfvoifb cord-307770-1igydu3y cord-314025-h9gj814e cord-313693-qmkrn7pr cord-299359-s8j78naz cord-313427-6y4zvrmn cord-310390-7pkbd3kg cord-315356-9zf2h0xr cord-325416-c0qj3yd9 cord-325068-j1lfq60o cord-321603-lbbsnriv cord-318358-glbr8kxh cord-314489-e5r5s5ee cord-327324-4c4a4bfz cord-324007-hapzf0fl cord-324707-9ld73wv1 cord-324307-2zbm4iwn cord-313499-8ijbesl8 cord-303240-tv1ta3z5 cord-326138-16kpn9db cord-318458-jadk2qbm cord-315180-itvc86cv cord-325455-e464idc0 cord-320562-zvsf3va0 cord-331731-c2r0kfaz cord-318204-t024w7h6 cord-317823-ztawznod cord-317940-yg91bsmm cord-321873-9l9zp6gm cord-339859-anatn295 cord-340956-1t3o24u5 cord-304487-ycvu5l5f cord-339004-49dkucxd cord-340317-gwqy6u9x cord-323125-qtlevnbt cord-317948-svgguadm cord-305394-wwabxlgr cord-312797-hohzjx74 cord-322448-s04e6po9 cord-312928-ef8hqs4s cord-329311-p68kr4ga cord-326494-qhxlh43t cord-329323-1cquorhs cord-325136-oyizfh2z cord-324607-rpwccvqi cord-327069-vjlisnui cord-331930-w2055c42 cord-329290-vqvujry3 cord-316970-n2dly3oa cord-317092-5qba9jiq cord-331719-uijwq8gx cord-322650-q8inhgtr cord-353342-2n6kqyeo cord-330214-28ah3nig cord-328267-tk0zc8il cord-332469-zegawla5 cord-322082-80ym2rsq cord-331465-humpwwk2 cord-318615-uhh3owcx cord-336563-hwemigk7 cord-335691-lsuwsm43 cord-326297-0r9pex1o cord-337972-otfloo64 cord-330951-k54e3lbu cord-327862-zcg3baym cord-328667-r5w09lb6 cord-338899-qt17jhg0 cord-335038-q32ghvsv cord-340678-2e2s1gof cord-331978-y4uo7o8g cord-330742-m5xx8861 cord-322204-kc7dy2za cord-335767-omm04fg5 cord-335907-93gwmo0v cord-333943-9d93na7s cord-341435-b36h69r1 cord-340579-cvze15cj cord-345045-nlui9d6e cord-341359-c34gyuv6 cord-348036-yub2cqz6 cord-344038-20n74z3o cord-341838-lkz8ro90 cord-349070-bqv03u2e cord-348144-t0chpsuh cord-349556-k312qkvh cord-348350-pac9ha4q cord-348392-e35cd9sg cord-348478-ho89o8mj cord-343827-jo61t3m0 cord-348178-6bjimde4 cord-350686-q2bu7o4i cord-351314-atsuh8e2 cord-350338-lcsa06gm cord-351231-aoz5jbf1 cord-352837-a29d5dkv cord-351348-lzo0dz7z cord-346502-x2b0ao3q cord-350972-0n4dumgg cord-351589-32kd9vva cord-349566-zx9kt144 cord-354265-udt2spoe cord-354877-n5du3bqt cord-352899-bt2xg0ha cord-353116-7t1prfkr cord-354009-1ek4s8oe cord-354011-v9t2b2ca cord-356316-ui11jr2h cord-356084-621qzpqd cord-353103-sdij1d90 cord-353862-7xe3fvd5 cord-354943-wxhbwcfr cord-355734-pz64534w cord-355618-7kfxc2w1 Creating transaction Updating wrd table ===== Reducing urls cord-273839-oasgagpc cord-271014-xzpvupms cord-260779-riw5xs3j cord-288432-n2y9cunc cord-002514-pp06m5xk cord-287676-qh7zeyyx cord-278045-hr3r17mz cord-292094-vmsdhccp cord-292372-kn27ghlv cord-296588-q2716lda cord-300411-ppcdkfxq cord-301066-62qe4fb0 cord-322448-s04e6po9 cord-324707-9ld73wv1 cord-331719-uijwq8gx cord-335038-q32ghvsv cord-341838-lkz8ro90 cord-350972-0n4dumgg cord-354943-wxhbwcfr cord-349070-bqv03u2e cord-336563-hwemigk7 cord-353342-2n6kqyeo cord-351348-lzo0dz7z Creating transaction Updating url table ===== Reducing named entities cord-007170-svsfu7fj cord-258304-86gqxajw cord-010570-ytv7dwr0 cord-001800-644lf8vn cord-032234-pfr4l1v9 cord-002514-pp06m5xk cord-007049-02p8ug67 cord-259243-1lkzcslx cord-281726-s1o5l7ns cord-007068-vcfs41eb cord-288432-n2y9cunc cord-280915-yk872yaz cord-254183-98o0dssj cord-011745-dbdtpojs cord-254458-bbcef8xt cord-261270-jkm9c5yv cord-266775-4npowkkz cord-278084-km04sz2s cord-015516-hx7ktq8j cord-277307-wabruzfs cord-260274-c3586tp6 cord-007064-nepgttxf cord-271014-xzpvupms cord-269973-sntnmqqd cord-007047-7ty9mxa9 cord-252761-ro5tj0tx cord-252423-ojmt4k2w cord-007325-g8ke9rfg cord-260630-vvpzp73r cord-266696-w9sb038q cord-260779-riw5xs3j cord-010599-nwp2if8d cord-266808-wyuodzyt cord-273956-mruywa71 cord-266150-wox7pnkr cord-010578-uib9h1lb cord-260457-m1jbpo5l cord-259471-lsdodl0a cord-279932-bilr71ay cord-271269-0gimxteg cord-289247-qc3to2xj cord-268233-ibxufjrv cord-273839-oasgagpc cord-280763-4bnv2t3f cord-266820-exl36jt3 cord-007321-7gi6xrci cord-278259-pbnnp9i1 cord-295525-emrwcx0m cord-007073-soov8q3q cord-280958-36ytqapi cord-015493-vf4et613 cord-291363-re45w37d cord-277788-6ls21tkr cord-295270-6ptaxg74 cord-265006-m1dmgcd1 cord-275454-an8xvow3 cord-280005-i9fp5rys cord-264660-tfktgy57 cord-012511-fl5llkoj cord-277611-3iynrfzq cord-257553-479x7av6 cord-007296-q9rn75qb cord-279828-es498qul cord-279550-7u2hksxm cord-266232-2ctfmjb8 cord-287676-qh7zeyyx cord-283788-04gwxo4b cord-288558-rthnj6wd cord-007050-ibmr5bev cord-281418-mvgp6qfv cord-258724-1qhen1bj cord-294853-8b0s5w4u cord-267152-m9m0aunk cord-282539-skzosh6u cord-290133-4ou7ubb4 cord-272956-0yumc7em cord-007075-sl45z4i0 cord-265242-y8t37p0b cord-268809-plgip4h6 cord-276995-b003vcdc cord-284782-51mbq7qb cord-285403-h8ahn8fw cord-256583-z3pd339v cord-273840-jjm7y07m cord-251945-v077hhgk cord-280954-wd89nka9 cord-275349-b35pt3mo cord-283780-h4lwzpl9 cord-252005-3ld5e7f5 cord-269455-pkjov371 cord-277410-lt19mijb cord-296631-43z3ee8m cord-001381-b0tlco4t cord-291286-diwigcy9 cord-287923-ev93r09i cord-278045-hr3r17mz cord-279167-fj36mzm5 cord-280571-ntgt5hy9 cord-287119-eo0evoog cord-294335-qnu19ru5 cord-292094-vmsdhccp cord-289598-t8upoq9a cord-291726-8670s4st cord-292546-un0blb3w cord-292372-kn27ghlv cord-294718-n3gx862b cord-297239-or6h6p9p cord-307660-onz6vfre cord-301066-62qe4fb0 cord-309091-te15ahvw cord-310476-mhm7r3qc cord-297612-swc2pitd cord-298539-yncda1us cord-299720-f0ny4ur5 cord-313617-hh7lccet cord-300411-ppcdkfxq cord-303603-4mi64bgm cord-303330-zh8wzza5 cord-303968-ikr6eeov cord-299274-gnbp7so5 cord-300013-6m1f4q5r cord-300550-l28tadhn cord-312905-8xlt92pl cord-299499-66qh3r75 cord-307342-3gkiukh4 cord-295940-siy32dj7 cord-294558-cqa58db8 cord-314025-h9gj814e cord-296588-q2716lda cord-313693-qmkrn7pr cord-307770-1igydu3y cord-321603-lbbsnriv cord-325068-j1lfq60o cord-313427-6y4zvrmn cord-315356-9zf2h0xr cord-325416-c0qj3yd9 cord-318358-glbr8kxh cord-324007-hapzf0fl cord-299359-s8j78naz cord-310390-7pkbd3kg cord-327324-4c4a4bfz cord-314489-e5r5s5ee cord-315180-itvc86cv cord-303240-tv1ta3z5 cord-318458-jadk2qbm cord-318204-t024w7h6 cord-313499-8ijbesl8 cord-326138-16kpn9db cord-320562-zvsf3va0 cord-324307-2zbm4iwn cord-317823-ztawznod cord-312928-ef8hqs4s cord-304487-ycvu5l5f cord-305394-wwabxlgr cord-325455-e464idc0 cord-329311-p68kr4ga cord-322448-s04e6po9 cord-316970-n2dly3oa cord-324607-rpwccvqi cord-332469-zegawla5 cord-326297-0r9pex1o cord-331731-c2r0kfaz cord-322204-kc7dy2za cord-336563-hwemigk7 cord-327862-zcg3baym cord-317948-svgguadm cord-326494-qhxlh43t cord-323125-qtlevnbt cord-317940-yg91bsmm cord-312797-hohzjx74 cord-317092-5qba9jiq cord-324707-9ld73wv1 cord-339859-anatn295 cord-325136-oyizfh2z cord-329323-1cquorhs cord-331719-uijwq8gx cord-329290-vqvujry3 cord-328267-tk0zc8il cord-330951-k54e3lbu cord-331930-w2055c42 cord-318615-uhh3owcx cord-328667-r5w09lb6 cord-335038-q32ghvsv cord-330214-28ah3nig cord-338899-qt17jhg0 cord-331465-humpwwk2 cord-331978-y4uo7o8g cord-337972-otfloo64 cord-333943-9d93na7s cord-340317-gwqy6u9x cord-339004-49dkucxd cord-330742-m5xx8861 cord-340678-2e2s1gof cord-335767-omm04fg5 cord-322650-q8inhgtr cord-340579-cvze15cj cord-341359-c34gyuv6 cord-341838-lkz8ro90 cord-349070-bqv03u2e cord-348478-ho89o8mj cord-327069-vjlisnui cord-335907-93gwmo0v cord-322082-80ym2rsq cord-348392-e35cd9sg cord-345045-nlui9d6e cord-344038-20n74z3o cord-349556-k312qkvh cord-348036-yub2cqz6 cord-352899-bt2xg0ha cord-351348-lzo0dz7z cord-348144-t0chpsuh cord-335691-lsuwsm43 cord-351231-aoz5jbf1 cord-350338-lcsa06gm cord-349566-zx9kt144 cord-352837-a29d5dkv cord-350686-q2bu7o4i cord-321873-9l9zp6gm cord-346502-x2b0ao3q cord-351314-atsuh8e2 cord-343827-jo61t3m0 cord-353103-sdij1d90 cord-353116-7t1prfkr cord-354011-v9t2b2ca cord-355618-7kfxc2w1 cord-356084-621qzpqd cord-348350-pac9ha4q cord-351589-32kd9vva cord-354943-wxhbwcfr cord-354877-n5du3bqt cord-353862-7xe3fvd5 cord-354009-1ek4s8oe cord-355734-pz64534w cord-353342-2n6kqyeo cord-356316-ui11jr2h cord-350972-0n4dumgg cord-348178-6bjimde4 cord-306495-o0ah1gj9 cord-307497-wtfvoifb cord-341435-b36h69r1 cord-354265-udt2spoe cord-340956-1t3o24u5 Creating transaction Updating ent table ===== Reducing parts of speech cord-007049-02p8ug67 cord-007047-7ty9mxa9 cord-007170-svsfu7fj cord-010578-uib9h1lb cord-258304-86gqxajw cord-007068-vcfs41eb cord-002514-pp06m5xk cord-257553-479x7av6 cord-007064-nepgttxf cord-001800-644lf8vn cord-277307-wabruzfs cord-007325-g8ke9rfg cord-259243-1lkzcslx cord-015516-hx7ktq8j cord-252761-ro5tj0tx cord-032234-pfr4l1v9 cord-266696-w9sb038q cord-266775-4npowkkz cord-260274-c3586tp6 cord-252423-ojmt4k2w cord-271014-xzpvupms cord-010570-ytv7dwr0 cord-266150-wox7pnkr cord-010599-nwp2if8d cord-279932-bilr71ay cord-280958-36ytqapi cord-007296-q9rn75qb cord-273956-mruywa71 cord-280763-4bnv2t3f cord-001381-b0tlco4t cord-260457-m1jbpo5l cord-279828-es498qul cord-288432-n2y9cunc cord-289247-qc3to2xj cord-266808-wyuodzyt cord-268233-ibxufjrv cord-275454-an8xvow3 cord-254183-98o0dssj cord-252005-3ld5e7f5 cord-007050-ibmr5bev cord-012511-fl5llkoj cord-284782-51mbq7qb cord-267152-m9m0aunk cord-277410-lt19mijb cord-273840-jjm7y07m cord-273839-oasgagpc cord-266820-exl36jt3 cord-011745-dbdtpojs cord-280915-yk872yaz cord-266232-2ctfmjb8 cord-256583-z3pd339v cord-269973-sntnmqqd cord-265006-m1dmgcd1 cord-281726-s1o5l7ns cord-278259-pbnnp9i1 cord-281418-mvgp6qfv cord-272956-0yumc7em cord-260630-vvpzp73r cord-260779-riw5xs3j cord-007321-7gi6xrci cord-291363-re45w37d cord-264660-tfktgy57 cord-276995-b003vcdc cord-283780-h4lwzpl9 cord-277611-3iynrfzq cord-283788-04gwxo4b cord-288558-rthnj6wd cord-282539-skzosh6u cord-261270-jkm9c5yv cord-251945-v077hhgk cord-015493-vf4et613 cord-290133-4ou7ubb4 cord-280954-wd89nka9 cord-280005-i9fp5rys cord-007075-sl45z4i0 cord-258724-1qhen1bj cord-265242-y8t37p0b cord-275349-b35pt3mo cord-254458-bbcef8xt cord-279550-7u2hksxm cord-269455-pkjov371 cord-268809-plgip4h6 cord-277788-6ls21tkr cord-287923-ev93r09i cord-271269-0gimxteg cord-285403-h8ahn8fw cord-280571-ntgt5hy9 cord-291286-diwigcy9 cord-278045-hr3r17mz cord-279167-fj36mzm5 cord-289598-t8upoq9a cord-278084-km04sz2s cord-287119-eo0evoog cord-259471-lsdodl0a cord-294335-qnu19ru5 cord-295525-emrwcx0m cord-292546-un0blb3w cord-292372-kn27ghlv cord-292094-vmsdhccp cord-291726-8670s4st cord-287676-qh7zeyyx cord-295270-6ptaxg74 cord-294718-n3gx862b cord-007073-soov8q3q cord-294853-8b0s5w4u cord-296631-43z3ee8m cord-299274-gnbp7so5 cord-299499-66qh3r75 cord-300411-ppcdkfxq cord-295940-siy32dj7 cord-309091-te15ahvw cord-310476-mhm7r3qc cord-301066-62qe4fb0 cord-313693-qmkrn7pr cord-294558-cqa58db8 cord-297239-or6h6p9p cord-318358-glbr8kxh cord-298539-yncda1us cord-307342-3gkiukh4 cord-313617-hh7lccet cord-303603-4mi64bgm cord-312905-8xlt92pl cord-307770-1igydu3y cord-300013-6m1f4q5r cord-307660-onz6vfre cord-296588-q2716lda cord-299359-s8j78naz cord-313427-6y4zvrmn cord-297612-swc2pitd cord-321603-lbbsnriv cord-315356-9zf2h0xr cord-300550-l28tadhn cord-307497-wtfvoifb cord-325068-j1lfq60o cord-303330-zh8wzza5 cord-314025-h9gj814e cord-299720-f0ny4ur5 cord-310390-7pkbd3kg cord-325416-c0qj3yd9 cord-303968-ikr6eeov cord-327324-4c4a4bfz cord-314489-e5r5s5ee cord-324007-hapzf0fl cord-324707-9ld73wv1 cord-326138-16kpn9db cord-324307-2zbm4iwn cord-303240-tv1ta3z5 cord-320562-zvsf3va0 cord-315180-itvc86cv cord-318458-jadk2qbm cord-325455-e464idc0 cord-313499-8ijbesl8 cord-318204-t024w7h6 cord-312928-ef8hqs4s cord-317940-yg91bsmm cord-323125-qtlevnbt cord-304487-ycvu5l5f cord-322448-s04e6po9 cord-317948-svgguadm cord-312797-hohzjx74 cord-306495-o0ah1gj9 cord-305394-wwabxlgr cord-321873-9l9zp6gm cord-317823-ztawznod cord-331719-uijwq8gx cord-329323-1cquorhs cord-326494-qhxlh43t cord-324607-rpwccvqi cord-331930-w2055c42 cord-329311-p68kr4ga parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. cord-316970-n2dly3oa parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. cord-332469-zegawla5 parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. cord-317092-5qba9jiq cord-322082-80ym2rsq cord-318615-uhh3owcx cord-322204-kc7dy2za cord-331978-y4uo7o8g cord-328667-r5w09lb6 parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. cord-322650-q8inhgtr parallel: Warning: No more processes: Decreasing number of running jobs to 91. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may 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cord-351589-32kd9vva cord-350972-0n4dumgg cord-349566-zx9kt144 cord-356316-ui11jr2h cord-351314-atsuh8e2 cord-351348-lzo0dz7z Creating transaction Updating pos table Building ./etc/reader.txt cord-292094-vmsdhccp cord-296588-q2716lda cord-336563-hwemigk7 cord-323125-qtlevnbt cord-353342-2n6kqyeo cord-346502-x2b0ao3q number of items: 242 sum of words: 532,257 average size in words: 2,583 average readability score: 51 nouns: patients; infection; study; cases; virus; disease; influenza; treatment; risk; data; pneumonia; coronavirus; infections; time; studies; results; testing; days; symptoms; case; transmission; children; use; therapy; test; analysis; age; health; samples; years; care; group; population; hospital; patient; community; control; laboratory; mortality; detection; i; outbreak; viruses; evidence; day; pandemic; antibody; syndrome; specimens; adults verbs: use; include; reported; associated; infect; based; shown; increase; comparing; identify; testing; perform; finding; confirmed; required; provides; detect; suggest; received; hospitalized; followed; developed; acquired; occur; consider; caused; reduced; obtaining; collected; treating; defined; determined; given; describing; needed; remains; assessed; indicating; evaluated; related; make; observed; present; lead; resulting; known; demonstrated; control; estimate; support adjectives: respiratory; clinical; viral; severe; acute; positive; high; covid-19; human; first; negative; higher; asymptomatic; available; specific; potential; lower; significant; different; important; medical; new; infectious; diagnostic; public; low; non; similar; early; novel; common; antibiotic; current; bacterial; chronic; rapid; possible; immune; likely; many; symptomatic; large; effective; several; recent; nasopharyngeal; real; key; single; additional adverbs: also; however; well; significantly; therefore; even; respectively; less; still; often; previously; especially; prior; highly; recently; first; currently; rapidly; particularly; clinically; approximately; frequently; potentially; furthermore; generally; now; relatively; likely; directly; later; finally; critically; alone; rather; usually; overall; early; moreover; least; yet; much; probably; possibly; commonly; worldwide; already; subsequently; newly; mainly; immediately pronouns: we; our; it; their; they; i; its; his; them; her; he; us; she; itself; themselves; one; my; your; me; you; ours; him; mg; himself; em; yourself; u; seniors(n=353; seasons[7; ourselves; mrnas; icd-9-cm; herself; hap_023; covid-19; cord-265242-y8t37p0b proper nouns: SARS; CoV-2; COVID-19; M; PCR; China; RT; HIV; CoV; RSV; Health; Coronavirus; United; States; RNA; Wuhan; MERS; Disease; A; March; Clin; sha; S.; Table; CI; CT; Dis; ICU; M.; April; CAP; HCoV; NP; H1N1; US; CDC; Hospital; Control; C; New; T; Prevention; Hong; TB; Kong; B; Diseases; January; East; Supplementary keywords: sars; covid-19; patient; pcr; hiv; respiratory; influenza; united; rsv; mers; cov-2; case; wuhan; virus; test; disease; cap; treatment; therapy; states; rna; laboratory; infection; h1n1; clinical; china; bal; vaccine; sciences; saliva; pwh; plwh; nl63; new; lrti; icu; hsct; household; health; hcq; ebola; east; covid; contact; cold; cfr; ards; antibody; antibiotic; africa one topic; one dimension: patients file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107923/ titles(s): Let Him Who Desires Peace Prepare for War: United States Hospitals and Severe Acute Respiratory Syndrome Preparedness three topics; one dimension: patients; sars; covid file(s): https://www.ncbi.nlm.nih.gov/pubmed/17278083/, https://www.ncbi.nlm.nih.gov/pubmed/26565003/, https://doi.org/10.1093/cid/ciaa1419 titles(s): Infectious Diseases Society of America/American Thoracic Society Consensus Guidelines on the Management of Community-Acquired Pneumonia in Adults | Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection | Risk Factors for COVID-19-associated hospitalization: COVID-19-Associated Hospitalization Surveillance Network and Behavioral Risk Factor Surveillance System five topics; three dimensions: covid sars transmission; sars cov patients; patients pneumonia influenza; virus patients respiratory; covid patients study file(s): https://www.ncbi.nlm.nih.gov/pubmed/32894747/, https://www.ncbi.nlm.nih.gov/pubmed/26565003/, https://www.ncbi.nlm.nih.gov/pubmed/17278083/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7109702/, https://doi.org/10.1093/cid/ciaa1419 titles(s): Reconsidering assumptions of adolescent and young adult SARS-CoV-2 transmission dynamics | Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection | Infectious Diseases Society of America/American Thoracic Society Consensus Guidelines on the Management of Community-Acquired Pneumonia in Adults | Infection with Borna Disease Virus: Molecular and Immunobiological Characterization of the Agent | Risk Factors for COVID-19-associated hospitalization: COVID-19-Associated Hospitalization Surveillance Network and Behavioral Risk Factor Surveillance System Type: cord title: journal-clinInfectDis-cord date: 2021-05-30 time: 15:05 username: emorgan patron: Eric Morgan email: emorgan@nd.edu input: facet_journal:"Clin Infect Dis" ==== make-pages.sh htm files ==== make-pages.sh complex files ==== make-pages.sh named enities ==== making bibliographics id: cord-307497-wtfvoifb author: Abu-Raya, Bahaa title: Predictors of refractory Coronavirus disease (COVID-19) pneumonia date: 2020-04-09 words: 511.0 sentences: 30.0 pages: flesch: 38.0 cache: ./cache/cord-307497-wtfvoifb.txt txt: ./txt/cord-307497-wtfvoifb.txt summary: In addition, refractory COVID-19 patients were more likely to receive oxygen, mechanical ventilation, expectorant, adjunctive treatment including corticosteroids, antiviral drugs and immune enhancers when compared to general COVID-19 patients. The authors have further attempted to explore predictive factors for refractory COVID-19 using a multivariate analysis showing that male sex, anorexia on admission and being afebrile are independent risk factors for the development of a refractory disease. Furthermore, out of this analysis the authors have found that patients with refractory COVID-19 were more likely to receive oxygen, expectorant, corticosteroids, lopinavir/ritonavir and immune enhancer. In their paper, the authors compared categorical and continuous variables between the two groups of patients and these variables that differed significantly between the two groups were included in the multivariate regression analysis. In their paper, the authors included the treatment introduced at the time of patient admission and/or hospitalization in the multivariate analysis aiming to identify independent risk factors for refractory COVID-19. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32271373/ doi: 10.1093/cid/ciaa409 id: cord-280954-wd89nka9 author: Ackerson, Bradley title: Severe Morbidity and Mortality Associated With Respiratory Syncytial Virus Versus Influenza Infection in Hospitalized Older Adults date: 2019-07-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Respiratory syncytial virus (RSV) is an important cause of serious respiratory illness in older adults. Comparison of RSV and influenza infection in hospitalized older adults may increase awareness of adult RSV disease burden. METHODS: Hospitalized adults aged ≥60 years who tested positive for RSV or influenza between 1 January 2011 and 30 June 2015 were identified from Kaiser Permanente Southern California electronic medical records. Baseline characteristics, comorbidities, utilization, and outcomes were compared. RESULTS: The study included 645 RSV- and 1878 influenza-infected hospitalized adults. Patients with RSV were older than those with influenza (mean, 78.5 vs 77.4 years; P = .035) and more likely to have congestive heart failure (35.3% vs 24.5%; P < .001) and chronic obstructive pulmonary disease (COPD) (29.8% vs 24.3%; P = .006) at baseline. In adjusted analyses, RSV infection was associated with greater odds of length of stay ≥7 days (odds ratio [OR] = 1.5; 95% confidence interval [CI], 1.2–1.8; P < .001); pneumonia (OR = 2.7; 95% CI, 2.2–3.2; P < .001); intensive care unit admission (OR = 1.3; 95% CI, 1.0–1.7; P = .023); exacerbation of COPD (OR = 1.7; 95% CI, 1.3–2.4; P = .001); and greater mortality within 1 year of admission (OR = 1.3; 95% CI, 1.0–1.6; P = .019). CONCLUSIONS: RSV infection may result in greater morbidity and mortality among older hospitalized adults than influenza. Increased recognition of adult RSV disease burden will be important in the evaluation and use of new RSV vaccines and antivirals. url: https://www.ncbi.nlm.nih.gov/pubmed/30452608/ doi: 10.1093/cid/ciy991 id: cord-323125-qtlevnbt author: Al Hosani, Farida Ismail title: Serologic Follow-up of Middle East Respiratory Syndrome Coronavirus Cases and Contacts—Abu Dhabi, United Arab Emirates date: 2019-02-01 words: 3706.0 sentences: 183.0 pages: flesch: 45.0 cache: ./cache/cord-323125-qtlevnbt.txt txt: ./txt/cord-323125-qtlevnbt.txt summary: BACKGROUND: Although there is evidence of person-to-person transmission of Middle East respiratory syndrome coronavirus (MERS-CoV) in household and healthcare settings, more data are needed to describe and better understand the risk factors and transmission routes in both settings, as well as the extent to which disease severity affects transmission. METHODS: A seroepidemiological investigation was conducted among MERS-CoV case patients (cases) and their household contacts to investigate transmission risk in Abu Dhabi, United Arab Emirates. In this investigation, we use serological detection of MERS-CoV antibodies to evaluate if asymptomatic or mildly ill case patients had detectable MERS-CoV antibodies, estimate transmission rates from known cases to their household contacts, and identify potential risk factors. For each MERS-CoV case identified in the investigation, clinical information, including symptoms, was collected using the International Severe Acute Respiratory and Emerging Infection Consortium form, which was filled out in real time by healthcare providers and subsequently verified by retrospective chart review. abstract: BACKGROUND: Although there is evidence of person-to-person transmission of Middle East respiratory syndrome coronavirus (MERS-CoV) in household and healthcare settings, more data are needed to describe and better understand the risk factors and transmission routes in both settings, as well as the extent to which disease severity affects transmission. METHODS: A seroepidemiological investigation was conducted among MERS-CoV case patients (cases) and their household contacts to investigate transmission risk in Abu Dhabi, United Arab Emirates. Cases diagnosed between 1 January 2013 and 9 May 2014 and their household contacts were approached for enrollment. Demographic, clinical, and exposure history data were collected. Sera were screened by MERS-CoV nucleocapsid protein enzyme-linked immunosorbent assay and indirect immunofluorescence, with results confirmed by microneutralization assay. RESULTS: Thirty-one of 34 (91%) case patients were asymptomatic or mildly symptomatic and did not require oxygen during hospitalization. MERS-CoV antibodies were detected in 13 of 24 (54%) case patients with available sera, including 1 severely symptomatic, 9 mildly symptomatic, and 3 asymptomatic case patients. No serologic evidence of MERS-CoV transmission was found among 105 household contacts with available sera. CONCLUSIONS: Transmission of MERS-CoV was not documented in this investigation of mostly asymptomatic and mildly symptomatic cases and their household contacts. These results have implications for clinical management of cases and formulation of isolation policies to reduce the risk of transmission. url: https://doi.org/10.1093/cid/ciy503 doi: 10.1093/cid/ciy503 id: cord-254458-bbcef8xt author: Ali, Farhana title: Throat Wash Testing and COVID-19 Disease: Should We Put Our Money Where Our Mouth Is? date: 2020-04-30 words: 1107.0 sentences: 76.0 pages: flesch: 59.0 cache: ./cache/cord-254458-bbcef8xt.txt txt: ./txt/cord-254458-bbcef8xt.txt summary: The tragedy that is the US aircraft carrier Theodore Roosevelt, in which 60 percent of the 600 sailors who tested positive for SARS-CoV-2 infection were asymptomatic, further highlights the need for accurate laboratory diagnostics for COVID-19 disease [2] . make the case that testing of throat wash samples may be more sensitive than testing of NP swabs for COVID-19 disease. Interestingly, there is biologic plausibility that a sample collected via the oral cavity (such as a throat wash) may yield higher results than a NP swab test based on a study by Xu et al. Finally, the authors'' detection of virus late in the patients'' clinical course emphasizes the uncertainty faced by policy makers as they try to determine the optimal length of isolation for an individual recovering from COVID-19 disease. Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32353114/ doi: 10.1093/cid/ciaa511 id: cord-260457-m1jbpo5l author: Allander, Tobias title: Human Bocavirus and Acute Wheezing in Children date: 2007-04-01 words: 3713.0 sentences: 209.0 pages: flesch: 49.0 cache: ./cache/cord-260457-m1jbpo5l.txt txt: ./txt/cord-260457-m1jbpo5l.txt summary: We investigated the presence of human bocavirus by quantitative polymerase chain reaction of nasopharyngeal aspirate specimens and selected serum samples obtained from 259 children (median age, 1.6 years) who had been hospitalized for acute expiratory wheezing. Human bocavirus DNA was frequently detected in serum specimens obtained from patients with acute wheezing, suggesting systemic infection. Results suggest a model for bocavirus infection in which high viral loads are potentially associated with respiratory symptoms and low viral loads indicate asymptomatic shedding. Of the 293 children who were randomized, 259 children (median age, 1.6 years; range, 3 months to 15 years) who had sufficient sample material available for complete virus diagnostic evaluation (nasopharyngeal aspirate specimens were used for PCR [for 16 viruses], virus culture [for 9 viruses], and antigen detection [for 7 viruses]; acute-and convalescent-phase serum samples were used for serologic testing [for 7 viruses]) were included in the present study. abstract: Background. Human bocavirus is a newly discovered parvovirus. It has been detected primarily in children with acute lower respiratory tract infection, but its occurrence, clinical profile, and role as a causative agent of respiratory tract disease are not clear. Methods. We investigated the presence of human bocavirus by quantitative polymerase chain reaction of nasopharyngeal aspirate specimens and selected serum samples obtained from 259 children (median age, 1.6 years) who had been hospitalized for acute expiratory wheezing. The samples were analyzed for 16 respiratory viruses by polymerase chain reaction, virus culture, antigen detection, and serological assays. Results. At least 1 potential etiologic agent was detected in 95% of children, and >1 agent was detected in 34% of children. Human bocavirus was detected in 49 children (19%). A large proportion of the cases were mixed infections with other viruses, but human bocavirus was the only virus detected in 12 children (5%). High viral loads of human bocavirus were noted mainly in the absence of other viral agents, suggesting a causative role for acute wheezing. In addition, infections that had uncertain clinical relevance and low viral loads were prevalent. Human bocavirus DNA was frequently detected in serum specimens obtained from patients with acute wheezing, suggesting systemic infection. Conclusions. Human bocavirus is prevalent among children with acute wheezing and can cause systemic infection. Results suggest a model for bocavirus infection in which high viral loads are potentially associated with respiratory symptoms and low viral loads indicate asymptomatic shedding. Therefore, quantitative polymerase chain reaction analysis may be important for additional studies of human bocavirus. url: https://www.ncbi.nlm.nih.gov/pubmed/17342639/ doi: 10.1086/512196 id: cord-303240-tv1ta3z5 author: Althoff, Keri N title: Contact tracing: Essential to the public health response and our understanding of the epidemiology of COVID-19 date: 2020-06-11 words: 1402.0 sentences: 106.0 pages: flesch: 61.0 cache: ./cache/cord-303240-tv1ta3z5.txt txt: ./txt/cord-303240-tv1ta3z5.txt summary: M a n u s c r i p t As the pandemic in the US continues to evolve, data from contact tracing can continue to inform our understanding about SARS-CoV-2 transmission and guide the public health response. Contact tracing that includes home-based molecular and/or serologic specimen collection to trigger isolation and quarantine may be especially critical when both testing and physical distancing are necessary to achieve the public health goals of epidemic control and mitigation of community transmission. "re-opening"), and test and trace strategies will again be deployed to facilitate epidemic control and interruption of SARS-CoV-2 transmission via isolation and quarantine. Test and trace initiatives will yield equally important information in the current phase of the epidemic as communities begins to "re-open." The contact tracers who will continue to log endless hours to protect the health of the population against COVID-19, and subsequently the stability of our healthcare systems, should be supported and commended. abstract: nan url: https://doi.org/10.1093/cid/ciaa757 doi: 10.1093/cid/ciaa757 id: cord-287676-qh7zeyyx author: Angoulvant, François title: COVID-19 pandemic: Impact caused by school closure and national lockdown on pediatric visits and admissions for viral and non-viral infections, a time series analysis date: 2020-06-03 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A time series analysis of 871,543 pediatric emergency visits revealed that the COVID-19 lockdown and school closure were associated with a significant decrease in infectious diseases disseminated through airborne or fecal-oral transmissions: common cold, gastro-enteritis, bronchiolitis, acute otitis. No change was found for urinary tract infections. url: https://www.ncbi.nlm.nih.gov/pubmed/32492117/ doi: 10.1093/cid/ciaa710 id: cord-261270-jkm9c5yv author: Annweiler, Cédric title: National French survey of COVID-19 symptoms in people aged 70 and over date: 2020-06-18 words: 1708.0 sentences: 114.0 pages: flesch: 57.0 cache: ./cache/cord-261270-jkm9c5yv.txt txt: ./txt/cord-261270-jkm9c5yv.txt summary: The following symptoms observed within the first 72 hours of SARS-CoV-2 infection (i.e., 72h from suspicion, possibly before diagnostic confirmation by RT-PCR test) were collected for each patient using yes/no questions: general signs (sudden deterioration of general condition, temperature, blood pressure), respiratory signs (cough, polypnea), ear nose and throat (ENT) signs (rhinorrhea, odynophagia, otalgia, conjunctivitis, dysgeusia or ageusia, anosmia), gastrointestinal signs (diarrhea, nausea or vomiting) and geriatric syndromes (falls, hypo or overactive delirium, altered consciousness). This national French survey shows that older adults with COVID-19 exhibit a paucisymptomatic clinical picture with less than 3 signs during the first 72h of the infection, generally combining general and respiratory signs (e.g. hyperthermia and cough) with peculiarities that should alert the clinician (e.g. sudden deterioration of general condition, diarrhea, lymphopenia, and/or geriatric syndromes including falls and delirium). abstract: The objective of this national French survey was to determine the COVID-19 semiology in seniors(n=353; mean,84.7±7.0y). 57.8% of patients exhibited ≤3symptoms, including thermal dysregulation(83.6%), cough(58.9%), asthenia(52.7%), polypnea(39.9%), gastrointestinal signs(24.4%). Patients≥80y exhibited falls(P=0.002) and asthenia(P=0.002). Patients with neurocognitive disorders exhibited delirium(P<0.001) and altered consciousness(P=0.001). Clinical peculiarities of COVID-19 were reported in seniors. url: https://doi.org/10.1093/cid/ciaa792 doi: 10.1093/cid/ciaa792 id: cord-355734-pz64534w author: Antonio-Villa, Neftali Eduardo title: Health-care workers with COVID-19 living in Mexico City: clinical characterization and related outcomes date: 2020-09-28 words: 3261.0 sentences: 215.0 pages: flesch: 49.0 cache: ./cache/cord-355734-pz64534w.txt txt: ./txt/cord-355734-pz64534w.txt summary: Physicians had higher risk for hospitalization and for severe outcomes compared with nurses and other HCWs. CONCLUSIONS: We report a high prevalence of SARS-CoV-2 infection in HCWs in Mexico City. The situation in Mexico is complex, given that SARS-CoV-2 infections coexist with a high prevalence of comorbidities associated with COVID-19 complications in a large proportion of patients, including HCWs. Furthermore, healthcare systems within Mexico are highly fragmented and quality of care and the ability to protect HCWs within each institution is highly heterogeneous due to structural inequalities, which overall could increase the disparities in risk among HCWs within marginalized communities (7) . Our results also show that comorbidities in HCWs, particularly those related to chronic noncommunicable diseases (e.g., diabetes, obesity and arterial hypertension), and the presentation of severe respiratory symptoms at the time of clinical assessment, increases the risk of adverse COVID-19 outcomes. abstract: BACKGROUND: Health-care workers (HCWs) could be at increased occupational risk for SARS-CoV-2 infection. Information regarding prevalence and risk factors for adverse outcomes in HCWs is scarce in Mexico. Here, we aimed to explore prevalence of SARS-CoV-2, symptoms, and risk factors associated with adverse outcomes in HCWs in Mexico City. METHODS: We explored data collected by the National Epidemiological Surveillance System in Mexico City. All cases underwent real-time RT-PCR test. We explored outcomes related to severe COVID-19 in HCWs and the diagnostic performance of symptoms to detect SARS-CoV-2 infection in HCWs. RESULTS: As of July 5 (th), 2020, 35,095 HCWs were tested for SARS-CoV-2 and 11,226 were confirmed (31.9%). Overall, 4,322 were nurses (38.5%), 3,324 physicians (29.6%), 131 dentists (1.16%) and 3,449 laboratory personnel and other HCWs (30.8%). After follow-up, 1,009 HCWs required hospitalization (9.00%), 203 developed severe outcomes (1.81%), and 93 required mechanical-ventilatory support (0.82%). Lethality was recorded in 226 (2.01%) cases. Symptoms associated with SARS-CoV-2 positivity were fever, cough, malaise, shivering, myalgias at evaluation but neither had significant predictive value. We also identified 341 asymptomatic SARS-CoV-2 infections (3.04%). Older HCWs with chronic non-communicable diseases, pregnancy, and severe respiratory symptoms were associated with higher risk for adverse outcomes. Physicians had higher risk for hospitalization and for severe outcomes compared with nurses and other HCWs. CONCLUSIONS: We report a high prevalence of SARS-CoV-2 infection in HCWs in Mexico City. No symptomatology can accurately discern HCWs with SARS-CoV-2 infection. Particular attention should focus on HCWs with risk factors to prevent adverse outcomes and reduce infection risk. url: https://www.ncbi.nlm.nih.gov/pubmed/32986819/ doi: 10.1093/cid/ciaa1487 id: cord-331731-c2r0kfaz author: Anugwom, Chimaobi M title: Inverse association between chronic hepatitis B infection and COVID-19: immune-exhaustion or coincidence? date: 2020-06-05 words: 711.0 sentences: 64.0 pages: flesch: 58.0 cache: ./cache/cord-331731-c2r0kfaz.txt txt: ./txt/cord-331731-c2r0kfaz.txt summary: M a n u s c r i p t Dear Editor, We read with great interest the report by Zhao et al, regarding a case of delayed immune response to SARS-CoV-2 in a patient with HIV and HCV co-infection [1] . It is unclear whether this is a simple epidemiological "misconnection" or if being chronically infected with HBV impacts the chances of clinically significant infection with SARS-CoV-2 leading to less hospital admissions, in a similar fashion as that reported by Zhao et al to HIV and HCV. Early virus clearance and delayed antibody response in a case of COVID-19 with a history of co-infection with HIV-1 and HCV Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series abstract: nan url: https://doi.org/10.1093/cid/ciaa592 doi: 10.1093/cid/ciaa592 id: cord-287923-ev93r09i author: Apisarnthanarak, Anucha title: Infection Prevention and Control in Asia: Current Evidence and Future Milestones date: 2017-05-15 words: 1310.0 sentences: 61.0 pages: flesch: 27.0 cache: ./cache/cord-287923-ev93r09i.txt txt: ./txt/cord-287923-ev93r09i.txt summary: This issue of Clinical Infectious Diseases focuses on 3 key themes of infection prevention and control in healthcare settings across the Asia-Pacific regions: (1) epidemiology and evidence to support prevention and control interventions, (2) enhancements to infection prevention and control in healthcare settings, and (3) practices associated with the containment of emerging infectious diseases and outbreaks. We thank the Infectious Diseases Association of Thailand for its partial sponsorship of this issue and share our hope that the collective experience from the study contributors reporting work in this issue will serve as a 2017 platform for improvement in the science and practice of infection prevention in the Asia-Pacific region and in other resource-limited settings. This article appears as part of the supplement "Infection Prevention in Asia Pacific, " sponsored by the Infectious Diseases Association of Thailand (IDAT) with additional author sponsorship. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/28475784/ doi: 10.1093/cid/cix071 id: cord-315356-9zf2h0xr author: Apisarnthanarak, Anucha title: Issues Relevant to the Adoption and Modification of Hospital Infection-Control Recommendations for Avian Influenza (H5N1 Infection) in Developing Countries date: 2007-11-15 words: 3003.0 sentences: 156.0 pages: flesch: 36.0 cache: ./cache/cord-315356-9zf2h0xr.txt txt: ./txt/cord-315356-9zf2h0xr.txt summary: In developing countries, health care worker preparedness training should address the modes of avian influenza transmission and specify how to implement appropriate infection-control strategies to prevent and control the spread of avian influenza. Pandemic influenza preparedness plans must include health care administrative support, mechanisms to rapidly create temporary isolation facilities, systems to restrict access to exposed health care workers, and plans to involve specialists to screen and identify cases early, to provide for continuous monitoring to ensure adherence to optimal infection-control practices, and to provide regular feedback to health care workers Given the experience of severe acute respiratory syndrome (SARS) outbreaks, which occurred in both designated "SARS hospitals" and "non-SARS hospitals" [40] [41] [42] , global preparedness plans should facilitate administrative, fiscal, and infrastructure support for routine occupational health and safety programs for HCWs, appropriate infection-control expertise, and infrastructure in health care settings, available PPE for HCWs, and epidemiological resources for the prevention and control of emerging infectious diseases. abstract: The reemergence of avian influenza (H5N1 infection) has heightened concern for a potential human influenza pandemic. Recommendations regarding preparation for a global avian influenza pandemic are available, and it is imperative that health care workers participate in preparedness planning and training. In developing countries, health care worker preparedness training should address the modes of avian influenza transmission and specify how to implement appropriate infection-control strategies to prevent and control the spread of avian influenza. We provide evidence for avian influenza transmission methods and identify prevention strategies relevant to infection control for hospitals in developing countries. Pandemic influenza preparedness plans must include health care administrative support, mechanisms to rapidly create temporary isolation facilities, systems to restrict access to exposed health care workers, and plans to involve specialists to screen and identify cases early, to provide for continuous monitoring to ensure adherence to optimal infection-control practices, and to provide regular feedback to health care workers url: https://www.ncbi.nlm.nih.gov/pubmed/17968831/ doi: 10.1086/522538 id: cord-346502-x2b0ao3q author: Arabi, Yaseen M title: Ribavirin and Interferon Therapy for Critically Ill Patients With Middle East Respiratory Syndrome: A Multicenter Observational Study date: 2019-06-25 words: 4076.0 sentences: 188.0 pages: flesch: 44.0 cache: ./cache/cord-346502-x2b0ao3q.txt txt: ./txt/cord-346502-x2b0ao3q.txt summary: BACKGROUND: The objective of this study was to evaluate the effect of ribavirin and recombinant interferon (RBV/rIFN) therapy on the outcomes of critically ill patients with Middle East respiratory syndrome (MERS), accounting for time-varying confounders. We evaluated the association of RBV/rIFN with 90-day mortality and MERS coronavirus (MERS-CoV) RNA clearance using marginal structural modeling to account for baseline and time-varying confounders. After adjusting for baseline and time-varying confounders using a marginal structural model, RBV/rIFN was not associated with changes in 90-day mortality (adjusted odds ratio, 1.03 [95% confidence interval {CI}, .73–1.44]; P = .87) or with more rapid MERS-CoV RNA clearance (adjusted hazard ratio, 0.65 [95% CI, .30–1.44]; P = .29). The objective of this study was to examine the effect of RBV/ rIFN therapy in a large cohort of critically ill patients with MERS on the 90-day mortality and MERS-CoV RNA clearance by accounting for baseline and time-varying confounders. abstract: BACKGROUND: The objective of this study was to evaluate the effect of ribavirin and recombinant interferon (RBV/rIFN) therapy on the outcomes of critically ill patients with Middle East respiratory syndrome (MERS), accounting for time-varying confounders. METHODS: This is a retrospective cohort study of critically ill patients with laboratory-confirmed MERS from 14 hospitals in Saudi Arabia diagnosed between September 2012 and January 2018. We evaluated the association of RBV/rIFN with 90-day mortality and MERS coronavirus (MERS-CoV) RNA clearance using marginal structural modeling to account for baseline and time-varying confounders. RESULTS: Of 349 MERS patients, 144 (41.3%) patients received RBV/rIFN (RBV and/or rIFN-α2a, rIFN-α2b, or rIFN-β1a; none received rIFN-β1b). RBV/rIFN was initiated at a median of 2 days (Q1, Q3: 1, 3 days) from intensive care unit admission. Crude 90-day mortality was higher in patients with RBV/rIFN compared to no RBV/rIFN (106/144 [73.6%] vs 126/205 [61.5%]; P = .02]. After adjusting for baseline and time-varying confounders using a marginal structural model, RBV/rIFN was not associated with changes in 90-day mortality (adjusted odds ratio, 1.03 [95% confidence interval {CI}, .73–1.44]; P = .87) or with more rapid MERS-CoV RNA clearance (adjusted hazard ratio, 0.65 [95% CI, .30–1.44]; P = .29). CONCLUSIONS: In this observational study, RBV/rIFN (RBV and/or rIFN-α2a, rIFN-α2b, or rIFN-β1a) therapy was commonly used in critically ill MERS patients but was not associated with reduction in 90-day mortality or in faster MERS-CoV RNA clearance. url: https://doi.org/10.1093/cid/ciz544 doi: 10.1093/cid/ciz544 id: cord-325455-e464idc0 author: Atchison, Christina title: Usability and acceptability of home-based self-testing for SARS-CoV-2 antibodies for population surveillance date: 2020-08-12 words: 3279.0 sentences: 204.0 pages: flesch: 57.0 cache: ./cache/cord-325455-e464idc0.txt txt: ./txt/cord-325455-e464idc0.txt summary: BACKGROUND: This study assesses acceptability and usability of home-based self-testing for SARS-CoV-2 antibodies using lateral flow immunoassays (LFIA). On a population level, by conducting seroprevalence surveys through widespread random sampling of the general public, and by adjusting for the sensitivity and specificity characteristics of the LFIA used, it is possible to estimate the levels of past infection with SARS-CoV-2 in the community (3) . Usability research on HIV selftesting has generally found good acceptability, the devices easy to use and high validity in interpretation of self-reported test results (7) (8) (9) . To mitigate against this, and given the scientific Our study is original because focusing on the acceptability and usability of LFIAs for self-testing for SARS-CoV-2 antibody in a home-based setting has not been done at such scale in the general population. Overall, our study has demonstrated that home-based self-testing LFIAs for use in large communitybased seroprevalence surveys of SARS-CoV-2 antibody are both acceptable and feasible. abstract: BACKGROUND: This study assesses acceptability and usability of home-based self-testing for SARS-CoV-2 antibodies using lateral flow immunoassays (LFIA). METHODS: We carried out public involvement and pilot testing in 315 volunteers to improve usability. Feedback was obtained through online discussions, questionnaires, observations and interviews of people who tried the test at home. This informed the design of a nationally representative survey of adults in England using two LFIAs (LFIA1 and LFIA2) which were sent to 10,600 and 3,800 participants, respectively, who provided further feedback. RESULTS: Public involvement and pilot testing showed high levels of acceptability, but limitations with the usability of kits. Most people reported completing the test; however, they identified difficulties with practical aspects of the kit, particularly the lancet and pipette, a need for clearer instructions and more guidance on interpretation of results. In the national study, 99.3% (8,693/8,754) of LFIA1 and 98.4% (2,911/2,957) of LFIA2 respondents attempted the test and 97.5% and 97.8% of respondents completed it, respectively. Most found the instructions easy to understand, but some reported difficulties using the pipette (LFIA1: 17.7%) and applying the blood drop to the cassette (LFIA2: 31.3%). Most respondents obtained a valid result (LFIA1: 91.5%; LFIA2: 94.4%). Overall there was substantial concordance between participant and clinician interpreted results (kappa: LFIA1 0.72; LFIA2 0.89). CONCLUSION: Impactful public involvement is feasible in a rapid response setting. Home self-testing with LFIAs can be used with a high degree of acceptability and usability by adults, making them a good option for use in seroprevalence surveys. url: https://doi.org/10.1093/cid/ciaa1178 doi: 10.1093/cid/ciaa1178 id: cord-258304-86gqxajw author: Bahl, Prateek title: Droplets and Aerosols generated by singing and the risk of COVID-19 for choirs date: 2020-09-18 words: 1553.0 sentences: 85.0 pages: flesch: 58.0 cache: ./cache/cord-258304-86gqxajw.txt txt: ./txt/cord-258304-86gqxajw.txt summary: title: Droplets and Aerosols generated by singing and the risk of COVID-19 for choirs The results of detailed particle tracking (in supplementary video) reveals that the maximum velocity of droplets expelled, specifically for certain syllables such as ''do'', ''fa'' and ''ti'', is approx. Figure 2c shows the velocity distribution of droplets that are visible while the subject was singing syllable ''sol'' & ''la'' and the direction in which these droplets are moving. Nevertheless, the droplets observed do not appear to be settling down rapidly and without adequate ventilation, these droplets can potentially saturate the indoor environment which can likely explain the very high attack rates of COVID-19 seen in choirs in the US and Europe (almost 87% in Skagit County, Washington) [1] . We note the present study only provides visual evidence of the droplets and aerosols expelled during singing and compare the associated velocities and directions with speaking and coughing. abstract: Choral singing has become a major risk during COVID-19 pandemic due to high infection rates. Our visualisation and velocimetry results reveal that majority of droplets expelled during singing follow the ambient airflow pattern. These results points toward the possibility of COVID-19 spread by small airborne droplets during singing. url: https://www.ncbi.nlm.nih.gov/pubmed/32945338/ doi: 10.1093/cid/ciaa1241 id: cord-351231-aoz5jbf1 author: Bartlett, John G. title: Why Infectious Diseases date: 2014-09-15 words: 5505.0 sentences: 276.0 pages: flesch: 43.0 cache: ./cache/cord-351231-aoz5jbf1.txt txt: ./txt/cord-351231-aoz5jbf1.txt summary: The value of the infectious disease practitioner is now magnified by the crisis of antibiotic resistance, the expanding consequences of international travel, the introduction of completely new pathogen diagnostics, and healthcare reform with emphasis on infection prevention and cost in dollars and lives. The point is that epidemics are the domain of infectious diseases and public health, with the expectation for management or prevention of outbreaks with requirements for detection, reporting, isolation, and case management. This began with a patient transferred from a New York City hospital with a KPC infection and became the source of an institutional outbreak that required extraordinary efforts to control, including a wall constructed to isolate cases, removal of plumbing (as a possible source), use of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) molecular diagnostics to detect cases and carriers, hydrogen peroxide room aerosols, and "whole house" surveillance cultures. The new healthcare system should value infectious disease expertise based on its important role in addressing resistance and costs associated with nosocomial infections. abstract: Infectious diseases is a broad discipline that is almost unique in contemporary medicine with its ability to cure and prevent disease, to identify specific disease causes (microbes), and to deal with diverse, sometimes massive outbreaks. The value of the infectious disease practitioner is now magnified by the crisis of antibiotic resistance, the expanding consequences of international travel, the introduction of completely new pathogen diagnostics, and healthcare reform with emphasis on infection prevention and cost in dollars and lives. Infectious disease careers have great personal rewards to the practitioner based on these observations. It is unfortunate that we have been so effective in our work, but relatively ineffective in convincing the healthcare system of this value. url: https://doi.org/10.1093/cid/ciu441 doi: 10.1093/cid/ciu441 id: cord-326494-qhxlh43t author: Beckerman, Karen Palmore title: Pregnancy and Pandemic Disease date: 2020-06-10 words: 1199.0 sentences: 95.0 pages: flesch: 59.0 cache: ./cache/cord-326494-qhxlh43t.txt txt: ./txt/cord-326494-qhxlh43t.txt summary: Globally, estimates suggest it is a disease of men (57%), however women (32%) and children < age 15 (11%) together make up close to half of those living with TB. 10 They report an unexpectedly high proportion of women (37%) living with TB, The strong implication of these pregnancy data, that exposure and transmission in the population studied is both continuous and ongoing, is striking. have provided proof of concept data that routine testing during pregnancy could be an ideal method of assessing the extent of community spread of both recognized endemic infection as well as emerging infectious diseases. Today, we continue to rely on universal HIV testing of pregnant women to estimate community HIV prevalence and to prevent vertical transmission, both in resource-rich and resource-limited regions. Tuberculosis infection in women of reproductive age -a cross-sectional study at antenatal care clinics in an Ethiopian city Control of maternal HIV-1 disease during pregnancy abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32520309/ doi: 10.1093/cid/ciaa741 id: cord-354011-v9t2b2ca author: Benkouiten, Samir title: Circulation of Respiratory Viruses Among Pilgrims During the 2012 Hajj Pilgrimage date: 2013-10-01 words: 3755.0 sentences: 172.0 pages: flesch: 49.0 cache: ./cache/cord-354011-v9t2b2ca.txt txt: ./txt/cord-354011-v9t2b2ca.txt summary: We performed a prospective survey among a cohort of pilgrims departing from Marseille, France, to Mecca in the Kingdom of Saudi Arabia (KSA) for the 2012 Hajj season. This study suggests a rapid acquisition of respiratory viruses among pilgrims during their stay in the KSA, most notably rhinovirus, and highlights the potential of spreading these infections in the pilgrims'' home countries upon their return. This study, including sample collection and laboratory methods, was conducted among a cohort of pilgrims departing from Marseille, France, to Mecca in the KSA for the 2012 Hajj season. Each sample was tested for the following viruses by real-time reverse transcription polymerase chain reaction (rRT-PCR): influenza A (FLUA) [11] , influenza B (FLUB) [11] , influenza C (FLUC), and A/2009/H1N1 [12] viruses; human respiratory syncytial virus A and B (RSVB) [13] ; human metapneumovirus (HMPV) [14] ; human rhinovirus (HRV) [15] ; MS2 bacteriophage; human adenovirus (HAdV) [16] ; and human enterovirus (HEV) [17] . abstract: Background. The Hajj is the oldest and largest annual mass gathering in the world and may increase the risk of spread of respiratory viruses. Methods. We performed a prospective survey among a cohort of pilgrims departing from Marseille, France, to Mecca in the Kingdom of Saudi Arabia (KSA) for the 2012 Hajj season. Nasal swabs were collected from participants and tested for 11 respiratory viruses by real-time reverse transcription polymerase chain reaction. Results. Of 165 participants sampled before departing to the KSA, 8 (4.8%) were positive for at least 1 virus (5 rhinovirus, 1 influenza C, 1 adenovirus, and 1 enterovirus). Seventy symptomatic pilgrims underwent additional nasal swabs during their pilgrimage in the KSA, of which 27 (38.6%) were positive for at least 1 virus (19 rhinovirus, 6 influenza A, 1 influenza C, 1 respiratory syncytial virus B, 1 metapneumovirus, 1 adenovirus, and 1 enterovirus). This was significantly higher than the 4.8% who were positive before departing for the KSA (P < .001). Of 154 pilgrims sampled before leaving the KSA, 17 (11%) were positive for at least 1 virus (13 rhinovirus, 3 adenovirus, 2 influenza B, and 1 enterovirus), which was also significantly higher than the percentage of positive pilgrims (4.8%), before departing for the KSA (P = .040). Conclusions. This study suggests a rapid acquisition of respiratory viruses among pilgrims during their stay in the KSA, most notably rhinovirus, and highlights the potential of spreading these infections in the pilgrims' home countries upon their return. url: https://www.ncbi.nlm.nih.gov/pubmed/23839997/ doi: 10.1093/cid/cit446 id: cord-353116-7t1prfkr author: Bhargava, Ashish title: Predictors for Severe COVID-19 Infection date: 2020-05-30 words: 2635.0 sentences: 188.0 pages: flesch: 55.0 cache: ./cache/cord-353116-7t1prfkr.txt txt: ./txt/cord-353116-7t1prfkr.txt summary: BACKGROUND: COVID-19 is a pandemic disease caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In multivariable logistic regression analysis, risk factors for severe infection included pre-existing renal disease (odds ratio [OR], 7.4; 95% CI 2.5-22.0), oxygen requirement at hospitalization (OR, 2.9; 95% CI, 1.3-6.7), acute renal injury (OR, 2.7; 95% CI 1.3-5.6) and initial CRP (OR,1.006; 95% CI, 1.001-1.01). CONCLUSIONS: Acute or pre-existing renal disease, supplemental oxygen at the time of hospitalization and initial CRP were independent predictors for the development of severe COVID-19 infections. The most common symptoms at the onset of illness in the studied cohort were cough (141 including higher white blood cell counts, lower lymphocyte and platelet counts, and increased C-reactive protein (CRP) levels compared with those patients with non-severe infection. In our study we report pre-existing renal disease, supplemental oxygen requirement at admission, acute renal insufficiency, and initial CRP value as independent predictors of severe COVID-19 infections. abstract: BACKGROUND: COVID-19 is a pandemic disease caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Predictors for severe COVID-19 infection have not been well defined. Determination of risk factors for severe infection would enable identifying patients who may benefit from aggressive supportive care and early intervention. METHODS: We conducted a retrospective observational study of 197 patients with confirmed COVID-19 infection admitted to a tertiary academic medical center. RESULTS: Of 197 hospitalized patients, the mean (SD) age of the cohort was 60.6 (16.2) years, 103 (52.3%) were male and 156 (82.1%) were black. Severe COVID-19 infection was noted in 74 (37.6%) patients, requiring intubation. Patients aged above 60 were significantly more likely to have severe infection. Patients with severe infection were significantly more likely to have diabetes, renal disease, chronic pulmonary disease and had significantly higher white blood cell counts, lower lymphocyte counts, and increased C-reactive protein (CRP) compared to patients with non-severe infection. In multivariable logistic regression analysis, risk factors for severe infection included pre-existing renal disease (odds ratio [OR], 7.4; 95% CI 2.5-22.0), oxygen requirement at hospitalization (OR, 2.9; 95% CI, 1.3-6.7), acute renal injury (OR, 2.7; 95% CI 1.3-5.6) and initial CRP (OR,1.006; 95% CI, 1.001-1.01). Race, age and socioeconomic status were not identified as independent predictors. CONCLUSIONS: Acute or pre-existing renal disease, supplemental oxygen at the time of hospitalization and initial CRP were independent predictors for the development of severe COVID-19 infections. Every 1 unit increase in CRP increased the risk of severe disease by 0.06%. url: https://www.ncbi.nlm.nih.gov/pubmed/32472676/ doi: 10.1093/cid/ciaa674 id: cord-336563-hwemigk7 author: Bhimraj, Adarsh title: Infectious Diseases Society of America Guidelines on the Treatment and Management of Patients with COVID-19 date: 2020-04-27 words: 8308.0 sentences: 448.0 pages: flesch: 42.0 cache: ./cache/cord-336563-hwemigk7.txt txt: ./txt/cord-336563-hwemigk7.txt summary: Given the rapidity of emerging literature, IDSA identified the need to develop living, frequently updated evidence-based guidelines to support patients, clinicians and other health-care professionals in their decisions about treatment and management of patients with COVID-19. Two RCTs of patients with confirmed COVID-19 with mild pneumonia (e.g., positive CT scan without oxygen requirement) or non-severe infection admitted to the hospital treated with hydroxychloroquine (HCQ) reported on mortality at 14 days, clinical progression (radiological progression on CT scan), clinical improvement, failure of virologic clearance (PCR), and adverse events (both) [11, 12] (Table 1 ). In addition, we identified four publications describing three trials of combination treatment with HCQ plus azithromycin (AZ) among hospitalized patients with COVID-19 reporting on the outcomes of mortality, failure of virologic clearance (assessed with PCR test), and adverse events (i.e., significant QT prolongation leading to treatment discontinuation) [13] [14] [15] [16] (Table 2) . abstract: BACKGROUND: There are many pharmacologic therapies that are being used or considered for treatment of COVID-19. There is a need for frequently updated practice guidelines on their use, based on critical evaluation of rapidly emerging literature. OBJECTIVE: Develop evidence-based rapid guidelines intended to support patients, clinicians and other health-care professionals in their decisions about treatment and management of patients with COVID-19. METHODS: IDSA formed a multidisciplinary guideline panel of infectious disease clinicians, pharmacists, and methodologists with varied areas of expertise. Process followed a rapid recommendation checklist. The panel prioritized questions and outcomes. Then a systematic review of the peer-reviewed and grey literature was conducted. The Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach was used to assess the certainty of evidence and make recommendations. RESULTS: The IDSA guideline panel agreed on 7 treatment recommendations and provided narrative summaries of other treatments undergoing evaluations. CONCLUSIONS: The panel expressed the overarching goal that patients be recruited into ongoing trials, which would provide much needed evidence on the efficacy and safety of various therapies for COVID-19, given that we could not make a determination whether the benefits outweigh harms for most treatments. url: https://doi.org/10.1093/cid/ciaa478 doi: 10.1093/cid/ciaa478 id: cord-268809-plgip4h6 author: Bielecki, Michel title: Social distancing alters the clinical course of COVID-19 in young adults: A comparative cohort study date: 2020-06-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Social distancing and stringent hygiene seem effective in reducing the number of transmitted virus particles, and therefore the infectivity, of coronavirus disease 2019 (COVID-19) and could alter the mode of transmission of the disease. However, it is not known if such practices can change the clinical course in infected individuals. METHODS: We prospectively studied an outbreak of COVID-19 in Switzerland among a population of 508 predominantly male soldiers with a median age of 21 years. We followed the number of infections in two spatially separated cohorts with almost identical baseline characteristics with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) before and after implementation of stringent social distancing. RESULTS: Of the 354 soldiers infected prior to the implementation of social distancing, 30% fell ill from COVID-19. While no soldier in a group of 154, in which infections appeared after implementation of social distancing, developed COVID-19 despite the detection of viral RNA in the nose and virus-specific antibodies within this group. CONCLUSIONS: Social distancing not only can slow the spread of SARS-CoV-2 in a cohort of young, healthy adults but can also prevent the outbreak of COVID-19 while still inducing an immune response and colonizing nasal passages. Viral inoculum during infection or mode of transmission may be key factors determining the clinical course of COVID-19. url: https://doi.org/10.1093/cid/ciaa889 doi: 10.1093/cid/ciaa889 id: cord-001800-644lf8vn author: Biggerstaff, Matthew title: Estimating the Potential Effects of a Vaccine Program Against an Emerging Influenza Pandemic—United States date: 2015-05-01 words: 4489.0 sentences: 175.0 pages: flesch: 43.0 cache: ./cache/cord-001800-644lf8vn.txt txt: ./txt/cord-001800-644lf8vn.txt summary: For the second scenario, we clinical attack rate of the influenza pandemic is 20% and the overall case fatality ratio is 0.53% (high-severity scenario); 10 million doses (left) or 30 million doses (right) of vaccine are administered each week; the vaccination program begins 16 weeks after, 8 weeks after, the same week as, 8 weeks before, and 16 weeks before the first cases of a novel influenza virus occur in the United States; and the efficacy is "H1N1pmd09 monovalent vaccine-like." 2009 H1N1-like vaccine effectiveness: 2 doses of vaccine administered 3 weeks apart required to be fully effective (62% for persons aged <60 years and 43% for persons ≥60 years) in protecting against subclinical and clinical cases, hospitalizations, and deaths. For an influenza pandemic with a 30% overall cumulative attack rate and high-severity scenario, we estimated that a vaccination program beginning the same week as the pandemic started in the United States that administered 10 million doses of vaccine with the moderate VE per week could avert 260 000 hospitalizations and 32 000 deaths (6% reduction) (Tables 2 and 3 ; Figures 2 and 3) . abstract: Background. Human illness from influenza A(H7N9) was identified in March 2013, and candidate vaccine viruses were soon developed. To understand factors that may impact influenza vaccination programs, we developed a model to evaluate hospitalizations and deaths averted considering various scenarios. Methods. We utilized a model incorporating epidemic curves with clinical attack rates of 20% or 30% in a single wave of illness, case hospitalization ratios of 0.5% or 4.2%, and case fatality ratios of 0.08% or 0.53%. We considered scenarios that achieved 80% vaccination coverage, various starts of vaccination programs (16 or 8 weeks before, the same week of, or 8 or 16 weeks after start of pandemic), an administration rate of 10 or 30 million doses per week (the latter rate is an untested assumption), and 2 levels of vaccine effectiveness (2 doses of vaccine required; either 62% or 80% effective for persons aged <60 years, and either 43% or 60% effective for persons aged ≥60 years). Results. The start date of vaccination campaigns most influenced impact; 141 000–2 200 000 hospitalizations and 11 000–281 000 deaths were averted when campaigns started before a pandemic, and <100–1 300 000 hospitalizations and 0–165 000 deaths were averted for programs beginning the same time as or after the introduction of the pandemic virus. The rate of vaccine administration and vaccine effectiveness did not influence campaign impact as much as timing of the start of campaign. Conclusions. Our findings suggest that efforts to improve the timeliness of vaccine production will provide the greatest impacts for future pandemic vaccination programs. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4610126/ doi: 10.1093/cid/ciu1175 id: cord-350686-q2bu7o4i author: Bilder, Christopher R title: Pool size selection when testing for SARS-CoV-2 date: 2020-06-16 words: 539.0 sentences: 55.0 pages: flesch: 71.0 cache: ./cache/cord-350686-q2bu7o4i.txt txt: ./txt/cord-350686-q2bu7o4i.txt summary: title: Pool size selection when testing for SARS-CoV-2 M a n u s c r i p t Dear Editor-Pooling samples has been proposed in multiple articles as an efficient way to test for SARS-CoV-2 [1] [2] [3] [4] . They concluded that "this pooling method can be applied immediately in current clinical testing laboratories." However, this research [1] and similar research of others [2] [3] missed answering a very important question: How does one choose the most efficient pool size relative to SARS-CoV-2 prevalence in samples? The efficiencies from pooling samples occur when pools test negative. For example, the most efficient pool size is four samples when prevalence is 10% (calculation to be discussed shortly). By changing the size to 32 samples in our example, only 3% of the pools will test negative. Pooling of samples for testing for SARS-CoV-2 in asymptomatic people abstract: nan url: https://doi.org/10.1093/cid/ciaa774 doi: 10.1093/cid/ciaa774 id: cord-273839-oasgagpc author: Bisno, Alan L. title: Diagnosis and Management of Group A Streptococcal Pharyngitis: A Practice Guideline date: 1997-09-17 words: 5771.0 sentences: 295.0 pages: flesch: 41.0 cache: ./cache/cord-273839-oasgagpc.txt txt: ./txt/cord-273839-oasgagpc.txt summary: Except under special circumstances, neither repeated bacteri-Evidence ologic testing (culture or RADT) of patients who have success-We reviewed a large number of clinical trials of diagnostic fully completed a course of antimicrobial therapy nor routine and treatment strategies for group A streptococcal pharyngitis. ple, studies of treatment were evaluated for randomization, A small percentage of patients will have recurrences of acute blinding, use of streptococcal typing to differentiate treatment pharyngitis that are associated with throat cultures (or RADTs) failures from new infections, duration and timing of follow-up positive for group A streptococci within a short period following examinations, and statistical power [1, 2] . Such tests are appropriate for streptococci in the upper respiratory tract and for the confirmation of the clinical diagnosis of acute streptococcal pharyngitis use by microbiology laboratory personnel, but most physicians who perform throat cultures would find it difficult to justify [12] (category A, grade II). abstract: This is the second in a series of practice guidelines commissioned by the Infectious Diseases Society of America through its Practice Guidelines Committee. The purpose of these guidelines is to provide assistance to clinicians when making decisions on treating the conditions specified in each guideline. The targeted providers are pediatricians, family practitioners, and internists. The targeted patients and setting for the acute pharyngitis guideline are pediatric, adolescent, and adult outpatients with a complaint of sore throat. Funding was provided by the IDSA. Panel members represented experts in adult and pediatric infectious diseases. The guidelines are evidence-based. A standard ranking system was used for the strength of the recommendations and the quality of the evidence cited in the literature reviewed. The document has been subjected to external review by peer reviewers as well as by the Practice Guidelines Committee and was approved by the IDSA Council. An executive summary, algorithms, and tables highlight the major recommendations. Indicators of quality will assist in guideline implementation. The guideline will be listed on the IDSA home page at http://www.idsociety.org. url: https://www.ncbi.nlm.nih.gov/pubmed/9314443/ doi: 10.1086/513768 id: cord-299274-gnbp7so5 author: Bodkin, Claire title: Pandemic Planning in Homeless Shelters: A pilot study of a COVID-19 testing and support program to mitigate the risk of COVID-19 outbreaks in congregate settings date: 2020-06-08 words: 1643.0 sentences: 113.0 pages: flesch: 59.0 cache: ./cache/cord-299274-gnbp7so5.txt txt: ./txt/cord-299274-gnbp7so5.txt summary: title: Pandemic Planning in Homeless Shelters: A pilot study of a COVID-19 testing and support program to mitigate the risk of COVID-19 outbreaks in congregate settings We tested 104 residents and 141 staff for COVID-19 who failed daily symptom screening in homeless shelters in Hamilton, Canada. The objective of this report is to describe our experience with shelter facility restructuring, daily symptom screening and rapid testing to mitigate the risk of COVID-19 in the homeless shelter setting in Hamilton, Ontario, Canada. Between March 17 and April 30, 2020, COVID-19 testing was performed on all shelter residents and staff who failed daily screening for potential COVID-19 related symptoms as well as staff and residents identified as close contacts of positive cases. We have thus far been successful in preventing large outbreaks in the shelter setting despite identifying positive cases in both staff and residents. abstract: We tested 104 residents and 141 staff for COVID-19 who failed daily symptom screening in homeless shelters in Hamilton, Canada. We detected one resident (1%), seven staff (5%) and one case of secondary spread. Shelter restructuring to allow physical distancing, testing and isolation can decrease outbreaks in shelters. url: https://www.ncbi.nlm.nih.gov/pubmed/32511704/ doi: 10.1093/cid/ciaa743 id: cord-340956-1t3o24u5 author: Borkenhagen, Laura K title: High Risk of Influenza Virus Infection Among Swine Workers: Examining a Dynamic Cohort in China date: 2019-09-01 words: 4184.0 sentences: 179.0 pages: flesch: 50.0 cache: ./cache/cord-340956-1t3o24u5.txt txt: ./txt/cord-340956-1t3o24u5.txt summary: Despite elevated titers, among the 187 study subjects for whom we had complete follow-up, participants working at swine CAFOs had significantly greater odds of seroconverting against both the swine H1N1 (odds ratio [OR] 19.16, 95% confidence interval [CI] 3.55–358.65) and swine H3N2 (OR 2.97, 95% CI 1.16–8.01) viruses, compared to unexposed and non-CAFO swine workers with less intense swine exposure. Conversely, higher odds of seroconversion against swine H3N2 virus were observed among the unexposed (OR 2.27, 95% CI 1.43-3.60) and CAFO-exposed (OR 1.98, 95% CI 1.11-3.42), when compared to the non-CAFO swine workers; the unexposed participants had higher geometric mean MN titers, compared to the other 2 groups, for all time points (Table 3) . In this report, we present the first 24 months of data from a 5-year prospective, cohort study of IAV among participants exposed and unexposed to swine in China. abstract: BACKGROUND: China is thought to be a hotspot for zoonotic influenza virus emergence, yet there have been few prospective studies examining the occupational risks of such infections. METHODS: We present the first 2 years of data collected from a 5-year, prospective, cohort study of swine-exposed and -unexposed participants at 6 swine farms in China. We conducted serological and virological surveillance to examine evidence for swine influenza A virus infection in humans. RESULTS: Of the 658 participants (521 swine-exposed and 137 swine-unexposed), 207 (31.5%) seroconverted against at least 1 swine influenza virus subtype (swine H1N1 or H3N2). Swine-exposed participants’ microneutralization titers, especially those enrolled at confined animal feeding operations (CAFOs), were higher against the swine H1N1 virus than were other participants at 12 and 24 months. Despite elevated titers, among the 187 study subjects for whom we had complete follow-up, participants working at swine CAFOs had significantly greater odds of seroconverting against both the swine H1N1 (odds ratio [OR] 19.16, 95% confidence interval [CI] 3.55–358.65) and swine H3N2 (OR 2.97, 95% CI 1.16–8.01) viruses, compared to unexposed and non-CAFO swine workers with less intense swine exposure. CONCLUSIONS: While some of the observed increased risk against swine viruses may have been explained by exposure to human influenza strains, study data suggest that even with elevated preexisting antibodies, swine-exposed workers were at high risk of infection with enzootic swine influenza A viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/31504322/ doi: 10.1093/cid/ciz865 id: cord-279828-es498qul author: Boulle, Andrew title: Risk factors for COVID-19 death in a population cohort study from the Western Cape Province, South Africa date: 2020-08-29 words: 3651.0 sentences: 148.0 pages: flesch: 44.0 cache: ./cache/cord-279828-es498qul.txt txt: ./txt/cord-279828-es498qul.txt summary: We used Cox-proportional hazards models adjusted for age, sex, location and comorbidities to examine the association between HIV, tuberculosis and COVID-19 death from 1 March-9 June 2020 among (i) public sector "active patients" (≥1 visit in the 3 years before March 2020), (ii) laboratory-diagnosed COVID-19 cases and (iii) hospitalized COVID-19 cases. We conducted a cohort study using de-identified data from the Western Cape Provincial Health Data Centre (WCPHDC) of public sector patients aged ≥20 years with documented sex and not known to have died before March 1, 2020 (before the first diagnosed COVID-19 case in South Africa, and several weeks before the first documented COVID-19 death) and included all follow up through June 9, 2020. We used Cox-proportional hazards models adjusted for age, sex and other comorbidities to examine the association between HIV, tuberculosis and COVID-19 death among (i) all public sector patients with ≥1 health visit in the 3 years before March 1, 2020 (considered "active patients"), (ii) laboratory-diagnosed COVID-19 cases and (iii) hospitalized COVID-19 cases. abstract: BACKGROUND: Risk factors for COVID-19 death in sub-Saharan Africa and the effects of HIV and tuberculosis on COVID-19 outcomes are unknown. METHODS: We conducted a population cohort study using linked data from adults attending public sector health facilities in the Western Cape, South Africa. We used Cox-proportional hazards models adjusted for age, sex, location and comorbidities to examine the association between HIV, tuberculosis and COVID-19 death from 1 March-9 June 2020 among (i) public sector “active patients” (≥1 visit in the 3 years before March 2020), (ii) laboratory-diagnosed COVID-19 cases and (iii) hospitalized COVID-19 cases. We calculated the standardized mortality ratio (SMR) for COVID-19 comparing HIV positive vs. negative adults using modelled population estimates. RESULTS: Among 3,460,932 patients (16% HIV positive), 22,308 were diagnosed with COVID-19, of whom 625 died. COVID-19 death was associated with male sex, increasing age, diabetes, hypertension and chronic kidney disease. HIV was associated with COVID-19 mortality (adjusted hazard ratio [aHR] 2.14; 95% confidence interval [CI] 1.70-2.70), with similar risks across strata of viral load and immunosuppression. Current and previous tuberculosis were associated with COVID-19 death (aHR [95%CI] 2.70 [1.81-4.04] and 1.51 [1.18-1.93] respectively). The SMR for COVID-19 death associated with HIV was 2.39 (95%CI 1.96-2.86); population attributable fraction 8.5% (95%CI 6.1-11.1). CONCLUSION: While our findings may over-estimate HIV- and tuberculosis-associated COVID-19 mortality risks due to residual confounding, both HIV and current tuberculosis were independently associated with increased COVID-19 mortality. The associations between age, sex and other comorbidities and COVID-19 mortality were similar to other settings. url: https://www.ncbi.nlm.nih.gov/pubmed/32860699/ doi: 10.1093/cid/ciaa1198 id: cord-300013-6m1f4q5r author: Brahier, Thomas title: Lung ultrasonography for risk stratification in patients with COVID-19: a prospective observational cohort study date: 2020-09-17 words: 3247.0 sentences: 220.0 pages: flesch: 54.0 cache: ./cache/cord-300013-6m1f4q5r.txt txt: ./txt/cord-300013-6m1f4q5r.txt summary: This study describes and compares LUS characteristics between patients with different clinical outcomes METHODS: Prospective observational study of PCR-confirmed COVID-19 adults with symptoms of lower respiratory tract infection in the emergency department (ED) of Lausanne University Hospital. We describe and compare early LUS findings (acquired within 24hours of presentation to the ED) between patient groups based on their outcome at 7 days after inclusion: 1) outpatients, 2) hospitalised and 3) intubated/death. Median normalized LUS score had a good level of discrimination between outpatients and others with area under the ROC of 0.80 (95% CI 0.68-0.92) CONCLUSIONS: Systematic LUS has potential as a reliable, cheap and easy-to-use triage tool for the early risk stratification in COVID-19 patients presenting in EDs Despite the potential of LUS as a cheap, portable and accessible point-of-care triage tool in acute respiratory disease (especially in low resource settings), a multinational consensus recently stated that the lack of studies limited specific recommendations for the management of COVID-19 patients (27) . abstract: BACKGROUND: Point-of-care lung ultrasound (LUS) is a promising pragmatic risk stratification tool in COVID-19. This study describes and compares LUS characteristics between patients with different clinical outcomes METHODS: Prospective observational study of PCR-confirmed COVID-19 adults with symptoms of lower respiratory tract infection in the emergency department (ED) of Lausanne University Hospital. A trained physician recorded LUS images using a standardized protocol. Two experts reviewed images blinded to patient outcome. We describe and compare early LUS findings (acquired within 24hours of presentation to the ED) between patient groups based on their outcome at 7 days after inclusion: 1) outpatients, 2) hospitalised and 3) intubated/death. Normalized LUS score was used to discriminate between groups RESULTS: Between March 6 and April 3 2020, we included 80 patients (17 outpatients, 42 hospitalized and 21 intubated/dead). 73 patients (91%) had abnormal LUS (70% outpatients, 95% hospitalised and 100% intubated/death; p=0.003). The proportion of involved zones was lower in outpatients compared with other groups (median 30% [IQR 0-40%], 44% [31-70%] and 70% [50-88%], p<0.001). Predominant abnormal patterns were bilateral and multifocal spread thickening of the pleura with pleural line irregularities (70%), confluent B lines (60%) and pathologic B lines (50%). Posterior inferior zones were more often affected. Median normalized LUS score had a good level of discrimination between outpatients and others with area under the ROC of 0.80 (95% CI 0.68-0.92) CONCLUSIONS: Systematic LUS has potential as a reliable, cheap and easy-to-use triage tool for the early risk stratification in COVID-19 patients presenting in EDs url: https://www.ncbi.nlm.nih.gov/pubmed/32940646/ doi: 10.1093/cid/ciaa1408 id: cord-351314-atsuh8e2 author: Bryson-Cahn, Chloe title: A Novel Approach for a Novel Pathogen: using a home assessment team to evaluate patients for 2019 novel coronavirus (SARS-CoV-2) date: 2020-03-12 words: 1255.0 sentences: 67.0 pages: flesch: 45.0 cache: ./cache/cord-351314-atsuh8e2.txt txt: ./txt/cord-351314-atsuh8e2.txt summary: Safe evaluation of persons for suspected infection with a special pathogen (including SARS-CoV-2) in the traditional healthcare environment is costly and resource intensive. It requires specialized rooms, use of personal protective equipment (PPE), monitored donning and doffing, logistically-complicated patient transportation from the community to the healthcare facility and back (typically through emergency medical services), and appropriate decontamination of transport and hospital environments. 4 The patient is evaluated by the physician, who gathers a focused history and All involved HAT members complete a daily log including temperature and respiratory and gastrointestinal symptom reporting through employee health for 14 days or until SARS-CoV-2 testing returns negative from the index visit. This model benefits both the public health and clinical healthcare systems by increasing safety and efficiency while reducing the costs and complexity of SARS-CoV-2 testing for patients who do not require emergency evaluation or hospitalization. abstract: Thousands of people in the United States have required testing for SARS-CoV-2. Evaluation for a special pathogen is resource intensive. We report an innovative approach to home assessment that, in collaboration with public health, enables safe evaluation and specimen collection outside the healthcare setting, avoiding unnecessary exposures and resource utilization. url: https://www.ncbi.nlm.nih.gov/pubmed/32166310/ doi: 10.1093/cid/ciaa256 id: cord-277611-3iynrfzq author: Buetti, Niccolò title: Risk factors for SARS-CoV-2 detection in blood of critically ill patients date: 2020-09-02 words: 810.0 sentences: 86.0 pages: flesch: 68.0 cache: ./cache/cord-277611-3iynrfzq.txt txt: ./txt/cord-277611-3iynrfzq.txt summary: In their multivariate analysis the authors showed that SARS-CoV-2 RNAaemia was strongly associated with the clinical class, with higher level RNAaemia among critically ill patients. Therefore, we conducted a similar study using prospectively collected data at the Bichat University Hospital, France, in order to identify risk factors for SARS-CoV-2 detection in blood in critically ill intubated patients. In order to identify risk factors for SARS-CoV-2 detection in blood, we used univariable and multivariable mixed-effect logistic models for clustered data (PROC GLIMMIX of SAS) and we adjusted for the time between symptoms'' onset and date of sampling. Using univariable mixed-effect models after adjusting for the time interval between onset of symptoms and date of sampling, we showed that immunosuppression (OR 12.16, 95% CI 1.74-84.93, p=0.013) and chronic renal failure (OR 5.98, A c c e p t e d M a n u s c r i p t 3 95% CI 1.14-31.35, p=0.035) increased the risk for SARS-CoV-2 detection in blood (Table) . abstract: nan url: https://doi.org/10.1093/cid/ciaa1315 doi: 10.1093/cid/ciaa1315 id: cord-331465-humpwwk2 author: Canaday, David H title: On setting expectations for a SARS-CoV-2 Vaccine date: 2020-06-04 words: 997.0 sentences: 67.0 pages: flesch: 45.0 cache: ./cache/cord-331465-humpwwk2.txt txt: ./txt/cord-331465-humpwwk2.txt summary: Therefore, the expectation that a SARS-CoV-2 vaccine can develop this level of protection from an immune naive state, especially in the setting of immunizing elderly individuals whose naive B and T cells are substantially diminished, needs to be set with caution. Data from several influenza studies suggest that increased CMI, specifically including both CD4+ and CD8+ T cells, helps mitigate influenza severity in older adults when infected despite vaccination [6] [7] [8] . We should expect all of the existing clinical trial candidates to have incomplete effectiveness, and we need to establish whether those that ineffectively recruit CMI have inferior disease mitigation when COVID-19 develops despite vaccination. Logically, none of the current clinical trials use a live attenuated vaccine, as we simply do not know enough about SARS-CoV-2 virology to safely put forward such a candidate. mRNA vaccines against H10N8 and H7N9 influenza viruses of pandemic potential are immunogenic and well tolerated in healthy adults in phase 1 randomized clinical trials abstract: The global coronavirus pandemic is unlike any other since 1918. A century of dramatic medical advances has produced a public expectation that the medical field will rapidly provide solutions to restore normalcy. In under 6 months, since SARS-CoV-2 was identified, the massive international effort to develop a SARS-CoV-2 vaccine has generated more than 140 vaccines in different stages of development with 9 already recruiting into clinical trials posted on clinicaltrials.gov. The long-term strategy to handle COVID-19 will almost certainly rely on vaccines. But, what type of protection can we realistically expect to achieve from vaccines and when? url: https://doi.org/10.1093/cid/ciaa726 doi: 10.1093/cid/ciaa726 id: cord-010570-ytv7dwr0 author: Casadevall, Arturo title: Return to the Past: The Case for Antibody-Based Therapies in Infectious Diseases date: 1995-07-17 words: 7469.0 sentences: 454.0 pages: flesch: 31.0 cache: ./cache/cord-010570-ytv7dwr0.txt txt: ./txt/cord-010570-ytv7dwr0.txt summary: In the preantibiotic era, passive antibody administration (serum therapy) was useful for the treatment of many infectious diseases. We briefly review the use of antibody-based therapy in the early 20th century and make the case for reintroducing passive antibody administration for the treatment ofinfectious diseases. Given the diminishing efficacy of existing antimicrobials because of widespread resistance and the difficulties of treating infections in immunosuppressed individuals, the reintroduction of antibody-based therapies is an option that should be given serious consideration. Thus, antibody therapy is still widely used in medicine, but its role in the treatment of infections is limited largely to viral and toxin neutralization and replacement therapy in patients with immunoglobulin deficiencies. In the past, serum therapy was effective against various pathogens despite the fact that immune sera contained only small amounts of specific antibody. Antibody-based therapies have traditionally been most effective in infections where viral and toxin neutralization modifies the course of the disease. abstract: In the preantibiotic era, passive antibody administration (serum therapy) was useful for the treatment of many infectious diseases. The introduction of antimicrobial chemotherapy in the 1940s led to the rapid abandonment of many forms of passive antibody therapy. Chemotherapy was more effective and less toxic than antibody therapy. In this last decade of the 20th century the efficacy of antimicrobial chemotherapy is diminishing because of the rapidly escalating number of immunocompromised individuals, the emergence of new pathogens, the reemergence of old pathogens, and widespread development of resistance to antimicrobial drugs. This diminishment in the effectiveness of chemotherapy has been paralleled by advances in monoclonal antibody technology that have made feasible the generation of human antibodies. This combination of factors makes passive antibody therapy an option worthy of serious consideration. We propose that for every pathogen there exists an antibody that will modify the infection to the benefit of the host. Such antibodies are potential antimicrobial agents. Antibody-based therapies have significant advantages and disadvantages relative to standard chemotherapy. The reintroduction of antibody-based therapy would require major changes in the practices of infectious disease specialists. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7197598/ doi: 10.1093/clinids/21.1.150 id: cord-282539-skzosh6u author: Casadevall, Arturo title: Implications of Coronavirus Disease 2019 (COVID-19) Antibody Dynamics for Immunity and Convalescent Plasma Therapy date: 2020-08-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32805024/ doi: 10.1093/cid/ciaa1213 id: cord-317940-yg91bsmm author: Chalumeau, Martin title: Transmission of Panton-Valentine Leukocidin–Producing Staphylococcus aureus to a Physician during Resuscitation of a Child date: 2005-08-01 words: 1045.0 sentences: 60.0 pages: flesch: 43.0 cache: ./cache/cord-317940-yg91bsmm.txt txt: ./txt/cord-317940-yg91bsmm.txt summary: title: Transmission of Panton-Valentine Leukocidin–Producing Staphylococcus aureus to a Physician during Resuscitation of a Child We report the first case of transmission of Panton-Valentine leukocidin–producing Staphylococcus aureus to a physician during the resuscitation of an infant with fatal pneumonia. We report the first case of transmission of Panton-Valentine leukocidin-producing Staphylococcus aureus to a physician during the resuscitation of an infant with fatal pneumonia. Severe respiratory diseases, in immunocompetent infants, and chronic furunculosis have been associated with Staphylococcus aureus strains producing Panton-Valentine leukocidin (PVL), a cytotoxin that causes leukocyte destruction and tissue necrosis [1] . S. aureus strains susceptible to methicillin were isolated from samples from the physician and from 5 other health care workers. aureus isolates from the infant (S1) and the physician (S2) but not from the isolates from the other health care workers. aureus strain from a patient to a health care worker during resuscitation. abstract: We report the first case of transmission of Panton-Valentine leukocidin–producing Staphylococcus aureus to a physician during the resuscitation of an infant with fatal pneumonia. The physician exhibited numerous furuncles. This case highlights the necessity for health care workers to protect themselves against transmission of infectious diseases from patient to care giver. url: https://www.ncbi.nlm.nih.gov/pubmed/16007520/ doi: 10.1086/431762 id: cord-312928-ef8hqs4s author: Chavanet, Pascal title: Viral Upper Respiratory Tract Infection and Otitis Media Complication in Young Children date: 2008-03-15 words: 590.0 sentences: 36.0 pages: flesch: 43.0 cache: ./cache/cord-312928-ef8hqs4s.txt txt: ./txt/cord-312928-ef8hqs4s.txt summary: title: Viral Upper Respiratory Tract Infection and Otitis Media Complication in Young Children [1] conducted a large, longitudinal observational study of children with upper respiratory infection and examined for otitis complicationeither acute otitis media or otitis media with effusion. Indeed, in this study, the rate of respiratory syncitial virus infection was found to be low, probably as a result of the method used (conventional assays, type of molecular technique, RT-PCR vs. In this study, children aged !1 year and those who attended day care centers had a greater risk of acquiring upper respiratory tract infection and otitis media, compared with older children and those who were cared for at home. This article is important, especially because the rate of complications of otitis in upper respiratory tract infection was longitudinally studied. Viral upper respiratory tract infection and otitis media complication in young children Rates of hospitalisation for influenza, respiratory syncytial virus and human metapneumovirus among infants and young children abstract: nan url: https://doi.org/10.1086/528686 doi: 10.1086/528686 id: cord-291726-8670s4st author: Che, Xiao-yan title: A Patient with Asymptomatic Severe Acute Respiratory Syndrome (SARS) and Antigenemia from the 2003–2004 Community Outbreak of SARS in Guangzhou, China date: 2006-07-01 words: 2584.0 sentences: 102.0 pages: flesch: 46.0 cache: ./cache/cord-291726-8670s4st.txt txt: ./txt/cord-291726-8670s4st.txt summary: Seventeen serum specimens were collected from 4 index case patients who exhibited recurrence of SARS with laboratory-confirmed SARS-CoV infection in Guangzhou City, China, from 22 December 2003 through 30 January 2004. The findings of these 2 assays had been validated previously with the use of serum specimens obtained from patients with serologically confirmed SARS, and the sensitivity and specificity of the N antigen-capture ELISA were documented [4] [5] [6] . Although none of the 4 index case patients showed evidence of secondary spread of the infection [1] , the direct detection of SARS-CoV N protein by the highly sensitive CIA a Serum samples in a serial 2-fold dilution (from 10-fold to 5120-fold). However, in the 2003-2004 community outbreak of SARS, none of the 4 index case patients with confirmed SARS had severe illness, and they all seemed to have acquired infection with SARS-CoV directly from animals. abstract: An asymptomatic case of severe acute respiratory syndrome (SARS) occurred early in 2004, during a community outbreak of SARS in Guangzhou, China. This was the first time that a case of asymptomatic SARS was noted in an individual with antigenemia and seroconversion. The asymptomatic case patient and the second index case patient with SARS in the 2003–2004 outbreak both worked in the same restaurant, where they served palm civets, which were found to carry SARS-associated coronaviruses. Epidemiological information and laboratory findings suggested that the findings for the patient with asymptomatic infection, together with the findings from previously reported serological analyses of handlers of wild animals and the 4 index case patients from the 2004 community outbreak, reflected a likely intermediate phase of animal-to-human transmission of infection, rather than a case of human-to-human transmission. This intermediate phase may be a critical stage for virus evolution and disease prevention. url: https://www.ncbi.nlm.nih.gov/pubmed/16758408/ doi: 10.1086/504943 id: cord-007064-nepgttxf author: Chemaly, Roy F title: A Phase II, Randomized, Double-blind, Placebo-Controlled Trial of Presatovir for the Treatment of Respiratory Syncytial Virus Upper Respiratory Tract Infection in Hematopoietic-Cell Transplant Recipients date: 2019-12-03 words: 5033.0 sentences: 227.0 pages: flesch: 42.0 cache: ./cache/cord-007064-nepgttxf.txt txt: ./txt/cord-007064-nepgttxf.txt summary: title: A Phase II, Randomized, Double-blind, Placebo-Controlled Trial of Presatovir for the Treatment of Respiratory Syncytial Virus Upper Respiratory Tract Infection in Hematopoietic-Cell Transplant Recipients This is the largest randomized, double blind, placebo-controlled clinical trial to date for the treatment of allogeneic and autologous HCT recipients with RSV URTIs. Presatovir treatment did not meet the coprimary endpoints of a greater time-weighted average change in the RSV viral load from Day 1 to 9 and the reduced development of LRTCs through Day 28, but was well tolerated, with a comparable safety profile relative to the placebo. In a post hoc analysis of patients with lymphopenia, the proportion who developed an LRTC through Day 28 was 51% lower following treatment with presatovir, as compared to the placebo; other post hoc analyses also indicated trends toward a treatment effect on LRTCs. The results suggest lessons for the design of future clinical trials of drugs for RSV or other respiratory viruses in transplant recipients or other immunocompromised patients. abstract: BACKGROUND: Hematopoietic-cell transplant (HCT) recipients are at risk for severe respiratory syncytial virus (RSV) infection. We evaluated the RSV fusion inhibitor presatovir in a randomized, double-blind, Phase II trial in HCT recipients with RSV upper respiratory tract infections. METHODS: Patients were stratified by lymphopenia (<200/µL) and ribavirin use; were randomized, stratified by lymphopenia (<200/μL) and ribavirin use, to receive oral presatovir at 200 mg or a placebo on Days 1, 5, 9, 13, and 17, and were followed through Day 28. The coprimary efficacy endpoints were the time-weighted average change in the nasal RSV viral load between Days 1 and 9 and the proportion of patients developing lower respiratory tract complications (LRTCs) through Day 28. RESULTS: From 23 January 2015 to 16 June 2017, 189 patients were randomly assigned to treatment (96 to presatovir and 93 to the placebo). Presatovir treatment, compared with the placebo treatment, did not significantly affect (prespecified α = 0.01) a time-weighted average decline in the RSV viral load from Day 1 to 9 (treatment difference, −0.33 log(10) copies/mL; 95% confidence interval [CI] −.64 to −.02 log(10) copies/mL; P = .040) or the progression to LRTC (11.2% vs 19.5%, respectively; odds ratio, 0.50; 95% CI, .22–1.18; P = .11). In a post hoc analysis among patients with lymphopenia, presatovir decreased LRTC development by Day 28 (2/15 [13.3%] vs 9/14 [64.3%], respectively; P = .008), compared with the placebo. Adverse events were similar for patients receiving presatovir and the placebo. CONCLUSIONS: Presatovir had a favorable safety profile in adult HCT recipients with RSV but did not achieve the coprimary endpoints. Exploratory analyses suggest an antiviral effect among patients with lymphopenia. CLINICAL TRIALS REGISTRATION: NCT02254408; EUDRA-CT#2014-002474-36. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7108134/ doi: 10.1093/cid/ciz1166 id: cord-288558-rthnj6wd author: Cheng, V. C. C. title: Viral Replication in the Nasopharynx Is Associated with Diarrhea in Patients with Severe Acute Respiratory Syndrome date: 2004-02-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The role of severe acute respiratory syndrome (SARS) coronavirus as an enteric pathogen was investigated in a cohort of 142 patients with SARS who were treated with a standard treatment protocol. Data from daily hematological, biochemical, radiological, and microbiological investigations were prospectively collected, and the correlation of these findings with diarrhea was retrospectively analyzed. Sixty-nine patients (48.6%) developed diarrhea at a mean (± standard deviation [SD]) of 7.6 ± 2.6 days after the onset of symptoms. The diarrhea was most severe at a mean (±SD) of 8.8 ± 2.4 days after onset, with a maximum frequency of 24 episodes per day (median, 5 episodes; range, 3–24 episodes). A higher mean virus load in nasopharyngeal specimens obtained on day 10 after the onset of symptoms was significantly associated with the occurrence of diarrhea (3.1 log(10) vs. 1.8 log(10) copies/mL; P = .01) and mortality (6.2 vs. 1.7 log(10) copies/mL; P < .01). However, diarrhea was not associated with mortality. The lung and the gastrointestinal tract may react differently to SARS coronavirus infection. Additional investigation of the role of SARS coronavirus in the pathogenesis of diarrhea in patients with SARS should be conducted. url: https://www.ncbi.nlm.nih.gov/pubmed/14765337/ doi: 10.1086/382681 id: cord-301066-62qe4fb0 author: Chiu, Susan S. title: Human Coronavirus NL63 Infection and Other Coronavirus Infections in Children Hospitalized with Acute Respiratory Disease in Hong Kong, China date: 2005-06-15 words: 3944.0 sentences: 220.0 pages: flesch: 56.0 cache: ./cache/cord-301066-62qe4fb0.txt txt: ./txt/cord-301066-62qe4fb0.txt summary: In 2001 and 2002, we performed prospective clinical and virological studies of children (age, р18 years) with acute respiratory tract infection who were admitted to Queen Mary Hospital (Hong Kong, China). We studied a systematic sample of children (age, р18 years) with acute respiratory infection admitted to Queen Mary Hospital during the period from August 2001 to March 2002. One child with HCoV-NL63 upper respiratory tract infection had positive results of only the consensus primer PCR, so no viral load could be measured. We documented that human coronavirus infection was a significant cause of hospitalization for children aged р18 years, accounting for 4.4% of all admissions for acute respiratory infections. A previous study showed that 8.2% of children aged !18 months who were admitted to a Chicago, Illinois, hospital with lower respiratory tract diseases had serological evidence of HCoV-229E or HCoV-OC43 infection [13] . abstract: Background. Human coronavirus NL63 (HCoV-NL63) is a recently discovered human coronavirus found to cause respiratory illness in children and adults that is distinct from the severe acute respiratory syndrome (SARS) coronavirus and human coronaviruses 229E (HCoV-229E) and OC43 (HCoV-OC43). Methods. We investigated the role that HCoV-NL63, HCoV-OC43, and HCoV-229E played in children hospitalized with fever and acute respiratory symptoms in Hong Kong during the period from August 2001 through August 2002. Results. Coronavirus infections were detected in 26 (4.4%) of 587 children studied; 15 (2.6%) were positive for HCoV-NL63, 9 (1.5%) were positive for HCoV-OC43, and 2 (0.3%) were positive for HCoV-229E. In addition to causing upper respiratory disease, we found that HCoV-NL63 can present as croup, asthma exacerbation, febrile seizures, and high fever. The mean age (± standard deviation [SD]) of the infected children was 30.7 ± 19.8 months (range, 6–57 months). The mean maximum temperature (±SD) for the 12 children who were febrile was 39.3°C ± 0.9°C, and the mean total duration of fever (±SD) for all children was 2.6 ± 1.2 days (range, 1–5 days). HCoV-NL63 infections were noted in the spring and summer months of 2002, whereas HCoV-OC43 infection mainly occurred in the fall and winter months of 2001. HCoV-NL63 viruses appeared to cluster into 2 evolutionary lineages, and viruses from both lineages cocirculated in the same season. Conclusions. HCoV-NL63 is a significant pathogen that contributes to the hospitalization of children, and it was estimated to have caused 224 hospital admissions per 100,000 population aged ⩽6 years each year in Hong Kong. url: https://www.ncbi.nlm.nih.gov/pubmed/15909257/ doi: 10.1086/430301 id: cord-278259-pbnnp9i1 author: Choi, Eun Hwa title: The Association of Newly Identified Respiratory Viruses with Lower Respiratory Tract Infections in Korean Children, 2000–2005 date: 2006-09-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Background. This study was performed to evaluate the associations of newly recognized viruses, namely, human metapneumovirus (hMPV), human coronavirus (HCoV)–NL63, and human bocavirus (HBoV) with lower respiratory tract infections (LRTIs) in previously healthy children. Methods. To determine the prevalences of 11 viruses—respiratory syncytial virus (RSV), adenovirus, rhinovirus, parainfluenza viruses (PIVs) 1 and 3, influenza viruses A and B, hMPV, HCoV, HCoV-NL63, and HBoV—among infants or children with LRTIs, in association with their epidemiologic characteristics, we performed multiplex reverse-transcriptase polymerase chain reaction on nasopharyngeal aspirates obtained from 515 children 5 years old with LRTIs during the period 2000–2005. Results. Viruses were identified in 312 (60.6%) of the 515 patients. RSV was detected in 122 (23.7%), HBoV in 58 (11.3%), adenovirus in 35 (6.8%), PIV-3 in 32 (6.2%), rhinovirus in 30 (5.8%), hMPV in 24 (4.7%), influenza A in 24 (4.7%), PIV-1 in 9 (1.7%), influenza B in 9 (1.7%), and HCoV-NL63 in 8 (1.6%). Coinfections with 2 viruses were observed in 36 patients (11.5%). Twenty-two patients (37.9%) infected with HBoV had a coinfection. Bronchiolitis was frequently diagnosed in patients who tested positive for RSV, PIV-3, or rhinovirus, whereas influenza A, PIV-1, and HCoV-NL63 were commonly found in patients with croup. The age distributions of patients with viral infections differed; notably, RSV was responsible for 77% of LRTIs that occurred in infants 3 months old. The number of hMPV infections peaked between February and April, whereas the number of HCoV-NL63 infections peaked between April and May. Conclusions. This study describes the features of LRTIs associated with newly identified viruses in children, compared with those associated with known viruses. Additional investigations are required to define the role of HBoV in LRTI. url: https://www.ncbi.nlm.nih.gov/pubmed/16886150/ doi: 10.1086/506350 id: cord-007321-7gi6xrci author: Chow, Anthony W. title: Evaluation of New Anti-Infective Drugs for the Treatment of Respiratory Tract Infections date: 1992-11-17 words: 16053.0 sentences: 825.0 pages: flesch: 31.0 cache: ./cache/cord-007321-7gi6xrci.txt txt: ./txt/cord-007321-7gi6xrci.txt summary: These guidelines for the evaluation of drugs for the treatment of respiratory tract infections include acute streptococcal pharyngitis and tonsillitis, acute otitis media, acute and chronic sinusitis, acute exacerbations of chronic bronchitis, and acute infectious pneumonia (table 1). This is often the case in otitis media, sinusitis, and pneumonia, when the use of invasive procedures such as tympanocentesis, sinus puncture, or transtracheal aspiration to confirm microbial eradication in the patient who is improving clinically generally is considered unjustified. Patients eligible for study entrance are children or adults with symptomatic pharyngitis or tonsillitis of acute onset clinically consistent with infection with group A I3-hemolytic streptococci and from whom group A (3-hemolytic streptococci have been isolated in cultures of throat -swab specimen or for whom a rapid screening test has indicated the presence of streptococci. abstract: These guidelines deal with the evaluation of anti-infective drugs for the treatment of respiratory tract infections. Five clinical entities are described: streptococcal pharyngitis and tonsillitis, otitis media, sinusitis, bronchitis, and pneumonia. A wide variety of microorganisms are potentially pathogenetic in these diseases; these guidelines focus on the bacterial infections. Inclusion of a patient in a trial of a new drug is based on the clinical entity, with the requirement that a reasonable attempt will be made to establish a specific microbial etiology. Microbiologic evaluation of efficacy requires isolation of the pathogen and testing for in vitro susceptibility. Alternatively, surrogate markers may be used to identify the etiologic agent. The efficacy of new drugs is evaluated with reference to anticipated response rates. Establishment of the microbial etiology of respiratory tract infections is hampered by the presence of “normal flora” of the nose, mouth, and pharynx, which may include asymptomatic carriage of potential pathogens. This issue is addressed for each category of infection described. For example, it is suggested that for initial phase 2 trials of acute otitis media and acute sinusitis tympanocentesis or direct sinus puncture be used to collect exudate for culture. Acute exacerbations of chronic bronchitis also present difficulties in the establishment of microbial etiology. These guidelines suggest that clinical trials employ an active control drug but leave open the possibility of a placebo-controlled trial. For pneumonia, the guidelines suggest the identification and enrollment of patients by the clinical type of pneumonia, e.g., atypical pneumonia or acute bacterial pneumonia, rather than by etiologic organism or according to whether it was community or hospital acquired. For each respiratory infection, the clinical response is judged as cure, failure, or indeterminate. Clinical improvement is not acceptable unless quantitative response measures can be applied. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7110372/ doi: 10.1093/clind/15.supplement_1.s62 id: cord-275454-an8xvow3 author: Clark, Andrew E title: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Screening With Specimen Pools: Time to Swim, or Too Deep for Comfort? date: 2020-09-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32986122/ doi: 10.1093/cid/ciaa1145 id: cord-307342-3gkiukh4 author: Clark, Eva title: Why contact tracing efforts have failed to curb COVID-19 transmission in much of the U.S date: 2020-08-06 words: 3272.0 sentences: 192.0 pages: flesch: 55.0 cache: ./cache/cord-307342-3gkiukh4.txt txt: ./txt/cord-307342-3gkiukh4.txt summary: By late April 2020, public discourse in the U.S. had shifted toward the idea of using more targeted case-based mitigation tactics (e.g., contact tracing) to combat COVID-19 transmission while allowing for the safe "re-opening" of society, in an effort to reduce the social, economic, and political ramifications associated with stricter approaches. This viewpoint offers a discussion of why testing-tracing efforts failed to sufficiently mitigate COVID-19 across much of the nation, with the hope that such deliberation will help the U.S. public health community better plan for the future. Partly for this reason, our nation rushed to espouse the idea of targeted, case-based COVID-19 management [3] [4] [5] [6] , focusing on expanded testing and contact tracing, while disregarding several major obstacles that set us apart from countries that succeeded in mounting a timely, targeted response. abstract: By late April 2020, public discourse in the U.S. had shifted toward the idea of using more targeted case-based mitigation tactics (e.g., contact tracing) to combat COVID-19 transmission while allowing for the safe “re-opening” of society, in an effort to reduce the social, economic, and political ramifications associated with stricter approaches. Expanded tracing-testing efforts were touted as a key solution that would allow for a precision approach, thus preventing economies from having to shut down again. However, it is now clear that many regions of the U.S. were unable to mount robust enough testing-tracing programs to prevent major resurgences of disease. This viewpoint offers a discussion of why testing-tracing efforts failed to sufficiently mitigate COVID-19 across much of the nation, with the hope that such deliberation will help the U.S. public health community better plan for the future. url: https://www.ncbi.nlm.nih.gov/pubmed/32761123/ doi: 10.1093/cid/ciaa1155 id: cord-353342-2n6kqyeo author: Corman, Victor M. title: Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection date: 2016-02-15 words: 4046.0 sentences: 223.0 pages: flesch: 52.0 cache: ./cache/cord-353342-2n6kqyeo.txt txt: ./txt/cord-353342-2n6kqyeo.txt summary: title: Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection The Middle East respiratory syndrome (MERS) coronavirus causes isolated cases and outbreaks of severe respiratory disease. We studied 37 adult patients infected with MERS coronavirus for viral load in the lower and upper respiratory tracts (LRT and URT, respectively), blood, stool, and urine. Quantitative data, such as viral loads and antibody titers, could enable comparisons with related diseases, in particular, severe acute respiratory syndrome (SARS), for which studies of natural history were conducted in the aftermath of the 2002-2003 epidemic [7] . DISCUSSION We studied quantitative viral excretion and serum antibody kinetics of a substantial group of hospitalized patients infected with MERS-CoV. Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays abstract: Background. The Middle East respiratory syndrome (MERS) coronavirus causes isolated cases and outbreaks of severe respiratory disease. Essential features of the natural history of disease are poorly understood. Methods. We studied 37 adult patients infected with MERS coronavirus for viral load in the lower and upper respiratory tracts (LRT and URT, respectively), blood, stool, and urine. Antibodies and serum neutralizing activities were determined over the course of disease. Results. One hundred ninety-nine LRT samples collected during the 3 weeks following diagnosis yielded virus RNA in 93% of tests. Average (maximum) viral loads were 5 × 10(6) (6 × 10(10)) copies/mL. Viral loads (positive detection frequencies) in 84 URT samples were 1.9 × 10(4) copies/mL (47.6%). Thirty-three percent of all 108 serum samples tested yielded viral RNA. Only 14.6% of stool and 2.4% of urine samples yielded viral RNA. All seroconversions occurred during the first 2 weeks after diagnosis, which corresponds to the second and third week after symptom onset. Immunoglobulin M detection provided no advantage in sensitivity over immunoglobulin G (IgG) detection. All surviving patients, but only slightly more than half of all fatal cases, produced IgG and neutralizing antibodies. The levels of IgG and neutralizing antibodies were weakly and inversely correlated with LRT viral loads. Presence of antibodies did not lead to the elimination of virus from LRT. Conclusions. The timing and intensity of respiratory viral shedding in patients with MERS closely matches that of those with severe acute respiratory syndrome. Blood viral RNA does not seem to be infectious. Extrapulmonary loci of virus replication seem possible. Neutralizing antibodies do not suffice to clear the infection. url: https://www.ncbi.nlm.nih.gov/pubmed/26565003/ doi: 10.1093/cid/civ951 id: cord-264660-tfktgy57 author: Creech, C Buddy title: It’s True Even in a Pandemic: Children are Not Merely Little Adults date: 2020-05-30 words: 980.0 sentences: 64.0 pages: flesch: 55.0 cache: ./cache/cord-264660-tfktgy57.txt txt: ./txt/cord-264660-tfktgy57.txt summary: In this issue of CID, Mehta et al (CID PAPER) provide a systematic review of pediatric COVID-19, evaluating the available literature to date to glean characteristics of disease and transmission. The authors report that children represent only 5% or less of diagnosed COVID cases and the data available at the time of review suggest that children are less likely to develop either severe pneumonia or the laboratory alterations commonly associated with severe disease, such as lymphopenia and elevated inflammatory markers. The authors also report that intrauterine transmission appears to be extremely uncommon and that newborns born to infected mothers are likely to experience either asymptomatic disease or mild disease. Taken together, it would appear that children experience a very different response to SARS-CoV-2 infection than adults and raises the hypothesis that dysregulated host responses may be the primary driver of disease severity. abstract: nan url: https://doi.org/10.1093/cid/ciaa680 doi: 10.1093/cid/ciaa680 id: cord-265242-y8t37p0b author: Cui, Wei title: Expression of Lymphocytes and Lymphocyte Subsets in Patients with Severe Acute Respiratory Syndrome date: 2003-09-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In a cohort of 38 patients with severe acute respiratory syndrome (SARS), we observed leukopenia in 47% of patients, lymphopenia in 84%, and T lymphopenia in 95%. CD4(+) T lymphocyte levels were reduced in 100% of patients, CD8(+) T lymphocyte levels were reduced in 87%, B lymphocyte levels were reduced in 76%, and natural killer cell levels were reduced in 55%. Our data suggested that these patients' immune systems were impaired during the course of SARS. The absolute counts of lymphocyte subsets demonstrated a clinical significance for patients with SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/12955652/ doi: 10.1086/378587 id: cord-292546-un0blb3w author: Dandachi, Dima title: Characteristics, Comorbidities, and Outcomes in a Multicenter Registry of Patients with HIV and Coronavirus Disease-19 date: 2020-09-09 words: 3438.0 sentences: 274.0 pages: flesch: 57.0 cache: ./cache/cord-292546-un0blb3w.txt txt: ./txt/cord-292546-un0blb3w.txt summary: BACKGROUND: People with HIV (PWH) may have numerous risk factors for acquiring Coronavirus disease-19 (COVID-19) and developing severe outcomes, but current data are conflicting. [12] [13] [14] [15] Some of these studies reported that PWH with COVID-19 had similar clinical characteristics and comparable risk of severe disease to the general population. Study variables included patient demographics, HIV-associated variables, underlying medical problems, COVID-19 clinical presentation as reported by patients, laboratory values, treatment, and clinical outcomes. In a multivariable analysis, older age, lower CD4 count, chronic lung disease, hypertension, and high comorbidity burden were significantly associated with severe outcomes (Table 4) . As reported in multiple other studies in people without HIV, we found that age, chronic lung disease, and comorbidity burden were associated with increased rates of severe outcomes. In addition, among HIV-specific factors, we found that a lower CD4 count (< 200 cells/mm3) was associated with poor outcomes, including higher hospitalization rates, lower ICU-free survival, and overall survival. abstract: BACKGROUND: People with HIV (PWH) may have numerous risk factors for acquiring Coronavirus disease-19 (COVID-19) and developing severe outcomes, but current data are conflicting. METHODS: Healthcare providers enrolled consecutively by non-random sampling PWH with lab-confirmed COVID-19, diagnosed at their facilities between April 1st and July 1st, 2020. De-identified data were entered into an electronic Research Electronic Data Capture (REDCap). The primary endpoint was severe outcome, defined as a composite endpoint of intensive care unit (ICU) admission, mechanical ventilation, or death. The secondary outcome was the need for hospitalization. RESULTS: 286 patients were included; the mean age was 51.4 years (SD, 14.4), 25.9% were female, and 75.4% were African-American or Hispanic. Most patients (94.3%) were on antiretroviral therapy (ART), 88.7% had HIV virologic suppression, and 80.8% had comorbidities. Within 30 days of positive SARS-CoV-2 testing, 164 (57.3%) patients were hospitalized, and 47 (16.5%) required ICU admission. Mortality rates were 9.4% (27/286) overall, 16.5% (27/164) among those hospitalized, and 51.5% (24/47) among those admitted to an ICU. The primary composite endpoint occurred in 17.5% (50/286) of all patients and 30.5% (50/164) of hospitalized patients. Older age, chronic lung disease, and hypertension were associated with severe outcomes. A lower CD4 count (<200 cells/mm³) was associated with the primary and secondary endpoints. There was no association between the antiretroviral regimen or lack of viral suppression and predefined outcomes. CONCLUSION: Severe clinical outcomes occurred commonly in PWH and COVID-19. The risk for poor outcomes was higher in those with comorbidities and lower CD4 cell counts, despite HIV viral suppression. url: https://doi.org/10.1093/cid/ciaa1339 doi: 10.1093/cid/ciaa1339 id: cord-341435-b36h69r1 author: Dawson, Patrick title: Loss of Taste and Smell as Distinguishing Symptoms of COVID-19 date: 2020-06-21 words: 1688.0 sentences: 104.0 pages: flesch: 56.0 cache: ./cache/cord-341435-b36h69r1.txt txt: ./txt/cord-341435-b36h69r1.txt summary: In a household study, loss of taste and/or smell was the fourth most reported symptom (26/42; 62%) among COVID-19 case-patients and had the highest positive predictive value (83%; 95% CI: 55–95%) among household contacts. This investigation provided an opportunity to identify household COVID-19 cases and describe their symptom profiles, including loss of taste and smell, prior to diagnosis. Among the 64 household members of COVID-19 index cases, loss of taste and/or smell was reported by 12 individuals, of whom 10 were positive for SARS-CoV-2. The positive predictive value (PPV) of any loss of taste and/or smell (83%, 95% CI: 55-95%) was higher than for fever (subjective or measured) and cough, two of the three classic symptoms, and equal to the third, shortness of breath (83%, 95% CI: 44-97%) ( Table 1 ). In the absence of confirmatory laboratory testing, CSTE criteria for a probable COVID-19 case now include loss of taste and/or smell in conjunction with other non-classic symptoms (3). abstract: In a household study, loss of taste and/or smell was the fourth most reported symptom (26/42; 62%) among COVID-19 case-patients and had the highest positive predictive value (83%; 95% CI: 55–95%) among household contacts. Olfactory and taste dysfunctions should be considered for COVID-19 case identification and testing prioritization. url: https://doi.org/10.1093/cid/ciaa799 doi: 10.1093/cid/ciaa799 id: cord-291286-diwigcy9 author: De Schutter, Iris title: Microbiology of Bronchoalveolar Lavage Fluid in Children With Acute Nonresponding or Recurrent Community-Acquired Pneumonia: Identification of Nontypeable Haemophilus influenzae as a Major Pathogen date: 2011-06-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Background. Precise etiologic diagnosis in pediatric community-acquired pneumonia (CAP) remains challenging. Methods. We conducted a retrospective study of CAP etiology in 2 groups of pediatric patients who underwent flexible bronchoscopy (FOB) with bronchoalveolar lavage (BAL); children with acute nonresponsive CAP (NR-CAP; n = 127) or recurrent CAP (Rec-CAP; n = 123). Procedural measures were taken to limit contamination risk and quantitative bacterial culture of BAL fluid (significance cutoff point, ≥10(4) colony-forming units/mL) was used. Blood culture results, serological test results, nasopharyngeal secretion findings, and pleural fluid culture results were also assessed, where available. Results. An infectious agent was detected in 76.0% of cases. In 51.2% of infections, aerobic bacteria were isolated, of which 75.0%, 28.9%, and 13.3% were Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae, respectively. Most (97.9%) of the H. influenzae strains were nontypeable (NTHi). H. influenzae was detected in 26.0% of NR-CAP cases and 51.2% of Rec-CAP cases, whereas Mycoplasma pneumoniae was the predominant pathogen in the NR-CAP group (accounting for 34.9% of cases) but not in the Rec-CAP group (19.3%). Viruses were found in 30.4% of cases, with respiratory syncytial virus, parainfluenzaviruses, and influenzaviruses detected most frequently. Mixed infections were found in 18.9% of NR-CAP cases and 30.1% of Rec-CAP cases. Conclusions. A variety of microorganisms were isolated with frequent mixed infection. NTHi was one of the major pathogens found, especially in association with recurrent CAP, possibly because of improved detection with the FOB with BAL procedure. This suggests that the burden of pediatric CAP could be reduced by addressing NTHi as a major causative pathogen. url: https://www.ncbi.nlm.nih.gov/pubmed/21628484/ doi: 10.1093/cid/cir235 id: cord-280958-36ytqapi author: Decker, Summer J title: 3D Printed Alternative to the Standard Synthetic Flocked Nasopharyngeal Swabs Used for COVID-19 testing date: 2020-09-10 words: 3513.0 sentences: 266.0 pages: flesch: 63.0 cache: ./cache/cord-280958-36ytqapi.txt txt: ./txt/cord-280958-36ytqapi.txt summary: BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, can be detected in respiratory samples by Real-time Reverse Transcriptase (RT)-PCR or other molecular methods. The performance of 3DP and FLNP swabs were compared in a clinical trial of symptomatic patients at three clinical sites (n=291) using three SARS-CoV-2 EUA tests: a modified version of the CDC Real-time Reverse Transcriptase (RT)-PCR Diagnostic Panel and two commercial automated formats, Roche Cobas and NeuMoDx. RESULTS: The cycle threshold (C(t)) values from the gene targets and the RNase P gene control in the CDC assay showed no significant differences between swabs for both gene targets (p=0.152 and p=0.092), with the RNase P target performing significantly better in the 3DP swabs (p & 0.001). Given the need for widespread testing, 3DP swabs printed on-site are an alternate to FLNP that can rapidly scale in response to acute needs when supply chain disruptions affect availability of collection kits. abstract: BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, can be detected in respiratory samples by Real-time Reverse Transcriptase (RT)-PCR or other molecular methods. Accessibility of diagnostic testing for COVID-19 has been limited by intermittent shortages of supplies required for testing, including flocked nasopharyngeal (FLNP) swabs. METHODS: We developed a 3D-printed nasopharyngeal (3DP) swab as a replacement of the FLNP swab. The performance of 3DP and FLNP swabs were compared in a clinical trial of symptomatic patients at three clinical sites (n=291) using three SARS-CoV-2 EUA tests: a modified version of the CDC Real-time Reverse Transcriptase (RT)-PCR Diagnostic Panel and two commercial automated formats, Roche Cobas and NeuMoDx. RESULTS: The cycle threshold (C(t)) values from the gene targets and the RNase P gene control in the CDC assay showed no significant differences between swabs for both gene targets (p=0.152 and p=0.092), with the RNase P target performing significantly better in the 3DP swabs (p & 0.001). The C(t) values showed no significant differences between swabs for both viral gene targets in the Roche cobas assay (p=0.05 and p=0.05) as well as the NeuMoDx assay (p=0.401 and p=0.484). The overall clinical correlation of COVID-19 diagnosis between all methods was 95.88% (Kappa 0.901). CONCLUSIONS: 3DP swabs were equivalent to standard FLNP in three testing platforms for SARS-CoV-2. Given the need for widespread testing, 3DP swabs printed on-site are an alternate to FLNP that can rapidly scale in response to acute needs when supply chain disruptions affect availability of collection kits. url: https://doi.org/10.1093/cid/ciaa1366 doi: 10.1093/cid/ciaa1366 id: cord-015493-vf4et613 author: Deresinski, Stan title: In the Literature date: 2007-10-15 words: 1565.0 sentences: 67.0 pages: flesch: 45.0 cache: ./cache/cord-015493-vf4et613.txt txt: ./txt/cord-015493-vf4et613.txt summary: Tetracyclines as an oral treatment option for patients with community-onset methicillin-resistant Staphylococcus aureus skin and soft-tissue infections. Subgroup analysis that included only the 225 episodes in which incision and drainage were performed at presentation confirmed that blactam antibiotic therapy was significantly associated with treatment failure. These results are consistent with those of several other recent studies that have found that administration of an antibiotic that inhibits the growth of MRSA improves outcomes, even in patients who have undergone incision and drainage. For example, in a similar retrospective study of 531 episodes of community-acquired MRSA SSTI, most of which were treated with incision and drainage, Ruhe et al. Although Ruhe and colleagues provide evidence of the benefit of doxycyline for the treatment of SSTI due to antibioticsusceptible MRSA, alternative antibiotic choices may be considered. Prospective randomized trial of empiric therapy with trimethoprim-sulfamethoxazole or doxycycline for outpatient skin and soft tissue infections in an area of high prevalence of methicillin-resistant Staphylococcus aureus abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107829/ doi: 10.1086/522526 id: cord-320562-zvsf3va0 author: Dookie, Navisha title: Tuberculosis Elimination in the Era of COVID-19: A Moving Target date: 2020-09-14 words: 1288.0 sentences: 85.0 pages: flesch: 53.0 cache: ./cache/cord-320562-zvsf3va0.txt txt: ./txt/cord-320562-zvsf3va0.txt summary: In this issue, Liu and colleagues describe the impact of a temporary disruption in health services due to COVID-19 mitigation measures on diagnosis and treatment of TB in the Jiangsu province of China. Thus, the resulting decline in case notifications is likely an unintended consequence of limited access to health care services during the pandemic. resulting from limited access to diagnosis and treatment, could potentially escalate TB related mortality have a lasting impact on TB burden. Thus, disruption to health care services will likely result in short term escalation in TB mortality and postlockdown surge in TB case notification, followed by a sustained increase in TB incidence and mortality over the next several years, with long-term consequences on TB elimination. The potential impact of the covid-19 response on tuberculosis in high-burden countries: a modelling analysis Potential impact of the COVID-19 pandemic on HIV, tuberculosis, and malaria in low-income and middle-income countries: a modelling study abstract: nan url: https://doi.org/10.1093/cid/ciaa1400 doi: 10.1093/cid/ciaa1400 id: cord-340317-gwqy6u9x author: Dora, Amy V title: Using Serologic Testing to Assess the Effectiveness of Outbreak Control Efforts, Serial PCR Testing, and Cohorting of Positive SARS-CoV-2 Patients in a Skilled Nursing Facility date: 2020-08-28 words: 1598.0 sentences: 109.0 pages: flesch: 55.0 cache: ./cache/cord-340317-gwqy6u9x.txt txt: ./txt/cord-340317-gwqy6u9x.txt summary: title: Using Serologic Testing to Assess the Effectiveness of Outbreak Control Efforts, Serial PCR Testing, and Cohorting of Positive SARS-CoV-2 Patients in a Skilled Nursing Facility Despite numerous outbreaks, the performance of serologic testing for SARS-CoV-2 in residents of skilled nursing facilities (SNF) is not well described; its utility in epidemiologic sero-surveillance studies and outbreak reporting is under evaluation. As our objective was to identify potentially missed cases of COVID-19 during serial surveillance testing, samples from residents with historically negative SARS-CoV-2 RT-PCR tests with DiaSorin IgG-positive results were re-tested on a second serologic testing platform (Abbott SARS-CoV-2 IgG Immunoassay) for IgG antibody specific to SARS-CoV-2 nucleocapsid. In a cohort of 150 nursing home residents tested for SARS-CoV-2 infection by RT-PCR, including 26 previously diagnosed with COVID-19, the sensitivity of the DiaSorin assay was 92% (24/26) and the specificity was 98% (122/124). abstract: We characterized serology following a nursing home outbreak where residents were serially tested by RT-PCR and positive residents were cohorted. When tested 46-76 days later, 24/26 RT-PCR-positive residents were seropositive; none of the 124 RT-PCR-negative residents had confirmed seropositivity, supporting serial SARS-CoV-2 RT-PCR testing and cohorting in nursing homes. url: https://www.ncbi.nlm.nih.gov/pubmed/32857830/ doi: 10.1093/cid/ciaa1286 id: cord-327069-vjlisnui author: Driscoll, Amanda J. title: Standardization of Laboratory Methods for the PERCH Study date: 2017-06-15 words: 4725.0 sentences: 221.0 pages: flesch: 42.0 cache: ./cache/cord-327069-vjlisnui.txt txt: ./txt/cord-327069-vjlisnui.txt summary: To build capacity at the sites, and in alignment with the priorities of the Bill & Melinda Gates Foundation, all PERCH testing was done locally, with the exception of quality assurance testing and a select subset of specialized assays, which were performed at the study reference laboratory (Canterbury Health Laboratories, Christchurch, New Zealand), which also served as the study specimen and isolate biorepository. Induced sputum, pleural fluid, and lung aspirate specimens were collected in saline in universal containers and either refrigerated at 2°C-8°C for a maximum of 24 hours, or frozen at -80°C prior to nucleic acid extraction. Organism identification was done according to standard microbiological methods that were documented in SOPs and clarified at each site at the outset; antimicrobial susceptibility testing followed the Clinical and Laboratory Standards Institute (CLSI) guidelines [15] . abstract: The Pneumonia Etiology Research for Child Health study was conducted across 7 diverse research sites and relied on standardized clinical and laboratory methods for the accurate and meaningful interpretation of pneumonia etiology data. Blood, respiratory specimens, and urine were collected from children aged 1–59 months hospitalized with severe or very severe pneumonia and community controls of the same age without severe pneumonia and were tested with an extensive array of laboratory diagnostic tests. A standardized testing algorithm and standard operating procedures were applied across all study sites. Site laboratories received uniform training, equipment, and reagents for core testing methods. Standardization was further assured by routine teleconferences, in-person meetings, site monitoring visits, and internal and external quality assurance testing. Targeted confirmatory testing and testing by specialized assays were done at a central reference laboratory. url: https://www.ncbi.nlm.nih.gov/pubmed/28575358/ doi: 10.1093/cid/cix081 id: cord-340579-cvze15cj author: Dudley, Joseph P title: Disparities in Age-Specific Morbidity and Mortality from SARS-CoV-2 in China and the Republic of Korea date: 2020-03-31 words: 1430.0 sentences: 74.0 pages: flesch: 46.0 cache: ./cache/cord-340579-cvze15cj.txt txt: ./txt/cord-340579-cvze15cj.txt summary: There is a need to gain greater understanding of the highest risk populations for infection and serious disease from the SARS-CoV-2 virus to support the development and implementation of effective public health surveillance and mitigation efforts, and minimize the adverse effects of the current COVID-19 Pandemic in countries worldwide [1] . The reported data on confirmed cases and fatalities from the SARS-CoV-2 indicate highly significant The available epidemiological and observational data from the ROK suggests that reduced rates of compliance with social distancing and self-quarantine recommendations among different sectors of the population -especially the younger adult and juvenile age cohorts --may have a significant impact on the age-specific rates of morbidity and mortality within the population as a whole. Comparison of Age-Specific Morbidity and Mortality Rates Among Reported Confirmed Cases from China and Republic of Korea Figure 1 abstract: We analyzed age- and sex-specific morbidity and mortality data from SARS-COV-2 pandemic in China and Republic of Korea (ROK). Data from China exhibit a Gaussian distribution with peak morbidity in the 50-59 years cohort, while the ROK data have a bimodal distribution with highest morbidity in the 20-29 years cohort. url: https://doi.org/10.1093/cid/ciaa354 doi: 10.1093/cid/ciaa354 id: cord-271014-xzpvupms author: Erikstrup, Christian title: Estimation of SARS-CoV-2 infection fatality rate by real-time antibody screening of blood donors date: 2020-06-25 words: 2366.0 sentences: 177.0 pages: flesch: 57.0 cache: ./cache/cord-271014-xzpvupms.txt txt: ./txt/cord-271014-xzpvupms.txt summary: title: Estimation of SARS-CoV-2 infection fatality rate by real-time antibody screening of blood donors The objective was to perform nationwide real-time seroprevalence surveying among blood donors as a tool to estimate previous SARS-CoV-2 infections and the population based IFR. We have initiated real-time nationwide anti-SARS-CoV-2 seroprevalence surveying of blood donations as a tool in monitoring the epidemic. Thus, numbers of patients tested positive for SARS-CoV-2, admitted to hospital, needing respiratory assistance or deceased from coronavirus disease 2019 (COVID-19) are updated on a daily basis. The objective of this study is to perform a seroprevalence survey among blood donors as a tool in the monitoring of the SARS-CoV-2 epidemic. In this survey of SARS-CoV-2 antibodies in Danish blood donors we found a seroprevalence of 1.9 (CI: 0.8-2.3) adjusted for the assay performance and a low IFR of 89/100,000 (CI: 72-211). The ratio between estimated antibody-positive individuals and confirmed COVID-19 cases is expected given the targeted early Danish SARS-CoV-2 testing strategy. abstract: BACKGROUND: The pandemic due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has tremendous consequences for our societies. Knowledge of the seroprevalence of SARS-CoV-2 is needed to accurately monitor the spread of the epidemic and to calculate the infection fatality rate (IFR). These measures may help the authorities to make informed decisions and adjust the current societal interventions. The objective was to perform nationwide real-time seroprevalence surveying among blood donors as a tool to estimate previous SARS-CoV-2 infections and the population based IFR. METHODS: Danish blood donors aged 17–69 years giving blood April 6 to May 3 were tested for SARS-CoV-2 immunoglobulin M and G antibodies using a commercial lateral flow test. Antibody status was compared between geographical areas and an estimate of the IFR was calculated. The seroprevalence was adjusted for assay sensitivity and specificity taking the uncertainties of the test validation into account when reporting the 95% confidence intervals (CI). RESULTS: The first 20,640 blood donors were tested and a combined adjusted seroprevalence of 1.9% (CI: 0.8-2.3) was calculated. The seroprevalence differed across areas. Using available data on fatalities and population numbers a combined IFR in patients younger than 70 is estimated at 89 per 100,000 (CI: 72-211) infections. CONCLUSIONS: The IFR was estimated to be slightly lower than previously reported from other countries not using seroprevalence data. The IFR is likely several fold lower than the current estimate. We have initiated real-time nationwide anti-SARS-CoV-2 seroprevalence surveying of blood donations as a tool in monitoring the epidemic. url: https://doi.org/10.1093/cid/ciaa849 doi: 10.1093/cid/ciaa849 id: cord-318204-t024w7h6 author: Fang, Ferric C title: The Laboratory Diagnosis of COVID-19-- Frequently-Asked Questions date: 2020-06-08 words: 2976.0 sentences: 218.0 pages: flesch: 51.0 cache: ./cache/cord-318204-t024w7h6.txt txt: ./txt/cord-318204-t024w7h6.txt summary: As communities attempt to re-open following periods of shutdown, the detection of both SARS-CoV-2 and specific antibodies recognizing the virus will become increasingly important as a means to assess infection and immunity in individuals and communities. In view of the less than ideal sensitivity of an NP swab to detect SARS-CoV-2 infection, it may be useful to repeat testing in a patient in whom the clinical suspicion is high (32) . Although the primary use of serologic tests is to determine prior exposure to SARS-CoV-2, the detection of specific antibodies may support the diagnosis of COVID-19 in a patient with a high clinical suspicion but negative PCR tests (57-59). Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China Early detection of SARS-CoV-2 antibodies in COVID-19 patients as a serologic marker of infection abstract: Diagnostic testing has played and will continue to play a major role in the COVID-19 pandemic. The ability to detect the SARS-CoV-2 coronavirus in respiratory secretions is essential to determine when an individual is infected and potentially infectious to others. Viral detection is used for the identification, management and isolation of individual patients. Viral detection is also used to determine when the virus has entered a community and how rapidly it is spreading. As communities attempt to re-open following periods of shutdown, the detection of both SARS-CoV-2 and specific antibodies recognizing the virus will become increasingly important as a means to assess infection and immunity in individuals and communities. Here we discuss questions commonly asked by clinicians about COVID-19 diagnostic testing. url: https://www.ncbi.nlm.nih.gov/pubmed/32511679/ doi: 10.1093/cid/ciaa742 id: cord-269455-pkjov371 author: Faust, Jeremy Samuel title: Towards a better case fatality estimate for SARS-CoV-2 during the early phase of the United States outbreak date: 2020-05-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32472126/ doi: 10.1093/cid/ciaa639 id: cord-280915-yk872yaz author: Flaherman, Valerie J title: Infant Outcomes Following Maternal Infection with SARS-CoV-2: First Report from the PRIORITY Study date: 2020-09-18 words: 1528.0 sentences: 98.0 pages: flesch: 54.0 cache: ./cache/cord-280915-yk872yaz.txt txt: ./txt/cord-280915-yk872yaz.txt summary: In a prospective U.S. registry of 263 infants born to mothers testing positive or negative for SARS-CoV-2, SARS-CoV-2 status was not associated with birth weight, difficulty breathing, apnea or upper or lower respiratory infection through 8 weeks of age. Currently, national and international guidelines for management of infants born to mothers with SARS-CoV-2 [6] [7] [8] are based on limited data without outcomes reported past the neonatal period. To address this urgent need, we report here early findings from infants born to mothers enrolled in the PRegnancy CoronavIrus Outcomes RegIsTrY (PRIORITY), an ongoing nationwide study of pregnant or recently pregnant women who have confirmed or suspected SARS-CoV-2. Among 263 initial infants enrolled in the PRIORITY study, adverse outcomes, including preterm birth, NICU admission, and respiratory disease did not differ between those born to mothers testing positive for SARS-CoV-2 and those born to mothers testing negative. abstract: Infant outcomes after maternal SARS-CoV-2 infection are not well-described. In a prospective U.S. registry of 263 infants born to mothers testing positive or negative for SARS-CoV-2, SARS-CoV-2 status was not associated with birth weight, difficulty breathing, apnea or upper or lower respiratory infection through 8 weeks of age. url: https://doi.org/10.1093/cid/ciaa1411 doi: 10.1093/cid/ciaa1411 id: cord-322650-q8inhgtr author: Fung, Yin-Wan Wendy title: Use of Clinical Criteria and Molecular Diagnosis to More Effectively Monitor Patients Recovering after Severe Acute Respiratory Syndrome Coronavirus Infection date: 2004-08-15 words: 1132.0 sentences: 64.0 pages: flesch: 50.0 cache: ./cache/cord-322650-q8inhgtr.txt txt: ./txt/cord-322650-q8inhgtr.txt summary: title: Use of Clinical Criteria and Molecular Diagnosis to More Effectively Monitor Patients Recovering after Severe Acute Respiratory Syndrome Coronavirus Infection In conclusion, voriconazole is highly active against Aspergillus species, but additional studies are needed to confirm that our low drug concentrations result from the method of sampling and not from poor efficacy of this molecule in the CSF. In early 2003, a novel severe acute respiratory syndrome (SARS) coronavirus (CoV) [1] spread around the world; ultimately, more than 8000 patients in 32 countries contracted SARS, many of whom died. The ERT method clearly demonstrated the presence of SARS CoV in all samples obtained from the patient on 16 June (table 1) , which was 1 day before his transfer to WTSH. More studies will be necessary to determine the infectivity status of patients who have ERT results positive for SARS CoV. Severe acute respiratory syndrome (SARS): laboratory diagnostic tests abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/15356838/ doi: 10.1086/422887 id: cord-322448-s04e6po9 author: Gadsby, Naomi J. title: Comprehensive Molecular Testing for Respiratory Pathogens in Community-Acquired Pneumonia date: 2016-04-01 words: 4371.0 sentences: 206.0 pages: flesch: 34.0 cache: ./cache/cord-322448-s04e6po9.txt txt: ./txt/cord-322448-s04e6po9.txt summary: Sputum (96%) or endotracheal aspirate (4%) specimens were cultured as per routine practice and also tested with fast multiplex real-time polymerase-chain reaction (PCR) assays for 26 respiratory bacteria and viruses. Comprehensive molecular testing of single lower respiratory tract (LRT) specimens achieved pathogen detection in 87% of CAP patients compared with 39% with culture-based methods. Comprehensive molecular testing significantly improves pathogen detection in CAP, particularly in antimicrobial-exposed patients, and requires only a single LRT specimen. The development of multiplex real-time polymerase-chain reaction (PCR) assays currently enables a respiratory specimen to be rapidly screened for a wide range of viral and atypical bacterial pathogens in a small number of reactions [10] [11] [12] [13] [14] [15] . As our study focused on testing sputum by molecular methods, our high level of pathogen detection for typical bacteria may not be directly comparable to results from other recent studies in hospitalized adult CAP. abstract: Background. The frequent lack of a microbiological diagnosis in community-acquired pneumonia (CAP) impairs pathogen-directed antimicrobial therapy. This study assessed the use of comprehensive multibacterial, multiviral molecular testing, including quantification, in adults hospitalized with CAP. Methods. Clinical and laboratory data were collected for 323 adults with radiologically-confirmed CAP admitted to 2 UK tertiary care hospitals. Sputum (96%) or endotracheal aspirate (4%) specimens were cultured as per routine practice and also tested with fast multiplex real-time polymerase-chain reaction (PCR) assays for 26 respiratory bacteria and viruses. Bacterial loads were also calculated for 8 bacterial pathogens. Appropriate pathogen-directed therapy was retrospectively assessed using national guidelines adapted for local antimicrobial susceptibility patterns. Results. Comprehensive molecular testing of single lower respiratory tract (LRT) specimens achieved pathogen detection in 87% of CAP patients compared with 39% with culture-based methods. Haemophilus influenzae and Streptococcus pneumoniae were the main agents detected, along with a wide variety of typical and atypical pathogens. Viruses were present in 30% of cases; 82% of these were codetections with bacteria. Most (85%) patients had received antimicrobials in the 72 hours before admission. Of these, 78% had a bacterial pathogen detected by PCR but only 32% were culture-positive (P < .0001). Molecular testing had the potential to enable de-escalation in number and/or spectrum of antimicrobials in 77% of patients. Conclusions. Comprehensive molecular testing significantly improves pathogen detection in CAP, particularly in antimicrobial-exposed patients, and requires only a single LRT specimen. It also has the potential to enable early de-escalation from broad-spectrum empirical antimicrobials to pathogen-directed therapy. url: https://www.ncbi.nlm.nih.gov/pubmed/26747825/ doi: 10.1093/cid/civ1214 id: cord-354265-udt2spoe author: Gersh, Felice title: Menopause status and COVID-19 date: 2020-09-23 words: 579.0 sentences: 45.0 pages: flesch: 51.0 cache: ./cache/cord-354265-udt2spoe.txt txt: ./txt/cord-354265-udt2spoe.txt summary: A c c e p t e d M a n u s c r i p t Dear Editor, We greatly appreciate the publication of this important research article, for its exploration of the connection of estradiol levels and menopausal status with outcomes from infections with SARS-CoV-2 in women. We advocate for the use of physiologically dosed human-identical transdermal estradiol as hormone replacement, combined with human-identical cyclic progesterone, in appropriate recently menopausal women. (8) Given the potential for serious negative effects ensuing from a state of estradiol deficiency, heightened by the COVID-19 pandemic, not only should appropriate postmenopausal women be considered for hormone replacement therapy, but women being treated with aromatase inhibitors and estrogen receptor antagonists should be counseled on the risks and benefits of those drugs, personalized in each case, in light of the findings of this study. Potential influence of menstrual status and sex hormones on female SARS-CoV-2 infection: A cross-sectional study from Multicentre in Wuhan abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32968797/ doi: 10.1093/cid/ciaa1447 id: cord-341838-lkz8ro90 author: Gervasoni, Cristina title: Clinical features and outcomes of HIV patients with coronavirus disease 2019 date: 2020-05-14 words: 1794.0 sentences: 117.0 pages: flesch: 59.0 cache: ./cache/cord-341838-lkz8ro90.txt txt: ./txt/cord-341838-lkz8ro90.txt summary: The aim of this retrospective study was to describe the clinical characteristics and outcomes of HIVinfected patients with a probable/proven diagnosis of SARS-CoV-2 infection who have been regularly followed up by our hospital. As in the general population, the large majority of our patients were males, but their mean age was nearly 10 years lower than that observed in HIV-negative COVID-19 patients. 16 Furthermore, the findings of this study document favourable outcomes in HIV patients treated mainly with integrase inhibitors (11% protease inhibitors), which apparently indicates that antiretroviral therapy does not play a key role, A c c e p t e d M a n u s c r i p t 8 although a potentially protective effect of tenofovir cannot be ruled out given its recently reported effect against SARS-CoV-2 RNA-dependent RNA polymerase. In conclusion, our findings suggest that HIV-positive patients with SARS-CoV-2 infection are not at greater risk of severe disease or death than HIV-negative patients. abstract: Little is known about the clinical outcomes of HIV patients infected with SARS-CoV-2. We describe 47 patients referred to our hospital between 21 February and 16 April 2020 with proven/probable COVID-19, 45 (96%) of whom fully recovered and two died. url: https://doi.org/10.1093/cid/ciaa579 doi: 10.1093/cid/ciaa579 id: cord-280571-ntgt5hy9 author: Ginocchio, Christine C. title: Strengths and Weaknesses of FDA-Approved/Cleared Diagnostic Devices for the Molecular Detection of Respiratory Pathogens date: 2011-05-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The rapid, sensitive, and specific identification of the microbial etiological characteristics of respiratory tract infections enhances the appropriate use of both antibiotics and antiviral agents and reduces the risk of nosocomial transmission. This article reviews the current nucleic acid amplification tests approved by the U.S. Food and Drug Administration (FDA) for the detection of respiratory pathogens. In addition, Emergency Use Authorization tests for the detection of 2009 influenza A H1N1 are discussed. The advantages and limitations of the current FDA-approved/cleared tests are reviewed. url: https://doi.org/10.1093/cid/cir046 doi: 10.1093/cid/cir046 id: cord-272956-0yumc7em author: Gnavi, Roberto title: Therapy With Agents Acting on the Renin-Angiotensin System and Risk of Severe Acute Respiratory Syndrome Coronavirus 2 Infection date: 2020-05-22 words: 1772.0 sentences: 90.0 pages: flesch: 51.0 cache: ./cache/cord-272956-0yumc7em.txt txt: ./txt/cord-272956-0yumc7em.txt summary: Exposure to agents acting on the renin-angiotensin system was not associated with a risk increase of COVID-19 infection in 2 Italian matched case-control studies, 1 nested in hypertensive patients and the other in patients with cardiovascular diseases or diabetes. Consequently, patients treated with ACE inhibitors (ACEIs) or angiotensin II receptor blockers (ARBs), in particular those with diabetes or cardiovascular disease, should be considered at higher risk of developing severe coronavirus disease 2019 (COVID-19) infection (CVi), and of experiencing unfavorable outcomes [2, 3] . As, to the best of our knowledge, a relationship between ACEI or ARB treatments and increased risk of CVi has never been demonstrated [8] , the aim of the present study was to determine whether an association exists between therapies based on agents acting on the RAAS and CVi in 2 populations at greater risk of being diagnosed with SARS-CoV-2 infection: hypertensive patients and patients who were affected by a cardio-cerebrovascular disease. abstract: Exposure to agents acting on the renin-angiotensin system was not associated with a risk increase of COVID-19 infection in 2 Italian matched case-control studies, 1 nested in hypertensive patients and the other in patients with cardiovascular diseases or diabetes. url: https://doi.org/10.1093/cid/ciaa634 doi: 10.1093/cid/ciaa634 id: cord-271269-0gimxteg author: Gourtsoyannis, John title: COVID-19: Possible reasons for the increased prevalence of Olfactory and Gustatory dysfunction observed in European studies date: 2020-05-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32474587/ doi: 10.1093/cid/ciaa685 id: cord-351348-lzo0dz7z author: Gu, Silan title: Alterations of the Gut Microbiota in Patients with COVID-19 or H1N1 Influenza date: 2020-06-04 words: 1994.0 sentences: 147.0 pages: flesch: 50.0 cache: ./cache/cord-351348-lzo0dz7z.txt txt: ./txt/cord-351348-lzo0dz7z.txt summary: METHODS: We conducted a cross-sectional study of 30 COVID-19 patients, 24 influenza A (H1N1) patients, and 30 matched healthy controls (HC) to identify differences in the gut microbiota by 16S ribosomal RNA (rRNA) gene V3-V4 region sequencing. Previous studies indicated that the intestinal flora was closely related to respiratory virus infection and could affect the occurrence and development of diseases through the gut-lung axis [13] . The analysis of group similarities indicated that differences in richness, diversity, A c c e p t e d M a n u s c r i p t and structure of the gut microbiota were not significantly different between general and severe COVID-19 patients (ANOSIM, p=0.426; Supplementary Figure S1 ), indicating that the experimental design was adequate. The gut microbiota signature of COVID-19 and H1N1 patients was analyzed to assess correlations between disease characteristics and the microbiome. abstract: BACKGROUND: Coronavirus disease 2019 (COVID-19) is an emerging serious global health problem. Gastrointestinal symptoms are common in COVID-19 patients, and SARS-CoV-2 RNA has been detected in stool specimens. However, the relationship between the gut microbiome and disease remains to be established. METHODS: We conducted a cross-sectional study of 30 COVID-19 patients, 24 influenza A (H1N1) patients, and 30 matched healthy controls (HC) to identify differences in the gut microbiota by 16S ribosomal RNA (rRNA) gene V3-V4 region sequencing. RESULTS: Compared with HC, COVID-19 patients had significantly reduced bacterial diversity, a significantly higher relative abundance of opportunistic pathogens, such as Streptococcus, Rothia, Veillonella and Actinomyces, and a lower relative abundance of beneficial symbionts. Five biomarkers showed high accuracy for distinguishing COVID-19 patients from HC with an area under the curve (AUC) up to 0.89. Patients with H1N1 displayed lower diversity and different overall microbial composition compared with COVID-19 patients. Seven biomarkers were selected to distinguish the two cohorts with an AUC of 0.94. CONCLUSION: The gut microbial signature of patients with COVID-19 was different from that of H1N1 patients and HC. Our study suggests the potential value of the gut microbiota as a diagnostic biomarker and therapeutic target for COVID-19, but further validation is needed. url: https://www.ncbi.nlm.nih.gov/pubmed/32497191/ doi: 10.1093/cid/ciaa709 id: cord-277307-wabruzfs author: Gu, Wei title: Associations of Early COVID-19 Cases in San Francisco with Domestic and International Travel date: 2020-05-21 words: 1096.0 sentences: 79.0 pages: flesch: 66.0 cache: ./cache/cord-277307-wabruzfs.txt txt: ./txt/cord-277307-wabruzfs.txt summary: In San Francisco, we validated a qRT-PCR test to detect SARS-CoV-2 infection from nasopharyngeal swab samples based on the EUA (Emergency Use Authorization)approved US CDC assay 3 . Those who did not have a recent travel history, a close contact who was COVID-19 positive, or were not a frontline healthcare worker were categorized as community transmission with an unknown source of infection and comprised 39% of cases. Viruses in the G clade comprise most of the genomes sequenced from patients in Europe 8, 9 , but notably have also been identified in the vast majority of cases associated with the New York SARS-CoV-2 outbreak in March to April of 2020, which occurred after the timeline of this study 11, 12 Viruses from two additional travel-associated cases from Europe (UC43) and New York (UC41) were mapped to other clades circulating in Europe (Figure 2) . Sequencing identifies multiple, early introductions of SARS-CoV2 to New York City Region abstract: In early-to-mid March 2020, 20 of 46 (43%) COVID-19 cases at a tertiary care hospital in San Francisco, California were travel-related. Cases were significantly associated with travel to Europe or New York (odds ratio 32.9). Viral genomes recovered from 9 of 12 (75%) cases co-clustered with lineages circulating in Europe. url: https://doi.org/10.1093/cid/ciaa599 doi: 10.1093/cid/ciaa599 id: cord-299499-66qh3r75 author: Guilamo-Ramos, Vincent title: Reconsidering assumptions of adolescent and young adult SARS-CoV-2 transmission dynamics date: 2020-09-07 words: 4199.0 sentences: 218.0 pages: flesch: 42.0 cache: ./cache/cord-299499-66qh3r75.txt txt: ./txt/cord-299499-66qh3r75.txt summary: In this viewpoint, we highlight evidence regarding the increased potential of AYA to transmit SARS-CoV-2 that, to date, has received little attention, discuss adolescent and young adult specific considerations for future COVID-19 control measures, and provide applied programmatic suggestions. Adolescents and young adults (AYA), who are between the ages of 10 and 24 years, account for approximately 20% of the total population in the United States (US), but the extent to which AYA contribute to forward transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not fully understood. In this viewpoint, we highlight evidence regarding the increased potential of AYA to transmit SARS-CoV-2 that, to date, has received little attention, discuss adolescent and young adultspecific considerations for future COVID-19 control measures, and provide applied programmatic suggestions. Adolescent and young adult-specific data Furthermore, behavioral factors unique to AYA may increase the risk of forward transmission of SARS-CoV-2 relative to both younger children and older adults. abstract: Evidence regarding the important role of adolescents and young adults (AYA) in accelerating and sustaining coronavirus disease 2019 (COVID-19) outbreaks is growing. Furthermore, data suggest two known factors that contribute to high severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmissibility—presymptomatic transmission and asymptomatic case presentations—may be amplified in AYA. However, AYA have not been prioritized as a key population in the public health response to the COVID-19 pandemic. Policy decisions that limit public health attention on AYA and are driven by the assumption of insignificant forward transmission from AYA pose a risk to inadvertently reinvigorate local transmission dynamics. In this viewpoint, we highlight evidence regarding the increased potential of AYA to transmit SARS-CoV-2 that, to date, has received little attention, discuss adolescent and young adult specific considerations for future COVID-19 control measures, and provide applied programmatic suggestions. url: https://www.ncbi.nlm.nih.gov/pubmed/32894747/ doi: 10.1093/cid/ciaa1348 id: cord-354943-wxhbwcfr author: Guo, Li title: Profiling Early Humoral Response to Diagnose Novel Coronavirus Disease (COVID-19) date: 2020-03-21 words: 3486.0 sentences: 181.0 pages: flesch: 55.0 cache: ./cache/cord-354943-wxhbwcfr.txt txt: ./txt/cord-354943-wxhbwcfr.txt summary: METHODS: The host humoral response against SARS-CoV-2, including IgA, IgM, and IgG response, was examined by using an ELISA-based assay on the recombinant viral nucleocapsid protein. The positive detection rate is significantly increased (98.6%) when combining IgM ELISA assay with PCR for each patient compared with a single qPCR test (51.9%). Western blot analysis showed that there was no cross-reactivity of SARS-CoV-2 rNP with human plasma positive for IgG antibodies against NL63, 229E, OC43, and HKU1. The antibody levels were then evaluated in the plasma samples of CCs and PCs. The appearance of IgM, IgA, and IgG antibodies against SARS-CoV-2 was positive as early as day 1 after the symptom onset ( Figure 3A) . These results suggest that IgM ELISA can increase the positive detection rate when combined with the PCR method and can be used for the early diagnosis of COVID-19 infections. abstract: BACKGROUND: The emergence of coronavirus disease 2019 (COVID-19) is a major healthcare threat. The current method of detection involves a quantitative polymerase chain reaction (qPCR)–based technique, which identifies the viral nucleic acids when present in sufficient quantity. False-negative results can be achieved and failure to quarantine the infected patient would be a major setback in containing the viral transmission. We aim to describe the time kinetics of various antibodies produced against the 2019 novel coronavirus (SARS-CoV-2) and evaluate the potential of antibody testing to diagnose COVID-19. METHODS: The host humoral response against SARS-CoV-2, including IgA, IgM, and IgG response, was examined by using an ELISA-based assay on the recombinant viral nucleocapsid protein. 208 plasma samples were collected from 82 confirmed and 58 probable cases (qPCR negative but with typical manifestation). The diagnostic value of IgM was evaluated in this cohort. RESULTS: The median duration of IgM and IgA antibody detection was 5 (IQR, 3–6) days, while IgG was detected 14 (IQR, 10–18) days after symptom onset, with a positive rate of 85.4%, 92.7%, and 77.9%, respectively. In confirmed and probable cases, the positive rates of IgM antibodies were 75.6% and 93.1%, respectively. The detection efficiency by IgM ELISA is higher than that of qPCR after 5.5 days of symptom onset. The positive detection rate is significantly increased (98.6%) when combining IgM ELISA assay with PCR for each patient compared with a single qPCR test (51.9%). CONCLUSIONS: The humoral response to SARS-CoV-2 can aid in the diagnosis of COVID-19, including subclinical cases. url: https://www.ncbi.nlm.nih.gov/pubmed/32198501/ doi: 10.1093/cid/ciaa310 id: cord-279167-fj36mzm5 author: Gwaltney, Jack M. title: Acute Community-Acquired Sinusitis date: 1996-12-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/8953061/ doi: 10.1093/clinids/23.6.1209 id: cord-306495-o0ah1gj9 author: Haidar, Ghady title: COVID-19, organ transplantation, and the nuances of immunomodulation: lessons learned and what comes next date: 2020-08-11 words: 1262.0 sentences: 74.0 pages: flesch: 47.0 cache: ./cache/cord-306495-o0ah1gj9.txt txt: ./txt/cord-306495-o0ah1gj9.txt summary: Thus, while morbidity and mortality related to COVID-19 in SOT recipients are substantial, A c c e p t e d M a n u s c r i p t 3 they appear to be driven by age and underlying medical conditions and unaffected by immunosuppression, corroborating the results of other studies in the general population. The study included only 30 lung transplant recipients was therefore unable to assess whether mortality in these patients is greatest (as is the case with sepsis [3] ), or whether COVID-19 precipitates acute or chronic lung allograft rejection. Furthermore, since all laboratory testing was done as standard of care, the study could not evaluate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viremia or the duration of SARS-CoV-2 PCR positivity, which may be longer than that of non-transplant patients. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32780792/ doi: 10.1093/cid/ciaa1193 id: cord-312797-hohzjx74 author: Hamelin, Marie-Ève title: Human Metapneumovirus: A New Player among Respiratory Viruses date: 2004-04-01 words: 3353.0 sentences: 170.0 pages: flesch: 41.0 cache: ./cache/cord-312797-hohzjx74.txt txt: ./txt/cord-312797-hohzjx74.txt summary: Despite the fact that prospective and case-control studies have been limited, the epidemiology and clinical manifestations associated with hMPV have been found to be reminiscent of those of the human respiratory syncytial virus, with most severe respiratory tract infections occurring in infants, elderly subjects, and immunocompromised hosts. In addition, studies have shown that hMPV is not a new pathogen, with serological evidence of human infection dating from 1958 in The Netherlands [4] and viral isolation for the past 10-20 years in Europe and Canada [4, 7] . Symptoms of both upper and lower respiratory tract infections have been associated with hMPV in young children, although most reports are biased towards description of the most severe symptomatology in hospitalized subjects. Virological features and clinical manifestations associated with human metapneumovirus: a new paramyxovirus responsible for acute respiratory-tract infections in all age groups abstract: The human metapneumovirus (hMPV) is a newly described member of the Paramyxoviridae family belonging to the Metapneumovirus genus. Since its initial description in 2001, hMPV has been reported in most parts of the world and isolated from the respiratory tract of subjects from all age groups. Despite the fact that prospective and case-control studies have been limited, the epidemiology and clinical manifestations associated with hMPV have been found to be reminiscent of those of the human respiratory syncytial virus, with most severe respiratory tract infections occurring in infants, elderly subjects, and immunocompromised hosts. Additional research is needed to define the pathogenesis of this viral infection and the host's specific immune response. url: https://www.ncbi.nlm.nih.gov/pubmed/15034830/ doi: 10.1086/382536 id: cord-344038-20n74z3o author: Han, Mi Seon title: Sequential analysis of viral load in a neonate and her mother infected with SARS-CoV-2 date: 2020-04-16 words: 1548.0 sentences: 110.0 pages: flesch: 67.0 cache: ./cache/cord-344038-20n74z3o.txt txt: ./txt/cord-344038-20n74z3o.txt summary: In this study, we described the clinical manifestation of COVID-19 in a neonate and her mother, and further analyzed the viral load kinetics of SARS-CoV-2 in clinical specimens from different sources. The neonate was febrile and SARS-CoV-2 RNA was detected in all of her clinical specimens, with high viral loads in the respiratory and stool samples. Her mother had mild symptoms with SARS-CoV-2 RNA detected in the respiratory and stool specimens at low titers. An interesting finding in this study is that SARS-CoV-2 RNA was detected in all of the neonate''s clinical specimens, including blood, urine, stool, and saliva along with the upper respiratory tract specimens. In comparison, although exposed to the same infection source, only the mother''s respiratory and stool specimens were positive for SARS-CoV-2 and at a much lower viral load. Recent studies have reported that SARS-CoV-2 RNA could be detected in different types of clinical specimens other than respiratory tract samples [9] . abstract: We report changes in viral load over time in a 27-day old neonate with COVID-19 who presented with fever, cough, and vomiting. SARS-CoV-2 RNA was detected in the nasopharynx, oropharynx, stool, saliva, plasma, and urine. The highest viral RNA copies in nasopharynx decreased over time while viral load in stool remained high. url: https://www.ncbi.nlm.nih.gov/pubmed/32297925/ doi: 10.1093/cid/ciaa447 id: cord-310390-7pkbd3kg author: Han, Xiaoyu title: Novel Coronavirus Pneumonia (COVID-19) Progression Course in 17 Discharged Patients: Comparison of Clinical and Thin-Section CT Features During Recovery date: 2020-03-30 words: 3174.0 sentences: 196.0 pages: flesch: 56.0 cache: ./cache/cord-310390-7pkbd3kg.txt txt: ./txt/cord-310390-7pkbd3kg.txt summary: title: Novel Coronavirus Pneumonia (COVID-19) Progression Course in 17 Discharged Patients: Comparison of Clinical and Thin-Section CT Features During Recovery BACKGROUND: To retrospectively analyze the evolution of clinical features and thin-section CT imaging of novel coronavirus pneumonia (COVID-19) in 17 discharged patients. Hence, this study aimed to analyze the serial thin-section CT changes of 17 discharged patients with COVID-19, and to compare the progression trend of imaging pattern and clinical parameters. The standard for survive and discharge of patients was according to the guideline of Diagnosis and Treatment of Pneumonia Caused by SARS-COV-2 (trial sixth version) published by the China Ministry of Health [22] , which include: temperature returning to normal for more than 3 days, both the clinical and chest imaging showing significant improvement, and two consecutive respiratory pathogen nucleic acid tests turning negative (the interval at least 24 hours). abstract: BACKGROUND: To retrospectively analyze the evolution of clinical features and thin-section CT imaging of novel coronavirus pneumonia (COVID-19) in 17 discharged patients. METHODS: Serial thin-section CT scans of 17 discharged patients with COVID-19 were obtained during recovery. Longitudinal changes of clinical parameters and CT pattern were documented in all patients during 4 weeks since admission. CT score was used to evaluate the extent of the disease. RESULTS: There was a marked improvement of fever, lymphocytes count, C-reactive protein and erythrocyte sedimentation rate within the first two weeks since admission. However, the mean CT score rapidly increased from the 1(st) to 3(rd) week, with a top score of 8.2 obtained in the 2(nd) week. During the 1(st) week, the main CT pattern was ground-glass opacities (GGO,76.5%). The frequency of GGO (52.9%) decreased in the 2(nd) week. Consolidation and mixed patterns (47.0%) were noted in the 2(nd) week. Thereafter, consolidations generally dissipated into GGO and the frequency of GGO increased in the 3(rd) week (76.5%) and 4(th) week (71.4%). Opacities were mainly located in the peripheral (76.5%), subpleural (47.1%) zones of the lungs, and presented as focal (35.3%) or multifocal (29.4%) in the 1(st) week and became more diffuse in the 2(nd) (47.1%) and 3(rd )week (58.8%), then showed reduced extent in 4(th )week (50%). CONCLUSIONS: The progression course of CT pattern was later than the clinical parameters within the first two weeks since admission; however, there was a synchronized improvement in both clinical and radiologic features in the 4(th) week. url: https://doi.org/10.1093/cid/ciaa271 doi: 10.1093/cid/ciaa271 id: cord-296588-q2716lda author: Hanson, Kimberly E title: Infectious Diseases Society of America Guidelines on the Diagnosis of COVID-19 date: 2020-06-16 words: 10179.0 sentences: 681.0 pages: flesch: 47.0 cache: ./cache/cord-296588-q2716lda.txt txt: ./txt/cord-296588-q2716lda.txt summary: OBJECTIVE: The IDSA''s goal was to develop an evidence-based diagnostic guideline to assists clinicians, clinical laboratorians, patients and policymakers in decisions related to the optimal use of SARS-CoV-2 nucleic acid amplification tests. It is important to note as well, that not all specimens were collected from the same patient at the same time, the time of collection from symptom onset was not provided in all studies and various approaches for establishing SARS-CoV-2 positivity were used to define positive results (i.e., clinical evaluation, detection different gene targets versus nucleic acid sequencing). While NP swab collection is widely used and the primary specimen type for commercial direct SARS-CoV-2 test platforms, based on current available evidence, clinical practice, and availability of testing resources, the panel believes there are comparable alternative methods for sampling the nasal passages. abstract: BACKGROUND: Accurate molecular diagnostic tests are necessary for confirming a diagnosis of coronavirus disease 2019 (COVID-19). Direct detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acids in respiratory tract specimens informs patient, healthcare institution and public health level decision-making. The numbers of available SARS-CoV-2 nucleic acid detection tests are rapidly increasing, as is the COVID-19 diagnostic literature. Thus, the Infectious Diseases Society of America (IDSA) recognized a significant need for frequently updated systematic reviews of the literature to inform evidence-based best practice guidance. OBJECTIVE: The IDSA’s goal was to develop an evidence-based diagnostic guideline to assists clinicians, clinical laboratorians, patients and policymakers in decisions related to the optimal use of SARS-CoV-2 nucleic acid amplification tests. In addition, we provide a conceptual framework for understanding molecular diagnostic test performance, discuss the nuance of test result interpretation in a variety of practice settings, and highlight important unmet research needs in the COVID-19 diagnostic testing space. METHODS: IDSA convened a multidisciplinary panel of infectious diseases clinicians, clinical microbiologists, and experts in systematic literature review to identify and prioritize clinical questions and outcomes related to the use of SARS-CoV-2 molecular diagnostics. Grading of Recommendations Assessment, Development and Evaluation (GRADE) methodology was used to assess the certainty of evidence and make testing recommendations. RESULTS: The panel agreed on 15 diagnostic recommendations. CONCLUSIONS: Universal access to accurate SARS-CoV-2 nucleic acid testing is critical for patient care, hospital infection prevention and the public response to the COVID-19 pandemic. Information on the clinical performance of available tests is rapidly emerging, but the quality of evidence of the current literature is considered low to very low. Recognizing these limitations, the IDSA panel weighed available diagnostic evidence and recommends nucleic acid testing for all symptomatic individuals suspected of having COVID-19. In addition, testing is recommended for asymptomatic individuals with known or suspected contact with a COVID-19 case. Testing asymptomatic individuals without known exposure is suggested when the results will impact isolation/quarantine/personal protective equipment (PPE) usage decisions, dictate eligibility for surgery, or inform administration of immunosuppressive therapy. Ultimately, prioritization of testing will depend on institutional-specific resources and the needs of different patient populations. url: https://www.ncbi.nlm.nih.gov/pubmed/32556191/ doi: 10.1093/cid/ciaa760 id: cord-326297-0r9pex1o author: Hartmann, Stacy title: Coronavirus 2019 (COVID-19) Infections Among Healthcare Workers, Los Angeles County, February - May 2020 date: 2020-08-17 words: 2195.0 sentences: 144.0 pages: flesch: 62.0 cache: ./cache/cord-326297-0r9pex1o.txt txt: ./txt/cord-326297-0r9pex1o.txt summary: The Los Angeles County Department of Public Health (LAC DPH) set out to understand the impact of COVID-19 on healthcare facilities and HCWs by tracking and analyzing data from case-patient interviews of HCWs. As of May 31st, over three months into the pandemic, nearly 5,500 positive HCWs were reported to LAC DPH, representing 9.6% of all cases. All LAC residents who test positive for COVID-19 are interviewed by LAC DPH using a standardized form that identifies if the case-patient worked in a high-risk environment, such as a healthcare setting. From case-patient interviews and/or emailed reports, LAC DPH recorded occupational setting, occupational role, date of symptom onset, date last worked, known exposure, and if hospitalized for each HCW. At the end of April, HCWs represented 12.8% of all LAC cases, whereas only 9.6% at the end of May. When asked if they had a known exposure to COVID-19, (Table 3) , healthcare exposures within their facility accounted for nearly 44%, including contact with either a positive patient, co-worker, or both. abstract: Across the world, healthcare workers (HCW) are at a greater risk of infection by the novel coronavirus 2019 (COVID-19) due to the nature of their work. The Los Angeles County Department of Public Health (LAC DPH) set out to understand the impact of COVID-19 on healthcare facilities and HCWs by tracking and analyzing data from case-patient interviews of HCWs. As of May 31st, over three months into the pandemic, nearly 5,500 positive HCWs were reported to LAC DPH, representing 9.6% of all cases. Cases reported working in 27 different setting types, including outpatient medical offices, correctional facilities, emergency medical services, etc., with the highest proportion from long-term care facilities (46.6%) and hospitals (27.7%). Case-patients included both clinical and non-clinical roles, with nearly half (49.4%) of positive HCWs being nurses. Over two-thirds of HCWs (68.6%) worked at some point during their infectious period and nearly half (47.9%) reported a known exposure to a positive patient and/or co-worker within their facility. Overall, compared to all LAC cases, HCWs reported lower rates of hospitalization (5.3% vs. 12.2%) and death (0.7% vs. 4.3%) from COVID-19. There are many factors that increase HCWs risk of infection, including high risk work environment, limited supply of personal protective equipment, and even pressure to help and work during a pandemic. In response to these data, LAC DPH created resources and provided guidance for healthcare facilities to best protect their patients and staff during the COVID-19 pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32803237/ doi: 10.1093/cid/ciaa1200 id: cord-010599-nwp2if8d author: Hayden, Frederick G. title: Efficacy and Safety of Oral Pleconaril for Treatment of Colds Due to Picornaviruses in Adults: Results of 2 Double-Blind, Randomized, Placebo-Controlled Trials date: 2003-06-15 words: 3985.0 sentences: 215.0 pages: flesch: 45.0 cache: ./cache/cord-010599-nwp2if8d.txt txt: ./txt/cord-010599-nwp2if8d.txt summary: More recently, retrospective analysis of 2 phase II randomized, double-blind, placebo-controlled studies found that pleconaril treatment provided clinical benefit for colds due to picornaviruses in previously healthy adults [10] . Calculations indicated that enrollment of 1000 subjects in each study was required to detect a 25% relative difference between treatment groups in the proportion of picornavirus-infected subjects reaching the primary end point (or an estimated 2-day difference in median time) with 90% power (2-sided test at the 5% level of significance [20] ). Among the picornavirus-infected (ITT-I) population, the time to reach the primary end point of illness alleviation was significantly shorter among pleconaril-treated subjects than among placebo recipients in each study (figure 1). severity score was reduced by 19% over the duration of the study for pleconaril recipients (table 4) , who also experienced significant reductions from baseline in symptom severity scores by day 2 of treatment, compared with placebo recipients (figure 2). abstract: The novel capsid-binding antiviral pleconaril inhibits in vitro replication of most rhinoviruses and enteroviruses. Oral pleconaril treatment was studied in 2 parallel randomized, double-blind, placebo-controlled trials. Among 1363 picornavirus-infected participants (65%) in the studies combined, the median time to alleviation of illness was 1 day shorter for pleconaril recipients than for placebo recipients (P > .001). Cold symptom scores and frequency of picornavirus cultured from nasal mucus specimens were lower among pleconaril recipients by day 2 of treatment. No treatment effects were seen in those without picornavirus infection. Pleconaril was associated with a higher incidence of nausea (6% vs. 4%) and diarrhea (9% vs. 7%) and with small increases in mean serum cholesterol levels and platelet counts, compared with baseline measurements. A subsequent 6-week prophylaxis study found that pleconaril induces cytochrome P-450 3A enzymes, which metabolize a variety of drugs, including ethinyl estradiol. Early pleconaril treatment was well tolerated and significantly reduced the duration and severity of colds due to picornaviruses in adults. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7199898/ doi: 10.1086/375069 id: cord-352837-a29d5dkv author: Hirsch, Hans H title: Spatiotemporal Virus Surveillance for Severe Acute Respiratory Infections in Resource-limited Settings: How Deep Need We Go? date: 2019-04-01 words: 1993.0 sentences: 79.0 pages: flesch: 36.0 cache: ./cache/cord-352837-a29d5dkv.txt txt: ./txt/cord-352837-a29d5dkv.txt summary: Given the technical and bioinformatic advances as well as the declining laboratory costs, the application of deep sequencing to identify etiologic agents in clinical samples has been approached in different pathologies, including those caused by community-acquired respiratory viruses (CARVs). With these caveats in mind, and given the significant global burden of viral respiratory tract disease in the very young and the very old [10] [11] [12] oropharyngeal (NP/OP) samples of SARI cases were identified through a national surveillance study conducted by the Uganda Virus Research Institute from 2010 through 2015. Taken together, this report from resource-limiting settings is also of relevance for resource-rich countries and raises the question about how to best expand current first-or second-line testing for respiratory viral pathogens including CMV, parvovirus B19, and measles, and how to move to more deep sequencing virome analysis and comprehensive metagenomics in the near future. abstract: nan url: https://doi.org/10.1093/cid/ciy663 doi: 10.1093/cid/ciy663 id: cord-315180-itvc86cv author: Hollingsworth, T Déirdre title: Counting Down the 2020 Goals for 9 Neglected Tropical Diseases: What Have We Learned From Quantitative Analysis and Transmission Modeling? date: 2018-06-15 words: 4494.0 sentences: 193.0 pages: flesch: 41.0 cache: ./cache/cord-315180-itvc86cv.txt txt: ./txt/cord-315180-itvc86cv.txt summary: In 2012, the World Health Organization set ambitious targets for eliminating many of these diseases as a public health problem by 2020, an aspiration that was supported by donations of treatments, intervention materials, and funding committed by a broad partnership of stakeholders in the London Declaration on NTDs. Alongside these efforts, there has been an increasing role for quantitative analysis and modeling to support the achievement of these goals through evaluation of the likely impact of interventions, the factors that could undermine these achievements, and the role of new diagnostics and treatments in reducing transmission. This article acts as an introduction for a special issue that aims to increase the accessibility of the results so far by summarizing insights from NTD models and identifying key themes for the control of these diseases. The modeling summarized in this issue highlights the value of vector control in reducing the infectiousness of all infected individuals, as well as the value of increasing diagnosis rates (Table 1) . abstract: The control of neglected tropical diseases (NTDs) has received huge investment in recent years, leading to large reductions in morbidity. In 2012, the World Health Organization set ambitious targets for eliminating many of these diseases as a public health problem by 2020, an aspiration that was supported by donations of treatments, intervention materials, and funding committed by a broad partnership of stakeholders in the London Declaration on NTDs. Alongside these efforts, there has been an increasing role for quantitative analysis and modeling to support the achievement of these goals through evaluation of the likely impact of interventions, the factors that could undermine these achievements, and the role of new diagnostics and treatments in reducing transmission. In this special issue, we aim to summarize those insights in an accessible way. This article acts as an introduction to the special issue, outlining key concepts in NTDs and insights from modeling as we approach 2020. url: https://doi.org/10.1093/cid/ciy284 doi: 10.1093/cid/ciy284 id: cord-001381-b0tlco4t author: Howie, Stephen R. C. title: Etiology of Severe Childhood Pneumonia in The Gambia, West Africa, Determined by Conventional and Molecular Microbiological Analyses of Lung and Pleural Aspirate Samples date: 2014-09-01 words: 2360.0 sentences: 123.0 pages: flesch: 46.0 cache: ./cache/cord-001381-b0tlco4t.txt txt: ./txt/cord-001381-b0tlco4t.txt summary: title: Etiology of Severe Childhood Pneumonia in The Gambia, West Africa, Determined by Conventional and Molecular Microbiological Analyses of Lung and Pleural Aspirate Samples Molecular analyses of lung aspirates from Gambian children with severe pneumonia detected pathogens more frequently than did culture and showed a predominance of bacteria, principally Streptococcus pneumoniae, >75% being of serotypes covered by current pneumococcal conjugate vaccines. influenzae), 16S rRNA PCR, multilocus sequence typing (MLST), molecular serotyping, and multiplex fast-track 33 PCR, all using standard methods (Supplementary Appendix 2) [2, [6] [7] [8] [9] [10] [11] [12] [13] , were performed at the MRC Unit in The Gambia, and multiplex MassTag PCR [14] was performed at Columbia University. This study also confirms that molecular methods are able to detect potential pathogens far more readily than culture and have a role in defining the etiology of pneumonia. abstract: Molecular analyses of lung aspirates from Gambian children with severe pneumonia detected pathogens more frequently than did culture and showed a predominance of bacteria, principally Streptococcus pneumoniae, >75% being of serotypes covered by current pneumococcal conjugate vaccines. Multiple pathogens were detected frequently, notably Haemophilus influenzae (mostly nontypeable) together with S. pneumoniae. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4130311/ doi: 10.1093/cid/ciu384 id: cord-335038-q32ghvsv author: Huang, Jiao title: Epidemiological, virological and serological features of COVID-19 cases in people living with HIV in Wuhan City: A population-based cohort study date: 2020-08-17 words: 3171.0 sentences: 231.0 pages: flesch: 59.0 cache: ./cache/cord-335038-q32ghvsv.txt txt: ./txt/cord-335038-q32ghvsv.txt summary: title: Epidemiological, virological and serological features of COVID-19 cases in people living with HIV in Wuhan City: A population-based cohort study METHODS: This population-based cohort study identified all COVID-19 cases among the whole PLWH in Wuhan city, China, by April 16, 2020. Previous studies have found that PLWH with low CD4 cell count, high HIV viral load and not taking antiretroviral treatment have an increased risk of other respiratory infections [9] . This indicates that COVID-19 cases in PLWH may have delayed viral clearance for SARS-CoV-2 because of immunosuppression, although clinical improvement of COVID-19 in PLWH was not worse than that of individuals without HIV infection as described in the present study and other published studies [25, 32] . CD4 cell count and the risk of AIDS or death in HIV-Infected adults on combination antiretroviral therapy with a suppressed viral load: a longitudinal cohort study from COHERE abstract: BACKGROUND: We aimed to describe the epidemiological, virological and serological features of coronavirus disease 2019 (COVID-19) cases in people living with HIV (PLWH). METHODS: This population-based cohort study identified all COVID-19 cases among the whole PLWH in Wuhan city, China, by April 16, 2020. The epidemiological, virological and serological features were analyzed based on the demographic data, temporal profile of nucleic acid test for SARS-CoV-2 during the disease, and SARS-CoV-2-specific IgM and IgG after recovery. RESULTS: From January 1 to April 16, 2020, 35 of 6001 PLWH have experienced COVID-19, with the cumulative incidence of COVID-19 to be 0.58% (95%CI: 0.42%-0.81%). Among the COVID-19 cases, 15 (42.86%) had severe illness, with 2 deaths. The incidence, case-severity and case-fatality of COVID-19 in PLWH were comparable to that in the entire population in Wuhan. 197 persons had cART discontinuation, of whom 4 persons experienced COVID-19. Risk factors for COVID-19 were age ≥50 years old and cART discontinuation. The median duration of SARS-CoV-2 viral shedding among confirmed COVID-19 cases in PLWH was 30 (IQR: 20-46) days. Cases with high HIV viral load (≥20 copies/ml) had lower IgM and IgG levels than those with low HIV viral load (<20 copies/ml) (median S/CO for IgM, 0.03 vs. 0.11, P<0.001; median S/CO for IgG, 10.16 vs. 17.04, P=0.069). CONCLUSIONS: Efforts need to maintain the persistent supply of antiretroviral treatment to elderly PLWH aged 50 years or above during the COVID-19 epidemic. The coinfection of HIV and SARS-CoV-2 might change the progression and prognosis of COVID-19 patients in PLWH. url: https://www.ncbi.nlm.nih.gov/pubmed/32803216/ doi: 10.1093/cid/ciaa1186 id: cord-284782-51mbq7qb author: Huang, Jing title: Care for the psychological status of frontline medical staff fighting against COVID-19 date: 2020-04-03 words: 314.0 sentences: 21.0 pages: flesch: 63.0 cache: ./cache/cord-284782-51mbq7qb.txt txt: ./txt/cord-284782-51mbq7qb.txt summary: key: cord-284782-51mbq7qb authors: Huang, Jing; Liu, Fangkun; Teng, Ziwei; Chen, Jindong; Zhao, Jingping; Wang, Xiaoping; Wu, Renrong title: Care for the psychological status of frontline medical staff fighting against COVID-19 cord_uid: 51mbq7qb Besides, a total of 6, 097 medical workers from different provinces in China were in Hubei province to assist in the COVID-19 by Jan 30, 2020 2 . For example, the emergency medical team from the Second Xiangya Hospital is able to set up field hospitals and ambulances to help and serve the With the increasing spreading of the virus worldwide, COVID-19 outbreak is now becoming a pandemic. None of the authors has any potential conflicts of interest to disclose. Timely mental health care for the 2019 novel coronavirus outbreak is urgently needed The immediate psychological and occupational impact of the 2003 SARS outbreak in a teaching hospital Protecting Health Care Workers during the COVID-19 Coronavirus Outbreak -Lessons from Taiwan''s SARS response abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32246142/ doi: 10.1093/cid/ciaa385 id: cord-335691-lsuwsm43 author: Jackson, Michael L. title: The Burden of Community-Acquired Pneumonia in Seniors: Results of a Population-Based Study date: 2004-12-01 words: 3625.0 sentences: 168.0 pages: flesch: 44.0 cache: ./cache/cord-335691-lsuwsm43.txt txt: ./txt/cord-335691-lsuwsm43.txt summary: To estimate rates of community-acquired pneumonia and to identify risk factors for this disease, we conducted a large, population-based cohort study of persons aged ⩾65 years that included both hospitalizations and outpatient visits for pneumonia. In multivariate analysis, age, male sex, current smoking, diabetes mellitus, congestive heart failure, lung cancer, serious nonlung cancer, COPD, asthma without COPD, dementia, stroke, receipt of prednisone, use of home oxygen services, greater number of outpatient visits, and hospitalization for pneumonia in the year prior to the study start date were independently associated with risk of all CAP (table 3) . A population-based study involving 4175 elderly persons in Finland found that crude CAP rates did not differ between men and women and that male sex was not significantly associated with CAP after accounting for age and certain chronic medical conditions and risk factors, including asthma, receipt of immunosuppressive therapy, and heart disease [21] . abstract: Background. Pneumonia is recognized as a leading cause of morbidity in seniors. However, the overall burden of this disease—and, in particular, the contribution of ambulatory cases to that burden—is not well defined. To estimate rates of community-acquired pneumonia and to identify risk factors for this disease, we conducted a large, population-based cohort study of persons aged ⩾65 years that included both hospitalizations and outpatient visits for pneumonia. Methods. The study population consisted of 46,237 seniors enrolled at Group Health Cooperative who were observed over a 3-year period. Pneumonia episodes presumptively identified by International Classification of Diseases, Ninth Revision, Clinical Modification codes assigned to medical encounters were validated by medical record review. Characteristics of participants were defined by administrative data sources. Results. The overall rate of community-acquired pneumonia ranged from 18.2 cases per 1000 person-years among persons aged 65–69 years to 52.3 cases per 1000 person-years among those aged ⩾85 years. In this population, 59.3% of all pneumonia episodes were treated on an outpatient basis. In multivariate analysis, risk factors for community-acquired pneumonia included age, male sex, chronic obstructive pulmonary disease, asthma, diabetes mellitus, congestive heart failure, and smoking. Conclusions. On the basis of these data, we estimate that roughly 915,900 cases of community-acquired pneumonia occur annually among seniors in the United States and that ∼1 of every 20 persons aged ⩾85 years will have a new episode of community-acquired pneumonia each year. url: https://www.ncbi.nlm.nih.gov/pubmed/15578365/ doi: 10.1086/425615 id: cord-333943-9d93na7s author: Jeong, Han Eol title: Association between NSAIDs use and adverse clinical outcomes among adults hospitalized with COVID-19 in South Korea: A nationwide study date: 2020-07-27 words: 3387.0 sentences: 218.0 pages: flesch: 47.0 cache: ./cache/cord-333943-9d93na7s.txt txt: ./txt/cord-333943-9d93na7s.txt summary: title: Association between NSAIDs use and adverse clinical outcomes among adults hospitalized with COVID-19 in South Korea: A nationwide study BACKGROUND: Non-steroidal anti-inflammatory drugs (NSAIDs) may exacerbate COVID-19 and worsen associated outcomes by upregulating the enzyme that SARS-CoV-2 binds to enter cells. [1, 2] Concerns exist that the use of nonsteroidal anti-inflammatory drugs (NSAIDs) may exacerbate COVID-19 by upregulating angiotensin-converting enzyme 2 (ACE2) expressions, [3, 4] the enzyme which SARS-CoV-2 binds to enter cells. This cohort study therefore aimed to examine the association between NSAIDs use, compared to non-use, and worsened clinical outcomes among adults hospitalized with A c c e p t e d M a n u s c r i p t page | 5 COVID-19 using South Korea''s nationwide healthcare database containing all COVID-19 patients. To our knowledge, this is the first population-based study conducted using all hospitalized patients with COVID-19 to assess the association between NSAID use and COVID-19 related outcomes. abstract: BACKGROUND: Non-steroidal anti-inflammatory drugs (NSAIDs) may exacerbate COVID-19 and worsen associated outcomes by upregulating the enzyme that SARS-CoV-2 binds to enter cells. To our knowledge, no study has examined the association between NSAID use and the risk of COVID-19-related outcomes. METHODS: We conducted a cohort study using South Korea’s nationwide healthcare database, which contains data of all subjects who received a test for COVID-19 (n=69,793) as of April 8, 2020. We identified adults hospitalized with COVID-19, where cohort entry was the date of hospitalization. NSAIDs users were those prescribed NSAIDs in the 7 days before and including cohort entry and non-users were those not prescribed NSAIDs during this period. Our primary outcome was a composite of in-hospital death, intensive care unit admission, mechanical ventilation use, and sepsis; our secondary outcomes were cardiovascular complications and acute renal failure. We conducted logistic regression analysis to estimate odds ratio (OR) with 95% confidence intervals (CI) using inverse probability of treatment weighting to minimize confounding. RESULTS: Of 1,824 adults hospitalized with COVID-19 (mean age 49.0 years; female 59%), 354 were NSAIDs users and 1,470 were non-users. Compared with non-use, NSAIDs use was associated with increased risks of the primary composite outcome (OR 1.54 [95% CI 1.13-2.11]) but insignificantly associated with cardiovascular complications (1.54 [0.96-2.48]) or acute renal failure (1.45 [0.49-4.14]). CONCLUSION: While awaiting the results of confirmatory studies, we suggest NSAIDs be used with caution among patients with COVID-19 as the harms associated with their use may outweigh their benefits in this population. url: https://doi.org/10.1093/cid/ciaa1056 doi: 10.1093/cid/ciaa1056 id: cord-349070-bqv03u2e author: Jiang, Shih Sheng title: Sensitive and Quantitative Detection of Severe Acute Respiratory Syndrome Coronavirus Infection by Real-Time Nested Polymerase Chain Reaction date: 2004-01-15 words: 2465.0 sentences: 110.0 pages: flesch: 51.0 cache: ./cache/cord-349070-bqv03u2e.txt txt: ./txt/cord-349070-bqv03u2e.txt summary: title: Sensitive and Quantitative Detection of Severe Acute Respiratory Syndrome Coronavirus Infection by Real-Time Nested Polymerase Chain Reaction In most of the cases, we and others have found that the single-step real time RT-PCR methods (as suggested by the World Health Organization [WHO] ; available at http://www.who.int/csr/sars/diagnostic tests/en/) could specifically detect SARS-CoV but were unable to proficiently detect !10 copies of virus per test, suggesting that the conventional RT-PCR assay may actually yield falsenegative results. In contrast, the second-round amplification by nested real-time PCR proficiently generated a signal of SARS-CoV DNA without apparent background, compared with no detectable signal for the negative control samples ( figure 1A ). After 25 cycles of first-round amplification and 25 cycles of nested PCR amplification, our assay could detect a theoretical single copy of extracted viral RNA (figure 1A), suggesting its superior sensitivity for detection of SARS-CoV. abstract: A quantitative, real-time, nested polymerase chain reaction (PCR) method, combining the high sensitivity of nested PCR with time-saving real-time instrumentation, was developed for large-scale screening for severe acute coronavirus (SARS) coronavirus. Forty-six clinical specimens were analyzed by this method, and results were compared with those obtained by conventional, single-round, real-time reverse-transcriptase PCR (RT-PCR) performed in parallel. Of the 17 positive results, 2 identified by our method were not detected by single-round, real-time RT-PCR, which suggests that real-time nested PCR has the potential for increased sensitivity, leading to earlier detection of SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/14699465/ doi: 10.1086/380841 id: cord-318458-jadk2qbm author: Jung, Chan-Young title: Association between Body Mass Index and Risk of COVID-19: A Nationwide Case-Control Study in South Korea date: 2020-08-25 words: 3657.0 sentences: 219.0 pages: flesch: 52.0 cache: ./cache/cord-318458-jadk2qbm.txt txt: ./txt/cord-318458-jadk2qbm.txt summary: METHODS: We examined the association between BMI level and the risk of COVID-19 infection in a nationwide case-control study comprised of 3,788 case patients confirmed with COVID-19 between January 24 and April 9, 2020 and 15,152 controls matched by age and sex, who were aged 20 years or more and underwent National Health Insurance Service (NHIS) health examinations between 2015−2017, using data from the Korean NHIS with linkage to the Korea Centers for Disease Control and Prevention data. In multivariable logistic regression models adjusted for sociodemographic, comorbidity, laboratory and medication data, there was a graded association between higher BMI levels and higher risk of COVID-19 infection; compared to normal weight individuals, the adjusted ORs in the overweight and obese individuals were 1.13 (95% CI, 1.03-1.25) and 1.26 (95% CI, 1.15-1.39), respectively. abstract: BACKGROUND: Increased body mass index (BMI) has been associated with higher risk of severe coronavirus disease 2019 (COVID-19) infections. However, whether obesity is a risk factor for contracting COVID-19 has been hardly investigated so far. METHODS: We examined the association between BMI level and the risk of COVID-19 infection in a nationwide case-control study comprised of 3,788 case patients confirmed with COVID-19 between January 24 and April 9, 2020 and 15,152 controls matched by age and sex, who were aged 20 years or more and underwent National Health Insurance Service (NHIS) health examinations between 2015−2017, using data from the Korean NHIS with linkage to the Korea Centers for Disease Control and Prevention data. Our primary exposure of interest was BMI level categorized into four groups; &18.5 (underweight), 18.5-22.9 (normal weight), 23-24.9 (overweight), and ≥25 kg/m (2) (obese). RESULTS: Of the entire 18,940 study population, 11,755 (62.1%) were women, and the mean (SD) age of the study participants was 53.7 (13.8) years. In multivariable logistic regression models adjusted for sociodemographic, comorbidity, laboratory and medication data, there was a graded association between higher BMI levels and higher risk of COVID-19 infection; compared to normal weight individuals, the adjusted ORs in the overweight and obese individuals were 1.13 (95% CI, 1.03-1.25) and 1.26 (95% CI, 1.15-1.39), respectively. This association was robust across age and sex subgroups. CONCLUSIONS: Higher BMI levels were associated with higher risk of contracting COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32841322/ doi: 10.1093/cid/ciaa1257 id: cord-324307-2zbm4iwn author: Kam, Kai-qian title: A Well Infant With Coronavirus Disease 2019 With High Viral Load date: 2020-02-28 words: 1914.0 sentences: 123.0 pages: flesch: 62.0 cache: ./cache/cord-324307-2zbm4iwn.txt txt: ./txt/cord-324307-2zbm4iwn.txt summary: A well 6-month-old infant with coronavirus disease 2019 (COVID-19) had persistently positive nasopharyngeal swabs up to day 16 of admission. A well 6-month-old infant with coronavirus disease 2019 (COVID-19) had persistently positive nasopharyngeal swabs up to day 16 of admission. Two specific real-time reverse-transcription polymerase chain reaction (rRT-PCR) methods, targeting the N and ORF1ab genes, were designed to detect the presence of SARS-CoV-2 in clinical samples. A nasopharyngeal specimen taken on admission and tested by rRT-PCR confirmed the diagnosis of COVID-19 infection with low cycle threshold (N gene, 15.57; Orf1ab gene, 13.73), suggesting high viral load. On day 2 of admission, he was found to be viremic with detection of SARS-CoV-2 in his blood sample via rRT-PCR. Repeat testing of his urine on day 9 of admission was negative, but his stool sample became positive for SARS-CoV-2. Similar to reports of adult COVID-19, we confirm the detection of SARS-CoV-2 RNA in the stool of our infant. abstract: A well 6-month-old infant with coronavirus disease 2019 (COVID-19) had persistently positive nasopharyngeal swabs up to day 16 of admission. This case highlights the difficulties in establishing the true incidence of COVID-19, as asymptomatic individuals can excrete the virus. These patients may play important roles in human-to-human transmission in the community. url: https://doi.org/10.1093/cid/ciaa201 doi: 10.1093/cid/ciaa201 id: cord-337972-otfloo64 author: Kao, Shang Jyh title: Mechanism of Fulminant Pulmonary Edema Caused by Enterovirus 71 date: 2004-06-15 words: 1949.0 sentences: 135.0 pages: flesch: 53.0 cache: ./cache/cord-337972-otfloo64.txt txt: ./txt/cord-337972-otfloo64.txt summary: Destruction of the medial, ventral, and caudal medulla may lead to sympathetic overactivation, causing blood to shift to the lungs. Destruction of the medial, ventral, and caudal medulla may lead to sympathetic overactivation, causing blood to shift to the lungs. Central sympathetic activation resulting in systemic vasoconstriction and the shift of blood volume to the pulmonary region of the circulatory system, as demonstrated in earlier findings from our laboratory, was used to explain centrogenic PE [2, 3] . In the present study, we report CNS lesions in patients associated with PE due to enterovirus infection. The present study also supports the contention that hyperglycemia, leukocytosis, and elevated protein levels in CSF are risk factors for the development of ARDS due to enterovirus infection [1, 2] . In this connection, we found that endogenous and exogenous nitric oxide reduced pulmonary hypertension but increased the capillary filtration coefficient and the extent of injury in an isolated rat''s lung that was subjected to ischemia and reperfusion [16] . abstract: Pulmonary edema (PE) may occur with enterovirus 71 (EV71) infection. We monitored arterial pressure (AP) and heart rate (HR) in patients with EV71 infection and analyzed the variability of AP and HR. Sympathetic activity, AP, and HR increased with respiratory stress. Thereafter, parasympathetic activity increased with decreases in AP and HR. The lungs showed edema with inducible nitric oxide synthase (iNOS) expression. Destruction of the medial, ventral, and caudal medulla may lead to sympathetic overactivation, causing blood to shift to the lungs. The pathogenesis of PE may also involve iNOS and nitric oxide. url: https://www.ncbi.nlm.nih.gov/pubmed/15227628/ doi: 10.1086/421021 id: cord-314489-e5r5s5ee author: Katsidzira, Leolin title: The SARS-CoV-2 epidemic in Zimbabwe: Quo vadis? date: 2020-05-11 words: 1948.0 sentences: 132.0 pages: flesch: 57.0 cache: ./cache/cord-314489-e5r5s5ee.txt txt: ./txt/cord-314489-e5r5s5ee.txt summary: The trajectory, and impact of the SARS-CoV-2 pandemic in sub-Saharan Africa is unclear, but it is seemingly varied between different countries, with most reporting low numbers. Using Zimbabwe as an example, we argue that the magnitude, and impact of the epidemic in most of sub-Saharan Africa is likely to be smaller than anticipated, with a reduced morbidity and mortality. This case strongly influenced the subsequent response to COVID-19 by both the government, and the private healthcare industry in Zimbabwe, and played a pivotal role in raising public awareness. There is a link between the volume of international flights, and the magnitude of the SARS-CoV-2 epidemic in sub-Saharan Africa [7, 11] . A potential source of higher than anticipated mortality from COVID-19 disease in sub-Saharan Africa is the high burden of HIV infection [5] . Moreover, considerable progress has It remains unclear whether complete lockdowns are the most ideal method to limit the spread of SARS-CoV-2 in sub-Saharan Africa [22] . abstract: The trajectory, and impact of the SARS-CoV-2 pandemic in sub-Saharan Africa is unclear, but it is seemingly varied between different countries, with most reporting low numbers. We use the situation in Zimbabwe to build an argument that the epidemic is likely to be attenuated in some countries with similar socio-economic and cultural structures. However, even an attenuated epidemic may overwhelm weak health systems, emphasising the importance of prevention. These prevention strategies should be tailored to the unique social and cultural networks of individual countries which may facilitate the spread of SARS-CoV 2. It is also equally important to maintain services for the major infectious diseases in the region such as tuberculosis and malaria. A breakdown of treatment and prevention services for these conditions may even overshadow the projected morbidity and mortality from COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32392333/ doi: 10.1093/cid/ciaa552 id: cord-329290-vqvujry3 author: Kempker, Russell R title: Loss of Smell and Taste Among Healthcare Personnel Screened for Coronavirus 2019 date: 2020-06-28 words: 1907.0 sentences: 90.0 pages: flesch: 55.0 cache: ./cache/cord-329290-vqvujry3.txt txt: ./txt/cord-329290-vqvujry3.txt summary: HCP with symptoms consistent with a viral-like illness were triaged to the employee health services staff for a virtual clinical assessment and then scheduled for SARS-CoV-2 testing. HCP with a positive SARS-CoV-2 test compared with those with a negative test had a higher mean number of symptoms and were more likely to have reported fever, chills, myalgia, and loss of smell or taste (Table 1 ). We are the first to evaluate the sensitivity of loss of smell and taste in distinguishing symptomatic HCP with and without a positive SARS-CoV-2 test and support their recent inclusion to the list of symptoms associated with COVID-19 provided by the CDC [4] . The high specificity and positive predictive value of loss of smell and/or taste for a positive SARS-CoV-2 test in our cohort highlights the utility of including these symptoms in COVID-19 screening algorithms. abstract: Among 283 symptomatic healthcare personnel (HCP) tested for SARS-CoV-2, 51 (18%) were positive. Among those 51 HCP, self reported loss of smell and taste were present in 51% and 52.9%, respectively, with either present in 60.8%. These symptoms had high specificity (93% each, 96% for either) for a positive SARS-CoV-2 test. url: https://doi.org/10.1093/cid/ciaa877 doi: 10.1093/cid/ciaa877 id: cord-287119-eo0evoog author: Kendall, Emily A title: When infections don’t reflect infectiousness: interpreting contact investigation data with care date: 2020-08-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://doi.org/10.1093/cid/ciaa1144 doi: 10.1093/cid/ciaa1144 id: cord-316970-n2dly3oa author: Kerbaj, Jad title: COVID-19: The New Caledonia experience date: 2020-05-16 words: 1444.0 sentences: 115.0 pages: flesch: 68.0 cache: ./cache/cord-316970-n2dly3oa.txt txt: ./txt/cord-316970-n2dly3oa.txt summary: Every passenger with fever or cough was hospitalized in the Centre Hospitalier Territorial CHT (the main island''s hospital, reference center in Infectious Diseases) and tested by SARS-CoV-2 reverse transcriptase Polymerase Chain Reaction (RT-PCR). On February 10, screening by SARS-CoV-2 RT-PCR started for all patients hospitalized for an Influenza like illness or a severe acute respiratory infection (SARI). All close contact to person confirmed with COVID-19 infection were isolated in a quarantine facility for 14 days. Iceland has quickly considered all travels outside the island as high risk, has done a large population screening and important tracking of SARS-A c c e p t e d M a n u s c r i p t 6 CoV-2 infections, associating these measures with quarantine, self-isolation and social distancing (8) . The surveillance, quarantine measures, the hospitalization of all detected COVID-19 positive patients and the rapid lockdown had probably an impact on stopping the spread. abstract: New Caledonia is a French associated territory in the South Pacific Ocean. While COVID-19 is expanding over the world, we seem to be well preserved with a total of 18 documented cases. We report the measures implemented on our island that probably helped containing an epidemic spread. url: https://doi.org/10.1093/cid/ciaa600 doi: 10.1093/cid/ciaa600 id: cord-322204-kc7dy2za author: Khalil, Asma title: SARS-CoV-2-specific antibody detection in healthcare workers in a UK maternity Hospital: Correlation with SARS-CoV-2 RT-PCR results date: 2020-08-08 words: 448.0 sentences: 50.0 pages: flesch: 60.0 cache: ./cache/cord-322204-kc7dy2za.txt txt: ./txt/cord-322204-kc7dy2za.txt summary: title: SARS-CoV-2-specific antibody detection in healthcare workers in a UK maternity Hospital: Correlation with SARS-CoV-2 RT-PCR results Universal healthcare worker (HCW) testing is potentially useful in ameliorating workforce depletion and reducing asymptomatic spread of SARS-CoV-2. Nasopharyngeal swab polymerase chain reaction (RT-PCR) can diagnose only current or recent infection; testing for antibody responses against SARS-CoV-2 could enhance the ability to expedite reinstatement of services, while ensuring patient and staff safety. Tests are now available for immunoglobulin (Ig) G against the SARS-CoV-2 nucleocapsid protein; the Abbott SARS-CoV-2 IgG ELISA is reported to have high specificity We previously reported that 32% of HCW testing positive for SARS-CoV-2 on nasopharyngeal swab were asymptomatic at the time. 2 Symptomatic and asymptomatic SARS-CoV-2 positive adults have similar viral loads and infectious virus isolation. Of those testing positive for SARS-CoV-2 IgG, 39% had an earlier negative nasopharyngeal swab. 5 Both symptomatic and asymptomatic infections were associated with SARS-COV-2 IgG antibodies, as were 10% of abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32770224/ doi: 10.1093/cid/ciaa893 id: cord-299720-f0ny4ur5 author: Kim, Seung Woo title: Risk Factors for Transmission of Middle East Respiratory Syndrome Coronavirus Infection During the 2015 Outbreak in South Korea date: 2017-03-01 words: 3914.0 sentences: 206.0 pages: flesch: 47.0 cache: ./cache/cord-299720-f0ny4ur5.txt txt: ./txt/cord-299720-f0ny4ur5.txt summary: title: Risk Factors for Transmission of Middle East Respiratory Syndrome Coronavirus Infection During the 2015 Outbreak in South Korea Transmission heterogeneity was observed during the 2015 Korean outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection. Transmission heterogeneity was a significant characteristic of the 2015 South Korean outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection [1] . Epidemiological reports from the outbreak were evaluated to collect data regarding basic demographic characteristics, medical history, MERS-CoV exposure, symptoms and their onset date(s), sampling date(s), contact history, and post-exposure infection control. In the univariate analyses, transmission was associated with underlying respiratory disease, Ct value, interval from symptom onset to diagnosis, number of contacts, and pre-isolation hospitalization or ER visits. It appears that both host infectivity and the number of contacts influenced MERS-CoV transmission, whereas super-spreading events were mostly associated with a greater likelihood of encountering other people under diverse environmental conditions. abstract: BACKGROUND. Transmission heterogeneity was observed during the 2015 Korean outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection. Only 22 of 186 cases transmitted the infection, and 5 super-spreading events caused 150 transmissions. We investigated the risk factors for MERS-CoV transmission. METHODS. Epidemiological reports were used to classify patients as nonspreaders, spreaders, or those associated with a super-spreading event (5 or more transmissions). Logistic regression analyses were used to evaluate the factors for MERS-CoV transmission. RESULTS. Compared to nonspreaders, spreaders exhibited a longer interval from symptom onset to isolation (7 days vs 3 days) and more frequent pre-isolation pneumonia diagnoses (68.2% vs 17.1%). Spreaders also exhibited higher values for pre-isolation contacts (149 vs 17.5), pre-isolation hospitalization (68.2% vs 16.5%), and emergency room (ER) visits (50% vs 7.3%). Spreaders exhibited lower cycle thresholds for the upE and ORF1a genes (22.7 vs 27.2 and 23.7 vs 27.9, respectively). In multivariate analysis, transmission was independently associated with the cycle threshold (odds ratio [OR], 0.84; 95% confidence interval [CI], 0.75–0.96) and pre-isolation hospitalization or ER visits (OR, 6.82; 95% CI, 2.06–22.84). The super-spreading events exhibited higher values for pre-isolation contacts (777 vs 78), pre-isolation ER visits (100% vs 35.3%), and doctor shopping (100% vs 47.1%) compared to non-super-spreading events. CONCLUSIONS. These findings indicate that transmission is determined by host infectivity and the number of contacts, whereas super-spreading events were determined by the number of contacts and hospital visits. These relationships highlight the importance of rapidly enforcing infection control measures to prevent outbreaks. url: https://www.ncbi.nlm.nih.gov/pubmed/27940937/ doi: 10.1093/cid/ciw768 id: cord-329323-1cquorhs author: Ko, Jean Y title: Risk Factors for COVID-19-associated hospitalization: COVID-19-Associated Hospitalization Surveillance Network and Behavioral Risk Factor Surveillance System date: 2020-09-18 words: 4184.0 sentences: 240.0 pages: flesch: 44.0 cache: ./cache/cord-329323-1cquorhs.txt txt: ./txt/cord-329323-1cquorhs.txt summary: Generalized Poisson regression models were used to calculate adjusted rate ratios (aRR) for hospitalization RESULTS: Among 5,416 adults, hospitalization rates were higher among those with ≥3 underlying conditions (versus without)(aRR: 5.0; 95%CI: 3.9, 6.3), severe obesity (aRR:4.4; 95%CI: 3.4, 5.7), chronic kidney disease (aRR:4.0; 95%CI: 3.0, 5.2), diabetes (aRR:3.2; 95%CI: 2.5, 4.1), obesity (aRR:2.9; 95%CI: 2.3, 3.5), hypertension (aRR:2.8; 95%CI: 2.3, 3.4), and asthma (aRR:1.4; 95%CI: 1.1, 1.7), after adjusting for age, sex, and race/ethnicity. BRFSS data were used to calculate weighted population estimates of community-dwelling adults with and without individual underlying medical conditions by age, sex, and race/ethnicity strata for the COVID-NET catchment area and served as the analytic A c c e p t e d M a n u s c r i p t 7 denominators. abstract: BACKGROUND: Data on risk factors for COVID-19-associated hospitalization are needed to guide prevention efforts and clinical care. We sought to identify factors independently associated with COVID-19-associated hospitalizations METHODS: U.S. community-dwelling adults (≥18 years) hospitalized with laboratory-confirmed COVID-19 during March 1–June 23, 2020 were identified from the COVID-19-Associated Hospitalization Surveillance Network (COVID-NET), a multi-state surveillance system. To calculate hospitalization rates by age, sex, and race/ethnicity strata, COVID-NET data served as the numerator and Behavioral Risk Factor Surveillance System estimates served as the population denominator for characteristics of interest. Underlying medical conditions examined included hypertension, coronary artery disease, history of stroke, diabetes, obesity [BMI ≥30 kg/m (2)], severe obesity [BMI≥40 kg/m (2)], chronic kidney disease, asthma, and chronic obstructive pulmonary disease. Generalized Poisson regression models were used to calculate adjusted rate ratios (aRR) for hospitalization RESULTS: Among 5,416 adults, hospitalization rates were higher among those with ≥3 underlying conditions (versus without)(aRR: 5.0; 95%CI: 3.9, 6.3), severe obesity (aRR:4.4; 95%CI: 3.4, 5.7), chronic kidney disease (aRR:4.0; 95%CI: 3.0, 5.2), diabetes (aRR:3.2; 95%CI: 2.5, 4.1), obesity (aRR:2.9; 95%CI: 2.3, 3.5), hypertension (aRR:2.8; 95%CI: 2.3, 3.4), and asthma (aRR:1.4; 95%CI: 1.1, 1.7), after adjusting for age, sex, and race/ethnicity. Adjusting for the presence of an individual underlying medical condition, higher hospitalization rates were observed for adults aged ≥65, 45-64 (versus 18-44 years), males (versus females), and non-Hispanic black and other race/ethnicities (versus non-Hispanic whites) CONCLUSION: Our findings elucidate groups with higher hospitalization risk that may benefit from targeted preventive and therapeutic interventions url: https://doi.org/10.1093/cid/ciaa1419 doi: 10.1093/cid/ciaa1419 id: cord-257553-479x7av6 author: Kortepeter, Mark G. title: Health Care Workers and Researchers Traveling to Developing-World Clinical Settings: Disease Transmission Risk and Mitigation date: 2010-12-01 words: 3967.0 sentences: 217.0 pages: flesch: 39.0 cache: ./cache/cord-257553-479x7av6.txt txt: ./txt/cord-257553-479x7av6.txt summary: title: Health Care Workers and Researchers Traveling to Developing-World Clinical Settings: Disease Transmission Risk and Mitigation This review provides practical advice for this special population of travelers, targeted to specific health care-related risks (needlestick, hemorrhagic fever viruses, severe viral respiratory disease, and tuberculosis), with suggestions for risk mitigation. Although no prophylaxis for hepatitis C virus (HCV) exposure exists, the needlestick transmission risk is lower (1.8%), and up to 20% of transmitted infections resolve spontaneously. The Centers for Disease Control and Prevention (CDC) recommends a 3-drug PEP regimen if the source patient is known to be infected with HIV and the source device is a hollow-bore needle or has visible blood contamination. During the pandemic, transmission to HCWs occurred after close, unprotected contact with symptomatic persons and was significantly mitigated once infection-control precautions were implemented; the degree of risk was related to the type and intensity of exposure (endotracheal intubation was significantly associated with contracting SARS) [27, 28] . abstract: With the recent emphasis on funding and training opportunities for global health and humanitarian aid and the increased interest in the field, many health care workers and medical researchers are traveling from resource-replete to resource-limited settings. This type of travel brings unique disease risks not routinely considered for the business or vacationing traveler. This review provides practical advice for this special population of travelers, targeted to specific health care-related risks (needlestick, hemorrhagic fever viruses, severe viral respiratory disease, and tuberculosis), with suggestions for risk mitigation. url: https://doi.org/10.1086/657115 doi: 10.1086/657115 id: cord-007325-g8ke9rfg author: Koskiniemi, Marjaleena title: CNS Manifestations Associated with Mycoplasma pneumoniae Infections: Summary of Cases at the University of Helsinki and Review date: 1993-08-17 words: 2324.0 sentences: 167.0 pages: flesch: 33.0 cache: ./cache/cord-007325-g8ke9rfg.txt txt: ./txt/cord-007325-g8ke9rfg.txt summary: title: CNS Manifestations Associated with Mycoplasma pneumoniae Infections: Summary of Cases at the University of Helsinki and Review CNS manifestations appear in one of 1,000 patients with Mycoplasma pneumoniae-associated infections. Encephalitis is the most frequent manifestation, but cases of meningitis, myelitis, and polyradiculitis, as well as many other symptoms (e.g., coma, ataxia, psychosis, and stroke), have been reported. Besides encephalitis, adult patients had meningitis, myelitis, and polyradiculitis, two cases of each (figure 2). Central nervous system disease associated with Mycoplasma pneumoniae infection: report of five cases and review of the literature Central nervous system manifestations associated with serologically verified Mycoplasma pneumoniae infection Two fatal cases of meningoencephalitis associated with Mycoplasma pneumoniae infection Central nervous system disease associated with Mycoplasma pneumoniae infection Neurological manifestations and Mycoplasma pneumoniae infection A brainstem syndrome associated with Mycoplasma pneumoniae infection-a report of two cases Antibodies to brain and other tissues in cases of Mycoplasma pneumoniae infection abstract: CNS manifestations appear in one of 1,000 patients with Mycoplasma pneumoniae-associated infections. Encephalitis is the most frequent manifestation, but cases of meningitis, myelitis, and polyradiculitis, as well as many other symptoms (e.g., coma, ataxia, psychosis, and stroke), have been reported. The onset of these manifestations is usually acute, with lowered consciousness, convulsions, pareses, and other neurological signs. Severe, even fatal, cases are known. The pathophysiology of CNS manifestations is unknown. To our knowledge, M. pneumoniae has never been isolated from brain tissue, but instead it has been recovered from CSF specimens in at least seven cases. Besides direct invasion of M. pneumoniae into the brain, neurotoxic or autoimmune reaction within the brain tissue is suspected. At neuropathological examination, edema, demyelination, and microthrombi have been described. Improved diagnostic methods may reveal the pathophysiology of CNS manifestations associated with M. pneumoniae infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7110383/ doi: 10.1093/clinids/17.supplement_1.s52 id: cord-265006-m1dmgcd1 author: Kow, Chia Siang title: Do the meta-analyses provide a clean bill of health to the use of renin-angiotensin system inhibitors in COVID-19? date: 2020-08-08 words: 842.0 sentences: 56.0 pages: flesch: 47.0 cache: ./cache/cord-265006-m1dmgcd1.txt txt: ./txt/cord-265006-m1dmgcd1.txt summary: In fact, we are aware of the publication of few systematic reviews and metaanalyses [2] [3] [4] [5] [6] [7] [8] which included these observational studies with questionable quality to determine the association between renin-angiotensin system (RAS) inhibitors use, including angiotensin converting enzyme (ACE) inhibitors and angiotensin receptor blockers (ARBs), and mortality/severity of COVID-19. A systematic review and meta-analysis to evaluate the clinical outcomes in COVID-19 patients on angiotensin-converting enzyme inhibitors or angiotensin receptor blockers ACEI/ARB use and risk of infection or severity or mortality of COVID-19: A systematic review and meta-analysis Outcomes of renin-angiotensin-aldosterone system blockers in patients with COVID-19: a systematic review and meta-analysis The use of renin angiotensin system inhibitor on mortality in patients with coronavirus disease 2019 (COVID-19): A systematic review and meta-analysis abstract: nan url: https://doi.org/10.1093/cid/ciaa1167 doi: 10.1093/cid/ciaa1167 id: cord-314025-h9gj814e author: Lai, Mary Y. Y. title: Survival of Severe Acute Respiratory Syndrome Coronavirus date: 2005-10-01 words: 3089.0 sentences: 159.0 pages: flesch: 58.0 cache: ./cache/cord-314025-h9gj814e.txt txt: ./txt/cord-314025-h9gj814e.txt summary: SARS-CoV GVU6109 can survive for 4 days in diarrheal stool samples with an alkaline pH, and it can remain infectious in respiratory specimens for >7 days at room temperature. Soon after the isolation of SARS-CoV in our laboratory, we were able to perform a survival study of the virus, and partial results were reported on the World Health Organization Communicable Disease Surveillance and Response Web site on SARS [6] . Here, we provide a full report of our study of the survival characteristics of SARS-CoV in different clinical sample matrices, as well as on various environmental surfaces in the laboratory and hospital. The present study demonstrates that SARS-CoV can survive in respiratory samples for 5 days at room temperature and for up to 3 weeks at 4ЊC. Our present data show that, at a high concentration of virus (10 6 TCID 50 / mL), SARS-CoV can survive for 4-5 days at room temperature in both respiratory and diarrheal stool samples. abstract: Background. The primary modes of transmission of severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) appear to be direct mucus membrane contact with infectious droplets and through exposure to formites. Knowledge of the survival characteristics of the virus is essential for formulating appropriate infection-control measures. Methods. Survival of SARS-CoV strain GVU6109 was studied in stool and respiratory specimens. Survival of the virus on different environmental surfaces, including a laboratory request form, an impervious disposable gown, and a cotton nondisposable gown, was investigated. The virucidal effects of sodium hypochlorite, house detergent, and a peroxygen compound (Virkon S; Antec International) on the virus were also studied. Results. SARS-CoV GVU6109 can survive for 4 days in diarrheal stool samples with an alkaline pH, and it can remain infectious in respiratory specimens for >7 days at room temperature. Even at a relatively high concentration (10(4) tissue culture infective doses/mL), the virus could not be recovered after drying of a paper request form, and its infectivity was shown to last longer on the disposable gown than on the cotton gown. All disinfectants tested were shown to be able to reduce the virus load by >3 log within 5 min. Conclusions. Fecal and respiratory samples can remain infectious for a long period of time at room temperature. The risk of infection via contact with droplet-contaminated paper is small. Absorbent material, such as cotton, is preferred to nonabsorptive material for personal protective clothing for routine patient care where risk of large spillage is unlikely. The virus is easily inactivated by commonly used disinfectants. url: https://www.ncbi.nlm.nih.gov/pubmed/16142653/ doi: 10.1086/433186 id: cord-338899-qt17jhg0 author: Lakshmi, Vemu title: Clinical Features and Molecular Diagnosis of Chikungunya Fever from South India date: 2008-05-01 words: 3623.0 sentences: 178.0 pages: flesch: 48.0 cache: ./cache/cord-338899-qt17jhg0.txt txt: ./txt/cord-338899-qt17jhg0.txt summary: Emergence or reemergence of severe arboviral hemorrhagic fevers caused by mosquitoborne viruses, such as dengue virus and Chikungunya (CHIK) virus, have been frequently reported in the Indian subcontinent in the past few years. We report clinical observations and laboratory investigations involving virus isolation methods and molecular assays performed for 296 clinically suspected cases of CHIK fever. Of particular interest was the applicability of a novel method of gene amplificatio called real-time loop-mediated isothermal amplifica tion (RT-LAMP) as a rapid, sensitive, and specifi real-time method to detect and quantify CHIK virus in the acute phase of the infection. All 132 patients who had clinically suspected CHIK virus but whose RT-PCR and RT-LAMP results were negative presented 17 days after the onset of fever; this may be the reason for the negative test results. The RT-LAMP allows rapid, realtime detection of CHIK virus in acute-phase serum samples, without requiring sophisticated equipment, and has potential usefulness for clinical diagnosis and surveillance of CHIK virus in developing countries. abstract: An epidemic of Chikungunya fever of unprecedented magnitude occurred in many parts of India in early 2006 after an interval of 33 years, and there has been a resurgence in some parts of South India since June 2007. The article highlights clinical manifestations of infection and various molecular tests that were used for diagnoses of Chikungunya virus infection. Of particular interest is the real-time loop-mediated isothermal amplification (RT LAMP) assay, which is rapid and cost-effective and can be adopted at ill-equipped laboratories. Clinical symptoms were characterized by a triad of fever, rash, and severe rheumatic manifestations. RT LAMP identified 20 additional Chikungunya virus—positive cases, compared with reverse-transcriptase polymerase chain reaction. Chikungunya virus was isolated from 20 randomly selected samples. Genotyping of the virus isolates revealed that the East Central South African genotype of Chikungunya virus was the etiologic agent of this epidemic. Molecular diagnosis is an important tool to identify such new vectorborne viral illnesses. url: https://www.ncbi.nlm.nih.gov/pubmed/18419449/ doi: 10.1086/529444 id: cord-309091-te15ahvw author: Larson, Derek title: A Case of Early Re-infection with SARS-CoV-2 date: 2020-09-19 words: 498.0 sentences: 57.0 pages: flesch: 63.0 cache: ./cache/cord-309091-te15ahvw.txt txt: ./txt/cord-309091-te15ahvw.txt summary: A c c e p t e d M a n u s c r i p t 3 Dear Editor, It is with great interest that we read the first report of re-infection from SARS-CoV-2, which represented an important data point in the ongoing COVID-19 pandemic [1] [2] [3] . 42-year-old healthy male military healthcare provider presented with cough, subjective fever, and myalgias on 21 March following a workplace COVID-19 exposure and tested positive by SARS-CoV-2 RT-PCR ( Figure 1 ). The SARS-CoV-2 genome from the re-infection sample was deposited in NCBI GenBank under Accession The identification of specific products, scientific instrumentation, or organization is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the author, DoD, or any component agency. COVID-19 re-infection by a phylogenetically distinct SARScoronavirus-2 strain confirmed by whole genome sequencing Persistent positivity and fluctuations of SARS-CoV-2 RNA in clinically-recovered COVID-19 patients Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32949240/ doi: 10.1093/cid/ciaa1436 id: cord-341359-c34gyuv6 author: Larson, Derek T title: Clinical Outcomes of Coronavirus Disease 2019 With Evidence-based Supportive Care date: 2020-05-30 words: 1203.0 sentences: 62.0 pages: flesch: 42.0 cache: ./cache/cord-341359-c34gyuv6.txt txt: ./txt/cord-341359-c34gyuv6.txt summary: This retrospective study of an institutional cohort including 135 patients with confirmed COVID-19 demonstrates positive outcomes when organizational standards of care consist of evidence-based supportive therapies. Following widespread use of therapeutic agents with limited data to support their use, calls were made to focus on the evidence-based care that has been the foundation of modern medical therapy for most acute respiratory viral infections [7, 8] . Our study is the first report of COVID-19 outcomes when institutional standards of care consist solely of known evidence-based practices of supportive care. Of those diagnosed with COVID-19, 21 (15.6%) had severe enough disease to necessitate hospitalization and 6 (4.4%) required care in the ICU. Our study demonstrates favorable outcomes for patients with mild to moderately severe COVID-19 disease when evidence-based supportive care is considered the institutional standard. abstract: Calls for adherence to evidence-based medicine have emerged during the initial wave of the COVID-19 pandemic but reports of outcomes are lacking. This retrospective study of an institutional cohort including 135 patients with confirmed COVID-19 demonstrates positive outcomes when organizational standards of care consist of evidence-based supportive therapies. url: https://www.ncbi.nlm.nih.gov/pubmed/32472675/ doi: 10.1093/cid/ciaa678 id: cord-275349-b35pt3mo author: Lenz, Heinz-Josef title: The Emergence of Baricitinib: A Story of Tortoises Versus Hares date: 2020-07-06 words: 1403.0 sentences: 63.0 pages: flesch: 37.0 cache: ./cache/cord-275349-b35pt3mo.txt txt: ./txt/cord-275349-b35pt3mo.txt summary: The artificial intelligence algorithms predicted that baricitinib would inhibit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection of cells [2] , (an effect later confirmed in human liver spheroids) [3] , combined with its better-known anti-inflammatory properties. Consequently, the combined potential antiviral and anti-inflammatory effects of this dually acting drug could be ideal for halting the progression of the disease in hospitalized patients, when taken for a limited duration. This new paper in the journal extends the previous published reports of baricitinib treatment in mild-tomoderate COVID19 patients and provides further evidence that baricitinib could be a potential treatment for unwell hospitalized patients with this disease, independent of severity. One would be advised to remain vigilant of such signals reflecting thromboembolic or infection risk in randomized controlled trials testing a variety of immunomodulatory therapies in COVID-19 patients, either alone or in combination, especially in view of associations between clots and SARS-CoV-2 infection [10] . abstract: nan url: https://doi.org/10.1093/cid/ciaa940 doi: 10.1093/cid/ciaa940 id: cord-252005-3ld5e7f5 author: Lewis, Nathaniel M title: Household Transmission of SARS-CoV-2 in the United States date: 2020-08-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Although many viral respiratory illnesses are transmitted within households, the evidence base for SARS-CoV-2 is nascent. We sought to characterize SARS-CoV-2 transmission within US households and estimate the household secondary infection rate (SIR) to inform strategies to reduce transmission. METHODS: We recruited laboratory-confirmed COVID-19 patients and their household contacts in Utah and Wisconsin during March 22–April 25, 2020. We interviewed patients and all household contacts to obtain demographics and medical histories. At the initial household visit, 14 days later, and when a household contact became newly symptomatic, we collected respiratory swabs from patients and household contacts for testing by SARS-CoV-2 rRT-PCR and sera for SARS-CoV-2 antibodies testing by enzyme-linked immunosorbent assay (ELISA). We estimated SIR and odds ratios (OR) to assess risk factors for secondary infection, defined by a positive rRT-PCR or ELISA test. RESULTS: Thirty-two (55%) of 58 households had evidence of secondary infection among household contacts. The SIR was 29% (n = 55/188; 95% confidence interval [CI]: 23–36%) overall, 42% among children (<18 years) of the COVID-19 patient and 33% among spouses/partners. Household contacts to COVID-19 patients with immunocompromised conditions had increased odds of infection (OR: 15.9, 95% CI: 2.4–106.9). Household contacts who themselves had diabetes mellitus had increased odds of infection (OR: 7.1, 95% CI: 1.2–42.5). CONCLUSIONS: We found substantial evidence of secondary infections among household contacts. People with COVID-19, particularly those with immunocompromising conditions or those with household contacts with diabetes, should take care to promptly self-isolate to prevent household transmission. url: https://www.ncbi.nlm.nih.gov/pubmed/33185244/ doi: 10.1093/cid/ciaa1166 id: cord-312905-8xlt92pl author: Li, Guanjian title: Asymptomatic and Presymptomatic Infectors: Hidden Sources of COVID-19 Disease date: 2020-04-09 words: 690.0 sentences: 61.0 pages: flesch: 58.0 cache: ./cache/cord-312905-8xlt92pl.txt txt: ./txt/cord-312905-8xlt92pl.txt summary: At the time of writing this paper, the authors claimed that "evidence regarding transmission from individuals with asymptomatic infection or mild illness is limited", but that the current evidence may need an update. Recently, two epidemiological studies on COVID-19 have reported that typically asymptomatic carriers transmit the virus to close contacts, resulting in aggregated infection of symptomatic COVID-19 diseases [2, 3] . This study used a prospective design to follow up the viral load and clinical manifestations of 2147 close contacts of symptomatic and asymptomatic COVID-19 cases. The authors suggested that the transmission ability of asymptomatic individuals should not be ignored. First Mildly Ill, Non-Hospitalized Case of Coronavirus Disease 2019 (COVID-19) Without Viral Transmission in the United States Clinical characteristics of 24 asymptomatic infections with COVID-19 screened among close contacts in Nanjing The epidemiological characteristics of infection in close contacts of COVID-19 in Ningbo city abstract: nan url: https://doi.org/10.1093/cid/ciaa418 doi: 10.1093/cid/ciaa418 id: cord-348178-6bjimde4 author: Li, Ling title: Biosafety Level 3 Laboratory for Autopsies of Patients with Severe Acute Respiratory Syndrome: Principles, Practices, and Prospects date: 2005-09-15 words: 3684.0 sentences: 205.0 pages: flesch: 52.0 cache: ./cache/cord-348178-6bjimde4.txt txt: ./txt/cord-348178-6bjimde4.txt summary: title: Biosafety Level 3 Laboratory for Autopsies of Patients with Severe Acute Respiratory Syndrome: Principles, Practices, and Prospects A specially designed biosafety level 3 (BSL-3) autopsy laboratory was constructed and divided into a clean area, a semicontaminated area, a contaminated area, and 2 buffer zones. Our experience suggests that BSL-3 laboratory operating principles should be among the special requirements for performing autopsies of contaminated bodies and that they can safeguard the clinicians and the environment involved in these procedures. According to the guidelines of World Health Organization and the Centers for Disease Control and Prevention (CDC) in the United States, SARS-CoV fulfills the criteria for a biohazard group 3 pathogen. The biosafety of our BSL-3 autopsy laboratory has been ensured in 4 ways: through the design of the facility, use of PPE, decontamination, and administrative regulation. Interim laboratory biosafety guidelines for handling and processing specimens associated with severe acute respiratory syndrome (SARS) abstract: Background. During the outbreak of the emergent severe acute respiratory syndrome (SARS) infection, >30% of the ∼8000 infected persons were health care workers. The highly infectious nature of SARS coronavirus (SARS-CoV) compelled our pathologists to consider biosafety issues in the autopsy room and for tissue processing procedures. Methods. A specially designed biosafety level 3 (BSL-3) autopsy laboratory was constructed and divided into a clean area, a semicontaminated area, a contaminated area, and 2 buffer zones. High-efficiency particulate air filters were placed in the air supply and exhaust systems. Laminar air flow was from the clean areas to the less clean areas. The negative pressures of the contaminated, semicontaminated, and clean areas were approximately -50 pa, -25 pa, and -5 pa, respectively. Personal protective equipment, including gas mask, impermeable protective clothing, and 3 layers of gloves worn during autopsies; the equipment was decontaminated before it was allowed to exit the facility. Strict BSL-3 practices were followed. Results. When a given concentration of particulate sarin simulant was introduced into the contaminated area, it could not be detected in either the semicontaminated area or clean area, and particles >0.3 μm in size were not detected in the exhaust air. A total of 16 complete postmortem examinations for probable and suspected SARS were performed during a 2-month period. Of these, 7 reported confirmed cases of SARS. None of the 23 pathologists and technicians who participated in these autopsies was infected with SARS-CoV. Conclusions. Our experience suggests that BSL-3 laboratory operating principles should be among the special requirements for performing autopsies of contaminated bodies and that they can safeguard the clinicians and the environment involved in these procedures. url: https://www.ncbi.nlm.nih.gov/pubmed/16107979/ doi: 10.1086/432720 id: cord-353862-7xe3fvd5 author: Li, Na title: Maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia: a case-control study date: 2020-03-30 words: 3515.0 sentences: 199.0 pages: flesch: 52.0 cache: ./cache/cord-353862-7xe3fvd5.txt txt: ./txt/cord-353862-7xe3fvd5.txt summary: METHODS: We conducted a case-control study to compare clinical characteristics, maternal and neonatal outcomes of pregnant women with and without COVID-19 pneumonia. An earlier study by Chen et al reported nine pregnant women with COVID-19 pneumonia, who took cesarean section in a tertiary hospital of Wuhan [8] . To date, none of previous studies have investigated the adverse effects of COVID-19 infection on pregnancy, by comparing maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia to those without pneumonia. Similar to two previous reports of nine and one pregnant women with confirmed COVID-19 infection [8, 22] , we did not find any evidence to support the vertical transmission of SARS-CoV-2 from mother to fetus via placenta or during cesarean section. Second, we collected the data of sixteen pregnant women with laboratory confirmed COVID-19 pneumonia and eighteen suspected cases with typical CT imaging. abstract: BACKGROUND: The ongoing epidemics of coronavirus disease 2019 (COVID-19) have caused serious concerns about its potential adverse effects on pregnancy. There are limited data on maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia. METHODS: We conducted a case-control study to compare clinical characteristics, maternal and neonatal outcomes of pregnant women with and without COVID-19 pneumonia. RESULTS: During January 24 to February 29, 2020, there were sixteen pregnant women with confirmed COVID-19 pneumonia and eighteen suspected cases who were admitted to labor in the third trimester. Two had vaginal delivery and the rest took cesarean section. Few patients presented respiratory symptoms (fever and cough) on admission, but most had typical chest CT images of COVID-19 pneumonia. Compared to the controls, COVID-19 pneumonia patients had lower counts of white blood cells (WBC), neutrophils, C-reactive protein (CRP), and alanine aminotransferase (ALT) on admission. Increased levels of WBC, neutrophils, eosinophils, and CRP were found in postpartum blood tests of pneumonia patients. There were three (18.8%) and three (16.7%) of the mothers with confirmed or suspected COVID-19 pneumonia had preterm delivery due to maternal complications, which were significantly higher than the control group. None experienced respiratory failure during hospital stay. COVID-19 infection was not found in the newborns and none developed severe neonatal complications. CONCLUSION: Severe maternal and neonatal complications were not observed in pregnant women with COVID-19 pneumonia who had vaginal delivery or caesarean section. Mild respiratory symptoms of pregnant women with COVID-19 pneumonia highlight the need of effective screening on admission. url: https://www.ncbi.nlm.nih.gov/pubmed/32249918/ doi: 10.1093/cid/ciaa352 id: cord-332469-zegawla5 author: Li, Wei title: The characteristics of household transmission of COVID-19 date: 2020-04-17 words: 2513.0 sentences: 164.0 pages: flesch: 64.0 cache: ./cache/cord-332469-zegawla5.txt txt: ./txt/cord-332469-zegawla5.txt summary: Secondary attack rates of SARS-CoV-2 to the contact members were computed and the risk factors for transmission within household were estimated. The secondary attack rate to contacts who were spouses of index cases was 27.8% comparing with 17.3% to other adult members in the households. Spouse relationship was another risk factor for the infection of SARS-CoV-2 to household contacts and the secondary attack rate to individuals who were spouses of index cases was 27.8%, compared to 17.3% to other members in the households (OR 2.21, 95% CI 1.18 to 4.12, p=0.013). The gender, symptoms and the time between onset of illness of index patients and hospitalization were not related to the secondary attack rates of SARS-CoV-2 to household contacts (Table 3 The results showed no infected contacts in the households with index cases who implemented quarantine immediately after appearance of symptoms, and so the secondary attack rate was zero. abstract: BACKGROUND: Since December 2019, SARS-CoV-2 virus has extended to most parts of China with more than 80 thousand cases and to at least 100 countries with more than 60 thousand international cases by March 15, 2020. Here we applied household cohort study to determine the features of household transmission of COVID-19. METHODS: Total 105 index patients and 392 household contacts were enrolled. Both index patients and household members were inspected by SARS-CoV-2 RT-PCR. The information of all recruited people was extracted from medical records and confirmed or supplemented by telephone interviews. The baseline characteristics of index cases and contact patients were described. Secondary attack rates of SARS-CoV-2 to the contact members were computed and the risk factors for transmission within household were estimated. RESULTS: Secondary transmission of SARS-CoV-2 developed in 64 of 392 household contacts (16.3%). The secondary attack rate to children was 4% comparing with 17.1% to adults. The secondary attack rate to the contacts within the households with index patients quarantined by themselves since onset of symptoms was 0% comparing with 16.9% to the contacts without index patients quarantined. The secondary attack rate to contacts who were spouses of index cases was 27.8% comparing with 17.3% to other adult members in the households. CONCLUSION: The secondary attack rate of SARS-CoV-2 in household is 16.3%. Ages of household contacts and spouse relationship with index case are risk factors for transmission of SARS-CoV-2 within household. Quarantine of index patients at home since onset of symptom is useful to prevent the transmission of SARS-Co-2 within household. url: https://doi.org/10.1093/cid/ciaa450 doi: 10.1093/cid/ciaa450 id: cord-348036-yub2cqz6 author: Lighter, Jennifer title: Obesity in patients younger than 60 years is a risk factor for Covid-19 hospital admission date: 2020-04-09 words: 722.0 sentences: 62.0 pages: flesch: 69.0 cache: ./cache/cord-348036-yub2cqz6.txt txt: ./txt/cord-348036-yub2cqz6.txt summary: title: Obesity in patients younger than 60 years is a risk factor for Covid-19 hospital admission Covid-19 disease, caused by SARS-CoV-2 infection includes a spectrum of illness; from asymptomatic infection [2] to severe pneumonia characterized by acute respiratory injury in about 20% of patients presenting to medical care [3] . A c c e p t e d M a n u s c r i p t years were 2.2 (95% CI 1.7-2.9, p<.0001) and 3.6 (95% CI 2.5-5.3, p=<.0001) times more likely to be admitted to acute and critical care compared to patients in the same age category who had BMI <30. Though patients aged <60 years are generally considered a lower risk group of Covid-19 disease severity, based on data from our institution, obesity appears to be a previously unrecognized risk factor for hospital admission and need for critical care. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32271368/ doi: 10.1093/cid/ciaa415 id: cord-288432-n2y9cunc author: Liu, Kun title: Population movement, city closure in Wuhan and geographical expansion of the 2019-nCoV pneumonia infection in China in January 2020 date: 2020-04-17 words: 2357.0 sentences: 144.0 pages: flesch: 58.0 cache: ./cache/cord-288432-n2y9cunc.txt txt: ./txt/cord-288432-n2y9cunc.txt summary: BACKGROUND: The unprecedented outbreak of 2019-nCoV pneumonia infection in Wuhan City caused global concern, the outflowing population from Wuhan was believed to be a main reason for the rapid and large-scale spread of the disease, so the government implemented a city closure measure to prevent its transmission considering the large amount of travelling before the Chinese New Year. METHODS: Based on the daily reported new cases and the population movement data between January 1 and 31, we examined the effects of population outflow from Wuhan on the geographical expansion of the infection in other provinces and cities of China, as well as the impacts of the city closure in Wuhan in different scenarios of closing dates. Thus, we conducted this study with the following objectives: 1) to evaluate the impacts of the population movement on the spatial transmission of the 2019-nCoV cases at the provincial and city levels in China; 2) to estimate the potential outbreak risk at areas with the population outflowed from Wuhan; 3) to evaluate the effectiveness of the city closure measures on the epidemic control. abstract: BACKGROUND: The unprecedented outbreak of 2019-nCoV pneumonia infection in Wuhan City caused global concern, the outflowing population from Wuhan was believed to be a main reason for the rapid and large-scale spread of the disease, so the government implemented a city closure measure to prevent its transmission considering the large amount of travelling before the Chinese New Year. METHODS: Based on the daily reported new cases and the population movement data between January 1 and 31, we examined the effects of population outflow from Wuhan on the geographical expansion of the infection in other provinces and cities of China, as well as the impacts of the city closure in Wuhan in different scenarios of closing dates. RESULTS: We observed a significantly positive association between population movement and the number of the 2019-nCoV cases. The spatial distribution of cases per unit outflow population indicated that some areas with large outflow population might have been underestimated for the infection, such as Henan and Hunan provinces. Further analysis revealed that if the city closure policy was implemented two days earlier, 1420 (95% CI: 1059, 1833) cases could have been prevented, and if two days later, 1462 (95% CI: 1090, 1886) more cases would be possible. CONCLUSIONS: Our findings suggest that population movement might be one important trigger for the transmission of 2019-nCoV infection in China, and the policy of city closure is effective to control the epidemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32302377/ doi: 10.1093/cid/ciaa422 id: cord-328267-tk0zc8il author: Liu, Qiao title: Collateral Impact of the Covid-19 Pandemic on Tuberculosis Control in Jiangsu Province, China date: 2020-08-28 words: 1667.0 sentences: 119.0 pages: flesch: 50.0 cache: ./cache/cord-328267-tk0zc8il.txt txt: ./txt/cord-328267-tk0zc8il.txt summary: title: Collateral Impact of the Covid-19 Pandemic on Tuberculosis Control in Jiangsu Province, China We compared tuberculosis case notifications, tuberculosis treatment outcomes, and diagnostic screening for multidrug resistance (MDR) among tuberculosis patients from 2015-2020 before and after the Covid-19 pandemic began in China. We A c c e p t e d M a n u s c r i p t Discussion This is the first data from China reporting the potential indirect impact on tuberculosis control of the Covid-19 pandemic. In addition, reductions in treatment completion and MDR screening during this time period suggest that both deterred health care seeking and community disease management are likely drivers of these trends. Our analysis suggests that collateral effects of the Covid-19 pandemic on tuberculosis control are substantial, with a reduction of 36%-52% in tuberculosis notifications in 2020 compared to 2015-2019. abstract: The Covid-19 pandemic may impede global tuberculosis elimination goals. In Jiangsu Province, China, tuberculosis notifications dropped 52% in 2020 compared to 2015–2019. Treatment completion and screening for drug resistance decreased continuously in 2020. Urgent attention must be paid to tuberculosis control efforts during and after the Covid-19 pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32857838/ doi: 10.1093/cid/ciaa1289 id: cord-348144-t0chpsuh author: Lucas, Alexander H. title: Carbohydrate Moieties as Vaccine Candidates date: 2005-09-01 words: 5556.0 sentences: 238.0 pages: flesch: 29.0 cache: ./cache/cord-348144-t0chpsuh.txt txt: ./txt/cord-348144-t0chpsuh.txt summary: We discuss the cellular basis of carbohydrate immunity, newly identified glycotope processing pathways and recognition capabilities, and the synthetic and microarray technologies that are being developed that will permit new experimental approaches to carbohydrate vaccine development and the exploration of the interaction of the immune system with self and nonself glycans. It has long been known that bactericidal and/or opsonic antibodies directed against capsular polysaccharide (PS) glycotopes protect against invasive diseases caused by encapsulated bacteria, and, accordingly, vaccine development has focused on the elicitation of these antibody specificities. Purified microbial PS vaccines have been in use for 140 years, but they have proven to be variably immunogenic and variably efficacious in protecting susceptible populations against invasive meningococcal, pneumococcal, and Haemophilus influenzae type b (Hib) diseases [1, 2] . Significant variation in serotype-specific immunogenicity of the sevenvalent Streptococcus pneumoniae capsular polysaccharide-CRM197 conjugate vaccine occurs despite vigorous T cell help induced by the carrier protein abstract: Carbohydrate epitopes or glycotopes are structurally diverse, occur in a variety of chemical contexts, and are present on the surfaces of cells in the body and on the surfaces of pathogens. These various structures and modes of presentation affect how they are perceived and processed by the body and dictate the outcome of the immune response directed against them. This review focuses on mechanisms of carbohydrate immunity, with an emphasis on carbohydrate vaccines that have been or are being developed for protection against encapsulated bacterial pathogens. We discuss the cellular basis of carbohydrate immunity, newly identified glycotope processing pathways and recognition capabilities, and the synthetic and microarray technologies that are being developed that will permit new experimental approaches to carbohydrate vaccine development and the exploration of the interaction of the immune system with self and nonself glycans. url: https://www.ncbi.nlm.nih.gov/pubmed/16080094/ doi: 10.1086/432582 id: cord-300550-l28tadhn author: Luers, Jan C title: Olfactory and Gustatory Dysfunction in Coronavirus Disease 19 (COVID-19) date: 2020-05-01 words: 1755.0 sentences: 129.0 pages: flesch: 65.0 cache: ./cache/cord-300550-l28tadhn.txt txt: ./txt/cord-300550-l28tadhn.txt summary: In this cross-sectional study, two-thirds of European patients with polymerase chain reaction confirmed COVID-19 reported olfactory and gustatory dysfunction, indicating the significance of this history in the early diagnostics. First of all, patients were asked for the onset of fever, cough, sore throat, rhinitis, muscle aches, headache, diarrhea, reduced olfaction, and a reduced sense of taste during COVID-19. To investigate factors related to reduced olfaction as well as to a reduced sense of taste two general linear models were used with explanatory variables of age, gender, TNSS, fever, cough, sore throat, rhinitis, and headache, respectively. In addition, fever, cough, sore throat, rhinitis, headache, and TNSS were also not associated with reduced olfaction or reduced sense of taste (p ≥ 0.05, respectively). Our study shows for the first time that both olfactory and gustatory dysfunction is very common in COVID-19 patients, with olfactory dysfunction even leveling the symptom ''cough'' at > 70%. abstract: Coronavirus-disease-2019 (COVID-19) caused by the severe-acute-respiratory-syndrome-coronavirus-2 (SARS-CoV-2) shows a rapid spread over-the-world. Given scarce resources, non-laboratory diagnostics is crucial. In this cross-sectional study, two-thirds of European patients with polymerase chain reaction confirmed COVID-19 reported olfactory and gustatory dysfunction, indicating the significance of this history in the early diagnostics. url: https://doi.org/10.1093/cid/ciaa525 doi: 10.1093/cid/ciaa525 id: cord-327862-zcg3baym author: Luo, Yiqi Ruben title: Kinetics of SARS-CoV-2 Antibody Avidity Maturation and Association with Disease Severity date: 2020-09-14 words: 1141.0 sentences: 93.0 pages: flesch: 59.0 cache: ./cache/cord-327862-zcg3baym.txt txt: ./txt/cord-327862-zcg3baym.txt summary: The kinetics of IgG avidity maturation during SARS-CoV-2 infection was studied. It was found that there was a strong correlation between IgG avidity and days since symptom onset, and peak readings were significantly higher in severe than mild disease cases. 3, 4 Here we report the development of a method to characterize SARS-CoV-2 IgG avidity maturation in COVID-19 patients from initial diagnosis through convalescence. The IgG avidity assay was established on a novel label-free immunoassay platform Gator Analyzer (Gator Bio, Palo Alto, CA) to measure SARS-CoV-2 IgG avidity to the virus spike protein receptor-binding domain (RBD). The signal increase in the final step, which is proportional to the quantity of RBD-IgG-Anti-IgG immune complex on the sensing probe, was measured. As other isotypes of antibodies might bind to RBD in the second step, the measurement of the RBD-IgG-Anti-IgG immune complex enhanced the assay specificity. Magnitude and kinetics of anti-SARS-CoV-2 antibody responses and their relationship to disease severity abstract: The kinetics of IgG avidity maturation during SARS-CoV-2 infection was studied. The IgG avidity assay used a novel label-free immunoassay technology. It was found that there was a strong correlation between IgG avidity and days since symptom onset, and peak readings were significantly higher in severe than mild disease cases. url: https://doi.org/10.1093/cid/ciaa1389 doi: 10.1093/cid/ciaa1389 id: cord-303330-zh8wzza5 author: Magleby, Reed title: Impact of SARS-CoV-2 Viral Load on Risk of Intubation and Mortality Among Hospitalized Patients with Coronavirus Disease 2019 date: 2020-06-30 words: 3557.0 sentences: 204.0 pages: flesch: 51.0 cache: ./cache/cord-303330-zh8wzza5.txt txt: ./txt/cord-303330-zh8wzza5.txt summary: In two studies of hospitalized patients in China, those with severe presentations of COVID-19 had higher viral loads than those with mild presentations, but the impact of SARS-CoV-2 viral load on the risk of intubation or death was not evaluated [10, 11] . We hypothesized that assessing SARS-CoV-2 viral load by analyzing Ct values from an initial NP swab sample could be a clinically valuable tool to identify patients at highest risk of intubation and death and provide insights into the pathogenesis of COVID-19. We therefore conducted this retrospective analysis of SARS-CoV-2 viral loads on admission, clinical presentations, and outcomes at two affiliated New York City hospitals using a high-throughput RT-PCR assay. In conclusion, we found that admission SARS-CoV-2 viral loads, as determined by Ct values that are generated with standard-of-care diagnostic assays, are independently associated with intubation and death among hospitalized patients with COVID-19. abstract: BACKGROUND: Patients hospitalized with coronavirus disease 2019 (COVID-19) frequently require mechanical ventilation and have high mortality rates, but the impact of viral burden on these outcomes is unknown. METHODS: We conducted a retrospective cohort study of patients hospitalized with COVID-19 from March 30 to April 30, 2020 at two hospitals in New York City. SARS-CoV-2 viral load was assessed using cycle threshold (Ct) values from a reverse transcription-polymerase chain reaction assay applied to nasopharyngeal swab samples. We compared patient characteristics and outcomes among patients with high, medium, and low admission viral loads and assessed whether viral load was independently associated with risk of intubation and in-hospital mortality. RESULTS: We evaluated 678 patients with COVID-19. Higher viral load was associated with increased age, comorbidities, smoking status, and recent chemotherapy. In-hospital mortality was 35.0% with a high viral load (Ct<25; n=220), 17.6% with a medium viral load (Ct 25-30; n=216), and 6.2% with a low viral load (Ct>30; n=242; P<0.001). The risk of intubation was also higher in patients with a high viral load (29.1%), compared to those with a medium (20.8%) or low viral load (14.9%; P<0.001). High viral load was independently associated with mortality (adjusted odds ratio [aOR] 6.05; 95% confidence interval [CI]: 2.92-12.52; P<0.001) and intubation (aOR 2.73; 95% CI: 1.68-4.44; P<0.001) in multivariate models. CONCLUSIONS: Admission SARS-CoV-2 viral load among hospitalized patients with COVID-19 independently correlates with the risk of intubation and in-hospital mortality. Providing this information to clinicians could potentially be used to guide patient care. url: https://doi.org/10.1093/cid/ciaa851 doi: 10.1093/cid/ciaa851 id: cord-260630-vvpzp73r author: Mandell, Lionel A. title: Etiologies of Acute Respiratory Tract Infections date: 2005-08-15 words: 2623.0 sentences: 120.0 pages: flesch: 52.0 cache: ./cache/cord-260630-vvpzp73r.txt txt: ./txt/cord-260630-vvpzp73r.txt summary: In this issue of Clinical Infectious Diseases, there are 2 articles that provide us with some insight into the various etiologic agents that can cause acute respiratory tract infection (ARTI) in general practice patients in The Netherlands [1] and into the significance of the human metapneumovirus (hMPV) in patients with community-acquired pneumonia (CAP) and exacerbations of chronic obstructive pulmonary disease (COPD) in Quebec, Canada [2] . The objectives of the Dutch study were to estimate the incidence of influenza-like illnesses (ILIs) and of other ARTIs in patients visiting their general practitioners (to determine the etiologic agents) and to test the hypothesis that asymptomatic persons with subclinical infection may act as sources of transmission [1] . Nose and throat swab specimens were obtained from case patients and control subjects, and viral cultures and PCR tests were performed for detection of adenovirus, coronavirus, enterovirus, hMPV, influenza virus, parainfluenza virus, rhinovirus, and respiratory syncytial virus (RSV), as well as for Mycoplasma pneumoniae, Chlamydophila pneumoniae, and Chlamydophila psittaci. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/16028159/ doi: 10.1086/432019 id: cord-292094-vmsdhccp author: Mandell, Lionel A. title: Infectious Diseases Society of America/American Thoracic Society Consensus Guidelines on the Management of Community-Acquired Pneumonia in Adults date: 2007-03-01 words: 28389.0 sentences: 1424.0 pages: flesch: 37.0 cache: ./cache/cord-292094-vmsdhccp.txt txt: ./txt/cord-292094-vmsdhccp.txt summary: Severity-of-illness scores, such as the CURB-65 criteria (confusion, uremia, respiratory rate, low blood pressure, age 65 years or greater), or prognostic models, such as the Pneumonia Severity Index (PSI), can be used to identify patients with CAP who may be candidates for outpatient treatment. A respiratory fluoroquinolone should be used for penicillin-allergic patients.) Increasing resistance rates have suggested that empirical therapy with a macrolide alone can be used only for the treat-ment of carefully selected hospitalized patients with nonsevere disease and without risk factors for infection with drug-resistant pathogens. Advantages include the high specificity, the ability of some assays to distinguish between influenza A and B, the rapidity with which the results can be obtained, the possibly reduced use of antibacterial agents, and the utility of establishing this diagnosis for epidemiologic purposes, especially in hospitalized patients who may require infection control precautions. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/17278083/ doi: 10.1086/511159 id: cord-351589-32kd9vva author: Mang, Sebastian title: Pneumocystis Jirovecii Pneumonia and SARS-CoV-2 Co-Infection in newly diagnosed HIV-1 infection date: 2020-07-01 words: 561.0 sentences: 58.0 pages: flesch: 60.0 cache: ./cache/cord-351589-32kd9vva.txt txt: ./txt/cord-351589-32kd9vva.txt summary: title: Pneumocystis Jirovecii Pneumonia and SARS-CoV-2 Co-Infection in newly diagnosed HIV-1 infection We report the case of a 52-year-old male from our intensive care unit (ICU) who developed acute respiratory failure due to Covid-19, Pneumocystis jirovecii Pneumonia (PJP) and newly diagnosed HIV, stage 3 [2] . He deteriorated further despite escalated pressure-controlled invasive ventilation and was finally transferred to our intensive care unit on 13 th May, 2020, for possible initiation of extracorporeal membrane oxygenation (ECMO). As a potential sign for subacute manifestation, airway changes, pleural changes, fibrosis, and nodules were present (Figure 1 Over the next two weeks, his state improved significantly. Why Aren''t People Living with HIV at Higher Risk for Developing Severe Coronavirus Disease 2019 (COVID-19) Radiological findings from 81 patients with COVID-19 pneumonia in Wuhan, China: a descriptive study. Coronavirus Disease 2019 (COVID-19) CT Findings: A Systematic Review and Meta-analysis abstract: nan url: https://doi.org/10.1093/cid/ciaa906 doi: 10.1093/cid/ciaa906 id: cord-313427-6y4zvrmn author: Mani, Nandita S title: Prevalence of COVID-19 Infection and Outcomes Among Symptomatic Healthcare Workers in Seattle, Washington date: 2020-06-16 words: 3433.0 sentences: 226.0 pages: flesch: 57.0 cache: ./cache/cord-313427-6y4zvrmn.txt txt: ./txt/cord-313427-6y4zvrmn.txt summary: Using data from these testing centers, we report the prevalence of SARS-CoV-2 infection among symptomatic employees and describe the clinical characteristics and outcomes among employees with COVID-19. Multiple factors have been reported to contribute to the risk of infections in HCWs, including lack of awareness during the early weeks of the outbreak, inadequate personal protective equipment (PPE) supply and training, insufficient rapid diagnostic testing for COVID-19, long work hours in high-risk environments, and ongoing community spread and household exposures. [12] [13] [14] A c c e p t e d M a n u s c r i p t Early and high-throughput testing for SARS-CoV-2 among symptomatic employees is essential to prevent nosocomial transmission of COVID-19 to patients, minimize clusters among HCWs, and maintain staffing during the pandemic. HCWs. 16 Here we describe the approach to establishing high-throughput employee testing centers, the prevalence of infections among symptomatic frontline versus non-frontline staff, and clinical outcomes associated with COVID-19 in these employees. abstract: BACKGROUND: Healthcare workers (HCW) serving on the front lines of the coronavirus disease 2019 (COVID-19) pandemic have been at increased risk for infection due to SARS-CoV-2 in some settings. Healthcare-acquired infection has been reported in similar epidemics, but there are limited data on the prevalence of COVID-19 among HCWs and their associated clinical outcomes in the United States. METHODS: We established two high-throughput employee testing centers in Seattle, Washington with drive-through and walk-through options for symptomatic employees in the University of Washington Medicine system and its affiliated organizations. Using data from these testing centers, we report the prevalence of SARS-CoV-2 infection among symptomatic employees and describe the clinical characteristics and outcomes among employees with COVID-19. RESULTS: Between March 12 and April 23, a total of 3,477 symptomatic employees were tested for COVID-19 at two employee testing centers; 185 (5.3%) employees tested positive for COVID-19. The prevalence of SARS-CoV-2 was similar when comparing frontline HCWs (5.2%) to non-frontline staff (5.5%). Among 174 positive employees reached for follow-up at least 14 days after diagnosis, 6 reported COVID-related hospitalization; all recovered. CONCLUSIONS: During the study period, we observed that the prevalence of positive SARS-CoV-2 tests among symptomatic HCWs was comparable to that of symptomatic non-frontline staff. Reliable and rapid access to testing for employees is essential to preserve the health, safety, and availability of the healthcare workforce during this pandemic and to facilitate the rapid return of SARS-CoV-2 negative employees to work. url: https://www.ncbi.nlm.nih.gov/pubmed/32548613/ doi: 10.1093/cid/ciaa761 id: cord-252761-ro5tj0tx author: Marriott, Deborah title: Concomitant marked decline in prevalence of SARS-CoV-2 and other respiratory viruses among symptomatic patients following public health interventions in Australia: data from St Vincent’s Hospital and associated screening clinics, Sydney, NSW. date: 2020-08-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Our Australian hospital tested almost 22,000 symptomatic people over 11 weeks for SARS-CoV-2 in a multiplex PCR assay. Following travel bans and physical distancing, SARS-CoV-2 and other respiratory viruses diagnoses fell dramatically. Increasing rhinovirus diagnoses as social control measures were relaxed may indirectly indicate an elevated risk of COVID-19 resurgence url: https://doi.org/10.1093/cid/ciaa1256 doi: 10.1093/cid/ciaa1256 id: cord-348350-pac9ha4q author: Martin-Blondel, G title: Hydroxychloroquine in COVID-19 patients: what still needs to be known about the kinetics date: 2020-05-11 words: 1824.0 sentences: 136.0 pages: flesch: 59.0 cache: ./cache/cord-348350-pac9ha4q.txt txt: ./txt/cord-348350-pac9ha4q.txt summary: Different dosage regimens of hydroxychloroquine are used to manage COVID-19 patients, without information on the pharmacokinetics in this population.Blood samples (n=101) were collected from 57 COVID-19 patients for 7 days and concentrations were compared with simulated kinetic profiles.Hydroxychloroquine exposure is low and cannot be predicted by other populations. Because of the severity of COVID-19 and the pharmacokinetics of hydroxychloroquine in SLE patients [5] , a loading dose was rapidly included in the new hospital regimens to optimize drug distribution in tissues and more precisely in the lungs. For each regimen applied at the Toulouse University Hospital, an example of the expected kinetic profiles for a body weight of 80 kg (the median weight in our population) are presented in Figure 1 with the corresponding serum concentration for each patient. abstract: Different dosage regimens of hydroxychloroquine are used to manage COVID-19 patients, without information on the pharmacokinetics in this population.Blood samples (n=101) were collected from 57 COVID-19 patients for 7 days and concentrations were compared with simulated kinetic profiles.Hydroxychloroquine exposure is low and cannot be predicted by other populations. url: https://www.ncbi.nlm.nih.gov/pubmed/32392332/ doi: 10.1093/cid/ciaa558 id: cord-278084-km04sz2s author: Martino, Rodrigo title: Respiratory Virus Infections in Adults with Hematologic Malignancies: A Prospective Study date: 2003-01-01 words: 3119.0 sentences: 167.0 pages: flesch: 48.0 cache: ./cache/cord-278084-km04sz2s.txt txt: ./txt/cord-278084-km04sz2s.txt summary: On multivariate analysis, the only variable that predicted progression to pneumonia in patients with an upper respiratory tract infection was the presence of respiratory syncytial virus, whereas lymphocytopenia had a nonsignificant trend. We performed a prospective 2-year study to assess the role of respiratory virus infections in the pathogenesis of URTI and LRTI and risk factors for severe LRTI in an adult clinical hematology department. All adult patients with a hematologic malignancy (including HSCT recipients) who had signs and symptoms of a URTI or LRTI in the inpatient and outpatient settings underwent a detailed clinical evaluation, and samples from the upper and/or lower respiratory tracts were screened for the presence of respiratory viruses. A first episode of infection was defined as the period during which the patient had symptoms of URTI and/ or LRTI, regardless of whether a respiratory virus was isolated. abstract: During a 2-year period, 157 consecutive episodes of respiratory virus infections that occurred in 130 patients with upper or lower respiratory tract infection were analyzed for respiratory viruses. A respiratory virus was identified in 75 episodes (48%), and several viruses were found in 13 episodes: there were a total of 56 influenza A virus infections, 14 respiratory syncytial virus infections, 8 adenovirus infections, 8 infections with parainfluenza virus types 1 or 3, and 7 enterovirus infections. On multivariate analysis, the only variable that predicted progression to pneumonia in patients with an upper respiratory tract infection was the presence of respiratory syncytial virus, whereas lymphocytopenia had a nonsignificant trend. Also, among the 38 patients who had pneumonia at any time during the episode, both respiratory syncytial virus and lymphocytopenia were commonly found. For both epidemiological and therapeutic considerations, frequent screening for respiratory viruses should be incorporated into the routine diagnostic study of patients with hematologic malignancies. url: https://www.ncbi.nlm.nih.gov/pubmed/12491194/ doi: 10.1086/344899 id: cord-007075-sl45z4i0 author: Marty, Francisco M title: A Phase 2b, Randomized, Double-blind, Placebo-Controlled Multicenter Study Evaluating Antiviral Effects, Pharmacokinetics, Safety, and Tolerability of Presatovir in Hematopoietic Cell Transplant Recipients with Respiratory Syncytial Virus (RSV) Infection of the Lower Respiratory Tract date: 2019-12-03 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Presatovir significantly reduced nasal viral load, signs, and symptoms of respiratory syncytial virus (RSV) infection in a human challenge study. We evaluated presatovir in hematopoietic-cell transplant (HCT) recipients with RSV lower respiratory tract infection (LRTI). METHODS: Patients with confirmed RSV in upper and lower respiratory tract and new chest X-ray abnormalities were randomized (1:1), stratified by supplemental oxygen and ribavirin use, to receive oral presatovir 200 mg or placebo every 4 days for 5 doses. The primary endpoint was time-weighted average change in nasal RSV viral load through day 9. Secondary endpoints included supplemental oxygen-free days, incident respiratory failure requiring mechanical ventilation, and all-cause mortality. RESULTS: From January 31, 2015, to March 20, 2017, 60 patients from 17 centers were randomized (31 presatovir, 29 placebo); 59 received study treatment (50 allogeneic, 9 autologous HCT). In the efficacy population (29 presatovir, 28 placebo), presatovir treatment did not significantly reduce time-weighted average change in viral load (−1.12 vs −1.09 log(10) copies/mL; treatment difference −0.02 log(10) copies/mL, 95% confidence interval: −.62, .57; P = .94), median supplemental oxygen-free days (26 vs 28 days, P = .84), incident respiratory failure (10.3 vs 10.7%, P = .98), or all-cause mortality (0 vs 7.1%, P = .19) versus placebo. Adverse events were similar between arms (presatovir 80%, placebo 79%). Resistance-associated substitutions in RSV fusion protein emerged in 6/29 presatovir-treated patients. CONCLUSIONS: Presatovir treatment was well tolerated in HCT patients with RSV LRTI but did not improve virologic or clinical outcomes versus placebo. CLINICAL TRIALS REGISTRATION: www.clinicaltrials.gov, NCT02254421; EudraCT, #2014-002475-29 url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7108198/ doi: 10.1093/cid/ciz1167 id: cord-303603-4mi64bgm author: Martínez-Urbistondo, Diego title: Early Combination of Tocilizumab and Corticosteroids: An Upgrade in Anti-inflammatory Therapy for Severe Coronavirus Disease (COVID) date: 2020-07-04 words: 656.0 sentences: 40.0 pages: flesch: 47.0 cache: ./cache/cord-303603-4mi64bgm.txt txt: ./txt/cord-303603-4mi64bgm.txt summary: title: Early Combination of Tocilizumab and Corticosteroids: An Upgrade in Anti-inflammatory Therapy for Severe Coronavirus Disease (COVID) In our experience, the early administration of corticosteroids associated to tocilizumab, according to the previously published recommendations by the Spanish Ministry of Health [6] , may solve this high failure rate. In the HM Sanchinarro Hospital, a 200 bed teaching institution, we consecutively and ambispectively collected the outcome of 136 patients who received tocilizumab plus corticosteroids to treat severe COVID, defined as a SpO2/FiO2 <325 with bilateral pneumonia and a clinical diagnosis of infection by SARS-CoV-2. Generalized linear and Cox regression models, adjusted by age, sex, interaction between age and sex, CCI, time from onset to admission, dose of corticosteroids and tocilizumab and C-reactive protein and D-dimer levels at anti-inflammatory therapy administration, showed benefit in the use of ET in COVID patients (Relative Risk, 0.18, P = .01, and Hazard Ratio, 0.13, P = .01, respectively). abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32621739/ doi: 10.1093/cid/ciaa910 id: cord-273956-mruywa71 author: Mathers, Amy J title: The practical challenges of making clinical use of the quantitative value for SARS-CoV-2 viral load across several dynamics date: 2020-07-10 words: 1326.0 sentences: 81.0 pages: flesch: 61.0 cache: ./cache/cord-273956-mruywa71.txt txt: ./txt/cord-273956-mruywa71.txt summary: title: The practical challenges of making clinical use of the quantitative value for SARS-CoV-2 viral load across several dynamics As the numbers of patients infected with SARS-CoV-2 continues to increase in the United States so does access diagnostic molecular testing especially for hospitalized patients. However, interpreting a low Ct value at the time of hospital admission can A c c e p t e d M a n u s c r i p t only be applied for prognosis of patients in this context while learning about the natural history of a novel infection. As most laboratory reports are not context aware this may mean that additional information for interpretation of the Ct value may need to be amended to the report so that we can use this valuable data to understand how it can help us care for patients infected with SARS-CoV-2. abstract: nan url: https://doi.org/10.1093/cid/ciaa958 doi: 10.1093/cid/ciaa958 id: cord-010578-uib9h1lb author: Mawle, Alison C. title: Seroepidemiology of Chronic Fatigue Syndrome: A Case-Control Study date: 1995-12-17 words: 2570.0 sentences: 164.0 pages: flesch: 49.0 cache: ./cache/cord-010578-uib9h1lb.txt txt: ./txt/cord-010578-uib9h1lb.txt summary: We performed serological testing for a large number of infectious agents in 26 patients from Atlanta who had chronic fatigue syndrome (CFS) and in 50 controls matched by age, race, and sex. We performed serological testing for a large number of infectious agents in 26 patients from Atlanta who had chronic fatigue syndrome (CFS) and in 50 controls matched by age, race, and sex. We conducted serological tests for a large number of infectious agents as part of a case-control study assessing risk factors for CFS. Antibodies against human T-lymphotrophic virus types I and II were detected with an ELISA, and confirmatory testing was performed by western blotting [5] . All other agents tested were detected in ;;:::25% of CFS cases, and antibody levels were compared between cases and controls. Evidence for active Epstein-Barr virus infection in patients with persistent unexplained illness: elevated anti-early antigen antibodies abstract: We performed serological testing for a large number of infectious agents in 26 patients from Atlanta who had chronic fatigue syndrome (CFS) and in 50 controls matched by age, race, and sex. We did not find any agent associated with CFS. In addition, we did not find elevated levels of antibody to any of a wide range of agents examined. In particular, we did not find elevated titers of antibody to any herpesvirus, nor did we find evidence of enteroviral exposure in this group of patients. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7197952/ doi: 10.1093/clinids/21.6.1386 id: cord-331978-y4uo7o8g author: Maxwell, Daniel N title: “The Art of War” in the Era of Coronavirus Disease 2019 (COVID-19) date: 2020-03-04 words: 1520.0 sentences: 83.0 pages: flesch: 53.0 cache: ./cache/cord-331978-y4uo7o8g.txt txt: ./txt/cord-331978-y4uo7o8g.txt summary: With rapidly increasing cases and local community transmission in multiple countries outside of China, including the United States, the outbreak has entered a new phase, which requires a shift in primary battle strategy from a focus on containment in China to international mitigation. As cases of COVID-19 explode internationally, a strategic shift is required away from primarily containment, keeping the virus "out there", to home-based mitigation and public health responses. Now, the task is bearing the burden of identifying, isolating, triaging and managing the rising number of cases, necessitating total engagement of the medical community, public health sector, governments and society as a whole. As Sun Tzu noted, "If in training soldiers'' commands are habitually enforced, the army will be well-disciplined." 1 The authors also highlight improvements in infection prevention and control (IPC) infrastructure, administrative controls, and public health coordination compared to their 2003 SARS experience. abstract: nan url: https://doi.org/10.1093/cid/ciaa229 doi: 10.1093/cid/ciaa229 id: cord-355618-7kfxc2w1 author: McAteer, John title: The VACCINES Act, Deciphering Vaccine Hesitancy in the Time of COVID19 date: 2020-04-13 words: 1893.0 sentences: 106.0 pages: flesch: 48.0 cache: ./cache/cord-355618-7kfxc2w1.txt txt: ./txt/cord-355618-7kfxc2w1.txt summary: In his statement of support 7 , the WHO Director-General Dr. Tedros Ghebreyesus asserted that "These online efforts must be matched by tangible steps by governments and the health sector to promote trust in vaccination and respond to the needs and concerns of parents." In order to adequately respond to these needs and concerns, which differ depending on the cultural, societal, and personal beliefs of a particular region, the WHO recommends that each country take steps to develop an understanding of vaccine hesitancy at a local level on an ongoing basis 8 . In recognition of these missed opportunities and in response to declining immunization rates and increasing national skepticism on the safety of vaccines, Congress has introduced bipartisan legislation to expand research into vaccine hesitancy. The bipartisan VACCINES Act is an important step in supporting evidence-based research into vaccine hesitancy. Association between vaccine refusal and vaccine-preventable diseases in the United States: a review of measles and pertussis abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32282038/ doi: 10.1093/cid/ciaa433 id: cord-007049-02p8ug67 author: McGeer, Allison title: Let Him Who Desires Peace Prepare for War: United States Hospitals and Severe Acute Respiratory Syndrome Preparedness date: 2004-07-15 words: 1613.0 sentences: 92.0 pages: flesch: 48.0 cache: ./cache/cord-007049-02p8ug67.txt txt: ./txt/cord-007049-02p8ug67.txt summary: In June 2003, the Centers for Disease Control and Prevention (CDC) surveyed members of the Infectious Disease Society of America Emerging Infections Network (EIN) about SARS preparedness in their hospitals. Of the 456 EIN members responding to the survey in this issue of Clinical Infectious Diseases [2] , 381 (83%) reported that patients with respiratory symptoms in their emergency department (ED) would be screened for a travel history. A careful assessment of exposures in SARS outbreaks, particularly those due to superspreading events and transmission despite compliance with isolation precautions, is needed to determine whether airborne spread occurs [10, [13] [14] [15] . At least 2 analyses of risks associated with health care worker infection despite the use of precautions now identify that 12 h of infection-control training and confidence that precautions would be protective are associated with substantial reductions in the risk of infection (Toronto SARS hospital investigation, unpublished data; Lau et al. Hospital preparedness for severe acute respiratory syndrome in the United States: views from a national survey of infectious diseases consultants abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107923/ doi: 10.1086/421784 id: cord-324007-hapzf0fl author: McGeer, Allison J. title: Diagnostic Testing or Empirical Therapy for Patients Hospitalized with Suspected Influenza: What to Do? date: 2009-01-01 words: 2893.0 sentences: 142.0 pages: flesch: 37.0 cache: ./cache/cord-324007-hapzf0fl.txt txt: ./txt/cord-324007-hapzf0fl.txt summary: In a retrospective study of adult patients with influenza who were admitted to the Prince of Wales Hospital in Hong Kong during the 2004-2005 influenza season with fever and respiratory and systemic symptoms, a clinically and statistically significant reduction in length of hospital stay was associated with treatment with oseltamivir [14] . The accumulating evidence suggests that, for patients with acute cardiorespiratory illness requiring hospital admission during influenza season, consideration should be given to either prompt laboratory diagnostic testing and treatment for influenza virus-infected patients or empirical antiviral therapy for influenza. The best choice is made on a case-by-case basis and depends on the severity of illness in the patient being admitted (since earlier therapy for pneumonia is more effective), the probability of influenza virus infection in the individual patient, and the sensitivity of the rapid diagnostic tests available. abstract: Accumulating evidence supports the use of specific diagnostic tests and antiviral therapies for seriously ill patients with influenza. Among available diagnostic tests, reverse-transcriptase polymerase chain reaction is faster than culture and more sensitive than commercial antigen assays. Current neuraminidase inhibitors were approved on the basis of their efficacy in ambulatory patients, but seriously ill patients who receive these agents are less likely to die, even when treatment is initiated >48 h after symptom onset. For patients hospitalized with suspected influenza, it is unclear which circumstances warrant diagnostic testing and which warrant the use of empirical therapy. Rapid antigen assays may reduce the unnecessary use of other tests and medications but are relatively insensitive, thus eliminating many patients with influenza as candidates for treatment. Empirical antiviral therapy ensures that all patients receive treatment promptly, at a cost equivalent to that of diagnostic tests alone, but results in the receipt of treatment by many patients without influenza. For patients hospitalized with suspected influenza, clinicians need to combine these approaches in order to optimize patient care. url: https://doi.org/10.1086/591852 doi: 10.1086/591852 id: cord-012511-fl5llkoj author: Meltzer, Martin I. title: Standardizing Scenarios to Assess the Need to Respond to an Influenza Pandemic date: 2015-05-01 words: 4122.0 sentences: 207.0 pages: flesch: 56.0 cache: ./cache/cord-012511-fl5llkoj.txt txt: ./txt/cord-012511-fl5llkoj.txt summary: We were tasked to evaluate the 6 following interventions: invasive mechanical ventilators, influenza antiviral drugs for treatment (but not large-scale prophylaxis), influenza vaccines, respiratory protective devices for healthcare workers and surgical face masks for patients, school closings to reduce transmission, and airport-based screening to identify those ill with novel influenza virus entering the United States. To allow easy comparison between results (a specification), we standardized a risk space defined by using ranges of transmission and clinical severity from a previously published influenza severity assessment framework ( Figure 1 ) [5] . Standardized epidemiological curves-contact matrix: To model the 4 epidemic curves (Figure 2 ), we built a simple, nonprobabilistic (ie, deterministic) model in which we divided the population into 4 age groups (0-10, 11-20, 21-60, ≥61 years). abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4481578/ doi: 10.1093/cid/civ088 id: cord-324707-9ld73wv1 author: Mitjà, Oriol title: Hydroxychloroquine for Early Treatment of Adults with Mild Covid-19: A Randomized-Controlled Trial date: 2020-07-16 words: 4268.0 sentences: 263.0 pages: flesch: 54.0 cache: ./cache/cord-324707-9ld73wv1.txt txt: ./txt/cord-324707-9ld73wv1.txt summary: Study outcomes were the reduction of viral RNA load in nasopharyngeal swabs up to 7 days after treatment start, patient disease progression using the WHO scale up to 28 days, and time to complete resolution of symptoms. Adult patients aged 18 years or more were eligible if they had mild symptoms of Covid-19 (i.e., fever, acute cough, shortness of breath, sudden olfactory or gustatory loss, or influenza-like-illness) for less than five days before enrollment, were non-hospitalized, and had a positive PCR test for SARS-CoV-2 in the baseline nasopharyngeal swab. We estimated that a sample size of 280 patients would provide the trial with 80% power to detect a difference of 0.5 log 10 in the mean reduction of SARS-CoV-2 viral load at a two-sided significance level of α = 0.05, assuming an expected standard deviation of 1.5 [23] . abstract: BACKGROUND: No therapeutics have yet been proven effective for the treatment of mild-illness caused by SARS-CoV-2. We aimed to determine whether early treatment with hydroxychloroquine (HCQ) would be more efficacious than no-treatment for outpatients with mild Covid-19. METHODS: We conducted a multicenter, open label, randomized controlled trial in Catalonia (Spain) between March 17, and May 26, 2020. Eligible Covid-19 cases were non-hospitalized adult patients with recently confirmed SARS-CoV-2 infection and less than five days of symptoms. Patients were assigned to receive HCQ (800 mg on day 1, followed by 400 mg once daily for 6 days) or no antiviral treatment (not-placebo controlled). Study outcomes were the reduction of viral RNA load in nasopharyngeal swabs up to 7 days after treatment start, patient disease progression using the WHO scale up to 28 days, and time to complete resolution of symptoms. Adverse events were assessed up to 28 days. RESULTS: A total of 293 patients were eligible for intention-to-treat analysis: 157 in the control arm and 136 in the intervention arm. The mean age was 41.6 years (SD 12.6), mean viral load at baseline was 7.90 (SD 1.82) Log(10) copies/mL, and median time from symptom onset to randomization was 3 days. No significant differences were found in the mean reduction of viral load at day 3 (-1.41 vs. -1.41 Log(10) copies/mL in the control and intervention arm, respectively; difference 0.01 [95% CI -0.28;0.29]) or at day 7 (-3.37 vs. -3.44; d –0.07 [-0.44;0.29]). This treatment regimen did not reduce risk of hospitalization (7.1%, control vs. 5.9%, intervention; RR 0.75 [0.32;1.77]) nor shortened the time to complete resolution of symptoms (12 days, control vs. 10 days, intervention; p = 0.38). No relevant treatment-related AEs were reported. CONCLUSIONS: In patients with mild Covid-19, no benefit was observed with HCQ beyond the usual care. url: https://doi.org/10.1093/cid/ciaa1009 doi: 10.1093/cid/ciaa1009 id: cord-322082-80ym2rsq author: Monto, Arnold S title: Lessons From Influenza Pandemics of the Last 100 Years date: 2020-03-01 words: 4089.0 sentences: 229.0 pages: flesch: 46.0 cache: ./cache/cord-322082-80ym2rsq.txt txt: ./txt/cord-322082-80ym2rsq.txt summary: Since this was the first true pandemic since 1918, there was immediate concern about its potential impact and great relief when it was found to resemble seasonal influenza with morbidity highest in children and mortality at the extremes of age [26, 27] (Figure 3 ). However, the new A(H3N2) virus completely replaced the previous subtype, and its variants, more than 50 years later, have been responsible for the greatest proportion of mortality from influenza viruses. In the United States, there was particular attention directed to nonpharmaceutical interventions, a result of the recognition that pandemic-specific vaccines would be available relatively late and that influenza-specific antiviral drugs, while important, would be limited in quantity. " The latter issue has been made worse by the repeated recognition of the pandemic potential of different avian influenza virus variants that have infected humans [63] [64] [65] . abstract: Seasonal influenza is an annual occurrence, but it is the threat of pandemics that produces universal concern. Recurring reports of avian influenza viruses severely affecting humans have served as constant reminders of the potential for another pandemic. Review of features of the 1918 influenza pandemic and subsequent ones helps in identifying areas where attention in planning is critical. Key among such issues are likely risk groups and which interventions to employ. Past pandemics have repeatedly underscored, for example, the vulnerability of groups such as pregnant women and taught other lessons valuable for future preparedness. While a fundamental difficulty in planning for the next pandemic remains their unpredictability and infrequency, this uncertainty can be mitigated, in part, by optimizing the handling of the much more predictable occurrence of seasonal influenza. Improvements in antivirals and novel vaccine formulations are critical in lessening the impact of both pandemic and seasonal influenza. url: https://www.ncbi.nlm.nih.gov/pubmed/31420670/ doi: 10.1093/cid/ciz803 id: cord-007068-vcfs41eb author: Moradi, Tony title: Use of Procalcitonin and a Respiratory Polymerase Chain Reaction Panel to Reduce Antibiotic Use via an Electronic Medical Record Alert date: 2019-10-22 words: 3669.0 sentences: 197.0 pages: flesch: 38.0 cache: ./cache/cord-007068-vcfs41eb.txt txt: ./txt/cord-007068-vcfs41eb.txt summary: We sought to determine whether an automated electronic medical record best practice alert (BPA) based on procalcitonin and respiratory polymerase chain reaction (PCR) results could help reduce inappropriate antibiotic use in patients with likely viral respiratory illness. In the study group, a BPA alerted providers of the diagnostic results suggesting viral infection and prompted them to reassess the need for antibiotics. CONCLUSIONS: The automated antimicrobial stewardship BPA effectively reduced antibiotic use and discharge prescribing rates when diagnostics suggested viral respiratory tract infection, without a higher rate for reinitiation of antibiotics after discontinuation. The aim of our study was to determine if antibiotic use could be reduced by deploying an automated antimicrobial stewardship provider alert that prompted antibiotic de-escalation if 3 criteria were met: PCT <0.25 ng/mL, virus detected on respiratory PCR, and active use of systemic antibiotics. abstract: BACKGROUND: Respiratory tract infections are often viral and but are frequently treated with antibiotics, providing a significant opportunity for antibiotic de-escalation in patients. We sought to determine whether an automated electronic medical record best practice alert (BPA) based on procalcitonin and respiratory polymerase chain reaction (PCR) results could help reduce inappropriate antibiotic use in patients with likely viral respiratory illness. METHODS: This multisite, pre–post, quasi-experimental study included patients 18 years and older with a procalcitonin level <0.25 ng/mL and a virus identified on respiratory PCR within 48 hours of each other, and 1 or more systemic antibiotics ordered. In the study group, a BPA alerted providers of the diagnostic results suggesting viral infection and prompted them to reassess the need for antibiotics. The primary outcome measured was total antibiotic-days of therapy. RESULTS: The BPA reduced inpatient antibiotic-days of therapy by a mean of 2.2 days compared with patients who met criteria but did not have the alert fire (8.0 vs 5.8 days, respectively, P < .001). The BPA also reduced the percentage of patients prescribed antibiotics on discharge (20% vs 47.8%, P < .001), whereas there was no difference in need for antibiotic escalation after initial discontinuation (7.6% vs 4.3%, P = .198). CONCLUSIONS: The automated antimicrobial stewardship BPA effectively reduced antibiotic use and discharge prescribing rates when diagnostics suggested viral respiratory tract infection, without a higher rate for reinitiation of antibiotics after discontinuation. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7108168/ doi: 10.1093/cid/ciz1042 id: cord-348392-e35cd9sg author: Moraleda, Cinta title: Multi-Inflammatory Syndrome in Children related to SARS-CoV-2 in Spain date: 2020-07-25 words: 1759.0 sentences: 165.0 pages: flesch: 66.0 cache: ./cache/cord-348392-e35cd9sg.txt txt: ./txt/cord-348392-e35cd9sg.txt summary: Some clusters of children with a multisystem inflammatory syndrome associated with SARS-CoV-2 infection (MIS-C) have been reported. MIS-C is a potentially severe condition that presents in children with recent SARS-CoV-2 infection. This is a case series of children with MIS-C associated with SARS-CoV-2 enrolled in the Epidemiological Study of COVID-19 in Children of the Spanish Society of Pediatrics (EPICO-AEP), from March 1 st to June 1 st, 2020. Inclusion criteria included positivity in real-time polymerase chain reaction (RT-PCR) positive, IgM or IgG in lateral-flow rapid test, ELISA or immuno chemiluminescence serology (see Table 1 ), or severe disease suggestive of MIS-C and recent household contact with a confirmed patient with COVID-19. In this registry, entry criteria was COVID-19 disease, differently from the previous reports that include patient without SARS-CoV-2 1,3 . MIS-C is a potentially severe condition that presents in some children after SARS-CoV-2 infection. abstract: Some clusters of children with a multisystem inflammatory syndrome associated with SARS-CoV-2 infection (MIS-C) have been reported. We describe the epidemiological and clinical features of children with MIS-C in Spain. MIS-C is a potentially severe condition that presents in children with recent SARS-CoV-2 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32710613/ doi: 10.1093/cid/ciaa1042 id: cord-007296-q9rn75qb author: Muether, Philipp S. title: Variant Effect of First- and Second-Generation Antihistamines as Clues to Their Mechanism of Action on the Sneeze Reflex in the Common Cold date: 2001-11-01 words: 2975.0 sentences: 163.0 pages: flesch: 46.0 cache: ./cache/cord-007296-q9rn75qb.txt txt: ./txt/cord-007296-q9rn75qb.txt summary: Treatment with first-generation antihistamines reduces sneezing, rhinorrhea, nasal mucus weight, and, in some instances, cough in subjects with experimental or natural colds; however, treatment with second-generation antihistamines has not been effective for these complaints in trials in subjects with natural colds. The effectiveness of first-generation antihistamines in blocking sneezing in colds may be due primarily to neuropharmacological manipulation of histaminic and muscarinic receptors in the medulla. Also, treatment with first-generation antihistamines is highly effective in reducing sneezing in subjects with experimental and natural colds [3] [4] [5] . Therefore, it would be desirable to confirm the results of the natural cold studies by testing a second-generation antihistamine in the rhinovirus challenge model, which provides more precision in the measurement of sneezing. Although the study was originally designed to determine whether loratadine by down-regulating expression of intercellular adhesion molecule-1 (ICAM-1) on nasal epithelial cells reduces rhinovirus infection rates, it provides heretoforemissing information on the results of testing a second-generation antihistamine in the virus challenge mode. abstract: Treatment with first-generation antihistamines reduces sneezing, rhinorrhea, nasal mucus weight, and, in some instances, cough in subjects with experimental or natural colds; however, treatment with second-generation antihistamines has not been effective for these complaints in trials in subjects with natural colds. This article reports the negative results of a clinical trial with loratadine, a second-generation antihistamine, in adults in the rhinovirus challenge model. This finding in the highly controlled setting of the challenge model confirms the earlier negative studies with second-generation antihistamines in natural colds. First-generation antihistamines block both histaminic and muscarinic receptors as well as passing the blood-brain barrier. Second-generation antihistamines mainly block histaminic receptors and do not pass the blood-brain barrier. The effectiveness of first-generation antihistamines in blocking sneezing in colds may be due primarily to neuropharmacological manipulation of histaminic and muscarinic receptors in the medulla. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7110240/ doi: 10.1086/322518 id: cord-268233-ibxufjrv author: Nagappa, Bharathnag title: Seroconversion rate and diagnostic accuracy of serological tests for COVID-19 date: 2020-05-30 words: 610.0 sentences: 52.0 pages: flesch: 69.0 cache: ./cache/cord-268233-ibxufjrv.txt txt: ./txt/cord-268233-ibxufjrv.txt summary: We read the recent article by Zhao J et al which studied the antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019 [1] . However in results, the authors have mentioned that only 112 out of 173 participants tested positive for RNA over complete duration of the study, which contradicts the methodology. Third, Antibody tests in this study population should be interpreted cautiously since 1) there is plausibility to have cross reaction to antibodies related to other corona virus strains and 2) also diseases caused by other corona virus present with similar symptoms as COVID-19, and symptomatic patients might have antibodies which may lead to increased false positivity rate. Therefore present study should carefully interpret the serological tests and sensitivity should be calculated only in participants tested positive for RNA. Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019 abstract: nan url: https://doi.org/10.1093/cid/ciaa676 doi: 10.1093/cid/ciaa676 id: cord-266808-wyuodzyt author: Nagler, Arielle R title: Early Results from SARS-CoV-2 PCR testing of Healthcare Workers at an Academic Medical Center in New York City date: 2020-06-28 words: 1590.0 sentences: 117.0 pages: flesch: 57.0 cache: ./cache/cord-266808-wyuodzyt.txt txt: ./txt/cord-266808-wyuodzyt.txt summary: title: Early Results from SARS-CoV-2 PCR testing of Healthcare Workers at an Academic Medical Center in New York City Over the following eight weeks three groups were tested: 1) symptomatic staff with fever or respiratory illness; 2) asymptomatic employees with self-reported exposure to COVID-19 which included any degree or duration of contact with an individual who had a documented COVID-19 infection in the work place or in the community; and 3) all employees who were returning to work in services that had been suspended during the epidemic''s peak. Positivity rates amongst all groups of employees being tested including symptomatic employees, asymptomatic employees with self-reported exposure to COVID-19, and employees being screened for returning work declined over time ( Figure 1 ). Thus during this testing program, most NYULH employees had continued exposure to COVID patients, yet A c c e p t e d M a n u s c r i p t employees still demonstrated sharp declines in COVID infection rates. abstract: COVID-19 RT-PCR employee-testing was implemented across NYU Langone. Over eight-weeks, 14,764 employees were tested: 33% of symptomatic employees, 8% of asymptomatic employees reporting COVID-19 exposure, 3% of employees returning to work were positive. Positivity rates declined over time possibly reflecting the importance of community transmission and efficacy of PPE. url: https://doi.org/10.1093/cid/ciaa867 doi: 10.1093/cid/ciaa867 id: cord-318358-glbr8kxh author: Naik, George O A title: COVID-19 and the RAAS date: 2020-06-20 words: 715.0 sentences: 64.0 pages: flesch: 54.0 cache: ./cache/cord-318358-glbr8kxh.txt txt: ./txt/cord-318358-glbr8kxh.txt summary: Further to Thomas Hanff et al [1] timely call for epidemiological and clinical investigations of COVID-19 infectious disease, measurements of the renin angiotensin aldosterone system (RAAS) components, as sub-studies would be insightful of this pandemic. Angiotensin-converting enzyme 2 (ACE 2) participates in the coronavirus (SARS-CoV-2) cell entry. Drugs that block RAAS also affect ACE 2 expression: it is down regulated by renin inhibition (RI) and up regulated by angiotensin-converting enzyme inhibitors (ACEIs), angiotensin receptor blockers (ARBs) (1) and mineralocorticoid receptor antagonists (MRAs) [2] . Such perturbations would also indirectly influence other RAAS components, and the coordination between circulating and local tissue expressions, as shown in Figure 1 ACE 2 is distributed throughout the body and is abundantly expressed in the lung, small intestine, and in blood vessels of many organs including the brain, heart, kidney and testis [4] . Mineralocorticoid receptor blocker increases angiotensin-converting enzyme 2 activity in congestive heart failure patients abstract: nan url: https://doi.org/10.1093/cid/ciaa818 doi: 10.1093/cid/ciaa818 id: cord-277788-6ls21tkr author: Nelson, Brian C title: Clinical Outcomes Associated with Methylprednisolone in Mechanically Ventilated Patients with COVID-19 date: 2020-08-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: The efficacy and safety of methylprednisolone in mechanically ventilated patients with acute respiratory distress syndrome due to coronavirus disease 2019 (COVID-19) are unclear. In this study, we evaluated the association between use of methylprednisolone and key clinical outcomes. METHODS: Clinical outcomes associated with the use of methylprednisolone were assessed in an unmatched, case-control study; a subset of patients also underwent propensity-score matching. Patients were admitted between March 1 and April 12, 2020. The primary outcome was ventilator-free days by 28 days after admission. Secondary outcomes included extubation, mortality, discharge, positive cultures, and hyperglycemia. RESULTS: A total of 117 patients met inclusion criteria. Propensity matching yielded a cohort of 42 well-matched pairs. Groups were similar except for hydroxychloroquine and azithromycin use, which were more common in patients who did not receive methylprednisolone. Mean ventilator free-days were significantly higher in patients treated with methylprednisolone (6.21±7.45 versus 3.14±6.22; P = 0.044). The probability of extubation was also increased in patients receiving methylprednisolone (45% versus 21%; P = 0.021), and there were no significant differences in mortality (19% versus 36%; P = 0.087). In a multivariable linear regression analysis, only methylprednisolone use was associated with higher number of ventilator-free days (P = 0.045). The incidence of positive cultures and hyperglycemia were similar between groups. CONCLUSIONS: Methylprednisolone was associated with increased ventilator-free days and higher probability of extubation in a propensity-score matched cohort. Randomized, controlled studies are needed to further define methylprednisolone use in patients with COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32772069/ doi: 10.1093/cid/ciaa1163 id: cord-294853-8b0s5w4u author: Nolen, Leisha D title: Impact of Social Distancing and Travel Restrictions on non-COVID-19 Respiratory Hospital Admissions in Young Children in Rural Alaska date: 2020-09-05 words: 922.0 sentences: 52.0 pages: flesch: 50.0 cache: ./cache/cord-294853-8b0s5w4u.txt txt: ./txt/cord-294853-8b0s5w4u.txt summary: title: Impact of Social Distancing and Travel Restrictions on non-COVID-19 Respiratory Hospital Admissions in Young Children in Rural Alaska Hospitalizations due to non-COVID-19 respiratory illnesses decreased dramatically after social distancing was implemented in a high-risk population in rural Alaska. People in the remote Yukon-Kuskokwim Delta (YKD) region of Alaska have a high burden of respiratory illnesses, with up to ten times the rate of infant hospitalization for pneumonia compared to the general US population [4] and the highest reported rates of infant RSV hospitalization in the United States, reaching 259 per 1,000 We compared the total, ARI, and RSV hospitalization rate in YKD children <3 years in the first 5 months of 2020 to the previous ten respiratory illness seasons. One limitation of our study is the inability to distinguish what proportion of the decline in ARI hospitalizations in YKD children is due to avoidance of care versus a decrease in circulation of respiratory pathogens secondary to the health mandates. abstract: Hospitalizations due to non-COVID-19 respiratory illnesses decreased dramatically after social distancing was implemented in a high-risk population in rural Alaska. Our data from the past ten respiratory seasons show that this decline is unprecedented. This demonstrates the potential secondary benefits of implementing social distancing and travel restrictions on respiratory illnesses. url: https://doi.org/10.1093/cid/ciaa1328 doi: 10.1093/cid/ciaa1328 id: cord-297612-swc2pitd author: Nosyk, Bohdan title: Contact tracing for COVID-19: An opportunity to reduce health disparities and End the HIV/AIDS Epidemic in the US date: 2020-04-27 words: 1637.0 sentences: 104.0 pages: flesch: 57.0 cache: ./cache/cord-297612-swc2pitd.txt txt: ./txt/cord-297612-swc2pitd.txt summary: title: Contact tracing for COVID-19: An opportunity to reduce health disparities and End the HIV/AIDS Epidemic in the US We argue that COVID-19 contact tracing may provide a unique opportunity to also conduct widespread HIV testing, among other health promotion activities. M a n u s c r i p t Massive SARS-CoV2 testing and contact tracing at a scale and speed never before seen have been proposed as critical components of a COVID-19 public health strategy that could, in theory, safely allow us to relax social distancing measures and begin to bring back the world we left behind before a cure or effective vaccine is delivered. Aside from the potentially profound health benefits of a combination implementation approach, pairing COVID-19 contact tracing with testing for HIV may serve to offset the immense costs of such an approach. abstract: SARS-CoV2 testing and contact tracing have been proposed as critical components of a safe and effective COVID-19 public health strategy. We argue that COVID-19 contact tracing may provide a unique opportunity to also conduct widespread HIV testing, among other health promotion activities. url: https://www.ncbi.nlm.nih.gov/pubmed/32339245/ doi: 10.1093/cid/ciaa501 id: cord-259471-lsdodl0a author: Pagliano, Pasquale title: Is Hydroxychloroquine a Possible Postexposure Prophylaxis Drug to Limit the Transmission to Healthcare Workers Exposed to Coronavirus Disease 2019? date: 2020-03-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32211764/ doi: 10.1093/cid/ciaa320 id: cord-339859-anatn295 author: Paret, Michal title: SARS-CoV-2 infection (COVID-19) in febrile infants without respiratory distress date: 2020-04-17 words: 1286.0 sentences: 105.0 pages: flesch: 59.0 cache: ./cache/cord-339859-anatn295.txt txt: ./txt/cord-339859-anatn295.txt summary: title: SARS-CoV-2 infection (COVID-19) in febrile infants without respiratory distress We report two cases of SARS-CoV-2 infection (COVID-19) in infants presenting with fever in the absence of respiratory distress who required hospitalization for evaluation of possible invasive bacterial infections. The diagnoses resulted from routine isolation and real-time RT-PCR-based testing for SARS-CoV-2 for febrile infants in an outbreak setting. [2] [3] [4] Even in the setting of asymptomatic or mildly symptomatic infection, children may represent a source of SARS-CoV-2 spread in community or hospital settings, so understanding the spectrum of COVID-19 illness in infants, particularly regarding conditions that result in hospitalization, is crucial to establishment of effective infection control interventions. Vital signs and pertinent laboratory findings appear in the A real-time RT-PCR assay performed at the New York State Department of Health detected SARS-CoV-2 RNA in the patient''s NP sample. abstract: We report two cases of SARS-CoV-2 infection (COVID-19) in infants presenting with fever in the absence of respiratory distress who required hospitalization for evaluation of possible invasive bacterial infections. The diagnoses resulted from routine isolation and real-time RT-PCR-based testing for SARS-CoV-2 for febrile infants in an outbreak setting. url: https://doi.org/10.1093/cid/ciaa452 doi: 10.1093/cid/ciaa452 id: cord-356316-ui11jr2h author: Patel, Monita R title: Performance of oropharyngeal swab testing compared to nasopharyngeal swab testing for diagnosis of COVID-19 —United States, January-February 2020 date: 2020-06-16 words: 1181.0 sentences: 88.0 pages: flesch: 62.0 cache: ./cache/cord-356316-ui11jr2h.txt txt: ./txt/cord-356316-ui11jr2h.txt summary: Among 146 nasopharyngeal (NP) and oropharyngeal (OP) swab pairs collected ≤7 days since illness onset, CDC real-time RT-PCR SARS-CoV-2 assay diagnostic results were 95.2% concordant. Current US Centers for Disease Control and Prevention (CDC) guidelines identify nasopharyngeal (NP) and oropharyngeal (OP) swabs as acceptable upper respiratory specimens to test for presence of SARS-CoV-2 ribonucleic acid (RNA) (1) . Overall, among persons with specimens collected early in the illness course, SARS-CoV-2 RNA diagnostic results were highly concordant between OP and NP swabs. Current Infectious Diseases Society of America Guidelines specifically recommend collection of NP, mid-turbinate or nasal swabs rather than OP swabs alone for all symptomatic persons; our findings suggest this recommendation may be particularly relevant for persons later in the illness course and who may have lower amount of SARS-CoV-2 viral RNA (7). Together, our findings support CDC guidelines that identify NP and OP swabs as acceptable specimens for SARS-CoV-2 RNA testing; but suggest that NP swab may comparatively be a more sensitive specimen type for testing persons later in the illness course. abstract: Among 146 nasopharyngeal (NP) and oropharyngeal (OP) swab pairs collected ≤7 days since illness onset, CDC real-time RT-PCR SARS-CoV-2 assay diagnostic results were 95.2% concordant. However, NP swab Ct values were lower (indicating more virus) in 66.7% of concordant-positive pairs, suggesting NP swabs may more accurately detect amount of SARS-CoV-2. url: https://doi.org/10.1093/cid/ciaa759 doi: 10.1093/cid/ciaa759 id: cord-348478-ho89o8mj author: Pawlotsky, Jean-Michel title: SARS-CoV-2 pandemic : Time to revive the cyclophilin inhibitor alisporivir date: 2020-05-15 words: 2100.0 sentences: 138.0 pages: flesch: 48.0 cache: ./cache/cord-348478-ho89o8mj.txt txt: ./txt/cord-348478-ho89o8mj.txt summary: This Viewpoint summarizes the strong scientific arguments supporting the use of alisporivir, a non-immunosuppressive analogue of cyclosporine A with potent cyclophilin inhibition properties that has reached Phase 3 clinical development, for the treatment of COVID-19. They include the strong cyclophilin dependency of the lifecycle of many coronaviruses, including SARS-CoV and MERS-CoV, and preclinical data showing strong antiviral and cytoprotective properties of alisporivir in various models of coronavirus infection, including SARS-CoV-2. It has indeed been shown that the lifecycles of human coronaviruses 229E (HCoV-229E) and NL-63 (HCoV-NL63), responsible for mild respiratory infections in humans, of feline infectious peritonitis coronavirus (FPIV), responsible for a fatal disease in cats, and of SARS-CoV were highly dependent on cyclophilin A (and possibly also cyclophilin B for FPIV) [18] [19] [20] [21] [22] . Human coronavirus NL63 replication is cyclophilin A-dependent and inhibited by non-immunosuppressive cyclosporine Aderivatives including alisporivir Inhibition of SARS-CoV-2 infection by the cyclophilin inhibitor Alisporivir (Debio 025) abstract: December 2019 saw the emergence of a new epidemic of pneumonia of varying severity, called COVID-19, caused by a newly identified coronavirus, SARS-CoV-2. No therapeutic option is available to treat this infection that has already killed more than 235,000 people worldwide. This Viewpoint summarizes the strong scientific arguments supporting the use of alisporivir, a non-immunosuppressive analogue of cyclosporine A with potent cyclophilin inhibition properties that has reached Phase 3 clinical development, for the treatment of COVID-19. They include the strong cyclophilin dependency of the lifecycle of many coronaviruses, including SARS-CoV and MERS-CoV, and preclinical data showing strong antiviral and cytoprotective properties of alisporivir in various models of coronavirus infection, including SARS-CoV-2. Alisporivir should be tested without delay on both virological and clinical endpoints in patients with or at-risk of severe forms of SARS-CoV-2 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32409832/ doi: 10.1093/cid/ciaa587 id: cord-325068-j1lfq60o author: Pene, Frédéric title: Coronavirus 229E-Related Pneumonia in Immunocompromised Patients date: 2003-10-01 words: 2583.0 sentences: 134.0 pages: flesch: 35.0 cache: ./cache/cord-325068-j1lfq60o.txt txt: ./txt/cord-325068-j1lfq60o.txt summary: The results of inoculation tests performed with HUH7 cells were also positive, revealing corona-like particles that were subsequently identified as coronavirus 229E by RT-PCR performed on both culture supernatant and BAL fluid specimens. However, respiratory symptoms only appeared after completion of antiviral treatment and improvement of skin eruptions, and both viral culture and PCR for VZV performed on BAL fluid specimens were negative. The prevalence of coronavirus pulmonary infections among immunocompromised patients is unknown, and it is probably largely underestimated in the absence of the routine performance of sensitive cell culture, RT-PCR, or electron microscopy on BAL fluid specimens. Thus, only 1 case of coronavirus-associated pneumonia was previously described in an immunocompromised patient following autologous bone marrow transplantation, with the diagnosis based on the presence of viral particles in BAL fluid specimens [22] . abstract: Coronaviruses strains 229E and OC43 have been associated with various respiratory illnesses ranging from the self-resolving common cold to severe pneumonia. Although chronic underlying conditions are major determinants of severe respiratory virus infections, few data about coronavirus-related pneumonia in immunocompromised patients are available. Here we report 2 well-documented cases of pneumonia related to coronavirus 229E, each with a different clinical presentation. Diagnosis was made on the basis of viral culture and electron microscopy findings that exhibited typical crown-like particles and through amplification of the viral genome by reverse transcriptase—polymerase chain reaction. On the basis of this report, coronaviruses should be considered as potential causative microorganisms of pneumonia in immunocompromised patients. url: https://www.ncbi.nlm.nih.gov/pubmed/13130404/ doi: 10.1086/377612 id: cord-303968-ikr6eeov author: Perinel, Sophie title: Towards Optimization of Hydroxychloroquine Dosing in Intensive Care Unit COVID-19 Patients date: 2020-04-07 words: 1933.0 sentences: 125.0 pages: flesch: 61.0 cache: ./cache/cord-303968-ikr6eeov.txt txt: ./txt/cord-303968-ikr6eeov.txt summary: Apart from the ongoing clinical evaluation of the efficacy of HCQ, little information is available concerning the modalities of administration of this drug for Intensive Care Unit (ICU) patients, especially in the context of COVID-19. M a n u s c r i p t Treatment Patients received 200 mg of oral HCQ, three times daily, as suggested by a recent study [9] . To more clearly understand HCQ PK and the effect of the dosing regimen, a simulation based on a PK population study in patients with rheumatoid arthritis was performed [2] . In this study, we demonstrated that the 200 mg three times daily dosing regimen is inappropriate to reach a supposed target blood level of 1 -2 mg/L in this population. This regimen could constitute an appropriate option, although the results of our study suggest that 800 mg once daily on the first day can more rapidly reach therapeutic levels in ICU patients. abstract: Hydroxychloroquine (HCQ) appears to be a promising treatment for COVID-19. However, all ongoing clinical trials with HCQ use different dosing regimens, resulting on various concentrations PK studies are therefore needed to define the optimal dosing regimen. url: https://www.ncbi.nlm.nih.gov/pubmed/32255489/ doi: 10.1093/cid/ciaa394 id: cord-325136-oyizfh2z author: Pham, Quang Thai title: The first 100 days of SARS-CoV-2 control in Vietnam date: 2020-08-01 words: 2655.0 sentences: 164.0 pages: flesch: 53.0 cache: ./cache/cord-325136-oyizfh2z.txt txt: ./txt/cord-325136-oyizfh2z.txt summary: METHODS: Clinical and demographic data on the first 270 SARS-CoV-2 infected cases and the timing and nature of Government control measures, including numbers of tests and quarantined individuals, were analysed. Data from 270 SARS-CoV-2-confirmed cases to May 1 st 2020 included their age, gender, nationality, dates of symptom onset (if any), entry to the country and quarantine (if any), hospital admission and discharge, and the results of RT-PCR tests. The epidemic timeline for Vietnam, including the numbers quarantined and hospitalised, tests performed, cases confirmed, population movements, and the timing and nature of major Government-led control measures are summarised in Figure 1 . Entry of airline passengers into Vietnam from Wuhan city and elsewhere in China was monitored and progressively limited ( Table 1) After further measures to prevent entry of infected international travellers (Table 1) Forty-three percent (89/208) of discharged cases never developed symptoms, and this was not significantly associated with age, gender, nationality, or origin of infection (imported or domestically-acquired). abstract: BACKGROUND: One hundred days after SARS-CoV-2 was first reported in Vietnam on January 23(rd), 270 cases were confirmed, with no deaths. We describe the control measures used by the Government and their relationship with imported and domestically-acquired case numbers, with the aim of identifying the measures associated with successful SARS-CoV-2 control. METHODS: Clinical and demographic data on the first 270 SARS-CoV-2 infected cases and the timing and nature of Government control measures, including numbers of tests and quarantined individuals, were analysed. Apple and Google mobility data provided proxies for population movement. Serial intervals were calculated from 33 infector-infectee pairs and used to estimate the proportion of pre-symptomatic transmission events and time-varying reproduction numbers. RESULTS: A national lockdown was implemented between April 1(st) and 22(nd). Around 200 000 people were quarantined and 266 122 RT-PCR tests conducted. Population mobility decreased progressively before lockdown. 60% (163/270) of cases were imported; 43% (89/208) of resolved infections remained asymptomatic for the duration of infection. The serial interval was 3·24 days, and 27·5% (95% confidence interval, 15·7%-40·0%) of transmissions occurred pre-symptomatically. Limited transmission amounted to a maximum reproduction number of 1·15 (95% confidence interval, 0·37-2·36). No community transmission has been detected since April 15(th). CONCLUSIONS: Vietnam has controlled SARS-CoV-2 spread through the early introduction of mass communication, meticulous contact-tracing with strict quarantine, and international travel restrictions. The value of these interventions is supported by the high proportion of asymptomatic and imported cases, and evidence for substantial pre-symptomatic transmission. url: https://doi.org/10.1093/cid/ciaa1130 doi: 10.1093/cid/ciaa1130 id: cord-283788-04gwxo4b author: Pinninti, Swetha title: Comparing Nasopharyngeal and Mid-Turbinate Nasal Swab Testing for the Identification of SARS-CoV-2 date: 2020-06-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Testing of paired mid-turbinate (MT) nasal and nasopharyngeal (NP) swabs, collected by trained personnel from 40 patients with COVID-19 showed more NP (76/95, 80%) than MT swabs tested positive (61/95, 64%; p=0.02). Among samples collected a week after study enrollment, fewer MT than NP samples were positive (45% vs 76%; p=0.001). url: https://www.ncbi.nlm.nih.gov/pubmed/32596725/ doi: 10.1093/cid/ciaa882 id: cord-280763-4bnv2t3f author: Piñana, José Luis title: Clinical Effectiveness of Influenza Vaccination After Allogeneic Hematopoietic Stem Cell Transplantation: A Cross-sectional, Prospective, Observational Study date: 2019-06-01 words: 4162.0 sentences: 190.0 pages: flesch: 35.0 cache: ./cache/cord-280763-4bnv2t3f.txt txt: ./txt/cord-280763-4bnv2t3f.txt summary: METHODS: In this prospective, cross-sectional study, we retrospectively analyzed the effect of inactivated trivalent influenza vaccination on the prevalence of influenza RVI in a consecutive cohort of 136 allo-HSCT adult recipients who developed 161 RVI over 5 flu seasons (from 2013 to 2018). The influenza virus has a significant impact on morbidity and mortality in allogeneic hematopoietic stem cell transplantation patients (allo-HSCT), leading to complications ranging from self-limited upper-respiratory tract infections to life-threatening or fatal pneumonias [1] [2] [3] [4] . We conducted a prospective, cross-sectional, observational epidemiological study of community-acquired respiratory virus (CARV) respiratory tract disease (RTD) in allo-HSCT recipients who developed upper RTD (URTD) and/or lower RTD (LRTD) symptoms after transplant. In this study, we report the prevalence of influenza RTD according to the vaccination status over 5 consecutive influenza seasons in a consecutive series of allo-HSCT recipients with virologically-documented respiratory virus infections (RVIs). abstract: BACKGROUND: Vaccination is the primary method for preventing influenza respiratory virus infection (RVI). Although the influenza vaccine is able to achieve serological responses in some allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipients, its clinical benefits are still uncertain. METHODS: In this prospective, cross-sectional study, we retrospectively analyzed the effect of inactivated trivalent influenza vaccination on the prevalence of influenza RVI in a consecutive cohort of 136 allo-HSCT adult recipients who developed 161 RVI over 5 flu seasons (from 2013 to 2018). Respiratory viruses in upper– and/or lower–respiratory tract specimens were tested using multiplex polymerase chain reaction panel assays. RESULTS: Overall, we diagnosed 74 episodes (46%) of influenza RVI in 70 allo-HSCT recipients. Influenza RVI occurred in 51% of the non-vaccinated compared to 36% of the vaccinated recipients (P = .036). A multivariate analysis showed that influenza vaccination was associated with a lower prevalence of influenza RVI (odds ratio [OR] 0.39, P = .01). A multivariate risk factor analysis of lower–respiratory tract disease (LRTD) identified 2 conditions associated with the probability of influenza RVI progression: influenza vaccination (OR 0.12, 95% confidence interval [CI] 0.014–1, P = .05) and a high-risk immunodeficiency score (OR 36, 95% CI 2.26–575, P = .011). Influenza vaccination was also associated with a lower likelihood of an influenza-related hospital admission (14% vs 2%, P = .04). CONCLUSIONS: This study shows that influenza vaccination may have a clinical benefit in allo-HSCT recipients with virologically-confirmed RVI, in terms of a lower influenza RVI prevalence, slower LRTD progression, and lower likelihood of hospital admission. url: https://doi.org/10.1093/cid/ciy792 doi: 10.1093/cid/ciy792 id: cord-279932-bilr71ay author: Plotkin, Stanley A title: The Value of Human Challenges in Severe Acute Respiratory Syndrome Coronavirus 2 Vaccine Development date: 2020-07-16 words: 1119.0 sentences: 61.0 pages: flesch: 52.0 cache: ./cache/cord-279932-bilr71ay.txt txt: ./txt/cord-279932-bilr71ay.txt summary: A number of people, including Nguyen et al [1] in this issue and others [2] [3] [4] [5] [6] [7] elsewhere, have proposed the use of human challenge trials as a way of confirming the protective ability of candidate vaccines, in order to allow emergency use in high-risk groups and to facilitate the way to eventual licensure and use in the general population. The idea behind human challenge trials is to recruit young, healthy volunteers who have the lowest chance of serious disease, who would be given vaccine candidates and then be challenged with SARS-CoV-2 in order to determine whether the vaccines protect. Aside from the ethical issues, the principal objection to human challenge trials with SARS-CoV-2 is the absence of a reliable rescue medication for the treatment of serious disease. Evaluating use cases for human challenge trials in accelerating SARS-CoV-2 vaccine development abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32674139/ doi: 10.1093/cid/ciaa1013 id: cord-330951-k54e3lbu author: Pollett, S title: Social media and the new world of scientific communication during the COVID19 pandemic date: 2020-05-12 words: 813.0 sentences: 49.0 pages: flesch: 51.0 cache: ./cache/cord-330951-k54e3lbu.txt txt: ./txt/cord-330951-k54e3lbu.txt summary: The human and social toll of the COVID19 pandemic has already spurred several major public health ''lessons learned'', and the theme of effective and responsible scientific communication is among them. This discussion also serves as a succinct primer on some of the pivotal epidemiological analyses (and their communication) during the early phases of the COVID19 outbreak, as seen through the lens of a Twitterfeed. The expansion of the outbreak has demanded a rapid response from public health authorities; fundamental epidemiological and scientific evidence has been acquired at break-neck speed to support those decisions. We propose that Twitter has played a fundamental -but often precarious -role in permitting real-time global communication between scientists during the COVID19 epidemic, on a scale not seen before. This discussion also serves as a succinct primer on some of the pivotal epidemiological analyses (and their communication) during the early phases of the COVID19 outbreak, as seen through the lens of a Twitter-feed. abstract: The human and social toll of the COVID19 pandemic has already spurred several major public health ‘lessons learned’, and the theme of effective and responsible scientific communication is among them. We propose that Twitter has played a fundamental – but often precarious - role in permitting real-time global communication between scientists during the COVID19 epidemic, on a scale not seen before. Here, we discuss three key facets to Twitter-enabled scientific exchange during public health emergencies, including some major draw-backs. This discussion also serves as a succinct primer on some of the pivotal epidemiological analyses (and their communication) during the early phases of the COVID19 outbreak, as seen through the lens of a Twitter- feed. url: https://doi.org/10.1093/cid/ciaa553 doi: 10.1093/cid/ciaa553 id: cord-032234-pfr4l1v9 author: Poloni, Chad title: Evaluating Immune Dysregulation in Patients With COVID-19 Requires a More Accurate Definition of the CD45RA(+) T-cell Phenotype date: 2020-06-04 words: 679.0 sentences: 42.0 pages: flesch: 49.0 cache: ./cache/cord-032234-pfr4l1v9.txt txt: ./txt/cord-032234-pfr4l1v9.txt summary: The recently published study conducted in Wuhan, China, by Qin et al indicated dysregulation of the immune response specifically related to T lymphocytes, suggesting that they are highly involved in the pathophysiology of COVID-19 [1] . T-cell dysregulation is a major contributor to age-related changes of the immune system in the elderly, where T-cell responses become defective. Qin et al sought to characterize the T-lymphocyte responses in COVID-19, with aims to differentiate between nonsevere and severe cases. The Wuhan study also identified several differences in T-cell populations between the severe and nonsevere COVID-19 cases. This terminally differentiated T-cell population has been associated with immune dysregulation in the elderly and is further characterized by low CD28 and increased CD57 expression [9] . Improved characterization of terminally differentiated CD45RA + T cells, along with screening for IRP positivity, may be beneficial in identifying those with potential for severe COVID-19. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7499531/ doi: 10.1093/cid/ciaa664 id: cord-329311-p68kr4ga author: Prebensen, Christian title: SARS-CoV-2 RNA in plasma is associated with ICU admission and mortality in patients hospitalized with COVID-19 date: 2020-09-05 words: 1454.0 sentences: 111.0 pages: flesch: 61.0 cache: ./cache/cord-329311-p68kr4ga.txt txt: ./txt/cord-329311-p68kr4ga.txt summary: title: SARS-CoV-2 RNA in plasma is associated with ICU admission and mortality in patients hospitalized with COVID-19 Routine biochemistry was taken at admission and study-specific samples of EDTA plasma and serum were taken at three time points; baseline (enrollment), day 3 (1 day) and day 9 ( 2 days) in patients who were still hospitalized (details in Supplementary Figure 1) . SARS-CoV-2 RNAemia was detected in at least one sample in 58/123 (47%) patients, and in a significantly higher proportion of patients who were admitted to the ICU or died (80% vs. RNAemia was significantly more frequent at all time points in patients who reached the primary endpoint, whereas RNA loads were significantly higher at baseline and day 3 ( Table 1 , Supplementary Figure 2A ). In this prospective study of patients hospitalized with COVID-19 we detected SARS-CoV-2 RNAemia in 47% of included patients, and a significantly higher frequency of RNAemia and higher RNA loads in and similarly found that RNAemia was associated with ICU admission and hospital mortality [3] . abstract: The clinical significance of SARS-CoV-2 RNA in the circulation is unknown. In this prospective cohort study, we detected viral RNA in the plasma of 58/123 (47%) patients hospitalized with COVID-19. RNA was detected more frequently, and levels were higher, in patients who were admitted to the ICU and/or died. url: https://www.ncbi.nlm.nih.gov/pubmed/32888003/ doi: 10.1093/cid/ciaa1338 id: cord-330742-m5xx8861 author: Qian, Jie title: Age-dependent gender differences of COVID-19 in mainland China: comparative study date: 2020-05-30 words: 3535.0 sentences: 214.0 pages: flesch: 61.0 cache: ./cache/cord-330742-m5xx8861.txt txt: ./txt/cord-330742-m5xx8861.txt summary: METHODS: We used the national surveillance database of COVID-19 in mainland China to compared gender differences in attack rate (AR), proportion of severe and critical cases (PSCC) and case fatality rate (CFR) in relation to age, affected province, and onset-to-diagnosis interval. After adjusting for age, affected province and onset-to-diagnosis interval, the female-to-male difference in AR, PSCC and CFR remained significant in multivariate logistic regression analyses. In this study, we used the surveillance data containing all confirmed cases in mainland China as of April 28, 2020 to evaluated gender-specific differences in attack rate, proportion of severe and critical cases, and case fatality in relation to age, affected province and onset-to-diagnosis interval, in order to provide evidence-based guidance for more effective and equitable interventions and treatments. abstract: BACKGROUND: The ongoing pandemic of novel coronavirus disease 2019 (COVID-19) is challenging global public health system. Sex-differences in infectious diseases are a common but neglected problem. METHODS: We used the national surveillance database of COVID-19 in mainland China to compared gender differences in attack rate (AR), proportion of severe and critical cases (PSCC) and case fatality rate (CFR) in relation to age, affected province, and onset-to-diagnosis interval. RESULTS: The overall AR was significantly higher in female population than in males (63.9 versus 60.5 per million persons; P ˂ .001). By contrast, PSCC and CFR were significantly lower among female patients (16.9% and 4.0%) than among males (19.5% and 7.2%), with ORs of 0.87 and 0.57, respectively (both P ˂ .001). The female-to-male differences were age-dependent, which were significant among people aged 50–69 years for AR, and in the patients of 30-years or older for both PSCC and CFR (all P ≤ .001). The AR, PSCC and CFR varied greatly from province to province. However, female-to-male differences in AR, PSCC and CFR were significant in the epicenter, Hubei province, where 82.2% confirmed cases and 97.4% deaths occurred. After adjusting for age, affected province and onset-to-diagnosis interval, the female-to-male difference in AR, PSCC and CFR remained significant in multivariate logistic regression analyses. CONCLUSIONS: We elucidate an age-dependent gender dimorphism for COVID-19, in which the females have higher susceptibility but lower severity and fatality. Further epidemiological and biological investigations are required to better understand the sex-specific differences for effective interventions. url: https://doi.org/10.1093/cid/ciaa683 doi: 10.1093/cid/ciaa683 id: cord-343827-jo61t3m0 author: Qian, Qun title: Direct evidence of active SARS-CoV-2 replication in the intestine date: 2020-07-08 words: 1314.0 sentences: 98.0 pages: flesch: 53.0 cache: ./cache/cord-343827-jo61t3m0.txt txt: ./txt/cord-343827-jo61t3m0.txt summary: We investigated the presence of virions and pathological changes in surgical rectal tissues of a clinically confirmed COVID-19 patient with rectal adenocarcinoma. RNA of SARS-CoV-2 was detected in surgically resected rectal specimens, but not in samples collected on 37 day after discharge. Notably, coincidence with rectal tissues of surgical specimens tested nucleic acid positive for SARS-CoV-2, typical coronavirus virions in rectal tissue were observed under electron microscopy. Notably, fecal samples remained positive for SARS-CoV-2 RNA nearly 5 weeks after the viral clearance from the upper respiratory tract in COVID-19 patients [8] . To clarify the above questions, we performed a retrospective study to detect the presence of SARS-CoV-2 virions and determine the pathological changes in rectal tissues of this patient. Samples of rectal tissues, succus entericus and intestinal mucosa of ileostomy, and rectal mucosa were tested for SARS-CoV-2 nucleic acid using qRT-PCR. abstract: BACKGROUND: Currently, there is no direct evidence to prove the active SARS-CoV-2 replication in the intestinal tract and relevant pathological changes in the colon and rectum. We investigated the presence of virions and pathological changes in surgical rectal tissues of a clinically confirmed COVID-19 patient with rectal adenocarcinoma. METHODS: Here, the clinical data were collected during hospitalization and follow-up of this patient. Quantitative RT-PCR was performed on the rectal tissue specimens obtained from surgical resection, succus entericus and intestinal mucosa of ileostomy, and rectal mucosa during follow-up after recovery. Ultrathin sections of surgical samples were observed for SARS-CoV-2 virions using electron microscopy. Histopathological examination was performed using hematoxylin-eosin stain. Immunohistochemical analysis and immunofluorescence were carried out on rectal tissues to evaluate the distribution of SARS-CoV-2 antigen, and immune cell infiltrations. RESULTS: The patient had fever and cough on day 3 postoperatively, was diagnosed with COVID-19 on day 7, and was discharged from the hospital on day 41. RNA of SARS-CoV-2 was detected in surgically resected rectal specimens, but not in samples collected on 37 day after discharge. Notably, coincidence with rectal tissues of surgical specimens tested nucleic acid positive for SARS-CoV-2, typical coronavirus virions in rectal tissue were observed under electron microscopy. Moreover, abundant lymphocytes and macrophages (some are SARS-CoV-2 positive) infiltrating the lamina propria were found with no significant mucosal damage. CONCLUSIONS: We firstly reported that direct evidence of the active SARS-CoV-2 replication in the patient's rectum during the incubation period, which might explain SARS-CoV-2 fecal-oral transmission. url: https://doi.org/10.1093/cid/ciaa925 doi: 10.1093/cid/ciaa925 id: cord-252423-ojmt4k2w author: Qu, Bing title: Monologue of a physician who tested persistently positive for COVID-19 date: 2020-05-11 words: 1100.0 sentences: 95.0 pages: flesch: 72.0 cache: ./cache/cord-252423-ojmt4k2w.txt txt: ./txt/cord-252423-ojmt4k2w.txt summary: The COVID-19, as other new infectious diseases, has presented us unprecedented challenges and put us into huge dilemma. As a physician on clinical frontline, I had been treating patients actively and wishing them an early recovery, but never expecting that I would be infected. As in the early stage we knew little about COVID-19 and the possibility that someone with COVID-19 can transmit the virus even if they are not showing symptoms, many healthcare professionals were infected. According to a Press Conference of the WHO-China Joint Mission on COVID-19 on February 24, 3387 medical staff have been reported to be infected, among which over 90% were from Hubei province. Exploring the reasons for healthcare workers infected with novel coronavirus disease 2019 (COVID-19) in China Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China abstract: nan url: https://doi.org/10.1093/cid/ciaa551 doi: 10.1093/cid/ciaa551 id: cord-356084-621qzpqd author: Qu, Jiuxin title: Profile of IgG and IgM antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) date: 2020-04-27 words: 1578.0 sentences: 98.0 pages: flesch: 61.0 cache: ./cache/cord-356084-621qzpqd.txt txt: ./txt/cord-356084-621qzpqd.txt summary: title: Profile of IgG and IgM antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) We profiled the serological responses to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) nucleocapsid (N) protein and spike (S) glycoprotein. In this study, we investigated the humoral immunity of hospitalized patients, analyzed the profile of IgG and IgM antibodies against the SARS-CoV-2 in 41 COVID-19 patients between three and 43 days of their illness. Li et al., reported that both IgG and IgM antibody levels increased to detectable levels from the second week of illness in 20 SARS-CoV patients [5] . found that acute lung injury in Chinese macaques caused by SARS-CoV could be mediated by higher anti-spike IgG [9] , and we detected high levels of IgG antibody in critical patients. Longitudinal profile of immunoglobulin G (IgG), IgM, and IgA antibodies against the severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein in patients with pneumonia due to the SARS coronavirus abstract: We profiled the serological responses to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) nucleocapsid (N) protein and spike (S) glycoprotein. The majority of the patients developed robust antibody responses between 17 and 23 days after illness onset. Delayed, but stronger antibody responses were observed in critical patients. url: https://doi.org/10.1093/cid/ciaa489 doi: 10.1093/cid/ciaa489 id: cord-335767-omm04fg5 author: Raabe, Vanessa N title: Importance of Pediatric Inclusion in COVID-19 Therapeutic Trials date: 2020-05-27 words: 1468.0 sentences: 57.0 pages: flesch: 32.0 cache: ./cache/cord-335767-omm04fg5.txt txt: ./txt/cord-335767-omm04fg5.txt summary: Not only do children and the medical community lose out on opportunities to gain the highest level of clinical evidence for efficacy in a vulnerable population, but due to the lack of availability of pediatric trials, many children hospitalized for COVID-19 are receiving off-label use of therapeutic agents with unproven benefit against COVID-19. In addition to offering enhanced safety monitoring, enrollment of children in clinical trials ensures that parents and older children are fully informed of the potential risks and benefits associated with use of the therapeutic agent, a conversation often omitted when medications are prescribed off-label. Inclusion of children in these clinical trials is feasible under current regulations, provides direct benefit to pediatric trial participants from a safety perspective compared to off-label prescribing, and provides systematic collection of the highest quality of evidence for COVID-19 therapeutics in a vulnerable population where SARS-CoV-2 infection behaves differently from adults. abstract: Pediatric patients are excluded from most coronavirus disease 2019 (COVID-19) therapeutic trials. We outline a rationale for the inclusion of children in COVID-19 therapeutic trials, which enabled us to include children of all ages in a therapeutic COVID-19 trial at our institution. url: https://doi.org/10.1093/cid/ciaa656 doi: 10.1093/cid/ciaa656 id: cord-321603-lbbsnriv author: Rao, Mohan title: Comparing nasopharyngeal swab and early morning saliva for the identification of SARS-CoV-2 date: 2020-08-06 words: 2186.0 sentences: 172.0 pages: flesch: 59.0 cache: ./cache/cord-321603-lbbsnriv.txt txt: ./txt/cord-321603-lbbsnriv.txt summary: The aim of this study was to compare patient-performed testing based on a morning saliva sample with the current standard testing method, healthcare worker-collected sampling via a nasopharyngeal swab (NPS). METHODS: This was a prospective single center study which recruited 217 asymptomatic adult male participants in a COVID-19 quarantine center who had tested positive for SARS-CoV-2 8-10 days prior isolation. The current standard sampling techniques such as NPS and OPS used for surveillance and serial monitoring of infected patients are exposing healthcare workers to SARS-CoV-2 virus and other unknown pathogens via aerosols from swabbing and jeopardizing physical distancing. This prospective single center diagnostic study was conducted among 217 individuals who were tested positive for SARS-CoV-2 via NPS at a COVID-19 quarantine center, MAEPS. Nevertheless, we had 72 individuals with their saliva specimen tested positive for SARS-CoV-2 while they were test negative for nasopharyngeal swab. Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs. abstract: BACKGROUND: The ideal SARs-CoV-2 testing method would be accurate and also be patient-performed to reduce exposure to healthcare workers. The aim of this study was to compare patient-performed testing based on a morning saliva sample with the current standard testing method, healthcare worker-collected sampling via a nasopharyngeal swab (NPS). METHODS: This was a prospective single center study which recruited 217 asymptomatic adult male participants in a COVID-19 quarantine center who had tested positive for SARS-CoV-2 8-10 days prior isolation. Paired NPS and saliva specimens were collected and processed within 5 hours of sample collection. Real time reverse transcriptase polymerase chain reaction (RT-PCR) targeting Envelope (E) and RNA-dependent RNA polymerase (RdRp) genes was performed and the results were compared. RESULTS: Overall, 160 of the 217 (74%) participants tested positive for Covid-19 based on saliva, NPS, or both testing methods. The detection rate for SARS-CoV-2 was higher in saliva compared to NPS testing (93.1%, 149/160 vs 52.5%, 84/160, p<0.001). The concordance between the two tests was 45.6% (virus was detected in both saliva and NPS in 73/160), while 47.5% were discordant (87/160 tested positive for one while negative for the other). The Ct values for E and RdRp genes were significantly lower in saliva specimens compared to NP swab specimens. CONCLUSIONS: Our findings demonstrate that saliva is a better alternative specimen for detection of SARS-CoV-2. Taking into consideration, the simplicity of specimen collection, shortage of PPE and the transmissibility of the virus, saliva could enable self-collection for an accurate SARS-CoV-2 surveillance testing. url: https://doi.org/10.1093/cid/ciaa1156 doi: 10.1093/cid/ciaa1156 id: cord-307770-1igydu3y author: Rawson, Timothy M title: Bacterial and fungal co-infection in individuals with coronavirus: A rapid review to support COVID-19 antimicrobial prescribing date: 2020-05-02 words: 2998.0 sentences: 266.0 pages: flesch: 45.0 cache: ./cache/cord-307770-1igydu3y.txt txt: ./txt/cord-307770-1igydu3y.txt summary: title: Bacterial and fungal co-infection in individuals with coronavirus: A rapid review to support COVID-19 antimicrobial prescribing Articles presenting clinical data for patients with coronavirus infection (defined as SARS-1, MERS, SARS-COV-2, and other coronavirus) and bacterial/fungal co-infection reported in English, Mandarin, or Italian were included. CONCLUSIONS: Despite frequent prescription of broad-spectrum empirical antimicrobials in patients with coronavirus associated respiratory infections, there is a paucity of data to support the association with respiratory bacterial/fungal co-infection. In terms of antimicrobial prescribing bacterial/fungal co-infection of the respiratory tract; some patients presenting to hospital with SARS-COV-2 infection have a clinical phenotype that is not dissimilar from atypical bacterial pneumonia. [13] We performed a review of the medical literature to explore commonly reported bacterial/fungal co-infections in patients admitted to hospital with coronavirus lower respiratory tract infections. It is not clear whether these patients were in critical or nonSelection of empiric antimicrobial therapy for respiratory bacterial/fungal co-infection and recommendations for duration of treatment require several considerations. abstract: BACKGROUND: To explore and describe the current literature surrounding bacterial/fungal co-infection in patients with coronavirus infection. METHODS: MEDLINE, EMBASE, and Web of Science were searched using broad based search criteria relating to coronavirus and bacterial co-infection. Articles presenting clinical data for patients with coronavirus infection (defined as SARS-1, MERS, SARS-COV-2, and other coronavirus) and bacterial/fungal co-infection reported in English, Mandarin, or Italian were included. Data describing bacterial/fungal co-infections, treatments, and outcomes were extracted. Secondary analysis of studies reporting antimicrobial prescribing in SARS-COV-2 even in the absence of co-infection was performed. RESULTS: 1007 abstracts were identified. Eighteen full texts reported bacterial/fungal co-infection were included. Most studies did not identify or report bacterial/fungal coinfection (85/140;61%). 9/18 (50%) studies reported on COVID-19, 5/18 (28%) SARS-1, 1/18 (6%) MERS, and 3/18 (17%) other coronavirus. For COVID-19, 62/806 (8%) patients were reported as experiencing bacterial/fungal co-infection during hospital admission. Secondary analysis demonstrated wide use of broad-spectrum antibacterials, despite a paucity of evidence for bacterial coinfection. On secondary analysis, 1450/2010 (72%) of patients reported received antimicrobial therapy. No antimicrobial stewardship interventions were described. For non-COVID-19 cases bacterial/fungal co-infection was reported in 89/815 (11%) of patients. Broad-spectrum antibiotic use was reported. CONCLUSIONS: Despite frequent prescription of broad-spectrum empirical antimicrobials in patients with coronavirus associated respiratory infections, there is a paucity of data to support the association with respiratory bacterial/fungal co-infection. Generation of prospective evidence to support development of antimicrobial policy and appropriate stewardship interventions specific for the COVID-19 pandemic are urgently required. url: https://www.ncbi.nlm.nih.gov/pubmed/32358954/ doi: 10.1093/cid/ciaa530 id: cord-007047-7ty9mxa9 author: Reller, L. Barth title: Implications of New Technology for Infectious Diseases Practice date: 2006-11-15 words: 4095.0 sentences: 190.0 pages: flesch: 38.0 cache: ./cache/cord-007047-7ty9mxa9.txt txt: ./txt/cord-007047-7ty9mxa9.txt summary: Problems with currently available molecular assays include a lack of knowledge about the extent of microbial nucleic acid in "normal" hosts, concentration of agent material in small volume samples, lack of microbiologist expertise, lack of adequate reimbursement, and difficulty with validation based on conventional methods. Infectious diseases clinicians have relied on these expert workers, and Reliable molecular diagnostic tests are not readily available for many infectious agents Commercial tests should only be used for validated specimen types Transportation problems, low concentrations of infectious agent, primer binding site genetic changes, final assay volume, inhibition, contamination, nonspecific amplification, and operator error lead to false-negative and false-positive amplification results Genomic bacterial sequencing is subject to error because of sequence homology among different bacteria, database problems, and mutations A number of nucleic acid hybridization and amplification methods are now in use, including direct probe hybridization (AdvanDx FISH for Staphylococcus aureus [AdvanDx] and GenProbe for group A streptococci [GenProbe]), hybrid capture (Digene for human papillomavirus; Digene), PCR, branched-chain DNA (bDNA; Bayer Diagnostics), and transcription-mediated amplification (Probe-Tec for Chlamydia and N. abstract: New assays for the diagnosis of infectious diseases—particularly those that use molecular technologies—will revolutionize infectious diseases practices, but the fulfillment of the promise is several years away. Problems with currently available molecular assays include a lack of knowledge about the extent of microbial nucleic acid in “normal” hosts, concentration of agent material in small volume samples, lack of microbiologist expertise, lack of adequate reimbursement, and difficulty with validation based on conventional methods. Clinicians must appreciate the shortcomings of new technology to use it effectively and appropriately. However, we are realizing tangible progress in our ability to detect new etiological agents; the availability of rapid, accurate diagnostic tests for previously difficult infections; and advances into new, human response—based paradigms for diagnostic testing. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107913/ doi: 10.1086/508536 id: cord-007170-svsfu7fj author: Richt, J. A. title: Infection with Borna Disease Virus: Molecular and Immunobiological Characterization of the Agent date: 1992-06-17 words: 6125.0 sentences: 325.0 pages: flesch: 42.0 cache: ./cache/cord-007170-svsfu7fj.txt txt: ./txt/cord-007170-svsfu7fj.txt summary: Studies on BDV may help to illuminate several important areas of neurobiology, including the mechanisms regulating the replication of a new type of RNA virus in the nuclei of neural cells, the neuroinvasiveness and neurotropism of such viruses, their T cell-mediated immunopathology, tolerance in newborn animals to persistent viral infection of the central nervous system, and behavioral diseases and eating disorders induced by such agents. Persistently infected MDCK (Madin-Darby canine kidney) cells are widely used in indirect immunofluorescence assays for the detection of BDV-specific antibodies in serum and CSF of affected animals and humans [18, 20] . The pathological changes in the brain and retina of BDVinfected animals resemble certain types of encephalitis and Most studies on the pathogenesis of BDV infection have involved experimentally inoculated Lewis rats. Although infection of newborn rats resulted in persistent viral replication in the CNS as well as in visceral organs, these animals developed no inflammatory response or signs of Borna disease. abstract: Borna disease virus (BDV), which seems to be distinct from all other known viruses, exhibits a unique mechanism of pathogenesis. This review highlights several aspects of the biology of infection with this virus and summarizes the preliminary characterization of the agent. Studies on BDV may help to illuminate several important areas of neurobiology, including the mechanisms regulating the replication of a new type of RNA virus in the nuclei of neural cells, the neuroinvasiveness and neurotropism of such viruses, their T cell-mediated immunopathology, tolerance in newborn animals to persistent viral infection of the central nervous system, and behavioral diseases and eating disorders induced by such agents. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7109702/ doi: 10.1093/clinids/14.6.1240 id: cord-297239-or6h6p9p author: Ridgway, Jessica P. title: Influenza Among Afebrile and Vaccinated Healthcare Workers date: 2015-06-01 words: 2674.0 sentences: 145.0 pages: flesch: 46.0 cache: ./cache/cord-297239-or6h6p9p.txt txt: ./txt/cord-297239-or6h6p9p.txt summary: To prevent transmission of influenza from healthcare workers (HCWs) to patients, many hospitals exclude febrile HCWs from working, but allow afebrile HCWs with respiratory symptoms to have contact with patients. During the 2013–2014 influenza season at our hospital, an influenza-positive HCW with respiratory symptoms but no fever was linked to a case of possible healthcare-associated influenza in a patient. In accordance with the CDC''s guidelines, our hospital''s routine sick policy at the time prohibited febrile HCWs from working, but not those with respiratory symptoms in the absence of fever. Given the risk of influenza transmission to patients from afebrile employees with influenza, we implemented a temporary mandatory influenza-testing policy for all HCWs with respiratory symptoms. To prevent healthcare-associated influenza, hospitals should consider more stringent infection control measures for HCWs with respiratory symptoms, even if no fever is present. abstract: Background. To prevent transmission of influenza from healthcare workers (HCWs) to patients, many hospitals exclude febrile HCWs from working, but allow afebrile HCWs with respiratory symptoms to have contact with patients. During the 2013–2014 influenza season at our hospital, an influenza-positive HCW with respiratory symptoms but no fever was linked to a case of possible healthcare-associated influenza in a patient. Therefore, we implemented a temporary policy of mandatory influenza testing for HCWs with respiratory symptoms. Methods. From 3 January through 28 February 2014, we tested HCWs with respiratory symptoms for influenza and other respiratory pathogens by polymerase chain reaction of flocked nasopharyngeal swabs. HCWs also reported symptoms and influenza vaccination status, and underwent temperature measurement. We calculated the proportion of influenza-positive HCWs with fever and prior influenza vaccination. Results. Of 449 HCWs, 243 (54%) had a positive test for any respiratory pathogen; 34 (7.6%) HCWs tested positive for influenza. An additional 7 HCWs were diagnosed with influenza by outside physicians. Twenty-one (51.2%) employees with influenza had fever. Among influenza-infected HCWs, 20 had previously received influenza vaccination, 18 had declined the vaccine, and 3 had unknown vaccination status. There was no significant difference in febrile disease among influenza-infected employees who had received the influenza vaccine and those who had not received the vaccine (45% vs 61%; P = .32). Conclusions. Nearly half of HCWs with influenza were afebrile prior to their diagnosis. HCWs with respiratory symptoms but no fever may pose a risk of influenza transmission to patients and coworkers. url: https://www.ncbi.nlm.nih.gov/pubmed/25733370/ doi: 10.1093/cid/civ163 id: cord-266820-exl36jt3 author: Rivera, Frida title: Prevalence of SARS-CoV-2 asymptomatic infections in two large academic health systems in Wisconsin date: 2020-08-19 words: 873.0 sentences: 76.0 pages: flesch: 61.0 cache: ./cache/cord-266820-exl36jt3.txt txt: ./txt/cord-266820-exl36jt3.txt summary: title: Prevalence of SARS-CoV-2 asymptomatic infections in two large academic health systems in Wisconsin We aim to determine the prevalence of asymptomatic SARS-CoV-2 infection at two hospital systems in two counties in Wisconsin. This study aims to determine the prevalence of asymptomatic SARS-CoV-2 infection at two hospital systems in two counties with markedly different rates of COVID-19. From April 6, 2020 to June 04, 2020, a total of 11,654 asymptomatic patients were tested for SARS-CoV-2, and 61 (0.52%) were positive [Froedtert Health, 38; UW Health, 23]. During the study period, we observed a low prevalence of asymptomatic SARS-CoV-2 infections in these two academic health systems in South Wisconsin. This low prevalence of asymptomatic infections has been recently reported in other areas with high COVID-19 rates, such as Boston and Philadelphia [4, 5] ; however, these two studies included pregnant women and children. In contrast, two hospitals in New York City reported a prevalence of SARS-CoV-2 asymptomatic infections of 14% among women admitted for delivery. abstract: SARS-CoV-2 asymptomatic infections may play a critical role in disease transmission. We aim to determine the prevalence of asymptomatic SARS-CoV-2 infection at two hospital systems in two counties in Wisconsin. The SARS-CoV-2 prevalence was 1% or lower at both systems despite the higher incidence of COVID-19 in Milwaukee county url: https://doi.org/10.1093/cid/ciaa1225 doi: 10.1093/cid/ciaa1225 id: cord-324607-rpwccvqi author: Rojek, Amanda M title: Core Minimal Datasets to Advance Clinical Research for Priority Epidemic Diseases date: 2020-02-15 words: 1260.0 sentences: 63.0 pages: flesch: 39.0 cache: ./cache/cord-324607-rpwccvqi.txt txt: ./txt/cord-324607-rpwccvqi.txt summary: Among the noteworthy successes of vaccine trials, and the commendable efforts to implement clinical treatment trials during Ebola outbreaks, we should also focus on strengthening the collection and curation of epidemiological and observational data that can improve the conception and design of clinical research. Table 1 identifies some key domains that could contribute to a core minimal dataset that informs clinical trial design for each priority pathogen. While these data have their most important benefits in improving patient management (through better recognition of disease complications and informing supportive care) and public health control, patient-based data are also used to determine key parameters for clinical trials, such as the inclusion criteria, the nature and rate of clinically relevant outcomes, and potential confounders. A systematic review and meta-analysis of patient data from the west Africa (2013-16) Ebola virus disease epidemic abstract: The Ebola virus disease outbreak in west Africa has prompted significant progress in responding to the clinical needs of patients affected by emerging infectious disease outbreaks. Among the noteworthy successes of vaccine trials, and the commendable efforts to implement clinical treatment trials during Ebola outbreaks, we should also focus on strengthening the collection and curation of epidemiological and observational data that can improve the conception and design of clinical research. url: https://doi.org/10.1093/cid/ciz760 doi: 10.1093/cid/ciz760 id: cord-349556-k312qkvh author: Roldán-Santiago, Ernesto title: SARS-CoV-2 spreads to lymph nodes and strongly expands CD4+ T(EMRA) cells in a patient with mild COVID-19 date: 2020-09-18 words: 1831.0 sentences: 148.0 pages: flesch: 64.0 cache: ./cache/cord-349556-k312qkvh.txt txt: ./txt/cord-349556-k312qkvh.txt summary: title: SARS-CoV-2 spreads to lymph nodes and strongly expands CD4+ T(EMRA) cells in a patient with mild COVID-19 After a FNAP we demonstrate that SARS-CoV-2 is found in lymph nodes (LNs) even in mild disease along with a strong expansion of terminally differentiated effector memory CD4+T-cells , a cell population that is practically absent in LN. Naive or central memory cells, which are the two main CD4+ subsets that are usually detected in normal or reactive LN that are or are not infected by EBV (Fig. 1B) , switched almost completely to effector memory and especially to T EMRA T-cells (Fig. 1A) . The findings strongly suggest that the enlarged LN was a consequence of EBV rather than SARS-CoV-2 infection, but this co-infection was an excellent opportunity to assess the presence of coronavirus in LNs from patients with mild symptoms. This case suggests that virus reaches LNs , regardless of disease severity.The other relevant finding of this study is an unexpected expansion of CD4+ T EMRA in the patient''s cervical LN. abstract: A woman with mild Covid-19 developed cervical adenopathy, being diagnosed of Epstein−Barr virus infectious mononucleosis. After a FNAP we demonstrate that SARS-CoV-2 is found in lymph nodes (LNs) even in mild disease along with a strong expansion of terminally differentiated effector memory CD4+T-cells , a cell population that is practically absent in LN. url: https://doi.org/10.1093/cid/ciaa1422 doi: 10.1093/cid/ciaa1422 id: cord-298539-yncda1us author: Ruan, Linhui title: New measures for COVID-19 response: a lesson from the Wenzhou experience date: 2020-04-03 words: 1233.0 sentences: 73.0 pages: flesch: 53.0 cache: ./cache/cord-298539-yncda1us.txt txt: ./txt/cord-298539-yncda1us.txt summary: This is the result of the more than 90,000 people who return to Wenzhou from Wuhan during On January 17 when the first case of COVID-19 was confirmed, the Wenzhou New Coronavirus Pneumonia Prevention and Control Committee launched emergency epidemic prevention and control measures, which in general consisted of two phases. The main measures included (1) centralizing the confirmed and suspected patients in designated hospitals for treatment, (2) identifying and investigating all returnees from Wuhan using a big data network and persuading them to undergo 14-day home quarantine, and (3) centralizing and medically observing individuals who had been exposed to a confirmed COVID-19 patient. However, the numbers of new cases in these cities were meaningfully reduced after implementation of most aggressive social distancing and quarantining measures, which was similar to Wenzhou second-phase measures on February 10 ( Figure 1A) . abstract: As the outbreak of COVID-19 has spread globally, determining how to prevent the spread is of paramount importance. We reported the effectiveness of different responses of four affected cities in preventing the COVID-19 spread. We expect Wenzhou anti-COVID-19 measures may provide experience for cities around the world that are experiencing this epidemic. url: https://doi.org/10.1093/cid/ciaa386 doi: 10.1093/cid/ciaa386 id: cord-331719-uijwq8gx author: Russek-Cohen, Estelle title: FDA Perspectives on Diagnostic Device Clinical Studies for Respiratory Infections date: 2011-05-01 words: 4838.0 sentences: 205.0 pages: flesch: 41.0 cache: ./cache/cord-331719-uijwq8gx.txt txt: ./txt/cord-331719-uijwq8gx.txt summary: In the former circumstance, a clinical reference method is considered to be the best available method for establishing the presence or absence of the target organism [1] but the reference method cannot incorporate results reported by the new device; for example, a new enzymelinked immunosorbent assay (ELISA) could not be used as one of the diagnostic criteria for the reference method in a study used to evaluate the performance of the assay. In a clinical study with only 5 specimens positive for a specific pathogen (via the reference method) and an observed sensitivity of 5/5 (100%) results in a lower confidence bound of only 55.6%, meaning diagnostic performance is very uncertain. Detailed information regarding the design of studies for a CLIA waiver application, including the minimal performance criteria acceptable for a CLIA-waived device, is described in ''''FDA guidance for industry and FDA staff: recommendations for Clinical Laboratory Improvement Amendments of 1988 (CLIA) waiver applications for manufacturers of in vitro diagnostic devices'''' [9] . abstract: Two pathways are described for submission to FDA for clearance of a diagnostic device: a Premarket Application (PMA), which can lead to approval of a diagnostic device, and a Premarket Notification, which can lead to clearance. The latter is often called a 510(k), named for the statute providing for this path. Recent FDA clearance of molecular-based multiplex panels represents the beginning of a new era for the diagnosis of respiratory infections. The ability to test for multiple pathogens simultaneously, accompanied by the increasing availability of molecular-based assays for newly recognized respiratory pathogens will likely have a major impact on patient care, drug development, and public health epidemiology. We provide a general overview of how FDA evaluates new diagnostics for respiratory tract infections and the agency’s expectations for sponsors developing new tests in this area. url: https://doi.org/10.1093/cid/cir056 doi: 10.1093/cid/cir056 id: cord-295940-siy32dj7 author: Saito, Makoto title: Gargle lavage as a safe and sensitive alternative to swab samples to diagnose COVID-19: a case report in Japan date: 2020-04-02 words: 533.0 sentences: 48.0 pages: flesch: 66.0 cache: ./cache/cord-295940-siy32dj7.txt txt: ./txt/cord-295940-siy32dj7.txt summary: title: Gargle lavage as a safe and sensitive alternative to swab samples to diagnose COVID-19: a case report in Japan Moreover, the sensitivity for virus detection is low with these swabs; viral load is reportedly higher in sputum samples. 3 Here we report a case in which gargle lavage samples yielded a positive PCR result. Additional gargle lavage samples and oropharyngeal swabs were collected and tested on Days 8 and 9 and found to be positive, with a slightly higher amount of viral genome in the gargle lavage sample (Supplement Figure 3) . For other respiratory pathogens, gargle lavage samples have been reported to be more sensitive than throat swabs. 1 Gargle lavage thus offers a safer and possibly more sensitive alternative or additional option for diagnosing COVID-19. SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients Comparison of gargle samples and throat swab samples for the detection of respiratory pathogens abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32241023/ doi: 10.1093/cid/ciaa377 id: cord-277410-lt19mijb author: Salvatore, Phillip P title: Epidemiological Correlates of PCR Cycle Threshold Values in the Detection of SARS-CoV-2 date: 2020-09-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Detection of SARS-CoV-2 infection has principally been performed through the use of real-time reverse-transcription PCR (rRT-PCR) testing. Results of such tests can be reported as cycle threshold (Ct) values, which may provide semi-quantitative or indirect measurements of viral load. Previous reports have examined temporal trends in Ct values over the course of a SARS-CoV-2 infection. METHODS: Using testing data collected during a prospective household transmission investigation of outpatient and mild COVID-19 cases, we examined the relationship between Ct values of the viral RNA N1 target and demographic, clinical, and epidemiological characteristics collected through participant interviews and daily symptom diaries. RESULTS: We found Ct values are lowest (corresponding to higher viral RNA concentration) soon after symptom onset and are significantly correlated with time elapsed since onset (p<0.001); within 7 days after symptom onset, the median Ct value was 26.5 compared with a median Ct value of 35.0 occurring 21 days after onset. Ct values were significantly lower among participants under 18 years of age (p=0.01) and those reporting upper respiratory symptoms at the time of sample collection (p=0.001) and were higher among participants reporting no symptoms (p=0.05). CONCLUSIONS: These results emphasize the importance of early testing for SARS-CoV-2 among individuals with symptoms of respiratory illness and allows cases to be identified and isolated when their viral shedding may be highest. url: https://www.ncbi.nlm.nih.gov/pubmed/32986120/ doi: 10.1093/cid/ciaa1469 id: cord-291363-re45w37d author: Sanville, Bradley title: A Community Transmitted Case of Severe Acute Respiratory Distress Syndrome due to SARS CoV2 in the United States date: 2020-03-30 words: 1308.0 sentences: 86.0 pages: flesch: 53.0 cache: ./cache/cord-291363-re45w37d.txt txt: ./txt/cord-291363-re45w37d.txt summary: title: A Community Transmitted Case of Severe Acute Respiratory Distress Syndrome due to SARS CoV2 in the United States The current novel coronavirus (SARS CoV2) outbreak, which was identified in December 2019 in Wuhan, Hubei, China has spread rapidly causing a significant public health crisis worldwide 1 . Two healthcare workers in contact with the patient at the outside hospital have subsequently tested positive for SARS CoV2. Overall, these reviews note a case fatality rate of 1.40-3.46%, though this may be considerably lower when accounting for a likely large number of mild or asymptomatic patients that were not tested 6, 9, 10 DeWit and colleagues from the NIH, Gilead, and Columbia University successfully treated rhesus macaques against a model of MERS 13 . As noted in a recent editorial, diagnosis becomes even more difficult considering the likelihood of a large number of mild or asymptomatic patients who are not formally identified with a SARS CoV2 infection 18, 19 . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32227197/ doi: 10.1093/cid/ciaa347 id: cord-328667-r5w09lb6 author: Schwartz, David A title: The Effects of Pregnancy on Women with COVID-19: Maternal and Infant Outcomes date: 2020-05-11 words: 1518.0 sentences: 88.0 pages: flesch: 48.0 cache: ./cache/cord-328667-r5w09lb6.txt txt: ./txt/cord-328667-r5w09lb6.txt summary: In contrast, some pregnant women might be asymptomatic or have only mild or nonspecific symptoms from an infectious disease, resulting in their escaping detection as having infection even when the embryo or fetus is severely affected. [9] evaluated for the first time the effects of being pregnant on COVID-19 disease and pneumonia using a case-control experimental design conducted at the Maternal and Child Health Hospital of Hubei Province, a 1900-bed tertiary medical center in Wuhan, China. To accomplish this, the authors enrolled two cohorts of pregnant women with COVID-19 and pneumonia -one consisting of 16 pregnant women with pneumonia and rt-PCR confirmed SARS-CoV-2 infection, and the other with 18 pregnant women with pneumonia who were clinically and radiologically suspected of having COVID-19 but had negative rt-PCR test results. An analysis of 38 pregnant women with COVID-19, their newborn infants, and maternal-fetal transmission of SARS-CoV-2: Maternal coronavirus infections and pregnancy outcomes Maternal and neonatal outcomes of pregnant women with COVID-19 pneumonia: a case-control study abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32392330/ doi: 10.1093/cid/ciaa559 id: cord-313617-hh7lccet author: Sigel, Keith title: Covid-19 and People with HIV Infection: Outcomes for Hospitalized Patients in New York City date: 2020-06-28 words: 2565.0 sentences: 190.0 pages: flesch: 56.0 cache: ./cache/cord-313617-hh7lccet.txt txt: ./txt/cord-313617-hh7lccet.txt summary: We collected data on baseline clinical characteristics, laboratory values, HIV infection status, COVID-19 treatment, and outcomes from this group and matched comparators (one PWH to up to five patients by age, sex, race/ethnicity and calendar week of infection). INTERPRETATION: We found no differences in adverse outcomes associated with HIV infection for hospitalized COVID-19 patients compared to a demographically similar patient group. We then compared differences in time to death to assess disease trajectory for hospitalized patients by HIV status by fitting unadjusted cumulative incidence function curves with hospital discharge as a competing risk. [7] To compare cumulative incidence of death by HIV status accounting for potential confounding factors we then fit a multivariable survival model using Fine-Grey competing risk methods, including demographics, COVID-19 severity, comorbid conditions and laboratory values that differed by HIV status. abstract: BACKGROUND: There have been limited data regarding the clinical impact of COVID-19 disease on people with HIV (PWH). In this study we compared outcomes for PWH with COVID-19 disease to a matched comparison group. DESIGN: We identified 88 PWH hospitalized with laboratory confirmed COVID-19 in our hospital system in New York between March 12 and April 23, 2020. We collected data on baseline clinical characteristics, laboratory values, HIV infection status, COVID-19 treatment, and outcomes from this group and matched comparators (one PWH to up to five patients by age, sex, race/ethnicity and calendar week of infection). We compared baseline clinical characteristics and outcomes (death, mechanical ventilation, hospital discharge) for these two groups, as well as cumulative incidence of death by HIV status. RESULTS: Patients did not differ significantly by HIV status by age, sex or race/ethnicity due to the matching algorithm. PWH hospitalized with COVID-19 had high proportions of HIV virologic control on antiretroviral therapy. PWH had greater proportions of smoking (p<0.001) and comorbid illness than demographically similar uninfected comparators. There was no difference in COVID-19 severity on admission by HIV status (p=0.15). Poor outcomes for hospitalized PWH were frequent but similar to proportions in comparators; 18% required mechanical ventilation and ultimately 21% died during follow-up (compared with 23% and 20% respectively). There was similar cumulative incidence of death over time by HIV status (p=0.94). INTERPRETATION: We found no differences in adverse outcomes associated with HIV infection for hospitalized COVID-19 patients compared to a demographically similar patient group. url: https://doi.org/10.1093/cid/ciaa880 doi: 10.1093/cid/ciaa880 id: cord-350972-0n4dumgg author: Sing, Chor-Wing title: Long-term outcome of short-course high-dose glucocorticoids for SARS: a 17-year follow-up in SARS survivors date: 2020-07-16 words: 1789.0 sentences: 143.0 pages: flesch: 59.0 cache: ./cache/cord-350972-0n4dumgg.txt txt: ./txt/cord-350972-0n4dumgg.txt summary: title: Long-term outcome of short-course high-dose glucocorticoids for SARS: a 17-year follow-up in SARS survivors Results showed that high-dose glucocorticoids greatly increased long-term risk of avascular necrosis, but not other major diseases. Hong Kong had an outbreak of severe acute respiratory syndrome (SARS; caused by SARS-CoV-1) in 2003, resulting in 1,755 cases and 299 deaths 3 Short course of very-high-dose (VHD) glucocorticoids was used for the treatment of SARS, especially to prevent cytokine storm. To understand the long-term consequences of VHD glucocorticoids, we studied the clinical outcomes of SARS survivors after 17 years. We identified SARS survivors using an electronic medical record database, Clinical Data Analysis and Reporting System (CDARS) of the Hong Kong Hospital Authority, the details of which have been described elsewhere. In this retrospective study of SARS survivors with 17 years of follow-up, a short-course use of VHD glucocorticoids was not associated with major diseases except AVN. abstract: Use of high-dose glucocorticoids for coronavirus disease 2019 (COVID-19; caused by SARS-CoV-2) is controversial because of safety concerns. We examined long-term consequences in severe acute respiratory syndrome (SARS; caused by SARS-CoV-1) survivors. Results showed that high-dose glucocorticoids greatly increased long-term risk of avascular necrosis, but not other major diseases. url: https://doi.org/10.1093/cid/ciaa992 doi: 10.1093/cid/ciaa992 id: cord-317092-5qba9jiq author: Singh, Tulika title: Lessons from COVID-19 in children: Key hypotheses to guide preventative and therapeutic strategies date: 2020-05-08 words: 4971.0 sentences: 355.0 pages: flesch: 49.0 cache: ./cache/cord-317092-5qba9jiq.txt txt: ./txt/cord-317092-5qba9jiq.txt summary: The current pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), reveals a peculiar trend of milder disease and lower case fatality in children compared to adults. Understanding differences in children''s immunity, host cellular factors required for virus replication, and physiology can provide insights into the correlates of protection from SARS-CoV-2 and other CoVs. In this review, we summarize current pediatric-specific knowledge on clinical disease, transmission, risks for severe disease, protective immunity, and novel therapies and vaccines in trial. 38 For example, a regulator of lung morphogenesis that is lower in childhood, nuclear factor kappa-light-chainenhancer of activated B cells (NF-b), plays a pathologic role in inflammatory diseases and should be evaluated as a protective host factor in pediatric versus adult SARS-CoV-2 infections. In this review, we evaluated recent reports on the pathology and immunity to SARS-CoV-2 infection and offered several hypotheses for how these features may differ in children versus adults, and how they may differentially modulate disease in these populations. abstract: The current pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), reveals a peculiar trend of milder disease and lower case fatality in children compared to adults. Consistent epidemiologic evidence of reduced severity of infection in children across different populations and countries suggests there are underlying biologic differences between children and adults that mediate differential disease pathogenesis. This presents a unique opportunity to learn about disease modifying host factors from pediatric populations. Our review summarizes the current knowledge of pediatric clinical disease, role in transmission, risks for severe disease, protective immunity, as well as novel therapies and vaccine trials for children. We then define key hypotheses and areas for future research that can use the pediatric model of disease, transmission, and immunity to develop preventive and therapeutic strategies for people of all age groups. url: https://www.ncbi.nlm.nih.gov/pubmed/32382748/ doi: 10.1093/cid/ciaa547 id: cord-340678-2e2s1gof author: Skowronski, Danuta M title: Influenza vaccine does not increase the risk of coronavirus or other non-influenza respiratory viruses: retrospective analysis from Canada, 2010-11 to 2016-17 date: 2020-05-22 words: 1646.0 sentences: 113.0 pages: flesch: 45.0 cache: ./cache/cord-340678-2e2s1gof.txt txt: ./txt/cord-340678-2e2s1gof.txt summary: Influenza vaccine effectiveness against influenza and non-influenza respiratory viruses (NIRV) was assessed by test-negative design using historic datasets of the community-based Canadian Sentinel Practitioner Surveillance Network (SPSN), spanning 2010-11 to 2016-17. Here, we use historic datasets of the community-based Canadian Sentinel Practitioner Surveillance Network (SPSN) to assess the association between influenza vaccine and NIRV risk, notably seasonal coronaviruses. Conversely, influenza vaccine had no effect on non-influenza causes of ILI, with the likelihood of vaccination among NIRV cases relative to test-negative controls approaching unity. In combined NIRV analysis, relative to pan-negative controls, Wolff adjusted for age and excluded specimens that tested influenza-positive. We illustrate the impact of this bias in Supplementary_Material_3, where we have re-analyzed Wolff''s data as well as our own, comparing influenza vaccine effect against NIRV when influenza testpositive specimens are properly excluded (as per TND prerequisite) or improperly included (as per Wolff [4] ) within the control group. abstract: Influenza vaccine effectiveness against influenza and non-influenza respiratory viruses (NIRV) was assessed by test-negative design using historic datasets of the community-based Canadian Sentinel Practitioner Surveillance Network (SPSN), spanning 2010-11 to 2016-17. Vaccine significantly reduced the risk of influenza illness by >40% with no effect on coronaviruses or other NIRV risk. url: https://doi.org/10.1093/cid/ciaa626 doi: 10.1093/cid/ciaa626 id: cord-281418-mvgp6qfv author: Soccal, P. M. title: Upper and Lower Respiratory Tract Viral Infections and Acute Graft Rejection in Lung Transplant Recipients date: 2010-07-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Background. Lung transplant recipients are frequently exposed to respiratory viruses and are particularly at risk for severe complications. The aim of this study was to assess the association among the presence of a respiratory virus detected by molecular assays in bronchoalveolar lavage (BAL) fluid, respiratory symptoms, and acute rejection in adult lung transplant recipients. Methods. Upper (nasopharyngeal swab) and lower (BAL) respiratory tract specimens from 77 lung transplant recipients enrolled in a cohort study and undergoing bronchoscopy with BAL and transbronchial biopsies were screened using 17 different polymerase chain reaction—based assays. Results. BAL fluid and biopsy specimens from 343 bronchoscopic procedures performed in 77 patients were analyzed. We also compared paired nasopharyngeal and BAL fluid specimens collected in a subgroup of 283 cases. The overall viral positivity rate was 29.3% in the upper respiratory tract specimens and 17.2% in the BAL samples (P < .001). We observed a significant association between the presence of respiratory symptoms and positive viral detection in the lower respiratory tract (P = .012). Conversely, acute rejection was not associated with the presence of viral infection (odds ratio, 0.41; 95% confidence interval, 0.20–0.88). The recovery of lung function was significantly slower when acute rejection and viral infection were both present. Conclusions. A temporal relationship exists between acute respiratory symptoms and positive viral nucleic acid detection in BAL fluid from lung transplant recipients. We provide evidence suggesting that respiratory viruses are not associated with acute graft rejection during the acute phase of infection. url: https://doi.org/10.1086/653529 doi: 10.1086/653529 id: cord-260274-c3586tp6 author: Somers, Emily C title: Tocilizumab for treatment of mechanically ventilated patients with COVID-19 date: 2020-07-11 words: 3645.0 sentences: 218.0 pages: flesch: 37.0 cache: ./cache/cord-260274-c3586tp6.txt txt: ./txt/cord-260274-c3586tp6.txt summary: CONCLUSIONS: In this cohort of mechanically ventilated COVID-19 patients, tocilizumab was associated with lower mortality despite higher superinfection occurrence. At our institution, IL-6 blockade with tocilizumab is considered for patients with severe COVID-19 and suspected hyperinflammation based on rapidly worsening respiratory status and elevated inflammatory markers, with the majority of usage occurring in patients requiring mechanical ventilation. Using our COVID-19 Rapid Response Registry infrastructure, we performed an observational study of outcomes in patients with COVID-19 requiring mechanical ventilation, comparing those treated with tocilizumab with those who were not. In this observational, controlled study of patients with severe COVID-19 necessitating mechanical ventilation, receipt of tocilizumab was independently associated with improved survival. To date, the risk of superinfection in mechanically ventilated patients with severe COVID-19 remains poorly described and the incremental risk associated with a single dose of tocilizumab is not well characterized. abstract: BACKGROUND: Severe COVID-19 can manifest in rapid decompensation and respiratory failure with elevated inflammatory markers, consistent with cytokine release syndrome for which IL-6 blockade is approved treatment. METHODS: We assessed effectiveness and safety of IL-6 blockade with tocilizumab in a single-center cohort of patients with COVID-19 requiring mechanical ventilation. The primary endpoint was survival probability post-intubation; secondary analyses included an ordinal illness severity scale integrating superinfections. Outcomes in patients who received tocilizumab compared to tocilizumab-untreated controls were evaluated using multivariable Cox regression with propensity score inverse probability weighting (IPTW). RESULTS: 154 patients were included, of whom 78 received tocilizumab and 76 did not. Median follow-up was 47 days (range 28-67). Baseline characteristics were similar between groups, although tocilizumab-treated patients were younger (mean 55 vs. 60 years), less likely to have chronic pulmonary disease (10% vs. 28%), and had lower D-dimer values at time of intubation (median 2.4 vs. 6.5 mg/dL). In IPTW-adjusted models, tocilizumab was associated with a 45% reduction in hazard of death [hazard ratio 0.55 (95% CI 0.33, 0.90)] and improved status on the ordinal outcome scale [odds ratio per 1-level increase: 0.58 (0.36, 0.94)]. Though tocilizumab was associated with an increased proportion of patients with superinfections (54% vs. 26%; p<0.001), there was no difference in 28-day case fatality rate among tocilizumab-treated patients with versus without superinfection [22% vs. 15%; p=0.42]. Staphylococcus aureus accounted for ~50% of bacterial pneumonia. CONCLUSIONS: In this cohort of mechanically ventilated COVID-19 patients, tocilizumab was associated with lower mortality despite higher superinfection occurrence. url: https://doi.org/10.1093/cid/ciaa954 doi: 10.1093/cid/ciaa954 id: cord-313499-8ijbesl8 author: Stowell, Sean title: Role of serology in the COVID-19 pandemic date: 2020-05-01 words: 1211.0 sentences: 61.0 pages: flesch: 39.0 cache: ./cache/cord-313499-8ijbesl8.txt txt: ./txt/cord-313499-8ijbesl8.txt summary: In this issue of Clinical Infections Diseases, F Xiang et al present a serologic study of 85 nucleic acid test (NAT) SARS-CoV-2 positive patients and 24 NAT negative patients who had symptoms suspicious for COVID-19 1 . Serological testing consisted of an enzyme linked immunosorbent assay designed to detect IgM and IgG antibodies against the N protein of SARS-CoV-2. In patients with suspected COVID-19 who tested NAT negative, IgM antibodies were detected in 87.5% and IgG was present in 70.8%. In the case of COVID-19, while serological analysis may be helpful in examining exposure, such approaches can be more challenging to interpret in patients with acute infection. Despite these considerations, the results of this manuscript suggest repeat serological testing may be informative in the acute setting, especially in patients who continue to follow a COVID-19-like disease course despite NAT negativity. Additional testing, such as NAT testing, may be warranted in serological positive individuals to determine potential risk for infecting others. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32357206/ doi: 10.1093/cid/ciaa510 id: cord-299359-s8j78naz author: Sundaram, Maria E. title: Influenza Vaccination Is Not Associated With Detection of Noninfluenza Respiratory Viruses in Seasonal Studies of Influenza Vaccine Effectiveness date: 2013-09-15 words: 3247.0 sentences: 157.0 pages: flesch: 35.0 cache: ./cache/cord-299359-s8j78naz.txt txt: ./txt/cord-299359-s8j78naz.txt summary: We investigated the association between influenza infection, vaccination, and detection of other respiratory viruses among children <5 years old and adults ≥50 years old with acute respiratory illness who participated in seasonal studies of influenza vaccine effectiveness. This could theoretically contribute to overestimation of true VE (ie, bias away from the null); therefore, a key assumption of the test-negative control design of influenza vaccine effectiveness studies is that the proportion of noninfluenza viral illness does not differ by influenza vaccination status [9] . The goals of this study were to determine if influenza vaccination is associated with detection of noninfluenza respiratory viruses and to determine if vaccine effectiveness estimates differ when different control groups are used in the analysis. For participants in these age groups, multiplex reverse transcription polymerase chain reaction (RT-PCR) testing was subsequently performed to detect other respiratory viruses, providing an opportunity to investigate the relationship between influenza vaccination and infection with other viral pathogens. abstract: Background. The test-negative control study design is the basis for observational studies of influenza vaccine effectiveness (VE). Recent studies have suggested that influenza vaccination increases the risk of noninfluenza respiratory virus infection. Such an effect could create bias in VE studies using influenza-negative controls. We investigated the association between influenza infection, vaccination, and detection of other respiratory viruses among children <5 years old and adults ≥50 years old with acute respiratory illness who participated in seasonal studies of influenza vaccine effectiveness. Methods. Nasal/nasopharyngeal samples collected from 2004–2005 through 2009–2010 were tested for 19 respiratory virus targets using a multiplex reverse-transcription polymerase chain reaction (RT-PCR) platform. Vaccination status was determined using a validated registry. Adjusted odds ratios for influenza and vaccination status were calculated using three different control groups: influenza-negative, other respiratory virus positive, and pan-negative. Results. Influenza was detected in 12% of 2010 children and 20% of 1738 adults. Noninfluenza respiratory viruses were detected in 70% of children and 38% of adults without influenza. The proportion vaccinated did not vary between virus-positive controls and pan-negative controls in children (P = .62) or adults (P = .33). Influenza infection was associated with reduced odds of vaccination, but adjusted odds ratios differed by no more than 0.02 when the analysis used influenza-negative or virus-positive controls. Conclusions. Influenza vaccination was not associated with detection of noninfluenza respiratory viruses. Use of influenza-negative controls did not generate a biased estimate of vaccine effectiveness due to an effect of vaccination on other respiratory virus infections. url: https://www.ncbi.nlm.nih.gov/pubmed/23748138/ doi: 10.1093/cid/cit379 id: cord-294718-n3gx862b author: Tam, Patrick C K title: Detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breast milk of a mildly symptomatic patient with coronavirus disease 2019 (COVID-19) date: 2020-05-30 words: 1606.0 sentences: 135.0 pages: flesch: 61.0 cache: ./cache/cord-294718-n3gx862b.txt txt: ./txt/cord-294718-n3gx862b.txt summary: title: Detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breast milk of a mildly symptomatic patient with coronavirus disease 2019 (COVID-19) Although RNA has been detected in various clinical samples, no reports to date have documented SARS-CoV-2 in human milk. This case report describes an actively breastfeeding patient with COVID-19 infection with detectable viral RNA in human milk. The first sampling of human milk occurred five days following maternal symptom onset with no episodes of breastfeeding in those five days prior to collection of the sample. An additional six samples of human milk were collected with one further sample demonstrating detectable SARS-COV-2 RNA (Figure 1 ). These samples continued to have detectable RNA sixty-six days following infant symptom onset (Figure 1 ). To our knowledge, this is the first case of detectable SARS-CoV-2 RNA from human milk in a patient with COVID-19. abstract: SARS-CoV-2 is a novel coronavirus and causative pathogen to the pandemic illness COVID-19. Although RNA has been detected in various clinical samples, no reports to date have documented SARS-CoV-2 in human milk. This case report describes an actively breastfeeding patient with COVID-19 infection with detectable viral RNA in human milk. url: https://doi.org/10.1093/cid/ciaa673 doi: 10.1093/cid/ciaa673 id: cord-011745-dbdtpojs author: Thompson, Mark G. title: Effectiveness of Nonadjuvanted Monovalent Influenza A(H1N1)pdm09 Vaccines for Preventing Reverse Transcription Polymerase Chain Reaction–Confirmed Pandemic Influenza Hospitalizations: Case-Control Study of Children and Adults at 10 US Influenza Surveillance Network Sites date: 2013-12-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: During 2009–2010, we examined 217 patients hospitalized with laboratory-confirmed pandemic influenza in 9 Influenza Hospitalization Surveillance Network sites and 413 age- and community-matched controls and found that a single dose of monovalent nonadjuvanted influenza A(H1N1)pdm09 vaccine was 50% (95% confidence interval, 13%–71%) effective in preventing hospitalization associated with A(H1N1)pdm09 virus infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7314184/ doi: 10.1093/cid/cit551 id: cord-251945-v077hhgk author: Titanji, Boghuma K title: Response to Correspondence: Baricitinib as Treatment of COVID-19 Friend or Foe of the Pancreas? Cerda-Contreras et.al date: 2020-08-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32797235/ doi: 10.1093/cid/ciaa1212 id: cord-295270-6ptaxg74 author: Titanji, Boghuma K title: Response to Correspondence: Baricitinib – Impact on COVID-19 Coagulopathy? Jorgensen et. al. date: 2020-08-14 words: 501.0 sentences: 54.0 pages: flesch: 63.0 cache: ./cache/cord-295270-6ptaxg74.txt txt: ./txt/cord-295270-6ptaxg74.txt summary: authors: Titanji, Boghuma K; Farley, Monica M; Schinazi, Raymond F; Marconi, Vincent C Baricitinib through its immunomodulatory effects as highlighted by Jorgensen et.al may in fact be beneficial in terms of reducing coagulopathy in patients with COVID-19, which is thought to be primarily mediated by hyper-inflammation and endothelial damage. All of the cohort studies of baricitinib for COVID-19 treatment led to significant decline in inflammatory M a n u s c r i p t markers for patients who received the drug 2,3,8 . Regarding baricitinib, ACTT2 should provide clarity on the VTE issue in the near future and its role in the treatment of COVID-19 in moderate to severe patients. Ruxolitinib in treatment of severe coronavirus disease 2019 (COVID-19): A multicenter, single-blind, randomized controlled trial Use of Baricitinib in patients with moderate and severe COVID-19 Vincent Marconi and Raymond F Schinazi are partially funded by -Emory University Center for AIDS Research (AI050409). abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32797226/ doi: 10.1093/cid/ciaa1210 id: cord-307660-onz6vfre author: Titanji, Boghuma K title: Use of Baricitinib in Patients with Moderate and Severe COVID-19 date: 2020-06-29 words: 1084.0 sentences: 75.0 pages: flesch: 51.0 cache: ./cache/cord-307660-onz6vfre.txt txt: ./txt/cord-307660-onz6vfre.txt summary: Coronavirus Infectious Disease-19 (COVID-19), caused by Severe Acute Respiratory Virus Syndrome Coronavirus-2 (SARS-CoV-2) has led to over 8 million confirmed infections worldwide with an estimated global mortality of 5.6% as of June 17 th 2020 1 . Patients had laboratory confirmed COVID-19, diagnosed by quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR) testing of oropharyngeal, nasopharyngeal or tracheal aspirate samples and were treated at the discretion of the medical team with a combination of hydroxychloroquine and baricitinib if they fulfilled at least one of the following criteria: 1) evidence of pneumonia on lung imaging and requiring supplemental oxygen on admission or development of a new oxygen requirement during the course of their hospitalization 2) moderate disease requiring hospitalization (e.g., severe diarrhea requiring volume resuscitation, encephalopathy, evidence of end-A c c e p t e d M a n u s c r i p t organ damage); 3) elevated or rising inflammatory markers during hospitalization. abstract: Cytokine storm and hyperinflammation are associated with increased mortality in COVID-19. In this small uncontrolled cohort of patients with moderate-severe COVID-19, treatment with baricitinib plus hydroxychloroquine was associated with recovery in 11 of 15 patients. Baricitinib for the treatment of COVID-19 should be further investigated in randomized controlled clinical trials. url: https://doi.org/10.1093/cid/ciaa879 doi: 10.1093/cid/ciaa879 id: cord-269973-sntnmqqd author: To, Kelvin Kai-Wang title: Unique SARS-CoV-2 clusters causing a large COVID-19 outbreak in Hong Kong date: 2020-08-05 words: 1860.0 sentences: 139.0 pages: flesch: 63.0 cache: ./cache/cord-269973-sntnmqqd.txt txt: ./txt/cord-269973-sntnmqqd.txt summary: However, the number of COVID-19 cases remained relatively low due to the early implementation of stringent public health measures, including border control, voluntary community-wide wearing of face masks, hand hygiene and social distancing, prompt isolation of suspected cases, and testing and quarantine of close contacts and travelers from epidemic areas [2, 3] . Spike protein D614G mutation was not found in any genomes during the first wave, which mainly involved travelers from mainland China or other parts of Asia, or the linked local cases. The majority of genomes from locally-acquired cases (91%) during this third wave belong to a cluster HK1, a unique cluster within the GR clade, which is characterized by 4 non-synonymous mutations (nsp3 A85V, nsp15 A231V, spike protein S12F, NP A12G) and 1 synonymous mutation (NP C29144T). Two unique SARS-CoV-2 clusters have been identified during this large summer outbreak in Hong Kong shortly after the easing of social distancing policies. abstract: After two months of relative quiescence, a large COVID-19 outbreak occurred in Hong Kong in July 2020 after gradual relaxation of social distancing policy. Two unique SARS-CoV-2 phylogenetic clusters have been identified among locally-acquired cases, with most genomes belonging to cluster HK1 which is phylogenetically related to SARS-CoV-2 reported overseas. url: https://www.ncbi.nlm.nih.gov/pubmed/32756996/ doi: 10.1093/cid/ciaa1119 id: cord-295525-emrwcx0m author: To, Kelvin Kai-Wang title: Consistent Detection of 2019 Novel Coronavirus in Saliva date: 2020-02-12 words: 1912.0 sentences: 110.0 pages: flesch: 55.0 cache: ./cache/cord-295525-emrwcx0m.txt txt: ./txt/cord-295525-emrwcx0m.txt summary: The 2019 novel coronavirus (2019-nCoV) was detected in the self-collected saliva of 91.7% (11/12) of patients. The 2019 novel coronavirus (2019-nCoV) was detected in the self-collected saliva of 91.7% (11/12) of patients. We have previously demonstrated that saliva has a high concordance rate of greater than 90% with nasopharyngeal specimens in the detection of respiratory viruses, including coronaviruses [5, 6] . A patient is considered to have laboratory-confirmed infection if 2019-nCoV was detected in their nasopharyngeal or sputum specimens. For patient K, the first saliva specimen collected on the day of hospital admission tested negative. The use of saliva is preferred over nasopharyngeal or oropharyngeal specimens for serial viral load monitoring because this would reduce the discomfort to the patient and reduce the health hazards to healthcare workers during repeated sampling. Our results have demonstrated the potential for saliva to be a noninvasive specimen type for the diagnosis and viral load monitoring of 2019-nCoV. abstract: The 2019 novel coronavirus (2019-nCoV) was detected in the self-collected saliva of 91.7% (11/12) of patients. Serial saliva viral load monitoring generally showed a declining trend. Live virus was detected in saliva by viral culture. Saliva is a promising noninvasive specimen for diagnosis, monitoring, and infection control in patients with 2019-nCoV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32047895/ doi: 10.1093/cid/ciaa149 id: cord-266150-wox7pnkr author: Torres, Juan Pablo title: SARS-CoV-2 antibody prevalence in blood in a large school community subject to a Covid-19 outbreak: a cross-sectional study date: 2020-07-10 words: 4202.0 sentences: 222.0 pages: flesch: 53.0 cache: ./cache/cord-266150-wox7pnkr.txt txt: ./txt/cord-266150-wox7pnkr.txt summary: Once these forms were signed, a copy was emailed to participants for their records and they were directed to a secure survey that i) asked basic demographic questions, ii) requested information on any previous RT-PCR test for SARS-CoV-2 and potential contact with any Covid-19 positive cases, and iii) asked about symptoms experienced since the outbreak (date and duration in days of each symptom). Among students, antibody positive children were younger, had a higher PCR positivity rate (in those who underwent PCR testing during the outbreak), and were more likely to self-report contact with one or more confirmed cases, as compared to seronegative children ( Table 2 ). Overall, PCR testing and contact history was significantly higher in staff compared to students, which in addition to the higher antibody positivity observed in this study, support the more significant role of adults within the outbreak, in proportion to the overall population. abstract: BACKGROUND: A SARS-CoV-2 outbreak affecting 52 people from a large school community in Santiago, Chile was identified (March 12), nine days after the first country case. We assessed the magnitude of the outbreak and the role students and staff played using a self-administered antibody detection test and survey. METHODS: The school was closed on March 13, and the entire community was placed under quarantine. We implemented a home-delivery, self-administered, IgG/IgM antibody test and survey to a classroom stratified sample of students and all staff from May 4-19. We aimed to determine overall seroprevalence rates by age group, reported symptoms, contact exposure and to explore dynamics of transmission. RESULTS: Antibody positivity rates were 9.9% (95%CI: 8.2-11.8) for 1,009 students and 16.6% (95%CI: 12.1-21.9) for 235 staff. Among students, positivity was associated with younger age (P=0.01), lower grade level (P=0.05), prior RT-PCR positivity (P=0.03), and history of contact with a confirmed case (P<0.001). Among staff, positivity was higher in teachers (P=0.01) and in those previously RT-PCR positive (P<0.001). Excluding RT-PCR positive individuals, antibody positivity was associated with fever in adults and children (P=0.02; P=0.002), abdominal pain in children (P=0.001), and chest pain in adults (P=0.02). Within antibody positive individuals, 40% of students and 18% of staff reported no symptoms (P=0.01). CONCLUSIONS: Teachers were more affected during the outbreak and younger children were at higher infection risk, likely because index case(s) were teachers and/or parents from preschool. Self-administered antibody testing, supervised remotely, proved to be a suitable and rapid tool. Our study provides useful information for school re-openings. url: https://doi.org/10.1093/cid/ciaa955 doi: 10.1093/cid/ciaa955 id: cord-266232-2ctfmjb8 author: Trubiano, Jason A title: Alterations in smell or taste – Classic COVID-19? date: 2020-05-28 words: 693.0 sentences: 74.0 pages: flesch: 66.0 cache: ./cache/cord-266232-2ctfmjb8.txt txt: ./txt/cord-266232-2ctfmjb8.txt summary: A c c e p t e d M a n u s c r i p t Dear Editor, There are increased reports of loss of smell (anosmia) and taste (ageusia) in patients with confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causing coronavirus disease 2019 , in particular in the setting of mild disease. Luers and colleagues described from a retrospective adult cohort of confirmed SARS-CoV-2 from Germany (n = 72) that 74% of patients reported anosmia and 69% ageusia [7] . prior to this also described from a retrospective cohort study of COVID-19 patients interviewed 5-6 days post diagnosis that 64.4% reported alternations in taste or smell [1] . It is important for clinicians to realize that ansomia and ageusia are likely to be commonly reported symptoms in other upper respiratory tract infections, when appropriately asked (8.9% of our COVID-19 test negative group) [3, 8] . Self-reported olfactory and taste disorders in SARS-CoV-2 patients: a cross-sectional study abstract: nan url: https://doi.org/10.1093/cid/ciaa655 doi: 10.1093/cid/ciaa655 id: cord-331930-w2055c42 author: Tso, Eugene Y. K. title: Persistence of Physical Symptoms in and Abnormal Laboratory Findings for Survivors of Severe Acute Respiratory Syndrome date: 2004-05-01 words: 529.0 sentences: 34.0 pages: flesch: 61.0 cache: ./cache/cord-331930-w2055c42.txt txt: ./txt/cord-331930-w2055c42.txt summary: title: Persistence of Physical Symptoms in and Abnormal Laboratory Findings for Survivors of Severe Acute Respiratory Syndrome Sir-We performed a cross-sectional study to assess the physical symptoms in and abnormal laboratory findings for survivors of severe acute respiratory syndrome (SARS) at their first follow-up visit after discharge from Princess Margaret Hospital (Hong Kong, China). The median interval (‫ע‬SD) between the onset of SARS symptoms and the first follow-up visit was weeks. Symptoms reported at the first followup visit included palpitation (45.1% of patients), exertional dyspnea (41.9%), malaise (40.3%), easy forgetfulness (30.6%), chest discomfort (22.5%), hand tremor (21%), dizziness (17.7%), depression (16.1%), myalgia (12.9%), headache (9.6%), diarrhoea (8.1%), cough (8.1%), insomnia (6.5%), and hair loss over the scalp (3.2%). Laboratory findings included the following mean values (‫ע‬SD): hemoglobin of patients. However, for 1 female patient, PCR of a stool sample obtained 35 days after the onset of SARS symptoms was positive for SARS-CoV RNA. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/15127357/ doi: 10.1086/383580 id: cord-273840-jjm7y07m author: Vabret, Astrid title: Detection of the New Human Coronavirus HKU1: A Report of 6 Cases date: 2006-03-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Background. Human coronavirus HKU1 (HCoV-HKU1), a new group 2 coronavirus, was first characterized in 2005 from 2 adults with pneumonia in Hong Kong, China. To the best of our knowledge, there is no other report to date about the detection of this new virus. We report a molecular method allowing for the detection of HCoV-HKU1 and also report the clinical presentation of 6 infected patients. Methods. We screened 141 specimens (135 nasal samples and 6 stool samples) received in February and March 2005 in our laboratory and obtained from 135 hospitalized patients (61.5% of whom were <5 years old and 34.1% of whom were >20 years old) for HCoV-HKU1. Results. HCoV-HKU1 was detected in 6 (4.4%) of the 135 nasal specimens and in 2 (33.3%) of the 6 stool samples; the positive samples were obtained from 6 patients (5 children and 1 adult). The clinical presentation of these 6 patients was as follows: 3 were admitted to the hospital for acute enteric disease resulting in severe dehydration associated with upper respiratory symptoms; 1 had fever, otitis, and febrile seizure; 1 had a sample obtained to investigate failure to thrive; and 1 had a sample obtained for exploration of X-linked agammaglobulinemia and hyperleucocytosis. Conclusion. HCoV-HKU1 can be detected in respiratory and stool samples from children and adults in a part of the world other than Hong Kong. Our results suggest that HCoV-HKU1 could be associated with respiratory and enteric diseases, and its detection can be related to a persistent asymptomatic infection in patients with poor underlying conditions. url: https://www.ncbi.nlm.nih.gov/pubmed/16447108/ doi: 10.1086/500136 id: cord-352899-bt2xg0ha author: Van Kerkhove, Maria D. title: Interpreting Results From Environmental Contamination Studies of Middle East Respiratory Syndrome Coronavirus date: 2016-10-15 words: 804.0 sentences: 41.0 pages: flesch: 44.0 cache: ./cache/cord-352899-bt2xg0ha.txt txt: ./txt/cord-352899-bt2xg0ha.txt summary: authors: Van Kerkhove, Maria D.; Peiris, Malik J. Researchers in Korea have recently published studies [4, 5] evaluating environmental and/or air contamination by MERS-CoV and should be commended for their efforts to evaluate the hospital outbreaks in their country. To fully understand the possible role of environmental contamination, including the possible detection of MERS-CoV in the air, additional studies must be conducted to see whether these results can be replicatedfor example, in hospitals in the Middle East where patients with MERS-CoV are treated, to evaluate virus persistence in hospital environments. A more complete understanding of the results of environmental and air contamination studies will have important implications for the application of infection prevention and control measures [8] currently used in hospitals treating patients with MERS-CoV, possibly leading to more detailed recommendations. Environmental contamination and viral shedding in MERS patients during MERS-CoV outbreak in South Korea Middle East respiratory syndrome coronavirus (MERS-CoV) abstract: nan url: https://doi.org/10.1093/cid/ciw478 doi: 10.1093/cid/ciw478 id: cord-354877-n5du3bqt author: Vasoo, Shawn title: Rapid Antigen Tests for Diagnosis of Pandemic (Swine) Influenza A/H1N1 date: 2009-10-01 words: 1783.0 sentences: 96.0 pages: flesch: 45.0 cache: ./cache/cord-354877-n5du3bqt.txt txt: ./txt/cord-354877-n5du3bqt.txt summary: During the period from 1 May 2009 through 2 June 2009, a convenience sample of 84 positive, nonduplicate nasopharyngeal specimens were tested using 3 different rapid antigen test kits: BD Directigen EZ Flu A+B test (Becton Dickinson), BinaxNOW Influenza A&B (Inverness Medical), and QuickVue Influenza A+B Test (Quidel). Patient charts were reviewed, if available, for potential factors that may have been associated with rapid antigen test result; these included patient age, duration of symptoms before presentation, inpatient or emergency department versus outpatient status, and the median number of RT-PCR fluorescence intensity (MFI) units. Because of the widespread interest regarding the clinical performance of rapid antigen tests for detection of pandemic influenza A/H1N1 virus, we used a convenience sample of positive specimens to allow for a quick yet relatively accurate assessment of these tests. abstract: We found that the sensitivities of 3 rapid influenza antigen tests for pandemic influenza A/H1N1 virus were low to moderate: BD Directigen EZ Flu A+B test (Becton Dickinson), 46.7%; BinaxNOW Influenza A&B (Inverness Medical), 38.3%; and QuickVue Influenza A+B Test (Quidel), 53.3%. A patient with influenza-like illness who has a negative rapid antigen test result should undergo further testing using reverse-transcription polymerase chain reaction. url: https://www.ncbi.nlm.nih.gov/pubmed/19725784/ doi: 10.1086/644743 id: cord-002514-pp06m5xk author: Venkatesan, Sudhir title: Impact of Outpatient Neuraminidase Inhibitor Treatment in Patients Infected With Influenza A(H1N1)pdm09 at High Risk of Hospitalization: An Individual Participant Data Metaanalysis date: 2017-05-15 words: 4019.0 sentences: 173.0 pages: flesch: 40.0 cache: ./cache/cord-002514-pp06m5xk.txt txt: ./txt/cord-002514-pp06m5xk.txt summary: title: Impact of Outpatient Neuraminidase Inhibitor Treatment in Patients Infected With Influenza A(H1N1)pdm09 at High Risk of Hospitalization: An Individual Participant Data Metaanalysis While evidence exists to support the effectiveness of neuraminidase inhibitors (NAIs) in reducing mortality when given to hospitalized patients with A(H1N1)pdm09 virus infection, the impact of outpatient treatment on hospitalization has not been clearly established. In patients with laboratory-confirmed or clinically diagnosed A(H1N1)pdm09 influenza, after adjustment for community-based antibiotic treatment and propensity score, the likelihood of hospital admission in patients with outpatient or community-based NAI treatment was 0.24 (95% CI, 0.20-0.30) when compared to no NAI treatment in the community (Table 2) . Our main findings ( Table 2) suggest that NAI treatment in the community for patients with severe pandemic influenza substantially reduced the likelihood of hospital admission due to influenza A(H1N1)pdm09. Effectiveness of neuraminidase inhibitors in reducing mortality in patients admitted to hospital with influenza A H1N1pdm09 virus infection: a meta-analysis of individual participant data abstract: BACKGROUND. While evidence exists to support the effectiveness of neuraminidase inhibitors (NAIs) in reducing mortality when given to hospitalized patients with A(H1N1)pdm09 virus infection, the impact of outpatient treatment on hospitalization has not been clearly established. We investigated the impact of outpatient NAI treatment on subsequent hospitalization in patients with A(H1N1)pdm09 virus infection. METHODS. We assembled general community and outpatient data from 9 clinical centers in different countries collected between January 2009 and December 2010. We standardized data from each study center to create a pooled dataset and then used mixed-effects logistic regression modeling to determine the effect of NAI treatment on hospitalization. We adjusted for NAI treatment propensity and preadmission antibiotic use, including “study center” as a random intercept to account for differences in baseline hospitalization rate between centers. RESULTS. We included 3376 patients with influenza A(H1N1)pdm09, of whom 3085 (91.4%) had laboratory-confirmed infection. Eight hundred seventy-three patients (25.8%) received outpatient or community-based NAI treatment, 928 of 2395 (38.8%) with available data had dyspnea or respiratory distress, and hospitalizations occurred in 1705 (50.5%). After adjustment for preadmission antibiotics and NAI treatment propensity, preadmission NAI treatment was associated with decreased odds of hospital admission compared to no NAI treatment (adjusted odds ratio, 0.24; 95% confidence interval, 0.20–0.30). CONCLUSIONS. In a population with confirmed or suspected A(H1N1)pdm09 and at high risk of hospitalization, outpatient or community-based NAI treatment significantly reduced the likelihood of requiring hospital admission. These data suggest that community patients with severe influenza should receive NAI treatment. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411393/ doi: 10.1093/cid/cix127 id: cord-305394-wwabxlgr author: Venter, W D Francois title: COVID-19: First data from Africa date: 2020-08-31 words: 1469.0 sentences: 78.0 pages: flesch: 54.0 cache: ./cache/cord-305394-wwabxlgr.txt txt: ./txt/cord-305394-wwabxlgr.txt summary: This data is from an ongoing surveillance cohort that has previously generated rich data on disease patterns in the Western Cape, and currently continues to provide near real-time updates on the impact of PCR-confirmed SARS-CoV-2 on factors ranging from death to oxygen consumption within hospitals. Key strengths of the paper include a dataset covering over 3 million healthcare users in the Western Cape Province, and the use of both hospitalized and nonhospitalized cases and deaths Davies'' data shows similar mortality risk factors, including age, sex, diabetes (especially uncontrolled diabetes), hypertension and renal disease to other cohorts from richer countries. For South Africa, a sigh of relief at a relatively small increase in mortality in HIV and TB should be quickly tempered; diabetes was the second commonest cause of death in the country pre-COVID-19, and most patients in the country have poor glucose control, a major risk factor from Davies'' data (7) . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32865552/ doi: 10.1093/cid/ciaa1293 id: cord-254183-98o0dssj author: Waggoner, Jesse J. title: Rare and Emerging Viral Infections in Transplant Recipients date: 2013-10-15 words: 3927.0 sentences: 236.0 pages: flesch: 44.0 cache: ./cache/cord-254183-98o0dssj.txt txt: ./txt/cord-254183-98o0dssj.txt summary: In this review, we first discuss viral diagnostics and the developing field of viral discovery and then focus on rare and emerging viruses in the transplant population: human T-cell leukemia virus type 1; hepatitis E virus; bocavirus; KI and WU polyomaviruses; coronaviruses HKU1 and NL63; influenza, H1N1; measles; dengue; rabies; and lymphocytic choriomeningitis virus. Detection and reporting of such rare pathogens in transplant recipients is critical to patient care and improving our understanding of posttransplant infections. In a multicenter review of 85 cases of acute HEV infection, 65.9% of the solid organ transplant (SOT) recipients developed chronic hepatitis of whom 14.3% developed cirrhosis. Cases of lymphocytic choriomeningitis virus (LCMV) transmitted through organ transplantation (4 clusters, including 14 cases and 11 deaths) document the ability of this pathogen to cause severe disease in the immunocompromised host [10, [49] [50] [51] . Human T-cell leukemia virus type I-associated myelopathy following living-donor liver transplantation abstract: Emerging viral pathogens include newly discovered viruses as well as previously known viruses that are either increasing, or threatening to increase in incidence. While often first identified in the general population, they may affect transplant recipients, in whom their manifestations may be atypical or more severe. Enhanced molecular methods have increased the rate of viral discovery but have not overcome the problem of demonstrating pathogenicity. At the same time, improved clinical diagnostic methods have increased the detection of reemerging viruses in immunocompromised patients. In this review, we first discuss viral diagnostics and the developing field of viral discovery and then focus on rare and emerging viruses in the transplant population: human T-cell leukemia virus type 1; hepatitis E virus; bocavirus; KI and WU polyomaviruses; coronaviruses HKU1 and NL63; influenza, H1N1; measles; dengue; rabies; and lymphocytic choriomeningitis virus. Detection and reporting of such rare pathogens in transplant recipients is critical to patient care and improving our understanding of posttransplant infections. url: https://www.ncbi.nlm.nih.gov/pubmed/23839998/ doi: 10.1093/cid/cit456 id: cord-007073-soov8q3q author: Wang, Claire Y T title: Parechovirus A Infections in Healthy Australian Children During the First 2 Years of Life: A Community-based Longitudinal Birth Cohort Study date: 2019-08-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Hospital-based studies identify parechovirus (PeV), primarily PeV-A3, as an important cause of severe infections in young children. However, few community-based studies have been published and the true PeV infection burden is unknown. We investigated PeV epidemiology in healthy children participating in a community-based, longitudinal birth cohort study. METHODS: Australian children (n = 158) enrolled in the Observational Research in Childhood Infectious Diseases (ORChID) study were followed from birth until their second birthday. Weekly stool and nasal swabs and daily symptom diaries were collected. Swabs were tested for PeV by reverse-transcription polymerase chain reaction and genotypes determined by subgenomic sequencing. Incidence rate, infection characteristics, clinical associations, and virus codetections were investigated. RESULTS: PeV was detected in 1423 of 11 124 (12.8%) and 17 of 8100 (0.2%) stool and nasal swabs, respectively. Major genotypes among the 306 infection episodes identified were PeV-A1 (47.9%), PeV-A6 (20.1%), and PeV-A3 (18.3%). The incidence rate was 144 episodes (95% confidence interval, 128–160) per 100 child-years. First infections appeared at a median age of 8 (interquartile range, 6.0–11.7) months. Annual seasonal peaks changing from PeV-A1 to PeV-A3 were observed. Infection was positively associated with age ≥6 months, summer season, nonexclusive breastfeeding at age <3 months, and formal childcare attendance before age 12 months. Sole PeV infections were either asymptomatic (38.4%) or mild (32.7%), while codetection with other viruses in stool swabs was common (64.4%). CONCLUSIONS: In contrast with hospital-based studies, this study showed that diverse and dynamically changing PeV genotypes circulate in the community causing mild or subclinical infections in children. Parechovirus can cause severe illnesses in children. However, studies focus mainly on hospitalized populations. True disease burden in the community remains largely unknown. From our community-based cohort, we found diverse parechovirus genotypes in the community, causing mild or subclinical infections in children. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7108192/ doi: 10.1093/cid/ciz761 id: cord-279550-7u2hksxm author: Wang, Kai title: Longitudinal dynamics of the neutralizing antibody response to SARS-CoV-2 infection date: 2020-08-03 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Coronavirus disease 2019 (COVID-19) is a global pandemic with no licensed vaccine or specific antiviral agents for therapy. Little is known about the longitudinal dynamics of SARS-CoV-2-specific neutralizing antibodies (NAbs) in COVID-19 patients. METHODS: Blood samples (n=173) were collected from 30 COVID-19 patients over a 3-month period after symptom onset and analyzed for SARS-CoV-2-specific NAbs, using the lentiviral pseudotype assay, coincident with the levels of IgG and proinflammatory cytokines. RESULTS: SARS-CoV-2-specific NAb titers were low for the first 7–10 d after symptom onset and increased after 2–3 weeks. The median peak time for NAbs was 33 d (IQR 24–59 d) after symptom onset. NAb titers in 93·3% (28/30) of the patients declined gradually over the 3-month study period, with a median decrease of 34·8% (IQR 19·6–42·4%). NAb titers increased over time in parallel with the rise in IgG antibody levels, correlating well at week 3 (r = 0·41, p & 0·05). The NAb titers also demonstrated a significant positive correlation with levels of plasma proinflammatory cytokines, including SCF, TRAIL, and M-CSF. CONCLUSIONS: These data provide useful information regarding dynamic changes in NAbs in COVID-19 patients during the acute and convalescent phases. url: https://doi.org/10.1093/cid/ciaa1143 doi: 10.1093/cid/ciaa1143 id: cord-350338-lcsa06gm author: Wang, Kun title: Clinical and laboratory predictors of in-hospital mortality in patients with COVID-19: a cohort study in Wuhan, China date: 2020-05-03 words: 2469.0 sentences: 157.0 pages: flesch: 51.0 cache: ./cache/cord-350338-lcsa06gm.txt txt: ./txt/cord-350338-lcsa06gm.txt summary: title: Clinical and laboratory predictors of in-hospital mortality in patients with COVID-19: a cohort study in Wuhan, China We then validated these models by randomly collecting COVID-19 patients in the Infection department of Union Hospital in Wuhan from January 1, 2020, to February 20, 2020. The laboratory model developed with age, high-sensitivity C-reactive protein (hsCRP), peripheral capillary oxygen saturation (SpO2), neutrophil and lymphocyte count, D-dimer, aspartate aminotransferase (AST) and glomerular filtration rate (GFR) had a significantly stronger discriminatory power than the clinical model (p=0.0157), with AUC of 0.98 (95% CI, 0.92-0.99); threshold, -2.998; sensitivity, 100.00%; specificity, 92.82% and NPV, 100.00%. We developed a clinical model and laboratory model for predicting the in-hospital mortality of COVID-19 patients, the AUCs (95% CI) were 0.88 (0.80, 0.95) and 0.98 (0.92, 0.99) in training cohort, and 0.83 (0.68, 0.93) and 0.88 (0.77, 0.95) in validation cohort, respectively. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China abstract: BACKGROUND: This study aimed to develop mortality-prediction models for patients with Coronavirus disease 2019 (COVID-19). METHODS: The training cohort were consecutive patients with COVID-19 in the First People’s Hospital of Jiangxia District in Wuhan from January 7, 2020 to February 11, 2020. We selected baseline clinical and laboratory data through the stepwise Akaike information criterion and ensemble XGBoost model to build mortality-prediction models. We then validated these models by randomly collecting COVID-19 patients in the Infection department of Union Hospital in Wuhan from January 1, 2020, to February 20, 2020. RESULTS: 296 patients with COVID-19 were enrolled in the training cohort, 19 of whom died during hospitalization and 277 were discharged from the hospital. The clinical model developed with age, history of hypertension and coronary heart disease showed AUC of 0.88 (95% CI, 0.80-0.95); threshold, -2.6551; sensitivity, 92.31%; specificity, 77.44% and negative predictive value (NPV), 99.34%. The laboratory model developed with age, high-sensitivity C-reactive protein (hsCRP), peripheral capillary oxygen saturation (SpO2), neutrophil and lymphocyte count, D-dimer, aspartate aminotransferase (AST) and glomerular filtration rate (GFR) had a significantly stronger discriminatory power than the clinical model (p=0.0157), with AUC of 0.98 (95% CI, 0.92-0.99); threshold, -2.998; sensitivity, 100.00%; specificity, 92.82% and NPV, 100.00%. In the subsequent validation cohort (N=44), the AUCs (95% CI) were 0.83 (0.68, 0.93) and 0.88 (0.75, 0.96) for clinical model and laboratory model, respectively. CONCLUSIONS: We developed two predictive models for the in-hospital mortality of patients with COVID-19 in Wuhan and validated in patients from another center. url: https://doi.org/10.1093/cid/ciaa538 doi: 10.1093/cid/ciaa538 id: cord-280005-i9fp5rys author: Wang, Mengmei title: Treatment of COVID-19 Patients with Prolonged Post-Symptomatic Viral Shedding with Leflunomide -- a Single-Center, Randomized, Controlled Clinical Trial date: 2020-09-21 words: 3185.0 sentences: 172.0 pages: flesch: 49.0 cache: ./cache/cord-280005-i9fp5rys.txt txt: ./txt/cord-280005-i9fp5rys.txt summary: title: Treatment of COVID-19 Patients with Prolonged Post-Symptomatic Viral Shedding with Leflunomide -a Single-Center, Randomized, Controlled Clinical Trial CONCLUSIONS: In COVID-19 patients with prolonged PCR positivity, no benefit in terms of the duration of viral shedding was observed with the combined treatment of leflunomide and IFN α-2a beyond IFN α-2a alone. Based on that background, we conducted a prospective randomized, controlled, open-label trial, to evaluate the efficacy and safety of oral leflunomide to treat hospitalized COVID-19 patients with prolonged post-symptomatic viral shedding. Fifty eligible patients were randomly assigned to a combination treatment group that received leflunomide (50 mg, q12h, three consecutive times, orally; then 20 mg, once a day for 8 days; a total course of 10 days) plus nebulized IFN -2a (3 million IU each time, adding 2 ml of sterilized water, atomization inhalation twice daily for 10 days), or to a control group that received nebulized IFN -2a This was an open-label, prospective randomized, controlled trial, which was conducted at East Campus, Renmin Hospital of Wuhan University. abstract: OBJECTIVE: To evaluate the efficacy and safety of leflunomide, an approved dihydroorotate dehydrogenase inhibitor, to treat COVID-19 patients with prolonged post-symptomatic viral shedding. METHODS: We conducted a prospective, randomized, controlled, open-label trial involving hospitalized adult COVID-19 patients with prolonged PCR positivity. Patients were randomly assigned to receive either leflunomide (50 mg, q12h, three consecutive times, orally; then 20 mg, once daily for 8 days), in addition to nebulized interferon alpha 2a (IFN α-2a, 3 million IU each time, twice daily for 10 days), or nebulized IFN α-2a alone for 10 days. The primary end point was the duration of viral shedding. RESULTS: A total of 50 COVID-19 patients with prolonged PCR positivity were randomized into 2 groups; 26 were assigned to the leflunomide group, and 24 were assigned to the interferon alone group. Treatment with leflunomide was not associated with a difference from the interferon alone group in the duration of viral shedding (hazard ratio for negative RT-PCR, 0.70; 95% confidence interval, 0.391-1.256; P=0.186). In addition, the patients given leflunomide did not have a substantially shorter length of hospital stay than patients treated with interferon alone, with median (IQRs) durations of 29.0 (19.3-47.3) days and 33.0 (29.3-42.8) days, respectively, P=0.170. Two leflunomide recipients were unable to complete the full 10-day course of administration due to adverse events. CONCLUSIONS: In COVID-19 patients with prolonged PCR positivity, no benefit in terms of the duration of viral shedding was observed with the combined treatment of leflunomide and IFN α-2a beyond IFN α-2a alone. url: https://www.ncbi.nlm.nih.gov/pubmed/32955081/ doi: 10.1093/cid/ciaa1417 id: cord-294558-cqa58db8 author: Wang, Yubo title: Characterization of an asymptomatic cohort of SARS-COV-2 infected individuals outside of Wuhan, China date: 2020-05-22 words: 2858.0 sentences: 214.0 pages: flesch: 57.0 cache: ./cache/cord-294558-cqa58db8.txt txt: ./txt/cord-294558-cqa58db8.txt summary: BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, resulting in the coronavirus disease COVID-19) is highly transmissible among people. METHODS: We identified close contacts of confirmed COVID-19 cases in northeast Chongqing who were RT-PCR+ yet remained asymptomatic throughout their infections. In December 2019 a novel coronavirus, which was later named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), caused a large outbreak of infectious disease, designated COVID-19. Symptomatic COVID-19 patients and asymptomatic cases are both a source of infection and patients in the incubation period can transmit SARS-CoV-2 to other persons [7] [8] [9] [10] . Epidemiological data collection was achieved by interviewing each patient and their family members, including the dates and times of close contact with (working together, living or gathering) or to exposure individuals from the affected area (not only Wuhan) with confirmed or suspected SARS-CoV-2 infection. abstract: BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, resulting in the coronavirus disease COVID-19) is highly transmissible among people. Asymptomatic infections are also an important source of infection. Here, we aimed to further clarify the epidemiologic and clinical characteristics of asymptomatic SARS-CoV-2 infections. METHODS: We identified close contacts of confirmed COVID-19 cases in northeast Chongqing who were RT-PCR+ yet remained asymptomatic throughout their infections. We stratified this cohort by normal versus abnormal findings on chest CT, and compared the strata regarding comorbidities, demographics, laboratory findings, viral transmission and other factors. RESULTS: Between January and March, 2020, we identified and hospitalized 279 RT-PCR+ contacts of COVID-19 patients. Of these, 63 (23%) remained asymptomatic until discharge; 29 had abnormal and 34 had normal chest CT findings. The mean cohort age was 39.3 years, and 87.3% had no comorbidities. Mean time to diagnosis after close contact with a COVID-19 index patient was 16.0 days (range 1 to 29), and 13.4 days and 18.7 days for those with abnormal and normal CT findings, respectively (p < 0.05). Nine subjects (14.3%) transmitted the virus to others; 4 and 5 were in the abnormal and normal CT strata, respectively. The median length of nucleic acid turning negative in asymptomatic COVID-19 patients was 13 days, compared to 10.4 days in those with normal chest CT (p < 0.05). CONCLUSIONS: A portion of these asymptomatic individuals, with and without abnormal chest CT scans, were capable of transmitting the virus to others. Given the frequency and potential infectiousness of asymptomatic infections, testing of traced contacts is essential. Studies of the impact of treatment on asymptomatic RT-PCR+ individuals on disease progression and transmission should be undertaken. url: https://doi.org/10.1093/cid/ciaa629 doi: 10.1093/cid/ciaa629 id: cord-354009-1ek4s8oe author: Wang, Yun title: Spatiotemporal Characteristics of COVID-19 Epidemic in the United States date: 2020-07-08 words: 3143.0 sentences: 207.0 pages: flesch: 59.0 cache: ./cache/cord-354009-1ek4s8oe.txt txt: ./txt/cord-354009-1ek4s8oe.txt summary: We characterized the dynamics of COVID-19 epidemic through detecting weekly hotspots of newly confirmed cases using Spatial and Space-Time Scan Statistics and quantifying the trends of incidence of COVID-19 by county characteristics using the Joinpoint analysis. The results would enhance our understanding of small area-based spatiotemporal dynamics of COVID-19 outbreak, thus help inform multilevel strategies to control the spread of coronavirus and appropriate allocations of public health and healthcare resources in the United States. To identify the characteristics of counties with a high burden of COVID-19, we examined county-level geographic and sociodemographic factors, including rural-urban context, distance to the nearest core airport, population density, percentage of non-white minority population, percentage of population 65 years or older, and percentage of population below the federal poverty line. abstract: BACKGROUND: A range of near-real-time online/mobile mapping dashboards and applications have been used to track the COVID-19 pandemic worldwide. It remains unknown about small area-based spatiotemporal patterns of COVID-19 in the United States. METHODS: We obtained county-based counts of COVID-19 cases confirmed in the United States from January 22 to May 13, 2020 (N=1,386,050). We characterized the dynamics of COVID-19 epidemic through detecting weekly hotspots of newly confirmed cases using Spatial and Space-Time Scan Statistics and quantifying the trends of incidence of COVID-19 by county characteristics using the Joinpoint analysis. RESULTS: Along with the national plateau reached in early April, COVID-19 incidence significantly decreased in the Northeast (estimated weekly percentage changes [EWPC]: -16.6%), but remained increasing in the Midwest, South and West Regions (EWPCs: 13.2%, 5.6%, and 5.7%, respectively). Higher risks of clustering and incidence of COVID-19 were consistently observed in metropolitan vs rural counties, counties closest to core airports, most populous counties, and counties with highest proportion of racial/ethnic minority counties. However, geographic differences in the incidence have shrunk since early April, driven by a significant decrease in the incidence in these counties (EWPC range: -2.0% – -4.2%) and a consistent increase in other areas (EWPC range: 1.5% – 20.3%). CONCLUSIONS: To substantially decrease the nationwide incidence of COVID-19, strict social distancing measures should be continuously implemented, especially in geographic areas with increasing risks, including rural areas. Spatiotemporal characteristics and trends of COVID-19 should be considered in decision-making on the timeline of re-opening for states and localities. url: https://doi.org/10.1093/cid/ciaa934 doi: 10.1093/cid/ciaa934 id: cord-326138-16kpn9db author: Weinstein, Robert A. title: Laboratory-Acquired Infections date: 2009-07-01 words: 3648.0 sentences: 183.0 pages: flesch: 38.0 cache: ./cache/cord-326138-16kpn9db.txt txt: ./txt/cord-326138-16kpn9db.txt summary: Although the precise risk of infection after an exposure remains poorly defined, surveys of laboratory-acquired infections suggest that Brucella species, Shigella species, Salmonella species, Mycobacterium tuberculosis, and Neisseria meningitidis are the most common causes. Surveys of diagnostic laboratory workers in the United Kingdom conducted since 1971 have reported that tuberculosis and enteric infections (especially shigellosis) were the most common laboratory-acquired infections [7, 8] . Similar results were obtained from a survey of clinical microbiology laboratories in Utah from the period 1978-1992, with shigellosis reported to be the most common laboratory-acquired infection [10] . Although no controlled studies have been performed to assess the benefit of postexposure prophylaxis (PEP), it should be considered for laboratory workers who have high-risk exposure to Brucella species (e.g., because of direct manipulation of Brucella cultures outside of laminar-flow BSCs). Viral agents transmitted through blood and bodily fluids cause most of the laboratory-acquired infections in diagnostic laboratories and among health care workers [1] . abstract: Laboratory-acquired infections due to a wide variety of bacteria, viruses, fungi, and parasites have been described. Although the precise risk of infection after an exposure remains poorly defined, surveys of laboratory-acquired infections suggest that Brucella species, Shigella species, Salmonella species, Mycobacterium tuberculosis, and Neisseria meningitidis are the most common causes. Infections due to the bloodborne pathogens (hepatitis B virus, hepatitis C virus, and human immunodeficiency virus) remain the most common reported viral infections, whereas the dimorphic fungi are responsible for the greatest number of fungal infections. Because of the increasing attention on the role of the laboratory in bioterrorism preparation, I discuss the risk of laboratory-acquired infection with uncommon agents, such as Francisella tularensis and Bacillus anthracis. Physicians who care for a sick laboratory worker need to consider the likelihood of an occupationally acquired infection while advising exposed laboratory workers about postexposure prophylaxis. In addition, physicians should be aware of the importance of alerting the laboratory if infection with a high-risk agent is suspected. url: https://doi.org/10.1086/599104 doi: 10.1086/599104 id: cord-290133-4ou7ubb4 author: Weiss, Martin M. title: Rethinking Smallpox date: 2004-12-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The potential consequences of a competently executed smallpox attack have not been adequately considered by policy makers. The possibility of release of an aerosolized and/or bioengineered virus must be anticipated and planned for. The transmission and infectivity of variola virus are examined. Arguments for and against pre-event vaccination are offered. The likely morbidity and mortality that would ensue from implementation of a mass pre-event vaccination program, within reasonable boundaries, are known. The extent of contagion that could result from an aerosolized release of virus is unknown and may have been underestimated. Pre-event vaccination of first responders is urged, and voluntary vaccination programs should be offered to the public. Two defenses against a vaccine-resistant, engineered variola virus are proposed for consideration. Methisazone, an overlooked drug, is reported to be effective for prophylaxis only. The extent of reduction in the incidence of smallpox with use of this agent is uncertain. It is useless for treatment of clinical smallpox. N-100 respirators (face masks) worn by uninfected members of the public may prevent transmission of the virus. url: https://www.ncbi.nlm.nih.gov/pubmed/15578369/ doi: 10.1086/425745 id: cord-304487-ycvu5l5f author: Wertheim, Joel O title: A glimpse into the origins of genetic diversity in SARS-CoV-2 date: 2020-03-04 words: 1202.0 sentences: 74.0 pages: flesch: 43.0 cache: ./cache/cord-304487-ycvu5l5f.txt txt: ./txt/cord-304487-ycvu5l5f.txt summary: Evolution tinkers with these viruses in bats, and the epidemiological consequences are seen both in pathogenic zoonotic diseases (e.g., SARS, MERS, and COVID-19) and in the less-virulent circulating coronaviruses causing common colds. Molecular epidemiology can use the genetic variation of SARS-CoV-2 to trace its history and better understand clusters of transmission. However, deep-sequencing of viral genomes from 7 patients (including this probable transmission pair), the authors detect substantial variation in the number and frequency of minority variants within different individuals. The evolutionary history of MERS-CoV in its intermediate host, camels, is littered with recombination events [6] . However, as the number of infections increases and the circulating viruses become more genetically distinct, natural selection will become more efficient, making viral adaptation more of a possibility. For now, SARS-CoV-2 genetic variation is likely evolutionarily inconsequential and will be more important for facilitating molecular epidemiology in tracing the origins of novel clusters of viral infection. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32129842/ doi: 10.1093/cid/ciaa213 id: cord-276995-b003vcdc author: Wiese, Andrew D title: Social distancing measures: evidence of interruption of seasonal influenza activity and early lessons of the SARS-CoV-2 pandemic date: 2020-06-20 words: 818.0 sentences: 54.0 pages: flesch: 39.0 cache: ./cache/cord-276995-b003vcdc.txt txt: ./txt/cord-276995-b003vcdc.txt summary: And while novel surveillance systems have been implemented to monitor SARS-CoV-2 activity, pre-existing surveillance systems have the advantage of allowing comparison to trends in prior years to assess the impact of social distancing measures on the activity of influenza and other respiratory pathogens. In this issue of the journal, Hyunju Lee and colleagues describe the use of national influenza surveillance data to assess the impact of social distancing measures, implemented in response to the SARS-CoV-2 pandemic, on seasonal influenza activity in Korea. [1] [2] [3] In this study, investigators compared the A c c e p t e d M a n u s c r i p t While surveillance data are helpful to identify abnormal activity of certain diseases of public health interest, and to demonstrate the impact of major interventions, such as implementation of social distancing measures, it is important to understand the limitations and strengths of specific surveillance systems. abstract: nan url: https://doi.org/10.1093/cid/ciaa834 doi: 10.1093/cid/ciaa834 id: cord-327324-4c4a4bfz author: Wilkinson, Robert J title: Tuberculosis and type 2 Diabetes Mellitus: an inflammatory danger signal in the time of COVID-19 date: 2020-06-13 words: 872.0 sentences: 61.0 pages: flesch: 43.0 cache: ./cache/cord-327324-4c4a4bfz.txt txt: ./txt/cord-327324-4c4a4bfz.txt summary: title: Tuberculosis and type 2 Diabetes Mellitus: an inflammatory danger signal in the time of COVID-19 Active tuberculosis has a transcriptomic signature dominated by a neutrophil-driven type 1 and 2 interferoninducible gene profile. The exaggerated inflammation that characterizes HIV-tuberculosis-associated immune reconstitution inflammatory syndrome is triggered by Toll-like receptor and inflammasome signalling [14] . Male sex and diabetes have been identified in virtually every study as risk factors for severe COVID-19 infection, associated in the largest study to date with an adjusted hazard ratio for in-hospital death of 1.99 (male sex) and 1.50 for controlled (HbA1c < 58 mmol/mol) and 2.36 for uncontrolled DM [18] . Diabetes mellitus increases the risk of active tuberculosis: a systematic review of 13 observational studies HIV-tuberculosis-associated immune reconstitution inflammatory syndrome is characterized by Toll-like receptor and inflammasome signalling Complement pathway gene activation and rising circulating immune complexes characterize early disease in HIV-associated tuberculosis abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32533824/ doi: 10.1093/cid/ciaa747 id: cord-313693-qmkrn7pr author: Wong, Bonnie C. K. title: Possible Role of Aerosol Transmission in a Hospital Outbreak of Influenza date: 2010-11-15 words: 4196.0 sentences: 222.0 pages: flesch: 46.0 cache: ./cache/cord-313693-qmkrn7pr.txt txt: ./txt/cord-313693-qmkrn7pr.txt summary: Airflow measurements were conducted, and concentrations of hypothetical virus-laden aerosols at different ward locations were estimated using computational fluid dynamics modeling. A major nosocomial outbreak of severe acute respiratory syndrome (SARS) occurred at PWH in 2003 [15, 23] ; since then, all patients hospitalized with acute febrile respiratory illnesses are put on droplet precautions; if influenza is confirmed, the patients will be isolated or cohorted in designated wards [21, 22] . Dispersion of the hypothetical virus-laden aerosols, originated from the index patient''s bed through the entire ward, was analyzed by computational fluid dynamics (CFD) method. In clinical studies, virus-laden particles less than 5-6 mm (ie, within the respirable aerosol fraction) have been detected in exhaled breaths of patients with influenza and in the air sampled from an acute healthcare setting during seasonal peak [19, 35, 36] . In conclusion, our findings suggest a possible role of aerosol transmission of influenza in an acute ward setting. abstract: Background. We examined the role of aerosol transmission of influenza in an acute ward setting. Methods. We investigated a seasonal influenza A outbreak that occurred in our general medical ward (with open bay ward layout) in 2008. Clinical and epidemiological information was collected in real time during the outbreak. Spatiotemporal analysis was performed to estimate the infection risk among patients. Airflow measurements were conducted, and concentrations of hypothetical virus-laden aerosols at different ward locations were estimated using computational fluid dynamics modeling. Results. Nine inpatients were infected with an identical strain of influenza A/H3N2 virus. With reference to the index patient's location, the attack rate was 20.0% and 22.2% in the “same” and “adjacent” bays, respectively, but 0% in the “distant” bay (P=.04). Temporally, the risk of being infected was highest on the day when noninvasive ventilation was used in the index patient; multivariate logistic regression revealed an odds ratio of 14.9 (95% confidence interval, 1.7–131.3; P=.015). A simultaneous, directional indoor airflow blown from the “same” bay toward the “adjacent” bay was found; it was inadvertently created by an unopposed air jet from a separate air purifier placed next to the index patient's bed. Computational fluid dynamics modeling revealed that the dispersal pattern of aerosols originated from the index patient coincided with the bed locations of affected patients. Conclusions. Our findings suggest a possible role of aerosol transmission of influenza in an acute ward setting. Source and engineering controls, such as avoiding aerosol generation and improving ventilation design, may warrant consideration to prevent nosocomial outbreaks. url: https://doi.org/10.1086/656743 doi: 10.1086/656743 id: cord-318615-uhh3owcx author: Xiang, Fei title: Antibody Detection and Dynamic Characteristics in Patients with COVID-19 date: 2020-04-19 words: 2365.0 sentences: 133.0 pages: flesch: 53.0 cache: ./cache/cord-318615-uhh3owcx.txt txt: ./txt/cord-318615-uhh3owcx.txt summary: METHODS: The antibodies against SARS-CoV-2 were detected by an enzyme-linked immunosorbent assay (ELISA) based on the recombinant nucleocapsid protein of SARS-CoV-2 in patients with confirmed or suspected COVID-19 at 3-40 days after symptom onset. Here, we detected dynamics characteristics and magnitude of antibody response in patients with COVID-19, and evaluated serodiagnostic value of ELISA-based IgM, IgG tests for COVID-19 pneumonia. Detection of IgM and IgG Antibody on Different Periods (Table 2.) We evaluated specificity of IgM and IgG antibodies based on ELISA from 216 serum sample of 85 confirmed COVID-19 pneumonia patients. To evaluate the diagnostic potential of serological IgM and IgG antibodies detection, 66 patients with confirmed COVID-19 pneumonia were evaluated and compare to standard RT-PCR assays. * Specific IgM and IgG antibodies against SARS-CoV-2 from 216 serum samples of 85 confirmed COVID-19 pneumonia cases were tested with ELISA. abstract: BACKGROUND: The corona virus disease 2019 (COVID-19) caused by the corona virus 2 (SARS-CoV-2) has been rapidly spreading nationwide and abroad. A serologic test to identify antibody dynamics and response to SARS-CoV-2 was developed. METHODS: The antibodies against SARS-CoV-2 were detected by an enzyme-linked immunosorbent assay (ELISA) based on the recombinant nucleocapsid protein of SARS-CoV-2 in patients with confirmed or suspected COVID-19 at 3-40 days after symptom onset. The gold standard for COVID-19 diagnosis was nucleic acid testing for SARS-CoV-2 by RT-PCR. The serodiagnostic power of the specific IgM and IgG antibodies against SARS-CoV-2 was investigated in terms of sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and consistency rate. RESULTS: The seroconversion of specific IgM and IgG antibodies were observed as early as the 4(th) day after symptom onset. In the confirmed patients with COVID-19, sensitivity, specificity, PPV, NPV, and consistency rate of IgM were 77.3% (51/66), 100%, 100%, 80.0%, and 88.1%, and those of IgG were 83.3.3% (55/66), 95.0%, 94.8%, 83.8%, and 88.9 %. In patients with suspected COVID-19, sensitivity, specificity, PPV, NPV, and consistency rate of IgM were 87.5% (21/24), 100%, 100%, 95.2%, and 96.4%, and those of IgG were 70.8% (17/24), 96.6%, 85.0%, 89.1%, and 88.1%. Both antibodies performed well in serodiagnosis for COVID-19 rely on great specificity. CONCLUSIONS: The antibodies against SARS-CoV-2 can be detected in the middle and later stage of the illness. Antibody detection may play an important role in the diagnosis of COVID-19 as complement approach for viral nucleid acid assays. url: https://www.ncbi.nlm.nih.gov/pubmed/32306047/ doi: 10.1093/cid/ciaa461 id: cord-317948-svgguadm author: Xiao, Ai Tang title: Profile of RT-PCR for SARS-CoV-2: a preliminary study from 56 COVID-19 patients date: 2020-04-19 words: 1290.0 sentences: 96.0 pages: flesch: 58.0 cache: ./cache/cord-317948-svgguadm.txt txt: ./txt/cord-317948-svgguadm.txt summary: title: Profile of RT-PCR for SARS-CoV-2: a preliminary study from 56 COVID-19 patients To date, an outbreak of infectious diseases--coronavirus disease 2019 (COVID-19) associated with Severe Acute Respiratory Syndrome Coronavirus -2 (SARS-CoV-2) continues in Wuhan, China and threatens countries such as Korea, Italy, Iraq and Japan, etc. Currently no study reported the viral dynamics of SARS-CoV-2 infection in a long observation period. Therefore, we collected clinical specimens from 56 COVID-19 patients and reported the results of SARS-CoV-2 detection during the disease course. If two consecutive negative results were achieved, the period between symptoms onset and the date of first negative RT-PCR test result was defined as viral nucleic acid conversion time. In first 3 weeks after symptoms onset, majority results of RT-PCR for SARS-CoV-2 were positive. [14] [15] [16] This preliminary study has found evidence of the dynamic profile of SARS-CoV-2 in non-ICU COVID-19 patients during disease course. abstract: A novel coronavirus (COVID-19) pandemic threatens the world. Here, we first studied the dynamics profile of SARS-CoV-2 from 56 recovered COVID-19 patients. We found virus shedding was up to 6 weeks after onset of symptoms. Prolonged observation period is necessary for older patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32306036/ doi: 10.1093/cid/ciaa460 id: cord-266775-4npowkkz author: Xu, Jun title: Detection of Severe Acute Respiratory Syndrome Coronavirus in the Brain: Potential Role of the Chemokine Mig in Pathogenesis date: 2005-10-15 words: 3449.0 sentences: 167.0 pages: flesch: 46.0 cache: ./cache/cord-266775-4npowkkz.txt txt: ./txt/cord-266775-4npowkkz.txt summary: In the present study, we isolated a SARS coronavirus strain from a brain tissue specimen obtained from a patient with SARS with significant central nervous symptoms. In the present study, we isolated a SARS-CoV strain from a brain tissue specimen obtained during autopsy from a patient with SARS who became severely sick and showed significant central nervous symptoms during the course of his illness. Immunohistochemistry stains for N protein of severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) in a specimen of brain tissue obtained from the patient with SARS during autopsy. With regard to the superinfection with invasive Aspergillus in the brain and other organs of the patient, we think that severe immunodepression resulting from the damage to the immune system induced by SARS-CoV infection, combined with high-dosage treatment with a corticosteroid, provided access for conditional pathogens, causing a superinfection with invasive Aspergillus in multiple organs [24] . abstract: Background. Previous studies have shown that common human coronavirus might be neurotropic, although it was first isolated as a pathogen of the respiratory tract. We noticed that a few patients with severe acute respiratory syndrome (SARS) experienced central nervous symptoms during the course of illness. In the present study, we isolated a SARS coronavirus strain from a brain tissue specimen obtained from a patient with SARS with significant central nervous symptoms. Methods. Using transmission electronic microscopy and nested reverse transcription–polymerase chain reaction, the causative pathogen was identified in cultures of a brain tissue specimen obtained from the patient with SARS. Histopathologic examination of the brain tissue was performed using the methods of immunohistochemistry analysis and double immunofluorescence staining. Fifteen cytokines and chemokines were detected in the blood of the patient with SARS by means of a bead-based multiassay system. Results. A fragment specific for SARS human coronavirus was amplified from cultures of the brain suspension, and transmission electronic microscopy revealed the presence of an enveloped virus morphologically compatible with a coronavirus isolated in the cultures. Pathologic examination of the brain tissue revealed necrosis of neuron cells and broad hyperplasia of gliocytes. Immunostaining demonstrated that monokine induced by interferon-Γ (Mig) was expressed in gliocytes with the infiltration of CD68(+) monocytes/macrophages and CD3(+) T lymphocytes in the brain mesenchyme. Cytokine/chemokine assay revealed that levels of interferon-Γ–inducible protein 10 and Mig in the blood were highly elevated, although the levels of other cytokines and chemokines were close to normal. Conclusions. This study provides direct evidence that SARS human coronavirus is capable of infecting the central nervous system, and that Mig might be involved in the brain immunopathology of SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/16163626/ doi: 10.1086/444461 id: cord-007050-ibmr5bev author: Xu, Wei title: Serological Investigation of Subclinical Influenza A(H7H9) Infection Among Healthcare and Non–Healthcare Workers in Zhejiang Province, China date: 2013-09-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107925/ doi: 10.1093/cid/cit396 id: cord-300411-ppcdkfxq author: Xu, Xiao-Ke title: Reconstruction of Transmission Pairs for novel Coronavirus Disease 2019 (COVID-19) in mainland China: Estimation of Super-spreading Events, Serial Interval, and Hazard of Infection date: 2020-06-18 words: 1957.0 sentences: 140.0 pages: flesch: 55.0 cache: ./cache/cord-300411-ppcdkfxq.txt txt: ./txt/cord-300411-ppcdkfxq.txt summary: title: Reconstruction of Transmission Pairs for novel Coronavirus Disease 2019 (COVID-19) in mainland China: Estimation of Super-spreading Events, Serial Interval, and Hazard of Infection METHODS: A unique database with detailed demographic characteristics, travel history, social relationships, and epidemiological timelines for 1,407 transmission pairs that formed 643 transmission clusters in mainland China was reconstructed from 9,120 COVID-19 confirmed cases reported during January 15 February 29, 2020. CONCLUSIONS: Non-negligible frequency of super-spreading events, short serial intervals, and a higher risk of being infected outside of households for male people of working age indicate a significant barrier to the identification and management of COVID-19 cases, which requires enhanced non-pharmaceutical interventions to mitigate this pandemic. We have built a line-list database with detailed demographic information, travel history, epidemiological timelines, and social relationships for 1,407 transmission pairs that formed 643 transmission clusters in mainland China outside Hubei Province. abstract: BACKGROUND: Knowledge on the epidemiological features and transmission patterns of COVID-19 is accumulating. Detailed line-list data with household settings can advance the understanding of COVID-19 transmission dynamics. METHODS: A unique database with detailed demographic characteristics, travel history, social relationships, and epidemiological timelines for 1,407 transmission pairs that formed 643 transmission clusters in mainland China was reconstructed from 9,120 COVID-19 confirmed cases reported during January 15 - February 29, 2020. Statistical model fittings were used to identify the super-spreaders and estimate serial interval distributions. Age and gender-stratified hazard of infection were estimated for household versus non-household transmissions. RESULTS: There were 34 primary cases identified as super-spreaders, with 5 super-spreading events occurred within households. Mean and standard deviation of serial intervals were estimated as 5.0 (95% CrI: 4.4, 5.5) and 5.2 (95% CrI: 4.9, 5.7) days for household transmissions and 5.2 (95% CrI: 4.6, 5.8) and 5.3 (95% CrI: 4.9, 5.7) days for non-household transmissions, respectively. Hazard of being infected outside of households is higher for age between 18 and 64 years, whereas hazard of being infected within households is higher for young and old people. CONCLUSIONS: Non-negligible frequency of super-spreading events, short serial intervals, and a higher risk of being infected outside of households for male people of working age indicate a significant barrier to the identification and management of COVID-19 cases, which requires enhanced non-pharmaceutical interventions to mitigate this pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32556265/ doi: 10.1093/cid/ciaa790 id: cord-289247-qc3to2xj author: Yamaoka, Yutaro title: Whole nucleocapsid protein of SARS-CoV-2 may cause false positive results in serological assays date: 2020-05-23 words: 729.0 sentences: 58.0 pages: flesch: 62.0 cache: ./cache/cord-289247-qc3to2xj.txt txt: ./txt/cord-289247-qc3to2xj.txt summary: The nucleocapsid protein (NP) of SARS-CoV-2 is one of the widely used antigens in serodiagnostics of the novel Coronavirus disease . They have generated recombinant whole nucleocapsid protein (rNP) of SARS-CoV-2 using Escherichia coli expression system and used it to develop an enzyme linked immunosorbent assay (ELISA) to detect anti-SARS-CoV-2 antibodies in plasma. Although the amino acid sequences of the entire nucleocapsid proteins (NP) of SARS-CoV and other common Coronaviruses are dissimilar to that of SARS-CoV-2 [1] , the conserved residues at the Nterminal domain of NP show a high degree of similarity (Figure-1A) . Evaluation of inapparent nosocomial severe acute respiratory syndrome coronavirus infection in Vietnam by use of highly specific recombinant truncated nucleocapsid protein-based enzyme-linked immunosorbent assay Novel Immunoglobulin M Capture Enzyme-Linked Immunosorbent Assay for Diagnosis of Severe Acute Respiratory Syndrome Coronavirus Infection Development of Monoclonal Antibody and Diagnostic Test for Middle East Respiratory Syndrome Coronavirus Using Cell-Free Synthesized Nucleocapsid Antigen abstract: nan url: https://doi.org/10.1093/cid/ciaa637 doi: 10.1093/cid/ciaa637 id: cord-267152-m9m0aunk author: Yang, Philip title: Investigating the sex differences in COVID-19: Another step forward, but many unanswered questions date: 2020-06-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://doi.org/10.1093/cid/ciaa776 doi: 10.1093/cid/ciaa776 id: cord-353103-sdij1d90 author: Yao, Xueting title: In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date: 2020-03-09 words: 3449.0 sentences: 191.0 pages: flesch: 52.0 cache: ./cache/cord-353103-sdij1d90.txt txt: ./txt/cord-353103-sdij1d90.txt summary: title: In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Using the PBPK models, hydroxychloroquine concentrations in lung fluid were simulated under 5 different dosing regimens to explore the most effective regimen whilst considering the drug''s safety profile. Based on PBPK models results, a loading dose of 400 mg twice daily of hydroxychloroquine sulfate given orally, followed by a maintenance dose of 200 mg given twice daily for 4 days is recommended for SARS-CoV-2 infection, as it reached three times the potency of chloroquine phosphate when given 500 mg twice daily 5 days in advance. In this study we aimed to: (i) investigate the antiviral and prophylactic activity of hydroxychloroquine and chloroquine in vitro, (ii) build a PBPK model for hydroxychloroquine and chloroquine using data from literature, and, (iii) predict drug concentrations under different dosing regimens using the developed PBPK models. abstract: BACKGROUND: The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) first broke out in Wuhan (China) and subsequently spread worldwide. Chloroquine has been sporadically used in treating SARS-CoV-2 infection. Hydroxychloroquine shares the same mechanism of action as chloroquine, but its more tolerable safety profile makes it the preferred drug to treat malaria and autoimmune conditions. We propose that the immunomodulatory effect of hydroxychloroquine also may be useful in controlling the cytokine storm that occurs late-phase in critically ill SARS-CoV-2 infected patients. Currently, there is no evidence to support the use of hydroxychloroquine in SARS-CoV-2 infection. METHODS: The pharmacological activity of chloroquine and hydroxychloroquine was tested using SARS-CoV-2 infected Vero cells. Physiologically-based pharmacokinetic models (PBPK) were implemented for both drugs separately by integrating their in vitro data. Using the PBPK models, hydroxychloroquine concentrations in lung fluid were simulated under 5 different dosing regimens to explore the most effective regimen whilst considering the drug’s safety profile. RESULTS: Hydroxychloroquine (EC(50)=0.72 μM) was found to be more potent than chloroquine (EC(50)=5.47 μM) in vitro. Based on PBPK models results, a loading dose of 400 mg twice daily of hydroxychloroquine sulfate given orally, followed by a maintenance dose of 200 mg given twice daily for 4 days is recommended for SARS-CoV-2 infection, as it reached three times the potency of chloroquine phosphate when given 500 mg twice daily 5 days in advance. CONCLUSIONS: Hydroxychloroquine was found to be more potent than chloroquine to inhibit SARS-CoV-2 in vitro. url: https://www.ncbi.nlm.nih.gov/pubmed/32150618/ doi: 10.1093/cid/ciaa237 id: cord-317823-ztawznod author: Yehya, Nadir title: Statewide Interventions and Covid-19 Mortality in the United States: An Observational Study date: 2020-07-08 words: 3509.0 sentences: 228.0 pages: flesch: 56.0 cache: ./cache/cord-317823-ztawznod.txt txt: ./txt/cord-317823-ztawznod.txt summary: Historical analysis of the 1918-1919 influenza pandemic during the second wave of infections that examined 43 cities in the United States demonstrated an association between earlier school closures and bans on public gatherings with lower mortality [5] . Therefore, we assessed the association between the timing of emergency declarations and school closures, two specific statewide distancing measures, and subsequent Covid-19 mortality. Second, because deaths per million is a common method to compare localities, we provide an analysis testing the association between deaths per million at the state level after multivariable adjustment relative to timing of emergency declarations or statewide school closures. States implementing emergency declarations or school closures later in the course of the pandemic experienced higher Covid-19 mortality, with each day of delay increasing mortality risk 5 to 6%. abstract: BACKGROUND: Social distancing is encouraged to mitigate viral spreading during outbreaks. However, the association between distancing and patient-centered outcomes in Covid-19 has not been demonstrated. In the United States social distancing orders are implemented at the state level with variable timing of onset. Emergency declarations and school closures were two early statewide interventions. METHODS: To determine whether later distancing interventions were associated with higher mortality, we performed a state-level analysis in 55,146 Covid-19 non-survivors. We tested the association between timing of emergency declarations and school closures with 28-day mortality using multivariable negative binomial regression. Day 1 for each state was set to when they recorded ≥ 10 deaths. We performed sensitivity analyses to test model assumptions. RESULTS: At time of analysis, 37 of 50 states had ≥ 10 deaths and 28 follow-up days. Both later emergency declaration (adjusted mortality rate ratio [aMRR] 1.05 per day delay, 95% CI 1.00 to 1.09, p=0.040) and later school closure (aMRR 1.05, 95% CI 1.01 to 1.09, p=0.008) were associated with more deaths. When assessing all 50 states and setting day 1 to the day a state recorded its first death, delays in declaring an emergency (aMRR 1.05, 95% CI 1.01 to 1.09, p=0.020) or closing schools (aMRR 1.06, 95% CI 1.03 to 1.09, p<0.001) were associated with more deaths. Results were unchanged when excluding New York and New Jersey. CONCLUSIONS: Later statewide emergency declarations and school closure were associated with higher Covid-19 mortality. Each day of delay increased mortality risk 5 to 6%. url: https://www.ncbi.nlm.nih.gov/pubmed/32634828/ doi: 10.1093/cid/ciaa923 id: cord-256583-z3pd339v author: Yen, Muh-Yong title: Traffic Control Bundling Is Essential for Protecting Healthcare Workers and Controlling the 2014 Ebola Epidemic date: 2015-03-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/25512433/ doi: 10.1093/cid/ciu978 id: cord-310476-mhm7r3qc author: Yi, Huiguang title: 2019 novel coronavirus is undergoing active recombination date: 2020-03-04 words: 737.0 sentences: 48.0 pages: flesch: 48.0 cache: ./cache/cord-310476-mhm7r3qc.txt txt: ./txt/cord-310476-mhm7r3qc.txt summary: The single origin of 2019-nCov indicates a persistent animal to human transmission is unlikely, otherwise, multiple nodes with above characteristics should be observed. To quantify the significance of recombination over recurring sequencing error/mutations, Phi [6] and Max Chi-squared tests [7] in the software PhiPack [8] were performed. It showed p-values of 0.03 and 0.005 for Phi and Max Chi-squared, respectively, indicating the presence of recombinants in 2019-nCoV population. Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32130405/ doi: 10.1093/cid/ciaa219 id: cord-278045-hr3r17mz author: Yokota, Isao title: Mass screening of asymptomatic persons for SARS-CoV-2 using saliva date: 2020-09-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: COVID-19 has rapidly evolved to become a global pandemic due largely to the transmission of its causative virus through asymptomatic carriers. Detection of SARS-CoV-2 in asymptomatic people is an urgent priority for the prevention and containment of disease outbreaks in communities. However, few data are available in asymptomatic persons regarding the accuracy of PCR testing. Additionally, although self-collected saliva has significant logistical advantages in mass screening, its utility as an alternative specimen in asymptomatic persons is yet to be determined. METHODS: We conducted a mass-screening study to compare the utility of nucleic acid amplification, such as reverse transcriptase polymerase chain reaction (RT-PCR) testing, using nasopharyngeal swabs (NPS) and saliva samples from each individual in two cohorts of asymptomatic persons: the contact tracing cohort and the airport quarantine cohort. RESULTS: In this mass-screening study including 1,924 individuals, the sensitivity of nucleic acid amplification testing with nasopharyngeal and saliva specimens were 86% (90%CI:77-93%) and 92% (90%CI:83-97%), respectively, with specificities greater than 99.9%. The true concordance probability between the nasopharyngeal and saliva tests was estimated at 0.998 (90%CI:0.996-0.999) on the estimated airport prevalence at 0.3%. In positive individuals, viral load was highly correlated between NPS and saliva. CONCLUSION: Both nasopharyngeal and saliva specimens had high sensitivity and specificity. Self-collected saliva is a valuable specimen to detect SARS-CoV-2 in mass screening of asymptomatic persons. url: https://doi.org/10.1093/cid/ciaa1388 doi: 10.1093/cid/ciaa1388 id: cord-289598-t8upoq9a author: Yoon, Jane C title: COVID-19 Prevalence among People Experiencing Homelessness and Homelessness Service Staff during Early Community Transmission in Atlanta, Georgia, April–May 2020 date: 2020-09-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: In response to reported COVID-19 outbreaks among people experiencing homelessness (PEH) in other U.S. cities, we conducted multiple, proactive, facility-wide testing events for PEH living sheltered and unsheltered and homelessness service staff in Atlanta, Georgia. We describe SARS-CoV-2 prevalence and associated symptoms and review shelter infection prevention and control (IPC) policies METHODS: PEH and staff were tested for SARS-CoV-2 by reverse transcription polymerase chain reaction (RT-PCR) during April 7–May 6, 2020. A subset of PEH and staff was screened for symptoms. Shelter assessments were conducted concurrently at a convenience sample of shelters using a standardized questionnaire RESULTS: Overall, 2,875 individuals at 24 shelters and nine unsheltered outreach events underwent SARS-CoV-2 testing and 2,860 (99.5%) had conclusive test results. SARS-CoV-2 prevalence was 2.1% (36/1,684) among PEH living sheltered, 0.5% (3/628) among PEH living unsheltered, and 1.3% (7/548) among staff. Reporting fever, cough, or shortness of breath in the last week during symptom screening was 14% sensitive and 89% specific for identifying COVID-19 cases compared with RT-PCR. Prevalence by shelter ranged 0%–27.6%. Repeat testing 3–4 weeks later at four shelters documented decreased SARS-CoV-2 prevalence (0%–3.9%). Nine of 24 shelters completed shelter assessments and implemented IPC measures as part of the COVID-19 response CONCLUSIONS: PEH living in shelters experienced higher SARS-CoV-2 prevalence compared with PEH living unsheltered. Facility-wide testing in congregate settings allowed for identification and isolation of COVID-19 cases and is an important strategy to interrupt SARS-CoV-2 transmission url: https://doi.org/10.1093/cid/ciaa1340 doi: 10.1093/cid/ciaa1340 id: cord-258724-1qhen1bj author: Young, Barnaby E title: Viral dynamics and immune correlates of COVID-19 disease severity date: 2020-08-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Key knowledge gaps remain in the understanding of viral dynamics and immune response of SARS-CoV-2 infection. METHODS: We evaluated these characteristics and established their association with clinical severity in a prospective observational cohort study of 100 patients with PCR-confirmed SARS-CoV-2 infection (mean age 46 years, 56% male, 38% with comorbidities). Respiratory samples (n=74) were collected for viral culture, serum samples for measurement of IgM/IgG levels (n=30), and plasma samples for levels of inflammatory cytokines and chemokines (n=81). Disease severity was correlated with results from viral culture, serologic testing, and immune markers. RESULTS: 57 (57%) patients developed viral pneumonia, of whom 20 (20%) required supplemental oxygen including 12 (12%) invasive mechanical ventilation. Viral culture from respiratory samples was positive for 19 of 74 patients (26%). No virus was isolated when the PCR cycle threshold (Ct) value was >30 or >14 days after symptom onset. Seroconversion occurred at a median of 12.5 days (IQR 9-18) for IgM and 15.0 days (IQR 12-20) for IgG; 54/62 patients (87.1%) sampled at day 14 or later seroconverted. Severe infections were associated with earlier seroconversion and higher peak IgM and IgG levels. Levels of IP-10, HGF, IL-6, MCP-1, MIP-1α, IL-12p70, IL-18, VEGF-A, PDGF-BB and IL-1RA significantly correlated with disease severity. CONCLUSION: We found virus viability was associated with lower PCR Ct value in early illness. A stronger antibody response was associated with disease severity. The overactive proinflammatory immune signatures offers targets for host-directed immunotherapy which should be evaluated in randomised controlled trials. url: https://www.ncbi.nlm.nih.gov/pubmed/32856707/ doi: 10.1093/cid/ciaa1280 id: cord-294335-qnu19ru5 author: Yousaf, Anna R title: A prospective cohort study in non-hospitalized household contacts with SARS-CoV-2 infection: symptom profiles and symptom change over time date: 2020-07-28 words: 3221.0 sentences: 179.0 pages: flesch: 50.0 cache: ./cache/cord-294335-qnu19ru5.txt txt: ./txt/cord-294335-qnu19ru5.txt summary: We assessed symptoms reported by household contacts on the collection date of their first RT-PCRpositive NP specimen (Figure 1 , Subset A), and categorized symptoms as constitutional (fever, chills, myalgia, or fatigue), upper respiratory (runny nose, nasal congestion, or sore throat), lower respiratory (cough, difficulty breathing, shortness of breath, wheezing, or chest pain), neurologic (headache, loss of taste, or loss of smell), and gastrointestinal (nausea/vomiting, diarrhea, or abdominal pain). We identified and prospectively followed household contacts who were asymptomatic at the time they initially tested positive for SARS-CoV-2 by PCR ( Figure 1 , Subset B) to see if they developed symptoms during the study period. The symptom profiles and demographic characteristics of our cohort of SARS-CoV-2 RT-PCR positive household contacts differ from those described in inpatient populations [3] [4] [5] 12] . abstract: BACKGROUND: Improved understanding of SARS-CoV-2 spectrum of disease is essential for clinical and public health interventions. There are limited data on mild or asymptomatic infections, but recognition of these individuals is key as they contribute to viral transmission. We describe the symptom profiles from individuals with mild or asymptomatic SARS-CoV-2 infection. METHODS: From March 22 to April 22, 2020 in Wisconsin and Utah, we enrolled and prospectively observed 198 household contacts exposed to SARS-CoV-2. We collected and tested nasopharyngeal (NP) specimens by RT-PCR two or more times during a 14-day period. Contacts completed daily symptom diaries. We characterized symptom profiles on the date of first positive RT-PCR test and described progression of symptoms over time. RESULTS: We identified 47 contacts, median age 24 (3-75) years, with detectable SARS-CoV-2 by RT-PCR. The most commonly reported symptoms on the day of first positive RT-PCR test were upper respiratory (n=32, 68%) and neurologic (n=30, 64%); fever was not commonly reported (n=9, 19%). Eight (17%) individuals were asymptomatic at the date of first positive RT-PCR collection; two (4%) had preceding symptoms that resolved and six (13%) subsequently developed symptoms. Children less frequently reported lower respiratory symptoms (age <18: 21%, age 18-49: 60%, age 50+ years: 69%; p=0.03). CONCLUSIONS: Household contacts with lab-confirmed SARS-CoV-2 infection reported mild symptoms. When assessed at a single time-point, several contacts appeared to have asymptomatic infection; however, over time all developed symptoms. These findings are important to inform infection control, contact tracing, and community mitigation strategies. url: https://doi.org/10.1093/cid/ciaa1072 doi: 10.1093/cid/ciaa1072 id: cord-281726-s1o5l7ns author: Yu, Ignatius T. S. title: Temporal-Spatial Analysis of Severe Acute Respiratory Syndrome among Hospital Inpatients date: 2005-05-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Background. We report the temporal-spatial spread of severe acute respiratory syndrome (SARS) among inpatients in a hospital ward during a major nosocomial outbreak and discuss possible mechanisms for the outbreak. Methods. All inpatients who had stayed in the same ward as the initial index case patient for any duration before isolation were recruited into a cohort and followed up to document the occurrence of SARS. The normalized concentration of virus-laden aerosols at different locations of the ward was estimated by use of computational fluid dynamics modeling. The attack rates in the various subgroups stratified by bed location were calculated. Multivariate Cox proportional hazards regression was used to document important risk factors. Results. The overall attack rate of SARS was 41% (30 of 74 subjects). It was 65%, 52%, and 18% in the same bay, adjacent bay, and distant bays, respectively (P = .001). Computation fluid dynamics modeling indicated that the normalized concentration of virus-laden aerosols was highest in the same bay and lowest in the distant bays. Cox regression indicated that staying in the ward on 6 or 10 March entailed higher risk, as well as staying in the same or adjacent bays. The epidemic curve showed 2 peaks, and stratified analyses by bed location suggested >1 generation of spread. Conclusions. The temporal-spatial spread of SARS in the ward was consistent with airborne transmission, as modeled by use of computational fluid dynamics. Infected health care workers likely acted as secondary sources in the latter phase of the outbreak. url: https://www.ncbi.nlm.nih.gov/pubmed/15825024/ doi: 10.1086/428735 id: cord-339004-49dkucxd author: Yu, Ignatius Tak-Sun title: Severe Acute Respiratory Syndrome Beyond Amoy Gardens: Completing the Incomplete Legacy date: 2014-03-01 words: 1772.0 sentences: 78.0 pages: flesch: 55.0 cache: ./cache/cord-339004-49dkucxd.txt txt: ./txt/cord-339004-49dkucxd.txt summary: The temporal and spatial distributions of the 2003 severe acute respiratory syndrome (SARS) outbreak in Amoy Gardens of Hong Kong was reexamined using all confirmed cases. The temporal and spatial distributions of the 2003 severe acute respiratorysyndrome (SARS) outbreak in Amoy Gardens of Hong Kong was reexamined using all confirmed cases. In 2004, we analyzed the temporal and spatial distributions of the initial 187 cases in 7 blocks (A-G) of Amoy Gardens, a residential building complex with 19 buildings, where the largest community outbreak of SARS took place. Considering that cases in Telford Gardens and Tak Bo Garden with symptom onset during 24-29 March were most likely resulting from the common source originating in block E of Amoy Gardens, the distance of airborne transmission in that outbreak could be >200 m. In conclusion, the airborne spread in the largest community outbreak of SARS in 2003 actually extended beyond the Amoy Gardens and affected residential buildings >200 m from the source. abstract: The temporal and spatial distributions of the 2003 severe acute respiratory syndrome (SARS) outbreak in Amoy Gardens of Hong Kong was reexamined using all confirmed cases. The outbreak actually extended to nearby residential complexes. Airborne spread was the most likely explanation, and the SARS coronavirus could have spread over a distance of 200 m. url: https://www.ncbi.nlm.nih.gov/pubmed/24319085/ doi: 10.1093/cid/cit797 id: cord-325416-c0qj3yd9 author: Zachariah, Philip title: Symptomatic Infants have Higher Nasopharyngeal SARS-CoV-2 Viral Loads but Less Severe Disease than Older Children date: 2020-05-20 words: 502.0 sentences: 59.0 pages: flesch: 67.0 cache: ./cache/cord-325416-c0qj3yd9.txt txt: ./txt/cord-325416-c0qj3yd9.txt summary: title: Symptomatic Infants have Higher Nasopharyngeal SARS-CoV-2 Viral Loads but Less Severe Disease than Older Children A report published in this journal described the presence of a high nasopharyngeal (NP) viral load of severe acute respiratory coronavirus 2 (SARS-CoV-2) in a well infant [4] . While some data have suggested a higher disease severity in infants [2, 6] , how NP viral load correlates with severity across the pediatric age spectrum has not been firmly established. For each patient, we extracted age, time from reported symptom onset to the date of test, and severity of disease during hospitalization. Our report suggests symptomatic infants have higher NP viral loads at presentation but develop less severe disease as compared to older children and adolescents. A Well Infant with Coronavirus Disease 2019 (COVID-19) with High Viral Load Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32433729/ doi: 10.1093/cid/ciaa608 id: cord-345045-nlui9d6e author: Zahn, Matthew title: Infectious Diseases Physicians: Improving and Protecting the Public’s Health: Why Equitable Compensation Is Critical date: 2019-07-15 words: 3570.0 sentences: 170.0 pages: flesch: 37.0 cache: ./cache/cord-345045-nlui9d6e.txt txt: ./txt/cord-345045-nlui9d6e.txt summary: Unfortunately, much of this work is undercompensated despite the proven efficacy of public health interventions such as hospital acquired infection prevention, antimicrobial stewardship, disease surveillance, and outbreak response. Here, we examine compensation data for ID physicians compared to their value in population and public health settings and suggest policy recommendations to address the pay disparities that exist between cognitive and procedural specialties that prevent more medical students and residents from entering the field. In 2015, 8515 ID physicians were practicing in the United States [5] , often combining clinical care with work as educators, epidemiologists, public health leaders, antimicrobial stewardship or infection prevention and control directors, researchers, administrators, and policymakers. Further, the work of ID physicians provides broader public protection against infectious threats through community and healthcare facility-based infection control and prevention activities, surveillance, outbreak response, and other public health activities. abstract: Infectious diseases (ID) physicians play a crucial role in public health in a variety of settings. Unfortunately, much of this work is undercompensated despite the proven efficacy of public health interventions such as hospital acquired infection prevention, antimicrobial stewardship, disease surveillance, and outbreak response. The lack of compensation makes it difficult to attract the best and the brightest to the field of ID, threatening the future of the ID workforce. Here, we examine compensation data for ID physicians compared to their value in population and public health settings and suggest policy recommendations to address the pay disparities that exist between cognitive and procedural specialties that prevent more medical students and residents from entering the field. All ID physicians should take an active role in promoting the value of the subspecialty to policymakers and influencers as well as trainees. url: https://doi.org/10.1093/cid/ciy888 doi: 10.1093/cid/ciy888 id: cord-283780-h4lwzpl9 author: Zhang, John J Y title: Risk Factors of Severe Disease and Efficacy of Treatment in Patients Infected with COVID-19: A Systematic Review, Meta-Analysis and Meta-Regression Analysis date: 2020-05-14 words: 3118.0 sentences: 221.0 pages: flesch: 50.0 cache: ./cache/cord-283780-h4lwzpl9.txt txt: ./txt/cord-283780-h4lwzpl9.txt summary: title: Risk Factors of Severe Disease and Efficacy of Treatment in Patients Infected with COVID-19: A Systematic Review, Meta-Analysis and Meta-Regression Analysis We conducted a systematic review and meta-analysis of all published studies up to March 15, 2020 which reported COVID-19 clinical features and/or treatment outcomes. To address this gap in the literature, we conducted a systematic review, meta-analysis and meta-regression to 1) investigate the predictive value of laboratory investigations for severe disease and adverse outcomes, and 2) evaluate the efficacy of antivirals and corticosteroids for COVID-19. Among the patients with antiviral use reported in our meta-analysis, overall rates of mortality, ICU admission and ARDS were 5.7%, 11.8% and 20.2%, respectively. Our meta-analysis suggested that the use of corticosteroids is associated with disease severity (ICU admission) and higher ARDS rates. To the best of our knowledge, this is the first systematic review and meta-analysis of COVID-19 to describe specific laboratory predictors of severe disease and adverse outcomes. abstract: The coronavirus disease 2019 (COVID-19) pandemic spread globally in the beginning of 2020. At present, predictors of severe disease and the efficacy of different treatments are not well-understood. We conducted a systematic review and meta-analysis of all published studies up to March 15, 2020 which reported COVID-19 clinical features and/or treatment outcomes. 45 studies reporting 4203 patients were included. Pooled rates of intensive care unit (ICU) admission, mortality and acute respiratory distress syndrome (ARDS) were 10.9%, 4.3% and 18.4%, respectively. On meta-regression, ICU admission was predicted by raised leukocyte count (p<0.0001), raised alanine aminotransferase (p=0.024), raised aspartate transaminase (p=0.0040), elevated lactate dehydrogenase (LDH) (p<0.0001) and increased procalcitonin (p<0.0001). ARDS was predicted by elevated LDH (p<0.0001), while mortality was predicted by raised leukocyte count (p=0.0005) and elevated LDH (p<0.0001). Treatment with lopinavir-ritonavir showed no significant benefit in mortality and ARDS rates. Corticosteroids were associated with a higher rate of ARDS (p=0.0003). url: https://www.ncbi.nlm.nih.gov/pubmed/32407459/ doi: 10.1093/cid/ciaa576 id: cord-285403-h8ahn8fw author: Zhang, Liangsheng title: Origin and Evolution of the 2019 Novel Coronavirus date: 2020-02-03 words: 830.0 sentences: 48.0 pages: flesch: 57.0 cache: ./cache/cord-285403-h8ahn8fw.txt txt: ./txt/cord-285403-h8ahn8fw.txt summary: To the Editor-The 2019 novel coronavirus disease (2019-nCoV or COVID-19) recently reported from Wuhan (China), which has cases in Thailand, Japan, South Korea, and the United States, has been confirmed as a new coronavirus [1] . Based on our phylogenomic analysis of the recently released genomic data of 2019-nCoV, we showed that the 2019-nCoV is most closely related to 2 severe acute respiratory syndrome (SARS)-like CoV sequences that were isolated in bats during 2015 to 2017 [2] , suggesting that the bats'' CoV and the human 2019-nCoV share a recent common ancestor ( Figure 1A) . This market also sells wild animals or mammals, which were likely intermediate hosts of 2019-nCoV, which originated from bat hosts ( Figure 1B ). The 2019-nCoVs have long branches (0.09) for the 2 isolated in the phylogenomic tree ( Figure 1A) , indicating that the 2019-nCoVs likely share bat hosts. There were 3 genotypes present in samples from Guangdong province, indicating that the 6 strains were infected from different places in Wuhan. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32011673/ doi: 10.1093/cid/ciaa112 id: cord-330214-28ah3nig author: Zhao, Jiao title: Relationship between the ABO Blood Group and the COVID-19 Susceptibility date: 2020-08-04 words: 1109.0 sentences: 72.0 pages: flesch: 64.0 cache: ./cache/cord-330214-28ah3nig.txt txt: ./txt/cord-330214-28ah3nig.txt summary: To explore any relationship between the ABO blood group and the COVID-19 susceptibility, we compared ABO blood group distributions in 2,173 COVID-19 patients with local control populations, and found that blood group A was associated with an increased risk of infection, whereas group O was associated with a decreased risk. Here, we investigated the relationship between the ABO blood type and the susceptibility to COVID-19 in patients from three hospitals in Wuhan and Shenzhen, China. These results showed associations between ABO blood groups and COVID-19 susceptibility. The COVID-19 risk significantly increased for blood group A ( Figure 1 shows the estimates of ORs of the risk of ABO blood groups for COVID-19 on the pooled data from the three hospitals by random effects models. In this study, we found that ABO blood groups displayed different association risks for the infection with SARS-CoV-2 resulting in COVID-19. In the 285 patients from Shenzhen, we also found that blood group AB had an increased risk of infection. abstract: To explore any relationship between the ABO blood group and the COVID-19 susceptibility, we compared ABO blood group distributions in 2,173 COVID-19 patients with local control populations, and found that blood group A was associated with an increased risk of infection, whereas group O was associated with a decreased risk. url: https://www.ncbi.nlm.nih.gov/pubmed/32750119/ doi: 10.1093/cid/ciaa1150 id: cord-321873-9l9zp6gm author: Zhou, Bo title: The duration of viral shedding of discharged patients with severe COVID-19 date: 2020-04-17 words: 608.0 sentences: 49.0 pages: flesch: 64.0 cache: ./cache/cord-321873-9l9zp6gm.txt txt: ./txt/cord-321873-9l9zp6gm.txt summary: title: The duration of viral shedding of discharged patients with severe COVID-19 However, little studies have focused on clinical characteristics of discharged patients with severe COVID-19, especially the duration of viral shedding. The RT-PCR tests were performed on throat swabs following a previously described method 3 Moreover, another study displayed that four patients with COVID-19 who met the criteria for hospital discharge in China had positive RT-PCR test results 5 to 13 days later 6 , suggesting that recovered patients might still be virus carriers. Based on the results, we did not observe shortening of viral shedding time in the above groups, so it implied that all patients with severe COVID-19 should complete adequate course of treatment, regardless of sex and age. Clinical features of patients infected with 2019 novel coronavirus in Wuhan Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study abstract: The 2019 coronavirus disease (COVID-19) has drawn global intensive attention(1-3). Most of studies paid attention to epidemiological, clinical, and radiological features of inpatients with COVID-19(1-3). However, little studies have focused on clinical characteristics of discharged patients with severe COVID-19, especially the duration of viral shedding. url: https://www.ncbi.nlm.nih.gov/pubmed/32302000/ doi: 10.1093/cid/ciaa451 id: cord-266696-w9sb038q author: Zhou, Yi-Hua title: Is the Immune System Impaired in Patients with Severe Acute Respiratory Syndrome? date: 2004-03-15 words: 1306.0 sentences: 67.0 pages: flesch: 56.0 cache: ./cache/cord-266696-w9sb038q.txt txt: ./txt/cord-266696-w9sb038q.txt summary: [1] recently described pronounced lymphopenia and low counts of CD4 + cells, CD8 + cells, and B cells in patients with severe acute respiratory syndrome (SARS). Low counts of both CD4 + and CD8 + cells in the peripheral circulation do not always indicate that the immune system is impaired: redistribution of lymphocytes among peripheral and secondary lymphoid organs and migration of these cells to inflamed tissues caused by infections may also result in lymphopenia. We believe that Zhou and Chen [1] need more data to support their conclusion that the immune function of B cells in our patients appeared not to be impaired because specific anti-SARS-CoV could be detected as early as 10 days after the onset of illness. Is the immune system impaired in patients with severe acute respiratory syndrome The clinical pathology of severe acute respiratory syndrome (SARS): a report from China abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/14999642/ doi: 10.1086/382081 id: cord-349566-zx9kt144 author: de Alencar, Julio Cesar Garcia title: Double-blind, randomized, placebo-controlled trial with N-acetylcysteine for treatment of severe acute respiratory syndrome caused by COVID-19 date: 2020-09-23 words: 2957.0 sentences: 213.0 pages: flesch: 55.0 cache: ./cache/cord-349566-zx9kt144.txt txt: ./txt/cord-349566-zx9kt144.txt summary: title: Double-blind, randomized, placebo-controlled trial with N-acetylcysteine for treatment of severe acute respiratory syndrome caused by COVID-19 There is still no robust experimental confirmation for this fact; however, increased serum AngII levels have been reported in patients with severe Covid-19 cases [7] and enhanced expression of ACE2 in adults, compared to children, has been advocated to cause the difference of disease prevalence in these age ranges [8] . Therefore, we designed a double-blind, placebo-controlled, randomized clinical trial to determine whether NAC (in doses used to treat acute liver failure), is able to protect alveolar cells and avoid respiratory failure in patients with severe acute respiratory syndrome caused by (confirmed or suspect) Covid-19. This is a double-blind, randomized, placebo-controlled trial to assess the effectiveness and safety of intravenous NAC to prevent respiratory failure in patients with confirmed or suspect severe Covid-19. abstract: BACKGROUND: A local increase in angiotensin 2 after inactivation of angiotensin-converting enzyme 2 by SARS-CoV-2 may induce a redox imbalance in alveolar epithelium cells, causing apoptosis, increased inflammation and, consequently, impaired gas exchange. We hypothesized that N-acetylcysteine (NAC) administration could restore this redox homeostasis and suppress unfavorable evolution in Covid-19 patients. OBJECTIVE: To determine whether NAC in high doses can avoid respiratory failure in patients with Covid-19. METHODS: It was a double-blind, randomized, placebo-controlled, unicentric trial, conducted at the Emergency Department of Hospital das Clínicas, São Paulo, Brazil. We enrolled 135 patients with severe Covid-19 (confirmed or suspected), with an oxyhemoglobin saturation of less than 94% or respiratory rate higher than 24 breaths/min. Patients were randomized to receive NAC 21 g (approximately 300 mg/kg) for 20 hours, or dextrose 5%. Primary endpoint was the need for mechanical ventilation. Secondary endpoints were time of mechanical ventilation, admission to ICU, time in ICU, and mortality. RESULTS: Baseline characteristics were very similar in the two groups, with no significant difference in age, sex, comorbidities, medicines taken, and disease severity. Also, groups were similar in laboratory tests and chest CT scan findings. Sixteen patients (23.9%) in the Placebo group were submitted to endotracheal intubation and mechanical ventilation, compared to 14 patients (20.6%) in the NAC group (p=0.675). No difference was observed in secondary endpoints. CONCLUSION: Administration of NAC in high doses did not affect the evolution of severe Covid-19. url: https://doi.org/10.1093/cid/ciaa1443 doi: 10.1093/cid/ciaa1443 id: cord-292372-kn27ghlv author: de Chaisemartin, Clément title: BCG vaccination in infancy does not protect against COVID-19. Evidence from a natural experiment in Sweden date: 2020-08-23 words: 2819.0 sentences: 151.0 pages: flesch: 56.0 cache: ./cache/cord-292372-kn27ghlv.txt txt: ./txt/cord-292372-kn27ghlv.txt summary: Instead, this paper takes advantage of a rare nationwide natural experiment that took place in Sweden in 1975, where discontinuation of newborns BCG vaccination led to a dramatic fall of the BCG coverage rate, thus allowing us to estimate the BCG''s effect without the biases associated with cross-country comparisons. found that countries with universal Bacillus Calmette-Guérin (BCG) childhood vaccination policies tend to be less affected by the COVID-19 pandemic, in terms of their number of cases and deaths [7] . In this study, we took advantage of a change in vaccination policy in Sweden to investigate the link between BCG vaccination in infancy and Covid-19 cases, hospitalizations and deaths, using a regression discontinuity approach. For instance, this study estimates the effect of universal BCG vaccination for individuals born around April 1st 1975, who are in their mid-forties during the COVID-19 pandemic, and cannot be generalized to the entire population. abstract: BACKGROUND: The Bacille Calmette-Guérin (BCG) tuberculosis vaccine has immunity benefits against respiratory infections. Accordingly, it has been hypothesized to have a protective effect against COVID-19. Recent research found that countries with universal BCG childhood vaccination policies tend to be less affected by the COVID-19 pandemic. However, such ecological studies are biased by numerous confounders. Instead, this paper takes advantage of a rare nationwide natural experiment that took place in Sweden in 1975, where discontinuation of newborns BCG vaccination led to a dramatic fall of the BCG coverage rate, thus allowing us to estimate the BCG’s effect without the biases associated with cross-country comparisons. METHODS: Numbers of COVID-19 cases and hospitalizations were recorded for birth cohorts born just before and just after 1975, representing 1,026,304 and 1,018,544 individuals, respectively. We used regression discontinuity to assess the effect of BCG vaccination on Covid-19 related outcomes. This method used on such a large population allows for a high precision that would be hard to achieve using a randomized controlled trial. RESULTS: The odds ratio for Covid-19 cases and Covid-19 related hospitalizations were 1·0005 (CI95: [0·8130-1·1881]) and 1·2046 (CI95: [0·7532-1·6560]), allowing us to reject fairly modest effects of universal BCG vaccination. We can reject with 95% confidence that universal BCG vaccination reduces the number of cases by 19% and the number of hospitalizations by 25%. CONCLUSIONS: While the effect of a recent vaccination must be evaluated, we provide strong evidence that receiving the BCG vaccine at birth does not have a protective effect against COVID-19 among middle-aged individuals. url: https://doi.org/10.1093/cid/ciaa1223 doi: 10.1093/cid/ciaa1223 id: cord-296631-43z3ee8m author: de Feria, Alejandro title: ACE inhibitors/ARB use and COVID-19. Time to change practice or keep gathering data? date: 2020-07-04 words: 896.0 sentences: 70.0 pages: flesch: 60.0 cache: ./cache/cord-296631-43z3ee8m.txt txt: ./txt/cord-296631-43z3ee8m.txt summary: This mechanism of entry, in combination with the findings of the previously mentioned risk factors, raised concerns that angiotensin-converting enzyme inhibitors (ACEi) and angiotensin receptor blockers (ARBs) could increase both the susceptibility and severity of SARS CoV-2 infection. An international, multicenter study which included electronic records from 169 hospitals in 11 countries on three continents again confirmed that advanced age (>65), heart failure, coronary disease, and hypertension (among other factors) increased risk for in hospital mortality with COVID-19, but ACEi/ARB therapy showed no harm [4] . In contrast to these findings, early studies out of China suggested that ARB therapy may improve clinical outcomes in COVID-19 infection [5, 6] . The current study is unique in that it focuses on patients with "severe COVID" disease and found that chronic ACE inhibitor and ARB use was associated with an increased risk of acute kidney injury, as well as a signal for a dosage effect. abstract: nan url: https://doi.org/10.1093/cid/ciaa819 doi: 10.1093/cid/ciaa819 id: cord-335907-93gwmo0v author: de Man, Peter title: Outbreak of COVID-19 in a nursing home associated with aerosol transmission as a result of inadequate ventilation date: 2020-08-28 words: 564.0 sentences: 57.0 pages: flesch: 73.0 cache: ./cache/cord-335907-93gwmo0v.txt txt: ./txt/cord-335907-93gwmo0v.txt summary: title: Outbreak of COVID-19 in a nursing home associated with aerosol transmission as a result of inadequate ventilation Recently, we were involved in an outbreak in a Dutch nursing home that was likely to be the result of aerosol transmission in a setting of inadequate ventilation. In total, 17 (81%) residents from one of the seven wards in a nursing home with psychogeriatric residents were diagnosed with COVID-19 as confirmed by RT-PCR ( Figure 1 ) [2] . To prevent and control COVID-19 infections all HCWs in this nursing home had been assigned to specific wards and did wear surgical masks during patient contacts since April 26, 2020 [4] . Because of the remarkable increase of COVID-19 infections in a very short time period despite the use of surgical masks, the ventilation system of the outbreak ward was investigated in addition to routine source and contact tracing. In this situation, low CO2 production by inactive nursing home patients might have limited the ventilation with outside air. abstract: nan url: https://doi.org/10.1093/cid/ciaa1270 doi: 10.1093/cid/ciaa1270 id: cord-015516-hx7ktq8j author: nan title: In the Literature date: 2005-10-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107963/ doi: 10.1086/497097 id: cord-260779-riw5xs3j author: van Griensven, Johan title: The Use of Ebola Convalescent Plasma to Treat Ebola Virus Disease in Resource-Constrained Settings: A Perspective From the Field date: 2016-01-01 words: 3825.0 sentences: 199.0 pages: flesch: 46.0 cache: ./cache/cord-260779-riw5xs3j.txt txt: ./txt/cord-260779-riw5xs3j.txt summary: The clinical evaluation of convalescent plasma (CP) for the treatment of Ebola virus disease (EVD) in the current outbreak, predominantly affecting Guinea, Sierra Leone, and Liberia, was prioritized by the World Health Organization in September 2014. The World Health Organization (WHO) guidelines recommend both convalescent whole blood (CWB) and CP for use against Ebola virus disease (EVD) [12] . Blood transfusion is routinely done in all 3 high-transmission countries involved in the current EVD outbreak; however, plasma has numerous advantages in these settings. Use of convalescent whole blood or plasma collected from patients recovered from Ebola virus disease for transfusion, as an empirical treatment during outbreaks. Treatment of Ebola hemorrhagic fever with blood transfusions from convalescent patients. Clinical trial to evaluate the efficacy and safety of convalescent plasma for Ebola treatment (EVD001). Acute respiratory distress syndrome after convalescent plasma use: treatment of a patient with Ebola virus disease Large-scale convalescent blood and plasma transfusion therapy for Ebola virus disease abstract: The clinical evaluation of convalescent plasma (CP) for the treatment of Ebola virus disease (EVD) in the current outbreak, predominantly affecting Guinea, Sierra Leone, and Liberia, was prioritized by the World Health Organization in September 2014. In each of these countries, nonrandomized comparative clinical trials were initiated. The Ebola-Tx trial in Conakry, Guinea, enrolled 102 patients by 7 July 2015; no severe adverse reactions were noted. The Ebola-CP trial in Sierra Leone and the EVD001 trial in Liberia have included few patients. Although no efficacy data are available yet, current field experience supports the safety, acceptability, and feasibility of CP as EVD treatment. Longer-term follow-up as well as data from nontrial settings and evidence on the scalability of the intervention are required. CP sourced from within the outbreak is the most readily available source of anti-EVD antibodies. Until the advent of effective antivirals or monoclonal antibodies, CP merits further evaluation. url: https://www.ncbi.nlm.nih.gov/pubmed/26261205/ doi: 10.1093/cid/civ680 id: cord-259243-1lkzcslx author: Álvarez-Aragón, Luis Miguel title: Inquiring into Benefits of Independent Activation of Non-Classical Renin-Angiotensin System in the Clinical Prognosis and Reduction of COVID-19 mortality date: 2020-04-08 words: 755.0 sentences: 54.0 pages: flesch: 53.0 cache: ./cache/cord-259243-1lkzcslx.txt txt: ./txt/cord-259243-1lkzcslx.txt summary: title: Inquiring into Benefits of Independent Activation of Non-Classical Renin-Angiotensin System in the Clinical Prognosis and Reduction of COVID-19 mortality We have read with great interest the elegant manuscript by Hanff et al [1] proposing a very interesting association between the classical renin-angiotensin system (RAS) and angiotensinconverting enzyme 2 (ACE2) dysregulation present in cardiovascular disease (CVD) and the high mortality index in patients with CVD and coronavirus disease 2019 (COVID-19). On the one hand, it will decrease the proinflammatory effect of Angiotensin II with its subsequent benefit on decreasing the risk of acute respiratory distress syndrome (ARDS) observed in these patients, and on the other hand, it will increase ACE2 expression and therefore the virulence of SARS-Cov2. In addition, in vitro studies in human renal cells treated with SLGT2 inhibitors have shown an increment in Angiotensin(1-7) due to the independent activation of the non-classical RES, leading to important anti-inflammatory and anti-M a n u s c r i p t fibrotic effects [6, 7] . abstract: nan url: https://doi.org/10.1093/cid/ciaa402 doi: 10.1093/cid/ciaa402 ==== 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