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Tatro, Grant; Poltavskiy, Eduard; Mooso, Benjamin; Hon, Simson; Bang, Heejung; Polage, Christopher title: Rapid Multiplex Testing for Upper Respiratory Pathogens in the Emergency Department: A Randomized Controlled Trial date: 2019-11-05 journal: Open Forum Infect Dis DOI: 10.1093/ofid/ofz481 sha: doc_id: 347255 cord_uid: fl9lur4h file: cache/cord-347465-yu6oj30v.json key: cord-347465-yu6oj30v authors: Kurskaya, Olga; Ryabichenko, Tatyana; Leonova, Natalya; Shi, Weifeng; Bi, Hongtao; Sharshov, Kirill; Kazachkova, Eugenia; Sobolev, Ivan; Prokopyeva, Elena; Kartseva, Tatiana; Alekseev, Alexander; Shestopalov, Alexander title: Viral etiology of acute respiratory infections in hospitalized children in Novosibirsk City, Russia (2013 – 2017) date: 2018-09-18 journal: PLoS One DOI: 10.1371/journal.pone.0200117 sha: doc_id: 347465 cord_uid: yu6oj30v file: cache/cord-344889-1y4ieamp.json key: cord-344889-1y4ieamp authors: Cameron, Robert J.; de Wit, Deo; Welsh, Toni N.; Ferguson, John; Grissell, Terry V.; Rye, Peter J. title: Virus infection in exacerbations of chronic obstructive pulmonary disease requiring ventilation date: 2006-05-24 journal: Intensive Care Med DOI: 10.1007/s00134-006-0202-x sha: doc_id: 344889 cord_uid: 1y4ieamp file: cache/cord-342853-n3e6yawi.json key: cord-342853-n3e6yawi authors: Naghipour, Mohammadreza; Cuevas, Luis E.; Bakhshinejad, Tahereh; Dove, Winifred; Hart, C. Anthony title: Human bocavirus in Iranian children with acute respiratory infections date: 2007-03-26 journal: J Med Virol DOI: 10.1002/jmv.20815 sha: doc_id: 342853 cord_uid: n3e6yawi file: cache/cord-343325-cbrly7f5.json key: cord-343325-cbrly7f5 authors: Denault, André Y.; Delisle, Stéphane; Canty, David; Royse, Alistair; Royse, Colin; Serra, Ximena Cid; Gebhard, Caroline E.; Couture, Étienne J.; Girard, Martin; Cavayas, Yiorgos Alexandros; Peschanski, Nicolas; Langevin, Stéphan; Ouellet, Paul title: A proposed lung ultrasound and phenotypic algorithm for the care of COVID-19 patients with acute respiratory failure date: 2020-05-21 journal: Can J Anaesth DOI: 10.1007/s12630-020-01704-6 sha: doc_id: 343325 cord_uid: cbrly7f5 file: cache/cord-344271-5aynmdsk.json key: cord-344271-5aynmdsk authors: de Souza Luna, Luciano Kleber; Panning, Marcus; Grywna, Klaus; Pfefferle, Susanne; Drosten, Christian title: Spectrum of Viruses and Atypical Bacteria in Intercontinental Air Travelers with Symptoms of Acute Respiratory Infection date: 2007-03-01 journal: J Infect Dis DOI: 10.1086/511432 sha: doc_id: 344271 cord_uid: 5aynmdsk file: cache/cord-346290-my8ow5ee.json key: cord-346290-my8ow5ee authors: Nelson, Philipp P.; Papadopoulos, Nikolaos G.; Skevaki, Chrysanthi title: Respiratory Viral Pathogens date: 2020-05-28 journal: Reference Module in Biomedical Sciences DOI: 10.1016/b978-0-12-801238-3.11635-6 sha: doc_id: 346290 cord_uid: my8ow5ee file: cache/cord-347509-2ysw9a0a.json key: cord-347509-2ysw9a0a authors: Aronen, Matti; Viikari, Laura; Vuorinen, Tytti; Langen, Henriikka; Hämeenaho, Mira; Sadeghi, Mohammadreza; Söderlund‐Venermo, Maria; Viitanen, Matti; Jartti, Tuomas title: Virus Etiology of Airway Illness in Elderly Adults date: 2016-06-20 journal: J Am Geriatr Soc DOI: 10.1111/jgs.14175 sha: doc_id: 347509 cord_uid: 2ysw9a0a file: cache/cord-349279-wbb7h2zu.json key: cord-349279-wbb7h2zu authors: Walker, Gregory J.; Stelzer‐Braid, Sacha; Shorter, Caroline; Honeywill, Claire; Wynn, Matthew; Willenborg, Christiana; Barnes, Phillipa; Kang, Janice; Pierse, Nevil; Crane, Julian; Howden‐Chapman, Philippa; Rawlinson, William D. title: Viruses associated with acute respiratory infection in a community‐based cohort of healthy New Zealand children date: 2019-05-07 journal: J Med Virol DOI: 10.1002/jmv.25493 sha: doc_id: 349279 cord_uid: wbb7h2zu file: cache/cord-346673-kyc1wks5.json key: cord-346673-kyc1wks5 authors: NICKBAKHSH, S.; THORBURN, F.; VON WISSMANN, B.; McMENAMIN, J.; GUNSON, R. N.; MURCIA, P. R. title: Extensive multiplex PCR diagnostics reveal new insights into the epidemiology of viral respiratory infections date: 2016-03-02 journal: Epidemiol Infect DOI: 10.1017/s0950268816000339 sha: doc_id: 346673 cord_uid: kyc1wks5 file: cache/cord-347246-0vofftmj.json key: cord-347246-0vofftmj authors: Everitt, J I; Richter, C B title: Infectious diseases of the upper respiratory tract: implications for toxicology studies. date: 1990-04-17 journal: Environ Health Perspect DOI: nan sha: doc_id: 347246 cord_uid: 0vofftmj file: cache/cord-348490-dqabq6d8.json key: cord-348490-dqabq6d8 authors: Maeder, Muriel N.; Rabezanahary, Henintsoa M.; Zafindraibe, Norosoa J.; Randriatiana, Martin Raoelina; Rasamoelina, Tahinamandranto; Rakotoarivo, Andry T.; Vanhems, Philippe; Hoffmann, Jonathan; Bénet, Thomas; Rakoto Andrianarivelo, Mala; Rakoto-Alson, Olivat A. title: Sickle-cell disease in febrile children living in a rural village of Madagascar and association with malaria and respiratory infections date: 2016-12-01 journal: BMC Hematol DOI: 10.1186/s12878-016-0069-1 sha: doc_id: 348490 cord_uid: dqabq6d8 file: cache/cord-349226-xzlc1pni.json key: cord-349226-xzlc1pni authors: Khatiwada, Saroj; Subedi, Astha title: Lung microbiome and coronavirus disease 2019 (COVID-19): possible link and implications date: 2020-08-05 journal: Hum Microb J DOI: 10.1016/j.humic.2020.100073 sha: doc_id: 349226 cord_uid: xzlc1pni file: cache/cord-346253-0mnsm6s4.json key: cord-346253-0mnsm6s4 authors: Ahanchian, Hamid; Jones, Carmen M; Chen, Yueh-sheng; Sly, Peter D title: Respiratory viral infections in children with asthma: do they matter and can we prevent them? date: 2012-09-13 journal: BMC Pediatr DOI: 10.1186/1471-2431-12-147 sha: doc_id: 346253 cord_uid: 0mnsm6s4 file: cache/cord-346096-aml84iv1.json key: cord-346096-aml84iv1 authors: Bailey, Emily S.; Choi, Jessica Y.; Zemke, Juliana; Yondon, Myagmarsukh; Gray, Gregory C. title: Molecular surveillance of respiratory viruses with bioaerosol sampling in an airport date: 2018-09-17 journal: Trop Dis Travel Med Vaccines DOI: 10.1186/s40794-018-0071-7 sha: doc_id: 346096 cord_uid: aml84iv1 file: cache/cord-347262-q88g1561.json key: cord-347262-q88g1561 authors: Schutzer‐Weissmann, J.; Magee, D.J.; Farquhar‐Smith, P. title: Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection risk during elective peri‐operative care: a narrative review date: 2020-07-11 journal: Anaesthesia DOI: 10.1111/anae.15221 sha: doc_id: 347262 cord_uid: q88g1561 file: cache/cord-346887-dl0wc4u2.json key: cord-346887-dl0wc4u2 authors: Cho, Hye Jung; Shim, So‐Yeon; Son, Dong Woo; Sun, Yong Han; Tchah, Hann; Jeon, In‐Sang title: Respiratory viruses in neonates hospitalized with acute lower respiratory tract infections date: 2012-12-11 journal: Pediatr Int DOI: 10.1111/j.1442-200x.2012.03727.x sha: doc_id: 346887 cord_uid: dl0wc4u2 file: cache/cord-349287-mwj2qby4.json key: cord-349287-mwj2qby4 authors: Mackay, Ian M.; Arden, Katherine E. title: MERS coronavirus: diagnostics, epidemiology and transmission date: 2015-12-22 journal: Virol J DOI: 10.1186/s12985-015-0439-5 sha: doc_id: 349287 cord_uid: mwj2qby4 file: cache/cord-349606-lup6tm2s.json key: cord-349606-lup6tm2s authors: Biill Primo, Osvaldo Vinícius; Lourenço, Edmir Américo; Passos, Saulo Duarte title: Detection of Respiratory Viruses in Nasopharyngeal Swab and Adenoid Tissue from Children Submitted to Adenoidectomy: Pre- and Postoperative Analysis date: 2014-02-17 journal: Int Arch Otorhinolaryngol DOI: 10.1055/s-0034-1368135 sha: doc_id: 349606 cord_uid: lup6tm2s file: cache/cord-346539-kxnrf5g5.json key: cord-346539-kxnrf5g5 authors: Riggioni, Carmen; Comberiati, Pasquale; Giovannini, Mattia; Agache, Ioana; Akdis, Mübeccel; Alves‐Correia, Magna; Antó, Josep M.; Arcolaci, Alessandra; Kursat Azkur, Ahmet; Azkur, Dilek; Beken, Burcin; Boccabella, Cristina; Bousquet, Jean; Breiteneder, Heimo; Carvalho, Daniela; De las Vecillas, Leticia; Diamant, Zuzana; Eguiluz‐Gracia, Ibon; Eiwegger, Thomas; Eyerich, Stefanie; Fokkens, Wytske; Gao, Ya‐dong; Hannachi, Farah; Johnston, Sebastian L.; Jutel, Marek; Karavelia, Aspasia; Klimek, Ludger; Moya, Beatriz; Nadeau, Kari; O'Hehir, Robyn; O'Mahony, Liam; Pfaar, Oliver; Sanak, Marek; Schwarze, Jürgen; Sokolowska, Milena; Torres, María J.; van de Veen, Willem; van Zelm, Menno C.; Wang, De Yun; Zhang, Luo; Jiménez‐Saiz, Rodrigo; Akdis, Cezmi A. title: A compendium answering 150 questions on COVID‐19 and SARS‐CoV‐2 date: 2020-06-14 journal: Allergy DOI: 10.1111/all.14449 sha: doc_id: 346539 cord_uid: kxnrf5g5 file: cache/cord-349956-h4i2t2cr.json key: cord-349956-h4i2t2cr authors: Hoang, Van-Thuan; Dao, Thi-Loi; Ly, Tran Duc Anh; Belhouchat, Khadidja; Chaht, Kamel Larbi; Gaudart, Jean; Mrenda, Bakridine Mmadi; Drali, Tassadit; Yezli, Saber; Alotaibi, Badriah; Fournier, Pierre-Edouard; Raoult, Didier; Parola, Philippe; de Santi, Vincent Pommier; Gautret, Philippe title: The dynamics and interactions of respiratory pathogen carriage among French pilgrims during the 2018 Hajj date: 2019-11-21 journal: Emerg Microbes Infect DOI: 10.1080/22221751.2019.1693247 sha: doc_id: 349956 cord_uid: h4i2t2cr file: cache/cord-350928-vj5qlzpj.json key: cord-350928-vj5qlzpj authors: Arnott, Alicia; Vong, Sirenda; Rith, Sareth; Naughtin, Monica; Ly, Sowath; Guillard, Bertrand; Deubel, Vincent; Buchy, Philippe title: Human bocavirus amongst an all‐ages population hospitalised with acute lower respiratory infections in Cambodia date: 2012-04-25 journal: Influenza Other Respir Viruses DOI: 10.1111/j.1750-2659.2012.00369.x sha: doc_id: 350928 cord_uid: vj5qlzpj file: cache/cord-351008-p0n1fdxw.json key: cord-351008-p0n1fdxw authors: Monge, Susana; Duijster, Janneke; Kommer, Geert Jan; van de Kassteele, Jan; Krafft, Thomas; Engelen, Paul; Valk, Jens P.; de Waard, Jan; de Nooij, Jan; Riezebos‐Brilman, Annelies; van der Hoek, Wim; van Asten, Liselotte title: Ambulance dispatch calls attributable to influenza A and other common respiratory viruses in the Netherlands (2014‐2016) date: 2020-05-14 journal: Influenza Other Respir Viruses DOI: 10.1111/irv.12731 sha: doc_id: 351008 cord_uid: p0n1fdxw file: cache/cord-349560-8n65rgfz.json key: cord-349560-8n65rgfz authors: Kleines, Michael; Häusler, Martin; Krüttgen, Alexander; Scheithauer, Simone title: WU Polyomavirus (WUPyV): A Recently Detected Virus Causing Respiratory Disease? date: 2009-11-04 journal: Viruses DOI: 10.3390/v1030678 sha: doc_id: 349560 cord_uid: 8n65rgfz file: cache/cord-354918-129inbwq.json key: cord-354918-129inbwq authors: Kotsimbos, T.; McCormack, J. title: Respiratory infectious disease: complacency with empiricism in the age of molecular science. We can do better! date: 2007-06-04 journal: Intern Med J DOI: 10.1111/j.1445-5994.2007.01424.x sha: doc_id: 354918 cord_uid: 129inbwq file: cache/cord-351323-cbejbm5v.json key: cord-351323-cbejbm5v authors: Roy Mukherjee, Tapasi; Chanda, Shampa; Mullick, Satarupa; De, Papiya; Dey‐Sarkar, Malay; Chawla‐Sarkar, Mamta title: Spectrum of respiratory viruses circulating in eastern India: Prospective surveillance among patients with influenza‐like illness during 2010–2011 date: 2013-06-13 journal: J Med Virol DOI: 10.1002/jmv.23607 sha: doc_id: 351323 cord_uid: cbejbm5v 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-351046-yq7287k9.json key: cord-351046-yq7287k9 authors: Schubert, Gena; Haverland, Josh; Wyst, Craig Vander; McGreevy, Jon title: How Much Drool Is Too Much?() date: 2019-12-13 journal: Clin Pediatr Emerg Med DOI: 10.1016/j.cpem.2019.100742 sha: doc_id: 351046 cord_uid: yq7287k9 file: cache/cord-351990-aham72b9.json key: cord-351990-aham72b9 authors: Radin, Jennifer M.; Hawksworth, Anthony W.; Kammerer, Peter E.; Balansay, Melinda; Raman, Rema; Lindsay, Suzanne P.; Brice, Gary T. title: Epidemiology of Pathogen-Specific Respiratory Infections among Three US Populations date: 2014-12-30 journal: PLoS One DOI: 10.1371/journal.pone.0114871 sha: doc_id: 351990 cord_uid: aham72b9 file: cache/cord-353698-gj8sx3zy.json key: cord-353698-gj8sx3zy authors: Bibiano-Guillen, C.; Arias-Arcos, B.; Collado-Escudero, C.; Mir-Montero, M.; Corella-Montoya, F.; Torres-Macho, J.; Buendía-Garcia, M.J.; Larrainzar-Garijo, R. title: Adapted Diving Mask (ADM) device as respiratory support with oxygen output during COVID-19 pandemic date: 2020-10-28 journal: Am J Emerg Med DOI: 10.1016/j.ajem.2020.10.043 sha: doc_id: 353698 cord_uid: gj8sx3zy file: cache/cord-352222-zq9o66i4.json key: cord-352222-zq9o66i4 authors: Rajatonirina, Soatiana; Razanajatovo, Norosoa Harline; Ratsima, Elisoa Hariniana; Orelle, Arnaud; Ratovoson, Rila; Andrianirina, Zo Zafitsara; Andriatahina, Todisoa; Ramparany, Lovasoa; Herindrainy, Perlinot; Randrianirina, Frédérique; Heraud, Jean-Michel; Richard, Vincent title: Outcome Risk Factors during Respiratory Infections in a Paediatric Ward in Antananarivo, Madagascar 2010–2012 date: 2013-09-12 journal: PLoS One DOI: 10.1371/journal.pone.0072839 sha: doc_id: 352222 cord_uid: zq9o66i4 file: cache/cord-353308-e4s8el0s.json key: cord-353308-e4s8el0s authors: Parashar, Umesh D; Anderson, Larry J title: Severe acute respiratory syndrome: review and lessons of the 2003 outbreak date: 2004-05-20 journal: Int J Epidemiol DOI: 10.1093/ije/dyh198 sha: doc_id: 353308 cord_uid: e4s8el0s file: cache/cord-352684-4o623x3n.json key: cord-352684-4o623x3n authors: Tan, M. Y.; Tan, L. N.; Aw, M. M.; Quak, S. H.; Karthik, S. V. title: Bocavirus infection following paediatric liver transplantation date: 2016-10-23 journal: Pediatr Transplant DOI: 10.1111/petr.12840 sha: doc_id: 352684 cord_uid: 4o623x3n file: cache/cord-355165-xc6ythgp.json key: cord-355165-xc6ythgp authors: van den Wijngaard, Cees; van Asten, Liselotte; van Pelt, Wilfrid; Nagelkerke, Nico J.D.; Verheij, Robert; de Neeling, Albert J.; Dekkers, Arnold; van der Sande, Marianne A.B.; van Vliet, Hans; Koopmans, Marion P.G. title: Validation of Syndromic Surveillance for Respiratory Pathogen Activity date: 2008-06-17 journal: Emerg Infect Dis DOI: 10.3201/eid1406.071467 sha: doc_id: 355165 cord_uid: xc6ythgp file: cache/cord-353786-284qn075.json key: cord-353786-284qn075 authors: Chen, Zhi-Min; Fu, Jun-Fen; Shu, Qiang; Chen, Ying-Hu; Hua, Chun-Zhen; Li, Fu-Bang; Lin, Ru; Tang, Lan-Fang; Wang, Tian-Lin; Wang, Wei; Wang, Ying-Shuo; Xu, Wei-Ze; Yang, Zi-Hao; Ye, Sheng; Yuan, Tian-Ming; Zhang, Chen-Mei; Zhang, Yuan-Yuan title: Diagnosis and treatment recommendations for pediatric respiratory infection caused by the 2019 novel coronavirus date: 2020-02-05 journal: World J Pediatr DOI: 10.1007/s12519-020-00345-5 sha: doc_id: 353786 cord_uid: 284qn075 Reading metadata file and updating bibliogrpahics === updating bibliographic database Building study carrel named keyword-respiratory-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: 88888 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-021277-smw6owql author: nan title: Respiratory distress syndrome: recent research date: 2013-02-17 pages: extension: .txt txt: ./txt/cord-021277-smw6owql.txt cache: ./cache/cord-021277-smw6owql.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-021277-smw6owql.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 88802 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 88929 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: 87034 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: 89036 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: 89442 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: 88245 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: 89089 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: 89500 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 89419 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: 89793 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: 89872 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: Resource temporarily unavailable parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-001070-zlzag6a8 author: Camargo, C.N. title: Human rhinovirus infections in symptomatic and asymptomatic subjects date: 2012-06-01 pages: extension: .txt txt: ./txt/cord-001070-zlzag6a8.txt cache: ./cache/cord-001070-zlzag6a8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-001070-zlzag6a8.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 89492 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: 89908 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-000877-usz7pnvu author: Abdel-Moneim, Ahmed S. title: Detection of Bocavirus in Children Suffering from Acute Respiratory Tract Infections in Saudi Arabia date: 2013-01-30 pages: extension: .txt txt: ./txt/cord-000877-usz7pnvu.txt cache: ./cache/cord-000877-usz7pnvu.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-000877-usz7pnvu.txt' === file2bib.sh === id: cord-020267-0axms5fp author: nan title: RIBAVIRIN AND RESPIRATORY SYNCYTIAL VIRUS date: 1986-02-15 pages: extension: .txt txt: ./txt/cord-020267-0axms5fp.txt cache: ./cache/cord-020267-0axms5fp.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-020267-0axms5fp.txt' === file2bib.sh === id: cord-251986-ajlpb9li author: Li, Yan‐Chao title: The neuroinvasive potential of SARS‐CoV2 may play a role in the respiratory failure of COVID‐19 patients date: 2020-03-11 pages: extension: .txt txt: ./txt/cord-251986-ajlpb9li.txt cache: ./cache/cord-251986-ajlpb9li.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-251986-ajlpb9li.txt' /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-003488-pfzy8p5v author: Cruces, Pablo title: Respiratory mechanics in infants with severe bronchiolitis on controlled mechanical ventilation date: 2017-10-06 pages: extension: .txt txt: ./txt/cord-003488-pfzy8p5v.txt cache: ./cache/cord-003488-pfzy8p5v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003488-pfzy8p5v.txt' === file2bib.sh === id: cord-009860-qebenhxz author: Falsey, Ann R. title: Viral Respiratory Infections in the Institutionalized Elderly: Clinical and Epidemiologic Findings date: 2015-04-27 pages: extension: .txt txt: ./txt/cord-009860-qebenhxz.txt cache: ./cache/cord-009860-qebenhxz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-009860-qebenhxz.txt' === file2bib.sh === id: cord-023711-xz5ftnat author: MORENO-LÓPEZ, J. title: Acute Respiratory Disease in Cattle date: 2013-11-17 pages: extension: .txt txt: ./txt/cord-023711-xz5ftnat.txt cache: ./cache/cord-023711-xz5ftnat.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-023711-xz5ftnat.txt' === file2bib.sh === id: cord-007176-61e9obb3 author: Jackson, George Gee title: Viroses Causing Common Respiratory Infections in Man. III. Respiratory Syncytial Viroses and Coronavimses date: 1973-11-17 pages: extension: .txt txt: ./txt/cord-007176-61e9obb3.txt cache: ./cache/cord-007176-61e9obb3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007176-61e9obb3.txt' === file2bib.sh === id: cord-007234-hcpa8ej5 author: Renwick, Neil title: A Recently Identified Rhinovirus Genotype Is Associated with Severe Respiratory-Tract Infection in Children in Germany date: 2007-12-15 pages: extension: .txt txt: ./txt/cord-007234-hcpa8ej5.txt cache: ./cache/cord-007234-hcpa8ej5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007234-hcpa8ej5.txt' === file2bib.sh === id: cord-006325-3no74e74 author: Jeannoël, M. title: Microorganisms associated with respiratory syncytial virus pneumonia in the adult population date: 2018-10-23 pages: extension: .txt txt: ./txt/cord-006325-3no74e74.txt cache: ./cache/cord-006325-3no74e74.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-006325-3no74e74.txt' === file2bib.sh === id: cord-017107-sg8n12hs author: Suri, H. S. title: Epidemiology of Acute Respiratory Failure and Mechanical Ventilation date: 2008 pages: extension: .txt txt: ./txt/cord-017107-sg8n12hs.txt cache: ./cache/cord-017107-sg8n12hs.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-017107-sg8n12hs.txt' === file2bib.sh === id: cord-253761-wjm8ju3v author: Haidopoulou, Katerina title: Human bocavirus infections in hospitalized Greek children date: 2010-03-09 pages: extension: .txt txt: ./txt/cord-253761-wjm8ju3v.txt cache: ./cache/cord-253761-wjm8ju3v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-253761-wjm8ju3v.txt' === file2bib.sh === id: cord-001162-z8cbbit3 author: Yun, Heather C. title: Pandemic Influenza Virus 2009 H1N1 and Adenovirus in a High Risk Population of Young Adults: Epidemiology, Comparison of Clinical Presentations, and Coinfection date: 2014-01-08 pages: extension: .txt txt: ./txt/cord-001162-z8cbbit3.txt cache: ./cache/cord-001162-z8cbbit3.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-001162-z8cbbit3.txt' === file2bib.sh === id: cord-254770-ot9ys10r author: Uçkay, Ilker title: Low incidence of severe respiratory syncytial virus infections in lung transplant recipients despite the absence of specific therapy date: 2009-10-17 pages: extension: .txt txt: ./txt/cord-254770-ot9ys10r.txt cache: ./cache/cord-254770-ot9ys10r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-254770-ot9ys10r.txt' === file2bib.sh === id: cord-002801-6myqgme3 author: Yoon, Byung Woo title: Possible therapeutic effect of orally administered ribavirin for respiratory syncytial virus-induced acute respiratory distress syndrome in an immunocompetent patient: a case report date: 2017-12-20 pages: extension: .txt txt: ./txt/cord-002801-6myqgme3.txt cache: ./cache/cord-002801-6myqgme3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002801-6myqgme3.txt' === file2bib.sh === id: cord-003798-nki2sasr author: Vidaur, Loreto title: Human metapneumovirus as cause of severe community-acquired pneumonia in adults: insights from a ten-year molecular and epidemiological analysis date: 2019-07-24 pages: extension: .txt txt: ./txt/cord-003798-nki2sasr.txt cache: ./cache/cord-003798-nki2sasr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-003798-nki2sasr.txt' === file2bib.sh === id: cord-002227-x1ddi8wg author: Li, Wanli title: Emergency treatment and nursing of children with severe pneumonia complicated by heart failure and respiratory failure: 10 case reports date: 2016-07-29 pages: extension: .txt txt: ./txt/cord-002227-x1ddi8wg.txt cache: ./cache/cord-002227-x1ddi8wg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002227-x1ddi8wg.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 87398 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-000285-7p3b6tyf author: HARTERT, Tina V. title: The Tennessee Children's Respiratory Initiative: Objectives, design and recruitment results of a prospective cohort study investigating infant viral respiratory illness and the development of asthma and allergic diseases date: 2010-04-08 pages: extension: .txt txt: ./txt/cord-000285-7p3b6tyf.txt cache: ./cache/cord-000285-7p3b6tyf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-000285-7p3b6tyf.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 86107 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-007030-mewo9w43 author: Hashim, Suhana title: The prevalence and preventive measures of the respiratory illness among Malaysian pilgrims in 2013 hajj season date: 2016-02-08 pages: extension: .txt txt: ./txt/cord-007030-mewo9w43.txt cache: ./cache/cord-007030-mewo9w43.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-007030-mewo9w43.txt' === file2bib.sh === id: cord-023728-fgcldn4e author: Bower, John title: Croup in Children (Acute Laryngotracheobronchitis) date: 2014-10-31 pages: extension: .txt txt: ./txt/cord-023728-fgcldn4e.txt cache: ./cache/cord-023728-fgcldn4e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-023728-fgcldn4e.txt' === file2bib.sh === id: cord-017784-4r3fpmlb author: Foccillo, Giampiero title: The Infections Causing Acute Respiratory Failure in Elderly Patients date: 2019-08-06 pages: extension: .txt txt: ./txt/cord-017784-4r3fpmlb.txt cache: ./cache/cord-017784-4r3fpmlb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-017784-4r3fpmlb.txt' === file2bib.sh === id: cord-010368-plpghewn author: Kenmoe, Sebastien title: Association of early viral lower respiratory infections and subsequent development of atopy, a systematic review and meta-analysis of cohort studies date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-010368-plpghewn.txt cache: ./cache/cord-010368-plpghewn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-010368-plpghewn.txt' === file2bib.sh === id: cord-005583-hmv8jjfl author: Peters, M. J. title: Acute hypoxemic respiratory failure in children: case mix and the utility of respiratory severity indices date: 2013-12-27 pages: extension: .txt txt: ./txt/cord-005583-hmv8jjfl.txt cache: ./cache/cord-005583-hmv8jjfl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-005583-hmv8jjfl.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-253148-3t4o27xp author: Chow, Brian D.W. title: Evidence of human bocavirus circulating in children and adults, Cleveland, Ohio date: 2008-09-19 pages: extension: .txt txt: ./txt/cord-253148-3t4o27xp.txt cache: ./cache/cord-253148-3t4o27xp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253148-3t4o27xp.txt' === file2bib.sh === id: cord-005818-3mzwliiy author: Speer, C. P. title: Surfactantsubstitutionstherapie: Ein entscheidender Durchbruch in der Behandlung des Atemnotsyndroms Frühgeborener date: 2014-04-24 pages: extension: .txt txt: ./txt/cord-005818-3mzwliiy.txt cache: ./cache/cord-005818-3mzwliiy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-005818-3mzwliiy.txt' /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-016070-e9ix35x3 author: Perret Pérez, Cecilia title: Pneumonia Caused by Emerging Viral Agents date: 2020-02-01 pages: extension: .txt txt: ./txt/cord-016070-e9ix35x3.txt cache: ./cache/cord-016070-e9ix35x3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016070-e9ix35x3.txt' === file2bib.sh === id: cord-254265-8i86c8kt author: Camps, Marta title: Prevalence of human metapneumovirus among hospitalized children younger than 1 year in Catalonia, Spain date: 2008-06-12 pages: extension: .txt txt: ./txt/cord-254265-8i86c8kt.txt cache: ./cache/cord-254265-8i86c8kt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-254265-8i86c8kt.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-003357-4qrg6lqu author: Wang, Yingchen title: Prevalence of Common Respiratory Viral Infections and Identification of Adenovirus in Hospitalized Adults in Harbin, China 2014 to 2017 date: 2018-11-27 pages: extension: .txt txt: ./txt/cord-003357-4qrg6lqu.txt cache: ./cache/cord-003357-4qrg6lqu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003357-4qrg6lqu.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-005774-7z6uyn6p author: Hammer, J. title: Infant lung function testing in the intensive care unit date: 1995 pages: extension: .txt txt: ./txt/cord-005774-7z6uyn6p.txt cache: ./cache/cord-005774-7z6uyn6p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-005774-7z6uyn6p.txt' === file2bib.sh === id: cord-011095-79ce5900 author: Meskill, Sarah D. title: Respiratory Virus Co-infection in Acute Respiratory Infections in Children date: 2020-01-24 pages: extension: .txt txt: ./txt/cord-011095-79ce5900.txt cache: ./cache/cord-011095-79ce5900.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-011095-79ce5900.txt' === file2bib.sh === id: cord-010233-772e35kx author: Monto, Arnold S. title: Respiratory illness caused by picornavirus infection: a review of clinical outcomes date: 2002-01-03 pages: extension: .txt txt: ./txt/cord-010233-772e35kx.txt cache: ./cache/cord-010233-772e35kx.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-010233-772e35kx.txt' === file2bib.sh === id: cord-007222-31o180fz author: MUFSON, MAURICE A. title: EPIDEMIOLOGY OF RESPIRATORY SYNCYTIAL VIRUS INFECTION AMONG INFANTS AND CHILDREN IN CHICAGO date: 1973-08-17 pages: extension: .txt txt: ./txt/cord-007222-31o180fz.txt cache: ./cache/cord-007222-31o180fz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-007222-31o180fz.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-000602-z5p3a64x author: Bhat, Niranjan title: Use and Evaluation of Molecular Diagnostics for Pneumonia Etiology Studies date: 2012-03-08 pages: extension: .txt txt: ./txt/cord-000602-z5p3a64x.txt cache: ./cache/cord-000602-z5p3a64x.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-000602-z5p3a64x.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-252037-rj61mzqj author: Gerna, G. title: Changing circulation rate of human metapneumovirus strains and types among hospitalized pediatric patients during three consecutive winter-spring seasons date: 2005-06-28 pages: extension: .txt txt: ./txt/cord-252037-rj61mzqj.txt cache: ./cache/cord-252037-rj61mzqj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252037-rj61mzqj.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-004397-ypli7wtu author: Ma, Zhan-Ying title: Suspension microarray-based comparison of oropharyngeal swab and bronchoalveolar lavage fluid for pathogen identification in young children hospitalized with respiratory tract infection date: 2020-02-22 pages: extension: .txt txt: ./txt/cord-004397-ypli7wtu.txt cache: ./cache/cord-004397-ypli7wtu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-004397-ypli7wtu.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 88071 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 89186 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: 98139 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: 584 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: 755 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-007445-2folsh35 author: Tuffaha, Amjad title: THE ROLE OF RESPIRATORY VIRUSES IN ACUTE AND CHRONIC ASTHMA date: 2000-06-01 pages: extension: .txt txt: ./txt/cord-007445-2folsh35.txt cache: ./cache/cord-007445-2folsh35.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-007445-2folsh35.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-017897-mbwm0ytg author: Chiumello, Davide title: The Acute Respiratory Distress Syndrome: Diagnosis and Management date: 2018-10-01 pages: extension: .txt txt: ./txt/cord-017897-mbwm0ytg.txt cache: ./cache/cord-017897-mbwm0ytg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-017897-mbwm0ytg.txt' === file2bib.sh === id: cord-048447-chz8luni author: Duffett, Mark title: Surfactant therapy for acute respiratory failure in children: a systematic review and meta-analysis date: 2007-06-15 pages: extension: .txt txt: ./txt/cord-048447-chz8luni.txt cache: ./cache/cord-048447-chz8luni.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-048447-chz8luni.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-016020-awanrm9u author: Fox, Julie D. title: Respiratory Pathogens date: 2007 pages: extension: .txt txt: ./txt/cord-016020-awanrm9u.txt cache: ./cache/cord-016020-awanrm9u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-016020-awanrm9u.txt' === file2bib.sh === id: cord-048197-9785vg6d author: Domachowske, Joseph B title: Gene expression in epithelial cells in response to pneumovirus infection date: 2001-05-11 pages: extension: .txt txt: ./txt/cord-048197-9785vg6d.txt cache: ./cache/cord-048197-9785vg6d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-048197-9785vg6d.txt' === file2bib.sh === id: cord-225826-bwghyhqx author: Jiang, Zheng title: Combining Visible Light and Infrared Imaging for Efficient Detection of Respiratory Infections such as COVID-19 on Portable Device date: 2020-04-15 pages: extension: .txt txt: ./txt/cord-225826-bwghyhqx.txt cache: ./cache/cord-225826-bwghyhqx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-225826-bwghyhqx.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-017140-k4lzwfge author: Andersen, Bjørg Marit title: Protection of Upper Respiratory Tract, Mouth and Eyes date: 2018-09-25 pages: extension: .txt txt: ./txt/cord-017140-k4lzwfge.txt cache: ./cache/cord-017140-k4lzwfge.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017140-k4lzwfge.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-003917-bswndfvk author: Lalle, Eleonora title: Pulmonary Involvement during the Ebola Virus Disease date: 2019-08-24 pages: extension: .txt txt: ./txt/cord-003917-bswndfvk.txt cache: ./cache/cord-003917-bswndfvk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-003917-bswndfvk.txt' === file2bib.sh === id: cord-021894-lq8yr710 author: Cunningham, Steve title: Bronchiolitis date: 2018-03-13 pages: extension: .txt txt: ./txt/cord-021894-lq8yr710.txt cache: ./cache/cord-021894-lq8yr710.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-021894-lq8yr710.txt' === file2bib.sh === id: cord-017126-7ebo3cy3 author: nan title: Lungenversagen date: 2007 pages: extension: .txt txt: ./txt/cord-017126-7ebo3cy3.txt cache: ./cache/cord-017126-7ebo3cy3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017126-7ebo3cy3.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 812 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: 1021 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: 1889 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-023712-nptuuixw author: Bower, John title: Bronchiolitis date: 2014-10-31 pages: extension: .txt txt: ./txt/cord-023712-nptuuixw.txt cache: ./cache/cord-023712-nptuuixw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-023712-nptuuixw.txt' === file2bib.sh === id: cord-018408-ttae193b author: Haddad, Imad Y. title: Pneumonia and Empyema date: 2008-11-15 pages: extension: .txt txt: ./txt/cord-018408-ttae193b.txt cache: ./cache/cord-018408-ttae193b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-018408-ttae193b.txt' === file2bib.sh === id: cord-017252-88b3preq author: Morgan, Carrie I. title: Pneumonia date: 2014-02-20 pages: extension: .txt txt: ./txt/cord-017252-88b3preq.txt cache: ./cache/cord-017252-88b3preq.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-017252-88b3preq.txt' === file2bib.sh === id: cord-020700-iko8gy1e author: Calvo, Cristina title: Respiratory viral infections in a cohort of children during the first year of life and their role in the development of wheezing() date: 2017-07-06 pages: extension: .txt txt: ./txt/cord-020700-iko8gy1e.txt cache: ./cache/cord-020700-iko8gy1e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-020700-iko8gy1e.txt' === file2bib.sh === id: cord-151024-qe7c2uks author: Koca, Caglar title: Molecular Communication Theoretical Modeling and Analysis of SARS-CoV2 Transmission in Human Respiratory System date: 2020-11-07 pages: extension: .txt txt: ./txt/cord-151024-qe7c2uks.txt cache: ./cache/cord-151024-qe7c2uks.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-151024-qe7c2uks.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 2814 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: 3239 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: 2428 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: 3053 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: 3065 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-018421-wy3mtafh author: Waghmare, Alpana title: Rhinovirus, Coronavirus, Enterovirus, and Bocavirus After Hematopoietic Cell Transplantation or Solid Organ Transplantation date: 2016-02-15 pages: extension: .txt txt: ./txt/cord-018421-wy3mtafh.txt cache: ./cache/cord-018421-wy3mtafh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018421-wy3mtafh.txt' === file2bib.sh === id: cord-253145-1fbj1rdv author: Fox, Julie D. title: Nucleic acid amplification tests for detection of respiratory viruses date: 2007-10-31 pages: extension: .txt txt: ./txt/cord-253145-1fbj1rdv.txt cache: ./cache/cord-253145-1fbj1rdv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253145-1fbj1rdv.txt' === file2bib.sh === id: cord-015893-e0fofgxq author: Ryhal, Bruce title: Viral Disease, Air Pollutants, Nanoparticles, and Asthma date: 2011-05-03 pages: extension: .txt txt: ./txt/cord-015893-e0fofgxq.txt cache: ./cache/cord-015893-e0fofgxq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-015893-e0fofgxq.txt' === file2bib.sh === id: cord-016451-k8m2xz0e author: Chertow, Daniel S. title: Influenza, Measles, SARS, MERS, and Smallpox date: 2020-01-03 pages: extension: .txt txt: ./txt/cord-016451-k8m2xz0e.txt cache: ./cache/cord-016451-k8m2xz0e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016451-k8m2xz0e.txt' === file2bib.sh === id: cord-253223-us0ey8dq author: Chow, Brian D.W. title: The Human Bocaviruses: A Review and Discussion of Their Role in Infection date: 2009-11-03 pages: extension: .txt txt: ./txt/cord-253223-us0ey8dq.txt cache: ./cache/cord-253223-us0ey8dq.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-253223-us0ey8dq.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 2890 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 4029 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-002590-24o2viv3 author: Rahe, Michael C. title: Mechanisms of Adaptive Immunity to Porcine Reproductive and Respiratory Syndrome Virus date: 2017-06-13 pages: extension: .txt txt: ./txt/cord-002590-24o2viv3.txt cache: ./cache/cord-002590-24o2viv3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-002590-24o2viv3.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-006261-yw5k8qkz author: Heath, Gregory W. title: Exercise and Upper Respiratory Tract Infections: Is There a Relationship? date: 2012-10-23 pages: extension: .txt txt: ./txt/cord-006261-yw5k8qkz.txt cache: ./cache/cord-006261-yw5k8qkz.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-006261-yw5k8qkz.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 4916 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: 3323 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: 4035 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: 3687 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: 3920 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: 4093 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: 4963 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: 5651 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-018319-tylkbh4h author: Chemaly, Roy F. title: Respiratory Viruses date: 2011-01-04 pages: extension: .txt txt: ./txt/cord-018319-tylkbh4h.txt cache: ./cache/cord-018319-tylkbh4h.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-018319-tylkbh4h.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 3318 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-027550-yyqsatqw author: Mammas, Ioannis N. title: Update on current views and advances on RSV infection (Review) date: 2020-06-15 pages: extension: .txt txt: ./txt/cord-027550-yyqsatqw.txt cache: ./cache/cord-027550-yyqsatqw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-027550-yyqsatqw.txt' /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-022337-f3a349cb author: Busse, William W. title: Infections date: 2007-05-09 pages: extension: .txt txt: ./txt/cord-022337-f3a349cb.txt cache: ./cache/cord-022337-f3a349cb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-022337-f3a349cb.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 91. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-258386-aiwzgkq3 author: MCLAREN, Rodney A. title: Delivery For Respiratory Compromise Among Pregnant Women With COVID-19 date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-258386-aiwzgkq3.txt cache: ./cache/cord-258386-aiwzgkq3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258386-aiwzgkq3.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 5089 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 === id: cord-254766-585iu5ey author: Tauro, Sharyn title: Molecular and cellular mechanisms in the viral exacerbation of asthma date: 2008-08-13 pages: extension: .txt txt: ./txt/cord-254766-585iu5ey.txt cache: ./cache/cord-254766-585iu5ey.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254766-585iu5ey.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-007796-zggk0x2q author: Lindemans, Caroline A. title: The Immune Response to Viral Lower Respiratory Tract Infection date: 2005 pages: extension: .txt txt: ./txt/cord-007796-zggk0x2q.txt cache: ./cache/cord-007796-zggk0x2q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-007796-zggk0x2q.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 7266 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-256827-tht5h1tu author: Jain, Neemisha title: Upper respiratory tract infections date: 2001 pages: extension: .txt txt: ./txt/cord-256827-tht5h1tu.txt cache: ./cache/cord-256827-tht5h1tu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256827-tht5h1tu.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-017715-99ri6x0y author: Zhou, Bo-Ping title: SARS date: 2015-07-25 pages: extension: .txt txt: ./txt/cord-017715-99ri6x0y.txt cache: ./cache/cord-017715-99ri6x0y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017715-99ri6x0y.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-003492-rodqdtfj author: Montaner-Tarbes, Sergio title: Key Gaps in the Knowledge of the Porcine Respiratory Reproductive Syndrome Virus (PRRSV) date: 2019-02-20 pages: extension: .txt txt: ./txt/cord-003492-rodqdtfj.txt cache: ./cache/cord-003492-rodqdtfj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-003492-rodqdtfj.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 91. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 5854 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 90. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 7267 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 91. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 8378 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 90. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 8142 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 90. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-256788-h4iv8crq author: Sumino, Kaharu title: Antiviral IFN-γ responses of monocytes at birth predict respiratory tract illness in the first year of life date: 2012-03-27 pages: extension: .txt txt: ./txt/cord-256788-h4iv8crq.txt cache: ./cache/cord-256788-h4iv8crq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-256788-h4iv8crq.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 7686 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 9111 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 89. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 8060 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: 9157 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-257073-dm80bxnd author: Akmatov, Manas K. title: E-mail-based symptomatic surveillance combined with self-collection of nasal swabs: a new tool for acute respiratory infection epidemiology date: 2011-08-17 pages: extension: .txt txt: ./txt/cord-257073-dm80bxnd.txt cache: ./cache/cord-257073-dm80bxnd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-257073-dm80bxnd.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 91. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 9377 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: 6274 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: 7721 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: 7929 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: 8797 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: 8951 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: 9460 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: 8377 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: 6498 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-016882-c9ts2g7w author: Ribeiro, Edna title: Viruses Present Indoors and Analyses Approaches date: 2017-06-12 pages: extension: .txt txt: ./txt/cord-016882-c9ts2g7w.txt cache: ./cache/cord-016882-c9ts2g7w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-016882-c9ts2g7w.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 8516 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-255901-nl9k8uwd author: Barasheed, Osamah title: Uptake and effectiveness of facemask against respiratory infections at mass gatherings: a systematic review date: 2016-03-29 pages: extension: .txt txt: ./txt/cord-255901-nl9k8uwd.txt cache: ./cache/cord-255901-nl9k8uwd.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-255901-nl9k8uwd.txt' === file2bib.sh === id: cord-018302-lmly43rd author: Renaud, Christian title: Respiratory Syncytial Virus and Human Metapneumovirus Infection in Transplant Recipients date: 2016-02-15 pages: extension: .txt txt: ./txt/cord-018302-lmly43rd.txt cache: ./cache/cord-018302-lmly43rd.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-018302-lmly43rd.txt' === file2bib.sh === id: cord-258336-zs04l3s0 author: Leotte, Jaqueline title: Impact and seasonality of human rhinovirus infection in hospitalized patients for two consecutive years date: 2017-06-30 pages: extension: .txt txt: ./txt/cord-258336-zs04l3s0.txt cache: ./cache/cord-258336-zs04l3s0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-258336-zs04l3s0.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-129086-ra2njvcz author: Kumar, Sanjay title: The perspective of fluid flow behavior of respiratory droplets and aerosols through the facemasks in context of SARS-CoV-2 date: 2020-10-10 pages: extension: .txt txt: ./txt/cord-129086-ra2njvcz.txt cache: ./cache/cord-129086-ra2njvcz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-129086-ra2njvcz.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 90. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 89. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 87927 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 88. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 91. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 9447 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: 9522 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: 10723 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 89. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 9970 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === 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 === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 10066 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-256065-zz2907h0 author: Barral-Arca, Ruth title: A Meta-Analysis of Multiple Whole Blood Gene Expression Data Unveils a Diagnostic Host-Response Transcript Signature for Respiratory Syncytial Virus date: 2020-03-06 pages: extension: .txt txt: ./txt/cord-256065-zz2907h0.txt cache: ./cache/cord-256065-zz2907h0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-256065-zz2907h0.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-264079-u0nkjexi author: Murphy, Dianne title: The use of gowns and masks to control respiratory illness in pediatric hospital personnel date: 1981-11-30 pages: extension: .txt txt: ./txt/cord-264079-u0nkjexi.txt cache: ./cache/cord-264079-u0nkjexi.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-264079-u0nkjexi.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 11200 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: 11903 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 11233 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: 12302 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: 11290 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-252012-hdjbxah8 author: McErlean, Peter title: Viral diversity in asthma: Immunology and Allergy Clinics of North America: Asthma and Infectious Disease date: 2010-11-01 pages: extension: .txt txt: ./txt/cord-252012-hdjbxah8.txt cache: ./cache/cord-252012-hdjbxah8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252012-hdjbxah8.txt' === file2bib.sh === id: cord-257656-z7zx46gd author: Ljubin-Sternak, Sunčanica title: The Emerging Role of Rhinoviruses in Lower Respiratory Tract Infections in Children – Clinical and Molecular Epidemiological Study From Croatia, 2017–2019 date: 2019-12-03 pages: extension: .txt txt: ./txt/cord-257656-z7zx46gd.txt cache: ./cache/cord-257656-z7zx46gd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257656-z7zx46gd.txt' === file2bib.sh === id: cord-260871-dtn5t8ka author: Silva, Marcus Tulius T. title: SARS-CoV-2: Should We Be Concerned about the Nervous System? date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-260871-dtn5t8ka.txt cache: ./cache/cord-260871-dtn5t8ka.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260871-dtn5t8ka.txt' === file2bib.sh === id: cord-267274-3ygl3stc author: Britton, Philip N title: COVID-19 public health measures and respiratory syncytial virus date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-267274-3ygl3stc.txt cache: ./cache/cord-267274-3ygl3stc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267274-3ygl3stc.txt' === file2bib.sh === id: cord-257244-gryp0khc author: Edwards, M. R. title: The potential of anti‐infectives and immunomodulators as therapies for asthma and asthma exacerbations date: 2017-08-10 pages: extension: .txt txt: ./txt/cord-257244-gryp0khc.txt cache: ./cache/cord-257244-gryp0khc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257244-gryp0khc.txt' === file2bib.sh === id: cord-257299-z9u12yqb author: Mansi, N. title: Ear, nose and throat manifestation of viral systemic infections in pediatric patients date: 2009-12-31 pages: extension: .txt txt: ./txt/cord-257299-z9u12yqb.txt cache: ./cache/cord-257299-z9u12yqb.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-257299-z9u12yqb.txt' === file2bib.sh === id: cord-272143-6ej3eibd author: Benavides‐Nieto, Marta title: The role of respiratory viruses in children with humoral immunodeficiency on immunoglobulin replacement therapy date: 2018-12-21 pages: extension: .txt txt: ./txt/cord-272143-6ej3eibd.txt cache: ./cache/cord-272143-6ej3eibd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272143-6ej3eibd.txt' === file2bib.sh === id: cord-268388-kkhuzf3p author: Sharif-Yakan, Ahmad title: Emergence of MERS-CoV in the Middle East: Origins, Transmission, Treatment, and Perspectives date: 2014-12-04 pages: extension: .txt txt: ./txt/cord-268388-kkhuzf3p.txt cache: ./cache/cord-268388-kkhuzf3p.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-268388-kkhuzf3p.txt' === file2bib.sh === id: cord-278031-vpq4yghn author: Zumla, Alimuddin title: Rapid diagnostics urgently needed for killer infections date: 2013-06-30 pages: extension: .txt txt: ./txt/cord-278031-vpq4yghn.txt cache: ./cache/cord-278031-vpq4yghn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-278031-vpq4yghn.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 14844 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: 14528 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: 14415 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: 14283 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: 14894 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: 14892 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: 14652 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: 15142 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-264059-jf4j00bp author: Lee, Chien-Chang title: Combining Procalcitonin and Rapid Multiplex Respiratory Virus Testing for Antibiotic Stewardship in Older Adult Patients With Severe Acute Respiratory Infection date: 2019-11-30 pages: extension: .txt txt: ./txt/cord-264059-jf4j00bp.txt cache: ./cache/cord-264059-jf4j00bp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-264059-jf4j00bp.txt' === file2bib.sh === id: cord-261598-w2tyongu author: Babady, N Esther title: The FilmArray® respiratory panel: an automated, broadly multiplexed molecular test for the rapid and accurate detection of respiratory pathogens date: 2014-01-09 pages: extension: .txt txt: ./txt/cord-261598-w2tyongu.txt cache: ./cache/cord-261598-w2tyongu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261598-w2tyongu.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 15563 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: 14692 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: 15240 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-261941-xf1k5uj1 author: Stackhouse, Robin A. title: Severe acute respiratory syndrome and tuberculosis date: 2005-03-01 pages: extension: .txt txt: ./txt/cord-261941-xf1k5uj1.txt cache: ./cache/cord-261941-xf1k5uj1.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-261941-xf1k5uj1.txt' === file2bib.sh === id: cord-282420-0fcyjw7l author: Lu, Cheng-wei title: 2019-nCoV transmission through the ocular surface must not be ignored date: 2020-02-06 pages: extension: .txt txt: ./txt/cord-282420-0fcyjw7l.txt cache: ./cache/cord-282420-0fcyjw7l.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-282420-0fcyjw7l.txt' === file2bib.sh === id: cord-261025-y49su5uc author: Sampathkumar, Priya title: SARS: Epidemiology, Clinical Presentation, Management, and Infection Control Measures date: 2003-07-31 pages: extension: .txt txt: ./txt/cord-261025-y49su5uc.txt cache: ./cache/cord-261025-y49su5uc.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-261025-y49su5uc.txt' === file2bib.sh === id: cord-263927-hnsyas9q author: Peci, Adriana title: Community‐acquired respiratory viruses and co‐infection among patients of Ontario sentinel practices, April 2009 to February 2010 date: 2012-08-09 pages: extension: .txt txt: ./txt/cord-263927-hnsyas9q.txt cache: ./cache/cord-263927-hnsyas9q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263927-hnsyas9q.txt' === file2bib.sh === id: cord-258139-x4js9vqe author: Callan, Robert J title: Biosecurity and bovine respiratory disease date: 2005-03-04 pages: extension: .txt txt: ./txt/cord-258139-x4js9vqe.txt cache: ./cache/cord-258139-x4js9vqe.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-258139-x4js9vqe.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-262366-cmjnb0al author: Gerna, Giuseppe title: Genetic variability of human coronavirus OC43‐, 229E‐, and NL63‐like strains and their association with lower respiratory tract infections of hospitalized infants and immunocompromised patients date: 2006-05-23 pages: extension: .txt txt: ./txt/cord-262366-cmjnb0al.txt cache: ./cache/cord-262366-cmjnb0al.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262366-cmjnb0al.txt' === file2bib.sh === id: cord-260472-xvvfguht author: Papadopoulos, Nikolaos G. title: Antimicrobial strategies: An option to treat allergy? date: 2007-01-31 pages: extension: .txt txt: ./txt/cord-260472-xvvfguht.txt cache: ./cache/cord-260472-xvvfguht.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260472-xvvfguht.txt' === file2bib.sh === id: cord-265445-bazcczdj author: Arias-Bravo, Guisselle title: Overnutrition in Infants Is Associated With High Level of Leptin, Viral Coinfection and Increased Severity of Respiratory Infections: A Cross-Sectional Study date: 2020-02-18 pages: extension: .txt txt: ./txt/cord-265445-bazcczdj.txt cache: ./cache/cord-265445-bazcczdj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265445-bazcczdj.txt' === file2bib.sh === id: cord-270647-vn4kirrx author: Romero-Espinoza, Jose A. title: Virome and bacteriome characterization of children with pneumonia and asthma in Mexico City during winter seasons 2014 and 2015 date: 2018-02-15 pages: extension: .txt txt: ./txt/cord-270647-vn4kirrx.txt cache: ./cache/cord-270647-vn4kirrx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-270647-vn4kirrx.txt' === file2bib.sh === id: cord-272596-yxvg8357 author: WU, Jian Jun title: Detection of Human Bocavirus in Children with Acute Respiratory Tract Infections in Lanzhou and Nanjing, China date: 2014-11-30 pages: extension: .txt txt: ./txt/cord-272596-yxvg8357.txt cache: ./cache/cord-272596-yxvg8357.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-272596-yxvg8357.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 17292 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: 16981 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: 15222 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: 17604 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-276005-ifn88mjd author: da Silva Filho, Luiz Vicente Ribeiro Ferreira title: The Differential Clinical Impact of Human Coronavirus Species in Children With Cystic Fibrosis date: 2012-08-01 pages: extension: .txt txt: ./txt/cord-276005-ifn88mjd.txt cache: ./cache/cord-276005-ifn88mjd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276005-ifn88mjd.txt' === file2bib.sh === id: cord-274900-s7ft1491 author: Tatarelli, P. title: Prevalence and clinical impact of VIral Respiratory tract infections in patients hospitalized for Community-Acquired Pneumonia: the VIRCAP study date: 2019-11-30 pages: extension: .txt txt: ./txt/cord-274900-s7ft1491.txt cache: ./cache/cord-274900-s7ft1491.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274900-s7ft1491.txt' === file2bib.sh === id: cord-275166-qduf08kp author: Assane, Dieng title: Viral and Bacterial Etiologies of Acute Respiratory Infections Among Children Under 5 Years in Senegal date: 2018-02-13 pages: extension: .txt txt: ./txt/cord-275166-qduf08kp.txt cache: ./cache/cord-275166-qduf08kp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275166-qduf08kp.txt' === file2bib.sh === id: cord-270258-9vgpphiu author: Ko, Jae-Hoon title: Predictive factors for pneumonia development and progression to respiratory failure in MERS-CoV infected patients date: 2016-08-09 pages: extension: .txt txt: ./txt/cord-270258-9vgpphiu.txt cache: ./cache/cord-270258-9vgpphiu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270258-9vgpphiu.txt' === file2bib.sh === id: cord-281754-auqh3vtr author: nan title: EMERGING RESPIRATORY DISEASE - CORONAVIRUSES date: 2017-09-12 pages: extension: .txt txt: ./txt/cord-281754-auqh3vtr.txt cache: ./cache/cord-281754-auqh3vtr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-281754-auqh3vtr.txt' === file2bib.sh === id: cord-274127-12x5cc8i author: Jeong, Ji Hun title: Comparison of sputum and nasopharyngeal swabs for detection of respiratory viruses date: 2014-05-06 pages: extension: .txt txt: ./txt/cord-274127-12x5cc8i.txt cache: ./cache/cord-274127-12x5cc8i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274127-12x5cc8i.txt' === file2bib.sh === id: cord-268038-9jjpc1a2 author: Boukhvalova, M title: Treatment with novel RSV Ig RI-002 controls viral replication and reduces pulmonary damage in immunocompromised Sigmodon hispidus date: 2015-09-14 pages: extension: .txt txt: ./txt/cord-268038-9jjpc1a2.txt cache: ./cache/cord-268038-9jjpc1a2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268038-9jjpc1a2.txt' === file2bib.sh === id: cord-260225-bc1hr0fr author: Sirpilla, Olivia title: SARS-CoV-2-Encoded Proteome and Human Genetics: From Interaction-Based to Ribosomal Biology Impact on Disease and Risk Processes date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-260225-bc1hr0fr.txt cache: ./cache/cord-260225-bc1hr0fr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-260225-bc1hr0fr.txt' === file2bib.sh === id: cord-283399-iz4l9i0d author: O’Gorman, C. title: Human metapneumovirus in adults: a short case series date: 2006-03-14 pages: extension: .txt txt: ./txt/cord-283399-iz4l9i0d.txt cache: ./cache/cord-283399-iz4l9i0d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-283399-iz4l9i0d.txt' === file2bib.sh === id: cord-272878-6f0q661e author: Schnepf, Nathalie title: High Burden of Non-Influenza Viruses in Influenza-Like Illness in the Early Weeks of H1N1v Epidemic in France date: 2011-08-17 pages: extension: .txt txt: ./txt/cord-272878-6f0q661e.txt cache: ./cache/cord-272878-6f0q661e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272878-6f0q661e.txt' === file2bib.sh === id: cord-282533-w6kl74c8 author: Li, Jin title: Rapid detection of respiratory organisms with the FilmArray respiratory panel in a large children’s hospital in China date: 2018-10-11 pages: extension: .txt txt: ./txt/cord-282533-w6kl74c8.txt cache: ./cache/cord-282533-w6kl74c8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282533-w6kl74c8.txt' === file2bib.sh === id: cord-283604-fqc9jp0l author: Chen, Meng title: Adenoviruses Associated with Acute Respiratory Diseases Reported in Beijing from 2011 to 2013 date: 2015-03-27 pages: extension: .txt txt: ./txt/cord-283604-fqc9jp0l.txt cache: ./cache/cord-283604-fqc9jp0l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-283604-fqc9jp0l.txt' === file2bib.sh === id: cord-284905-h8xovybl author: MUSK, A.W. (Bill) title: Respiratory infections and lung function in an Australian Aboriginal community date: 2008-02-05 pages: extension: .txt txt: ./txt/cord-284905-h8xovybl.txt cache: ./cache/cord-284905-h8xovybl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284905-h8xovybl.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-281418-mvgp6qfv.txt cache: ./cache/cord-281418-mvgp6qfv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281418-mvgp6qfv.txt' === file2bib.sh === id: cord-268324-86a0n0dc author: Charitos, Ioannis A title: Special features of SARS-CoV-2 in daily practice date: 2020-09-26 pages: extension: .txt txt: ./txt/cord-268324-86a0n0dc.txt cache: ./cache/cord-268324-86a0n0dc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268324-86a0n0dc.txt' === file2bib.sh === id: cord-262673-j2ot35lt author: Ahmed-Hassan, Hanaa title: Innate Immune Responses to Highly Pathogenic Coronaviruses and Other Significant Respiratory Viral Infections date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-262673-j2ot35lt.txt cache: ./cache/cord-262673-j2ot35lt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262673-j2ot35lt.txt' === file2bib.sh === id: cord-282867-kbyxdegu author: Shah, Sayed Zulfiqar Ali title: Scaling the Need, Benefits, and Risks Associated with COVID-19 Acute and Postacute Care Rehabilitation: A Review date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-282867-kbyxdegu.txt cache: ./cache/cord-282867-kbyxdegu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-282867-kbyxdegu.txt' === file2bib.sh === id: cord-291217-fpte1q9m author: Adams, Madeleine title: Management of bronchiolitis date: 2009-05-13 pages: extension: .txt txt: ./txt/cord-291217-fpte1q9m.txt cache: ./cache/cord-291217-fpte1q9m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-291217-fpte1q9m.txt' === file2bib.sh === id: cord-289139-5ljqnc39 author: Mengelle, C. title: The use of a multiplex real-time PCR assay for diagnosing acute respiratory viral infections in children attending an emergency unit date: 2014-09-03 pages: extension: .txt txt: ./txt/cord-289139-5ljqnc39.txt cache: ./cache/cord-289139-5ljqnc39.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289139-5ljqnc39.txt' === file2bib.sh === id: cord-284266-tbndldhr author: Schippa, Serena title: Nasal Microbiota in RSV Bronchiolitis date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-284266-tbndldhr.txt cache: ./cache/cord-284266-tbndldhr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284266-tbndldhr.txt' === file2bib.sh === id: cord-286449-ekvzaae2 author: McManus, Terence E. title: Respiratory viral infection in exacerbations of COPD date: 2008-07-30 pages: extension: .txt txt: ./txt/cord-286449-ekvzaae2.txt cache: ./cache/cord-286449-ekvzaae2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286449-ekvzaae2.txt' === file2bib.sh === id: cord-283910-k10j5dzd author: Fretzayas, Andrew title: Etiology and clinical features of viral bronchiolitis in infancy date: 2017-05-04 pages: extension: .txt txt: ./txt/cord-283910-k10j5dzd.txt cache: ./cache/cord-283910-k10j5dzd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-283910-k10j5dzd.txt' === file2bib.sh === id: cord-022084-hap7flng author: ARRUDA, EURICO title: Respiratory Tract Viral Infections date: 2009-05-15 pages: extension: .txt txt: ./txt/cord-022084-hap7flng.txt cache: ./cache/cord-022084-hap7flng.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-022084-hap7flng.txt' === file2bib.sh === id: cord-275605-mbiojk39 author: Benkouiten, Samir title: Clinical respiratory infections and pneumonia during the Hajj pilgrimage: A systematic review date: 2018-12-04 pages: extension: .txt txt: ./txt/cord-275605-mbiojk39.txt cache: ./cache/cord-275605-mbiojk39.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-275605-mbiojk39.txt' === file2bib.sh === id: cord-296777-6xz2aslj author: Oosterhof, L title: Fatal lower respiratory tract disease with human corona virus NL63 in an adult haematopoietic cell transplant recipient date: 2009-10-12 pages: extension: .txt txt: ./txt/cord-296777-6xz2aslj.txt cache: ./cache/cord-296777-6xz2aslj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296777-6xz2aslj.txt' === file2bib.sh === id: cord-017364-d9zmdm23 author: Crowe, James E. title: Paramyxoviruses: Respiratory Syncytial Virus and Human Metapneumovirus date: 2014-02-27 pages: extension: .txt txt: ./txt/cord-017364-d9zmdm23.txt cache: ./cache/cord-017364-d9zmdm23.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-017364-d9zmdm23.txt' === file2bib.sh === id: cord-282303-idh7io9v author: Hassan, Md. Zakiul title: Contamination of hospital surfaces with respiratory pathogens in Bangladesh date: 2019-10-28 pages: extension: .txt txt: ./txt/cord-282303-idh7io9v.txt cache: ./cache/cord-282303-idh7io9v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-282303-idh7io9v.txt' === file2bib.sh === id: cord-289282-4oz6r7op author: Hon, Kam Lun title: Overview: The history and pediatric perspectives of severe acute respiratory syndromes: Novel or just like SARS date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-289282-4oz6r7op.txt cache: ./cache/cord-289282-4oz6r7op.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-289282-4oz6r7op.txt' === file2bib.sh === id: cord-284372-v95fzp8n author: Coyle, Peter V title: A touchdown nucleic acid amplification protocol as an alternative to culture backup for immunofluorescence in the routine diagnosis of acute viral respiratory tract infections date: 2004-10-25 pages: extension: .txt txt: ./txt/cord-284372-v95fzp8n.txt cache: ./cache/cord-284372-v95fzp8n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284372-v95fzp8n.txt' === file2bib.sh === id: cord-280857-0o1ikwks author: Goligher, Ewan C. title: Clinical strategies for implementing lung and diaphragm-protective ventilation: avoiding insufficient and excessive effort date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-280857-0o1ikwks.txt cache: ./cache/cord-280857-0o1ikwks.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-280857-0o1ikwks.txt' === file2bib.sh === id: cord-281051-i229xv0o author: Bishop-Williams, Katherine E. title: A protocol for a systematic literature review: comparing the impact of seasonal and meteorological parameters on acute respiratory infections in Indigenous and non-Indigenous peoples date: 2017-01-26 pages: extension: .txt txt: ./txt/cord-281051-i229xv0o.txt cache: ./cache/cord-281051-i229xv0o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281051-i229xv0o.txt' === file2bib.sh === id: cord-292587-hp4zd8lr author: Rubino, Ilaria title: Respiratory Protection against Pandemic and Epidemic Diseases date: 2017-10-31 pages: extension: .txt txt: ./txt/cord-292587-hp4zd8lr.txt cache: ./cache/cord-292587-hp4zd8lr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-292587-hp4zd8lr.txt' === file2bib.sh === id: cord-282668-bs634hti author: Niang, Mbayame Ndiaye title: Respiratory viruses in patients with influenza-like illness in Senegal: Focus on human respiratory adenoviruses date: 2017-03-22 pages: extension: .txt txt: ./txt/cord-282668-bs634hti.txt cache: ./cache/cord-282668-bs634hti.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-282668-bs634hti.txt' === file2bib.sh === id: cord-291618-166wvdbt author: Mikulska, Małgorzata title: Epidemiology of viral respiratory tract infections in an outpatient haematology facility date: 2013-10-06 pages: extension: .txt txt: ./txt/cord-291618-166wvdbt.txt cache: ./cache/cord-291618-166wvdbt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-291618-166wvdbt.txt' === file2bib.sh === id: cord-278935-3lgud7l8 author: Chen, Zheng‐Rong title: Clinical and epidemiological profiles of lower respiratory tract infection in hospitalized children due to human bocavirus in a subtropical area of China date: 2014-04-30 pages: extension: .txt txt: ./txt/cord-278935-3lgud7l8.txt cache: ./cache/cord-278935-3lgud7l8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278935-3lgud7l8.txt' === file2bib.sh === id: cord-286443-t0asknzu author: Emerson, Julia title: Home Self-Collection of Nasal Swabs for Diagnosis of Acute Respiratory Virus Infections in Children With Cystic Fibrosis date: 2013-07-14 pages: extension: .txt txt: ./txt/cord-286443-t0asknzu.txt cache: ./cache/cord-286443-t0asknzu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-286443-t0asknzu.txt' === file2bib.sh === id: cord-276927-rxudwp2v author: Barbas, Carmen Sílvia Valente title: Goal-Oriented Respiratory Management for Critically Ill Patients with Acute Respiratory Distress Syndrome date: 2012-08-23 pages: extension: .txt txt: ./txt/cord-276927-rxudwp2v.txt cache: ./cache/cord-276927-rxudwp2v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-276927-rxudwp2v.txt' === file2bib.sh === id: cord-281085-lqniqui0 author: Nosalova, Gabriela title: Pharmacological modulation of cough reflex date: 2006-12-31 pages: extension: .txt txt: ./txt/cord-281085-lqniqui0.txt cache: ./cache/cord-281085-lqniqui0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-281085-lqniqui0.txt' === file2bib.sh === id: cord-295074-fsbp4fky author: Broor, Shobha title: Rates of respiratory virus-associated hospitalization in children aged <5 years in rural northern India date: 2013-11-21 pages: extension: .txt txt: ./txt/cord-295074-fsbp4fky.txt cache: ./cache/cord-295074-fsbp4fky.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295074-fsbp4fky.txt' === file2bib.sh === id: cord-300510-fhpkdqr0 author: Mojoli, Francesco title: Our recommendations for acute management of COVID-19 date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-300510-fhpkdqr0.txt cache: ./cache/cord-300510-fhpkdqr0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300510-fhpkdqr0.txt' === file2bib.sh === id: cord-291961-usl8z6ep author: Zheng, Wen-zhi title: Human polyomavirus type six in respiratory samples from hospitalized children with respiratory tract infections in Beijing, China date: 2015-10-13 pages: extension: .txt txt: ./txt/cord-291961-usl8z6ep.txt cache: ./cache/cord-291961-usl8z6ep.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-291961-usl8z6ep.txt' === file2bib.sh === id: cord-293354-55nawxos author: Kenmoe, Sebastien title: Viral etiology of severe acute respiratory infections in hospitalized children in Cameroon, 2011–2013 date: 2016-05-09 pages: extension: .txt txt: ./txt/cord-293354-55nawxos.txt cache: ./cache/cord-293354-55nawxos.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293354-55nawxos.txt' === file2bib.sh === id: cord-286472-pqtem19t author: McFee, R.B. title: MIDDLE EAST RESPIRATORY SYNDROME (MERS) CORONAVIRUS date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-286472-pqtem19t.txt cache: ./cache/cord-286472-pqtem19t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-286472-pqtem19t.txt' === file2bib.sh === id: cord-291639-hioh2s35 author: Alfredo, Potena title: Pathophysiology of viral-induced exacerbations of COPD date: 2007-12-17 pages: extension: .txt txt: ./txt/cord-291639-hioh2s35.txt cache: ./cache/cord-291639-hioh2s35.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-291639-hioh2s35.txt' === file2bib.sh === id: cord-295189-bz3gi15h author: Jennings, Lance C. title: Respiratory viruses in airline travellers with influenza symptoms: Results of an airport screening study date: 2015-03-14 pages: extension: .txt txt: ./txt/cord-295189-bz3gi15h.txt cache: ./cache/cord-295189-bz3gi15h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295189-bz3gi15h.txt' === file2bib.sh === id: cord-285096-g9y3au1a author: Mitchell, Judy A. title: Tropism and pathological findings associated with canine respiratory coronavirus (CRCoV) date: 2013-03-23 pages: extension: .txt txt: ./txt/cord-285096-g9y3au1a.txt cache: ./cache/cord-285096-g9y3au1a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-285096-g9y3au1a.txt' === file2bib.sh === id: cord-303299-p15irs4e author: Dzien, Alexander title: Will the COVID-19 pandemic slow down in the Northern hemisphere by the onset of summer? An epidemiological hypothesis date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-303299-p15irs4e.txt cache: ./cache/cord-303299-p15irs4e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303299-p15irs4e.txt' === file2bib.sh === id: cord-016499-5iqpl23p author: Mackay, Ian M. title: Rhinoviruses date: 2014-02-27 pages: extension: .txt txt: ./txt/cord-016499-5iqpl23p.txt cache: ./cache/cord-016499-5iqpl23p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016499-5iqpl23p.txt' === file2bib.sh === id: cord-301254-093yih5n author: Brittain-Long, Robin title: Prospective evaluation of a novel multiplex real-time PCR assay for detection of fifteen respiratory pathogens—Duration of symptoms significantly affects detection rate date: 2010-01-18 pages: extension: .txt txt: ./txt/cord-301254-093yih5n.txt cache: ./cache/cord-301254-093yih5n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301254-093yih5n.txt' === file2bib.sh === id: cord-300711-yibdumij author: Shatizadeh, Somayeh title: Epidemiological and clinical evaluation of children with respiratory virus infections date: 2014-09-22 pages: extension: .txt txt: ./txt/cord-300711-yibdumij.txt cache: ./cache/cord-300711-yibdumij.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300711-yibdumij.txt' === file2bib.sh === id: cord-292836-1o2ynvy3 author: Ogimi, Chikara title: What’s New With the Old Coronaviruses? date: 2020-04-21 pages: extension: .txt txt: ./txt/cord-292836-1o2ynvy3.txt cache: ./cache/cord-292836-1o2ynvy3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-292836-1o2ynvy3.txt' === file2bib.sh === id: cord-284889-hth8nf5b author: Tsukagoshi, Hiroyuki title: Molecular epidemiology of respiratory viruses in virus-induced asthma date: 2013-09-12 pages: extension: .txt txt: ./txt/cord-284889-hth8nf5b.txt cache: ./cache/cord-284889-hth8nf5b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284889-hth8nf5b.txt' === file2bib.sh === id: cord-310508-zgqbfmzl author: Alavi-Moghaddam, Mostafa title: A Novel Coronavirus Outbreak from Wuhan City in China, Rapid Need for Emergency Departments Preparedness and Response; a Letter to Editor date: 2020-02-02 pages: extension: .txt txt: ./txt/cord-310508-zgqbfmzl.txt cache: ./cache/cord-310508-zgqbfmzl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-310508-zgqbfmzl.txt' === file2bib.sh === id: cord-296605-p67twx7a author: LAU, Arthur Chun-Wing title: Management of Critically Ill Patients with Severe Acute Respiratory Syndrome (SARS) date: 2004-03-10 pages: extension: .txt txt: ./txt/cord-296605-p67twx7a.txt cache: ./cache/cord-296605-p67twx7a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296605-p67twx7a.txt' === file2bib.sh === id: cord-294933-oc2glu4a author: Cinesi Gómez, César title: Clinical consensus recommendations regarding non-invasive respiratory support in the adult patient with acute respiratory failure secondary to SARS-CoV-2 infection date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-294933-oc2glu4a.txt cache: ./cache/cord-294933-oc2glu4a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-294933-oc2glu4a.txt' === file2bib.sh === id: cord-299379-ch7a39d6 author: De Conto, Flora title: Epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in Northern Italy() date: 2019-01-17 pages: extension: .txt txt: ./txt/cord-299379-ch7a39d6.txt cache: ./cache/cord-299379-ch7a39d6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299379-ch7a39d6.txt' === file2bib.sh === id: cord-302111-kg0dmgq0 author: Darden, Dijoia B. title: The Clinical Presentation and Immunology of Viral Pneumonia and Implications for Management of Coronavirus Disease 2019 date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-302111-kg0dmgq0.txt cache: ./cache/cord-302111-kg0dmgq0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302111-kg0dmgq0.txt' === file2bib.sh === id: cord-306450-sh2mrhoq author: Appak, Özgür title: Viral respiratory infections diagnosed by multiplex polymerase chain reaction in pediatric patients date: 2019-01-03 pages: extension: .txt txt: ./txt/cord-306450-sh2mrhoq.txt cache: ./cache/cord-306450-sh2mrhoq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306450-sh2mrhoq.txt' === file2bib.sh === id: cord-294544-iutcduix author: Kesson, Alison M. title: Respiratory virus infections date: 2007-09-06 pages: extension: .txt txt: ./txt/cord-294544-iutcduix.txt cache: ./cache/cord-294544-iutcduix.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-294544-iutcduix.txt' === file2bib.sh === id: cord-300019-8vxqr3mc author: Shi, Ting title: The Etiological Role of Common Respiratory Viruses in Acute Respiratory Infections in Older Adults: A Systematic Review and Meta-analysis date: 2019-03-08 pages: extension: .txt txt: ./txt/cord-300019-8vxqr3mc.txt cache: ./cache/cord-300019-8vxqr3mc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-300019-8vxqr3mc.txt' === file2bib.sh === id: cord-308979-qhlvd2mt author: Sumino, Kaharu C. title: Detection of Severe Human Metapneumovirus Infection by Real-Time Polymerase Chain Reaction and Histopathological Assessment date: 2005-09-15 pages: extension: .txt txt: ./txt/cord-308979-qhlvd2mt.txt cache: ./cache/cord-308979-qhlvd2mt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308979-qhlvd2mt.txt' === file2bib.sh === id: cord-303606-ypkia5x1 author: Lee, So-lun title: Is respiratory viral infection really an important trigger of asthma exacerbations in children? date: 2011-03-30 pages: extension: .txt txt: ./txt/cord-303606-ypkia5x1.txt cache: ./cache/cord-303606-ypkia5x1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-303606-ypkia5x1.txt' === file2bib.sh === id: cord-301011-xbuqd0j5 author: Felten-Barentsz, Karin M title: Recommendations for Hospital-Based Physical Therapists Managing Patients With COVID-19 date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-301011-xbuqd0j5.txt cache: ./cache/cord-301011-xbuqd0j5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301011-xbuqd0j5.txt' === file2bib.sh === id: cord-312024-qdgqif5j author: Talbot, H. Keipp title: The Diagnosis of Viral Respiratory Disease in Older Adults date: 2010-02-01 pages: extension: .txt txt: ./txt/cord-312024-qdgqif5j.txt cache: ./cache/cord-312024-qdgqif5j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 10 resourceName b'cord-312024-qdgqif5j.txt' === file2bib.sh === id: cord-299835-92karhpl author: Ho, Khek Y. title: Mild Illness Associated with Severe Acute Respiratory Syndrome Coronavirus Infection: Lessons from a Prospective Seroepidemiologic Study of Health-Care Workers in a Teaching Hospital in Singapore date: 2004-02-17 pages: extension: .txt txt: ./txt/cord-299835-92karhpl.txt cache: ./cache/cord-299835-92karhpl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299835-92karhpl.txt' === file2bib.sh === id: cord-292828-29jbf9ik author: Alsaleh, Asma N title: Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control date: 2014-01-09 pages: extension: .txt txt: ./txt/cord-292828-29jbf9ik.txt cache: ./cache/cord-292828-29jbf9ik.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-292828-29jbf9ik.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-303935-qdehf6rb author: Yun, Heather C. title: Changes in Clinical Presentation and Epidemiology of Respiratory Pathogens Associated With Acute Respiratory Illness in Military Trainees After Reintroduction of Adenovirus Vaccine date: 2015-09-01 pages: extension: .txt txt: ./txt/cord-303935-qdehf6rb.txt cache: ./cache/cord-303935-qdehf6rb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-303935-qdehf6rb.txt' === file2bib.sh === id: cord-266822-ecq50ye2 author: Rath, Barbara title: Influenza and other respiratory viruses: standardizing disease severity in surveillance and clinical trials date: 2017-05-12 pages: extension: .txt txt: ./txt/cord-266822-ecq50ye2.txt cache: ./cache/cord-266822-ecq50ye2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-266822-ecq50ye2.txt' === file2bib.sh === id: cord-313749-f2ct57em author: Brittain-Long, Robin title: Multiplex real-time PCR for detection of respiratory tract infections date: 2007-12-26 pages: extension: .txt txt: ./txt/cord-313749-f2ct57em.txt cache: ./cache/cord-313749-f2ct57em.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313749-f2ct57em.txt' === file2bib.sh === id: cord-293897-p30wz7b7 author: Waghmare, Alpana title: Respiratory viruses date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-293897-p30wz7b7.txt cache: ./cache/cord-293897-p30wz7b7.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-293897-p30wz7b7.txt' === file2bib.sh === id: cord-300116-r93w4jm3 author: Yi, Hana title: Profiling bacterial community in upper respiratory tracts date: 2014-11-13 pages: extension: .txt txt: ./txt/cord-300116-r93w4jm3.txt cache: ./cache/cord-300116-r93w4jm3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-300116-r93w4jm3.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 3 resourceName b'cord-312797-hohzjx74.txt' === file2bib.sh === id: cord-299952-xvtt8fz8 author: Gao, LuLu title: A randomized controlled trial of low-dose recombinant human interferons α-2b nasal spray to prevent acute viral respiratory infections in military recruits date: 2010-06-17 pages: extension: .txt txt: ./txt/cord-299952-xvtt8fz8.txt cache: ./cache/cord-299952-xvtt8fz8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-299952-xvtt8fz8.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 1 resourceName b'cord-312928-ef8hqs4s.txt' === file2bib.sh === id: cord-303040-ha8gufh8 author: Park, Won-Ju title: Respiratory Syncytial Virus Outbreak in the Basic Military Training Camp of the Republic of Korea Air Force date: 2015-01-14 pages: extension: .txt txt: ./txt/cord-303040-ha8gufh8.txt cache: ./cache/cord-303040-ha8gufh8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303040-ha8gufh8.txt' === file2bib.sh === id: cord-287156-3plpi6i9 author: Lassandro, Giuseppe title: Children in Coronaviruses’ Wonderland: What Clinicians Need to Know date: 2020-07-01 pages: extension: .txt txt: ./txt/cord-287156-3plpi6i9.txt cache: ./cache/cord-287156-3plpi6i9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287156-3plpi6i9.txt' === file2bib.sh === id: cord-301988-cevv81h3 author: Hassoun, Ali title: Seasonal variation of respiratory pathogen colonization in asymptomatic health care professionals: A single-center, cross-sectional, 2-season observational study date: 2015-08-01 pages: extension: .txt txt: ./txt/cord-301988-cevv81h3.txt cache: ./cache/cord-301988-cevv81h3.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-301988-cevv81h3.txt' === file2bib.sh === id: cord-306411-dutbxfl4 author: Eifan, Saleh A. title: Respiratory Tract Viral Infections and Coinfections Identified by Anyplex™ II RV16 Detection Kit in Pediatric Patients at a Riyadh Tertiary Care Hospital date: 2017-11-21 pages: extension: .txt txt: ./txt/cord-306411-dutbxfl4.txt cache: ./cache/cord-306411-dutbxfl4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-306411-dutbxfl4.txt' === file2bib.sh === id: cord-306315-vt2e0crh author: Elabbadi, Alexandre title: Respiratory virus-associated infections in HIV-infected adults admitted to the intensive care unit for acute respiratory failure: a 6-year bicenter retrospective study (HIV-VIR study) date: 2020-09-14 pages: extension: .txt txt: ./txt/cord-306315-vt2e0crh.txt cache: ./cache/cord-306315-vt2e0crh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 26 resourceName b'cord-306315-vt2e0crh.txt' === file2bib.sh === id: cord-307261-0a3iztns author: Hayden, Randall T. title: Comparison of two broadly multiplexed PCR systems for viral detection in clinical respiratory tract specimens from immunocompromised children date: 2012-01-30 pages: extension: .txt txt: ./txt/cord-307261-0a3iztns.txt cache: ./cache/cord-307261-0a3iztns.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-307261-0a3iztns.txt' === file2bib.sh === id: cord-306278-c4q4la5c author: Esposito, Susanna title: Epidemiology and Clinical Characteristics of Respiratory Infections Due to Adenovirus in Children Living in Milan, Italy, during 2013 and 2014 date: 2016-04-05 pages: extension: .txt txt: ./txt/cord-306278-c4q4la5c.txt cache: ./cache/cord-306278-c4q4la5c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306278-c4q4la5c.txt' === file2bib.sh === id: cord-312615-q333qgps author: Knobbe, Rebecca B title: Pathogens Causing Respiratory Tract Infections in Children Less Than 5 Years of Age in Senegal date: 2019-12-30 pages: extension: .txt txt: ./txt/cord-312615-q333qgps.txt cache: ./cache/cord-312615-q333qgps.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-312615-q333qgps.txt' === file2bib.sh === id: cord-296836-aizquh16 author: Brenner, Hermann title: Vitamin D Insufficiency and Deficiency and Mortality from Respiratory Diseases in a Cohort of Older Adults: Potential for Limiting the Death Toll during and beyond the COVID-19 Pandemic? date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-296836-aizquh16.txt cache: ./cache/cord-296836-aizquh16.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296836-aizquh16.txt' === file2bib.sh === id: cord-307874-0obomty2 author: Pardon, Bart title: Bovine Respiratory Disease Diagnosis: What Progress Has Been Made in Infectious Diagnosis? date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-307874-0obomty2.txt cache: ./cache/cord-307874-0obomty2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307874-0obomty2.txt' === file2bib.sh === id: cord-312613-1nl7q6cy author: Luz Garcia-Garcia, M. title: Pediatric Asthma and Viral Infection() date: 2016-03-26 pages: extension: .txt txt: ./txt/cord-312613-1nl7q6cy.txt cache: ./cache/cord-312613-1nl7q6cy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-312613-1nl7q6cy.txt' === file2bib.sh === id: cord-316956-nnqi0dj1 author: Gamiño‐Arroyo, Ana E. title: Epidemiology and clinical characteristics of respiratory syncytial virus infections among children and adults in Mexico date: 2016-08-18 pages: extension: .txt txt: ./txt/cord-316956-nnqi0dj1.txt cache: ./cache/cord-316956-nnqi0dj1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-316956-nnqi0dj1.txt' === file2bib.sh === id: cord-286337-qk90xb3a author: Hanada, Shigeo title: Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia date: 2018-11-16 pages: extension: .txt txt: ./txt/cord-286337-qk90xb3a.txt cache: ./cache/cord-286337-qk90xb3a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286337-qk90xb3a.txt' === file2bib.sh === id: cord-017499-51yy7y9n author: Freye, Enno title: Mechanism of Action of Opioids and Clinical Effects date: 2008 pages: extension: .txt txt: ./txt/cord-017499-51yy7y9n.txt cache: ./cache/cord-017499-51yy7y9n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-017499-51yy7y9n.txt' === file2bib.sh === id: cord-315949-7id5mitl author: Sentilhes, Anne‐Charlotte title: Respiratory virus infections in hospitalized children and adults in Lao PDR date: 2013-06-25 pages: extension: .txt txt: ./txt/cord-315949-7id5mitl.txt cache: ./cache/cord-315949-7id5mitl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315949-7id5mitl.txt' === file2bib.sh === id: cord-303322-d69o3z8d author: Chang, Anne B title: Randomized placebo-controlled trial on azithromycin to reduce the morbidity of bronchiolitis in Indigenous Australian infants: rationale and protocol date: 2011-04-14 pages: extension: .txt txt: ./txt/cord-303322-d69o3z8d.txt cache: ./cache/cord-303322-d69o3z8d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-303322-d69o3z8d.txt' === file2bib.sh === id: cord-316727-ktrlohm9 author: Razavi, Seyed Mansour title: Treatment and prevention of acute respiratory infections among Iranian hajj pilgrims: a 5-year follow up study and review of the literature date: 2014-05-10 pages: extension: .txt txt: ./txt/cord-316727-ktrlohm9.txt cache: ./cache/cord-316727-ktrlohm9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316727-ktrlohm9.txt' === file2bib.sh === id: cord-312691-ynh84b98 author: Mohd, Hamzah A. title: Predictors of MERS-CoV infection: A large case control study of patients presenting with ILI at a MERS-CoV referral hospital in Saudi Arabia date: 2016-09-24 pages: extension: .txt txt: ./txt/cord-312691-ynh84b98.txt cache: ./cache/cord-312691-ynh84b98.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-312691-ynh84b98.txt' === file2bib.sh === id: cord-312952-9gbb4own author: WARDZYŃSKA, ALEKSANDRA title: The profile of respiratory pathogens in induced sputum of elderly and non-elderly asthmatics date: 2020-01-20 pages: extension: .txt txt: ./txt/cord-312952-9gbb4own.txt cache: ./cache/cord-312952-9gbb4own.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312952-9gbb4own.txt' === file2bib.sh === id: cord-309120-05bg7rfa author: Niazi, Sadegh title: The role of respiratory droplet physicochemistry in limiting and promoting the airborne transmission of human coronaviruses: A critical review() date: 2020-11-06 pages: extension: .txt txt: ./txt/cord-309120-05bg7rfa.txt cache: ./cache/cord-309120-05bg7rfa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309120-05bg7rfa.txt' === file2bib.sh === id: cord-314841-b5l6epy3 author: Falsey, Ann Regina title: Respiratory viral infections date: 2019-08-15 pages: extension: .txt txt: ./txt/cord-314841-b5l6epy3.txt cache: ./cache/cord-314841-b5l6epy3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-314841-b5l6epy3.txt' === file2bib.sh === id: cord-306480-wgl4zrnb author: Subissi, Lorenzo title: Capturing respiratory syncytial virus season in Belgium using the influenza severe acute respiratory infection surveillance network, season 2018/19 date: 2020-10-01 pages: extension: .txt txt: ./txt/cord-306480-wgl4zrnb.txt cache: ./cache/cord-306480-wgl4zrnb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306480-wgl4zrnb.txt' === file2bib.sh === id: cord-322573-1fw1ehzd author: Vicente, Diego title: Human Bocavirus, a Respiratory and Enteric Virus date: 2007-04-17 pages: extension: .txt txt: ./txt/cord-322573-1fw1ehzd.txt cache: ./cache/cord-322573-1fw1ehzd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-322573-1fw1ehzd.txt' === file2bib.sh === id: cord-320286-9tumplp3 author: Bastien, Nathalie title: Human Bocavirus Infection, Canada date: 2006-05-17 pages: extension: .txt txt: ./txt/cord-320286-9tumplp3.txt cache: ./cache/cord-320286-9tumplp3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320286-9tumplp3.txt' === file2bib.sh === id: cord-320107-wels9wt7 author: Gottlieb, Jens title: Community-Acquired Respiratory Viruses date: 2018-03-26 pages: extension: .txt txt: ./txt/cord-320107-wels9wt7.txt cache: ./cache/cord-320107-wels9wt7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-320107-wels9wt7.txt' === file2bib.sh === id: cord-315037-lmur80te author: Lin, Chien-Yu title: Increased Detection of Viruses in Children with Respiratory Tract Infection Using PCR date: 2020-01-15 pages: extension: .txt txt: ./txt/cord-315037-lmur80te.txt cache: ./cache/cord-315037-lmur80te.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-315037-lmur80te.txt' === file2bib.sh === id: cord-321284-0y69n1ea author: El Kholy, A. A. title: The use of multiplex PCR for the diagnosis of viral severe acute respiratory infection in children: a high rate of co-detection during the winter season date: 2016-06-10 pages: extension: .txt txt: ./txt/cord-321284-0y69n1ea.txt cache: ./cache/cord-321284-0y69n1ea.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321284-0y69n1ea.txt' === file2bib.sh === id: cord-257220-fe2sacjj author: Butler, J. E. title: Porcine reproductive and respiratory syndrome (PRRS): an immune dysregulatory pandemic date: 2014-07-01 pages: extension: .txt txt: ./txt/cord-257220-fe2sacjj.txt cache: ./cache/cord-257220-fe2sacjj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-257220-fe2sacjj.txt' === file2bib.sh === id: cord-323112-e78zpa9c author: WATERER, Grant title: Respiratory infections: A current and future threat date: 2009-07-16 pages: extension: .txt txt: ./txt/cord-323112-e78zpa9c.txt cache: ./cache/cord-323112-e78zpa9c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323112-e78zpa9c.txt' === file2bib.sh === id: cord-319675-mwy3t1ny author: Gu, Li title: Sustained Viremia and High Viral Load in Respiratory Tract Secretions Are Predictors for Death in Immunocompetent Adults with Adenovirus Pneumonia date: 2016-08-17 pages: extension: .txt txt: ./txt/cord-319675-mwy3t1ny.txt cache: ./cache/cord-319675-mwy3t1ny.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319675-mwy3t1ny.txt' === file2bib.sh === id: cord-311275-ysr9nqun author: Chuaychoo, Benjamas title: Clinical manifestations and outcomes of respiratory syncytial virus infection in adult hospitalized patients date: 2019-07-03 pages: extension: .txt txt: ./txt/cord-311275-ysr9nqun.txt cache: ./cache/cord-311275-ysr9nqun.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-311275-ysr9nqun.txt' === file2bib.sh === id: cord-308201-lavcsqov author: Desforges, Marc title: Human Coronaviruses and Other Respiratory Viruses: Underestimated Opportunistic Pathogens of the Central Nervous System? date: 2019-12-20 pages: extension: .txt txt: ./txt/cord-308201-lavcsqov.txt cache: ./cache/cord-308201-lavcsqov.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308201-lavcsqov.txt' === file2bib.sh === id: cord-302833-6kntd89t author: Radonovich, Lewis J. title: The Respiratory Protection Effectiveness Clinical Trial (ResPECT): a cluster-randomized comparison of respirator and medical mask effectiveness against respiratory infections in healthcare personnel date: 2016-06-02 pages: extension: .txt txt: ./txt/cord-302833-6kntd89t.txt cache: ./cache/cord-302833-6kntd89t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-302833-6kntd89t.txt' === file2bib.sh === id: cord-322657-q4aeood2 author: Jartti, Tuomas title: Respiratory Picornaviruses and Respiratory Syncytial Virus as Causative Agents of Acute Expiratory Wheezing in Children date: 2004-06-17 pages: extension: .txt txt: ./txt/cord-322657-q4aeood2.txt cache: ./cache/cord-322657-q4aeood2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-322657-q4aeood2.txt' === file2bib.sh === id: cord-327264-j0efi5vc author: Waterer, Grant title: Respiratory infections in the Asia‐Pacific region date: 2017-05-24 pages: extension: .txt txt: ./txt/cord-327264-j0efi5vc.txt cache: ./cache/cord-327264-j0efi5vc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-327264-j0efi5vc.txt' === file2bib.sh === id: cord-323066-tvguutak author: Praznik, Ajda title: Risk factors for bronchiolitis severity: A retrospective review of patients admitted to the university hospital from central region of Slovenia date: 2018-08-09 pages: extension: .txt txt: ./txt/cord-323066-tvguutak.txt cache: ./cache/cord-323066-tvguutak.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323066-tvguutak.txt' === file2bib.sh === id: cord-319814-tyqb473m author: Zhang, Dingmei title: Epidemiology characteristics of respiratory viruses found in children and adults with respiratory tract infections in southern China date: 2014-06-11 pages: extension: .txt txt: ./txt/cord-319814-tyqb473m.txt cache: ./cache/cord-319814-tyqb473m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319814-tyqb473m.txt' === file2bib.sh === id: cord-323009-frej2qmb author: Nakouné, Emmanuel title: First introduction of pandemic influenza A/H1N1 and detection of respiratory viruses in pediatric patients in Central African Republic date: 2013-02-08 pages: extension: .txt txt: ./txt/cord-323009-frej2qmb.txt cache: ./cache/cord-323009-frej2qmb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323009-frej2qmb.txt' === file2bib.sh === id: cord-324898-bjxpuqhr author: Lazzeri, Marta title: How Italian respiratory physiotherapists have faced and are facing the coronavirus disease 2019 pandemic date: 2020-08-03 pages: extension: .txt txt: ./txt/cord-324898-bjxpuqhr.txt cache: ./cache/cord-324898-bjxpuqhr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324898-bjxpuqhr.txt' === file2bib.sh === id: cord-315934-h70j2jmt author: Yu, Jianxing title: Respiratory Syncytial Virus Seasonality, Beijing, China, 2007–2015 date: 2019-06-17 pages: extension: .txt txt: ./txt/cord-315934-h70j2jmt.txt cache: ./cache/cord-315934-h70j2jmt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315934-h70j2jmt.txt' === file2bib.sh === id: cord-284332-p4c1fneh author: Bosma, Karen J. title: Pharmacotherapy for Prevention and Treatment of Acute Respiratory Distress Syndrome: Current and Experimental Approaches date: 2012-09-19 pages: extension: .txt txt: ./txt/cord-284332-p4c1fneh.txt cache: ./cache/cord-284332-p4c1fneh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-284332-p4c1fneh.txt' === file2bib.sh === id: cord-324601-s3rgxtg6 author: Mhimbira, F. title: Prevalence and clinical significance of respiratory viruses and bacteria detected in tuberculosis patients compared to household contact controls in Tanzania: a cohort study date: 2019-01-31 pages: extension: .txt txt: ./txt/cord-324601-s3rgxtg6.txt cache: ./cache/cord-324601-s3rgxtg6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324601-s3rgxtg6.txt' === file2bib.sh === id: cord-326004-wg47sd06 author: Wilson, Patrick T title: Respiratory Pathogens in Children 1 Month to 5 Years of Age Presenting With Undifferentiated Acute Respiratory Distress in 2 District-Level Hospitals in Ghana date: 2018-09-03 pages: extension: .txt txt: ./txt/cord-326004-wg47sd06.txt cache: ./cache/cord-326004-wg47sd06.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326004-wg47sd06.txt' === file2bib.sh === id: cord-323551-22v2hn3v author: Galanti, M. title: Rates of asymptomatic respiratory virus infection across age groups date: 2019-04-15 pages: extension: .txt txt: ./txt/cord-323551-22v2hn3v.txt cache: ./cache/cord-323551-22v2hn3v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323551-22v2hn3v.txt' === file2bib.sh === id: cord-318591-ssnlfjap author: Pecego, AC title: Etiology, clinical, and epidemiological characteristics of severe respiratory infection in people living with HIV date: 2020-01-22 pages: extension: .txt txt: ./txt/cord-318591-ssnlfjap.txt cache: ./cache/cord-318591-ssnlfjap.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-318591-ssnlfjap.txt' === file2bib.sh === id: cord-325635-don9qjpz author: Turner, Paul title: Respiratory virus surveillance in hospitalised pneumonia patients on the Thailand-Myanmar border date: 2013-09-16 pages: extension: .txt txt: ./txt/cord-325635-don9qjpz.txt cache: ./cache/cord-325635-don9qjpz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325635-don9qjpz.txt' === file2bib.sh === id: cord-321756-a7eh4dkb author: Kwofie, Theophilus B title: Respiratory viruses in children hospitalized for acute lower respiratory tract infection in Ghana date: 2012-04-10 pages: extension: .txt txt: ./txt/cord-321756-a7eh4dkb.txt cache: ./cache/cord-321756-a7eh4dkb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321756-a7eh4dkb.txt' === file2bib.sh === id: cord-329306-p5wmqmvj author: Kim, Kiwook title: Rhinovirus Associated Severe Respiratory Failure in Immunocompetent Adult Patient date: 2014-09-30 pages: extension: .txt txt: ./txt/cord-329306-p5wmqmvj.txt cache: ./cache/cord-329306-p5wmqmvj.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-329306-p5wmqmvj.txt' === file2bib.sh === id: cord-328086-ji2emajn author: Zhou, Jie‐ying title: Human bocavirus and human metapneumovirus in hospitalized children with lower respiratory tract illness in Changsha, China date: 2018-01-11 pages: extension: .txt txt: ./txt/cord-328086-ji2emajn.txt cache: ./cache/cord-328086-ji2emajn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328086-ji2emajn.txt' === file2bib.sh === id: cord-325783-pqonn0as author: Nicholls, John M title: Lung pathology of fatal severe acute respiratory syndrome date: 2003-05-24 pages: extension: .txt txt: ./txt/cord-325783-pqonn0as.txt cache: ./cache/cord-325783-pqonn0as.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325783-pqonn0as.txt' === file2bib.sh === id: cord-320950-x02zp349 author: Esposito, Susanna title: Multiplex Platforms for the Identification of Respiratory Pathogens: Are They Useful in Pediatric Clinical Practice? date: 2019-06-04 pages: extension: .txt txt: ./txt/cord-320950-x02zp349.txt cache: ./cache/cord-320950-x02zp349.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320950-x02zp349.txt' === file2bib.sh === id: cord-317619-o7qfugjw author: Nye, Steven title: Viral Infection in the Development and Progression of Pediatric Acute Respiratory Distress Syndrome date: 2016-11-24 pages: extension: .txt txt: ./txt/cord-317619-o7qfugjw.txt cache: ./cache/cord-317619-o7qfugjw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-317619-o7qfugjw.txt' === file2bib.sh === id: cord-324432-k0g3r1lw author: Maykowski, Philip title: Seasonality and clinical impact of human parainfluenza viruses date: 2018-08-29 pages: extension: .txt txt: ./txt/cord-324432-k0g3r1lw.txt cache: ./cache/cord-324432-k0g3r1lw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324432-k0g3r1lw.txt' === file2bib.sh === id: cord-321851-ku4z34lu author: Alosaimi, Bandar title: MERS-CoV infection is associated with downregulation of genes encoding Th1 and Th2 cytokines/chemokines and elevated inflammatory innate immune response in the lower respiratory tract date: 2020-02-29 pages: extension: .txt txt: ./txt/cord-321851-ku4z34lu.txt cache: ./cache/cord-321851-ku4z34lu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-321851-ku4z34lu.txt' === file2bib.sh === id: cord-314190-fvdock94 author: Florin, Todd A title: Viral bronchiolitis date: 2017-01-01 pages: extension: .txt txt: ./txt/cord-314190-fvdock94.txt cache: ./cache/cord-314190-fvdock94.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-314190-fvdock94.txt' === file2bib.sh === id: cord-327493-v2iatbol author: Kwon, Hyo Jin title: Clinical manifestations of respiratory adenoviral infection among hospitalized children in Korea date: 2013-08-05 pages: extension: .txt txt: ./txt/cord-327493-v2iatbol.txt cache: ./cache/cord-327493-v2iatbol.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327493-v2iatbol.txt' === file2bib.sh === id: cord-318229-29cgwivt author: Baier, Claas title: Molecular characteristics and successful management of a respiratory syncytial virus outbreak among pediatric patients with hemato-oncological disease date: 2018-02-13 pages: extension: .txt txt: ./txt/cord-318229-29cgwivt.txt cache: ./cache/cord-318229-29cgwivt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-318229-29cgwivt.txt' === file2bib.sh === id: cord-322524-bq9ok8h1 author: Belongia, Edward A title: Clinical Features, Severity, and Incidence of RSV Illness During 12 Consecutive Seasons in a Community Cohort of Adults ≥60 Years Old date: 2018-11-27 pages: extension: .txt txt: ./txt/cord-322524-bq9ok8h1.txt cache: ./cache/cord-322524-bq9ok8h1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-322524-bq9ok8h1.txt' === file2bib.sh === id: cord-324843-r43u7sld author: Kockuzu, Esra title: Comprehensive Analysis of Severe Viral Infections of Respiratory Tract admitted to PICUs during the Winter Season in Turkey date: 2019-06-17 pages: extension: .txt txt: ./txt/cord-324843-r43u7sld.txt cache: ./cache/cord-324843-r43u7sld.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-324843-r43u7sld.txt' === file2bib.sh === id: cord-328742-r4ht266w author: Heo, Jung Yeon title: Molecular Epidemiology of Human Adenovirus–Associated Febrile Respiratory Illness in Soldiers, South Korea(1) date: 2018-07-17 pages: extension: .txt txt: ./txt/cord-328742-r4ht266w.txt cache: ./cache/cord-328742-r4ht266w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-328742-r4ht266w.txt' === file2bib.sh === id: cord-329877-vish6v8e author: Lapinsky, Stephen E. title: ICU management of severe acute respiratory syndrome date: 2003-05-09 pages: extension: .txt txt: ./txt/cord-329877-vish6v8e.txt cache: ./cache/cord-329877-vish6v8e.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-329877-vish6v8e.txt' === file2bib.sh === id: cord-324217-secnz2ta author: Pasdaran, A. title: Volatile oils: Potential agents for the treatment of respiratory infections date: 2016-08-05 pages: extension: .txt txt: ./txt/cord-324217-secnz2ta.txt cache: ./cache/cord-324217-secnz2ta.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-324217-secnz2ta.txt' === file2bib.sh === id: cord-326163-u8nh8cr3 author: van Benten, Inesz J. title: RSV‐induced bronchiolitis but not upper respiratory tract infection is accompanied by an increased nasal IL‐18 response date: 2003-08-18 pages: extension: .txt txt: ./txt/cord-326163-u8nh8cr3.txt cache: ./cache/cord-326163-u8nh8cr3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-326163-u8nh8cr3.txt' === file2bib.sh === id: cord-325611-tu1bn4hu author: Pérez-Sautu, Unai title: Target-independent high-throughput sequencing methods provide evidence that already known human viral pathogens play a main role in respiratory infections with unexplained etiology date: 2019-07-23 pages: extension: .txt txt: ./txt/cord-325611-tu1bn4hu.txt cache: ./cache/cord-325611-tu1bn4hu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325611-tu1bn4hu.txt' === file2bib.sh === id: cord-325830-mrtpihc7 author: Nelson, Philipp P. title: Current and Future Point-of-Care Tests for Emerging and New Respiratory Viruses and Future Perspectives date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-325830-mrtpihc7.txt cache: ./cache/cord-325830-mrtpihc7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-325830-mrtpihc7.txt' === file2bib.sh === id: cord-324786-8k81jetq author: Chang, Anne B title: Antibiotics for bronchiectasis exacerbations in children: rationale and study protocol for a randomised placebo-controlled trial date: 2012-08-31 pages: extension: .txt txt: ./txt/cord-324786-8k81jetq.txt cache: ./cache/cord-324786-8k81jetq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-324786-8k81jetq.txt' === file2bib.sh === id: cord-332055-lrpfzsog author: DeVos, Elizabeth title: Approach to Adult Patients with Acute Dyspnea date: 2015-11-27 pages: extension: .txt txt: ./txt/cord-332055-lrpfzsog.txt cache: ./cache/cord-332055-lrpfzsog.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-332055-lrpfzsog.txt' === file2bib.sh === id: cord-306266-8qdrshz3 author: Scully, Crispian title: Respiratory medicine date: 2014-06-25 pages: extension: .txt txt: ./txt/cord-306266-8qdrshz3.txt cache: ./cache/cord-306266-8qdrshz3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306266-8qdrshz3.txt' === file2bib.sh === id: cord-324775-3x5os79m author: Crowe, J.E. title: Human Respiratory Viruses date: 2008-07-30 pages: extension: .txt txt: ./txt/cord-324775-3x5os79m.txt cache: ./cache/cord-324775-3x5os79m.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-324775-3x5os79m.txt' === file2bib.sh === id: cord-329263-o5e2go23 author: Kaplan, Nasser M. title: Molecular epidemiology and disease severity of respiratory syncytial virus in relation to other potential pathogens in children hospitalized with acute respiratory infection in Jordan date: 2007-11-26 pages: extension: .txt txt: ./txt/cord-329263-o5e2go23.txt cache: ./cache/cord-329263-o5e2go23.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329263-o5e2go23.txt' === file2bib.sh === id: cord-330079-pdaowkop author: Xu, Lin title: Surveillance and Genome Analysis of Human Bocavirus in Patients with Respiratory Infection in Guangzhou, China date: 2012-09-11 pages: extension: .txt txt: ./txt/cord-330079-pdaowkop.txt cache: ./cache/cord-330079-pdaowkop.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-330079-pdaowkop.txt' === file2bib.sh === id: cord-331288-elnwn7l5 author: Grützmacher, Kim title: Human quarantine: Toward reducing infectious pressure on chimpanzees at the Taï Chimpanzee Project, Côte d'Ivoire date: 2017-01-17 pages: extension: .txt txt: ./txt/cord-331288-elnwn7l5.txt cache: ./cache/cord-331288-elnwn7l5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-331288-elnwn7l5.txt' === file2bib.sh === id: cord-328829-yywxmioq author: Boixeda, Ramon title: Microbiological study of patients hospitalized for acute exacerbation of chronic obstructive pulmonary disease (AE-COPD) and the usefulness of analytical and clinical parameters in its identification (VIRAE study) date: 2012-05-25 pages: extension: .txt txt: ./txt/cord-328829-yywxmioq.txt cache: ./cache/cord-328829-yywxmioq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-328829-yywxmioq.txt' === file2bib.sh === id: cord-336335-spap39b7 author: Silva, Denise R title: Respiratory viral infections and effects of meteorological parameters and air pollution in adults with respiratory symptoms admitted to the emergency room date: 2013-08-26 pages: extension: .txt txt: ./txt/cord-336335-spap39b7.txt cache: ./cache/cord-336335-spap39b7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336335-spap39b7.txt' === file2bib.sh === id: cord-331520-o9e4qqn4 author: Kistler, Christine E. title: The Winter Respiratory Viral Season During the COVID-19 Pandemic date: 2020-10-26 pages: extension: .txt txt: ./txt/cord-331520-o9e4qqn4.txt cache: ./cache/cord-331520-o9e4qqn4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331520-o9e4qqn4.txt' === file2bib.sh === id: cord-337747-7sb03moe author: Lagare, Adamou title: Molecular detection of respiratory pathogens among children aged younger than 5 years hospitalized with febrile acute respiratory infections: A prospective hospital‐based observational study in Niamey, Niger date: 2019-10-11 pages: extension: .txt txt: ./txt/cord-337747-7sb03moe.txt cache: ./cache/cord-337747-7sb03moe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-337747-7sb03moe.txt' === file2bib.sh === id: cord-330919-dep3v1pt author: Whyte, Claire S title: Fibrinolytic abnormalities in acute respiratory distress syndrome (ARDS) and versatility of thrombolytic drugs to treat COVID‐19 date: 2020-04-23 pages: extension: .txt txt: ./txt/cord-330919-dep3v1pt.txt cache: ./cache/cord-330919-dep3v1pt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-330919-dep3v1pt.txt' === file2bib.sh === id: cord-326122-5m1727m1 author: Wishaupt, Jérôme O. title: PCR testing for Paediatric Acute Respiratory Tract Infections date: 2014-08-04 pages: extension: .txt txt: ./txt/cord-326122-5m1727m1.txt cache: ./cache/cord-326122-5m1727m1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326122-5m1727m1.txt' === file2bib.sh === id: cord-330343-p7a8chn4 author: Kelly-Cirino, Cassandra title: An updated roadmap for MERS-CoV research and product development: focus on diagnostics date: 2019-02-01 pages: extension: .txt txt: ./txt/cord-330343-p7a8chn4.txt cache: ./cache/cord-330343-p7a8chn4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-330343-p7a8chn4.txt' === file2bib.sh === id: cord-335116-c83xyev5 author: Proença-Módena, José Luiz title: Respiratory viruses are continuously detected in children with chronic tonsillitis throughout the year date: 2014-07-21 pages: extension: .txt txt: ./txt/cord-335116-c83xyev5.txt cache: ./cache/cord-335116-c83xyev5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335116-c83xyev5.txt' === file2bib.sh === id: cord-327685-fymfqvp3 author: Channappanavar, Rudragouda title: Pathogenic human coronavirus infections: causes and consequences of cytokine storm and immunopathology date: 2017-05-02 pages: extension: .txt txt: ./txt/cord-327685-fymfqvp3.txt cache: ./cache/cord-327685-fymfqvp3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327685-fymfqvp3.txt' === file2bib.sh === id: cord-333355-ykmp4ven author: Kuchar, E. title: Pathophysiology of Clinical Symptoms in Acute Viral Respiratory Tract Infections date: 2015-03-19 pages: extension: .txt txt: ./txt/cord-333355-ykmp4ven.txt cache: ./cache/cord-333355-ykmp4ven.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-333355-ykmp4ven.txt' === file2bib.sh === id: cord-336562-5qmzne98 author: Auten, Richard title: Pediatric pulmonology year in review 2016: Part 2 date: 2017-04-25 pages: extension: .txt txt: ./txt/cord-336562-5qmzne98.txt cache: ./cache/cord-336562-5qmzne98.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336562-5qmzne98.txt' === file2bib.sh === id: cord-332926-8hdkpkgz author: Meissner, H. Cody title: Bronchiolitis date: 2017-07-18 pages: extension: .txt txt: ./txt/cord-332926-8hdkpkgz.txt cache: ./cache/cord-332926-8hdkpkgz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332926-8hdkpkgz.txt' === file2bib.sh === id: cord-335055-gzuug3p5 author: Kwiyolecha, Elizabeth title: Patterns of viral pathogens causing upper respiratory tract infections among symptomatic children in Mwanza, Tanzania date: 2020-10-28 pages: extension: .txt txt: ./txt/cord-335055-gzuug3p5.txt cache: ./cache/cord-335055-gzuug3p5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335055-gzuug3p5.txt' === file2bib.sh === id: cord-007417-az8xd66p author: Hansbro, Nicole G. title: Understanding the mechanisms of viral induced asthma: New therapeutic directions date: 2008-01-29 pages: extension: .txt txt: ./txt/cord-007417-az8xd66p.txt cache: ./cache/cord-007417-az8xd66p.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-007417-az8xd66p.txt' === file2bib.sh === id: cord-332361-pdoln3nr author: Khor, Chee-Sieng title: Epidemiology and seasonality of respiratory viral infections in hospitalized children in Kuala Lumpur, Malaysia: a retrospective study of 27 years date: 2012-03-20 pages: extension: .txt txt: ./txt/cord-332361-pdoln3nr.txt cache: ./cache/cord-332361-pdoln3nr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-332361-pdoln3nr.txt' === file2bib.sh === id: cord-304876-txaoz7oh author: Jordan, Paul C title: Nucleosides for the treatment of respiratory RNA virus infections date: 2018-03-21 pages: extension: .txt txt: ./txt/cord-304876-txaoz7oh.txt cache: ./cache/cord-304876-txaoz7oh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-304876-txaoz7oh.txt' === file2bib.sh === id: cord-336420-1a2u9p4t author: Söderman, Martina title: Frequent Respiratory Viral Infections in Children with Febrile Neutropenia - A Prospective Follow-Up Study date: 2016-06-16 pages: extension: .txt txt: ./txt/cord-336420-1a2u9p4t.txt cache: ./cache/cord-336420-1a2u9p4t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336420-1a2u9p4t.txt' === file2bib.sh === id: cord-340104-6n0sn5lk author: Fagbo, Shamsudeen F. title: Acute viral respiratory infections among children in MERS‐endemic Riyadh, Saudi Arabia, 2012–2013 date: 2016-07-29 pages: extension: .txt txt: ./txt/cord-340104-6n0sn5lk.txt cache: ./cache/cord-340104-6n0sn5lk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-340104-6n0sn5lk.txt' === file2bib.sh === id: cord-336743-udokbcki author: Lilitsis, Emmanouil title: Inspiratory effort and breathing pattern change in response to varying the assist level: a physiological study date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-336743-udokbcki.txt cache: ./cache/cord-336743-udokbcki.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336743-udokbcki.txt' === file2bib.sh === id: cord-328501-mbwgi56x author: Pang, Junxiong title: Risk factors for febrile respiratory illness and mono-viral infections in a semi-closed military environment: a case-control study date: 2015-07-25 pages: extension: .txt txt: ./txt/cord-328501-mbwgi56x.txt cache: ./cache/cord-328501-mbwgi56x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-328501-mbwgi56x.txt' === file2bib.sh === id: cord-337562-pkejb0a9 author: Bialasiewicz, Seweryn title: Merkel Cell Polyomavirus DNA in Respiratory Specimens from Children and Adults date: 2009-03-17 pages: extension: .txt txt: ./txt/cord-337562-pkejb0a9.txt cache: ./cache/cord-337562-pkejb0a9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337562-pkejb0a9.txt' === file2bib.sh === id: cord-333026-9f6ecg30 author: Kompanikova, J. title: Microbiologic Methods in the Diagnostics of Upper Respiratory Tract Pathogens date: 2017-03-03 pages: extension: .txt txt: ./txt/cord-333026-9f6ecg30.txt cache: ./cache/cord-333026-9f6ecg30.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333026-9f6ecg30.txt' === file2bib.sh === id: cord-331973-avjw4kx1 author: Das, Shubhagata title: Laboratory Diagnosis of Respiratory Tract Infections in Children – the State of the Art date: 2018-10-18 pages: extension: .txt txt: ./txt/cord-331973-avjw4kx1.txt cache: ./cache/cord-331973-avjw4kx1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331973-avjw4kx1.txt' === file2bib.sh === id: cord-340811-w4x4falm author: Frizzelli, Annalisa title: What happens to people’s lungs when they get coronavirus disease 2019? date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-340811-w4x4falm.txt cache: ./cache/cord-340811-w4x4falm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-340811-w4x4falm.txt' === file2bib.sh === id: cord-319877-izn315hb author: de Wit, Emmie title: SARS and MERS: recent insights into emerging coronaviruses date: 2016-06-27 pages: extension: .txt txt: ./txt/cord-319877-izn315hb.txt cache: ./cache/cord-319877-izn315hb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-319877-izn315hb.txt' === file2bib.sh === id: cord-339852-9rq7zzqs author: Theamboonlers, Apiradee title: Human Coronavirus Infection among Children with Acute Lower Respiratory Tract Infection in Thailand date: 2006-11-30 pages: extension: .txt txt: ./txt/cord-339852-9rq7zzqs.txt cache: ./cache/cord-339852-9rq7zzqs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-339852-9rq7zzqs.txt' === file2bib.sh === id: cord-335505-s013j5ex author: Zhang, Chen title: Viral Etiology and Clinical Profiles of Children with Severe Acute Respiratory Infections in China date: 2013-08-22 pages: extension: .txt txt: ./txt/cord-335505-s013j5ex.txt cache: ./cache/cord-335505-s013j5ex.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-335505-s013j5ex.txt' === file2bib.sh === id: cord-339039-6gyo9rya author: Bonvehí, Pablo E. title: Transmission and Control of Respiratory Viral Infections in the Healthcare Setting date: 2018-04-30 pages: extension: .txt txt: ./txt/cord-339039-6gyo9rya.txt cache: ./cache/cord-339039-6gyo9rya.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-339039-6gyo9rya.txt' === file2bib.sh === id: cord-339869-euikj8fv author: Cebey-López, Miriam title: Does Viral Co-Infection Influence the Severity of Acute Respiratory Infection in Children? date: 2016-04-20 pages: extension: .txt txt: ./txt/cord-339869-euikj8fv.txt cache: ./cache/cord-339869-euikj8fv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-339869-euikj8fv.txt' === file2bib.sh === id: cord-340280-m1j6v33y author: Jeon, Jae‐Hyun title: Incidence and seasonality of respiratory viruses causing acute respiratory infections in the Northern United Arab Emirates date: 2019-04-07 pages: extension: .txt txt: ./txt/cord-340280-m1j6v33y.txt cache: ./cache/cord-340280-m1j6v33y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-340280-m1j6v33y.txt' === file2bib.sh === id: cord-343042-9mue4eiv author: Bertozzi, Giuseppe title: Mistrial or Misdiagnosis: The Importance of Autopsy and Histopathological Examination in Cases of Sudden Infant Bronchiolitis-Related Death date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-343042-9mue4eiv.txt cache: ./cache/cord-343042-9mue4eiv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343042-9mue4eiv.txt' === file2bib.sh === id: cord-343074-dsubeaso author: Lee, Wan‐Ji title: Molecular epidemiology of a post‐influenza pandemic outbreak of acute respiratory infections in Korea caused by human adenovirus type 3 date: 2014-06-01 pages: extension: .txt txt: ./txt/cord-343074-dsubeaso.txt cache: ./cache/cord-343074-dsubeaso.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-343074-dsubeaso.txt' === file2bib.sh === id: cord-337137-0ey40gzw author: Lo, Anthony WI title: How the SARS coronavirus causes disease: host or organism? date: 2005-12-17 pages: extension: .txt txt: ./txt/cord-337137-0ey40gzw.txt cache: ./cache/cord-337137-0ey40gzw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337137-0ey40gzw.txt' === file2bib.sh === id: cord-342853-n3e6yawi author: Naghipour, Mohammadreza title: Human bocavirus in Iranian children with acute respiratory infections date: 2007-03-26 pages: extension: .txt txt: ./txt/cord-342853-n3e6yawi.txt cache: ./cache/cord-342853-n3e6yawi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-342853-n3e6yawi.txt' === file2bib.sh === id: cord-335567-ssnvr6nj author: Berry, Michael title: Identification of New Respiratory Viruses in the New Millennium date: 2015-03-06 pages: extension: .txt txt: ./txt/cord-335567-ssnvr6nj.txt cache: ./cache/cord-335567-ssnvr6nj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335567-ssnvr6nj.txt' === file2bib.sh === id: cord-331228-wbd0s4fo author: Shehata, Mahmoud M. title: Middle East respiratory syndrome coronavirus: a comprehensive review date: 2016-01-20 pages: extension: .txt txt: ./txt/cord-331228-wbd0s4fo.txt cache: ./cache/cord-331228-wbd0s4fo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-331228-wbd0s4fo.txt' === file2bib.sh === id: cord-342314-nx0a3nvd author: Gebru, Mu’uz title: Aerobic bacteriological studies on the respiratory tracts of apparently healthy and pneumonic camels (Camelus dromedaries) in selected districts of Afar Region, Ethiopia date: 2017-11-16 pages: extension: .txt txt: ./txt/cord-342314-nx0a3nvd.txt cache: ./cache/cord-342314-nx0a3nvd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-342314-nx0a3nvd.txt' === file2bib.sh === id: cord-342993-deuytbml author: Maffey, Alberto F. title: Viruses and atypical bacteria associated with asthma exacerbations in hospitalized children date: 2010-05-06 pages: extension: .txt txt: ./txt/cord-342993-deuytbml.txt cache: ./cache/cord-342993-deuytbml.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-342993-deuytbml.txt' === file2bib.sh === id: cord-347509-2ysw9a0a author: Aronen, Matti title: Virus Etiology of Airway Illness in Elderly Adults date: 2016-06-20 pages: extension: .txt txt: ./txt/cord-347509-2ysw9a0a.txt cache: ./cache/cord-347509-2ysw9a0a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347509-2ysw9a0a.txt' === file2bib.sh === id: cord-342133-khrljehj author: Principi, Nicola title: Bocavirus Infection in Otherwise Healthy Children with Respiratory Disease date: 2015-08-12 pages: extension: .txt txt: ./txt/cord-342133-khrljehj.txt cache: ./cache/cord-342133-khrljehj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-342133-khrljehj.txt' === file2bib.sh === id: cord-342476-0rupk21u author: van Rijn, Anneloes L. title: The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease date: 2019-10-24 pages: extension: .txt txt: ./txt/cord-342476-0rupk21u.txt cache: ./cache/cord-342476-0rupk21u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342476-0rupk21u.txt' === file2bib.sh === id: cord-312741-0au4nctt author: Lin, Panpan title: Coronavirus in human diseases: Mechanisms and advances in clinical treatment date: 2020-10-01 pages: extension: .txt txt: ./txt/cord-312741-0au4nctt.txt cache: ./cache/cord-312741-0au4nctt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312741-0au4nctt.txt' === file2bib.sh === id: cord-344271-5aynmdsk author: de Souza Luna, Luciano Kleber title: Spectrum of Viruses and Atypical Bacteria in Intercontinental Air Travelers with Symptoms of Acute Respiratory Infection date: 2007-03-01 pages: extension: .txt txt: ./txt/cord-344271-5aynmdsk.txt cache: ./cache/cord-344271-5aynmdsk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344271-5aynmdsk.txt' === file2bib.sh === id: cord-342915-r9kv67we author: Hayden, Frederick G. title: Advances in antivirals for non‐influenza respiratory virus infections date: 2013-11-01 pages: extension: .txt txt: ./txt/cord-342915-r9kv67we.txt cache: ./cache/cord-342915-r9kv67we.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342915-r9kv67we.txt' === file2bib.sh === id: cord-339009-wcoch07b author: File, Thomas M. title: Severe Acute Respiratory Syndrome: Pertinent Clinical Characteristics and Therapy date: 2012-08-23 pages: extension: .txt txt: ./txt/cord-339009-wcoch07b.txt cache: ./cache/cord-339009-wcoch07b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339009-wcoch07b.txt' === file2bib.sh === id: cord-349279-wbb7h2zu author: Walker, Gregory J. title: Viruses associated with acute respiratory infection in a community‐based cohort of healthy New Zealand children date: 2019-05-07 pages: extension: .txt txt: ./txt/cord-349279-wbb7h2zu.txt cache: ./cache/cord-349279-wbb7h2zu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349279-wbb7h2zu.txt' === file2bib.sh === id: cord-333286-lr32e0w4 author: Lehtoranta, Liisa title: Role of Probiotics in Stimulating the Immune System in Viral Respiratory Tract Infections: A Narrative Review date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-333286-lr32e0w4.txt cache: ./cache/cord-333286-lr32e0w4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333286-lr32e0w4.txt' === file2bib.sh === id: cord-341765-ml6eo8r3 author: Widhidewi, Ni Wayan title: Identification of viral etiology of acute respiratory tract infections in children and adults in Tabanan, Bali, Indonesia date: 2020-03-25 pages: extension: .txt txt: ./txt/cord-341765-ml6eo8r3.txt cache: ./cache/cord-341765-ml6eo8r3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341765-ml6eo8r3.txt' === file2bib.sh === id: cord-343390-y903mxcj author: Hoppe, Ingrid Bortolin Affonso Lux title: Bovine respiratory syncytial virus seroprevalence and risk factors in non-vaccinated dairy cattle herds in Brazil date: 2018-06-27 pages: extension: .txt txt: ./txt/cord-343390-y903mxcj.txt cache: ./cache/cord-343390-y903mxcj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-343390-y903mxcj.txt' === file2bib.sh === id: cord-347465-yu6oj30v author: Kurskaya, Olga title: Viral etiology of acute respiratory infections in hospitalized children in Novosibirsk City, Russia (2013 – 2017) date: 2018-09-18 pages: extension: .txt txt: ./txt/cord-347465-yu6oj30v.txt cache: ./cache/cord-347465-yu6oj30v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-347465-yu6oj30v.txt' === file2bib.sh === id: cord-347255-fl9lur4h author: May, Larissa title: Rapid Multiplex Testing for Upper Respiratory Pathogens in the Emergency Department: A Randomized Controlled Trial date: 2019-11-05 pages: extension: .txt txt: ./txt/cord-347255-fl9lur4h.txt cache: ./cache/cord-347255-fl9lur4h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347255-fl9lur4h.txt' === file2bib.sh === id: cord-343325-cbrly7f5 author: Denault, André Y. title: A proposed lung ultrasound and phenotypic algorithm for the care of COVID-19 patients with acute respiratory failure date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-343325-cbrly7f5.txt cache: ./cache/cord-343325-cbrly7f5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-343325-cbrly7f5.txt' === file2bib.sh === id: cord-342649-ysossker author: Scagnolari, Carolina title: Evaluation of viral load in infants hospitalized with bronchiolitis caused by respiratory syncytial virus date: 2012-03-10 pages: extension: .txt txt: ./txt/cord-342649-ysossker.txt cache: ./cache/cord-342649-ysossker.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342649-ysossker.txt' === file2bib.sh === id: cord-346096-aml84iv1 author: Bailey, Emily S. title: Molecular surveillance of respiratory viruses with bioaerosol sampling in an airport date: 2018-09-17 pages: extension: .txt txt: ./txt/cord-346096-aml84iv1.txt cache: ./cache/cord-346096-aml84iv1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346096-aml84iv1.txt' === file2bib.sh === id: cord-324950-ux7shvji author: Saade, Georges title: Coinfections and their molecular consequences in the porcine respiratory tract date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-324950-ux7shvji.txt cache: ./cache/cord-324950-ux7shvji.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-324950-ux7shvji.txt' === file2bib.sh === id: cord-344889-1y4ieamp author: Cameron, Robert J. title: Virus infection in exacerbations of chronic obstructive pulmonary disease requiring ventilation date: 2006-05-24 pages: extension: .txt txt: ./txt/cord-344889-1y4ieamp.txt cache: ./cache/cord-344889-1y4ieamp.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344889-1y4ieamp.txt' === file2bib.sh === id: cord-349606-lup6tm2s author: Biill Primo, Osvaldo Vinícius title: Detection of Respiratory Viruses in Nasopharyngeal Swab and Adenoid Tissue from Children Submitted to Adenoidectomy: Pre- and Postoperative Analysis date: 2014-02-17 pages: extension: .txt txt: ./txt/cord-349606-lup6tm2s.txt cache: ./cache/cord-349606-lup6tm2s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-349606-lup6tm2s.txt' === file2bib.sh === id: cord-333868-qrnsmhws author: Rothman, Richard E. title: Respiratory Hygiene in the Emergency Department date: 2006-08-23 pages: extension: .txt txt: ./txt/cord-333868-qrnsmhws.txt cache: ./cache/cord-333868-qrnsmhws.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-333868-qrnsmhws.txt' === file2bib.sh === id: cord-346887-dl0wc4u2 author: Cho, Hye Jung title: Respiratory viruses in neonates hospitalized with acute lower respiratory tract infections date: 2012-12-11 pages: extension: .txt txt: ./txt/cord-346887-dl0wc4u2.txt cache: ./cache/cord-346887-dl0wc4u2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346887-dl0wc4u2.txt' === file2bib.sh === id: cord-346290-my8ow5ee author: Nelson, Philipp P. title: Respiratory Viral Pathogens date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-346290-my8ow5ee.txt cache: ./cache/cord-346290-my8ow5ee.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346290-my8ow5ee.txt' === file2bib.sh === id: cord-345211-4ivqlsgt author: Murdoch, David R. title: How recent advances in molecular tests could impact the diagnosis of pneumonia date: 2016-03-07 pages: extension: .txt txt: ./txt/cord-345211-4ivqlsgt.txt cache: ./cache/cord-345211-4ivqlsgt.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345211-4ivqlsgt.txt' === file2bib.sh === id: cord-347246-0vofftmj author: Everitt, J I title: Infectious diseases of the upper respiratory tract: implications for toxicology studies. date: 1990-04-17 pages: extension: .txt txt: ./txt/cord-347246-0vofftmj.txt cache: ./cache/cord-347246-0vofftmj.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-347246-0vofftmj.txt' === file2bib.sh === id: cord-354918-129inbwq author: Kotsimbos, T. title: Respiratory infectious disease: complacency with empiricism in the age of molecular science. We can do better! date: 2007-06-04 pages: extension: .txt txt: ./txt/cord-354918-129inbwq.txt cache: ./cache/cord-354918-129inbwq.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-354918-129inbwq.txt' === file2bib.sh === id: cord-351008-p0n1fdxw author: Monge, Susana title: Ambulance dispatch calls attributable to influenza A and other common respiratory viruses in the Netherlands (2014‐2016) date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-351008-p0n1fdxw.txt cache: ./cache/cord-351008-p0n1fdxw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-351008-p0n1fdxw.txt' === file2bib.sh === id: cord-349226-xzlc1pni author: Khatiwada, Saroj title: Lung microbiome and coronavirus disease 2019 (COVID-19): possible link and implications date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-349226-xzlc1pni.txt cache: ./cache/cord-349226-xzlc1pni.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-349226-xzlc1pni.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-352684-4o623x3n author: Tan, M. Y. title: Bocavirus infection following paediatric liver transplantation date: 2016-10-23 pages: extension: .txt txt: ./txt/cord-352684-4o623x3n.txt cache: ./cache/cord-352684-4o623x3n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352684-4o623x3n.txt' === file2bib.sh === id: cord-343050-1pfqgvie author: Huang, Qiu Sue title: Southern Hemisphere Influenza and Vaccine Effectiveness Research and Surveillance date: 2015-06-09 pages: extension: .txt txt: ./txt/cord-343050-1pfqgvie.txt cache: ./cache/cord-343050-1pfqgvie.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-343050-1pfqgvie.txt' === file2bib.sh === id: cord-346673-kyc1wks5 author: NICKBAKHSH, S. title: Extensive multiplex PCR diagnostics reveal new insights into the epidemiology of viral respiratory infections date: 2016-03-02 pages: extension: .txt txt: ./txt/cord-346673-kyc1wks5.txt cache: ./cache/cord-346673-kyc1wks5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-346673-kyc1wks5.txt' === file2bib.sh === id: cord-343365-4y9fedcr author: Chang, Christopher title: Unmet Needs in Respiratory Diseases: “You Can’t Know Where You Are Going Until You Know Where You Have Been”—Anonymous date: 2013-11-30 pages: extension: .txt txt: ./txt/cord-343365-4y9fedcr.txt cache: ./cache/cord-343365-4y9fedcr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343365-4y9fedcr.txt' === file2bib.sh === id: cord-349956-h4i2t2cr author: Hoang, Van-Thuan title: The dynamics and interactions of respiratory pathogen carriage among French pilgrims during the 2018 Hajj date: 2019-11-21 pages: extension: .txt txt: ./txt/cord-349956-h4i2t2cr.txt cache: ./cache/cord-349956-h4i2t2cr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-349956-h4i2t2cr.txt' === file2bib.sh === id: cord-351323-cbejbm5v author: Roy Mukherjee, Tapasi title: Spectrum of respiratory viruses circulating in eastern India: Prospective surveillance among patients with influenza‐like illness during 2010–2011 date: 2013-06-13 pages: extension: .txt txt: ./txt/cord-351323-cbejbm5v.txt cache: ./cache/cord-351323-cbejbm5v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351323-cbejbm5v.txt' === file2bib.sh === id: cord-348490-dqabq6d8 author: Maeder, Muriel N. title: Sickle-cell disease in febrile children living in a rural village of Madagascar and association with malaria and respiratory infections date: 2016-12-01 pages: extension: .txt txt: ./txt/cord-348490-dqabq6d8.txt cache: ./cache/cord-348490-dqabq6d8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-348490-dqabq6d8.txt' === file2bib.sh === id: cord-347262-q88g1561 author: Schutzer‐Weissmann, J. title: Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection risk during elective peri‐operative care: a narrative review date: 2020-07-11 pages: extension: .txt txt: ./txt/cord-347262-q88g1561.txt cache: ./cache/cord-347262-q88g1561.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-347262-q88g1561.txt' === file2bib.sh === id: cord-339386-sxyeuiw1 author: McIntosh, Kenneth title: 157 Coronaviruses, Including Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) date: 2015-12-31 pages: extension: .txt txt: ./txt/cord-339386-sxyeuiw1.txt cache: ./cache/cord-339386-sxyeuiw1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339386-sxyeuiw1.txt' === file2bib.sh === id: cord-325353-tx6s4ggu author: Restori, Katherine H. title: Neonatal Immunity, Respiratory Virus Infections, and the Development of Asthma date: 2018-06-04 pages: extension: .txt txt: ./txt/cord-325353-tx6s4ggu.txt cache: ./cache/cord-325353-tx6s4ggu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-325353-tx6s4ggu.txt' === file2bib.sh === id: cord-350928-vj5qlzpj author: Arnott, Alicia title: Human bocavirus amongst an all‐ages population hospitalised with acute lower respiratory infections in Cambodia date: 2012-04-25 pages: extension: .txt txt: ./txt/cord-350928-vj5qlzpj.txt cache: ./cache/cord-350928-vj5qlzpj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-350928-vj5qlzpj.txt' === file2bib.sh === id: cord-351046-yq7287k9 author: Schubert, Gena title: How Much Drool Is Too Much?() date: 2019-12-13 pages: extension: .txt txt: ./txt/cord-351046-yq7287k9.txt cache: ./cache/cord-351046-yq7287k9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-351046-yq7287k9.txt' === file2bib.sh === id: cord-353698-gj8sx3zy author: Bibiano-Guillen, C. title: Adapted Diving Mask (ADM) device as respiratory support with oxygen output during COVID-19 pandemic date: 2020-10-28 pages: extension: .txt txt: ./txt/cord-353698-gj8sx3zy.txt cache: ./cache/cord-353698-gj8sx3zy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353698-gj8sx3zy.txt' === file2bib.sh === id: cord-353786-284qn075 author: Chen, Zhi-Min title: Diagnosis and treatment recommendations for pediatric respiratory infection caused by the 2019 novel coronavirus date: 2020-02-05 pages: extension: .txt txt: ./txt/cord-353786-284qn075.txt cache: ./cache/cord-353786-284qn075.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353786-284qn075.txt' === file2bib.sh === id: cord-345472-qrddwebe author: Sebina, Ismail title: The Contribution of Neutrophils to the Pathogenesis of RSV Bronchiolitis date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-345472-qrddwebe.txt cache: ./cache/cord-345472-qrddwebe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-345472-qrddwebe.txt' === file2bib.sh === id: cord-349560-8n65rgfz author: Kleines, Michael title: WU Polyomavirus (WUPyV): A Recently Detected Virus Causing Respiratory Disease? date: 2009-11-04 pages: extension: .txt txt: ./txt/cord-349560-8n65rgfz.txt cache: ./cache/cord-349560-8n65rgfz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-349560-8n65rgfz.txt' === file2bib.sh === id: cord-352222-zq9o66i4 author: Rajatonirina, Soatiana title: Outcome Risk Factors during Respiratory Infections in a Paediatric Ward in Antananarivo, Madagascar 2010–2012 date: 2013-09-12 pages: extension: .txt txt: ./txt/cord-352222-zq9o66i4.txt cache: ./cache/cord-352222-zq9o66i4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-352222-zq9o66i4.txt' === file2bib.sh === id: cord-355165-xc6ythgp author: van den Wijngaard, Cees title: Validation of Syndromic Surveillance for Respiratory Pathogen Activity date: 2008-06-17 pages: extension: .txt txt: ./txt/cord-355165-xc6ythgp.txt cache: ./cache/cord-355165-xc6ythgp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-355165-xc6ythgp.txt' === file2bib.sh === id: cord-351990-aham72b9 author: Radin, Jennifer M. title: Epidemiology of Pathogen-Specific Respiratory Infections among Three US Populations date: 2014-12-30 pages: extension: .txt txt: ./txt/cord-351990-aham72b9.txt cache: ./cache/cord-351990-aham72b9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-351990-aham72b9.txt' === file2bib.sh === id: cord-353308-e4s8el0s author: Parashar, Umesh D title: Severe acute respiratory syndrome: review and lessons of the 2003 outbreak date: 2004-05-20 pages: extension: .txt txt: ./txt/cord-353308-e4s8el0s.txt cache: ./cache/cord-353308-e4s8el0s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-353308-e4s8el0s.txt' === file2bib.sh === id: cord-346253-0mnsm6s4 author: Ahanchian, Hamid title: Respiratory viral infections in children with asthma: do they matter and can we prevent them? date: 2012-09-13 pages: extension: .txt txt: ./txt/cord-346253-0mnsm6s4.txt cache: ./cache/cord-346253-0mnsm6s4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-346253-0mnsm6s4.txt' === file2bib.sh === id: cord-023528-z9rc0ubj author: Wilkins, Pamela A. title: Disorders of Foals date: 2009-05-18 pages: extension: .txt txt: ./txt/cord-023528-z9rc0ubj.txt cache: ./cache/cord-023528-z9rc0ubj.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-023528-z9rc0ubj.txt' === file2bib.sh === id: cord-349287-mwj2qby4 author: Mackay, Ian M. title: MERS coronavirus: diagnostics, epidemiology and transmission date: 2015-12-22 pages: extension: .txt txt: ./txt/cord-349287-mwj2qby4.txt cache: ./cache/cord-349287-mwj2qby4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-349287-mwj2qby4.txt' === file2bib.sh === id: cord-346539-kxnrf5g5 author: Riggioni, Carmen title: A compendium answering 150 questions on COVID‐19 and SARS‐CoV‐2 date: 2020-06-14 pages: extension: .txt txt: ./txt/cord-346539-kxnrf5g5.txt cache: ./cache/cord-346539-kxnrf5g5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-346539-kxnrf5g5.txt' === file2bib.sh === id: cord-023509-tvqpv6fp author: Corrin, Bryan title: Occupational, environmental and iatrogenic lung disease date: 2011-03-02 pages: extension: .txt txt: ./txt/cord-023509-tvqpv6fp.txt cache: ./cache/cord-023509-tvqpv6fp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-023509-tvqpv6fp.txt' === file2bib.sh === id: cord-315339-dcui85lw author: Broadbent, Andrew J. title: Respiratory Virus Vaccines date: 2015-03-13 pages: extension: .txt txt: ./txt/cord-315339-dcui85lw.txt cache: ./cache/cord-315339-dcui85lw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-315339-dcui85lw.txt' === file2bib.sh === id: cord-275828-c6d6nk7x author: Mikasa, Keiichi title: JAID/JSC Guidelines for the Treatment of Respiratory Infectious Diseases: The Japanese Association for Infectious Diseases/Japanese Society of Chemotherapy – The JAID/JSC Guide to Clinical Management of Infectious Disease/Guideline-preparing Committee Respiratory Infectious Disease WG date: 2016-07-31 pages: extension: .txt txt: ./txt/cord-275828-c6d6nk7x.txt cache: ./cache/cord-275828-c6d6nk7x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-275828-c6d6nk7x.txt' === file2bib.sh === id: cord-026005-f2khcjdy author: López, Alfonso title: Respiratory System, Mediastinum, and Pleurae date: 2017-02-17 pages: extension: .txt txt: ./txt/cord-026005-f2khcjdy.txt cache: ./cache/cord-026005-f2khcjdy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-026005-f2khcjdy.txt' === file2bib.sh === id: cord-005646-xhx9pzhj author: nan title: 2nd World Congress on Pediatric Intensive Care 1996 Rotterdam, The Netherlands, 23–26 June 1996 Abstracts of Oral Presentations, Posters and Nursing Programme date: 1996 pages: extension: .txt txt: ./txt/cord-005646-xhx9pzhj.txt cache: ./cache/cord-005646-xhx9pzhj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 7 resourceName b'cord-005646-xhx9pzhj.txt' === file2bib.sh === id: cord-315598-qwh72inx author: Mendoza, Jose Luis Accini title: ACTUALIZACION DE LA DECLARACIÓN DE CONSENSO EN MEDICINA CRITICA PARA LA ATENCIÓN MULTIDISCIPLINARIA DEL PACIENTE CON SOSPECHA O CONFIRMACIÓN DIAGNÓSTICA DE COVID-19 date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-315598-qwh72inx.txt cache: ./cache/cord-315598-qwh72inx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 9 resourceName b'cord-315598-qwh72inx.txt' === file2bib.sh === id: cord-005814-ak5pq312 author: nan title: 8th European Congress of Intensive Care Medicine Athens - Greece, October 18–22, 1995 Abstracts date: 1995 pages: extension: .txt txt: ./txt/cord-005814-ak5pq312.txt cache: ./cache/cord-005814-ak5pq312.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 14 resourceName b'cord-005814-ak5pq312.txt' Que is empty; done keyword-respiratory-cord === reduce.pl bib === id = cord-005774-7z6uyn6p author = Hammer, J. title = Infant lung function testing in the intensive care unit date = 1995 pages = extension = .txt mime = text/plain words = 5005 sentences = 232 flesch = 45 summary = This review will focus on techniques which are used to measure thoracoabdominal asynchrony, tidal breathing flow-volume loops, small airway function (forced expiratory maneuvers), respiratory mechanics and lung volumes in critically ill infants and children. In 1989, Shannon [49] proposed in this Journal that the minimum physiological information needed for the intelligent use of mechanical ventilation (particularly if lower airway and/or pulmonary parenchymal disease was apparent) required the measurement of at least 4 variables: i) arterial partial pressure of carbon dioxide; ii) arterial oxygen saturation; iii) the mechanical time constant of the lung and iv) FRC. In 1989, Shannon [49] proposed in this Journal that the minimum physiological information needed for the intelligent use of mechanical ventilation (particularly if lower airway and/or pulmonary parenchymal disease was apparent) required the measurement of at least 4 variables: i) arterial partial pressure of carbon dioxide; ii) arterial oxygen saturation; iii) the mechanical time constant of the lung and iv) FRC. cache = ./cache/cord-005774-7z6uyn6p.txt txt = ./txt/cord-005774-7z6uyn6p.txt === reduce.pl bib === id = cord-000285-7p3b6tyf author = HARTERT, Tina V. title = The Tennessee Children's Respiratory Initiative: Objectives, design and recruitment results of a prospective cohort study investigating infant viral respiratory illness and the development of asthma and allergic diseases date = 2010-04-08 pages = extension = .txt mime = text/plain words = 3846 sentences = 169 flesch = 38 summary = The primary goals of the study are: (i) to investigate both the acute and the long-term health consequences of varying severity and aetiology of clinically significant viral respiratory tract infections on the outcomes of allergic rhinitis (AR) and early childhood asthma; and (ii) to identify the potentially modifiable factors that define children who are at greatest risk of developing asthma following infant respiratory viral infection. Thus, we designed the prospective TCRI to establish a base for the evaluation of both the risks and benefits of documented significant infant viral respiratory infection of varying severity and aetiology and other environmental exposures on childhood atopy outcomes and to establish a biospecimen repository for analyses including biomarker testing and genotyping. The TCRI is a prospective cohort of mother-infant dyads enrolled in a longitudinal investigation of the relationship of infant viral respiratory infection severity and aetiology and the interaction of other risk factors on the development of childhood asthma and allergic diseases. cache = ./cache/cord-000285-7p3b6tyf.txt txt = ./txt/cord-000285-7p3b6tyf.txt === reduce.pl bib === id = cord-003798-nki2sasr author = Vidaur, Loreto title = Human metapneumovirus as cause of severe community-acquired pneumonia in adults: insights from a ten-year molecular and epidemiological analysis date = 2019-07-24 pages = extension = .txt mime = text/plain words = 3501 sentences = 195 flesch = 41 summary = BACKGROUND: Information on the clinical, epidemiological and molecular characterization of human metapneumovirus in critically ill adult patients with severe community-acquired pneumonia (CAP) and the role of biomarkers identifying bacterial coinfection is scarce. METHODS: This is a retrospective epidemiological study of adult patients with hMPV severe CAP admitted to ICU during a ten-year period with admission PSI score ≥ 3. The main objective of this study was to describe the clinical and epidemiological characteristics of adults with severe pneumonia caused by hMPV who required intensive care unit (ICU) admission, over a long period of time. Interestingly, three patients (10.7%) were young adult patients without comorbidities and without bacterial coinfection that developed ARDS pointing out a main role of hMPV in the etiology of severe respiratory infections requiring mechanical ventilation. Main characteristics of immunosuppressed adult patients admitted to the Intensive Care Unit due to a severe community-acquired pneumonia associated with human metapneumovirus infection (Guipuzcoa, Basque Country, Spain, 2007-2017). cache = ./cache/cord-003798-nki2sasr.txt txt = ./txt/cord-003798-nki2sasr.txt === reduce.pl bib === id = cord-007176-61e9obb3 author = Jackson, George Gee title = Viroses Causing Common Respiratory Infections in Man. III. Respiratory Syncytial Viroses and Coronavimses date = 1973-11-17 pages = extension = .txt mime = text/plain words = 4090 sentences = 299 flesch = 50 summary = RS virus was estimated, from sucrose density gradient centrifugation studies, to be 90-120 nm in diameter [2] ; viral particles in infected cells measured 65 nm by electron microscopy. All adults tested possessed detectable levels of neutralizing antibody to RS virus before challenge, but the titer of naturally acquired antibody had no significant effect on subsequent RS infection of volunteers and was poorly correlated with development of mild clinical illnesses. The neutralization test is more sensitive than CF when serum from infants is used, but rises in neutralizing antibody have been detected in only half of the virus-positive infections in this age group. Virus structures were detected 6-8 hr later [17] .· Infection of WI-38 cells with strain 229E resulted in a reorganization of the cytoplasm, as determined by electron microscopy. Respiratory syncytial virus infection in adult volunteers. Respiratory syncytial virus infection in adult volunteers. Morphology and development of respiratory syncytial virus in cell culture cache = ./cache/cord-007176-61e9obb3.txt txt = ./txt/cord-007176-61e9obb3.txt === reduce.pl bib === id = cord-016070-e9ix35x3 author = Perret Pérez, Cecilia title = Pneumonia Caused by Emerging Viral Agents date = 2020-02-01 pages = extension = .txt mime = text/plain words = 3645 sentences = 174 flesch = 44 summary = The SARS coronavirus and MERS-CoV are two pathogens from the coronavirus family that predominantly cause serious lower tract respiratory infections with a high mortality rate, but they are genetically different viruses. This observation suggests that camels are the reservoirs of the virus, which can be transmitted to humans through direct contact with these animals or through consumption of their milk: 1599 cases had been diagnosed by July 2015, with 574 deaths [World Health Organization (WHO)]. HCoV-NL63 and HCoV-HKU1 are viruses that tend to manifest as a common cold, just as the usual coronaviruses HCoV-229E and HCoV-OC43; nevertheless, in small children, elderly patients, and immunosuppressed patients, they can cause serious respiratory disease with a high mortality rate. Isolated cases of avian origin in humans caused by the influenza H10N8 virus and H6N1 have been observed in China. cache = ./cache/cord-016070-e9ix35x3.txt txt = ./txt/cord-016070-e9ix35x3.txt === reduce.pl bib === id = cord-003488-pfzy8p5v author = Cruces, Pablo title = Respiratory mechanics in infants with severe bronchiolitis on controlled mechanical ventilation date = 2017-10-06 pages = extension = .txt mime = text/plain words = 3697 sentences = 229 flesch = 46 summary = Bronchiolitis is usually a self-limited disease, but some children may develop respiratory failure with increased work of breathing (WOB), hypoxemia and hypercarbia requiring mechanical ventilation (MV) in addition to usual supportive measures [7, 8] . These findings may seem unexpected and contradictory with the current understanding of severe bronchiolitis as a primarily obstructive airway disease with an increase in Abbreviations: mo months old, PF ratio PaO 2 /FIO 2 ratio, OI oxygenation index, PIM 2 Pediatric index of mortality 2, RSV respiratory syncytial virus, PNB preterm newborn, HMD hyaline membrane disease a Viral Studies were negative, but pneumococcal superinfection was diagnosed expiratory resistance, but they are supported by the observation done over a half century ago by Krieger et al. Correlation between respiratory system compliance and expiratory airway resistance measured in children on mechanical ventilation due to severe bronchiolitis. cache = ./cache/cord-003488-pfzy8p5v.txt txt = ./txt/cord-003488-pfzy8p5v.txt === reduce.pl bib === id = cord-000877-usz7pnvu author = Abdel-Moneim, Ahmed S. title = Detection of Bocavirus in Children Suffering from Acute Respiratory Tract Infections in Saudi Arabia date = 2013-01-30 pages = extension = .txt mime = text/plain words = 1826 sentences = 101 flesch = 51 summary = title: Detection of Bocavirus in Children Suffering from Acute Respiratory Tract Infections in Saudi Arabia Swabs samples from 80 children with respiratory tract infections were examined for the presence of HBoV. Human bocavirus (HBoV) was first found in children with acute respiratory tract infections in 2005 [1] . The current study aims to screen the epidemiological status and molecular phylogeny of HBoV isolates prevailing in pediatric patients with respiratory infection in Saudi Arabia. The current study investigated the prevalence of HBoV in patients suffering from respiratory tract infections in Saudi Arabia. Furthermore, the phylogenetic analysis results of three selected sequences showed that the Saudi HBoV1 strains obtained from respiratory samples belonged to group I human bocaviruses (Fig. 1) . Detection of human bocavirus in Japanese children with lower respiratory tract infections Frequent detection of viral coinfection in children hospitalized with acute respiratory tract infection using a real-time polymerase chain reaction cache = ./cache/cord-000877-usz7pnvu.txt txt = ./txt/cord-000877-usz7pnvu.txt === reduce.pl bib === id = cord-002227-x1ddi8wg author = Li, Wanli title = Emergency treatment and nursing of children with severe pneumonia complicated by heart failure and respiratory failure: 10 case reports date = 2016-07-29 pages = extension = .txt mime = text/plain words = 4023 sentences = 204 flesch = 40 summary = In the process of nursing children with severe pneumonia, intensive care was provided, including condition assessment and diagnosis, close observation of disease, keeping the airway unblocked, rational oxygen therapy, prevention and treatment of respiratory and circulatory failure, support of vital organs, complications, and health education. As a result, severe pneumonia produces corresponding clinical symptoms, such as respiratory failure, heart failure, toxic encephalopathy and intestinal paralysis, which endanger the lives of children in the short term, and is the first cause of death of pediatric inpatients (6, 7) . Type I respiratory failure also refers to the coexistence of hypoxemia and hypercapnia, impairment of ventilatory function and gas exchange functions, severe lung lesion, obstruction of trachea and bronchia caused by sticky secretions, blood change of PaO 2 <60 mmHg, and PaCO 2 >50 mmHg. Main clinical manifestations of children patients with type I pneumonia with respiratory failure include, poor mental state or dysphoria, polypnea, cyanosis of lips, dyspnea, nasal flaring and three depression signs. cache = ./cache/cord-002227-x1ddi8wg.txt txt = ./txt/cord-002227-x1ddi8wg.txt === reduce.pl bib === id = cord-007234-hcpa8ej5 author = Renwick, Neil title = A Recently Identified Rhinovirus Genotype Is Associated with Severe Respiratory-Tract Infection in Children in Germany date = 2007-12-15 pages = extension = .txt mime = text/plain words = 2510 sentences = 135 flesch = 40 summary = title: A Recently Identified Rhinovirus Genotype Is Associated with Severe Respiratory-Tract Infection in Children in Germany Here we report the investigation, by MassTag PCR, of pediatric respiratory-tract infections in Germany, studying 97 cases for which no pathogen was identified through routine laboratory evaluation. In an attempt to gather additional information on the potential pathogenicity, as well as temporal and geographic distribution, of rhinoviruses, including the recently identified genotype, we evaluated specimens collected, during the 2003-2006 seasons in Bad Kreuznach, Germany, from children hospitalized because of severe LRTI. In this study of samples collected, during a 3-year interval, from hospitalized children with severe undiagnosed respiratory infection, MassTag PCR allowed us to detect viral pathogens in 49 (51%) of 97 cases. Although we did not have samples to test for the presence of HRV in the lower respiratory tract, the high frequency at which HRV was identified as being the sole virus detected suggests a correlation between the agent and the observed LRTI symptoms. cache = ./cache/cord-007234-hcpa8ej5.txt txt = ./txt/cord-007234-hcpa8ej5.txt === reduce.pl bib === === reduce.pl bib === id = cord-002590-24o2viv3 author = Rahe, Michael C. title = Mechanisms of Adaptive Immunity to Porcine Reproductive and Respiratory Syndrome Virus date = 2017-06-13 pages = extension = .txt mime = text/plain words = 8016 sentences = 375 flesch = 34 summary = Pig immune response to general stimulus and to porcine reproductive and respiratory syndrome virus infection: A meta-analysis approach Antigen-specific B-cell responses to porcine reproductive and respiratory syndrome virus infection The Chinese highly pathogenic porcine reproductive and respiratory syndrome virus infection suppresses Th17 cells response in vivo Pathogenic and humoral immune responses to porcine reproductive and respiratory syndrome virus (PRRSV) are related to viral load in acute infection Porcine reproductive and respiratory syndrome virus-infected alveolar macrophages contain no detectable levels of viral proteins in their plasma membrane and are protected against antibody-dependent, complement-mediated cell lysis Polyclonal activation of B cells occurs in lymphoid organs from porcine reproductive and respiratory syndrome virus (PRRSV)-infected pigs The role of porcine reproductive and respiratory syndrome virus infection in immune phenotype and Th1/Th2 balance of dendritic cells Porcine reproductive and respiratory syndrome virus induces pronounced immune modulatory responses at mucosal tissues in the parental vaccine strain VR2332 infected pigs cache = ./cache/cord-002590-24o2viv3.txt txt = ./txt/cord-002590-24o2viv3.txt === reduce.pl bib === id = cord-004397-ypli7wtu author = Ma, Zhan-Ying title = Suspension microarray-based comparison of oropharyngeal swab and bronchoalveolar lavage fluid for pathogen identification in young children hospitalized with respiratory tract infection date = 2020-02-22 pages = extension = .txt mime = text/plain words = 3229 sentences = 183 flesch = 44 summary = title: Suspension microarray-based comparison of oropharyngeal swab and bronchoalveolar lavage fluid for pathogen identification in young children hospitalized with respiratory tract infection The primary purpose of this study was to compare the detection rates of OPS and paired BALF in detecting key respiratory pathogens using suspension microarray. In the present study, we used the suspension microarray, a multipathogen detection platform, to simultaneously detect viral and bacterial respiratory pathogens in matched OPS and BALF specimens from pediatric patients for comparison of the sensitivities between the two sample types. To compare the OPS and paired BALF for pathogens detection in young children with RTI, we tested the two sample types using suspension microarray. In the present study, we used suspension array to simultaneously detect multiple viral and bacterial pathogens in paired BALF and OPS specimens from symptomatic patients hospitalized with respiratory illness. We used suspension-array to compare BALF and paired OPS specimens for detecting multiple pathogens in children hospitalized with respiratory illness. cache = ./cache/cord-004397-ypli7wtu.txt txt = ./txt/cord-004397-ypli7wtu.txt === reduce.pl bib === id = cord-011095-79ce5900 author = Meskill, Sarah D. title = Respiratory Virus Co-infection in Acute Respiratory Infections in Children date = 2020-01-24 pages = extension = .txt mime = text/plain words = 4976 sentences = 276 flesch = 33 summary = One study in children under age 5 years old found that respiratory syncytial virus (RSV), human metapneumovirus (HMPV), and parainfluenza viruses (PIV) were more likely to be causative of disease [8] . In an evaluation of children under 18 years old admitted to the hospital with a diagnosis of pneumonia, the most common cause of infection, whether bacterial or viral, was RSV quickly followed by rhinovirus [12] . While some studies do have RSV and rhinovirus as the leading cause of pneumonia in children, another important common viral contributor is influenza [15] . [55] did a systemic review of patients of all ages with respiratory illnesses and found that studies that recruited young children were more likely to report high rates of co-infection and that there were inconclusive results on risk of hospitalization or ICU admission. Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children. cache = ./cache/cord-011095-79ce5900.txt txt = ./txt/cord-011095-79ce5900.txt === reduce.pl bib === id = cord-020267-0axms5fp author = nan title = RIBAVIRIN AND RESPIRATORY SYNCYTIAL VIRUS date = 1986-02-15 pages = extension = .txt mime = text/plain words = 1845 sentences = 84 flesch = 39 summary = In Britain RSV accounts for yearly hospitaladmission rates of 12 -5 to 24' 5 per 1000 among infants aged 1-3 months;3 and in North Carolina it is responsible for 24-50% of all admissions for pneumonia in children under 5 years of age.4 In hospital roughly 14% of RSV-infected infants require intensive care and 5% need assisted ventilation.s Although the mortality from RSV infection is generally low, it is especially high in infants with underlying congenital heart disease (37%, rising to 73% with concomitant pulmonary hypertension),5 and in the immunocompromised (23%),6 and is almost certainly raised in infants with bronchopulmonary dysplasia and cystic fibrosis. Striking improvements were noted in 2 infants treated with ribavirin aerosol for parainfluenza virus type 3 infection complicating severe combined immunodeficiency disease13,14-a combination often causing respiratory failure and death. Rather it should be considered for infants with bronchiolitis or pneumonia, and for high-risk patients with underlying cardiopulmonary disorders or immunodeficiency with probable RSV or influenza, and possibly parainfluenza infection. cache = ./cache/cord-020267-0axms5fp.txt txt = ./txt/cord-020267-0axms5fp.txt === reduce.pl bib === id = cord-018302-lmly43rd author = Renaud, Christian title = Respiratory Syncytial Virus and Human Metapneumovirus Infection in Transplant Recipients date = 2016-02-15 pages = extension = .txt mime = text/plain words = 10500 sentences = 459 flesch = 30 summary = Respiratory viral infections due to respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) cause infections in immunocompromised transplant patients ranging from mild upper respiratory infections to severe lower respiratory tract disease with respiratory failure. Surveillance studies of respiratory viruses from transplant centers have established the high frequency and the signifi cant clinical impact of respiratory viral infections in HSCT recipients overall [ 8 -15 , 46 , 47 ] as well as the relative importance of RSV in terms of morbidity and mortality (Table 31 -2 ). A retrospective MDACC study of confi rmed RSV infections in 280 allogeneic HSCT recipients from 1996 to 2009 utilized multivariable logistic regression to demonstrate that lack of ribavirin aerosol therapy at the upper respiratory tract disease stage was an important risk factor associated with RSV LRTI and all-cause mortality [ 99 ] . cache = ./cache/cord-018302-lmly43rd.txt txt = ./txt/cord-018302-lmly43rd.txt === reduce.pl bib === id = cord-023728-fgcldn4e author = Bower, John title = Croup in Children (Acute Laryngotracheobronchitis) date = 2014-10-31 pages = extension = .txt mime = text/plain words = 3887 sentences = 232 flesch = 53 summary = The term croup now generally refers to an acute respiratory tract illness characterized by a distinctive barking cough, hoarseness, and inspiratory stridor in a young child, usually between 6 months and 3 years old. From 1979 to 1997, croup cases associated with parainfluenza viruses, estimated from the National Hospital Discharge Survey, showed that the number of admissions among children younger than 5 years decreased by approximately one third. 14 The human coronaviruses (hCoV) have been identified in up to 7% of young children with acute respiratory tract infections, with the NL63 strain most often associated with croup. Although abrupt onset of stridor at night may be the initial indication of illness, most children have a prodrome of mild upper respiratory tract signs of rhinorrhea, cough, and sometimes fever 12 to 48 hours before the onset of the distinctive "rough and stridulous" cough of croup. cache = ./cache/cord-023728-fgcldn4e.txt txt = ./txt/cord-023728-fgcldn4e.txt === reduce.pl bib === id = cord-016451-k8m2xz0e author = Chertow, Daniel S. title = Influenza, Measles, SARS, MERS, and Smallpox date = 2020-01-03 pages = extension = .txt mime = text/plain words = 6141 sentences = 365 flesch = 41 summary = Influenza, measles, SARS, MERS, and smallpox illnesses are caused by highly infectious viral pathogens that induce critical illness. Measles infects and disrupts tissues throughout the body; however, severe disease is primarily due to lower respiratory tract and neurological complications [72] . Global epidemiology of avian influenza A H5N1 virus infection in humans, 1997-2015: a systematic review of individual case data Transmission of Middle East respiratory syndrome coronavirus infections in healthcare settings Viral shedding and antibody response in 37 patients with Middle East respiratory syndrome coronavirus infection Viral RNA in blood as indicator of severe outcome in Middle East respiratory syndrome coronavirus infection Clinical features and viral diagnosis of two cases of infection with Middle East respiratory syndrome coronavirus: a report of nosocomial transmission Clinical course and outcomes of critically ill patients with Middle East respiratory syndrome coronavirus infection cache = ./cache/cord-016451-k8m2xz0e.txt txt = ./txt/cord-016451-k8m2xz0e.txt === reduce.pl bib === id = cord-018319-tylkbh4h author = Chemaly, Roy F. title = Respiratory Viruses date = 2011-01-04 pages = extension = .txt mime = text/plain words = 8852 sentences = 467 flesch = 37 summary = Historically, the most common causes of respiratory infections in cancer patients were thought to be opportunistic bacteria and fungi, but newer diagnostic methods have revealed that respiratory viruses can cause serious morbidity and mortality in such patients, including leukemia patients and hematopoietic stem cell transplant (HSCT) recipients. Many viruses are known to cause respiratory tract infections, but the most common in hospitalized cancer patients are influenza viruses, respiratory syncytial virus (RSV), and parainfluenza viruses (PIV) [1, 2] . Although the combination of ribavirin and intravenous immunoglobulin (IVIG) or palivizumab has not been evaluated in a randomized trial, it is sometimes used in severely ill patients with RSV pneumonia, especially HSCT recipients, given that they have high mortality rates from this infection [3, 11, 14] . However, because other viruses can produce the same syndrome and influenza infection can produce other respiratory syndromes, a confirmatory test detecting the virus or viral antigens in nasal washes, throat swabs, respiratory tract secretions, or bronchoalveolar lavage specimens is needed in sporadic cases and in immunocompromised patients. cache = ./cache/cord-018319-tylkbh4h.txt txt = ./txt/cord-018319-tylkbh4h.txt === reduce.pl bib === id = cord-017107-sg8n12hs author = Suri, H. S. title = Epidemiology of Acute Respiratory Failure and Mechanical Ventilation date = 2008 pages = extension = .txt mime = text/plain words = 4109 sentences = 210 flesch = 39 summary = A recently completed, retrospective, community cohort study in Olmsted County, Minnesota included patients treated with NIV and found an even higher incidence of ALI, 156 per 100,000 person-years (personal communication, Rodrigo Cartin -Ceba), Mortality from ALI varies greatly depending upon the age of the patient, underlying chronic illnesses, ALI risk factors, and non-pulmonary organ dysfunctions [15] . In an international cohort study [4] , acute exacerbation of COPD was a principal indication for initiating mechanical ventilation in 13 % of patients with acute respiratory failure. The majority of patients with interstitial lung disease and acute respiratory failure admitted to the ICU require invasive mechanical ventilation . In a retrospective review [39] of 75 patients with interstitial lung disease who were mechanically ventilated at Mayo Clinic from 2003 to 2005, acute respiratory failure was the most common cause of ICU admiss ion (77 %), followed by sepsis (11 %) and cardiopulmonary arrest (4 %). cache = ./cache/cord-017107-sg8n12hs.txt txt = ./txt/cord-017107-sg8n12hs.txt === reduce.pl bib === id = cord-016499-5iqpl23p author = Mackay, Ian M. title = Rhinoviruses date = 2014-02-27 pages = extension = .txt mime = text/plain words = 23394 sentences = 1156 flesch = 45 summary = A convenience population of 15 healthy children (1-9 years old) without asthma were followed during at least three seasons, and picornaviruses were detected in 5 % of 740 specimens (21 % of infections) not associated with symptoms, The impact of HRV typing and of sampling based only on symptoms. Clinical features and complete genome characterization of a distinct human rhinovirus genetic cluster, probably representing a previously undetected HRV species, HRV-C, associated with acute respiratory illness in children Comparison of results of detection of rhinovirus by PCR and viral culture in human nasal wash specimens from subjects with and without clinical symptoms of respiratory illness Detection of human rhinovirus C viral genome in blood among children with severe respiratory infections in the Philippines cache = ./cache/cord-016499-5iqpl23p.txt txt = ./txt/cord-016499-5iqpl23p.txt === reduce.pl bib === id = cord-010233-772e35kx author = Monto, Arnold S. title = Respiratory illness caused by picornavirus infection: a review of clinical outcomes date = 2002-01-03 pages = extension = .txt mime = text/plain words = 4597 sentences = 241 flesch = 37 summary = The search terms used were picornavirus, rhinovirus, enterovirus, viral respiratory infection, upper respiratory infection, disease burden, economic, cost, complications, asthma, COPD, immunocompromised, elderly, otitis media, and sinusitis. In fact, because rhinovirus-induced illnesses are so common, they produce more restriction of activity and physician consultations annually than respiratory illnesses caused by other viruses or bacteria.s This article reviews the clinical impact and outcomes associated with picomavirusinduced respiratory infection in specific populations at risk for complications secondary to these infections. 15 In addition, these advances in technology have confirmed the results of earlier studies, further demonstrating the significance of rhinoviruses in causing or predisposing patients to otitis media and sinusitis and exacerbating other chronic respiratory diseases such as asthma, cystic fibrosis, and chronic obstructive pulmonary disease (COPD). cache = ./cache/cord-010233-772e35kx.txt txt = ./txt/cord-010233-772e35kx.txt === reduce.pl bib === id = cord-000602-z5p3a64x author = Bhat, Niranjan title = Use and Evaluation of Molecular Diagnostics for Pneumonia Etiology Studies date = 2012-03-08 pages = extension = .txt mime = text/plain words = 3608 sentences = 165 flesch = 26 summary = Although our final molecular diagnostic platform was ultimately selected on the basis of operational and strategic considerations determined by the specific context of PERCH, our review highlighted several conceptual and practical challenges in respiratory diagnostics that have broader relevance for the performance and interpretation of pneumonia research studies. Although our final molecular diagnostic platform was ultimately selected on the basis of operational and strategic considerations determined by the specific context of PERCH, our review highlighted several conceptual and practical challenges in respiratory diagnostics that have broader relevance for the performance and interpretation of pneumonia research studies. The specific research-related demands of PERCH added to these constraints, requiring that our diagnostic strategy must exclude any prior assumptions regarding the likely importance of specific pathogens; must include a full range of respiratory tract specimens, including upper respiratory swab or aspirate, induced sputum, lung aspirate, bronchoalveolar lavage, and pleural fluid; must be comprehensive, yet realistic; must appropriately balance the demands of accuracy and efficiency; must account for both clinical and research ethical issues; and must be feasible for use and support at all participating field sites. cache = ./cache/cord-000602-z5p3a64x.txt txt = ./txt/cord-000602-z5p3a64x.txt === reduce.pl bib === id = cord-023712-nptuuixw author = Bower, John title = Bronchiolitis date = 2014-10-31 pages = extension = .txt mime = text/plain words = 5404 sentences = 307 flesch = 41 summary = 12 Influenza A and B viruses frequently cause lower respiratory tract disease among children younger than 2 years of age, but the proportion manifesting as bronchiolitis is less than that observed with RSV. Although rapid diagnostic testing is generally unnecessary, it may be useful at times for implementing appropriate infection control, monitoring seasonal patterns of respiratory pathogens, restricting antimicrobial use, or providing confirmation of the diagnosis in children with unusual clinical presentations or severe disease. Timely diagnosis of specific viral respiratory pathogens may occasionally be necessary to guide specific antiviral therapy in children with high-risk conditions or severe illness with influenza or RSV. Although the risk of respiratory failure is relatively low for most children with RSV bronchiolitis, a small number of severely affected infants will require assisted ventilation in most intensive care units each year. Comparison of risk factors for human metapneumovirus and respiratory syncytial virus disease severity in young children cache = ./cache/cord-023712-nptuuixw.txt txt = ./txt/cord-023712-nptuuixw.txt === reduce.pl bib === id = cord-021277-smw6owql author = nan title = Respiratory distress syndrome: recent research date = 2013-02-17 pages = extension = .txt mime = text/plain words = 116 sentences = 16 flesch = 49 summary = key: cord-021277-smw6owql authors: nan title: Respiratory distress syndrome: recent research date: 2013-02-17 journal: nan DOI: 10.2165/00128413-199107860-00060 sha: doc_id: 21277 cord_uid: smw6owql nan In infants Effects In adults Use of corticosteroids in the adult respiratory distress syndrome -a clinical review Adult respiratory distress syndrome associated with parainfluenza virus type I in children Effects of prostaglandin EI on oxygen delivery and consumption in patients with the adult respiratory distress syndrome Prophylactic treatment with an aerosolized corticosteroid liposome in a porcine model of early ARDS induced by endotoxaemia Physiologic effects and side effects of prostaglandin E I in the adult respiratory distress syndrome respiratory distress and acute renal failure due to synergic bleomycin-cisplatin toxicity cache = ./cache/cord-021277-smw6owql.txt txt = ./txt/cord-021277-smw6owql.txt === reduce.pl bib === id = cord-017784-4r3fpmlb author = Foccillo, Giampiero title = The Infections Causing Acute Respiratory Failure in Elderly Patients date = 2019-08-06 pages = extension = .txt mime = text/plain words = 3573 sentences = 170 flesch = 31 summary = Severe community-acquired pneumonia and acute exacerbations of chronic obstructive pulmonary disease (AECOPD) are causes of acute respiratory failure (ARF) in elderly patients. This process termed immunosenescence or immune dysregulation, together changes in lung function who occur with advancing age, play a critical role in the manifestation of age-related pulmonary diseases such as infections (i.e., pneumonia), chronic obstructive pulmonary disease (COPD), and increased the risk for develop sepsis [1] . Triggering causes of ARF in advanced aged patients are especially acute heart decompensation, severe community-acquired pneumonia (CAP), acute exacerbations of COPD (AECOPD), and pulmonary embolism. Lower respiratory tract infections, including pneumonia and exacerbation of chronic obstructive pulmonary disease, are among the most common causes of ARF in elderly people and the most important cause of hospitalization. Antibiotic therapy and treatment failure in patients hospitalized for acute exacerbations of chronic obstructive pulmonary disease cache = ./cache/cord-017784-4r3fpmlb.txt txt = ./txt/cord-017784-4r3fpmlb.txt === reduce.pl bib === id = cord-018408-ttae193b author = Haddad, Imad Y. title = Pneumonia and Empyema date = 2008-11-15 pages = extension = .txt mime = text/plain words = 6160 sentences = 345 flesch = 33 summary = Second, patients with genetic or acquired immune defi ciency commonly develop severe pneumonia with opportunistic infections that usually do not infect healthy children. These immunocompromised patients commonly have been given chemo-radiotherapy for cancer or are receiving immune-suppressive agents to prevent rejection episodes following solid organ and hematopoietic stem cell transplantation. The pathogens that commonly produce CAP or VAP, such as Streptococcus pneumoniae, Gram-negative bacilli, and Staphylococcus aureus, are relatively virulent bacteria so that only a small inoculum is required and the aspiration is usually subtle. Bacterial organisms recovered from tracheal secretions obtained through an endotracheal tube may or may not refl ect the causative agent(s) responsible for lower respiratory tract infection. In addition, recipients of solid organ and hematopoietic stem cell transplantation (HSCT) are frequently given life-long treatment with immunosuppressive agents designed to prevent graft rejection or graft-versus-host disease. Early-onset nosocomial pneumonia and VAP are commonly caused by antibiotic-sensitive, community-acquired organisms (e.g., Strep. cache = ./cache/cord-018408-ttae193b.txt txt = ./txt/cord-018408-ttae193b.txt === reduce.pl bib === id = cord-010368-plpghewn author = Kenmoe, Sebastien title = Association of early viral lower respiratory infections and subsequent development of atopy, a systematic review and meta-analysis of cohort studies date = 2020-04-24 pages = extension = .txt mime = text/plain words = 3924 sentences = 204 flesch = 44 summary = Although not confirmed in all studies with a symmetric distribution of the 23 confounding factors investigated, the overall analyses showed that there was a relationship between childhood viral LRTI at < 5 years and serum test diagnosed-atopy (OR = 2.0, [95% CI = 1.0–4.1]), allergic rhinoconjunctivitis (OR = 1.7, [95% CI = 1.1–2.9]), hyperreactivity diagnosed by serum tests with food (OR = 5.3, [1.7–16.7]) or inhaled allergens (OR = 4.2, [95% CI = 2.1–8.5]), or furred animals (OR = 0.6, [95% CI = 0.5–0.9]). The purpose of this systematic review and meta-analysis of Long-term sEquelAe of lower Respiratory tract infections iN Early childhood (A LEARNED study) was to investigate the association between viral LRTI at <5 years and the atopy development at > 2 years. Pérez-Yarza in a systematic review including children younger than 3 years with HRSV respiratory infection from 1985 to 2006 also suggested controversial findings about the subsequent risk of allergic sensitization development defined by positive skin or serum tests specific for common allergens [11] . cache = ./cache/cord-010368-plpghewn.txt txt = ./txt/cord-010368-plpghewn.txt === reduce.pl bib === === reduce.pl bib === id = cord-003357-4qrg6lqu author = Wang, Yingchen title = Prevalence of Common Respiratory Viral Infections and Identification of Adenovirus in Hospitalized Adults in Harbin, China 2014 to 2017 date = 2018-11-27 pages = extension = .txt mime = text/plain words = 5191 sentences = 260 flesch = 47 summary = Conclusion: This study demonstrated that common respiratory viruses were partially responsible for hospitalized lower respiratory tract infections in adult patients from Harbin, China, with parainfluenza virus as the dominant viral pathogen. Viral infections played an important role in pediatric lower respiratory tract infections, and the corresponding common viral pathogens were influenza A and B virus (IAV and IBV), parainfluenza virus (PIV, type 1 to 3), respiratory syncytial virus (RSV) and human adenovirus (ADV) (Pavia, 2011) . In this report, the prevalence of common viruses in the lower respiratory tract infection of hospitalized adult patients from Harbin, China was explored in hopes of revealing the clinical and pathogenic features of respiratory viruses. The overall detection rate of viral infection among hospitalized adult patients in this report is 14.5%, which was consistent with the result of 16.8% in the age group above 14 years old by a national survey from 2009 to 2013 in China (Feng et al., 2014) . cache = ./cache/cord-003357-4qrg6lqu.txt txt = ./txt/cord-003357-4qrg6lqu.txt === reduce.pl bib === id = cord-002801-6myqgme3 author = Yoon, Byung Woo title = Possible therapeutic effect of orally administered ribavirin for respiratory syncytial virus-induced acute respiratory distress syndrome in an immunocompetent patient: a case report date = 2017-12-20 pages = extension = .txt mime = text/plain words = 2560 sentences = 144 flesch = 38 summary = title: Possible therapeutic effect of orally administered ribavirin for respiratory syncytial virus-induced acute respiratory distress syndrome in an immunocompetent patient: a case report Respiratory syncytial virus-induced severe pneumonia or acute respiratory distress syndrome in immunocompetent adults has been rarely described. We report a case of respiratory syncytial virus-induced acute respiratory distress syndrome occurring in a previously healthy man successfully treated with orally administered ribavirin. CONCLUSION: This case demonstrates the potential usefulness of orally administered ribavirin as a therapeutic option for severe respiratory syncytial virus infection, at least in an immunocompetent host. RSV-induced severe pneumonia or acute respiratory distress syndrome (ARDS) in immunocompromised patients is not uncommon. Here we report a case of ARDS due to RSV occurring in a previously healthy adult successfully treated with orally administered ribavirin. In addition, this case suggests that orally administered ribavirin could be a therapeutic option even for severe pneumonia or ARDS due to RSV, at least in immunocompetent hosts, especially if other antiviral agents are unavailable. cache = ./cache/cord-002801-6myqgme3.txt txt = ./txt/cord-002801-6myqgme3.txt === reduce.pl bib === id = cord-007445-2folsh35 author = Tuffaha, Amjad title = THE ROLE OF RESPIRATORY VIRUSES IN ACUTE AND CHRONIC ASTHMA date = 2000-06-01 pages = extension = .txt mime = text/plain words = 4973 sentences = 217 flesch = 34 summary = To more comprehensively evaluate the relationships among virus infection, atopy (cytokine dysregulation of Thl / Th2 imbalance), and immune system or lung developmental components, a rat model of virus-induced airway dysfunction has been studied extensively.'l' In this model, infection with PIV type 1 during a critical developmental time period (when the animals are weaning [ 3 4 weeks of age] as opposed to when they are neonates [4-5 days] or adults) produces chronic (8-12 weeks fol-lowing infection), episodic, reversible airway inflammation and remodeling with associated alterations in airway physiology (increased resistance and rnethacholine responsiveness) that resemble human asthma in high (brown Norway strain) but not low (F344 strain) IgEantibody producing rats.62 The temporal progression of this asthma-like syndrome is associated with a Thl / Th2 imbalance within the lung, and its development can be significantly attenuated by the exogenous administration of IFN-8 just prior to and during the viral infection in the brown Norway responder strain.lo2 This model further supports the concept of both genetic (atopy; cytokine dysregulation or imbalance) and environmental factors (virus infection) being important in the inception of the asthmatic phenotype, as well as a developmental component contributing. cache = ./cache/cord-007445-2folsh35.txt txt = ./txt/cord-007445-2folsh35.txt === reduce.pl bib === id = cord-017499-51yy7y9n author = Freye, Enno title = Mechanism of Action of Opioids and Clinical Effects date = 2008 pages = extension = .txt mime = text/plain words = 24955 sentences = 1278 flesch = 45 summary = Thus, -selective opioids like morphine, fentanyl and sufentanil, due to the high density of binding sites, mediate their main action within the brain stem and the midbrain. This sterospecificity of opiate action supports the concept of selective receptor binding to a site, which is able to distinguish in "handedness or goodness of fit" of an opioid molecule maximal response induced by administration of the active agent. On the other hand mixed agonist/antagonists, such as pentazocine, nalorphine, levallorphan, nalbuphine and butorphanol, demonstrate characteristics, which enable them to displace a pure agonist at the receptor site (antagonistic effect), but at the same time when administered by themselves, they induce opioid related effects such as analgesia and respiratory depression (agonistic effects; Table II-7) . However, a less potent opioid like codeine or tramadol, even when given in dosages higher than their therapeutic margin, will not induce a clinically relevant respiratory depressive effect ( Figure II-34) . cache = ./cache/cord-017499-51yy7y9n.txt txt = ./txt/cord-017499-51yy7y9n.txt === reduce.pl bib === id = cord-003917-bswndfvk author = Lalle, Eleonora title = Pulmonary Involvement during the Ebola Virus Disease date = 2019-08-24 pages = extension = .txt mime = text/plain words = 5545 sentences = 245 flesch = 40 summary = Filoviruses have become a worldwide public health concern, especially during the 2013–2016 Western Africa Ebola virus disease (EVD) outbreak—the largest outbreak, both by number of cases and geographical extension, recorded so far in medical history. During the 2013–2016 Western Africa outbreak, Ebola virus (EBOV) was detected in the lung of infected patients suggesting a role in lung pathogenesis. However, new evidences collected during the recent 2013-2016 Ebola outbreak hypothesized shedding of the virus in the lung and identified viral replication markers in sputum samples collected from EBOV infected patients [14] . However, new evidences collected during the recent 2013-2016 Ebola outbreak hypothesized shedding of the virus in the lung and identified viral replication markers in sputum samples collected from EBOV infected patients [14] . Interestingly, evidence collected in animal studies, in the epidemiological analysis of transmission chains, and in the most recent Ebola outbreaks suggests that EBOV may be able to cause primary pulmonary infection. cache = ./cache/cord-003917-bswndfvk.txt txt = ./txt/cord-003917-bswndfvk.txt === reduce.pl bib === id = cord-005818-3mzwliiy author = Speer, C. P. title = Surfactantsubstitutionstherapie: Ein entscheidender Durchbruch in der Behandlung des Atemnotsyndroms Frühgeborener date = 2014-04-24 pages = extension = .txt mime = text/plain words = 3927 sentences = 400 flesch = 27 summary = Die Surfactantsubstitution stellt einen entscheidenden Durchbruch in der Behandlung des Atemnotsyndroms dar.Durch eine prophylaktische Surfactantgabe oder die Therapie des manifesten Atemnotsyndroms konnten die akuten pulmonalen Komplikationen beatmeter Frühgeborener um 2/3 reduziert und die Sterblichkeit nahezu halbiert werden.Eine frühe Surfactantapplikation innerhalb der ersten 15 Lebensminuten ist besonders bei sehr unreifen Frühgeborenen einer späteren Behandlung bei manifestem Atemnotsyndrom überlegen.Als initiale Dosis werden 100 mg Phospholipide/kg empfohlen; einige Frühgeborene profitieren von einer Mehrfachbehandlung.Natürliche Surfactantpräparate haben eine bessere klinische Wirksamkeit als die zurzeit verfügbaren synthetischen Präparate.Es gibt einige Hinweise, dass eine Surfactanttherapie auch bei pulmonalen Erkrankungen Neugeborener einen therapeutischen Effekt haben kann; diese Erkrankungen wie Mekoniumaspirationssyndrom und neonatale Pneumonie führen u.a.über eine Inaktivierung von Surfactant zu einer sekundären Defizienz dieses oberflächenaktiven Systems. Fujiwara und Mitarbeiter (Morioka) berichteten 1980 erstmals von Frühgeborenen mit manifestem Atemnotsyndrom (engl: respiratory distress syndrom: RDS), die nach einer intratrachealen Applikation eines Rindersurfactants mit einer deutlichen Verbesserung des pulmonalen Gasaustausches reagierten [18] . cache = ./cache/cord-005818-3mzwliiy.txt txt = ./txt/cord-005818-3mzwliiy.txt === reduce.pl bib === id = cord-017252-88b3preq author = Morgan, Carrie I. title = Pneumonia date = 2014-02-20 pages = extension = .txt mime = text/plain words = 6424 sentences = 315 flesch = 32 summary = Despite immunizations and public health initiatives, the most common bacterial causes of CAP have remained largely unchanged over the last several decades and include: Streptococcus pneumoniae , Staphylococcus aureus , Haemophilus infl uenzae (including non-typable strains) and Moraxella catarrhalis [ 7 , 8 , 21 , 23 ] . Chest CT is helpful to further evaluate diffi cult cases, particularly immunocompromised children with ill-defi ned infi ltrates on CXR, complex empyema or effusion, or recurrent or chronic pneumonia [ 11 ] . Respiratory failure in an immunocompromised child frequently necessitates a chest CT to better visualize the pattern and extent of disease, aid in diagnosis of the etiology, determine the need for more invasive procedures, and to increase the sensitivity of assessing treatment response [ 11 ] . Etiology of community-acquired pneumonia in hospitalized school-age children: evidence for high prevalence of viral infections cache = ./cache/cord-017252-88b3preq.txt txt = ./txt/cord-017252-88b3preq.txt === reduce.pl bib === id = cord-009860-qebenhxz author = Falsey, Ann R. title = Viral Respiratory Infections in the Institutionalized Elderly: Clinical and Epidemiologic Findings date = 2015-04-27 pages = extension = .txt mime = text/plain words = 3461 sentences = 220 flesch = 52 summary = Serologic evidence of infection with respiratory syncytial virus (RSV) and parainfluenza were determined by enzyme immunoassay (EIA), and influenza by hemagglutination‐inhibition assay and EIA. This is despite the fact that each year many residents of nursing homes become ill with respiratory infections not proven to be influenza, either by culture or serology. The purpose of this study was to identify all common respiratory viruses which cause symptomatic dsease during the winter months in nursing home patients, by utilizing both viral cultures and serology, and to assess their clinical impact. Subjects Between December 11, 1989 and March 13, 1990 , the head nurse on each floor identified residents who had signs or symptoms of acute respiratory illness including nasal congestion, pharyngitis, cough, wheezing, or respiratory difficulty with or without fever. The groups of viruses responsible for most acute respiratory infections are rhinovirus, coronavirus, influenza, RSV, parainfluenza, and adeno~irus.~ An attempt was made to diagnose each of these pathogens, with the exception of coronavirus, utilizing either culture, serology, or both. cache = ./cache/cord-009860-qebenhxz.txt txt = ./txt/cord-009860-qebenhxz.txt === reduce.pl bib === id = cord-001070-zlzag6a8 author = Camargo, C.N. title = Human rhinovirus infections in symptomatic and asymptomatic subjects date = 2012-06-01 pages = extension = .txt mime = text/plain words = 630 sentences = 47 flesch = 38 summary = The role of rhinovirus asymptomatic infections in the transmission among close contacts subjects is unknown. We investigated HRV infections rates on selected populations of a pair of one child and one family member, health care workers (HCW), and immunocompromised patients with and without respiratory symptoms from June to September. One hundred and eleven health care workers (HCW) from São Paulo Hospital, 36 pairs of one child and one family member and 8 blood marrow transplanted hospitalized patients (BMT). Influenza and rhinovirus infections among health-care workers Acute Respiratory Infection and Influenza-Like Illness Viral Etiologies in Brazilian Adults Use of polymerase chain reaction for diagnosis of picornavirus infection in subjects with and without respiratory symptoms Rhinovirus transmission within families with children: Insidence of symptomatic and assymptomatic infections Viral respiratory infections in hospitalized and community control children in Alaska Frequent detection of respiratory viruses in adult recipients of stem cell transplants with the use of real-time polymerase chain reaction, compared with viral culture cache = ./cache/cord-001070-zlzag6a8.txt txt = ./txt/cord-001070-zlzag6a8.txt === reduce.pl bib === === reduce.pl bib === id = cord-251986-ajlpb9li author = Li, Yan‐Chao title = The neuroinvasive potential of SARS‐CoV2 may play a role in the respiratory failure of COVID‐19 patients date = 2020-03-11 pages = extension = .txt mime = text/plain words = 2250 sentences = 125 flesch = 47 summary = This virus shares highly homological sequence with SARS‐CoV, and causes acute, highly lethal pneumonia coronavirus disease 2019 (COVID‐19) with clinical symptoms similar to those reported for SARS‐CoV and MERS‐CoV. A growing body of evidence shows that neurotropism is one common feature of CoVs. 1, [9] [10] [11] [12] Therefore, it is urgent to make clear whether SARS-CoV-2 can gain access to the central nervous system (CNS) and induce neuronal injury leading to the acute respiratory distress. Mechanisms of host defense following severe acute respiratory syndrome-coronavirus (SARS-CoV) pulmonary infection of mice Exploring the pathogenesis of severe acute respiratory syndrome (SARS): the tissue distribution of the coronavirus (SARS-CoV) and its putative receptor, angiotensin-converting enzyme 2 (ACE2) Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for pathogenesis and virus transmission pathways Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients cache = ./cache/cord-251986-ajlpb9li.txt txt = ./txt/cord-251986-ajlpb9li.txt === reduce.pl bib === id = cord-253145-1fbj1rdv author = Fox, Julie D. title = Nucleic acid amplification tests for detection of respiratory viruses date = 2007-10-31 pages = extension = .txt mime = text/plain words = 5391 sentences = 270 flesch = 40 summary = Assays based on nucleic acid amplification and detection can be designed against a broad range of respiratory viruses and have been particularly useful for detection of recently identified viruses such as human metapneumovirus and coronaviruses NL63 and HKU1. Use of NATs allows assessment of the impact of a wider array of potential pathogens on respiratory infections than previously possible and target-specific (multiplex) approaches have proved feasible for enhanced broadspectrum respiratory virus diagnosis. Many feasibility studies have confirmed that NATs improve detection of potential pathogens from lower respiratory tract specimens as well as from respiratory swabs even where alternative methods such as DFA and culture are available (Hibbitts and Fox, 2002; Moore et al., 2004; Lee et al., 2006) . If individual NATs are utilized, multiple infections are identified frequently but use of real-time multiplex reactions may lead to competition between amplification and detection Table 1 Enhanced detection of respiratory viruses using NATs cache = ./cache/cord-253145-1fbj1rdv.txt txt = ./txt/cord-253145-1fbj1rdv.txt === reduce.pl bib === id = cord-005583-hmv8jjfl author = Peters, M. J. title = Acute hypoxemic respiratory failure in children: case mix and the utility of respiratory severity indices date = 2013-12-27 pages = extension = .txt mime = text/plain words = 3992 sentences = 207 flesch = 45 summary = In an individual patient, such a response to intervention should be indicated by their best, rather than worst, measure of gas exchange, Therefore, the purpose of the present prospective, single institution study of AHRF in children was to assess whether the best, early respiratory indices in non-survivors were significantly different from those who survived. Table 2 Comparison of previously published [2] [3] [4] [5] respiratory severity parameters with the present series (PPV positive predictive value for mortality, VI ventilation index, OI oxygenation index, PIP peak inspiratory pressure (cmH20), A-aDO 2 alveolar arterial oxygen gradient (mmHg), MAP mean airway pressure (cmH20), LR + the likelihood ratio for a positive test result, i.e. the ratio of finding the predictor in non-survivors to finding it in survivors) * indicates intermediate to high diagnostic impact, ns not significant Proposed PPV LR + PPV p predictors (95 % confidence interval) in present study cache = ./cache/cord-005583-hmv8jjfl.txt txt = ./txt/cord-005583-hmv8jjfl.txt === reduce.pl bib === id = cord-017715-99ri6x0y author = Zhou, Bo-Ping title = SARS date = 2015-07-25 pages = extension = .txt mime = text/plain words = 8853 sentences = 460 flesch = 46 summary = 2. The patient has been to or lived in areas reported with infectious SARS patients and patients suffering from secondary infections 2 weeks before the disease onset, who also have abovementioned clinical symptoms, not high peripheral blood white cell count and pulmonary shadows on chest X-ray fi lms. 3. The patient has been to or lived in areas reported with infectious SARS patients and patients suffering from secondary infections 2 weeks before the disease onset, who also have abovementioned clinical symptoms, pulmonary shadows on chest X-ray fi lms, and no obvious response to anti-infectious treatment. If the foci could not be absorbed for a long term in SARS recovery phase or patients still have symptoms but normal chest presentations, CT scan need to be carried out for further observation as it can better visualize the subtle pulmonary interstitial changes, such as lung interlobular septum thickening, intralobular septum thickening, subpleural linear shadow, and small ground-glassdensity lesion and regional and segmental bronchiectasis, and therefore is helpful for clinical diagnosis of pulmonary interstitial fi brosis. cache = ./cache/cord-017715-99ri6x0y.txt txt = ./txt/cord-017715-99ri6x0y.txt === reduce.pl bib === id = cord-021894-lq8yr710 author = Cunningham, Steve title = Bronchiolitis date = 2018-03-13 pages = extension = .txt mime = text/plain words = 6536 sentences = 351 flesch = 39 summary = Globally there are an estimated 33.8 million cases of RSV lower respiratory tract infection each year in children under 5 years of age, resulting in 3.4 million admissions to the hospital and 66 to 199 thousand deaths (with the majority in low-and middle-income countries). 42, 43 Severity of disease is associated with both infant risk factors (including lack of adaptive T cell response), 26,44 but also RSV virus specific factors (viral antigen load and direct cytotoxic effects). Respiratory syncytial virus genomic load and disease severity among children hospitalized with bronchiolitis: multicenter cohort studies in the United States and Finland Respiratory syncytial virus load, viral dynamics, and disease severity in previously healthy naturally infected children The risk of mortality among young children hospitalized for severe respiratory syncytial virus infection High incidence of pulmonary bacterial co-infection in children with severe respiratory syncytial virus (RSV) bronchiolitis cache = ./cache/cord-021894-lq8yr710.txt txt = ./txt/cord-021894-lq8yr710.txt === reduce.pl bib === id = cord-003492-rodqdtfj author = Montaner-Tarbes, Sergio title = Key Gaps in the Knowledge of the Porcine Respiratory Reproductive Syndrome Virus (PRRSV) date = 2019-02-20 pages = extension = .txt mime = text/plain words = 9579 sentences = 381 flesch = 31 summary = PRRSV is a complex disease and several gaps in the knowledge of its economic impact, biology and evolution, genetic polymorphism, mechanism of viral infections, elicitation of protective immune responses and novel control strategies, have been reviewed here (Box 1). Nonstructural proteins nsp2TF and nsp2N of porcine reproductive and respiratory syndrome virus (PRRSV) play important roles in suppressing host innate immune responses Immune responses in pigs infected with porcine reproductive and respiratory syndrome virus (PRRSV) Immunodominant epitopes in nsp2 of porcine reproductive and respiratory syndrome virus are dispensable for replication, but play an important role in modulation of the host immune response Nonstructural protein 11 (nsp11) of porcine reproductive and respiratory syndrome virus (PRRSV) promotes PRRSV infection in MARC-145 cells Immune response to ORF5a protein immunization is not protective against porcine reproductive and respiratory syndrome virus infection cache = ./cache/cord-003492-rodqdtfj.txt txt = ./txt/cord-003492-rodqdtfj.txt === reduce.pl bib === id = cord-001162-z8cbbit3 author = Yun, Heather C. title = Pandemic Influenza Virus 2009 H1N1 and Adenovirus in a High Risk Population of Young Adults: Epidemiology, Comparison of Clinical Presentations, and Coinfection date = 2014-01-08 pages = extension = .txt mime = text/plain words = 3365 sentences = 160 flesch = 41 summary = title: Pandemic Influenza Virus 2009 H1N1 and Adenovirus in a High Risk Population of Young Adults: Epidemiology, Comparison of Clinical Presentations, and Coinfection While coinfections with viral pathogens including 2009 H1N1 have been described in patients with respiratory infections, few prospective studies have related these to clinical presentation and outcomes in adults since molecular diagnostics became available, and none in the setting of high background rates of adenovirus. [12] [13] [14] [15] [16] [17] We sought to describe the epidemiology of 2009 H1N1 and adenovirus in a basic training population, and to correlate differences in clinical presentations and outcomes with each respective pathogen and in coinfections. Subject enrollment was variable throughout the study period, depending on rates of clinical illness within the training population, as well as availability of study personnel to enroll trainees, and given that 2009 H1N1 influenza virus PCR was done as part of clinical care, there could have been some differences in those who enrolled vs. cache = ./cache/cord-001162-z8cbbit3.txt txt = ./txt/cord-001162-z8cbbit3.txt === reduce.pl bib === id = cord-007796-zggk0x2q author = Lindemans, Caroline A. title = The Immune Response to Viral Lower Respiratory Tract Infection date = 2005 pages = extension = .txt mime = text/plain words = 9767 sentences = 518 flesch = 38 summary = In respect to the role of viruses in the pathogenesis of acute and chronic airway disease in children, it is of utmost importance that we gain a proper understanding of the underlying mechanisms involved in order to design effective therapeutic and preventive strategies. Epithelial cells are key regulators of the innate immune response against viral infections (Garofalo and Haeberle, 2000) , producing a number of inflammatory mediators in response to RSV infection. In summary, in RSV lower respiratory tract infections, cytotoxic CD8ϩ T-cells are involved in viral clearance while the humoral response is required for the protection against reinfection. The innate immune defense to viral respiratory tract infections consists of the mucosal layer, type 1 interferons, activated phagocytes, and NK-cells. A key question is whether the association with the development of asthma is merely an expression of increased susceptibility to both asthma and RSV-induced lower respiratory tract infections or whether true causality is involved. cache = ./cache/cord-007796-zggk0x2q.txt txt = ./txt/cord-007796-zggk0x2q.txt === reduce.pl bib === id = cord-254265-8i86c8kt author = Camps, Marta title = Prevalence of human metapneumovirus among hospitalized children younger than 1 year in Catalonia, Spain date = 2008-06-12 pages = extension = .txt mime = text/plain words = 4567 sentences = 227 flesch = 42 summary = In 67/99 children (67%) at least one viral pathogen was identified, the viruses detected most frequently were respiratory syncytial virus (35%), human metapneumovirus (25%) and rhinovirus (19%). The aim of the present study was to describe the role of human metapneumovirus and other common respiratory viruses including: influenza virus A, B, and C, parainfluenza 1-4 viruses, adenoviruses, respiratory syncytial virus A and B, rhinovirus, coronavirus 229E and OC43 and enterovirus as bronchiolitis, and bronchopneumonia pathogens among hospitalized children younger than 1 year, taking into account that in this age group respiratory viruses are the main etiological agents of lower respiratory tract infections [Shay et al., 1999; Smyth and Openshaw, 2006; Bush and Thomson, 2007] . Detection of human metapneumovirus RNA sequences in nasopharyngeal aspirates of young French children with acute bronchiolitis by real-time reverse transcriptase PCR and phylogenetic analysis cache = ./cache/cord-254265-8i86c8kt.txt txt = ./txt/cord-254265-8i86c8kt.txt === reduce.pl bib === === reduce.pl bib === id = cord-017364-d9zmdm23 author = Crowe, James E. title = Paramyxoviruses: Respiratory Syncytial Virus and Human Metapneumovirus date = 2014-02-27 pages = extension = .txt mime = text/plain words = 18331 sentences = 897 flesch = 37 summary = A virus causing a similar cytopathic effect in cultured cells was recovered from infants with respiratory illness shortly after, and studies of human antibodies in the serum of infants and children indicated that infection was common early in life [ 1 , 2 ] . Higher titers of virus in respiratory secretions usually are associated with increased severity of disease, in prospective studies of natural infection [ 114 ] or of clinical vaccine trials [ 115 ] . Most epidemiologic studies of MPV in children show that the virus is the second leading cause of lower respiratory infection after RSV. Acute lower respiratory tract infections by human metapneumovirus in children in Southwest China: a 2-year study The impact of infection with human metapneumovirus and other respiratory viruses in young infants and children at high risk for severe pulmonary disease Comparison of risk factors for human metapneumovirus and respiratory syncytial virus disease severity in young children cache = ./cache/cord-017364-d9zmdm23.txt txt = ./txt/cord-017364-d9zmdm23.txt === reduce.pl bib === id = cord-016882-c9ts2g7w author = Ribeiro, Edna title = Viruses Present Indoors and Analyses Approaches date = 2017-06-12 pages = extension = .txt mime = text/plain words = 10251 sentences = 466 flesch = 37 summary = It's well known that approximately 60% of total human respiratory and gastrointestinal infections are acquired indoor, since viruses have a rapid spread in the community and can be transmitted easily, especially in crowded and poorly ventilated environments, causing high morbidity and decline in quality of life and productivity. Viruses' inductors of Severe Acute Respiratory Syndrome (SARS), influenza and norovirus are transmitted from patients primarily by contact and/or droplet routes, while airborne transmission occurs over a limited distance (Srikanth et al., 2008) . It is well-known that viruses are shed in large numbers, with transmission routes extraordinary diverse, including direct contact with infected persons, faecal-oral transmission (through contaminated food and water), droplet and airborne transmission, and can survive for long periods on surfaces or fomites, emphasizing the possible role of surfaces in the transmission of viruses (Barker et al., 2001; La Rosa et al., 2013) . cache = ./cache/cord-016882-c9ts2g7w.txt txt = ./txt/cord-016882-c9ts2g7w.txt === reduce.pl bib === id = cord-020700-iko8gy1e author = Calvo, Cristina title = Respiratory viral infections in a cohort of children during the first year of life and their role in the development of wheezing() date = 2017-07-06 pages = extension = .txt mime = text/plain words = 3945 sentences = 228 flesch = 53 summary = INTRODUCTION: It is known that infants with viral respiratory infections severe enough to require hospital admission have a high risk of developing recurrent wheezing. The main aim of this study was to analyse symptomatic and asymptomatic respiratory viral infections during the first year of life in a cohort of infants, recruited at birth, and the development of recurrent wheezing. The objective of our prospective study was to analyse asymptomatic and symptomatic infections of varying severity in a cohort of newborns during the first year of life and assess their role in the development of recurrent wheezing. We defined ''first detected viral infection'' as PCR detecting a respiratory virus in a sample for the first time in the life of a child, whether the infection was asymptomatic, symptomatic and managed at the outpatient level, or symptomatic and requiring hospital admission. cache = ./cache/cord-020700-iko8gy1e.txt txt = ./txt/cord-020700-iko8gy1e.txt === reduce.pl bib === === reduce.pl bib === id = cord-023528-z9rc0ubj author = Wilkins, Pamela A. title = Disorders of Foals date = 2009-05-18 pages = extension = .txt mime = text/plain words = 42569 sentences = 2235 flesch = 44 summary = First, restriction of the thorax or the abdomen can result in impaired ventilation, which can occur easily when one restrains a foal and may result in spuriously abnormal arterial blood gas values (see the discussion on arterial blood gas evaluation, Respiratory Diseases Associated with Hypoxemia in the Neonate). Hypoxic ischemic encephalopathy (HIE), currently referred to as neonatal encephalopathy in the human literature, is one systemic manifestation of a broader syndrome of perinatal asphyxia syndrome (PAS), and management of foals with signs consistent with a diagnosis of HIE requires the clinician to examine other body systems fully and to provide therapy directed at treating other involved systems. Therapy for the various manifestations of hypoxiaischemia involves control of seizures, general cerebral support, correction of metabolic abnormalities, maintenance of normal arterial blood gas values, maintenance of tissue perfusion, maintenance of renal function, treatment of gastrointestinal dysfunction, prevention and recognition and early treatment of secondary infections, and general supportive care. cache = ./cache/cord-023528-z9rc0ubj.txt txt = ./txt/cord-023528-z9rc0ubj.txt === reduce.pl bib === id = cord-151024-qe7c2uks author = Koca, Caglar title = Molecular Communication Theoretical Modeling and Analysis of SARS-CoV2 Transmission in Human Respiratory System date = 2020-11-07 pages = extension = .txt mime = text/plain words = 5622 sentences = 353 flesch = 56 summary = We further provide the impulse response of SARS-CoV2-ACE2 receptor binding event to determine the proportion of the virus population reaching different regions of the respiratory tract. These results are especially important to understand the effect of SARS-CoV2 on the different human populations at different ages who have different mucus flow rates and ACE2 receptor concentrations in the different regions of the respiratory tract. • Determining impulse response of SARS-CoV2 infection process for the first time in literature • Calculating ACE2 receptor densities in the different regions of the respiratory tract: Based on the available data on surface parameters, we calculate ACE2 receptor density crudely. Due to the cylindrical symmetry assumption, we can make a longitudinal Upon entering the mucus and periciliary layer, viruses use their viral S-spike proteins to bind to ACE2 receptors on host cell surfaces [43] . cache = ./cache/cord-151024-qe7c2uks.txt txt = ./txt/cord-151024-qe7c2uks.txt === reduce.pl bib === id = cord-016020-awanrm9u author = Fox, Julie D. title = Respiratory Pathogens date = 2007 pages = extension = .txt mime = text/plain words = 4603 sentences = 220 flesch = 30 summary = In addition, despite the well-recognized association of viral infections with upper and lower respiratory tract infections, the current diagnostic virology procedures do not provide an answer rapidly enough to with parainfluenza virus type 4, human coronaviruses, rhinoviruses, and some enteroviruses would not ordinarily be identified without RNA detection methods. Published diagnostic methods for detection of respiratory pathogen DNA or RNA directly from clinical specimens utilize target amplification procedures such as polymerase chain reaction (PCR) or nucleic acid sequence-based amplification (NASBA).Although direct detection methods based on nucleic acid hybridization would be theoretically possible, the amount of target nucleic acid in specimens may be minimal and such methods would lack sensitivity compared to amplification methods, unless the organism was propagated before analysis. Thus, the molecular amplification procedures reported for direct detection of respiratory pathogens in clinical samples include PCR (e.g., Reference 19 and Figure 41 assays have utilized bacterial ribosomal RNA (rRNA; e.g., Reference 22 ). cache = ./cache/cord-016020-awanrm9u.txt txt = ./txt/cord-016020-awanrm9u.txt === reduce.pl bib === id = cord-022337-f3a349cb author = Busse, William W. title = Infections date = 2007-05-09 pages = extension = .txt mime = text/plain words = 7599 sentences = 391 flesch = 40 summary = There is also evidence that the viruses which cause wheezing with respiratory tract infections may be age dependent; for example, infants wheeze with RSV while older children have exacerbations of asthma with rhinovirus.^^ To extend these observations. However, as already discussed, the increased frequency of LARs to antigen was still noted 4 weeks after the viral infection, suggesting that a viral respiratory infection has a greater, and possibly more lasting, effect on factors that participate in the development of LARs. Virus-associated airway hyperresponsiveness is a multifactorial process involving a complex interplay of IgE-dependent reactions, epithelial activation or damage, autonomic nervous system dysfunction and, of particular interest and relevance to our discussion, enhanced allergic inflammation."^^ In IgE-mediated reactions, the tissue response, be it the skin, nose or airway, is influenced by I g E sensitization of mast cells and basophils, release of bronchospastic and inflammatory mediators from sensitized cells, and the response of the target organ, which in asthma is bronchial smooth muscle. cache = ./cache/cord-022337-f3a349cb.txt txt = ./txt/cord-022337-f3a349cb.txt === reduce.pl bib === id = cord-007030-mewo9w43 author = Hashim, Suhana title = The prevalence and preventive measures of the respiratory illness among Malaysian pilgrims in 2013 hajj season date = 2016-02-08 pages = extension = .txt mime = text/plain words = 3903 sentences = 237 flesch = 55 summary = The purpose of this study is to determine the prevalence of respiratory illness and its associated factors among Malaysian hajj pilgrims in 2013 and to describe its preventive measures. Malaysian hajj pilgrims with previous experience of hajj (OR 0.24; 95% CI 0.10–0.56) or umrah (OR 0.19; 95% CI 0.07–0.52) and those who have practiced good hand hygiene (OR 0.35; 95% CI 0.16–0.79) were found to be significantly associated with lower risk of having respiratory illness. All preventive measures which include hand hygiene, wearing face masks and influenza vaccination must be practiced together as bundle of care to reduce respiratory illness effectively. Data based on the social demographic, co-morbid illness, smoking habits, symptoms of respiratory illness, history of contact with respiratory ill patients, previous experience of hajj or umrah, the practice of preventive measures, influenza and pneumococcal vaccination and supplement intake against respiratory illness were obtained by a self-administered proforma. cache = ./cache/cord-007030-mewo9w43.txt txt = ./txt/cord-007030-mewo9w43.txt === reduce.pl bib === === reduce.pl bib === id = cord-023711-xz5ftnat author = MORENO-LÓPEZ, J. title = Acute Respiratory Disease in Cattle date = 2013-11-17 pages = extension = .txt mime = text/plain words = 1525 sentences = 85 flesch = 49 summary = Acute respiratory disease in cattle is not attributable to a single etiological agent. However, if PI3 virus or BVDV has been isolated, you have diagnosed the infection but not an "acute respiratory/enteric disease", because other viruses and also bacteria might be etiologically involved. At the end of the 1950s, "shipping fever" was described as a disease following massive transports to or from the enormous feedlots of the USA, and PI3 virus was isolated as the first virus of a condition with a multiple viral etiology. The types 4, 5 and 7 have been described each as a single causative agent of acute respiratory-enteric disease in Hungary and Japan, respectively. The isolation of these viruses from apparently healthy cattle as well as from those with acute respiratory-enteric disease indicates that they are widespread. A serosurvey of viruses during outbreaks of acute respiratory and/or enteric disease in Swedish cattle cache = ./cache/cord-023711-xz5ftnat.txt txt = ./txt/cord-023711-xz5ftnat.txt === reduce.pl bib === id = cord-027550-yyqsatqw author = Mammas, Ioannis N. title = Update on current views and advances on RSV infection (Review) date = 2020-06-15 pages = extension = .txt mime = text/plain words = 7970 sentences = 390 flesch = 35 summary = cache = ./cache/cord-027550-yyqsatqw.txt txt = ./txt/cord-027550-yyqsatqw.txt === reduce.pl bib === id = cord-022084-hap7flng author = ARRUDA, EURICO title = Respiratory Tract Viral Infections date = 2009-05-15 pages = extension = .txt mime = text/plain words = 19181 sentences = 1041 flesch = 43 summary = The Centers for Disease Control and Prevention (CDC) recommends the immunization of persons aged 50 years and older; residents of nursing homes; children and adults with chronic cardiovascular or pulmonary disease, including asthma; persons chronically ill with diabetes mellitus, renal dysfunction, or hemoglobinopathies; immunosuppressed patients including those with HIV infection; children and adolescents on chronic aspirin therapy who may develop postinfluenza Reye' s syndrome; women who will be pregnant during the influenza season; children aged 6 to 23 months; those who can transmit influenza to persons at high risk, such as health-care workers and household contacts of those at high risk including children 0 to 23 months of age; crew members of cruise ships; providers of essential services; and unimmunized travelers to areas where influenza may be circulating, including the tropics, the southern hemisphere between April and September, and those traveling in large organized tourist groups. cache = ./cache/cord-022084-hap7flng.txt txt = ./txt/cord-022084-hap7flng.txt === reduce.pl bib === id = cord-254770-ot9ys10r author = Uçkay, Ilker title = Low incidence of severe respiratory syncytial virus infections in lung transplant recipients despite the absence of specific therapy date = 2009-10-17 pages = extension = .txt mime = text/plain words = 2666 sentences = 165 flesch = 40 summary = 20 In Switzerland, pre-emptive therapy in cases of low-grade immunosuppression, prophylaxis in severe immunosuppression, and combined treatment with immunoglobulin (Ig), ribavirin, and palivizumab in cases of proven infection have been suggested for both BMT recipients and LTRs. 20 To get a better overview on the clinical evolution of RSV infections in LTRs we retrospectively searched our virology reports and identified 10 adult LTRs with proven lower respiratory tract RSV infection. Two patients were treated with ribavirin for 7 days (orally with 1,600 mg/day or intravenously with 10 mg/kg 3 times daily) concomitant with intravenous palivizumab (a single dose of 15 mg/kg) ( Table 1) , including Patient 3, who required anti-thymocyte globulins for non-responding conThe detection of RSV by PCR in respiratory secretions is highly sensitive and specific, 24 and is currently considered the best available test for the diagnosis of respiratory tract infections in adult lung transplant recipients. cache = ./cache/cord-254770-ot9ys10r.txt txt = ./txt/cord-254770-ot9ys10r.txt === reduce.pl bib === id = cord-015893-e0fofgxq author = Ryhal, Bruce title = Viral Disease, Air Pollutants, Nanoparticles, and Asthma date = 2011-05-03 pages = extension = .txt mime = text/plain words = 6327 sentences = 316 flesch = 49 summary = Sulfur dioxide, nitrogen dioxide, ozone, and particulate matter in air pollution may • exacerbate asthma, and patients should be cautioned to stay indoors when levels of these irritants are high. A study of children aged 6-8 years with asthma concluded that an asthma exacerbation was of a greater severity if a viral infection was present as opposed to a nonviral illness (7) . Inhaled corticosteroids and leukotriene receptor antagonists (LTRAs) are well known to control the number of wheezing exacerbations in school-age children with chronic persistent asthma, an effect that appears to encompass those episodes caused by viral illness. Viral respiratory infections, and to a lesser extent air pollution, are common triggers of exacerbations and may interact with individuals to affect the development of some forms of asthma. By understanding and anticipating respiratory viral infections and air pollution as important causes of asthma, the health care provider can provide superior care for those who suffer from this chronic disease. cache = ./cache/cord-015893-e0fofgxq.txt txt = ./txt/cord-015893-e0fofgxq.txt === reduce.pl bib === id = cord-253223-us0ey8dq author = Chow, Brian D.W. title = The Human Bocaviruses: A Review and Discussion of Their Role in Infection date = 2009-11-03 pages = extension = .txt mime = text/plain words = 5912 sentences = 401 flesch = 49 summary = [38] [39] [40] [42] [43] [44] In a recent casecontrol study on acute gastroenteritis, Arthur and colleagues 13 examined stool specimens for potential pathogens, including all three species of human bocavirus. The large percentage of coinfections associated with human bocavirus infections suggests that evaluation for further pathogens should be undertaken for any patient diagnosed with HBoV-1. Human bocavirus infection in children with respiratory tract disease Human bocavirus detection in nasopharyngeal aspirates of children without clinical symptoms of respiratory infection Detection of human bocavirus in Japanese children with lower respiratory tract infections High prevalence of human bocavirus detected in young children with severe acute lower respiratory tract disease by use of a standard PCR protocol and a novel real-time PCR protocol Human bocavirus DNA detected by quantitative real-time PCR in two children hospitalized for lower respiratory tract infection cache = ./cache/cord-253223-us0ey8dq.txt txt = ./txt/cord-253223-us0ey8dq.txt === reduce.pl bib === id = cord-006261-yw5k8qkz author = Heath, Gregory W. title = Exercise and Upper Respiratory Tract Infections: Is There a Relationship? date = 2012-10-23 pages = extension = .txt mime = text/plain words = 6209 sentences = 329 flesch = 44 summary = Few studies have investigated the common belief that moderate physical activity is beneficial in decreasing risk of respiratory tract infections and improving immune function. Laboratory and clinical studies suggest that changes in immune parameters associated with heavy train ing lead to adverse health effects, particularly an increase in the incidence or severity of upper respiratory tract infections. During this time, the women in the exercise group experienced fewer upper respiratory tract infection symptom days, improved cardiorespiratory fitness, and increased natural killer cell numbers compared with their sedentary controls. This study indicates that intensity of exercise may playa role, and that moderate activity may actually improve immune function and associated upper respiratory tract infection symptoms. Clinical studies examining the effects of moderate levels of physical activity have shown possible enhanced immune responses with a concomitant impact on the length and severity of an upper respiratory tract infection. The effects of moderate exercise training on natural killer cells and acute upper respiratory tract infections cache = ./cache/cord-006261-yw5k8qkz.txt txt = ./txt/cord-006261-yw5k8qkz.txt === reduce.pl bib === id = cord-006325-3no74e74 author = Jeannoël, M. title = Microorganisms associated with respiratory syncytial virus pneumonia in the adult population date = 2018-10-23 pages = extension = .txt mime = text/plain words = 1955 sentences = 108 flesch = 39 summary = A more severe outcome was observed for RSV-bacteria-associated pneumonia compared with RSV pneumonia: length of stay was significantly longer (16 days vs 10 days) and ICU hospitalization more frequent (66.7% vs 21.0%) (p < 0.05). In conclusion, we did not observe major differences in the epidemiology of bacterial superinfections in RSV-positive pneumonia compared to reports on post-influenza pneumonia. RSV and bacteria coinfection was statistically associated with a more severe outcome than RSV-positive pneumonia as length of stay was significantly longer (16 days vs 10 days) and ICU hospitalization more frequent (66.7% vs 21.0%) (p < 0.05). It is probably due to the systematic testing strategy associated to a Species distribution of pathogenic bacteria involved in RSV-positive pneumonia (CAP) and hospital-acquired pneumonia (HAP) sampling bias toward influenza-like illness. Clinical characteristics and outcome of respiratory syncytial virus infection among adults hospitalized with influenza-like illness in France cache = ./cache/cord-006325-3no74e74.txt txt = ./txt/cord-006325-3no74e74.txt === reduce.pl bib === id = cord-026005-f2khcjdy author = López, Alfonso title = Respiratory System, Mediastinum, and Pleurae date = 2017-02-17 pages = extension = .txt mime = text/plain words = 57323 sentences = 2749 flesch = 34 summary = Microscopic examination of properly collected, stored, and processed samples may reveal many erythrocytes and siderophages in pulmonary hemorrhage or left-sided heart failure; inclusion bodies or syncytial cells in viral pneumonias; increased number of leukocytes in pulmonary inflammation; abundant mucus in asthma or equine recurrent airway obstruction (RAO); the presence of pulmonary pathogens, such as parasites, fungi, and bacteria; or tumor cells in cases of pulmonary neoplasia. The portal of entry for the respiratory form is typically aerogenous, and the disease is generally transient; thus the primary viral-induced lesions in the nasal mucosa and lungs are rarely seen at necropsy unless complicated by secondary bacterial rhinitis, pharyngitis, or bronchopneumonia. Laryngeal edema occurs in pigs with edema disease; in horses with purpura hemorrhagica; in cattle with acute interstitial pneumonia; in cats with systemic anaphylaxis; and in all species as a result of trauma, improper endotracheal tubing, inhalation of irritant gases (e.g., smoke), local inflammation, and animal species is classified as fibrinous, catarrhal, purulent, or granulomatous (Figs. cache = ./cache/cord-026005-f2khcjdy.txt txt = ./txt/cord-026005-f2khcjdy.txt === reduce.pl bib === id = cord-048197-9785vg6d author = Domachowske, Joseph B title = Gene expression in epithelial cells in response to pneumovirus infection date = 2001-05-11 pages = extension = .txt mime = text/plain words = 4688 sentences = 193 flesch = 34 summary = The respiratory epithelial target cells respond to viral infection with specific alterations in gene expression, including production of chemoattractant cytokines, adhesion molecules, elements that are related to the apoptosis response, and others that remain incompletely understood. The transcription factor NF-IL-6 is also produced in response to RSV infection [13] , and participates in a co-operative manner with NF-κB in the regulation of IL-8 gene expression [11] , although later studies suggest that activator protein-1 may function preferentially in this role [14] . Again, as part of our systematic study of gene expression in response to pneumovirus infection, we found that human respiratory epithelial cells respond to RSV infection with increased expression of the cytoskeletal protein cytokeratin-17 [36] . Inhibiton of viral replication reverses respiratory syncytial virus-induced NF-κ κB activation and interleukin-8 gene expression in A549 cells Respiratory syncytial virus infection induces expression of the anti-apoptosis gene IEX-1L in human respiratory epithelial cells cache = ./cache/cord-048197-9785vg6d.txt txt = ./txt/cord-048197-9785vg6d.txt === reduce.pl bib === id = cord-017897-mbwm0ytg author = Chiumello, Davide title = The Acute Respiratory Distress Syndrome: Diagnosis and Management date = 2018-10-01 pages = extension = .txt mime = text/plain words = 4825 sentences = 215 flesch = 35 summary = In order to guarantee a better patient adaptation to the ventilator, to reduce the oxygen consumption related to the respiratory muscle activity and to guarantee a protective transpulmonary pressure, the use of neuromuscular blockers is accepted in clinical practice [49] . The indications for the prone positioning have changed over time: once it was used to improve arterial oxygenation in the most severe forms of respiratory failure [53, 54] ; while nowadays it aims to achieve a more homogeneous distribution of stress and strain within the lung parenchyma, acting in synergy with the remaining therapies and protecting against the ventilator induced lung injury [55] . Lung recruitability is better estimated according to the Berlin definition of acute respiratory distress syndrome at standard 5 cm H2O rather than higher positive end-expiratory pressure: a retrospective cohort study Ventilation strategy using low tidal volumes, recruitment maneuvers, and high positive end-expiratory pressure for acute lung injury and acute respiratory distress syndrome: a randomized controlled trial cache = ./cache/cord-017897-mbwm0ytg.txt txt = ./txt/cord-017897-mbwm0ytg.txt === reduce.pl bib === id = cord-018421-wy3mtafh author = Waghmare, Alpana title = Rhinovirus, Coronavirus, Enterovirus, and Bocavirus After Hematopoietic Cell Transplantation or Solid Organ Transplantation date = 2016-02-15 pages = extension = .txt mime = text/plain words = 5430 sentences = 264 flesch = 36 summary = Human rhinoviruses are the most common respiratory viruses detected in the upper respiratory tract of hematopoietic cell transplant and lung transplant recipients, and evidence on the impact on clinical outcomes is mounting. Due to the development of polymerase chain reaction (PCR) assays for viral detection, HRVs are now known to be the most common viruses detected from respiratory specimens in HCT recipients and can account for 25-40% of cases of viral respiratory infections in these patients [ 2 -4 ] (Figure 32-1 ). In that study, approximately one third of the adult HCT recipients who developed symptomatic HRV infections prior to engraftment had progression of upper respiratory tract symptoms to LRTI, and all cases with pneumonias were fatal. Rhinovirus as a cause of fatal lower respiratory tract infection in adult stem cell transplantation patients: a report of two cases Human Rhinovirus RNA Detection in the Lower Respiratory Tract of Hematopoietic Cell Transplant recipients: Association with Mortality. cache = ./cache/cord-018421-wy3mtafh.txt txt = ./txt/cord-018421-wy3mtafh.txt === reduce.pl bib === id = cord-017140-k4lzwfge author = Andersen, Bjørg Marit title = Protection of Upper Respiratory Tract, Mouth and Eyes date = 2018-09-25 pages = extension = .txt mime = text/plain words = 6161 sentences = 412 flesch = 59 summary = • Patient with suspected contagious respiratory infection-during transport, examination, treatment, etc.; use a face mask-also on the patient-to protect others and the environment from contamination. Department management is responsible for training, use and control of face masks, respirators and eye protection and that the equipment and written guidelines are available [5] . P3 mask is used by the surgical team and during all sterile procedures: in the case of operative treatment of patients with special types of airborne infection such as tuberculosis, etc., see above. However, surgical masks are not approved as protection against airborne infections: [5, 14, 24, 25] "Harmful microorganisms (bacteria, viruses, fungi) or components of microorganisms (e.g. endotoxins) may occur in air, either in dust, smoke or aerosols, or even finer distributed as droplet nuclei where all liquid has dried in. Transmission of microbes via small particles and droplet nuclei from influenza patients is not adequately controlled by the use of surgical mask [50] [51] [52] . cache = ./cache/cord-017140-k4lzwfge.txt txt = ./txt/cord-017140-k4lzwfge.txt === reduce.pl bib === id = cord-253761-wjm8ju3v author = Haidopoulou, Katerina title = Human bocavirus infections in hospitalized Greek children date = 2010-03-09 pages = extension = .txt mime = text/plain words = 2012 sentences = 114 flesch = 52 summary = To define the epidemiological profile and the clinical characteristics associated with HBoV infection in a population of children hospitalized with respiratory tract infection. MATERIAL AND METHODS: During a one-year period throat swab samples were collected from 370 previously healthy children, aged 14 days to 13 years, admitted to two different paediatric wards because of respiratory tract infection. The aim of the present study was to define the epidemiological profile and the clinical characteristics associated with HBoV in hospitalized children with respiratory tract infection (RTI) in Greece. One may argue that the fact that HBoV is prevalent in samples from patients with respiratory tract infection does not guarantee a causative role for the symptoms, especially when -as in this case -it is frequently detected in combination with other respiratory viruses of known pathogenic potential. Human bocavirus infection in young children in the United States: molecular epidemiological profile and clinical characteristics of a newly emerging respiratory virus cache = ./cache/cord-253761-wjm8ju3v.txt txt = ./txt/cord-253761-wjm8ju3v.txt === reduce.pl bib === id = cord-007222-31o180fz author = MUFSON, MAURICE A. title = EPIDEMIOLOGY OF RESPIRATORY SYNCYTIAL VIRUS INFECTION AMONG INFANTS AND CHILDREN IN CHICAGO date = 1973-08-17 pages = extension = .txt mime = text/plain words = 2723 sentences = 146 flesch = 49 summary = From January 1, 1967 to December 1971, the temporal pattern of respiratory syncytial virus infection was investigated in infants and children younger than 18 months hospitalized for acute lower respiratory tract disease. Of 4696 infants and children with acute lower respiratory tract disease admitted to the Cook County Hospital, 2530 were tested for virus infection by virus isolation or serologic procedures or both. This report describes the periodic pattern of RSV infection in infants and children with lower respiratory tract disease admitted to the Cook County Hospital in Chicago, between January 1, 1967 and December 31, 1971. The study group comprised infants and children younger than 18 months of age admitted to the Cook County Hospital because of acute lower respiratory tract disease. DISCUSSION This continuing surveillance study of virus infections in infants and young children with acute lower respiratory tract disease describes the cyclical pattern of occurrence of RSV infections. cache = ./cache/cord-007222-31o180fz.txt txt = ./txt/cord-007222-31o180fz.txt === reduce.pl bib === id = cord-253148-3t4o27xp author = Chow, Brian D.W. title = Evidence of human bocavirus circulating in children and adults, Cleveland, Ohio date = 2008-09-19 pages = extension = .txt mime = text/plain words = 2700 sentences = 200 flesch = 50 summary = STUDY DESIGN: From October 2005 through October 2006, we screened respiratory samples from children and adults negative for common respiratory pathogens for HBoV by PCR. CONCLUSIONS: HBoV circulates in Cleveland, OH, in children and adults with similar frequencies, and can warrant hospitalization and intensive care. We sought to further define the clinical and epidemiologic characteristics of HBoV in adult and pediatric patients in Cleveland, OH. Isolates positive for HBoV were screened for common respiratory viruses by RT-PCR with published primer sets. Forty samples (2.2%) tested positive for HBoV by PCR: 36 (90%) pediatric patients and 4 (10%) adult patients. Of pediatric patients who screened positive for HBoV, 27 (84.4%) were admitted to the hospital, including 9 (28.1%) who required intensive care. However, this report suggests that clinical disease associated with HBoV alone may be severe enough to require admission to the hospital in both adults and children and to the intensive care unit in children. cache = ./cache/cord-253148-3t4o27xp.txt txt = ./txt/cord-253148-3t4o27xp.txt === reduce.pl bib === id = cord-252037-rj61mzqj author = Gerna, G. title = Changing circulation rate of human metapneumovirus strains and types among hospitalized pediatric patients during three consecutive winter-spring seasons date = 2005-06-28 pages = extension = .txt mime = text/plain words = 2203 sentences = 116 flesch = 44 summary = In this study, we examined: i) the circulation rate of hMPV among the other respiratory viruses during 3 consecutive winter-spring seasons; ii) the relative circulation of the 2 types and the 4 subtypes of hMPV during the same 3-year period; iii) the relative impact of hMPV as compared to hRSV in determining admission to the hospital of infants with acute respiratory infections. The relative distribution of different respiratory viruses causing severe infections requiring admission to the hospital of infants and young children in three consecutive winter-spring seasons from 2001 through 2004 is reported in Table 2 Within the aliquot of patients found positive for some respiratory virus, no difference in the circulation rate was observed for respiratory virus infections caused by influenzavirus B, hPIVs, hAdVs, hCoVs, and coinfections along the three years studied. cache = ./cache/cord-252037-rj61mzqj.txt txt = ./txt/cord-252037-rj61mzqj.txt === reduce.pl bib === === reduce.pl bib === id = cord-017126-7ebo3cy3 author = nan title = Lungenversagen date = 2007 pages = extension = .txt mime = text/plain words = 4324 sentences = 512 flesch = 42 summary = Nach der „American-European Consensus Conference" (Bernard et al., 1994) wird zwischen einem ARDS — acute respiratory distress syndrom und einem ALI — acute lung injury unterschieden. Bei Patienten mit ALI/ARDS kann das Auftreten apoptotischer Vorgänge an pulmonalen epithelialen Zellen (Song Y et al., 1999 , Li et al., 2004 , Martin et al., 2005 (Abraham, 2003) derselben, sodass es zur Aufrechterhaltung eines von Leukozyten geführten inflammatorischen Prozesses kommt, der typisch für eine akute Lungenschädigung ist (Wang et al., 1999 , Yum et al., 2001 Die verminderte Apoptose der Neutrophilen ist bedingt durch: 1. Beneficial effects of the "Open lung Approach" with low distending pressures in acute respiratory distress syndrom; A prospective randomized study on mechanical ventilation Combining high-frequency oscillatory ventilation and recruitment maneuvers in adults with early acute respiratory distress syndrome: the treatment with oscillation and an Open Lung Strategy (TOOLS) trial pilot study Effect of alveolar recruitment maneuver in early acute respiratory distress syndrome according to antiderecruitment strategy, etiological category of diffuse lung injury, and body position of the patient cache = ./cache/cord-017126-7ebo3cy3.txt txt = ./txt/cord-017126-7ebo3cy3.txt === reduce.pl bib === id = cord-048447-chz8luni author = Duffett, Mark title = Surfactant therapy for acute respiratory failure in children: a systematic review and meta-analysis date = 2007-06-15 pages = extension = .txt mime = text/plain words = 3996 sentences = 215 flesch = 38 summary = The primary objective of the systematic review is to assess the effect of the administration of pulmonary surfactant compared with no therapy or with placebo on all-cause mortality (at or before hospital discharge) in mechanically ventilated children with acute respiratory failure. We used the following characteristics to assess the methodologic quality: allocation concealment (sealed envelopes or central randomization were considered adequate), blinding (which of the trial personnel and caregivers were blinded, and the methods used to ensure blinding), completeness of followup (assessed by the number of patients randomized for whom there were no outcomes), similarity of the groups at baseline (with respect to known prognostic factors: age, aetiology, severity of illness as measured by the Pediatric Risk of Mortality score, and immunosuppression), whether a standard or recommended strategy for mechanical ventilation was used, and whether a priori criteria for the use of co-interventions were used. cache = ./cache/cord-048447-chz8luni.txt txt = ./txt/cord-048447-chz8luni.txt === reduce.pl bib === === reduce.pl bib === id = cord-225826-bwghyhqx author = Jiang, Zheng title = Combining Visible Light and Infrared Imaging for Efficient Detection of Respiratory Infections such as COVID-19 on Portable Device date = 2020-04-15 pages = extension = .txt mime = text/plain words = 4812 sentences = 276 flesch = 56 summary = In this work, we perform the health screening through the combination of the RGB and thermal videos obtained from the dual-mode camera and deep learning architecture.We first accomplish a respiratory data capture technique for people wearing masks by using face recognition. In this study, we develop a portable and intelligent health screening device that uses thermal imaging to extract respiration data from masked people which is then used to do the health screening classification via deep learning architecture. After extracting breathing data from the video obtained from the thermal camera, a deep learning neural network is performed to work on the classification between healthy and abnormal respiration conditions. First, we combine the face recognition technology with dual-mode imaging to accomplish a respiratory data extraction method for people wearing masks, which is quite essential for current situation. Finally, we use a bidirectional GRU neural network with attention mechanism (BiGRU-AT) model to work on the classification task with the input respiration data. cache = ./cache/cord-225826-bwghyhqx.txt txt = ./txt/cord-225826-bwghyhqx.txt === reduce.pl bib === === reduce.pl bib === id = cord-007417-az8xd66p author = Hansbro, Nicole G. title = Understanding the mechanisms of viral induced asthma: New therapeutic directions date = 2008-01-29 pages = extension = .txt mime = text/plain words = 29677 sentences = 1459 flesch = 41 summary = Whether an infection induces disease depends on viral (type (E.g. RSV, RV)), host (genetic susceptibility, age, immune responses) and environmental (allergen exposure, season) factors. With respect to allergy RSV infection might only trigger defective immunity in genetically susceptible individuals or that allergic inflammatory and immune responses may promote the influx of virus-specific cells into the airways increasing inflammation and AHR (Schwarze et al., 1999c) . Nevertheless most studies suggest that Th1 responses may result in viral clearance and mild symptoms whereas an aberrant bias towards a Th2 phenotype may lead to more intense RSV-induced disease and promote the development of asthma . Animal models have been used to determine if RSV can induce the development of asthma by triggering pro-asthmatic immune responses that lead to variable airflow obstruction and airway inflammation. Further studies are required to elucidate the links between infection, immune responses and susceptibility to chronic respiratory diseases and why some individuals but not others develop persistent wheeze and asthma. cache = ./cache/cord-007417-az8xd66p.txt txt = ./txt/cord-007417-az8xd66p.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-129086-ra2njvcz author = Kumar, Sanjay title = The perspective of fluid flow behavior of respiratory droplets and aerosols through the facemasks in context of SARS-CoV-2 date = 2020-10-10 pages = extension = .txt mime = text/plain words = 8130 sentences = 466 flesch = 52 summary = However, in more recent times, the focus has shifted towards the theoretical investigations of fluid flow mechanisms involved in the virus-laden particles prevention by facemasks. 44 While these experimental studies are essential for the broad characterization and design evaluation of respiratory facemasks, further theoretical and numerical methods and algorithm-based investigations provide a better insight into the facemask's fluid flow dynamics and the droplet leakage through the facemask openings. The computational fluid flow models have shown their potentials in an improved prediction of the spreading of respiratory virus-laden droplets and aerosols, sensitive to the ambient environment, and crucial to the public health responses. The results revealed that the small droplets travel a larger distance and remain suspended in the air for a longer time under the influence of airflow, supporting the mandatory use of facemasks to prevent the virus. In recent years, the respiratory droplets flow behavior through the facemasks has typically well-predicted using the computational fluid dynamics (CFD) techniques. cache = ./cache/cord-129086-ra2njvcz.txt txt = ./txt/cord-129086-ra2njvcz.txt === reduce.pl bib === === reduce.pl bib === id = cord-023509-tvqpv6fp author = Corrin, Bryan title = Occupational, environmental and iatrogenic lung disease date = 2011-03-02 pages = extension = .txt mime = text/plain words = 42576 sentences = 2457 flesch = 45 summary = As a general rule, exposure to silica dust extends over many years, often 20 or more, before the symptoms of silicosis first appear: by the time the disease becomes overt clinically, much irreparable damage has been inflicted on the lungs. Confusingly, the term 'acute silicosis' has since been applied to a further effect of heavy dust exposure in tunnellers, sand blasters and silica flour workers, namely pulmonary alveolar lipoproteinosis (see below), 71, 72 whilst the terms 'accelerated silicosis' or 'cellular phase silicosis' have been substituted for 'acute silicosis' in referring to the rapid development of early cellular lesions. Asbestosis is defined as diffuse interstitial fibrosis of the lung caused by exposure to asbestos dust. The finely divided fume of several metals is highly toxic to the lungs and capable of producing severe acute and chronic damage to both the conductive airways and the alveoli, resulting in acute tracheobronchitis and bronchiolitis, diffuse alveolar damage, obliterative bronchiolitis and pulmonary fibrosis. cache = ./cache/cord-023509-tvqpv6fp.txt txt = ./txt/cord-023509-tvqpv6fp.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-005646-xhx9pzhj author = nan title = 2nd World Congress on Pediatric Intensive Care 1996 Rotterdam, The Netherlands, 23–26 June 1996 Abstracts of Oral Presentations, Posters and Nursing Programme date = 1996 pages = extension = .txt mime = text/plain words = 72031 sentences = 4734 flesch = 56 summary = Aims and methods The aim of both a prospective and retrospective survey conducted in German pediatric intensive care units in 1993 was to accumulate data on the epidemiology, risk factors, natural history and treatment strategies in a large group of pediatric ARDS patients who were treated in the tt~ee year period from 1991 to 1993.All patients had acute bilateral alveolar infiltration of noncardiogenic origin and a pO2~iO2 ratio < 150mmHg. The influence of sex, underlying disease and single organ failure was analyzed using the Fischer's exact test, the influence of additional organ failure on mortality was tested with the Cochran-Mantel-Haenszet statistics. cache = ./cache/cord-005646-xhx9pzhj.txt txt = ./txt/cord-005646-xhx9pzhj.txt === reduce.pl bib === === reduce.pl bib === id = cord-254766-585iu5ey author = Tauro, Sharyn title = Molecular and cellular mechanisms in the viral exacerbation of asthma date = 2008-08-13 pages = extension = .txt mime = text/plain words = 5251 sentences = 246 flesch = 39 summary = This review summarizes the evidence associated with factors that may contribute to the development or exacerbation of asthma including age, host factors, genetic polymorphisms, altered immune responses, and aspects of viral antigen expression. These observations suggest that respiratory viral infections lead to a prolonged period of increased antigen presentation in the airways resulting in de novo and memory T-cell responses not only to the virus but also to unrelated antigens including allergens. In addition to studies of primary infections, models studying the interactions between respiratory viral infections and allergen sensitization are essential in understanding the mechanisms of virus induced asthma exacerbations. These studies show that the immune responses to allergen sensitization and respiratory viral infections interact to cause persistent inflammation and AHR, symptomatic of the asthmatic response (Fig. 2) [53] . Recurrent respiratory syncytial virus infections in allergen sensitized mice lead to persistent airway inflammation and hyperresponsiveness cache = ./cache/cord-254766-585iu5ey.txt txt = ./txt/cord-254766-585iu5ey.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-252012-hdjbxah8 author = McErlean, Peter title = Viral diversity in asthma: Immunology and Allergy Clinics of North America: Asthma and Infectious Disease date = 2010-11-01 pages = extension = .txt mime = text/plain words = 5497 sentences = 299 flesch = 44 summary = Traditionally associated with acute respiratory illness (ARI) or symptoms of the "common cold," the respiratory viruses implicated in asthma exacerbations predominantly possess RNA genomes with a distinct genome organization (positive [1] or negative [À] sense), virus particle (virion) morphology (enveloped or nonenveloped), host cell receptor interaction, and well-defined annual or seasonal prevalence. These "newly identified viruses" (NIVs) including human metapneumovirus (HMPV; described pre-SARS), the human rhinovirus (HRV) species C (HRV-Cs), human coronaviruses (HCoVs)-NL63 and -HKU1, human bocavirus (HBoV), and the KI and WU polyomaviruses (KIPyV and WUPyV) are now the focus of intense research, and their involvement in asthma exacerbations is slowly beginning to be determined. 34 In a retrospective study of clinical samples taken over a 20-year period from young children (median age 14.5 months), the percentage of lower respiratory tract illness (LRTI; including asthma exacerbations and bronchiolitis) associated with any HCoV, HCoV-NL63, or HCoV-OC43 was estimated to be 4.6%, 2.6%, and 1.9%, respectively. cache = ./cache/cord-252012-hdjbxah8.txt txt = ./txt/cord-252012-hdjbxah8.txt === reduce.pl bib === id = cord-255901-nl9k8uwd author = Barasheed, Osamah title = Uptake and effectiveness of facemask against respiratory infections at mass gatherings: a systematic review date = 2016-03-29 pages = extension = .txt mime = text/plain words = 4522 sentences = 256 flesch = 50 summary = Studies conducted in community or health care settings found facemasks to be generally effective against influenza-like illness (ILI) or even against severe acute respiratory syndrome (SARS) but its effectiveness against respiratory infections at MGs remains unknown. 15, 17 A review of non-pharmaceutical interventions against respiratory tract infections among Hajj pilgrims presented data on the uptake of facemask and acknowledged that compliance was generally poor, but did not evaluate its effectiveness during Hajj. A few studies showed that providing educational session on protective measures against respiratory infections (including facemask) before Hajj was associated with significantly higher uptake of facemasks among pilgrims. 68 Focused studies are required to investigate factors influencing facemask compliance among attendees of Hajj and other MGs. In this systematic review, pooled data of facemask effectiveness showed that participants who used facemask during Hajj are about 20% less likely to suffer from respiratory infections compared to those who do not use it. cache = ./cache/cord-255901-nl9k8uwd.txt txt = ./txt/cord-255901-nl9k8uwd.txt === reduce.pl bib === id = cord-256065-zz2907h0 author = Barral-Arca, Ruth title = A Meta-Analysis of Multiple Whole Blood Gene Expression Data Unveils a Diagnostic Host-Response Transcript Signature for Respiratory Syncytial Virus date = 2020-03-06 pages = extension = .txt mime = text/plain words = 5643 sentences = 285 flesch = 44 summary = title: A Meta-Analysis of Multiple Whole Blood Gene Expression Data Unveils a Diagnostic Host-Response Transcript Signature for Respiratory Syncytial Virus We meta-analyzed seven transcriptome microarray studies from the public Gene Expression Omnibus (GEO) repository containing a total of 922 samples, including RSV, healthy controls, coronaviruses, enteroviruses, influenzas, rhinoviruses, and coinfections, from both adult and pediatric patients. RSV additionally induced over-representation of differential expressed pattern recognition receptor genes as compared to healthy controls (Table S3 ): (i) Toll-like receptors (TLR) cascades (R-HSA-168898; adjusted p-value = 1.23 × 10 −3 ), including TLR3 (R-HSA-168164; adjusted p-value = 2.45 × 10 −2 ), which are specialized in the recognition of conserved molecular features of different pathogens such as bacteria, viruses, fungi, and parasites; and (ii) C-type lectin receptors (R-HSA-5621481; adjusted p-value = 5.12 × 10 −6 ), capable of sensing glycans present in viral pathogens to activate antiviral immune responses such as phagocytosis, cytokine production, antigen processing and presentation, and subsequent T cell activation. cache = ./cache/cord-256065-zz2907h0.txt txt = ./txt/cord-256065-zz2907h0.txt === reduce.pl bib === id = cord-256788-h4iv8crq author = Sumino, Kaharu title = Antiviral IFN-γ responses of monocytes at birth predict respiratory tract illness in the first year of life date = 2012-03-27 pages = extension = .txt mime = text/plain words = 5026 sentences = 238 flesch = 47 summary = 9 In that regard a decrease in IFN-g production from cord blood mononuclear cells (CBMCs) stimulated by PHA or allergens has been associated with increased risk for acute respiratory tract illness during infancy. We assessed whether each of these immune end points could predict the development of respiratory tract illness during the first year of life in a prospective birth cohort of children at high risk for asthma and allergic disease. Together, these findings reinforce the association of a decreased IFN-g response to RSV with the development of increased viral respiratory tract infections in the first year of life. In this study we provide evidence that a decreased antiviral interferon response at the time of birth is selectively associated with an increase in acute respiratory tract infections in the first year of life among infants at high risk for asthma and allergic disease. cache = ./cache/cord-256788-h4iv8crq.txt txt = ./txt/cord-256788-h4iv8crq.txt === reduce.pl bib === id = cord-256827-tht5h1tu author = Jain, Neemisha title = Upper respiratory tract infections date = 2001 pages = extension = .txt mime = text/plain words = 2740 sentences = 201 flesch = 43 summary = Common cold is caused by viruses in most circumstances and does not require antimicrobial agent unless it is complicated by acute otitis media with effusion, tonsillitis, sinusitis, and lower respiratory tract infection. Five to six days after initiation of treatment, cephalexin and placebo groups did not differ in the presence of nasal discharge, incidence of complications, or parental opinion of benefit of medicationY Cough occurs in 60-80% of common cold and does not suggest a bacterial etiology. n Even in uncomplicated viral upper respiratory infection, as occurs in common cold, there is inflammation and congestion of both the nasal and the sinus mucosa. Persistence of signs and symptoms of upper respiratory infection i.e. rhinorrhea or cough for more than 10-14 days is a pointer towards sinusitis. cache = ./cache/cord-256827-tht5h1tu.txt txt = ./txt/cord-256827-tht5h1tu.txt === reduce.pl bib === id = cord-257073-dm80bxnd author = Akmatov, Manas K. title = E-mail-based symptomatic surveillance combined with self-collection of nasal swabs: a new tool for acute respiratory infection epidemiology date = 2011-08-17 pages = extension = .txt mime = text/plain words = 3515 sentences = 177 flesch = 46 summary = OBJECTIVE: We examined the feasibility of combining communication by e-mail and self-collection of nasal swabs for the prospective detection of acute respiratory infections in a non-medical setting. Conclusions: Combining e-mail-based symptomatic surveillance with nasal self-swabbing promises to be a powerful tool for the real-time identification of incident cases of acute respiratory infections and the associated pathogens in population-based studies. Conclusions: Combining e-mail-based symptomatic surveillance with nasal self-swabbing promises to be a powerful tool for the real-time identification of incident cases of acute respiratory infections and the associated pathogens in population-based studies. We tested the feasibility of combining real-time symptomatic surveillance with nasal self-swabbing for the prospective collection of epidemiologic and virological data on acute respiratory infections. Combining e-mail-based active symptomatic surveillance with self-collection of nasal swabs ensured prospective, accurate collection of data on incident episodes of acute respiratory infections and timely sample collection for the detection of respiratory pathogens. cache = ./cache/cord-257073-dm80bxnd.txt txt = ./txt/cord-257073-dm80bxnd.txt === reduce.pl bib === id = cord-258336-zs04l3s0 author = Leotte, Jaqueline title = Impact and seasonality of human rhinovirus infection in hospitalized patients for two consecutive years date = 2017-06-30 pages = extension = .txt mime = text/plain words = 3254 sentences = 180 flesch = 46 summary = Abstract Objectives To report epidemiological features, clinical characteristics, and outcomes of human rhinovirus (HRV) infections in comparison with other community acquired respiratory virus (CRV) infections in patients hospitalized for two consecutive years. The present study reports the epidemiological features, clinical characteristics, and outcomes of HRV infections in comparison with other CRV infections in patients hospitalized in a referral hospital in Southern Brazil, for two consecutive years. Patients hospitalized at an academic tertiary care center in Southern Brazil from whom respiratory samples were collected and sent for investigation, or who were diagnosed with SARI in 2012 or 2013, were included in the study. The medical records and influenza notification forms of patients with detectable respiratory virus were reviewed, focusing on epidemiology, clinical manifestation, outcome, laboratory findings, and diagnosis of SARI. In conclusion, HRV has a high prevalence in the hospitalized children and was present in cases of severe disease, including death. cache = ./cache/cord-258336-zs04l3s0.txt txt = ./txt/cord-258336-zs04l3s0.txt === reduce.pl bib === id = cord-257244-gryp0khc author = Edwards, M. R. title = The potential of anti‐infectives and immunomodulators as therapies for asthma and asthma exacerbations date = 2017-08-10 pages = extension = .txt mime = text/plain words = 5746 sentences = 317 flesch = 37 summary = Despite these important associations, the use of antiinfectives (antibiotics, antivirals, antifungals, vaccines) that specifically target known pathogens, or drugs that are based on or exploit microbe-host receptor interactions (toll-like receptor agonists, bacterial lysates) or are immunomodulators (vitamin D), and/or may work in part by altering our associated microbiology (probiotics) are, with the exception of severe asthma, seldom considered in asthma treatment, prevention and guidelines. Overall, antibiotic use is associated with asthma risk rather than protection at most stages of human development, including pregnancy, 10, 11 early life 12 and childhood, 13 although why this is so is a subject widely debated. 10 In retrospective studies, the association between antibiotic use and increased risk of asthma or wheezing in children is further confused due to the potential of reverse causation. Inhibiting virus replication through interfering with viral enzymes active within cells poses additional problems in drug discovery; however, several useful inhibitors for respiratory tract viruses have found their way into phase I/II clinical trials. cache = ./cache/cord-257244-gryp0khc.txt txt = ./txt/cord-257244-gryp0khc.txt === reduce.pl bib === === reduce.pl bib === id = cord-257656-z7zx46gd author = Ljubin-Sternak, Sunčanica title = The Emerging Role of Rhinoviruses in Lower Respiratory Tract Infections in Children – Clinical and Molecular Epidemiological Study From Croatia, 2017–2019 date = 2019-12-03 pages = extension = .txt mime = text/plain words = 4806 sentences = 221 flesch = 49 summary = title: The Emerging Role of Rhinoviruses in Lower Respiratory Tract Infections in Children – Clinical and Molecular Epidemiological Study From Croatia, 2017–2019 Therefore, we investigated the rhinovirus (RV) infection prevalence over a 2-year period, compared it with prevalence patterns of other common respiratory viruses, and explored clinical and molecular epidemiology of RV infections among 590 children hospitalized with acute respiratory infection in north-western and central parts of Croatia. Therefore, we investigated the rhinovirus (RV) infection prevalence over a 2-year period, compared it with prevalence patterns of other common respiratory viruses, and explored clinical and molecular epidemiology of RV infections among 590 children hospitalized with acute respiratory infection in north-western and central parts of Croatia. This study aims to determine the RV prevalence, compare it with prevalence patterns of other common respiratory viruses, as well as to explore clinical and molecular epidemiological features of RV infections among hospitalized children with acute respiratory infection. cache = ./cache/cord-257656-z7zx46gd.txt txt = ./txt/cord-257656-z7zx46gd.txt === reduce.pl bib === === reduce.pl bib === id = cord-257299-z9u12yqb author = Mansi, N. title = Ear, nose and throat manifestation of viral systemic infections in pediatric patients date = 2009-12-31 pages = extension = .txt mime = text/plain words = 5779 sentences = 291 flesch = 42 summary = Common childhood viral infections, such as measles and mumps are probably an unrecognized cause of acute or progressive damage to hearing [5] . Measles infection can be avoided by administering a reduced, live-virus vaccine to children between the ages of 12 and 15 months (MMR). The etiology of the acute forms in the respiratory airways is, initially, of a viral nature in most patients, with later, secondary bacterial infections on the mucous lesions caused by the viral agents [31] . Herpangina is an extremely contagious illness caused by a coxackievirus characterized by a presence of a vesicular exanthema at the velopharyngeal mucous level and acute or croup laryngotracheitis [38] [39] [40] [41] when viral infections are associated. The most common manifestation of the primary infection of this organism is infective mononucleosis (IM), a sometimes acute, but often asymptomatic clinical syndrome which more often strikes children, adolescents, and young adults [82] . Viral etiology and epidemiology of acute lower respiratory tract infections in children cache = ./cache/cord-257299-z9u12yqb.txt txt = ./txt/cord-257299-z9u12yqb.txt === reduce.pl bib === id = cord-258386-aiwzgkq3 author = MCLAREN, Rodney A. title = Delivery For Respiratory Compromise Among Pregnant Women With COVID-19 date = 2020-05-23 pages = extension = .txt mime = text/plain words = 896 sentences = 59 flesch = 49 summary = Of the remaining nine who continued to need respiratory support, seven 39 (77.8%) had iatrogenic preterm deliveries (six by cesarean delivery) for maternal respiratory 40 distress (needing increasing levels of respiratory support without improved oxygen saturation), 41 one had an early term delivery due to PROM, and one, now 30 weeks, has required intensive 42 care with high-flow nasal cannula for three weeks. Of the eight patients delivering with maternal respiratory distress, seven did not require 45 intubation, and one was intubated for emergent cesarean delivery, and remained on a ventilator 46 for 19 days. Of the eight patients delivering with maternal respiratory distress, seven did not require 45 intubation, and one was intubated for emergent cesarean delivery, and remained on a ventilator 46 for 19 days. cache = ./cache/cord-258386-aiwzgkq3.txt txt = ./txt/cord-258386-aiwzgkq3.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-258139-x4js9vqe author = Callan, Robert J title = Biosecurity and bovine respiratory disease date = 2005-03-04 pages = extension = .txt mime = text/plain words = 7688 sentences = 405 flesch = 37 summary = Alternatively, when the causative pathogens are endemic in a population and individual susceptibility is dependent on numerous interrelated factors, the management of animal resistance and risk factors may be proportionally more important for disease prevention than biosecurity practices. The authors emphasize five areas of biosecurity management that should be more rigorously applied for the reduction of respiratory disease prevalence in cattle, including (1) strategic vaccination, (2) calf biosecurity, (3) housing ventilation, (4) commingling and animal contact, and (5) bovine viral diarrhea virus control. Airborne pathogen concentration is a function of many factors, including animal type, housing system, stocking rate, bedding, humidity, dust particle density and size, and finally, elimination through ventilation. Because the pathogens involved in bovine respiratory disease are enzootic in the general cattle population, biosecurity practices aimed at the complete elimination of exposure are currently impractical. Because the pathogens involved in bovine respiratory disease are enzootic in the general cattle population, biosecurity practices aimed at the complete elimination of exposure are currently impractical. cache = ./cache/cord-258139-x4js9vqe.txt txt = ./txt/cord-258139-x4js9vqe.txt === reduce.pl bib === === 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-261598-w2tyongu author = Babady, N Esther title = The FilmArray® respiratory panel: an automated, broadly multiplexed molecular test for the rapid and accurate detection of respiratory pathogens date = 2014-01-09 pages = extension = .txt mime = text/plain words = 6030 sentences = 293 flesch = 39 summary = The FilmArray Respiratory Panel (RP) (BioFire Diagnostics, Inc., Salt Lake City, UT, USA) is the first multiplex molecular panel cleared by the US FDA for the detection of both bacterial and viral respiratory pathogens in nasopharygeal swabs. The FilmArray Respiratory Panel (RP) (BioFire Diagnostics, Inc., Salt Lake City, UT, USA) is the first multiplex molecular panel cleared by the US FDA for the detection of both bacterial and viral respiratory pathogens in nasopharygeal swabs. Although the infection usually remains limited to the upper respiratory tract in most patients, complications due to influenza viruses have been reported in HSCT and SOT patients, especially lung transplant recipients [18, 22, 23] . In 2008, the FDA cleared the first broadly multiplexed molecular assay, the xTAG Ò respiratory viral panel ( Two studies have evaluated the performance of the eSensor RVP compared to other multiplex respiratory panels including the FilmArray RP, the xTAG RVP and the xTAG RVP FAST and to laboratory developed tests [58, 59] . cache = ./cache/cord-261598-w2tyongu.txt txt = ./txt/cord-261598-w2tyongu.txt === reduce.pl bib === === reduce.pl bib === id = cord-257220-fe2sacjj author = Butler, J. E. title = Porcine reproductive and respiratory syndrome (PRRS): an immune dysregulatory pandemic date = 2014-07-01 pages = extension = .txt mime = text/plain words = 19650 sentences = 994 flesch = 44 summary = LDV elevates IgG levels in mice with little production of virus-specific antibodies [11, 21] , which is almost identical to what is seen in isolator piglets infected with PRRSV [22] (''The effect of age, rearing, complement and the role of mucosal immunity'' section). Polyclonal activation of B cells occurs in lymphoid organs from porcine reproductive and respiratory syndrome virus (PRRSV)-induced pigs The presence of alpha interferon at the time of infection alters the innate and adaptive immune responses to porcine reproductive and respiratory syndrome virus Interferon type I response in porcine reproductive and respiratory syndrome virus-infected MARC-145 cells Antigen-specific B cell responses to porcine reproductive and respiratory syndrome virus infection Antibody production and blastogenesis response in pigs experimentally infected with porcine reproductive and respiratory syndrome virus Neutralizing antibody responses of pigs infected with natural GP5 N-glycan mutants of porcine reproductive and respiratory syndrome virus cache = ./cache/cord-257220-fe2sacjj.txt txt = ./txt/cord-257220-fe2sacjj.txt === reduce.pl bib === id = cord-260225-bc1hr0fr author = Sirpilla, Olivia title = SARS-CoV-2-Encoded Proteome and Human Genetics: From Interaction-Based to Ribosomal Biology Impact on Disease and Risk Processes date = 2020-07-20 pages = extension = .txt mime = text/plain words = 8918 sentences = 582 flesch = 44 summary = Integrating evolutionary, structural, and interaction data with human proteins, we present how the SARS-CoV-2 proteome interacts with human disorders and risk factors ranging from cytokine storm, hyperferritinemic septic, coagulopathic, cardiac, immune, and rare disease-based genetics. The most noteworthy human genetic potential of SARS-CoV-2 is that of the nucleocapsid protein, where it is known to contribute to the inhibition of the biological process known as nonsense-mediated decay. As we understand more of the dynamic and complex biological pathways that the proteome of SARS-CoV-2 utilizes for entry into cells, for replication, and for release from human cells, we can understand more risk factors for severe/lethal outcomes in patients and novel pharmaceutical interventions that may mitigate future pandemics. Additional SARS-CoV-2 proteins with mentions include nsp12 (RNA-directed RNA polymerase, 20/71), nucleocapsid (N, 17/71), membrane (M, 5/48), envelope (E, 4/31), nsp5 (3CLPro/Mpro, 7/26), nsp8 (3/19), nsp16 (2′-O-methyltransferase, 3/14), ORF8 (1/10), nsp10 (3/9), nsp14 (guanine-N7 methyltransferase, 1/8), nsp3 (papain-like protease, 16/6), and nsp15 (uridylate-specific endoribonuclease, 16/4). cache = ./cache/cord-260225-bc1hr0fr.txt txt = ./txt/cord-260225-bc1hr0fr.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-264079-u0nkjexi author = Murphy, Dianne title = The use of gowns and masks to control respiratory illness in pediatric hospital personnel date = 1981-11-30 pages = extension = .txt mime = text/plain words = 2674 sentences = 152 flesch = 56 summary = title: The use of gowns and masks to control respiratory illness in pediatric hospital personnel Nosocomial disease often lengthens the hospital stay and, in some instances, may be severe or even fatal> ~ For certain viruses, particularly respiratory syncytial virus, there is a high frequency of infection in nursing, medical, and other stafP ..... Children with respiratory disease are usually placed in isolation and hospital personnel may be cohorted or required to wear gowns when administering patient care. The efficacy of this approach in the control of RSV therefore designed a prospective study to examine the effect of various control methods on the acquisition of symptomatic respiratory infections by medical personnel caring for infants with respiratory disease. We were unable to demonstrate any effect of adding the use of both gown and mask to the usual handwashing routine on the development of illness in personnel caring for infants with respiratory disease. cache = ./cache/cord-264079-u0nkjexi.txt txt = ./txt/cord-264079-u0nkjexi.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-261941-xf1k5uj1 author = Stackhouse, Robin A. title = Severe acute respiratory syndrome and tuberculosis date = 2005-03-01 pages = extension = .txt mime = text/plain words = 5420 sentences = 306 flesch = 55 summary = Recommendations for limiting secondary transmission are given based on the Centers for Disease Control and Prevention guidelines on infection control in health care facilities. It is confirmed through laboratory testing showing an acute rise in SARS-CoV antibody titers within 4 weeks of developing the disease. Patients who meet the criteria for suspect SARS should immediately be placed in a private respiratory isolation room that has been specially engineered to contain negative pressure in relation to the outside hallway and have a minimum of 12 air exchanges per hour. Prevention of transmission in medical facilities requires a combination of early identification, isolation, and treatment of infectious individuals with active disease, engineering controls, basic infection control measures, and the use of personal protective equipment. Hospital infection control guidance for severe acute respiratory syndrome (SARS) California Department of Health Services: severe acute respiratory syndrome (SARS)-infection control recommendations Infection control measures for operative procedures in severe acute respiratory syndrome-related patients cache = ./cache/cord-261941-xf1k5uj1.txt txt = ./txt/cord-261941-xf1k5uj1.txt === reduce.pl bib === id = cord-260871-dtn5t8ka author = Silva, Marcus Tulius T. title = SARS-CoV-2: Should We Be Concerned about the Nervous System? date = 2020-07-17 pages = extension = .txt mime = text/plain words = 4110 sentences = 263 flesch = 43 summary = Besides, several neurological manifestations had been described as complications of two other previous outbreaks of CoV diseases (SARS ad Middle East respiratory syndrome). Several neurological manifestations were described as complications of two other previous outbreaks of CoV diseases, namely, SARS and the Middle East respiratory syndrome (MERS). Stroke is one of the most frequent neurological diseases associated with SARS-CoV-2 infection, 8 and large-vessel stroke in younger patients was recently reported in five patients. Detection of SARS coronavirus RNA in the cerebrospinal fluid of a patient with severe acute respiratory syndrome Mechanisms of host defense following severe acute respiratory syndrome-coronavirus (SARS-CoV) pulmonary infection of mice Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 Central nervous system involvement by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the central nervous system cache = ./cache/cord-260871-dtn5t8ka.txt txt = ./txt/cord-260871-dtn5t8ka.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-262673-j2ot35lt author = Ahmed-Hassan, Hanaa title = Innate Immune Responses to Highly Pathogenic Coronaviruses and Other Significant Respiratory Viral Infections date = 2020-08-18 pages = extension = .txt mime = text/plain words = 8591 sentences = 472 flesch = 41 summary = Furthermore, respiratory epithelial cells and lung macrophages are capable of secreting a broad range of chemokines like IL-8, Macrophage inflammatory protein-1 (MIP-1), RANTES and cytokines including TNF-α, IL-6, IL-1β that influence the types of immune cells being recruited to the area in response to acute viral infections (177, 178) . Both Influenza and SARS virus can induce acute lung injury (ALI) which is accompanied by high levels of C5a, leading to the influx and activation of innate immune cells (199) (Figure 1) . Innate immune response of human alveolar type II cells infected with severe acute respiratory syndrome-coronavirus Middle East respiratory syndrome coronavirus shows poor replication but significant induction of antiviral responses in human monocytederived macrophages and dendritic cells Dynamic innate immune responses of human bronchial epithelial cells to severe acute respiratory syndrome-associated coronavirus infection Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells cache = ./cache/cord-262673-j2ot35lt.txt txt = ./txt/cord-262673-j2ot35lt.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-264059-jf4j00bp author = Lee, Chien-Chang title = Combining Procalcitonin and Rapid Multiplex Respiratory Virus Testing for Antibiotic Stewardship in Older Adult Patients With Severe Acute Respiratory Infection date = 2019-11-30 pages = extension = .txt mime = text/plain words = 4611 sentences = 251 flesch = 36 summary = 3 Initial studies demonstrated that such POC multiplex PCR systems identified previously under-evaluated viral or atypical infections in ED dyspneic patients, and the additional information on rapid respiratory infection testing may also change the physician's antibiotic-prescribing behavior, enabling more timely and appropriate treatment. In this study, we aimed to assess the impact of implementing a diagnostic algorithm that combines rapid respiratory viral surveillance and PCT tests on older patients presenting to the ED with severe acute respiratory illness. This prospective cohort study reports the clinical impact of rapid molecular diagnosis of respiratory pathogens in conjunction with PCT testing on older adult patients presenting to the ED with severe acute respiratory illness. The findings of our study support the use of rapid multiplex PCR respiratory panels in conjunction with the PCT test for early diagnosis of respiratory viral infection and to inform optimizing antibiotic use in older adult patients presenting to the ED with severe acute respiratory illness. cache = ./cache/cord-264059-jf4j00bp.txt txt = ./txt/cord-264059-jf4j00bp.txt === reduce.pl bib === === reduce.pl bib === id = cord-260472-xvvfguht author = Papadopoulos, Nikolaos G. title = Antimicrobial strategies: An option to treat allergy? date = 2007-01-31 pages = extension = .txt mime = text/plain words = 5105 sentences = 255 flesch = 30 summary = The association between upper respiratory viral infections and asthma exacerbations in children was demonstrated almost three decades ago using virus cultures and serological techniques [5] . Abbreviations: RTePCR, reverse transcriptionepolymerase chain reaction; RV, rhinovirus; PIV, parainfluenza virus; RSV, respiratory syncytial virus; MPV, human metapneumovirus; ICAM-1, intracellular adhesion molecule-1; IFN-b, interferon-beta; NGF, nerve growth factor; SP, substance P; NK1, neurokinin 1 receptor; MBL, mannose-binding lectin; LABA, long-acting b 2 agonists. In the human respiratory tract, all the above agents are able to produce a spectrum of clinical acute infection phenotypes, ranging from the common cold, croup and acute bronchiolitis, to pneumonia, although each virus has increased propensity for a particular clinical disease (e.g. parainfluenza for croup, RSV for severe bronchiolitis, influenza for pneumonia) [21, 22] . Rhinovirus is the key virus accounting for the majority of exacerbations both in children and adults and thus the effective treatment or prevention of that infection would be a major asset in asthma therapy. cache = ./cache/cord-260472-xvvfguht.txt txt = ./txt/cord-260472-xvvfguht.txt === reduce.pl bib === === reduce.pl bib === id = cord-268388-kkhuzf3p author = Sharif-Yakan, Ahmad title = Emergence of MERS-CoV in the Middle East: Origins, Transmission, Treatment, and Perspectives date = 2014-12-04 pages = extension = .txt mime = text/plain words = 2507 sentences = 141 flesch = 50 summary = Two years have passed since the initial description of the Middle East respiratory syndrome coronavirus (MERS-CoV), yet the epidemic is far from being controlled. First reported in 2012 [1] , Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel coronavirus and the first lineage 2C Betacoronavirus known to infect humans [2] . Middle east respiratory syndrome coronavirus (MERS-CoV) RNA and neutralising antibodies in milk collected according to local customs from dromedary camels, qatar Middle east respiratory syndrome coronavirus (MERS-CoV) in dromedary camels Epidemiological, demographic, and clinical characteristics of 47 cases of middle east respiratory syndrome coronavirus disease from saudi arabia: A descriptive study Clinical features and viral diagnosis of two cases of infection with middle east respiratory syndrome coronavirus: A report of nosocomial transmission Clinical features and virological analysis of a case of middle east respiratory syndrome coronavirus infection Ribavirin and interferon therapy in patients infected with the middle east respiratory syndrome coronavirus: An observational study cache = ./cache/cord-268388-kkhuzf3p.txt txt = ./txt/cord-268388-kkhuzf3p.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-265445-bazcczdj author = Arias-Bravo, Guisselle title = Overnutrition in Infants Is Associated With High Level of Leptin, Viral Coinfection and Increased Severity of Respiratory Infections: A Cross-Sectional Study date = 2020-02-18 pages = extension = .txt mime = text/plain words = 4565 sentences = 257 flesch = 50 summary = title: Overnutrition in Infants Is Associated With High Level of Leptin, Viral Coinfection and Increased Severity of Respiratory Infections: A Cross-Sectional Study Objective: To investigate the relationship of overnutrition (obese and overweight) with severity of illness in children hospitalized with acute lower respiratory infections (ALRIs), frequency of viral coinfections and leptin levels. However, the empirical evidence needed to estimate the impact of overnutrition (including overweight and obese conditions) on the severity of viral respiratory infections in children is still lacking (10) . Hence, the objective of this study was to estimate the relationship of overnutrition on severity of illness in infants (aged between 0 and 5 months) and children (aged between 6 and 24 months) hospitalized with ALRIs. Moreover, frequency of viral coinfection, RSV viral load and levels of leptin according to nutritional status were evaluated. cache = ./cache/cord-265445-bazcczdj.txt txt = ./txt/cord-265445-bazcczdj.txt === reduce.pl bib === id = cord-263927-hnsyas9q author = Peci, Adriana title = Community‐acquired respiratory viruses and co‐infection among patients of Ontario sentinel practices, April 2009 to February 2010 date = 2012-08-09 pages = extension = .txt mime = text/plain words = 3210 sentences = 210 flesch = 48 summary = Objectives To describe respiratory viruses, including co‐infection and associated attributes such as age, sex or comorbidity, in patients presenting with influenza‐like illness to a community sentinel network, during the pandemic A(H1N1)pdm09 in Ontario, Canada. In multinomial logistic regression analyses adjusted for age, sex, comorbidity, and timeliness of sample collection, single infection was less often detected in the elderly and co‐infection more often in patients <30 years of age. Co‐infection, but not single infection, was more likely detected in patients who had a sample collected within 2 days of symptom onset as compared to 3–7 days. [8] [9] [10] [11] [12] [13] Higher proportions of influenza A, respiratory syncytial virus (RSV), parainfluenza viruses, and rhinovirus, compared with other circulating viruses have been detected in patients with co-infections. 9, 15, 16, 20, 21 This study enrolled community patients presenting with (ILI) to a community sentinel network, during the influenza pandemic A(H1N1)pdm09 in Ontario, Canada and documented the profile of respiratory viruses causing ILI symptoms. cache = ./cache/cord-263927-hnsyas9q.txt txt = ./txt/cord-263927-hnsyas9q.txt === reduce.pl bib === id = cord-262366-cmjnb0al author = Gerna, Giuseppe title = Genetic variability of human coronavirus OC43‐, 229E‐, and NL63‐like strains and their association with lower respiratory tract infections of hospitalized infants and immunocompromised patients date = 2006-05-23 pages = extension = .txt mime = text/plain words = 5857 sentences = 304 flesch = 51 summary = title: Genetic variability of human coronavirus OC43‐, 229E‐, and NL63‐like strains and their association with lower respiratory tract infections of hospitalized infants and immunocompromised patients In the winter–spring seasons 2003–2004 and 2004–2005, 47 (5.7%) patients with acute respiratory infection associated with human coronavirus (hCoV) 229E‐, NL63‐, and OC43‐like strains were identified among 823 (597 immunocompetent and 226 immunocompromised) patients admitted to hospital with acute respiratory syndromes. © 2006 Wiley‐Liss, Inc. In the winter-spring seasons 2003-2004 and 2004-2005, 47 (5.7%) patients with acute respiratory infection associated with human coronavirus (hCoV) 229E-, NL63-, and OC43-like strains were identified among 823 (597 immunocompetent and 226 immunocompromised) patients admitted to hospital with acute respiratory syndromes. cache = ./cache/cord-262366-cmjnb0al.txt txt = ./txt/cord-262366-cmjnb0al.txt === reduce.pl bib === id = cord-272143-6ej3eibd author = Benavides‐Nieto, Marta title = The role of respiratory viruses in children with humoral immunodeficiency on immunoglobulin replacement therapy date = 2018-12-21 pages = extension = .txt mime = text/plain words = 1875 sentences = 133 flesch = 40 summary = We have evaluated these infections in children with humoral immunodeficiencies who required immunoglobulin replacement therapy, considering their relationship with symptoms, lung function, bacterial co‐infection, and outcomes. CONCLUSIONS: In our experience, viral respiratory tract infections can cause significant respiratory symptoms and impaired lung function, in children with HID, despite immunoglobulin replacement therapy. Children with severe T-cell immunodeficiencies present impaired clearance of respiratory viruses, and pulmonary complications of viral infections are leading causes of morbidity and mortality in this group of patients. 1 However, the role of respiratory viruses in children with other types of primary immunodeficiency (PID), mainly those with humoral immunodeficiencies (HID) or diseases of immune dysregulation, has hardly been studied. 2, 7 We report, to the best of our knowledge, the first study that analyses respiratory viruses in pediatric patients with predominantly antibody deficiency who required IRT, considering their relationship with clinical symptoms and pulmonary function, bacterial co-infection, treatment and outcomes. cache = ./cache/cord-272143-6ej3eibd.txt txt = ./txt/cord-272143-6ej3eibd.txt === reduce.pl bib === id = cord-267274-3ygl3stc author = Britton, Philip N title = COVID-19 public health measures and respiratory syncytial virus date = 2020-09-18 pages = extension = .txt mime = text/plain words = 1038 sentences = 56 flesch = 47 summary = We analysed three separate datasets from the SCHN electronic records from Jan 1, 2015, to June 30, 2020, in children younger than 16 years: (1) laboratory tests for respiratory syncytial virus by PCR; (2) hospital admissions for bronchiolitis coded by the ICD-10 Australian Modification (J21.0, J21.1, J21.8, and J21.9); and (3) emergency department attendances for acute respiratory illness coded by the Systematised Nomenclature of Medicine Clinical Terminology (appendix p 4). We observed concurrent lower frequencies of respiratory syncytial virus (A and B) detection, admission to hospital for bronchiolitis, and emergency department attendance for acute respiratory illnesses (appendix p 1) in 2020 compared with preceding years. The small uptick in emergency department attendances and bronchiolitis admissions in June, 2020 (appendix p 1) was not associated with increased respiratory syncytial virus detections. cache = ./cache/cord-267274-3ygl3stc.txt txt = ./txt/cord-267274-3ygl3stc.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-266822-ecq50ye2 author = Rath, Barbara title = Influenza and other respiratory viruses: standardizing disease severity in surveillance and clinical trials date = 2017-05-12 pages = extension = .txt mime = text/plain words = 10809 sentences = 556 flesch = 38 summary = Disease burden due to influenza and other respiratory viral infections is reported on a population level, but clinical scores measuring individual changes in disease severity are urgently needed. Standardized measures of disease severity are urgently needed for clinical trials of vaccines and antivirals currently in development for ARI caused by influenza (FLU), respiratory syncytial virus (RSV), human metapneumovirus (HMPV), adenovirus (ADV), or human rhinovirus (HRV) [9] [10] [11] [12] [13] [14] [15] [16] [17] . Considering the variability in disease presentations and courses of illness with influenza and other respiratory viral infections in children, the ViVI Disease Severity Score is not intended to be validated against future clinical events or outcomes. Our contributions are the following: (A) The design of a hospital-based surveillance program and a unique QM cohort of more than 6000 children, where an independent QM team monitored patients daily using standardized clinical assessments and virology at the National Reference Centre for Influenza and Other Respiratory Viruses. cache = ./cache/cord-266822-ecq50ye2.txt txt = ./txt/cord-266822-ecq50ye2.txt === reduce.pl bib === id = cord-261025-y49su5uc author = Sampathkumar, Priya title = SARS: Epidemiology, Clinical Presentation, Management, and Infection Control Measures date = 2003-07-31 pages = extension = .txt mime = text/plain words = 3952 sentences = 200 flesch = 49 summary = Severe acute respiratory syndrome (SARS) is a recently recognized febrile respiratory illness that first appeared in southern China in November 2002, has since spread to several countries, and has resulted in more than 8000 cases and more than 750 deaths. This article summarizes currently available information regarding the epidemiology, clinical features, etiologic agent, and modes of transmission of the disease, as well as infection control measures appropriate to contain SARS. An RT-PCR test specific for RNA from the SARS-CoV has been positive within the first 10 days after fever onset in respiratory specimens from most patients considered probable cases of SARS who have been tested and in stool samples in the second week of illness. Case definitions of SARS are currently based on the presence of epidemiological risk factors (close contact with patients with SARS or travel to SARS-affected areas) and a combination of fever and respiratory symptoms, with or without chest radiographic changes. Severe Acute Respiratory Syndrome (SARS) in Singapore: clinical features of index patient and initial contacts cache = ./cache/cord-261025-y49su5uc.txt txt = ./txt/cord-261025-y49su5uc.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-268324-86a0n0dc author = Charitos, Ioannis A title = Special features of SARS-CoV-2 in daily practice date = 2020-09-26 pages = extension = .txt mime = text/plain words = 6117 sentences = 279 flesch = 42 summary = The severe acute respiratory syndrome-coronavirus-2 (commonly known as SARS-CoV-2) is a novel coronavirus (designated as 2019-nCoV), which was isolated for the first time after the Chinese health authorities reported a cluster of pneumonia cases in Wuhan, China in December 2019. The clinical picture of critical patients with severe inflammatory-induced lung disease and with sepsis or septic shock needing intensive care support and mechanical ventilation is characterized by a wide range of signs and symptoms of life-threatening multiorgan dysfunction or failure, including dyspnoea, tachypnoea (respiratory rate of > 30/min), tachycardia, chest pain or tightness, hypoxemia, virus-induced distributive shock, cardiac dysfunction, elevations in multiple inflammatory cytokines, renal impairment with oliguria, altered mental status, functional alterations of organs expressed as laboratory data of hyperbilirubinemia, acidosis [serum lactate level > 2 mmol/L (18 mg/dL)], coagulopathy, and thrombocytopenia. cache = ./cache/cord-268324-86a0n0dc.txt txt = ./txt/cord-268324-86a0n0dc.txt === reduce.pl bib === === reduce.pl bib === id = cord-270647-vn4kirrx author = Romero-Espinoza, Jose A. title = Virome and bacteriome characterization of children with pneumonia and asthma in Mexico City during winter seasons 2014 and 2015 date = 2018-02-15 pages = extension = .txt mime = text/plain words = 3513 sentences = 201 flesch = 48 summary = OBJECTIVES: To describe the virome and bacteriome present in the upper respiratory tract of hospitalized children with a clinical diagnosis of asthma and pneumonia during an acute exacerbation and an acute respiratory illness ARI episode respectively. Both groups differ with respect to the associated virus and bacteria: while asthma exacerbations have been associated to a specific rhinovirus infection, pneumonia can be related to a wide range of bacterial, fungal and viral agents, with a high prevalence of Respiratory Syncytial Virus (RSV) [2, 7] . Here we describe the virome and bacteriome present in the Upper Respiratory Tract of hospitalized children clinically diagnosed with asthma and pneumonia, during an acute exacerbation and an ARI episode respectively, at the National Institute of Respiratory Diseases (INER, Mexico City) during 2014 and 2015 winter seasons. Prevalence of respiratory viral infection in children hospitalized for acute lower respiratory tract diseases, and association of rhinovirus and influenza virus with asthma exacerbations cache = ./cache/cord-270647-vn4kirrx.txt txt = ./txt/cord-270647-vn4kirrx.txt === reduce.pl bib === id = cord-270258-9vgpphiu author = Ko, Jae-Hoon title = Predictive factors for pneumonia development and progression to respiratory failure in MERS-CoV infected patients date = 2016-08-09 pages = extension = .txt mime = text/plain words = 3460 sentences = 171 flesch = 43 summary = To identify factors which can predict pneumonia development and progression to respiratory failure at the early course of the disease, we evaluated MERS-CoV infected patients managed in a tertiary care center during the 2015 MERS outbreak in Korea. To identify factors which can predict pneumonia development and progression to respiratory failure at the early course of the disease, we reviewed the electronic medical records of who were diagnosed with MERS-CoV infection and admitted at Samsung Medical Center, a 1950 tertiary care university hospital which managed the largest number of MERS-CoV infected patients as a single center during the 2015 Korean MERS outbreak. The present analysis of predictive factors for pneumonia development and progression to respiratory failure using variables obtained by day 3 of symptom onset could be conducted owing to the observation of entire clinical course of the disease from the exposure to MERS-CoV. cache = ./cache/cord-270258-9vgpphiu.txt txt = ./txt/cord-270258-9vgpphiu.txt === reduce.pl bib === === reduce.pl bib === id = cord-278031-vpq4yghn author = Zumla, Alimuddin title = Rapid diagnostics urgently needed for killer infections date = 2013-06-30 pages = extension = .txt mime = text/plain words = 1138 sentences = 71 flesch = 50 summary = 3 Clinicians are often unaware of the presence of more than one pathogen, although co-infections of bacteria 4 or other respiratory viruses 5 and infl uenza are well described, as are bacterial, viral, or parasitic infections with pulmonary tuberculosis. Global scientifi c and political attention is currently focused on two new viruses associated with severe RTIs and high mortality: the avian infl uenza A H7N9 virus from China and novel coronavirus from the Arabian Peninsula. 11 Although several new rapid molecular diagnostic plat forms capable of simultaneously identifying both pathogens and the genetic determinants of anti microbial resistance are emerging, 12 they do not seem to be well suited to clinical presentations or downstream manage ment strategies for patients with RTIs. Furthermore, none can identify new emerging organisms for which genetic sequences are unavailable. cache = ./cache/cord-278031-vpq4yghn.txt txt = ./txt/cord-278031-vpq4yghn.txt === reduce.pl bib === id = cord-268038-9jjpc1a2 author = Boukhvalova, M title = Treatment with novel RSV Ig RI-002 controls viral replication and reduces pulmonary damage in immunocompromised Sigmodon hispidus date = 2015-09-14 pages = extension = .txt mime = text/plain words = 4354 sentences = 230 flesch = 37 summary = These results indicate the potential of RI-002 to improve outcome of RSV infection in immunocompromised subjects not only by controlling viral replication, but also by reducing damage to lung parenchyma and epithelial airway lining, but further studies are needed. In this case, treatment with a drug that has strong antiviral activity may have a higher therapeutic efficacy in immunosuppressed patients compared with immunocompetent individuals infected with RSV because of the reduction in pulmonary damage caused by excessive viral replication. Although normal cotton rats treated with saline cleared RSV by day 10 post infection, immunosuppressed saline-treated animals had~6 log 10 PFU of virus in their lungs and noses at that time. To determine whether RI-002 has an effect on pulmonary pathology associated with prolonged RSV replication in immunosuppressed animals, lung tissue was collected for histopathology analysis on day 10 post infection. cache = ./cache/cord-268038-9jjpc1a2.txt txt = ./txt/cord-268038-9jjpc1a2.txt === reduce.pl bib === === reduce.pl bib === id = cord-272878-6f0q661e author = Schnepf, Nathalie title = High Burden of Non-Influenza Viruses in Influenza-Like Illness in the Early Weeks of H1N1v Epidemic in France date = 2011-08-17 pages = extension = .txt mime = text/plain words = 4177 sentences = 217 flesch = 45 summary = In the two academic hospitals, Saint-Louis hospital (SLS) in Paris and Tours hospital (TRS), influenza-like illness (ILI) was defined as a patient suffering from at least one general symptom (fever above 38uC, asthenia, myalgia, shivers or headache) and one respiratory symptom (cough, dyspnoea, rhinitis or pharyngitis), in agreement with the guidelines from the French Institut de Veille Sanitaire (InVS), a governmental institution responsible for surveillance and alert in all domains of public health [12] . Two hundred and twelve were positive for non influenza pathogens (189 single infections and 23 mixed infections with two, three or four viruses) and three additional single infections by influenza A were identified in SLS, including two by pandemic H1N1v and one by seasonal H3N2, as determined after molecular typing (data not shown). As RHV was the most frequent aetiology in ILI, we also compared clinical symptoms observed in patients with a single infection by RHV or by H1N1v (data not shown). cache = ./cache/cord-272878-6f0q661e.txt txt = ./txt/cord-272878-6f0q661e.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-272596-yxvg8357 author = WU, Jian Jun title = Detection of Human Bocavirus in Children with Acute Respiratory Tract Infections in Lanzhou and Nanjing, China date = 2014-11-30 pages = extension = .txt mime = text/plain words = 2953 sentences = 167 flesch = 48 summary = title: Detection of Human Bocavirus in Children with Acute Respiratory Tract Infections in Lanzhou and Nanjing, China In our study, 72.34% of HBoV1-positive patients had co-infection with 10 different respiratory viruses, which is similar to previous reports [12] [13] [14] [46] [47] [48] . Detection of human bocavirus in children with upper respiratory tract infection by polymerase chain reaction Detection of bocavirus in children suffering from acute respiratory tract infections in Saudi Arabia Detection of human bocavirus from children and adults with acute respiratory tract illness in Guangzhou, southern China Clinical relevance of human bocavirus with acute respiratory tract infection and diarrhea in children: a prospective case-control study Frequent detection of bocavirus DNA in German children with respiratory tract infections Human bocavirus infection in children with acute respiratory tract infection in India Human bocavirus in children with acute respiratory infections in Vietnam Human bocavirus infection in young children with acute respiratory tract infection in Lanzhou cache = ./cache/cord-272596-yxvg8357.txt txt = ./txt/cord-272596-yxvg8357.txt === reduce.pl bib === === reduce.pl bib === id = cord-274900-s7ft1491 author = Tatarelli, P. title = Prevalence and clinical impact of VIral Respiratory tract infections in patients hospitalized for Community-Acquired Pneumonia: the VIRCAP study date = 2019-11-30 pages = extension = .txt mime = text/plain words = 3812 sentences = 199 flesch = 39 summary = title: Prevalence and clinical impact of VIral Respiratory tract infections in patients hospitalized for Community-Acquired Pneumonia: the VIRCAP study Whilst epidemiology and clinical features of viral respiratory tract infections (VRTIs) were mainly explored in children and outpatients [7, 8] , a few data show increasing prevalence rates also in hospitalized patients, particularly in elderly and in presence of comorbidities such as asthma, chronic obstructive pulmonary disease or immunosuppression [9] [10] [11] . CAP was defined as acute lower respiratory tract infection characterized by the presence of two or more signs and symptoms (among fever, cough, dyspnoea, pleuritic pain, crackles or bronchial breath at pulmonary auscultation), associated with at least one among (a) radiological findings (opacity or infiltrate at radiography or computed tomography interpreted as pneumonia by the attending physician), (b) serum levels of inflammatory markers above normal values and (c) neutrophilic leucocytosis, in patients hospitalized no longer than 48 h [1] . cache = ./cache/cord-274900-s7ft1491.txt txt = ./txt/cord-274900-s7ft1491.txt === reduce.pl bib === === reduce.pl bib === id = cord-276927-rxudwp2v author = Barbas, Carmen Sílvia Valente title = Goal-Oriented Respiratory Management for Critically Ill Patients with Acute Respiratory Distress Syndrome date = 2012-08-23 pages = extension = .txt mime = text/plain words = 7991 sentences = 374 flesch = 35 summary = Rapid administration of antibiotics and resuscitative measures in case of sepsis and septic shock associated with protective ventilatory strategies and early short-term paralysis associated with differential ventilatory techniques (recruitment maneuvers with adequate positive end-expiratory pressure titration, prone position, and new extracorporeal membrane oxygenation techniques) in severe ARDS can help improve its prognosis. Incorporation of modified risk factors such as acute increase of respiratory rate, presence of tachypnea, detection of pulse oximeter desaturation, increased necessity of oxygen supplementation, presence of low pH, acidosis, or hypoxemia in an arterial blood gas sample in clinical practice can improve the clinicians' ability to perform early diagnosis and prompt therapeutic intervention in ARDS [17] . cache = ./cache/cord-276927-rxudwp2v.txt txt = ./txt/cord-276927-rxudwp2v.txt === reduce.pl bib === id = cord-274127-12x5cc8i author = Jeong, Ji Hun title = Comparison of sputum and nasopharyngeal swabs for detection of respiratory viruses date = 2014-05-06 pages = extension = .txt mime = text/plain words = 2721 sentences = 148 flesch = 49 summary = Paired specimens of nasopharyngeal swabs and sputum were obtained from 154 subjects, and RNA was extracted and tested for 16 different respiratory viruses using the Anyplex II RV16 Detection kit (Seegene, Seoul, Korea). The detection rates of respiratory viruses from sputum samples were significantly higher than those from nasopharyngeal swabs in adults using real‐time multiplex RT‐PCR. The aim of this study was to compare the detection rates of respiratory viruses in paired nasopharyngeal swabs and sputum samples from adult patients with respiratory symptoms using multiplex real-time RT-PCR. The present study found that the overall detection rate from sputum samples in adults was significantly higher than from nasopharyngeal swabs using multiplex real-time RT-PCR. In conclusion, the detection rates of respiratory viruses from sputum samples are significantly higher than those from nasopharyngeal swabs in adults using multiple real-time RT-PCR. cache = ./cache/cord-274127-12x5cc8i.txt txt = ./txt/cord-274127-12x5cc8i.txt === reduce.pl bib === id = cord-276005-ifn88mjd author = da Silva Filho, Luiz Vicente Ribeiro Ferreira title = The Differential Clinical Impact of Human Coronavirus Species in Children With Cystic Fibrosis date = 2012-08-01 pages = extension = .txt mime = text/plain words = 2485 sentences = 113 flesch = 42 summary = We investigated the clinical impact of human coronaviruses (HCoV) OC43, 229E, HKU1 and NL63 in pediatric patients with cystic fibrosis (CF) during routine and exacerbation visits. The proportion of cases with acute respiratory exacerbation among patients infected with different HCoV species was compared by χ 2 or Fisher exact tests. The identification of new species of HCoV [7, 8] and the emergence of SARS HCoV [6] highlighted the potential role of these viruses as causative agents of severe lower respiratory tract infections. However, most of the studies on the clinical impact of different HCoV species were only performed among children who were hospitalized for acute respiratory tract infections, with small sample sizes and short periods of sample collection [10] . New human coronavirus, HCoV-NL63, associated with severe lower respiratory tract disease in Australia cache = ./cache/cord-276005-ifn88mjd.txt txt = ./txt/cord-276005-ifn88mjd.txt === reduce.pl bib === id = cord-275166-qduf08kp author = Assane, Dieng title = Viral and Bacterial Etiologies of Acute Respiratory Infections Among Children Under 5 Years in Senegal date = 2018-02-13 pages = extension = .txt mime = text/plain words = 1877 sentences = 119 flesch = 44 summary = Adenovirus was the most prevalent virus (50%; n = 81), followed by influenza virus (45.68%, n = 74), rhinovirus (40.12%; n = 65), enterovirus (25.31%; n = 41), and respiratory syncytial virus (16.05%; n = 26), whereas Streptococcus pneumoniae (17%; n = 29), Moraxella catarrhalis (15.43%; n = 25), and Haemophilus influenzae (8.02%; n = 13) were the most commonly isolated bacteria. Respiratory tract infections (RTIs) such as acute otitis media, sinusitis, bronchitis, and community-acquired pneumonia are a leading cause of infectious disease-related morbidity, hospitalization, and mortality among children worldwide, particularly in low-income countries. 1 According to World Health Organization (WHO), the prevalence of hospitalized children under 5 years with acute respiratory infections (ARIs) is estimated to be 20% and 90% of those were due to pneumonia. 4, 5 However, primary infections with viral pathogens can predispose to secondary bacterial infections, and the most frequently isolated bacteria in ARIs include Streptococcus pneumonia and Haemophilus influenzae. cache = ./cache/cord-275166-qduf08kp.txt txt = ./txt/cord-275166-qduf08kp.txt === reduce.pl bib === === reduce.pl bib === id = cord-281754-auqh3vtr author = nan title = EMERGING RESPIRATORY DISEASE - CORONAVIRUSES date = 2017-09-12 pages = extension = .txt mime = text/plain words = 3626 sentences = 229 flesch = 49 summary = As a human virus the range of disease is broad, from cold like to severe multisystem involvement (These CoV infections are associated with short incubation periods (2-7 days), such as those found in SARS [2, 5, 6, 17, 18, 24, 25] . The etiology causing his illness was identified as severe acute respiratory syndrome coronavirus (SARS CoV); it was likely transmitted to at least 10 additional persons. Other pathogens, including members of the Paramyxoviridae family, and human metapneumovirus (hMPV) were considered as causative of this new clinical illness which became known as Severe Acute Respiratory Syndrome or SARS. Genomic sequence analysis seems to support the hypothesis that of SARS-CoV is an animal virus for which the normal host is still unknown and that developed the ability to productively infect humans or has the ability to cross species barriers [25] . cache = ./cache/cord-281754-auqh3vtr.txt txt = ./txt/cord-281754-auqh3vtr.txt === reduce.pl bib === id = cord-275605-mbiojk39 author = Benkouiten, Samir title = Clinical respiratory infections and pneumonia during the Hajj pilgrimage: A systematic review date = 2018-12-04 pages = extension = .txt mime = text/plain words = 5812 sentences = 282 flesch = 46 summary = METHOD: The MEDLINE/PubMed and Scopus databases were searched for all relevant papers published prior to February 2018 that evaluated the prevalence of clinical symptoms of respiratory infections, including pneumonia, among Hajj pilgrims, as well as their influenza and pneumococcal vaccination status. We carried out a systematic review of cohort and hospital studies that reported the prevalence of clinical symptoms of respiratory infections and pneumonia among pilgrims during the Hajj, and both their influenza and pneumococcal vaccination status, with the aim to provide data allowing the investigation of the impact of this large mass-gathering event on public health policies and services and to identify potential targets for preventive measures. For inclusion, the article had to meet the following criteria: (1) Original study involving Hajj pilgrims; (2) detailed description of the study population, including influenza and pneumococcal vaccination status when available; (3) clinical or self-reported respiratory symptoms and diseases. cache = ./cache/cord-275605-mbiojk39.txt txt = ./txt/cord-275605-mbiojk39.txt === reduce.pl bib === id = cord-282420-0fcyjw7l author = Lu, Cheng-wei title = 2019-nCoV transmission through the ocular surface must not be ignored date = 2020-02-06 pages = extension = .txt mime = text/plain words = 309 sentences = 27 flesch = 59 summary = key: cord-282420-0fcyjw7l authors: Lu, Cheng-wei; Liu, Xiu-fen; Jia, Zhi-fang cord_uid: 0fcyjw7l On Jan 22, Guangfa Wang, a member of the national expert panel on pneumonia, reported that he was infected by 2019nCoV during the inspection in Wuhan. Unprotected exposure of the eyes to 2019nCoV in the Wuhan Fever Clinic might have allowed the virus to infect the body. 4 Severe acute respiratory syndrome coronavirus (SARSCoV) is predominantly transmitted through direct or indirect contact with mucous membranes in the eyes, mouth, or nose. 5 The fact that exposed mucous membranes and unprotected eyes increased the risk of SARSCoV transmission 4 suggests that exposure of unprotected eyes to 2019nCoV could cause acute respiratory infection. The respiratory tract is probably not the only transmission route for 2019nCoV, and all ophthalmologists examining suspected cases should wear protective eyewear. *Cheng-wei Lu, Xiu-fen Liu, Zhi-fang Jia The severe acute respiratory syndrome cache = ./cache/cord-282420-0fcyjw7l.txt txt = ./txt/cord-282420-0fcyjw7l.txt === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 3558 sentences = 174 flesch = 40 summary = 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. 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. The present investigation was specifically designed to assess the epidemiology of respiratory viruses in bronchoalveolar lavage (BAL) fluid from lung transplant recipients and to analyze the relationship between these viruses and the presence of acute graft rejection. Because BAL fluid specimens were collected for a variety of clinical conditions, we were able to analyze the association among symptoms, the diagnosis suspected by the physician in charge, and the subsequent presence of a proven upper and/ or lower respiratory tract viral infection. cache = ./cache/cord-281418-mvgp6qfv.txt txt = ./txt/cord-281418-mvgp6qfv.txt === reduce.pl bib === === reduce.pl bib === id = cord-280857-0o1ikwks author = Goligher, Ewan C. title = Clinical strategies for implementing lung and diaphragm-protective ventilation: avoiding insufficient and excessive effort date = 2020-11-02 pages = extension = .txt mime = text/plain words = 6146 sentences = 274 flesch = 25 summary = This review summarizes practical strategies for achieving lung and diaphragm-protective targets at the bedside, focusing on inspiratory and expiratory ventilator settings, monitoring of inspiratory effort or respiratory drive, management of dyssynchrony, and sedation considerations. Several strategies can be used to facilitate lung and diaphragm protective ventilation, including modulation of ventilator inspiratory and expiratory assist, drugs that modify respiratory drive and/or effort, extracorporeal CO 2 removal (ECCO 2 R) and electrical stimulation of the respiratory muscles, as shown in Fig. 2 . [7] also showed that higher ECCO 2 R support reduced P 0.1 , respiratory muscle effort, and transpulmonary pressure in spontaneously breathing patients recovering from severe ARDS [74] . These preliminary findings suggest that partial neuromuscular blockade could be a feasible approach to achieving lung and diaphragm-protective ventilation targets in patients with high respiratory effort. cache = ./cache/cord-280857-0o1ikwks.txt txt = ./txt/cord-280857-0o1ikwks.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-282533-w6kl74c8 author = Li, Jin title = Rapid detection of respiratory organisms with the FilmArray respiratory panel in a large children’s hospital in China date = 2018-10-11 pages = extension = .txt mime = text/plain words = 3378 sentences = 174 flesch = 44 summary = METHODS: Nasopharyngeal swab or sputum specimens were collected from children aged 19 days to 15 years who were admitted to a hospital in Shanghai and diagnosed with RTIs. The specimens were tested with the FilmArray Respiratory Panel, a multiplex PCR assay that detects 16 viruses, Mycoplasma pneumoniae (M. CONCLUSIONS: FilmArray RP allows the rapid simultaneous detection of a wide number of respiratory organisms, with limited hands-on time, in Chinese pediatric patients with RTIs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-018-3429-6) contains supplementary material, which is available to authorized users. The aim of this study was to evaluate the application of FilmArray RP for the detection of respiratory organisms, and to provide information about the seasonality and prevalence of these organisms in pediatric patients with RTIs in a large children's hospital in China. cache = ./cache/cord-282533-w6kl74c8.txt txt = ./txt/cord-282533-w6kl74c8.txt === reduce.pl bib === id = cord-281085-lqniqui0 author = Nosalova, Gabriela title = Pharmacological modulation of cough reflex date = 2006-12-31 pages = extension = .txt mime = text/plain words = 6991 sentences = 415 flesch = 47 summary = As the pathological cough (especially its chronic form) has significant impact on patient's quality of life, observed either in physical activity or psychosocial domain, various treatment attitudes are used for different forms of cough (acute, subacute, chronic, productive, nonproductive, psychogenic, asthma-associated, or painful). The most important defensive reflex of the airways is cough, which, together with the mucociliary transport system, forms the main mechanism for cleaning of the respiratory tract (Korpas and Nosalova, 1991; Chung and Chang, 2002; Belvisi and Geppetti, 2004) . Although respiratory-modulated receptors play an important role in the function of the upper airways, they are not generally viewed as a primary factor in the elicitation of cough reflex. The antitussive activity of these agents is associated with their ability to lower the sensitivity of the cough center to nerve impulses coming from airways receptors (Fox, 1996b) . cache = ./cache/cord-281085-lqniqui0.txt txt = ./txt/cord-281085-lqniqui0.txt === reduce.pl bib === === reduce.pl bib === id = cord-283604-fqc9jp0l author = Chen, Meng title = Adenoviruses Associated with Acute Respiratory Diseases Reported in Beijing from 2011 to 2013 date = 2015-03-27 pages = extension = .txt mime = text/plain words = 3060 sentences = 127 flesch = 39 summary = To identify the types of human adenoviruses (HAdVs) causing respiratory illness in Beijing, a sentinel surveillance project on the viral aetiology of acute respiratory infection was initiated in 2011. The comparison results of the penton base, hexon, and fiber gene sequences of the Beijing HAdV-3, HAdV-4, HAdV-7, and HAdV-55 strains in this study and those from the GenBank database indicated significant spatial and temporal conservation and stability of sequences within the genome; however, the phylogenetic relationship indicated that both strain BJ04 and strain BJ09 isolated in 2012 and 2013, respectively, may have recombined between HAdV-1 genome and HAdV-2 genome within species HAdV-C, indicating intraspecies recombination. The comparison results of the penton base, hexon, and fiber gene sequences between the Beijing HAdV-3, HAdV-4, HAdV-7, and HAdV-55 strains in this study and the strains from the GenBank database indicated significant conservation and stability of the sequences within the genome across time and space. cache = ./cache/cord-283604-fqc9jp0l.txt txt = ./txt/cord-283604-fqc9jp0l.txt === reduce.pl bib === === reduce.pl bib === id = cord-281051-i229xv0o author = Bishop-Williams, Katherine E. title = A protocol for a systematic literature review: comparing the impact of seasonal and meteorological parameters on acute respiratory infections in Indigenous and non-Indigenous peoples date = 2017-01-26 pages = extension = .txt mime = text/plain words = 6404 sentences = 366 flesch = 44 summary = This protocol outlines our process for conducting a systematic review to investigate whether associations between ARI and seasonal or meteorological parameters differ between Indigenous and non-Indigenous groups residing in the same geographical region. This paper outlines a protocol for conducting a systematic review to investigate whether associations between ARI and seasonal or meteorological parameters differ between Indigenous and non-Indigenous groups residing in the same geographical region. This research builds from the United Nations Declaration of the Rights of Indigenous Peoples [13] understanding of the term Indigenous peoples, which states that an Indigenous person self-identifies as Indigenous; has historical continuity Table 1 Inclusion and exclusion criteria for a systematic literature review investigating the impact of seasonal and meteorological parameters on acute respiratory infection (ARI) in Indigenous and non-Indigenous peoples cache = ./cache/cord-281051-i229xv0o.txt txt = ./txt/cord-281051-i229xv0o.txt === reduce.pl bib === id = cord-282867-kbyxdegu author = Shah, Sayed Zulfiqar Ali title = Scaling the Need, Benefits, and Risks Associated with COVID-19 Acute and Postacute Care Rehabilitation: A Review date = 2020-08-26 pages = extension = .txt mime = text/plain words = 4542 sentences = 247 flesch = 39 summary = The main aim of this study is to review and summarize the evidence regarding the supportive role of physical rehabilitation techniques in managing COVID-19-associated pneumonia. In this review, we also emphasize the use of rehabilitation techniques in the management of pneumonia in COVID-19-infected patients. The purpose of this study was to review the evidence regarding the supportive role of treatment options available in physical rehabilitation to manage COVID-19 pneumonia effectively. Evidence strongly supports that many rehabilitation techniques including chest physiotherapy and physical therapy modalities can be of great support to manage COVID-19-associated pneumonia [9, 10] . Common problems identified in COVID-19 patients that could be managed by rehabilitation specialists in the postacute phase include musculoskeletal pain, joint pain, reduced range of motion, muscular weakness, neuropathy and myopathy, pulmonary dysfunction, dysphagia, dyspnea, confusion, and impaired activities of daily living. cache = ./cache/cord-282867-kbyxdegu.txt txt = ./txt/cord-282867-kbyxdegu.txt === reduce.pl bib === id = cord-284372-v95fzp8n author = Coyle, Peter V title = A touchdown nucleic acid amplification protocol as an alternative to culture backup for immunofluorescence in the routine diagnosis of acute viral respiratory tract infections date = 2004-10-25 pages = extension = .txt mime = text/plain words = 4717 sentences = 224 flesch = 43 summary = title: A touchdown nucleic acid amplification protocol as an alternative to culture backup for immunofluorescence in the routine diagnosis of acute viral respiratory tract infections To overcome this problem we developed a diagnostic molecular strip which combined a generic nested touchdown protocol with in-house primer master-mixes that could recognise 12 common respiratory viruses. CONCLUSIONS: The touchdown protocol with pre-dispensed primer master-mixes was suitable for replacing virus culture for the diagnosis of respiratory viruses which were negative by immunofluorescence. To test the feasibility of its routine use we needed to clinically validate its performance in a routine setting on specimens tested in parallel with our standard immunofluorescence protocol for the diagnosis of acute virus respiratory infections. In conclusion the use of the touchdown protocol with pre-dispensed and quality checked primer master-mixes was suitable for replacing virus culture for the diagnosis of respiratory viruses for immunofluorescence negative specimens. cache = ./cache/cord-284372-v95fzp8n.txt txt = ./txt/cord-284372-v95fzp8n.txt === reduce.pl bib === id = cord-284905-h8xovybl author = MUSK, A.W. (Bill) title = Respiratory infections and lung function in an Australian Aboriginal community date = 2008-02-05 pages = extension = .txt mime = text/plain words = 3449 sentences = 178 flesch = 43 summary = Background and objective: To investigate the association between serological evidence of past infections with common respiratory pathogens and lung function in members of an isolated community of Aborigines from tropical coastal north‐western Australia. 3 Studies of members of an isolated coastal Australian Aboriginal community in the tropical Kimberley region of Western Australia have shown that levels of lung function measured by FEV1 and FVC were lower than those of Australians of European descent. In this tropical Aboriginal community, serological evidence of the burden of previous infections with known viral and other respiratory pathogens was associated with significant decreases in the levels of airway function, consistent with airflow obstruction. The relationship of FEV1 and FEV1/FVC ratio with the total number of positive titres in this study suggests that repeated infections with common respiratory pathogens may have a cumulative detrimental effect on airway function or increase susceptibility to other agents such as tobacco smoke. cache = ./cache/cord-284905-h8xovybl.txt txt = ./txt/cord-284905-h8xovybl.txt === reduce.pl bib === id = cord-278935-3lgud7l8 author = Chen, Zheng‐Rong title = Clinical and epidemiological profiles of lower respiratory tract infection in hospitalized children due to human bocavirus in a subtropical area of China date = 2014-04-30 pages = extension = .txt mime = text/plain words = 4779 sentences = 236 flesch = 47 summary = title: Clinical and epidemiological profiles of lower respiratory tract infection in hospitalized children due to human bocavirus in a subtropical area of China Furthermore, epidemiological data shows that HBoV is present year-round with different incidence rates from 2.2% to 19% in children with lower respiratory tract infection [Manning et al., 2006; Weissbrich et al., 2006; Allander et al., 2007; Canducci et al., 2008] . The purpose of this study was to ascertain the frequency, seasonal, and clinical characteristics in hospitalized children with lower respiratory tract infection and evaluate the effects of meteorological factors on the incidence of HBoV in a subtropical region of China. Based on the data from this study, HBoV was the third most common pathogen after RSV and Mycoplasma pneumoniae with an incidence of 6.6% in all hospitalized children with lower respiratory tract infection in Suzhou area. cache = ./cache/cord-278935-3lgud7l8.txt txt = ./txt/cord-278935-3lgud7l8.txt === reduce.pl bib === id = cord-283910-k10j5dzd author = Fretzayas, Andrew title = Etiology and clinical features of viral bronchiolitis in infancy date = 2017-05-04 pages = extension = .txt mime = text/plain words = 4685 sentences = 260 flesch = 43 summary = Recent advances in laboratory diagnostic methods confer to the identifi cation of different viruses as etiologic pathogens of bronchiolitis, although respiratory syncytial virus (RSV) remains the main culprit The aim of this review was to present the clinical picture of bronchiolitis as a whole entity irrespective of the virology as well as in relation to the particular viral parthogens that are incriminated as etiological factors. We searched the databases with the following key words: viral bronchiolitis, clinical features, definition, epidemiology, etiology, guidelines, severity score, adenovirus, bocavirus, coronavirus, influenza, metapneumovirus, parainfluenza, respiratory synchytial virus, and rhinovirus. In 2006 American Academy of Pediatrics (AAP) published a clinical practice guideline for bronchiolitis, [3] that was updated in 2014 [4] according to which bronchiolitis is "a constellation of signs and symptoms including children younger than 2 years including a viral upper respiratory tract prodrome followed by increased respiratory effort and wheezing". cache = ./cache/cord-283910-k10j5dzd.txt txt = ./txt/cord-283910-k10j5dzd.txt === reduce.pl bib === id = cord-282668-bs634hti author = Niang, Mbayame Ndiaye title = Respiratory viruses in patients with influenza-like illness in Senegal: Focus on human respiratory adenoviruses date = 2017-03-22 pages = extension = .txt mime = text/plain words = 4623 sentences = 243 flesch = 47 summary = In the present study, we investigate the epidemiologic and viral molecular features of HAdVs circulating in Senegal after 4 consecutive years of sentinel surveillance of influenza-like Illness cases. In the present study, we investigate the epidemiologic and viral molecular features of HAdVs circulating in Senegal after 4 consecutive years of sentinel surveillance of influenzalike Illness cases. From January 2012 to December 2015 we collected specimens (nasal-pharyngeal and oral-pharyngeal swabs) and surveillance data for influenza and other viral respiratory pathogens from outpatients presenting with influenza-like-illness (ILI) at different sentinel sites in Senegal. So the circulation of such HAdV genome types in Senegal emphasizes the need to reinforce HAdV surveillance, especially in hospitalized patients, by including HAdV genome detection and genotyping in the documentation of severe respiratory infections. Molecular epidemiology of human adenovirus isolated from children hospitalized with acute respiratory infection in São Paulo, Brazil cache = ./cache/cord-282668-bs634hti.txt txt = ./txt/cord-282668-bs634hti.txt === reduce.pl bib === id = cord-284266-tbndldhr author = Schippa, Serena title = Nasal Microbiota in RSV Bronchiolitis date = 2020-05-13 pages = extension = .txt mime = text/plain words = 5521 sentences = 237 flesch = 34 summary = Our results indicated that infants with more severe bronchiolitis disease, caused by RSV-A infection, present significant perturbations of both the nasal microbiota structure and the microbial relationships. Evaluation of α diversity by the Shannon and Simpson indexes, as well as the number of observed OTUs, showed a significant lower biodiversity in the RSV-positive group with respect to the virus-negative one, suggesting the presence of a microbial shifts in the nasal microbiota of RSV-positive subjects (Figure 1a) . Evaluation of α diversity by the Shannon and Simpson indexes, as well as the number of observed OTUs, showed a significant lower biodiversity in the RSV-positive group with respect to the virus-negative one, suggesting the presence of a microbial shifts in the nasal microbiota of RSVpositive subjects (Figure 1a) . The main aim of the present study was to characterize the nasal microbiota in pediatric patients hospitalized for bronchiolitis from RSV and in infants affected by bronchiolitis but negative for a respiratory virus. cache = ./cache/cord-284266-tbndldhr.txt txt = ./txt/cord-284266-tbndldhr.txt === reduce.pl bib === id = cord-282303-idh7io9v author = Hassan, Md. Zakiul title = Contamination of hospital surfaces with respiratory pathogens in Bangladesh date = 2019-10-28 pages = extension = .txt mime = text/plain words = 4158 sentences = 203 flesch = 39 summary = With limited infection control practices in overcrowded Bangladeshi hospitals, surfaces may play an important role in the transmission of respiratory pathogens in hospital wards and pose a serious risk of infection for patients, health care workers, caregivers and visitors. With limited infection control practices in overcrowded Bangladeshi hospitals, surfaces may play an important role in the transmission of respiratory pathogens in hospital wards and pose a serious risk of infection for patients, health care workers, caregivers and visitors. Respiratory viral and bacterial pathogens, including Staphylococcus aureus, Streptococcus pyogenes, influenza viruses, respiratory syncytial virus, adenovirus, rhinoviruses and novel coronavirus strains, can survive on hospital surfaces for days, weeks or even months. This study identified that hospital surfaces in these Bangladeshi hospitals, were frequently contaminated with respiratory pathogens and pose a potential threat for fomite-borne transmission of respiratory infections to patients, healthcare workers and family caregivers. cache = ./cache/cord-282303-idh7io9v.txt txt = ./txt/cord-282303-idh7io9v.txt === reduce.pl bib === id = cord-285096-g9y3au1a author = Mitchell, Judy A. title = Tropism and pathological findings associated with canine respiratory coronavirus (CRCoV) date = 2013-03-23 pages = extension = .txt mime = text/plain words = 7120 sentences = 340 flesch = 50 summary = Following experimental infection in dogs, all five CRCoV isolates gave rise to clinical signs of respiratory disease consistent with that observed during natural infection. Following experimental infection in dogs, all five CRCoV isolates gave rise to clinical signs of respiratory disease consistent with that observed during natural infection. In that study we demonstrated that young dogs were susceptible to experimental infection with both CRCoV isolates, which gave rise to clinical signs of respiratory disease consistent with naturally occurring infection. Analyses specifically focused on the histopathological changes in the canine upper and lower respiratory tissues, virulence differences among CRCoV isolates derived from CIRD cases representing wide geographical locations; UK and USA [MO, NE, UT and MI] , and the demonstration of Koch's postulates. Consistent with observations made during naturally occurring infection, dogs in this study also displayed clinical signs of mild respiratory disease following viral challenge (nasal discharge, sneezing, and coughing); whilst the control group remained healthy. cache = ./cache/cord-285096-g9y3au1a.txt txt = ./txt/cord-285096-g9y3au1a.txt === reduce.pl bib === id = cord-283399-iz4l9i0d author = O’Gorman, C. title = Human metapneumovirus in adults: a short case series date = 2006-03-14 pages = extension = .txt mime = text/plain words = 1484 sentences = 83 flesch = 41 summary = This study was carried out to further the available information on adult cases of human metapneumovirus (hMPV), a recently described cause of respiratory infection. For adults presenting with respiratory symptoms and a background of pre-existing respiratory disease or who are immunocompromised, nucleic acid-based techniques are a cost-effective means of making the viral diagnosis in a clinically relevant time frame. In young children and elderly patients hMPV is most commonly associated with a clinical diagnosis of bronchiolitis or bronchitis, respectively, whereas in middle-aged adults, it may produce an influenza-like illness, which can be complicated by pneumonitis in the presence of immunocompromising factors [5] . This retrospective observational study reviewed all cases of hMPV detected in patients over 18 years of age, from the time the RT-PCR method was adopted in July 2003 through to January 2005. cache = ./cache/cord-283399-iz4l9i0d.txt txt = ./txt/cord-283399-iz4l9i0d.txt === reduce.pl bib === id = cord-284889-hth8nf5b author = Tsukagoshi, Hiroyuki title = Molecular epidemiology of respiratory viruses in virus-induced asthma date = 2013-09-12 pages = extension = .txt mime = text/plain words = 6955 sentences = 353 flesch = 43 summary = Previous studies have shown that respiratory syncytial virus (RSV), human rhinovirus (HRV), human metapneumovirus (HMPV), human parainfluenza virus (HPIV), and human enterovirus infections may be associated with virus-induced asthma. Therefore, in this article, we review molecular epidemiological studies of RSV, HRV, HPIV, and HMPV infection associated with virus-induced asthma. More than 200 different types of viruses are known to cause ARI, with respiratory syncytial virus (RSV), human rhinovirus (HRV), human metapneumovirus (HMPV), and human parainfluenza virus (HPIV) most commonly identified in ARI patients. In this review, we focus on molecular epidemiological studies of respiratory viruses, including RSV, HRV, HMPV, and HPIV infections, associated with virus-induced asthma. Thus, both the antigenicity of the viruses and host immune conditions may play important roles in the pathophysiology of severe respiratory infections such as bronchiolitis, pneumonia, and virus-induced asthma (Awomoyi et al., 2007) . cache = ./cache/cord-284889-hth8nf5b.txt txt = ./txt/cord-284889-hth8nf5b.txt === reduce.pl bib === id = cord-286443-t0asknzu author = Emerson, Julia title = Home Self-Collection of Nasal Swabs for Diagnosis of Acute Respiratory Virus Infections in Children With Cystic Fibrosis date = 2013-07-14 pages = extension = .txt mime = text/plain words = 4006 sentences = 185 flesch = 45 summary = title: Home Self-Collection of Nasal Swabs for Diagnosis of Acute Respiratory Virus Infections in Children With Cystic Fibrosis In the current study, we investigated the feasibility of home self-collection of NS in children with CF experiencing onset of new respiratory illness, with samples mailed to a central laboratory for respiratory virus detection by real-time PCR. If respiratory illness with onset of symptoms in the previous 7 days was present at a clinic visit, subjects were first asked to blow their nose to remove mucus that might inhibit PCR, and paired swabs were obtained as follows: a deep nasal (mid-turbinate) sample was collected by research staff, by first measuring from the opening of one naris to the nasal bridge, and then inserting a standard flexible nasopharyngeal flocked nylon swab (Copan Diagnostics Inc, Murrieta, CA; catalog No. 503CS01) until mild resistance was encountered, approximately one-half to two-thirds the length of the nose. cache = ./cache/cord-286443-t0asknzu.txt txt = ./txt/cord-286443-t0asknzu.txt === reduce.pl bib === id = cord-275828-c6d6nk7x author = Mikasa, Keiichi title = JAID/JSC Guidelines for the Treatment of Respiratory Infectious Diseases: The Japanese Association for Infectious Diseases/Japanese Society of Chemotherapy – The JAID/JSC Guide to Clinical Management of Infectious Disease/Guideline-preparing Committee Respiratory Infectious Disease WG date = 2016-07-31 pages = extension = .txt mime = text/plain words = 39672 sentences = 2522 flesch = 42 summary = -SBT/ABPC, intravenous drip, 3 g/3e4 times a day -CTRX, intravenous drip, 1 g/twice a day or 2 g/once a day -CTX, intravenous drip, 1e2 g/2e3 times a day -LVFX, intravenous drip, 500 mg/once a day (2) Cases of late-onset hospital-acquired pneumonia or ventilator-associated pneumonia in which the risk of resistant bacteria is high An antimicrobial drug with anti-pseudomonal activity that targets non-glucose-fermentative gram-negative rod should be administered [50, 51, 68] -To treat polymicrobial infection, the administration of an antimicrobial drug with an activity against obligate anaerobe is not always necessary [67, 70] . -SBT/ABPC, intravenous drip, 3 g/3e4 times a day -CTRX, intravenous drip, 2 g/once a day or 1 g/twice a day -CTX, intravenous drip, 1e2 g/2e3 times a day -LVFX, intravenous drip, 500 mg/once a day (2) Late-onset hospital-acquired pneumonia or cases in which there is a risk of multi-drug-resistant bacteria In addition to the above pathogens, the involvement of non-glucose-fermentative gram negative bacteria or ESBLproducing enteric bacteria must be considered. For the treatment of immunodeficiency-/blood disease-related pneumonia in children, antimicrobial drug therapy should also be basically selected, considering causative microorganisms. cache = ./cache/cord-275828-c6d6nk7x.txt txt = ./txt/cord-275828-c6d6nk7x.txt === reduce.pl bib === id = cord-284332-p4c1fneh author = Bosma, Karen J. title = Pharmacotherapy for Prevention and Treatment of Acute Respiratory Distress Syndrome: Current and Experimental Approaches date = 2012-09-19 pages = extension = .txt mime = text/plain words = 14516 sentences = 721 flesch = 37 summary = [47] Although both of these studies were conducted prior to the 1994 AECC definition, ARDS was strictly defined in the aforementioned studies, including a PaO 2 /FiO 2 ratio <150 or intrapulmonary shunt >20% in patients requiring mechanical ventilation and who had diffuse infiltrates on chest radiograph without clinical evidence of heart failure as pulmonary arterial occlusion pressures were <18 mmHg. Building on the results of these two studies, Sinuff and colleagues [48] developed practice guidelines for prophylactic ketoconazole use, and tested the implementation and efficacy of these guidelines in two ICUs (one control and one active comparator). [119] A phase II study enrolling 98 patients with ALI compared an antioxidant enteral feeding formula containing eicosapentaenoic acid, g-linolenic acid and antioxidant vitamins with placebo, and observed improved oxygenation, reduced pulmonary inflammation, fewer days of mechanical ventilation and fewer non-pulmonary organ failures in the treatment arm, although there was no difference in mortality between this approach and the control group. cache = ./cache/cord-284332-p4c1fneh.txt txt = ./txt/cord-284332-p4c1fneh.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-289282-4oz6r7op author = Hon, Kam Lun title = Overview: The history and pediatric perspectives of severe acute respiratory syndromes: Novel or just like SARS date = 2020-06-01 pages = extension = .txt mime = text/plain words = 3558 sentences = 269 flesch = 58 summary = title: Overview: The history and pediatric perspectives of severe acute respiratory syndromes: Novel or just like SARS The WHO coined the acronym SARS (severe acute respiratory syndrome) and subsequently the causative virus as SARS‐CoV. Clinical presentations and outcome of severe acute respiratory syndrome in children Clinical features, diagnosis, treatment and short-term outcome of severe acute respiratory syndrome (SARS) in children Severe acute respiratory syndrome (SARS) in children: epidemiology, presentation and management Screening for Middle East respiratory syndrome coronavirus infection in hospital patients and their healthcare worker and family contacts: a prospective descriptive study Middle East respiratory syndrome coronavirus in pediatrics: a report of seven cases from Saudi Arabia The epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (COVID-19) in China Comparative analysis of eleven healthcare-associated outbreaks of Middle East respiratory syndrome coronavirus (Mers-Cov) from 2015 to 2017 Overview: The history and pediatric perspectives of severe acute respiratory syndromes: Novel or just like SARS cache = ./cache/cord-289282-4oz6r7op.txt txt = ./txt/cord-289282-4oz6r7op.txt === reduce.pl bib === === reduce.pl bib === id = cord-286449-ekvzaae2 author = McManus, Terence E. title = Respiratory viral infection in exacerbations of COPD date = 2008-07-30 pages = extension = .txt mime = text/plain words = 3105 sentences = 205 flesch = 49 summary = A respiratory virus was detected in 37% of exacerbations, 12% of stable COPD patients and 12% of non-obstructed smokers, p < 0.0005. Studies using serology and viral culture identified respiratory viruses in 30% of patients during acute exacerbations of COPD. 8 The hypothesis tested in the present study was that acute respiratory viral infection is implicated in the pathogenesis of COPD exacerbations. The detection rate of respiratory viruses during exacerbations of COPD in this study (37%) is comparable to results obtained by Seemungal 9 Lower detection rates may be related to time of sampling as patients presenting to hospital had developed symptoms for a median of 5 days prior to admission. 21 However, several of the patients were seen at different time points during this study and the same virus was not detected by repeat sampling suggesting that those testing positive using the PCR screen were experiencing an acute viral infection. cache = ./cache/cord-286449-ekvzaae2.txt txt = ./txt/cord-286449-ekvzaae2.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-286472-pqtem19t author = McFee, R.B. title = MIDDLE EAST RESPIRATORY SYNDROME (MERS) CORONAVIRUS date = 2020-07-28 pages = extension = .txt mime = text/plain words = 5364 sentences = 291 flesch = 47 summary = This newly identified respiratory viral illness was caused by a novel coronavirus, which was initially designated as human betacoronavirus (2) (3) (4) (5) , but was eventually named Middle East Respiratory Syndrome Coronavirus (MERS CoV). It is important to consider multisystem function as well as pulmonary status in patients with severe respiratory illness, including suspected MERS CoV, especially those returning from regions where aggressive pathogens are noted. Patients recently returning from the Middle East, presenting with significant respiratory illness, with CT findings of peribronchial region abnormalities, organizing pneumonia, should be considered for MERS CoV infection, and if possible, queried about international travel and occupational exposures. Middle East Respiratory Syndrome Coronavirus (MERS CoV) Infection Feasibility, safety, clinical and laboratory effects of convalescent plasma therapy for patients with Middle East respiratory syndrome coronavirus infection: a study protocol cache = ./cache/cord-286472-pqtem19t.txt txt = ./txt/cord-286472-pqtem19t.txt === reduce.pl bib === id = cord-289139-5ljqnc39 author = Mengelle, C. title = The use of a multiplex real-time PCR assay for diagnosing acute respiratory viral infections in children attending an emergency unit date = 2014-09-03 pages = extension = .txt mime = text/plain words = 2574 sentences = 146 flesch = 51 summary = title: The use of a multiplex real-time PCR assay for diagnosing acute respiratory viral infections in children attending an emergency unit BACKGROUND: The use of a multiplex molecular technique to identify the etiological pathogen of respiratory viral infections might be a support as clinical signs are not characteristic. OBJECTIVES: The aim of the study was to evaluate a multiplex molecular real-time assay for the routine diagnosis of respiratory viruses, to analyze the symptoms associated with the pathogens detected and to determine the spread of virus during the period. This assay can detect 15 viruses: influenza viruses (IV) types A and B, parainfluenza viruses 1 to 4 (PiV), respiratory syncytial viruses A and B (RSV), rhinovirus (RV), coronaviruses 229E, OC43 and NL63 (CoV), human metapneumovirus (MPV) and adenovirus (ADV). RSV and RV were the most prevalent pathogens, particularly in the youngest children, and co-infections were associated with more severe respiratory symptoms. cache = ./cache/cord-289139-5ljqnc39.txt txt = ./txt/cord-289139-5ljqnc39.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-291217-fpte1q9m author = Adams, Madeleine title = Management of bronchiolitis date = 2009-05-13 pages = extension = .txt mime = text/plain words = 3536 sentences = 153 flesch = 32 summary = The most recent Cochrane review of 22 trials involving 1428 infants with bronchiolitis who received inhaled bronchodilators (including β 2 agonists, ipratropium and adrenergic agents) reported a significant improvement in overall average clinical score, but had no effect on either pulse oximetry measurements or on risk of hospitalization. However, a recent placebo-controlled study of montelukast in 53 infants with a first episode of bronchiolitis demonstrated absence of benefit, with no significant differences in length of hospitalization, clinical severity score, or inflammatory mediators between the two groups. Fluids (either enteral or parenteral) and oxygen are the mainstays, although cpap or mechanical ventilation are effective for respiratory failure • there is no role for bronchodilators, corticosteroids, antiviral agents, physiotherapy, nebulized dnase or antibiotics, but nebulized 3% hypertonic saline administered with a bronchodilator may decrease length of stay in hospital cache = ./cache/cord-291217-fpte1q9m.txt txt = ./txt/cord-291217-fpte1q9m.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-291618-166wvdbt author = Mikulska, Małgorzata title = Epidemiology of viral respiratory tract infections in an outpatient haematology facility date = 2013-10-06 pages = extension = .txt mime = text/plain words = 4043 sentences = 189 flesch = 37 summary = Viral respiratory tract infections (VRTI) are an important cause of morbidity and mortality in patients with hematologic malignancies, particularly in allogeneic haematopoietic stem cell transplantation (HSCT) recipients [1] [2] [3] . The symptoms of VRTI were divided into three main categories, and the rate of positive virological results was as follows: ILI 38 % (25 out of 65), fever only 30 % (9 out of 30) and upper VRTI symptoms 22 % (15 out of 67) (Fig. 1) Six patients had pneumonia; thus, BAL was performed and four viruses were detected (co-pathogens are reported in Table 2 ): one influenza A, two RSV and one coronavirus. Prospective study of the incidence, clinical features, and outcome of symptomatic upper and lower respiratory tract infections by respiratory viruses in adult recipients of hematopoietic stem cell transplants for hematologic malignancies cache = ./cache/cord-291618-166wvdbt.txt txt = ./txt/cord-291618-166wvdbt.txt === reduce.pl bib === id = cord-286337-qk90xb3a author = Hanada, Shigeo title = Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia date = 2018-11-16 pages = extension = .txt mime = text/plain words = 9806 sentences = 436 flesch = 22 summary = While the effects of these alterations on risk of secondary bacterial pneumonia have not been studied, potential mechanisms by which these changes might modulate susceptibility to secondary bacterial infections include alterations in the nature and magnitude of the immune response in the host (microbiome on host effects) and facilitating growth of pathogens in the absence of normal commensals (inter-microbial effects). Given the effects of viruses on enhancing bacterial adherence to the epithelium (86) (87) (88) , it is perhaps not surprising that multiple studies of human subjects as well as in animal models have shown that viral infections are associated with increased colonization by potentially pathogenic bacteria (known as "pathobionts"). Another study of patients with 2009 pandemic H1N1 influenza infection revealed that the predominant phyla of the upper respiratory tract (nasal and nasopharyngeal samples) in patients harboring pandemic H1N1 were Actinobacteria, Firmicutes, and Proteobacteria although normal controls were not included; however, the authors suggested that flu is associated with an expansion of Proteobacteria (109) which is generally less abundant in healthy hosts. cache = ./cache/cord-286337-qk90xb3a.txt txt = ./txt/cord-286337-qk90xb3a.txt === reduce.pl bib === === reduce.pl bib === id = cord-292587-hp4zd8lr author = Rubino, Ilaria title = Respiratory Protection against Pandemic and Epidemic Diseases date = 2017-10-31 pages = extension = .txt mime = text/plain words = 2608 sentences = 153 flesch = 34 summary = We expect that the development of technologies that overcome the existing challenges in current respiratory protective devices will lead to a timely and effective response to the next outbreak. We expect that the development of technologies that overcome the existing challenges in current respiratory protective devices will lead to a timely and effective response to the next outbreak. While effective management and availability of control measures are crucial to an outbreak response, the pathogens [ 1 1 4 _ T D $ D I F F ] (virus/bacteria/ fungi) captured on filters are an intrinsic concern because of fear of cross-infection, new aerosol release, and contaminated waste. Hence, production of a filter that inactivates the collected pathogens would bring key improvements to current surgical masks and respirators, resulting in increased protection, reduced risk of cross[ 1 0 9 _ T D $ D I F F ] -infection, and recyclability without decontamination ( Figure 1 ). cache = ./cache/cord-292587-hp4zd8lr.txt txt = ./txt/cord-292587-hp4zd8lr.txt === reduce.pl bib === id = cord-291639-hioh2s35 author = Alfredo, Potena title = Pathophysiology of viral-induced exacerbations of COPD date = 2007-12-17 pages = extension = .txt mime = text/plain words = 4434 sentences = 205 flesch = 34 summary = Many epidemiological and clinical studies have suggested a role for respiratory viral infections in the natural history of chronic obstructive pulmonary disease (COPD), particularly during their exacerbations highlighting the need for development of effective vaccines and/or treatment for these viruses. In this review we will provide an overview of the relationship between respiratory virus infection and the molecular mechanisms involved in the activation of airway infl ammation in COPD exacerbations. It has been postulated that bacterial colonization could contribute to increased susceptibility to viral infection in COPD patients for example by increasing ICAM-1 expression in bronchial epithelial cells either directly or through induced infl ammation (Sajjan et al 2006) . Despite growing clinical evidence for a role of respiratory viral infections in the pathogenesis of COPD exacerbations, the precise mechanisms of respiratory virus-induced airway infl ammation and of host defenses against respiratory viruses are poorly understood (Johnston 2005) . cache = ./cache/cord-291639-hioh2s35.txt txt = ./txt/cord-291639-hioh2s35.txt === reduce.pl bib === id = cord-287156-3plpi6i9 author = Lassandro, Giuseppe title = Children in Coronaviruses’ Wonderland: What Clinicians Need to Know date = 2020-07-01 pages = extension = .txt mime = text/plain words = 8021 sentences = 535 flesch = 43 summary = Among the seven coronaviruses that affect humans (SARS)-CoV, the Middle East respiratory syndrome (MERS)-CoV, and the most recent coronavirus disease 2019 (COVID-19) represent potential life-threatening diseases worldwide. Children appear to be less susceptible to develop severe clinical disease and present usually with mild and aspecific symptoms similar to other respiratory infections typical of childhood. 8, 9 Additionally, three HCoVs responsible for outbreaks involving high case fatality rates have been detected in humans in the last two decades: the severe acute respiratory syndrome (SARS)-CoV, the Middle East respiratory syndrome (MERS)-CoV and the new coronavirus disease 2019 (COVID-19) ( Table 1) . Principal features of severe acute respiratory syndrome (SARS)-CoV, the Middle East respiratory syndrome (MERS)-CoV and the most recent coronavirus disease 2019 (COVID19) . Clinical features and viral diagnosis of two cases of infection with Middle East Respiratory Syndrome coronavirus: a report of nosocomial transmission cache = ./cache/cord-287156-3plpi6i9.txt txt = ./txt/cord-287156-3plpi6i9.txt === reduce.pl bib === id = cord-292836-1o2ynvy3 author = Ogimi, Chikara title = What’s New With the Old Coronaviruses? date = 2020-04-21 pages = extension = .txt mime = text/plain words = 5194 sentences = 267 flesch = 44 summary = In this review, we discuss what is known about the virology, epidemiology, and disease associated with pediatric infection with the common community-acquired human coronaviruses, including species 229E, OC43, NL63, and HKU1, and the coronaviruses responsible for past world-wide epidemics due to severe acute respiratory syndrome and Middle East respiratory syndrome coronavirus. By contrast SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV) are highly pathogenic in humans, with high rates of severe pneumonia and fatal outcomes [21] . A large prospective surveillance study conducted in Norway from 2006 to 2015 that enrolled all hospitalized children aged ≤16 years with respiratory tract infections revealed that HCoVs OC43 and NL63 were detected most frequently and were epidemic every second winter [35] . Large surveillance studies of children and adults to evaluate the prevalence of all major respiratory viruses using multiplex PCR have been conducted in many settings, showing that HCoV infections are the fourth or sixth most common virus detected overall and across all age groups [33, 43] . cache = ./cache/cord-292836-1o2ynvy3.txt txt = ./txt/cord-292836-1o2ynvy3.txt === reduce.pl bib === id = cord-291961-usl8z6ep author = Zheng, Wen-zhi title = Human polyomavirus type six in respiratory samples from hospitalized children with respiratory tract infections in Beijing, China date = 2015-10-13 pages = extension = .txt mime = text/plain words = 2915 sentences = 162 flesch = 54 summary = METHODS: The VP1 gene of HPyV6 was detected with an established TaqMan real-time PCR from nasopharyngeal aspirate specimens collected from hospitalized children with respiratory tract infections. All 15 HPyV6-positive patients were diagnosed with lower respiratory tract infections, and their viral loads ranged from 1.38 to 182.42 copies/μl nasopharyngeal aspirate specimen. CONCLUSIONS: The prevalence of HPyV6 was 1.7 % in nasopharyngeal aspirate specimens from hospitalized children with respiratory tract infections, as analyzed by real-time PCR. Previous studies have indicated that a number of HPyVs are associated with human diseases, such as progressive multifocal leukoencephalopathy (JCPyV), hemorrhagic cystitis (BKPyV), Merkel cell carcinoma (MCPyV), and trichodysplasia spinulosa (TSPyV) [3, 7, 9, [17] [18] [19] . Because initial infections with most HPyVs occur in infancy, the prevalence of HPyV6 in NPAs from children was detected with real-time PCR. The detection rate for HPyV6 by real-time PCR assay was 1.7 % in 887 NPA samples collected from hospitalized children with RTI. cache = ./cache/cord-291961-usl8z6ep.txt txt = ./txt/cord-291961-usl8z6ep.txt === reduce.pl bib === === reduce.pl bib === id = cord-294933-oc2glu4a author = Cinesi Gómez, César title = Clinical consensus recommendations regarding non-invasive respiratory support in the adult patient with acute respiratory failure secondary to SARS-CoV-2 infection date = 2020-06-19 pages = extension = .txt mime = text/plain words = 5643 sentences = 337 flesch = 45 summary = The document provides clinical recommendations for the noninvasive respiratory support (noninvasive ventilation, high flow oxygen therapy with nasal cannula) in any patient with suspected or confirmed presentation of COVID-19 with acute respiratory failure. The document provides clinical recommendations for the noninvasive respiratory support (noninvasive ventilation, high flow oxygen therapy with nasal cannula) in any patient with suspected or confirmed presentation of COVID-19 with acute respiratory failure. The present document has been developed by consensus among the scientific societies involved in acute respiratory failure in adult patients, and seeks to provide a more detailed description of the recommendations on the use of non-invasive respiratory support (NIRS) in the management of acute respiratory failure (ARF) secondary to infection by the newly emergent SARS-CoV-2 coronavirus, which causes so-called COVID-19 disease, as a complement to the information emitted by the Spanish Ministry of Health, Consumer Affairs and Social Wellbeing (Ministerio de Sanidad, Consumo y Bienestar Social [MSC]), 1,2 which is frequently updated and establishes a series of general recommendations. cache = ./cache/cord-294933-oc2glu4a.txt txt = ./txt/cord-294933-oc2glu4a.txt === reduce.pl bib === id = cord-294544-iutcduix author = Kesson, Alison M. title = Respiratory virus infections date = 2007-09-06 pages = extension = .txt mime = text/plain words = 6057 sentences = 297 flesch = 38 summary = 1 This has enabled the identification of many viruses, including those commonly causing respiratory infections -influenza, RSV, PIV 1-4, adenoviruses, measles, enteroviruses, rhinoviruses, VZV, CMV and HSV. 3 After 24-72 h of culture, using pooled or single fluorescein isothiocyanate (FITC)-labelled monoclonal antibodies directed against influenza A and B, RSV, parainfluenza 1-3 and adenoviruses, rapid identification of a respiratory virus infection can be established. Diagnosis of rhinovirus infection rarely requires laboratory testing but virus isolation, detection of viral RNA by RT-PCR, antigen detection by DIF in cells from respiratory secretions or detection of a fourfold rise in antibody titres by neutralization test or EIA can be performed if required. Diagnosis of the specific cause of an acute pneumonia due to a particular viral agent is complicated by difficulty in obtaining appropriate lower respiratory tract samples for culture and in isolating or detecting certain pathogens, and additionally by the frequent asymptomatic shedding of some viruses, e.g. herpes simplex virus or adenoviruses. cache = ./cache/cord-294544-iutcduix.txt txt = ./txt/cord-294544-iutcduix.txt === reduce.pl bib === id = cord-296777-6xz2aslj author = Oosterhof, L title = Fatal lower respiratory tract disease with human corona virus NL63 in an adult haematopoietic cell transplant recipient date = 2009-10-12 pages = extension = .txt mime = text/plain words = 1195 sentences = 87 flesch = 53 summary = title: Fatal lower respiratory tract disease with human corona virus NL63 in an adult haematopoietic cell transplant recipient Community-acquired respiratory viruses are known to account for many cases of interstitial pneumonia as a common complication following allo-haematopoietic cell transplantation (HCT). 7 We present a case of fatal HCoV NL63 pulmonary infection during the late-engraftment phase, 5 months after an allo-HCT with a matched unrelated donor in a patient without active GVHD and receiving only modest immune suppressive treatment. The BAL fluid at day 11 of admission and the final PCR analysis post mortem were negative for HCoV NL63, suggesting that the patient had cleared the virus. Although evaluation for corona virus in symptomatic HCT patients is not routinely performed, we believe it should be considered in the differential diagnoses of respiratory failure or as a possible causative agent before the development of IPS after allo-HCT for haematological disease. cache = ./cache/cord-296777-6xz2aslj.txt txt = ./txt/cord-296777-6xz2aslj.txt === reduce.pl bib === id = cord-293354-55nawxos author = Kenmoe, Sebastien title = Viral etiology of severe acute respiratory infections in hospitalized children in Cameroon, 2011–2013 date = 2016-05-09 pages = extension = .txt mime = text/plain words = 3714 sentences = 238 flesch = 50 summary = title: Viral etiology of severe acute respiratory infections in hospitalized children in Cameroon, 2011–2013 This study was conducted to gain new insights into the timeliness of virus circulation and viral etiology among children aged ≤15 years, hospitalized for SARI. hBoV occurred intermittently all over the study period, while the prevalence of remaining viral etiologies was low, ranging from 0 to 5 positive samples per month for each virus, numbers which appeared insufficient to allow for the description of seasonal patterns. Viral etiology of hospitalized acute lower respiratory infections in children under 5 years of age -a systematic review and meta-analysis Viral etiology of acute lower respiratory tract infections in hospitalized young children in Northern Taiwan Frequent detection of viral coinfection in children hospitalized with acute respiratory tract infection using a real-time polymerase chain reaction Epidemiology and seasonality of respiratory viral infections in hospitalized children in Kuala Lumpur, Malaysia: a retrospective study of 27 years cache = ./cache/cord-293354-55nawxos.txt txt = ./txt/cord-293354-55nawxos.txt === reduce.pl bib === === reduce.pl bib === id = cord-296605-p67twx7a author = LAU, Arthur Chun-Wing title = Management of Critically Ill Patients with Severe Acute Respiratory Syndrome (SARS) date = 2004-03-10 pages = extension = .txt mime = text/plain words = 4846 sentences = 247 flesch = 38 summary = title: Management of Critically Ill Patients with Severe Acute Respiratory Syndrome (SARS) Most SARS patients would require high flow oxygen supplementation, 20–30% required intensive care unit (ICU) or high dependency care, and 13–26% developed acute respiratory distress syndrome (ARDS). The management of critically ill SARS patients requires timely institution of pharmacotherapy where applicable and supportive treatment (oxygen therapy, noninvasive and invasive ventilation). More than onethird of all the SARS patients required high flow oxygen therapy [4] , 20-30% required intensive care unit (ICU) admission or high dependency care, and 13-26% developed acute respiratory distress syndrome (ARDS) [5, 6] . Description and clinical treatment of an early outbreak of severe acute respiratory syndrome (SARS) in Guangzhou, PR China Evaluation of non-invasive positive pressure ventilation in treatment for patients with severe acute respiratory syndrome Clinical observation of non-invasive positive pressure ventilation (NIPPV) in the treatment of severe acute respiratory syndrome (SARS) cache = ./cache/cord-296605-p67twx7a.txt txt = ./txt/cord-296605-p67twx7a.txt === reduce.pl bib === id = cord-295074-fsbp4fky author = Broor, Shobha title = Rates of respiratory virus-associated hospitalization in children aged <5 years in rural northern India date = 2013-11-21 pages = extension = .txt mime = text/plain words = 3902 sentences = 177 flesch = 33 summary = Rates of respiratory virus-associated hospitalization in children aged <5 years in rural northern India Introduction Acute respiratory infections are recognized as an important cause of mortality, hospitalization, and healthcare utilization in young children globally. 17e20 Using data from population-based surveillance of approximately 9500 children for hospitalizations for acute medical illness in rural northern India and concomitant testing for respiratory viruses by real-time reverse transcription polymerase chain reaction (rRT-PCR), we estimate the incidence of respiratory virus-associated hospitalizations among children aged <5 years. Incidences were also calculated for children aged <6 months for RSV and influenza since maternal immunization with RSV and Among the 98 children with respiratory virus-associated illness, history of fever (82%) and cough (69%) were the most commonly reported symptoms. RSV and influenza viruses circulated with clearly defined but different seasonality and were infrequently detected among children without fever or respiratory symptoms or signs, similar to prior studies. cache = ./cache/cord-295074-fsbp4fky.txt txt = ./txt/cord-295074-fsbp4fky.txt === reduce.pl bib === id = cord-302111-kg0dmgq0 author = Darden, Dijoia B. title = The Clinical Presentation and Immunology of Viral Pneumonia and Implications for Management of Coronavirus Disease 2019 date = 2020-04-29 pages = extension = .txt mime = text/plain words = 4492 sentences = 257 flesch = 34 summary = Given the rapidly emerging pandemic associated with the novel severe acute respiratory syndrome coronavirus 2 causing coronavirus disease 2019, it is important to review the clinical presentation and immunologic changes associated with viral pneumonia. Given the rapidly emerging pandemic associated with the novel severe acute respiratory syndrome coronavirus 2 causing coronavirus disease 2019, it is important to review the clinical presentation and immunologic changes associated with viral pneumonia. Key Words: coronavirus; immunology; influenza virus; severe acute respiratory syndrome; viral pneumonia P neumonia is the leading infectious cause of hospitalization among adults and children in the United States (1) . Given the rapid spread of this virus and its association with severe pulmonary disease, the purpose of this review is to provide an overview of the presentation and immunology of viral pneumonia, principles of early management, and application to COVID-19. cache = ./cache/cord-302111-kg0dmgq0.txt txt = ./txt/cord-302111-kg0dmgq0.txt === reduce.pl bib === id = cord-293897-p30wz7b7 author = Waghmare, Alpana title = Respiratory viruses date = 2020-04-24 pages = extension = .txt mime = text/plain words = 5885 sentences = 307 flesch = 28 summary = 14,15 Many immunocompromised adults with PIV infection first present with symptoms of mild upper respiratory tract disease, but in contrast to RSV, influenza, and HMPV, detection of PIV-1 and PIV-3 in asymptomatic HCT recipients is relatively common, reported in 6 of 17 (35%) infection episodes in a prospective study. In immunocompromised hosts, including hematopoietic cell transplant recipients, solid organ transplant recipients, and oncology patients, respiratory viruses can be associated with significant clinical manifestations, including prolonged viral shedding, lower respiratory tract disease, the need for supplemental oxygen, late airflow obstruction, and even death. In immunocompromised hosts, including hematopoietic cell transplant recipients, solid organ transplant recipients, and oncology patients, respiratory viruses can be associated with significant clinical manifestations, including prolonged viral shedding, lower respiratory tract disease, the need for supplemental oxygen, late airflow obstruction, and even death. cache = ./cache/cord-293897-p30wz7b7.txt txt = ./txt/cord-293897-p30wz7b7.txt === reduce.pl bib === === reduce.pl bib === id = cord-300510-fhpkdqr0 author = Mojoli, Francesco title = Our recommendations for acute management of COVID-19 date = 2020-05-08 pages = extension = .txt mime = text/plain words = 1083 sentences = 73 flesch = 41 summary = 7. Perform early intubation if poor response to continuous positive airway pressure in terms of oxygenation: do not trust patients' relatively good respiratory mechanics and feeling of improved dyspnoea, since these patients may have relatively normal lung compliance and the only clinical sign of fatigue may be high respiratory rate. As soon as possible according to gas exchanges (PaO 2 /FiO 2 > 150 with FiO2 < 50%) and lung ultrasound score (≤ 12), start assisted ventilation with a sigh while maintaining moderate to high positive end-expiratory pressure to prevent derecruitment. Abbreviations SARS-CoV-2: Severe acute respiratory syndrome coronavirus 2; ICU: Intensive care unit Assessment of lung aeration and recruitment by CT scan and ultrasound in acute respiratory distress syndrome patients Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China The authors read and approved the final manuscript. cache = ./cache/cord-300510-fhpkdqr0.txt txt = ./txt/cord-300510-fhpkdqr0.txt === reduce.pl bib === id = cord-300019-8vxqr3mc author = Shi, Ting title = The Etiological Role of Common Respiratory Viruses in Acute Respiratory Infections in Older Adults: A Systematic Review and Meta-analysis date = 2019-03-08 pages = extension = .txt mime = text/plain words = 3968 sentences = 187 flesch = 43 summary = We aimed to identify all case-control studies investigating the potential role of respiratory viruses in the etiology of ARI in older adults aged ≥65 years. This review supports RSV, Flu, PIV, HMPV, AdV, RV, and CoV as important causes of ARI in older adults and provides quantitative estimates of the absolute proportion of virus-associated ARI cases to which a viral cause can be attributed. Although influenza virus (Flu) is the most widely recognized viral infection associated with respiratory illness, >25 viruses have been linked to pneumonia, causing a substantial disease burden in adults and elderly individuals. Therefore, we aimed to conduct a similar systematic review to identify all case-control studies since 1996 investigating the potential role of respiratory viruses in the etiology of ARIs in older adults aged ≥65 years. cache = ./cache/cord-300019-8vxqr3mc.txt txt = ./txt/cord-300019-8vxqr3mc.txt === reduce.pl bib === id = cord-295189-bz3gi15h author = Jennings, Lance C. title = Respiratory viruses in airline travellers with influenza symptoms: Results of an airport screening study date = 2015-03-14 pages = extension = .txt mime = text/plain words = 3264 sentences = 166 flesch = 48 summary = STUDY DESIGN: Data were collected from travellers arriving at Christchurch International Airport, New Zealand, during the winter 2008, via a symptom questionnaire, temperature testing, and respiratory sampling. CONCLUSIONS: The high prevalence of respiratory virus infections caused by viruses other than influenza in this study, many with overlapping symptotology to influenza, has important implications for any screening strategies for the prediction of influenza in airline travellers. In a 2008 study, we sought to assess the prevalence of influenza infection in symptomatic and asymptomatic arriving international airline travellers and whether using a symptom-screening questionnaire and temperature measurement could reliably predict seasonal influenza infection [16] . The high prevalence of respiratory virus infections caused by viruses other than influenza in this study, many with overlapping symptoms to influenza, has important implications for any screening strategy for the prediction of influenza in airline travellers. cache = ./cache/cord-295189-bz3gi15h.txt txt = ./txt/cord-295189-bz3gi15h.txt === reduce.pl bib === id = cord-292828-29jbf9ik author = Alsaleh, Asma N title = Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control date = 2014-01-09 pages = extension = .txt mime = text/plain words = 3915 sentences = 185 flesch = 45 summary = title: Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control We therefore investigated the impact of sample collection quality and the presence of visible mould in samples upon respiratory virus detection by real-time polymerase chain reaction (PCR) assays. Quality control measures, including monitoring human DNA loads using ERV3 as a marker for epithelial cell components in samples should be undertaken to optimize the validity of real-time PCR results for respiratory virus investigations in community-based studies. Importantly, when using highly sensitive polymerase chain reaction (PCR) assays the detection rates for respiratory viruses are similar in both anterior nasal swab specimens and samples collected by the more traditional method of nasopharyngeal aspiration [18, 19] . The ORChID project is an ongoing comprehensive community-based study using PCR assays to detect respiratory viruses in anterior nasal swab specimens taken weekly by parents from their infants throughout the first 2-years of life. cache = ./cache/cord-292828-29jbf9ik.txt txt = ./txt/cord-292828-29jbf9ik.txt === reduce.pl bib === id = cord-300116-r93w4jm3 author = Yi, Hana title = Profiling bacterial community in upper respiratory tracts date = 2014-11-13 pages = extension = .txt mime = text/plain words = 5063 sentences = 271 flesch = 39 summary = METHODS: We analyzed the upper respiratory tract bacterial content of 57 healthy asymptomatic people (17 health-care workers and 40 community people) and 59 patients acutely infected with influenza, parainfluenza, rhino, respiratory syncytial, corona, adeno, or metapneumo viruses using culture-independent pyrosequencing. In this study, our aim was to determine whether a viral infection-related bacterial profile exists in the respiratory tract and evaluate any disparities in the microbiota structure that develops depending on the infectious virus species. The microbiota profiles of healthy-adult and patient groups also differed in the relative composition of the microbiome, which was highlighted in the graph showing the abundant bacterial genera observed in the tested samples ( Figure 2 and Additional file 3: Figure S2 ). cache = ./cache/cord-300116-r93w4jm3.txt txt = ./txt/cord-300116-r93w4jm3.txt === reduce.pl bib === id = cord-005814-ak5pq312 author = nan title = 8th European Congress of Intensive Care Medicine Athens - Greece, October 18–22, 1995 Abstracts date = 1995 pages = extension = .txt mime = text/plain words = 179164 sentences = 12028 flesch = 56 summary = Results: In 5 patients with treated SS, 16 tests were performed (VL n=8; Dobu n=4; NA n=4 Method: Septic shock was defined as severe sepsis with either persistent hypotension (mean arterial pressure; MAP<70 mmHg) or the requirement for a noradrenaline (NA) infusion ~> 0.1 ~g/kg/min with a MAP _< 90mmHg. Cardiovascular support was limited to NA + dobutamine (DB), 546C88 was administered for up to 8 h at a fixed dose-rate of either i, 2.5, 5, 10 or 20 mg/kg/h iv. Methods: Fourteen cases were s~udied,their gestational age ranged from(27-32)ws.Continnous positive air way pressure was applied to six cases at Peep level from (3-6)cm H2o through nasal pronge,(group I),the other 8 cases were managed as routine,(group II).Blood gases, TcPO2,TcCo2,resp.rate,depth and pattern were monitored for assessment of tissue Oxygenation and ventilation, Results: Our rasults showed that early application of CPAP improve ventilation among (83.3%)of cases,while (16.7%)of cases need IMV.The cases of group II need IMV among (75%)of the studied cases during the second or the third day of life. cache = ./cache/cord-005814-ak5pq312.txt txt = ./txt/cord-005814-ak5pq312.txt === reduce.pl bib === id = cord-299379-ch7a39d6 author = De Conto, Flora title = Epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in Northern Italy() date = 2019-01-17 pages = extension = .txt mime = text/plain words = 4005 sentences = 274 flesch = 56 summary = title: Epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in Northern Italy() The viral etiology of ARTIs was investigated over 3 years (October 2012–September 2015) in 2575 children in Parma, Italy, using indirect immunofluorescent staining of respiratory samples for viral antigens, cell culture, and molecular assays. The simultaneous use of different diagnostic tools allowed us to identify a putative viral etiology in half the children examined and to provide an estimate of the epidemiology and seasonality of respiratory viruses associated with ARTIs. Acute respiratory tract infections (ARTIs) are a persistent public health problem (Lu et al., 2013) . This three-year (October 2012-September 2015) hospital-based survey in Parma (Northern Italy) aimed to determine the prevalence of respiratory virus infections, their seasonality, and any patterns of mixed infections in children with ARTIs by using indirect immunofluorescent staining of respiratory samples for viral antigens, cell culture, and molecular assays. cache = ./cache/cord-299379-ch7a39d6.txt txt = ./txt/cord-299379-ch7a39d6.txt === reduce.pl bib === id = cord-303606-ypkia5x1 author = Lee, So-lun title = Is respiratory viral infection really an important trigger of asthma exacerbations in children? date = 2011-03-30 pages = extension = .txt mime = text/plain words = 3525 sentences = 179 flesch = 46 summary = We performed a prospective cohort study from September 2003 to December 2004 to delineate attributing the effect of different respiratory viral infections including newly discovered ones to asthma exacerbations in children in Hong Kong. Plausible explanations for much lower virus detection rate than previously reported include improved personal hygiene and precautionary measures taken during respiratory tract infections in the immediate post-severe acute respiratory syndrome period together with a significant contribution of other adverse factors like environmental air pollution. Plausible explanations for much lower virus detection rate than previously reported include improved personal hygiene and precautionary measures taken during respiratory tract infections in the immediate post-severe acute respiratory syndrome period together with a significant contribution of other adverse factors like environmental air pollution. Thus, we carried out a prospective study to delineate the current role of different viral respiratory tract infections including newly discovered respiratory viruses in asthma exacerbation in children in our locality. cache = ./cache/cord-303606-ypkia5x1.txt txt = ./txt/cord-303606-ypkia5x1.txt === reduce.pl bib === id = cord-308979-qhlvd2mt author = Sumino, Kaharu C. title = Detection of Severe Human Metapneumovirus Infection by Real-Time Polymerase Chain Reaction and Histopathological Assessment date = 2005-09-15 pages = extension = .txt mime = text/plain words = 4296 sentences = 191 flesch = 40 summary = BackgroundInfections with common respiratory tract viruses can cause high mortality, especially in immunocompromised hosts, but the impact of human metapneumovirus (hMPV) in this setting was previously unknown MethodsWe evaluated consecutive bronchoalveolar lavage and bronchial wash fluid samples from 688 patients—72% were immunocompromised and were predominantly lung transplant recipients—for hMPV by use of quantitative real-time polymerase chain reaction (PCR), and positive results were correlated with clinical outcome and results of viral cultures, in situ hybridization, and lung histopathological assessment ResultsSix cases of hMPV infection were identified, and they had a similar frequency and occurred in a similar age range as other paramyxoviral infections. Each patient with high titers of hMPV exhibited a complicated clinical course requiring prolonged hospitalization ConclusionsOur results provide in situ evidence of hMPV infection in humans and suggest that hMPV is a cause of clinically severe lower respiratory tract infection that can be detected during bronchoscopy by use of real-time PCR and routine histopathological assessment cache = ./cache/cord-308979-qhlvd2mt.txt txt = ./txt/cord-308979-qhlvd2mt.txt === reduce.pl bib === id = cord-303935-qdehf6rb author = Yun, Heather C. title = Changes in Clinical Presentation and Epidemiology of Respiratory Pathogens Associated With Acute Respiratory Illness in Military Trainees After Reintroduction of Adenovirus Vaccine date = 2015-09-01 pages = extension = .txt mime = text/plain words = 4250 sentences = 199 flesch = 43 summary = title: Changes in Clinical Presentation and Epidemiology of Respiratory Pathogens Associated With Acute Respiratory Illness in Military Trainees After Reintroduction of Adenovirus Vaccine The Center for Advanced Molecular Detection at Joint Base San Antonio-Lackland prospectively collects demographic, clinical, and polymerase chain reaction data from respiratory specimens (throat swab and nasal wash) among Air Force trainees presenting for care of ARI. Acute respiratory illness in military trainees post-VI is associated with decreased severity of systemic symptoms and reduced fever and heart rate. The purpose of this study was to evaluate (1) changes in clinical presentations of ARI pre-and post-VI, and (2) reductions in proportions of disease due to Ad. We also sought to further evaluate for evidence of nonvaccine type serotype shift and to determine whether the frequencies of common non-Ad respiratory pathogens have changed after VI, in trainees presenting for care of ARI, which have not previously been described in the published literature. cache = ./cache/cord-303935-qdehf6rb.txt txt = ./txt/cord-303935-qdehf6rb.txt === reduce.pl bib === id = cord-300711-yibdumij author = Shatizadeh, Somayeh title = Epidemiological and clinical evaluation of children with respiratory virus infections date = 2014-09-22 pages = extension = .txt mime = text/plain words = 2024 sentences = 119 flesch = 48 summary = This study was performed to detect viruses in children with respiratory infections and describe their epidemiology and clinical characteristics. Methods: In this descriptive cross sectional study, throat swabs and wash specimens from 202 children younger than six years of age with diagnosis of a respiratory tract infection from a total of 897 specimens were evaluated using multiplex PCR method. Results: Respiratory viruses were detected in 92 children: respiratory synsytial virus, 16.8%; influenza virus, 5.4%; parainfluenza virus, 8.4%; adenovirus, 14.4% and human metapneumo virus 0.49% with male predominance and higher distribution in children younger than 1 year of age with preference in the cold months of year. In this study, AdVs followed by RSV were the most frequently detected viral agents in our patients (14.4%) which occurred mostly in the summer and winter months (August, September and February) in male children in all age groups. cache = ./cache/cord-300711-yibdumij.txt txt = ./txt/cord-300711-yibdumij.txt === reduce.pl bib === id = cord-299952-xvtt8fz8 author = Gao, LuLu title = A randomized controlled trial of low-dose recombinant human interferons α-2b nasal spray to prevent acute viral respiratory infections in military recruits date = 2010-06-17 pages = extension = .txt mime = text/plain words = 4447 sentences = 224 flesch = 50 summary = title: A randomized controlled trial of low-dose recombinant human interferons α-2b nasal spray to prevent acute viral respiratory infections in military recruits To assess the efficacy and safety of a low-dose recombinant human interferon α-2b (rIFNα-2b) nasal spray in preventing acute viral respiratory infections in military population, we performed this randomized controlled trial. To evaluate the efficacy and safety of this new nasal spray in preventing acute respiratory infections in military population, we performed this randomized, placebo-controlled, double-blind trial. In summary, this randomized controlled trial suggested that the recombinant human interferon ␣-2b nasal spray can be used to prevent common acute viral respiratory infections caused by Flu-A, Flu-B, PIV1-3 and ADV and was generally well tolerated among military recruits. The efficacy of preventing viral respiratory infections by the rIFN␣-2b nasal spray should be evaluated further in different population groups, such as children and the elderly, and more samples should be involved in the further study. cache = ./cache/cord-299952-xvtt8fz8.txt txt = ./txt/cord-299952-xvtt8fz8.txt === reduce.pl bib === id = cord-303040-ha8gufh8 author = Park, Won-Ju title = Respiratory Syncytial Virus Outbreak in the Basic Military Training Camp of the Republic of Korea Air Force date = 2015-01-14 pages = extension = .txt mime = text/plain words = 3618 sentences = 181 flesch = 48 summary = In the event of an outbreak of an acute febrile illness of a highly infective nature in facilities used by a young adult group, RSV should be considered among the possible causative agents. Recent studies indicate that RSV is an important cause of respiratory infection in elderly patients, either those with compromised immunity or inflicted with chronic illness, as well as in adult populations in a special environment, such as military personnel [7] [8] [9] [10] [11] . A case patient was a person, among military recruits in this boot camp, who was admitted to the medical care center in the boot camp with chief complaints of fever and symptoms of upper respiratory tract illness after May 26, 2011. In the event of an epidemic of acute febrile respiratory illness of a highly infective nature, it is recommended to conduct a test for RSV in the young adult population in the military facilities. cache = ./cache/cord-303040-ha8gufh8.txt txt = ./txt/cord-303040-ha8gufh8.txt === reduce.pl bib === id = cord-306266-8qdrshz3 author = Scully, Crispian title = Respiratory medicine date = 2014-06-25 pages = extension = .txt mime = text/plain words = 13246 sentences = 698 flesch = 42 summary = Other factors that have been studied include: ■ air pollution -There is an association between air pollution and aggravation of existing asthma ■ allergen avoidance -There is no consistent evidence of benefit ■ breast-feeding -There is evidence of a protective effect in relation to early asthma ■ electrolytes -There is no consistent evidence of benefit ■ fish oils and fatty acid -There is no consistent evidence of benefit ■ house dust mites -Measures to reduce the numbers of house dust mites do not affect asthma severity ■ immunotherapy -Allergenspecific immunotherapy is beneficial in allergic asthma ■ microbial exposure -There is insufficient evidence to indicate that the use of probiotics in pregnancy reduces the incidence of childhood asthma ■ modified milk formulae -There is no consistent evidence of benefit pets -There are no controlled trials on the benefits of removing pets from the home ■ tobacco -Exposure to cigarette smoke adversely affects quality of life, lung function, need for rescue medications and longterm control with inhaled steroids. cache = ./cache/cord-306266-8qdrshz3.txt txt = ./txt/cord-306266-8qdrshz3.txt === reduce.pl bib === id = cord-301254-093yih5n author = Brittain-Long, Robin title = Prospective evaluation of a novel multiplex real-time PCR assay for detection of fifteen respiratory pathogens—Duration of symptoms significantly affects detection rate date = 2010-01-18 pages = extension = .txt mime = text/plain words = 2860 sentences = 160 flesch = 48 summary = OBJECTIVES: The aim of the present study was to evaluate the diagnostic performance and clinical use of a novel multiplex PCR method in adults with community-acquired respiratory viral infection, and the impact of duration of symptoms on detection rates. CONCLUSIONS: Duration of symptoms significantly affects the detection rate of respiratory pathogens by multiplex real-time PCR in nasopharyngeal swab samples from adult patients with respiratory infections. The aim of the present study was to evaluate the diagnostic performance and clinical use of a novel multiplex PCR method in adults with community-acquired respiratory viral infection, and the impact of duration of symptoms on detection rates. All patients still positive for the same agent on follow-up had a higher Ct-value (corresponding to a lower Table 2 Follow-up (10 ± 2 days after initial visit) test result from analysis with real-time PCR of nasopharyngeal/throat swab specimens. cache = ./cache/cord-301254-093yih5n.txt txt = ./txt/cord-301254-093yih5n.txt === reduce.pl bib === id = cord-301011-xbuqd0j5 author = Felten-Barentsz, Karin M title = Recommendations for Hospital-Based Physical Therapists Managing Patients With COVID-19 date = 2020-06-18 pages = extension = .txt mime = text/plain words = 3952 sentences = 259 flesch = 39 summary = In line with international initiatives, this article aims to provide guidance and detailed recommendations for hospital-based physical therapists managing patients hospitalized with COVID-19 through a national approach in the Netherlands. A working group conducted a purposive scan of the literature and drafted initial recommendations based on the knowledge of symptoms in patients with COVID-19, and current practice for physical therapist management for patients hospitalized with lung disease and patients admitted to the intensive care unit (ICU). 12 In line with this international study 12 and the consensus statement of Italian respiratory therapists 13 we aim to provide guidance and detailed recommendations for hospital-based physical therapists managing patients hospitalized with COVID-19 through a national approach in the Netherlands. Physical therapist management for patients hospitalized with COVID-19 comprises elements of respiratory support and active mobilization. Physical therapist management for patients hospitalized with COVID-19 comprises elements of respiratory support and active mobilization. cache = ./cache/cord-301011-xbuqd0j5.txt txt = ./txt/cord-301011-xbuqd0j5.txt === reduce.pl bib === id = cord-299835-92karhpl author = Ho, Khek Y. title = Mild Illness Associated with Severe Acute Respiratory Syndrome Coronavirus Infection: Lessons from a Prospective Seroepidemiologic Study of Health-Care Workers in a Teaching Hospital in Singapore date = 2004-02-17 pages = extension = .txt mime = text/plain words = 3524 sentences = 163 flesch = 52 summary = title: Mild Illness Associated with Severe Acute Respiratory Syndrome Coronavirus Infection: Lessons from a Prospective Seroepidemiologic Study of Health-Care Workers in a Teaching Hospital in Singapore Participating HCWs completed a questionnaire and provided paired serum samples, which were analyzed by 2 different laboratories blinded to clinical data, by use of an enzyme-linked immunosorbent assay based on a protocol developed by the Centers for Disease Control and Prevention and a dot-blot immunoassay, with confirmation by a viral neutralization assay. Of the 372 HCWs participating in the present study, 8 were found to have positive antibodies to the SARS coronavirus in both samples by use of both test methods, and 6 had pneumonia and had been hospitalized for either probable or suspected SARS infection, whereas 2 had fever but did not have changes on chest radiographs. cache = ./cache/cord-299835-92karhpl.txt txt = ./txt/cord-299835-92karhpl.txt === reduce.pl bib === id = cord-307874-0obomty2 author = Pardon, Bart title = Bovine Respiratory Disease Diagnosis: What Progress Has Been Made in Infectious Diagnosis? date = 2020-05-23 pages = extension = .txt mime = text/plain words = 7061 sentences = 388 flesch = 43 summary = Evidence-based guidelines for precise interpretation of microbiologic tests results are lacking; however, approaches that have been practically useful for the management of bovine respiratory disease outbreaks are presented. However, naturally resistant to fluoroquinolones 71 Escherichia coli, Gallibacterium anatis, Enterobacter hormaechei, staphylococci, streptococci, fungi Secondary Single reports on cattle-specific strains isolated in pure culture in an outbreak of pneumonia in calves 52, [72] [73] [74] Multiple other bacterial species can be detected in the bovine respiratory tract. 10, 35, 54 However, with current knowledge on the interpretation of DNS results at the individual or group level, samples of the lower respiratory tract are likely a better option to evaluate potential involvement of opportunistic pathogens. In the example where the pathogen is causing the disease in 100% of affected calves, the risk of not finding an infected animal after sampling n cases is (1-Se)n , where Se is the test sensitivity. cache = ./cache/cord-307874-0obomty2.txt txt = ./txt/cord-307874-0obomty2.txt === reduce.pl bib === id = cord-308201-lavcsqov author = Desforges, Marc title = Human Coronaviruses and Other Respiratory Viruses: Underestimated Opportunistic Pathogens of the Central Nervous System? date = 2019-12-20 pages = extension = .txt mime = text/plain words = 8470 sentences = 473 flesch = 36 summary = Viruses infecting human CNS cells could then cause different types of encephalopathy, including encephalitis, and long-term neurological diseases. Even though no clear cause and effect link has ever been made with the onset of human neurological diseases, their neuropathogenicity is being increasingly recognized in humans, as several recent reports associated cases of encephalitis [244] , acute flaccid paralysis [271] and other neurological symptoms, including possible complications of HCoV infection such as Guillain-Barré syndrome or ADEM [249, [272] [273] [274] [275] [276] [277] [278] [279] . Like for several other respiratory viruses, accumulating evidence now indicate that HCoV are neuroinvasive in humans and we hypothesize that these recognized respiratory pathogens are potentially neurovirulent as well, as they could participate in short-and long-term neurological disorders either as a result of inadequate host immune responses and/or viral propagation in the CNS, which directly induces damage to resident cells. cache = ./cache/cord-308201-lavcsqov.txt txt = ./txt/cord-308201-lavcsqov.txt === reduce.pl bib === id = cord-312615-q333qgps author = Knobbe, Rebecca B title = Pathogens Causing Respiratory Tract Infections in Children Less Than 5 Years of Age in Senegal date = 2019-12-30 pages = extension = .txt mime = text/plain words = 4466 sentences = 284 flesch = 51 summary = The aim of this study was to identity the various respiratory pathogens causing acute respiratory tract infections in children below 5 years of age visiting a sub-urban primary care clinic in Senegal. CONCLUSIONS: This case-control study in a primary care setting in sub-Saharan Africa found influenza virus A and B, RSV, and S pneumoniae to be the main causes of acute respiratory tract infections in children below 5 years of age. Therefore, the aim of this case-control study was to investigate the prevalence of the different viruses and bacteria colonizing the airways and their association with the occurrence of ARTIs and severity of disease in children less than 5 years of age, visiting a sub-urban primary care clinic in Dakar, Senegal. This case-control study investigates the prevalence of the different viruses and bacteria colonizing the airways and their 6 Microbiology Insights association with the occurrence of ARTIs in children visiting a sub-urban primary care clinic in Senegal. cache = ./cache/cord-312615-q333qgps.txt txt = ./txt/cord-312615-q333qgps.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-310508-zgqbfmzl author = Alavi-Moghaddam, Mostafa title = A Novel Coronavirus Outbreak from Wuhan City in China, Rapid Need for Emergency Departments Preparedness and Response; a Letter to Editor date = 2020-02-02 pages = extension = .txt mime = text/plain words = 1243 sentences = 69 flesch = 44 summary = This report to World Health Organization (WHO), raised global public health concern because this is the third coronavirus âȂŞassociated acute respiratory illness outbreak. Clinical care of patients with suspected 2019-nCoV should focus on early recognition, immediate isolation (separation), implementation of appropriate infection prevention and control (IPC) measures and provision optimized supportive care. Both the health care worker (HCW) and the suspected case of acute respiratory illness (ALI) should wear a medical mask and the patient should better be directed to a separate area, an isolation room if available. At the time being, emergency preparedness and response for providing appropriate care to the patients suspected to coronavirus-associated acute respiratory illness (abovementioned plans) should be developed and implemented in the emergency departments, as the frontline of treating human infections of 2019-nCov in the hospitals. Clinical management of severe acute respiratory infection when novel coronavirus (2019-nCoV) infection is suspected: interim guidance cache = ./cache/cord-310508-zgqbfmzl.txt txt = ./txt/cord-310508-zgqbfmzl.txt === reduce.pl bib === id = cord-306278-c4q4la5c author = Esposito, Susanna title = Epidemiology and Clinical Characteristics of Respiratory Infections Due to Adenovirus in Children Living in Milan, Italy, during 2013 and 2014 date = 2016-04-05 pages = extension = .txt mime = text/plain words = 4660 sentences = 220 flesch = 48 summary = To evaluate the predominant human adenovirus (HAdV) species and types associated with pediatric respiratory infections, nasopharyngeal swabs were collected from otherwise healthy children attending an emergency room in Milan, Italy, due to a respiratory tract infection from January 1 to February 28 of two subsequent years, 2013 and 2014. To evaluate the circulation of the different HAdV types and the possible relationship between viral load, viral genetic characteristics, and the severity of infection, nasopharyngeal swabs were collected from otherwise healthy children consecutively attending the Emergency Room of the Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Italy, due to a respiratory tract infection. However, further studies are needed to identify the potential pathogenetic role of the different species and types of HAdV and the importance of viral load in the severity of infection. cache = ./cache/cord-306278-c4q4la5c.txt txt = ./txt/cord-306278-c4q4la5c.txt === reduce.pl bib === id = cord-303299-p15irs4e author = Dzien, Alexander title = Will the COVID-19 pandemic slow down in the Northern hemisphere by the onset of summer? An epidemiological hypothesis date = 2020-06-23 pages = extension = .txt mime = text/plain words = 1263 sentences = 70 flesch = 51 summary = The infection caused by the human corona virus COVID-19 (SARS-CoV2) resulted in a worldwide pandemic affecting several million people and causing severe disease and fatality mostly based on virus mediated lung failure [1, 2] . However, epidemics with respiratory virus such as not only influenza but also human corona viruses are prevalent in the Northern hemisphere over several months during the cold season and then disappear whereas influenza remains prevalent in tropical regions throughout the whole year [5] [6] [7] . The grey lines indicate seasons where no specific pandemic respiratory infections are recorded. If COVID-19 would behave similar to other respiratory viruses causing respiratory infections including human corona viruses which peak during winter time and early spring, there is hope that the COVID-19 pandemic can be slowed down by this seasonal trend [7, 9] . However, pandemics with new viruses such as the influenza H1N1v can circulate independent of typical respiratory viral seasons throughout the whole year [10] . cache = ./cache/cord-303299-p15irs4e.txt txt = ./txt/cord-303299-p15irs4e.txt === reduce.pl bib === id = cord-296836-aizquh16 author = Brenner, Hermann title = Vitamin D Insufficiency and Deficiency and Mortality from Respiratory Diseases in a Cohort of Older Adults: Potential for Limiting the Death Toll during and beyond the COVID-19 Pandemic? date = 2020-08-18 pages = extension = .txt mime = text/plain words = 4435 sentences = 192 flesch = 39 summary = We assessed the prevalence of vitamin D insufficiency and deficiency, defined by 25-hydroxyvitamin D (25(OH)D) blood levels of 30–50 and <30 nmol/L, respectively, and their association with mortality from respiratory diseases during 15 years of follow-up in a cohort of 9548 adults aged 50–75 years from Saarland, Germany. Vitamin D insufficiency and deficiency are common and account for a large proportion of respiratory disease mortality in older adults, supporting the hypothesis that vitamin D(3) supplementation could be helpful to limit the burden of the COVID-19 pandemic, particularly among women. We previously assessed the prevalence of vitamin D insufficiency and deficiency and their association with all-cause mortality and mortality from cardiovascular, cancer and respiratory diseases during a mean follow-up of 9.5 years in a cohort of 9548 adults aged 50-75 years from Saarland, Germany [4] [5] [6] [7] [8] . cache = ./cache/cord-296836-aizquh16.txt txt = ./txt/cord-296836-aizquh16.txt === reduce.pl bib === id = cord-306450-sh2mrhoq author = Appak, Özgür title = Viral respiratory infections diagnosed by multiplex polymerase chain reaction in pediatric patients date = 2019-01-03 pages = extension = .txt mime = text/plain words = 1742 sentences = 99 flesch = 52 summary = The aim of this study was to investigate the respiratory viruses in children admitted to a university hospital with acute respiratory tract infection during the last 8 years by a multiplex polymerase chain reaction (PCR) assay. where coinfections were the most frequent cause of the respiratory infections in the studied group and followed by RV/EV and influenza A/B, respectively ( Figure 1B ). In our study, the age relation was significant for RSV and HMPV which were detected in 89% (260 of 292) and 81% (84 of 104) of children under 5 years, respectively. Similar to RSV, HMPV infections were frequently seen in winter and spring months as it was the case in our study while 90% of the HMPV cases were detected between January and April. Epidemiologic analysis of respiratory viral infections mainly in hospitalized children and adults in Midwest University Medical Center after the implementation of a 14-virus multiplex nucleic acid amplification test cache = ./cache/cord-306450-sh2mrhoq.txt txt = ./txt/cord-306450-sh2mrhoq.txt === reduce.pl bib === id = cord-307261-0a3iztns author = Hayden, Randall T. title = Comparison of two broadly multiplexed PCR systems for viral detection in clinical respiratory tract specimens from immunocompromised children date = 2012-01-30 pages = extension = .txt mime = text/plain words = 4052 sentences = 206 flesch = 48 summary = title: Comparison of two broadly multiplexed PCR systems for viral detection in clinical respiratory tract specimens from immunocompromised children Samples were de-identified and assayed in parallel using two different, broadly multiplexed PCR systems: ResPlex™ II Panel v2.0 (ResPlex), Qiagen, Hilden, Germany and FilmArray(®) Respiratory Panel (FilmArray), Idaho Technology Inc., Salt Lake City, UT. Two broadly multiplexed PCR systems were compared to each other and to a panel of laboratory developed tests for the detection of respiratory viral pathogens in clinical respiratory tract specimens from pediatric immunocompromised children. FilmArray detected viral targets: adenovirus, bocavirus, coronavirus 229E, HKU1, NL63, OC43, enterovirus, hMPV, human rhinovirus, influenza virus types A and B, parainfluenza viruses 1, 2, 3 and 4, and RSV. The current study, to our knowledge, is the first reported that compares the FilmArray with the ResPlex II v2.0 for the direct detection of viral agents in clinical respiratory tract specimens from immunocompromised children. cache = ./cache/cord-307261-0a3iztns.txt txt = ./txt/cord-307261-0a3iztns.txt === reduce.pl bib === id = cord-301988-cevv81h3 author = Hassoun, Ali title = Seasonal variation of respiratory pathogen colonization in asymptomatic health care professionals: A single-center, cross-sectional, 2-season observational study date = 2015-08-01 pages = extension = .txt mime = text/plain words = 3067 sentences = 169 flesch = 40 summary = BACKGROUND: The purpose of this study was to determine the seasonal variance of potentially pathogenic bacterial and viral organisms in nasopharyngeal specimens obtained from asymptomatic health care professionals (HCPs) during the 2014 winter and summer months. Although asymptomatic HCPs certainly harbor a number of different potentially infectious agents, future studies are needed to determine whether colonized pathogens are transmitted or initiate infection in at-risk patient populations. Here, we describe the frequency and seasonal variation of bacterial and viral detections in asymptomatic health care professionals (HCPs) during the winter and summer months of 2014. 4 By elucidating changes in pathogen colonization rates in asymptomatic HCPs during different time periods in the year, health care organizations can monitor which potentially pathogenic agents are most prevalent in carriers in a health care setting and observe correlations with infection levels in at-risk hospitalized patients. cache = ./cache/cord-301988-cevv81h3.txt txt = ./txt/cord-301988-cevv81h3.txt === reduce.pl bib === id = cord-306315-vt2e0crh author = Elabbadi, Alexandre title = Respiratory virus-associated infections in HIV-infected adults admitted to the intensive care unit for acute respiratory failure: a 6-year bicenter retrospective study (HIV-VIR study) date = 2020-09-14 pages = extension = .txt mime = text/plain words = 4734 sentences = 244 flesch = 36 summary = CONCLUSIONS: Viruses are frequently identified in the respiratory tract of HIV-infected patients with acute respiratory failure that requires ICU admission, but with a non-viral copathogen in two-thirds of cases. Indeed, using nucleic acid amplification test such as multiplex polymerase chain reaction (mPCR), these pathogens have been shown highly prevalent (20-56%) in large cohorts of adult patients admitted to the ICU for all-cause ARF [7, 8] , community-acquired pneumonia [9, 10] , hospitalacquired pneumonia [11] , acute exacerbation of COPD [12, 13] , and asthma [14] , compared to asymptomatic adults [15, 16] . We investigated whether a respiratory virus-associated infection Table 2 Causative diagnosis of acute respiratory failure in 123 HIV-infected patients admitted to the ICU Data are presented as number (%). Viruses are frequently identified in the respiratory tract of HIV-infected patients with ARF that required ICU admission, but with a non-viral copathogen in two-thirds of cases. cache = ./cache/cord-306315-vt2e0crh.txt txt = ./txt/cord-306315-vt2e0crh.txt === reduce.pl bib === id = cord-312024-qdgqif5j author = Talbot, H. Keipp title = The Diagnosis of Viral Respiratory Disease in Older Adults date = 2010-02-01 pages = extension = .txt mime = text/plain words = 3423 sentences = 175 flesch = 39 summary = The increasing availability of new rapid and sensitive molecular diagnostics such as polymerase chain reaction testing, should provide more accurate and timely diagnoses of viral respiratory infections in older adults in the near future. This article summarizes what is known about the diagnosis of viral respiratory diseases in elderly adults, with the hope of increasing understanding of the utility and limitations of the currently available diagnostic tests for viral respiratory pathogens, such as culture, rapid antigen testing, polymerase chain reaction (PCR) testing, and serologic analysis. Compared with previous studies that have used viral culture for diagnosis, studies using PCR have more accurately detected the presence of viruses (including influenza virus, RSV, hMPV, parainfluenza virus, rhinoviruses, and coronaviruses) in the lower respiratory tract illness in older adults [5, 13, 31, 36, 40, 42] . cache = ./cache/cord-312024-qdgqif5j.txt txt = ./txt/cord-312024-qdgqif5j.txt === reduce.pl bib === id = cord-314841-b5l6epy3 author = Falsey, Ann Regina title = Respiratory viral infections date = 2019-08-15 pages = extension = .txt mime = text/plain words = 6006 sentences = 300 flesch = 32 summary = Analysis of the host transcriptional response during respiratory viral infection using in-vitro, animal models and natural and experimental human challenge have furthered the understanding of the mechanisms and predictors of severe disease and may identify potential therapeutic targets to prevent and ameliorate illness. In addition to sensitive and rapid diagnostic testing, new molecular techniques allow an understanding of viral evolution, mechanisms and predictors of severe disease, interrogation of vaccine responses, improved bacterial and viral diagnostics and associations of viral infections with non-respiratory medical events. A number of candidate genes influencing respiratory virus susceptibility have been identified in animal and human studies and involve host virus interactions, innate immune signaling, interferon related pathways and cytokine responses (Table 1) [49] [50] [51] [69] [70] [71] [72] [73] [74] [75] . In addition, two compartments, the respiratory epithelium and blood can be sampled in human studies and interrogated using different viruses or viral strains to develop gene signatures for prognosis, as indicators of severity and to identify potential therapeutic targets. cache = ./cache/cord-314841-b5l6epy3.txt txt = ./txt/cord-314841-b5l6epy3.txt === reduce.pl bib === id = cord-312613-1nl7q6cy author = Luz Garcia-Garcia, M. title = Pediatric Asthma and Viral Infection() date = 2016-03-26 pages = extension = .txt mime = text/plain words = 4089 sentences = 231 flesch = 48 summary = Respiratory viral infections, particularly respiratory syncytial virus (RSV) and rhinovirus, are the most importance risk factors for the onset of wheezing in infants and small children. The association between bronchiolitis caused by RSV and the development of recurrent wheezing and/or asthma was first described more than 40 years ago, but it is still unclear whether bronchiolitis causes chronic respiratory symptoms, or if it is a marker for children with a genetic predisposition for developing asthma in the medium or long term. In the Childhood Origins of Asthma (COAST) study, which followed a cohort of 289 newborns with high risk of developing asthma, lower respiratory tract infection associated with rhinovirus was the main risk factor for presenting recurrent wheezing at 3 and 6 years of life, with an odds ratio of 10 for rhinovirus bronchiolitis compared to 2.6 for RSV bronchiolitis. 3 found that 80% of asthma exacerbations in asthmatic children aged 9-11 years were associated with viral respiratory infection, of which two thirds were caused by rhinovirus. cache = ./cache/cord-312613-1nl7q6cy.txt txt = ./txt/cord-312613-1nl7q6cy.txt === reduce.pl bib === id = cord-303322-d69o3z8d author = Chang, Anne B title = Randomized placebo-controlled trial on azithromycin to reduce the morbidity of bronchiolitis in Indigenous Australian infants: rationale and protocol date = 2011-04-14 pages = extension = .txt mime = text/plain words = 5403 sentences = 287 flesch = 37 summary = Our randomised, placebo-controlled trial of azithromycin in Indigenous infants hospitalised with bronchiolitis is designed to determine whether it can reduce short-term (and potentially long-term) morbidity from respiratory illness in Australian Indigenous infants who are at high risk of developing chronic respiratory illness. Indigenous infants (aged ≤ 24-months, expected number = 200) admitted to one of two regional hospitals (Darwin, Northern Territory and Townsville, Queensland) with a clinical diagnosis of bronchiolitis and fulfilling inclusion criteria are randomised (allocation concealed) to either azithromycin (30 mg/kg/dose) or placebo administered once weekly for three doses. Indigenous infants (aged ≤ 24-months, expected number = 200) admitted to one of two regional hospitals (Darwin, Northern Territory and Townsville, Queensland) with a clinical diagnosis of bronchiolitis and fulfilling inclusion criteria are randomised (allocation concealed) to either azithromycin (30 mg/kg/dose) or placebo administered once weekly for three doses. cache = ./cache/cord-303322-d69o3z8d.txt txt = ./txt/cord-303322-d69o3z8d.txt === reduce.pl bib === id = cord-306411-dutbxfl4 author = Eifan, Saleh A. title = Respiratory Tract Viral Infections and Coinfections Identified by Anyplex™ II RV16 Detection Kit in Pediatric Patients at a Riyadh Tertiary Care Hospital date = 2017-11-21 pages = extension = .txt mime = text/plain words = 2641 sentences = 132 flesch = 38 summary = title: Respiratory Tract Viral Infections and Coinfections Identified by Anyplex™ II RV16 Detection Kit in Pediatric Patients at a Riyadh Tertiary Care Hospital This retrospective cohort study aimed to determine the etiological agents responsible for respiratory tract infections by Anyplex II RV16 detection kit (RV16, Seegene), involving 2266 pediatric patients with respiratory infections admitted to the Department of Pediatrics at King Abdul-Aziz Medical City, Ministry of National Guard, Riyadh, from July 2014 to June 2015. Different studies reported the detection of viruses like human respiratory syncytial virus A (RSV A), human respiratory syncytial virus B (RSV B), human adenovirus (AdV), Human metapneumovirus (HMPV), human coronavirus, and human parainfluenza virus (PIV). This study aimed to determine the distribution of 16 different viruses causing respiratory infections in children, by using RV16, and to compare data on demographic characteristics, symptoms, and single infections or coinfections. cache = ./cache/cord-306411-dutbxfl4.txt txt = ./txt/cord-306411-dutbxfl4.txt === reduce.pl bib === id = cord-315949-7id5mitl author = Sentilhes, Anne‐Charlotte title = Respiratory virus infections in hospitalized children and adults in Lao PDR date = 2013-06-25 pages = extension = .txt mime = text/plain words = 4098 sentences = 246 flesch = 49 summary = 8, 9 The purpose of this study was to describe during a limited period of time the viral etiology of acute lower respiratory infections (ALRI) in patients hospitalized in two Lao hospitals by using a set of five multiplex RT-PCR/PCR targeting 18 common respiratory viruses. In this study, we report for the first time in Lao PDR the viral etiologies in patients hospitalized for ALRIs. We identified 186 respiratory viruses in 162 (55%) patients of all ages using 5 multiplex PCR/RT-PCR. Human respiratory syncytial virus is frequently defined as the predominant virus associated with hospitalizations for ALRI in children aged ≤5 years. Respiratory virus coinfections being frequent, 5, 19, 44 it demonstrates the usefulness of the multiplex RT-PCR approach, which allows the detection of the most important viruses in only few reactions while multiple infections are often undetected in viral culture or by direct immunofluorescence. cache = ./cache/cord-315949-7id5mitl.txt txt = ./txt/cord-315949-7id5mitl.txt === reduce.pl bib === id = cord-302833-6kntd89t author = Radonovich, Lewis J. title = The Respiratory Protection Effectiveness Clinical Trial (ResPECT): a cluster-randomized comparison of respirator and medical mask effectiveness against respiratory infections in healthcare personnel date = 2016-06-02 pages = extension = .txt mime = text/plain words = 5090 sentences = 248 flesch = 39 summary = BACKGROUND: Although N95 filtering facepiece respirators and medical masks are commonly used for protection against respiratory infections in healthcare settings, more clinical evidence is needed to understand the optimal settings and exposure circumstances for healthcare personnel to use these devices. Healthcare personnel who work in outpatient settings will be cluster-randomized to wear N95 respirators or medical masks for protection against infections during respiratory virus season. Abbreviations ARI, acute respiratory illness; CDC, centers for disease control and prevention; DSMB, data safety monitoring board; HAI, hemagglutination inhibition antibody; HCP, healthcare personnel; ILI, influenza like illness; LCRI, Laboratory confirmed respiratory illness; MM, medical mask; N95, N95 respirator; NIOSH, National Institute for Occupational Safety and Health; OSHA, Occupational Safety and Health Administration; PPE, occupational protective equipment; ResPECT, respiratory protection effectiveness clinical trial; RPD, respiratory protective devices; RT-PCR, reverse-transcriptase polymerase chain reaction; US, United States. cache = ./cache/cord-302833-6kntd89t.txt txt = ./txt/cord-302833-6kntd89t.txt === reduce.pl bib === id = cord-316727-ktrlohm9 author = Razavi, Seyed Mansour title = Treatment and prevention of acute respiratory infections among Iranian hajj pilgrims: a 5-year follow up study and review of the literature date = 2014-05-10 pages = extension = .txt mime = text/plain words = 4673 sentences = 357 flesch = 50 summary = title: Treatment and prevention of acute respiratory infections among Iranian hajj pilgrims: a 5-year follow up study and review of the literature Background Respiratory diseases/syndromes are the most common causes of referring to physicians among pilgrims in Hajj. The main aim of our study was to determine types, frequencies, etiologies, and epidemiologic factors of respiratory diseases among Iranian Hajj pilgrims and to suggest some preventive and treatment strategies. The aim of our study was to determine types, frequencies, etiologies, and some of other epidemiologic factors of respiratory diseases among Iranian Hajj pilgrims and to suggest some preventive and treatment strategies based on our 10 years of experience and literature review. We used the results of above mentioned studies and reviewed the literature, and offered a guideline for the treatment and prevention of acute respiratory infections (ARIs) in Hajj.  Significant difference values of NBT test before and after travel showed that respiratory diseases of pilgrims might have infectious origins. cache = ./cache/cord-316727-ktrlohm9.txt txt = ./txt/cord-316727-ktrlohm9.txt === reduce.pl bib === id = cord-313749-f2ct57em author = Brittain-Long, Robin title = Multiplex real-time PCR for detection of respiratory tract infections date = 2007-12-26 pages = extension = .txt mime = text/plain words = 1566 sentences = 94 flesch = 50 summary = title: Multiplex real-time PCR for detection of respiratory tract infections STUDY DESIGN: An assay targeting influenza virus A (IfA) and B (IfB), parainfluenza 1-3 (PIV), human metapneumovirus (MPV), respiratory syncytial virus (RSV), rhinovirus (RV), enterovirus (EV), adenovirus (AdV), human coronaviruses (229E, OC43, NL63), M. We developed a real-time PCR procedure, based on automated specimen extraction and multiplex amplification, at a relatively low cost (D 33). We believe that a combination of low cost, high accuracy and prompt result delivery is the key to achieving a wide clinical use of molecular diagnostics of respiratory infections. Further studies of respiratory infection aetiologies in different patient categories, and of the clinical utility of this and similar multiplex assays, need to be carried out. Real-time RT-PCR detection of 12 respiratory viral infections in four triplex reactions Rapid and sensitive method using multiplex real-time PCR for diagnosis of infections by influenza A and influenza B viruses, respiratory syncytial virus, and parainfluenza viruses 1, 2, 3, and 4 cache = ./cache/cord-313749-f2ct57em.txt txt = ./txt/cord-313749-f2ct57em.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-306480-wgl4zrnb author = Subissi, Lorenzo title = Capturing respiratory syncytial virus season in Belgium using the influenza severe acute respiratory infection surveillance network, season 2018/19 date = 2020-10-01 pages = extension = .txt mime = text/plain words = 4135 sentences = 187 flesch = 48 summary = BACKGROUND: Respiratory syncytial virus (RSV) is a common cause of severe respiratory illness in young children (< 5 years old) and older adults (≥ 65 years old) leading the World Health Organization (WHO) to recommend the implementation of a dedicated surveillance in countries. AIM: We tested the capacity of the severe acute respiratory infection (SARI) hospital network to contribute to RSV surveillance in Belgium. CONCLUSION: With only marginal modifications in the case definition and the period of surveillance, the Belgian SARI network would be able to substantially contribute to RSV surveillance and burden evaluation in children and older adults, the two groups of particular interest for WHO. Nevertheless, the SARI case definition we used, even with a less strict fever criterion, allowed to follow RSV circulation in the children population aged < 5 years and to identify comorbidities/indicators potentially associated with disease severity. cache = ./cache/cord-306480-wgl4zrnb.txt txt = ./txt/cord-306480-wgl4zrnb.txt === reduce.pl bib === id = cord-309120-05bg7rfa author = Niazi, Sadegh title = The role of respiratory droplet physicochemistry in limiting and promoting the airborne transmission of human coronaviruses: A critical review() date = 2020-11-06 pages = extension = .txt mime = text/plain words = 2717 sentences = 180 flesch = 38 summary = title: The role of respiratory droplet physicochemistry in limiting and promoting the airborne transmission of human coronaviruses: A critical review() Airborne transmission is an accepted potential route for the spread of some viral infections (measles, chickenpox); however, aerosol features and infectious inoculum vary from one respiratory virus to another. This critical review identifies studies reporting instances of infected patients producing airborne human pathogenic coronaviruses, and evidence for the role of physical/chemical characteristics of human-generated droplets in altering embedded viruses' viability. Based on previous literature, healthy subjects can produce particles between 0.01 The aerosols generated through speech, coughing, sneezing, and breathing have been 178 surveyed in several studies (Table 1) 290 Hygroscopic salts influence the transport of water vapor, and allow for humidity dependent 359 droplet sizes as described by Köhler theory (Köhler, 1936) . Measurements of airborne influenza virus in 839 aerosol particles from human coughs Measurements of airborne influenza virus in 839 aerosol particles from human coughs cache = ./cache/cord-309120-05bg7rfa.txt txt = ./txt/cord-309120-05bg7rfa.txt === reduce.pl bib === id = cord-312741-0au4nctt author = Lin, Panpan title = Coronavirus in human diseases: Mechanisms and advances in clinical treatment date = 2020-10-01 pages = extension = .txt mime = text/plain words = 14665 sentences = 840 flesch = 42 summary = 160, 161 Once the PAMPs from invaded viruses are detected, RIG-I and MDA5 interact with the mitochondrial antiviral signaling protein (MAVs) that is a mitochondrial membrane-bound F I G U R E 2 Escape mechanisms of innate immune response of SARS-CoV and MERS-CoV adaptor molecule, followed by the activation of several kinase complexes and multiple subsequent transcription factors (IRF3, IRF7, and NF-κB). Antiviral peptides analogous derived from these regions exhibited inhibition to the spike protein-mediated cell-cell fusion and viral entry in viruses such as SARS-CoV, MERS-CoV, as well as HCoV-229E. Receptor-binding domain of severe acute respiratory syndrome coronavirus spike protein contains multiple conformation-dependent epitopes that induce highly potent neutralizing antibodies Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry Evidence that TMPRSS2 activates the severe acute respiratory syndrome coronavirus spike protein for membrane fusion and reduces viral control by the humoral immune response Inhibition of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infectivity by peptides analogous to the viral spike protein cache = ./cache/cord-312741-0au4nctt.txt txt = ./txt/cord-312741-0au4nctt.txt === reduce.pl bib === id = cord-316956-nnqi0dj1 author = Gamiño‐Arroyo, Ana E. title = Epidemiology and clinical characteristics of respiratory syncytial virus infections among children and adults in Mexico date = 2016-08-18 pages = extension = .txt mime = text/plain words = 2497 sentences = 138 flesch = 45 summary = title: Epidemiology and clinical characteristics of respiratory syncytial virus infections among children and adults in Mexico Respiratory syncytial virus (RSV) is the major infectious cause of lower respiratory tract illness in infants and young children around the world. 11 In the present study, 570 cases of RSV infection identified during four epidemic years in Mexico were evaluated to clarify the epidemiology of this infection and to assess the possible variations in demographic and clinical characteristics according to viral groups. 6 In this report, we analyzed the characteristics of 570 patients (399 children and 171 adults) with confirmed RSV infection included in the study during a 4-year period. Epidemiological and clinical data of hospitalizations associated with respiratory syncytial virus infection in children under 5 years of age in Spain: FIVE multicenter study Epidemiology and clinical characteristics of respiratory syncytial virus infections among children and adults in Mexico cache = ./cache/cord-316956-nnqi0dj1.txt txt = ./txt/cord-316956-nnqi0dj1.txt === reduce.pl bib === id = cord-304876-txaoz7oh author = Jordan, Paul C title = Nucleosides for the treatment of respiratory RNA virus infections date = 2018-03-21 pages = extension = .txt mime = text/plain words = 10962 sentences = 654 flesch = 46 summary = 42 Viral polymerase: An important molecular target for antiviral therapy Nucleoside analogs represent one of the dominant classes of antiviral agents due to their widespread use against the common chronic infections caused by human immunodeficiency virus (HIV), hepatitis B virus, and herpesviruses. 43 After being metabolized by host kinases to their triphosphate form, antiviral nucleotides compete with natural nucleoside triphosphates (NTPs) to bind to the active site of viral polymerases and alter DNA or RNA synthesis. 122 However, the results summarized here indicate that nucleoside analogs targeting the viral RNA polymerase of rhinovirus, EV71, and other enteroviruses have the potential to be efficacious in preclinical animal models, providing a rationale to conduct human studies with safer molecules sharing the same mode of action. Structure and functional analysis of the RNA-and viral phosphoprotein-binding domain of respiratory syncytial virus M2-1 protein cache = ./cache/cord-304876-txaoz7oh.txt txt = ./txt/cord-304876-txaoz7oh.txt === reduce.pl bib === id = cord-312952-9gbb4own author = WARDZYŃSKA, ALEKSANDRA title = The profile of respiratory pathogens in induced sputum of elderly and non-elderly asthmatics date = 2020-01-20 pages = extension = .txt mime = text/plain words = 2990 sentences = 167 flesch = 47 summary = While the majority of studies indicate that the detection rate of respiratory viruses in patients with asthma and healthy subjects is similar [10] , they have been found to differ with regard to the bacterial composition of the airways [11] . This technique was chosen for the present study, to test the hypothesis that elderly patients with asthma display a different profile of respiratory pathogens in the airways as compared to non-elderly asthmatics, and that this profile may be related to local airway and/or systemic inflammation. This study is the first to use the IS technique to compare detection rates of respiratory pathogens in the airways of elderly and non-elderly patients with asthma. Although the detection rate and profile of respiratory viruses in IS was similar in elderly and non-elderly patients with asthma, the presence of pathogens was associated with some clinical characteristics only in older subjects. cache = ./cache/cord-312952-9gbb4own.txt txt = ./txt/cord-312952-9gbb4own.txt === reduce.pl bib === id = cord-315339-dcui85lw author = Broadbent, Andrew J. title = Respiratory Virus Vaccines date = 2015-03-13 pages = extension = .txt mime = text/plain words = 28246 sentences = 1270 flesch = 39 summary = Although neutralizing antibodies directed against the HA globular head are highly efficient at preventing and clearing influenza virus infection, they can also FIGURE 3 In the memory phase, migratory lung DCs capture viral antigen retained on follicular DCs (FDCs) in tertiary lymphoid organs and present it to specific T cells in the respiratory draining lymph nodes. This explains why passively transferred IgG is effective at preventing severe disease from respiratory infections in experimental animals and why serum IgG antibodies are the main correlate of protection for parentally administered inactivated influenza vaccines in humans (Section Respiratory Virus Vaccines). Nasal administration of influenza vaccine with type I IFN was effective at inducing serum antigen-specific IgG2a and mucosal IgA antibody responses and at providing full protection against influenza virus challenge (Proietti et al., 2002) . cache = ./cache/cord-315339-dcui85lw.txt txt = ./txt/cord-315339-dcui85lw.txt === reduce.pl bib === id = cord-317619-o7qfugjw author = Nye, Steven title = Viral Infection in the Development and Progression of Pediatric Acute Respiratory Distress Syndrome date = 2016-11-24 pages = extension = .txt mime = text/plain words = 6733 sentences = 324 flesch = 35 summary = While the overall incidence of respiratory virus infection, in particular RSV and influenza A (H1N1) virus, leading to lower respiratory tract disease is widely studied (12, 13), the frequency of progression to pediatric ARDS has yet to be clearly determined. While post-pandemic studies suggest a decrease in influenza A (H1N1) virus disease severity and burden (20, 21), it continues to be a significant cause of severe illness and pediatric ARDS (22). In RSV infection, development of lower respiratory track disease in premature infants, with or without chronic neonatal lung disease is associated with a significantly higher risk of hospitalization, intensive care unit admission, need for mechanical ventilation, and death (12, [70] [71] [72] [73] . Disease severity and viral load are correlated in infants with primary respiratory syncytial virus infection in the community Motavizumab treatment of infants hospitalized with respiratory syncytial virus infection does not decrease viral load or severity of illness cache = ./cache/cord-317619-o7qfugjw.txt txt = ./txt/cord-317619-o7qfugjw.txt === reduce.pl bib === id = cord-312691-ynh84b98 author = Mohd, Hamzah A. title = Predictors of MERS-CoV infection: A large case control study of patients presenting with ILI at a MERS-CoV referral hospital in Saudi Arabia date = 2016-09-24 pages = extension = .txt mime = text/plain words = 3296 sentences = 167 flesch = 56 summary = title: Predictors of MERS-CoV infection: A large case control study of patients presenting with ILI at a MERS-CoV referral hospital in Saudi Arabia BACKGROUND: A case control study to better characterize the clinical features, laboratory, and radiological abnormalities associated with MERS-CoV infection in order to help with early identification of this syndrome from other respiratory infections. METHODS: Eighty patients admitted to a hospital in Riyadh, diagnosed with MERS-CoV infection based on RT-PCR were matched on age, sex, and the presence of a co-morbid condition on a basis of 1:2 to other patients admitted with respiratory symptoms and tested negative for MERS-CoV on RT-PCR. First cases of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infections in France, investigations and implications for the prevention of human-to-human transmission Laboratory-confirmed case of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infection in Malaysia: preparedness and response Middle East Respiratory Syndrome Coronavirus: a case-control study of hospitalized patients cache = ./cache/cord-312691-ynh84b98.txt txt = ./txt/cord-312691-ynh84b98.txt === reduce.pl bib === id = cord-315037-lmur80te author = Lin, Chien-Yu title = Increased Detection of Viruses in Children with Respiratory Tract Infection Using PCR date = 2020-01-15 pages = extension = .txt mime = text/plain words = 4190 sentences = 241 flesch = 42 summary = We performed a multiplex real-time polymerase chain reaction (PCR) to investigate the viral etiology in pediatric patients and compared the detection rates with those determined using traditional antigen tests and virus cultures. This study aims to detect respiratory viruses in children using PCR and to compare the detection power of this technique against that when using traditional antigen tests and virus cultures. For children with respiratory symptoms and with a clinical suspicion of virus infection, a test for RSV antigen test, human parainfluenza virus (PIV) type 3 antigen test, viral PCR for enterovirus, or viral cultures was prescribed by the judgment of pediatricians. The following multiplex PCR assays were performed for each sample to detect RNA/DNA of 15 respiratory viruses, including RSV A or B, FluA, FluB, human enterovirus (EV), MPV, human parainfluenza virus types 1-4, human rhinovirus (RV), coronavirus OC43/NL63/229E, human adenovirus (ADV), and human bocavirus (Boca). The present study demonstrates that PCR has higher detectability for respiratory viruses compared to traditional antigen tests and viral cultures. cache = ./cache/cord-315037-lmur80te.txt txt = ./txt/cord-315037-lmur80te.txt === reduce.pl bib === id = cord-311275-ysr9nqun author = Chuaychoo, Benjamas title = Clinical manifestations and outcomes of respiratory syncytial virus infection in adult hospitalized patients date = 2019-07-03 pages = extension = .txt mime = text/plain words = 3164 sentences = 199 flesch = 41 summary = There were a few data of adult hospitalized patients with RSV infection, with high complications, in Thailand; [3, 12, 13] however, additional clinical data are required for planning patient management and also disease prevention in this region. RSV, respiratory syncytial virus; ARI, acute respiratory illness; COPD, chronic obstructive pulmonary disease; HAP, hospital-acquired pneumonia; VAP, ventilator-associated pneumonia. The pre-existing coronary arterial disease (CAD) was the risk factor of overall cardiovascular complications in hospitalized adult patients with RSV infection with odds ratio 6.18, (95% CI 1.18-32.5), p = 0.03, adjusted for age, sex, HT, DLP, DM, pre-existing CHF, arrhythmia, and VHD. The prospective study of all adult hospitalized patients with acute respiratory illness should be conducted to determine the prevalence, clinical manifestations, and outcomes of the virus. Most of the adult hospitalized patients with RSV infections aged ≥ 50 years old and had pre-existing cardiopulmonary diseases, hematologic malignancy, immunocompromised hosts, and DM. cache = ./cache/cord-311275-ysr9nqun.txt txt = ./txt/cord-311275-ysr9nqun.txt === reduce.pl bib === id = cord-318591-ssnlfjap author = Pecego, AC title = Etiology, clinical, and epidemiological characteristics of severe respiratory infection in people living with HIV date = 2020-01-22 pages = extension = .txt mime = text/plain words = 4441 sentences = 234 flesch = 49 summary = We used the severe acute respiratory infection (SARI) definition to describe the etiology, clinical, and epidemiological characteristics in this population. [4] [5] [6] After the recent influenza A (H1N1, H5N1, and H7N9) and the Middle East Respiratory Virus (MERS-CoV) outbreaks, the WHO is encouraging and supporting countries to strengthen surveillance on severe acute respiratory infections (SARI) 7 but with limited information on PLWH regarding etiology and prognosis, despite their increased risk for respiratory infections and adverse outcomes. [8] [9] [10] So, in this study, we described how SARI is represented, according to clinical presentation, epidemiology and etiology in a population of PLWH with respiratory infection residing in a high-prevalence TB area. We observed two cases of influenza in the non-SARI group, respectively 20 and 30 days after symptom onset, and both patients developed respiratory failure that led to death (data not shown). cache = ./cache/cord-318591-ssnlfjap.txt txt = ./txt/cord-318591-ssnlfjap.txt === reduce.pl bib === id = cord-321284-0y69n1ea author = El Kholy, A. A. title = The use of multiplex PCR for the diagnosis of viral severe acute respiratory infection in children: a high rate of co-detection during the winter season date = 2016-06-10 pages = extension = .txt mime = text/plain words = 3345 sentences = 175 flesch = 46 summary = title: The use of multiplex PCR for the diagnosis of viral severe acute respiratory infection in children: a high rate of co-detection during the winter season This study confirms the high rate of detection of viral nucleic acids by multiplex PCR among hospitalized children admitted with SARI, as well as the high rate of co-detection of multiple viruses. Forty healthy age-matched asymptomatic children with no history of a recent respiratory tract infection during the previous 2 weeks, who were not admitted to the hospital, and who do not have any chronic underlying illness were included as a control group. This study confirms the high rate of detection of viral nucleic acids by multiplex PCR) among hospitalized children admitted with severe acute respiratory infection, as well as the high rate of detection of multiple viruses. cache = ./cache/cord-321284-0y69n1ea.txt txt = ./txt/cord-321284-0y69n1ea.txt === reduce.pl bib === id = cord-320107-wels9wt7 author = Gottlieb, Jens title = Community-Acquired Respiratory Viruses date = 2018-03-26 pages = extension = .txt mime = text/plain words = 3659 sentences = 220 flesch = 40 summary = Resolution of respiratory virus infection requires not only the elimination of the Keywords ► lung transplantation ► community-acquired respiratory viruses ► ribavirin ► bronchiolitis obliterns syndrome The incidence of community-acquired respiratory viruses (CARVs) is $15 cases per 100 patient-years after lung transplantation (LTx). The incidence of community-acquired respiratory viruses (CARVs) is $15 cases per 100 patient-years after lung transplantation (LTx). 8 In contrast to the nonimmunosuppressed host, CARV infection usually leads to more severe illness in the lung transplanted recipient with a higher incidence of respiratory failure. ALN-RSV01 for prevention of bronchiolitis obliterans syndrome after respiratory syncytial virus infection in lung transplant recipients Incidence and outcomes of respiratory viral infections in lung transplant recipients: a prospective study Upper and lower respiratory tract viral infections and acute graft rejection in lung transplant recipients Community-acquired respiratory viral infections in lung transplant recipients: a single season cohort study cache = ./cache/cord-320107-wels9wt7.txt txt = ./txt/cord-320107-wels9wt7.txt === reduce.pl bib === id = cord-320950-x02zp349 author = Esposito, Susanna title = Multiplex Platforms for the Identification of Respiratory Pathogens: Are They Useful in Pediatric Clinical Practice? date = 2019-06-04 pages = extension = .txt mime = text/plain words = 5863 sentences = 267 flesch = 41 summary = A systematic review and meta-analysis (Huang et al., 2018) of studies on the accuracy of FA-RP, Nanosphere Verigene RV+ test (Hologic, 2018; Luminex, 2018) Gen-Probe Prodesse assays (Hologic, 2018) in the detection of IV A, IV B virus, RSV, hMPV, and AV showed that all of these assays had high diagnostic accuracy, with an area under the receiver operating characteristic curve (AUROC) equal to or >0.98 for all tested viruses. In a study involving 46 children aged 6-36 months with bocavirus infection, it was shown that in 22% of cases, the virus persisted in the respiratory secretions for more than 30 days, despite the rapid disappearance of clinical manifestations (Wagner et al., 2016) . In conclusion, multiplex platforms, despite significantly increasing the possibility to detect which pathogens are present in the respiratory secretions of a child with a respiratory infection, do not offer any advantage in comparison to tradition diagnostic tests regarding the identification of the true etiologic agent of the disease. cache = ./cache/cord-320950-x02zp349.txt txt = ./txt/cord-320950-x02zp349.txt === reduce.pl bib === id = cord-322657-q4aeood2 author = Jartti, Tuomas title = Respiratory Picornaviruses and Respiratory Syncytial Virus as Causative Agents of Acute Expiratory Wheezing in Children date = 2004-06-17 pages = extension = .txt mime = text/plain words = 3169 sentences = 177 flesch = 45 summary = We studied the viral etiology of acute expiratory wheezing (bronchiolitis, acute asthma) in 293 hospitalized children in a 2-year prospective study in Finland. To prevent and treat acute expiratory wheezing illnesses in children, efforts should be focused on RSV, enterovirus, and rhinovirus infections. The purpose of the study was to investigate the role of 11 respiratory viruses in children hospitalized for acute expiratory wheezing. The supernatants of cell cultures exhibiting a cytopathogenic effect were further studied by antigen detection for adenovirus; influenza A and B viruses; parainfluenza virus types 1, 2, and 3; and RSV or by reverse transcription (RT)-PCR for enterovirus-es and rhinovirus. First, respiratory virus infection was detected in up to 90% of hospitalized children with acute expiratory wheezing. In conclusion, this study showed that acute expiratory wheezing necessitating hospitalization was most often associated with RSV, enterovirus, and rhinovirus infections. cache = ./cache/cord-322657-q4aeood2.txt txt = ./txt/cord-322657-q4aeood2.txt === reduce.pl bib === id = cord-314190-fvdock94 author = Florin, Todd A title = Viral bronchiolitis date = 2017-01-01 pages = extension = .txt mime = text/plain words = 7584 sentences = 404 flesch = 38 summary = The evidence and guideline recommendations consistently support a clinical diagnosis with the limited role for diagnostic testing for children presenting with the typical clinical syndrome of viral upper respiratory infection progressing to the lower respiratory tract. 24, 25, 27, 29, 30 Studies have investigated whether severity of illness, as measured by need for hospital admission, length of hospital stay, intensive care unit admission, repeated emergency department visits, and apnoea, is associated with specifi c viral infections or co-infections, but the evidence is confl icting. Recent studies suggest that higher respiratory syncytial virus genomic load, measured using quantitative PCR, might be associated with increased length of stay, use of respiratory support, and need for intensive care, in addition to recurrent wheezing, compared with lower viral loads. Systematic literature review assessing tobacco smoke exposure as a risk factor for serious respiratory syncytial virus disease among infants and young children cache = ./cache/cord-314190-fvdock94.txt txt = ./txt/cord-314190-fvdock94.txt === reduce.pl bib === id = cord-321851-ku4z34lu author = Alosaimi, Bandar title = MERS-CoV infection is associated with downregulation of genes encoding Th1 and Th2 cytokines/chemokines and elevated inflammatory innate immune response in the lower respiratory tract date = 2020-02-29 pages = extension = .txt mime = text/plain words = 5619 sentences = 299 flesch = 45 summary = Our results showed a downregulation of Th2, inadequate (partial) Th1 immune response and high expression levels of inflammatory cytokines IL-1α and IL-1β and the neutrophil chemoattractant chemokine IL-8 (CXCL8) in the lower respiratory tract of MERS-CoV infected patients. The lower respiratory tract samples from MERS-CoV infected patients and healthy non-infected controls were used to quantify expression levels of the main 12 human pro-inflammatory cytokines and chemokines (IL-1α, IL-1β, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12, IL-17A, IFN-γ, TNF-α, and GM-CSF). A side-by-side analysis of the data derived from the RT 2 -PCR profiling of pulmonary Th1/Th2 responses showed that genes encoding Th1 and Th2-related cytokines and chemokines were largely downregulated in the lower respiratory tract of MERS-CoV infected patients. Therefore, the high expression of inflammatory cytokines and downregulation of the Th1 and Th2 immune responses in the lower respiratory tracts of MERS-CoV infected patients may contribute to a more severe infection, higher case fatality, lung inflammation, and immunopathology. cache = ./cache/cord-321851-ku4z34lu.txt txt = ./txt/cord-321851-ku4z34lu.txt === reduce.pl bib === id = cord-322573-1fw1ehzd author = Vicente, Diego title = Human Bocavirus, a Respiratory and Enteric Virus date = 2007-04-17 pages = extension = .txt mime = text/plain words = 1296 sentences = 78 flesch = 48 summary = To determine the prevalence and clinical characteristics of HBoV, we investigated the presence of this virus in children with respiratory tract infection in our region (Gipúzkoa, Basque Country, Spain). To rule out the possibility that this result could have been due to fecal contamination resulting from swallowing respiratory secretions, and to determine whether the gastrointestinal tract is affected by this new respiratory virus, we studied its presence in patient feces in 527 episodes of acute gastroenteritis, unrelated to respiratory infection, in children <3 years of age, mainly from nonhospital centers (ambulatory clinics). From a second group of 520 children <3 years of age who came to the pediatric emergency unit of our hospital with an episode of acute respiratory infection during the same period, a similar frequency of HBoV detection was obtained (40/520, 7.7%) when nasopharyngeal aspirates were tested. Detection of human bocavirus in Japanese children with lower respiratory tract infections cache = ./cache/cord-322573-1fw1ehzd.txt txt = ./txt/cord-322573-1fw1ehzd.txt === reduce.pl bib === id = cord-315934-h70j2jmt author = Yu, Jianxing title = Respiratory Syncytial Virus Seasonality, Beijing, China, 2007–2015 date = 2019-06-17 pages = extension = .txt mime = text/plain words = 3994 sentences = 216 flesch = 52 summary = During July 2007–June 2015, we enrolled 4,225 hospitalized children with pneumonia in a study to determine the seasonality of respiratory syncytial virus (RSV) infection in Beijing, China. R espiratory syncytial virus (RSV) is a major cause of lower respiratory tract infection in young children worldwide (1-3); 2.7-3.8 million hospitalizations and 94,600-149,400 deaths occur each year among children <5 years of age as a result of RSV infection (4) . Several previous studies reported an RSV prevalence of 17%-33% among children with severe acute respiratory illness (15, 16) , but few have assessed the seasonality or trends of RSV infections in China. A sharp decrease in sample number and samples positive for RSV were observed each year during this event, resulting in a bimodal distribution curve ( Figure 1, During the study, 335 (8%) hospitalized children with pneumonia were admitted into the PICU, and 8 died (median age 1.4 years, range 4 months-13 years). cache = ./cache/cord-315934-h70j2jmt.txt txt = ./txt/cord-315934-h70j2jmt.txt === reduce.pl bib === id = cord-318229-29cgwivt author = Baier, Claas title = Molecular characteristics and successful management of a respiratory syncytial virus outbreak among pediatric patients with hemato-oncological disease date = 2018-02-13 pages = extension = .txt mime = text/plain words = 5698 sentences = 309 flesch = 47 summary = An outbreak case is a patient with a positive RSV laboratory testing in samples from the upper or lower respiratory tract and a definite or possible nosocomial onset. Considering bed and room occupancy on the ward during the outbreak, direct patient to patient transmission (e.g. via droplets or contaminated surfaces) in cases 1 and 2 as well as 3 and 4 seemed epidemiologically possible as each pair was accommodated in the same room before samples were tested positive for RSV. Overlying sequence information from different quasispecies detected in the samples are highlighted in a box measures, in particular single room accommodation for contact patients (quarantine), suspension of all social activities, and surgical masks for all HCWs and visitors at any time, addressed the postulated RSV transmission pathways during this outbreak. Outbreak of respiratory syncytial virus (RSV) infection in immunocompromised adults on a hematology ward cache = ./cache/cord-318229-29cgwivt.txt txt = ./txt/cord-318229-29cgwivt.txt === reduce.pl bib === id = cord-324217-secnz2ta author = Pasdaran, A. title = Volatile oils: Potential agents for the treatment of respiratory infections date = 2016-08-05 pages = extension = .txt mime = text/plain words = 7698 sentences = 407 flesch = 35 summary = The present chapter reviews natural traditional remedies used in the treatment of respiratory infections with the emphasis on antibacterial, antiviral, and antiinflammation activities of the volatile natural compounds (essential oils, etc.), and provides a brief view in some of structural activity relationships between antibacterial potencies and chemical structures of the essential oil's constituents. 10 Besides the antimicrobial activity of the essential oils in natural products, other characteristics such as high vapor pressure, low toxicity, and antiinflammatory potential create a worthwhile theme for using of these natural compounds for new drug development in respiratory infections. As a member of the phytochemicals, terpenoids have been observed as a model of lipid soluble agents, which have an impact on the activities of membrane catalyzed enzymes; for 3 SCREENING OF THE ANTIbACTERIAL EFFECTS OF ESSENTIAL OILS example, enzymes involved in respiratory pathways. 98 Among the natural chemical compounds, significant antiinflammatory activities of plant-based essential oil have been reported by many researchers, which showed the basis for folk and traditional uses of these herbs for treatment of inflammatory diseases. cache = ./cache/cord-324217-secnz2ta.txt txt = ./txt/cord-324217-secnz2ta.txt === reduce.pl bib === id = cord-323112-e78zpa9c author = WATERER, Grant title = Respiratory infections: A current and future threat date = 2009-07-16 pages = extension = .txt mime = text/plain words = 2670 sentences = 156 flesch = 39 summary = This review will focus on the human, pathogen and environmental factors that contribute to the continued global burden or respiratory diseases with a particular focus on areas where we might hope to see some progress in the coming decades. 14 While it is clear that strict infection control can reduce nosocomial infection rates, 15 the practical necessity of pooling vulnerable hosts together combined with the inevitable ageing of health-care facilities will ensure that nosocomial outbreaks continue to be a problem. In recent years the marked increase in tumour necrosis factor antagonists and monoclonal antibodies targeting specific lymphoid populations in patients with inflammatory arthritis (and especially rheumatoid disease) has significantly over taken patients on immunosuppressant therapy after solid organ transplantation as the major cause of iatrogenic immunosuppression. New therapeutic and diagnostic approaches coupled with clinical vigilance, strict infection control and solid public health measures are the hopes for reducing the burden of pulmonary infectious disease over the coming decades. cache = ./cache/cord-323112-e78zpa9c.txt txt = ./txt/cord-323112-e78zpa9c.txt === reduce.pl bib === id = cord-320286-9tumplp3 author = Bastien, Nathalie title = Human Bocavirus Infection, Canada date = 2006-05-17 pages = extension = .txt mime = text/plain words = 1425 sentences = 85 flesch = 59 summary = The virus was identified in clinical specimens from infants and children with respiratory tract illness. All specimens were negative for influenza viruses A and B; parainfluenza viruses 1, 2, and 3; adenovirus; and respiratory syncytial virus (RSV) by direct or indirect fluorescence assays or virus isolation and for human metapneumovirus (HMPV) by reverse transcription-polymerase chain reaction. Although a causal relationship still needs to be demonstrated by including a control group of healthy persons, detection of HBoV in respiratory tract specimens from patients with undiagnosed ARI suggests that this virus may be associated with respiratory illness. Most (89%) hospitalizations were in persons <5 years of age, which suggests that HBoV may cause more severe respiratory illness in infants and children, similar to disease caused by RSV (4, 5) , HMPV (6,7), human coronavirus NL63 (8) (9) (10) (11) (12) (13) (14) , and human coronavirus 229E (15) . cache = ./cache/cord-320286-9tumplp3.txt txt = ./txt/cord-320286-9tumplp3.txt === reduce.pl bib === id = cord-319675-mwy3t1ny author = Gu, Li title = Sustained Viremia and High Viral Load in Respiratory Tract Secretions Are Predictors for Death in Immunocompetent Adults with Adenovirus Pneumonia date = 2016-08-17 pages = extension = .txt mime = text/plain words = 3081 sentences = 164 flesch = 56 summary = At admission (on day 5–7 after illness onset), the patients in fatal cases presented higher initial viral loads in respiratory tract secretions (8.578 ± 2.115 vs 6.263 ± 1.225 Log(10) copies/ml, p = 0.023). Our results suggest that a higher initial viral load (10 8 copy/ml) in the respiratory tract samples on day 5-7 after disease onset is a predictor for fatal clinical outcome. In one case, as shown in Fig 2, even though the patient presented with a higher viral load (10 8.32 copies / ml) in tracheal aspiration, which may be associated fatal outcome, his clinical manifestation recovered gradually with a downward trend in the viral load in respiratory tract and whole blood samples. A higher initial viral load (10 8 copy/ml) in the respiratory tract on day 5-7 after disease onset and sustained viremia for 2 weeks or more may be associated with fatal clinical outcomes. cache = ./cache/cord-319675-mwy3t1ny.txt txt = ./txt/cord-319675-mwy3t1ny.txt === reduce.pl bib === id = cord-321756-a7eh4dkb author = Kwofie, Theophilus B title = Respiratory viruses in children hospitalized for acute lower respiratory tract infection in Ghana date = 2012-04-10 pages = extension = .txt mime = text/plain words = 3675 sentences = 204 flesch = 48 summary = The study was done to identify viruses associated with acute lower respiratory tract infection among children less than 5 years. Majority of acute lower respiratory tract infections (ALRTI) in developed countries have been reported to be often due to viral pathogens of which most common are RSV, PIV, influenza viruses, Adv, human Coronaviruses and Bocaviruses [5] [6] [7] . This study was done to determine the burden of respiratory viruses among children hospitalized at the Komfo Anokye Teaching Hospital for acute lower respiratory illness using the Real Time Polymerase Chain Reaction (RT-PCR). The overall prevalence is comparable to previous studies done in other developing countries [24] and the predominance of RSV is in accordance with the assertion that this virus is the single most frequent lower respiratory tract pathogen in infants and young children worldwide [25] [26] [27] . cache = ./cache/cord-321756-a7eh4dkb.txt txt = ./txt/cord-321756-a7eh4dkb.txt === reduce.pl bib === id = cord-319814-tyqb473m author = Zhang, Dingmei title = Epidemiology characteristics of respiratory viruses found in children and adults with respiratory tract infections in southern China date = 2014-06-11 pages = extension = .txt mime = text/plain words = 3480 sentences = 208 flesch = 51 summary = METHODS: In this work, a total of 14 237 nasopharyngeal swabs (14 237 patients from 25 hospitals) were analyzed, and seven respiratory viruses (influenza virus, respiratory syncytial virus, parainfluenza virus, adenovirus, human metapneumovirus, human coronavirus, human bocavirus) were detected using PCR/RT-PCR from nasopharyngeal swabs. Flu viruses were detected in 2632 specimens (18.50%), RSV in 1120 (7.86%), PIV in 494 (3.47%), ADV in 493 (3.47%), hMPV in 319 (2.24%), HCoV in 351 (2.47%), and HBoV in 180 (1.26%). A decline in the incidence of viral infections with age was observed for respiratory viruses, except for Flu. The detection rates of RSV, PIV, ADV, hMPV, HCoV, and HBoV among children ( 14 years) were higher than among adults (>14 years old). The total detection rates for the seven respiratory viruses in spring, summer, autumn, and winter were 44.31%, 41.15%, 41.66%, and 30.52%, respectively. cache = ./cache/cord-319814-tyqb473m.txt txt = ./txt/cord-319814-tyqb473m.txt === reduce.pl bib === id = cord-323066-tvguutak author = Praznik, Ajda title = Risk factors for bronchiolitis severity: A retrospective review of patients admitted to the university hospital from central region of Slovenia date = 2018-08-09 pages = extension = .txt mime = text/plain words = 3074 sentences = 178 flesch = 41 summary = METHODS: A retrospective chart review of all children <2 years old diagnosed with bronchiolitis at the University Medical Centre Ljubljana between May 2014 and April 2015, who were treated as outpatients (paediatric emergency department, PED group) or as inpatients in the standard hospital setting (WARD group) or in the paediatric intensive care unit (PICU group). 10 The objective of our study was to ascertain demographic characteristics, clinical findings and presumptive aetiologic agents (respiratory viruses demonstrated in nasopharyngeal swab) associated with bronchiolitis severity defined as length of hospitalization for >24 hours. Electronic medical records of patients included in the study were reviewed, and statistical analysis was performed for the following clinical and laboratory data: gender, chronological age at admission, prematurity (defined as birth before 37 weeks of gestation), birthweight, history of allergies, number of previous bronchiolitis episodes, clinical manifestations of bronchiolitis using the Wang Respiratory Score, 9 comorbidities (chronic lung disease, congenital heart disease, immune deficiency or neuromuscular diseases), body temperature at admission, treatment with bronchodilators, antibiotics or supplemental oxygen and respiratory virus detected in the nasopharyngeal swab. cache = ./cache/cord-323066-tvguutak.txt txt = ./txt/cord-323066-tvguutak.txt === reduce.pl bib === id = cord-323009-frej2qmb author = Nakouné, Emmanuel title = First introduction of pandemic influenza A/H1N1 and detection of respiratory viruses in pediatric patients in Central African Republic date = 2013-02-08 pages = extension = .txt mime = text/plain words = 2839 sentences = 149 flesch = 46 summary = FINDINGS: A prospective study was conducted in the Central African Republic (CAR) between January and December 2010 among infants and children aged 0–15 years attending sentinel sites for influenza-like illness or acute respiratory illness. The aim of the study reported here was to determine the circulation of 2009 pandemic influenza A/H1N1 virus (H1N1pdm09) by molecular methods and to identify the causative viruses, the incidence and the clinical features of acute respiratory illness among infants and young children at sentinel sites in Bangui and three rural areas. All infants and children aged between 0-15 years who attended sentinel sites in Bangui and three rural areas ( Figure 1 ) for influenza-like illness (ILI) or severe acute respiratory illness between January and December 2010 were included in the study (Figure 2A ). Abbreviations CAR: Central African Republic; ILI: Influenza-like illness; HRSV: Human respiratory syncytial virus; PIV: Parainfluenza viruses. cache = ./cache/cord-323009-frej2qmb.txt txt = ./txt/cord-323009-frej2qmb.txt === reduce.pl bib === id = cord-323551-22v2hn3v author = Galanti, M. title = Rates of asymptomatic respiratory virus infection across age groups date = 2019-04-15 pages = extension = .txt mime = text/plain words = 3120 sentences = 152 flesch = 39 summary = We enrolled 214 individuals at multiple New York City locations and tested weekly for respiratory viral pathogens, irrespective of symptom status, from fall 2016 to spring 2018. Here, we document rates of asymptomatic respiratory virus infection through a large-scale community study across multiple age groups. For the entire duration of the study, participants provided a daily report rating nine respiratory illness-related symptoms (fever, chills, muscle pain, watery eyes, runny nose, sneezing, sore throat, cough, chest pain), which were recorded on a Likert scale (0 = none, 1 = mild, 2 = moderate, 3 = severe). Pairwise comparisons between single infections and coinfections across all eight definitions showed that testing positive for multiple viruses was not associated with more severe symptoms. Figure 3 shows that while children were most frequently infected with a respiratory virus (they presented with the highest number of viral shedding events per season), they recorded (as reported by their parents) the lowest symptom scores on average. cache = ./cache/cord-323551-22v2hn3v.txt txt = ./txt/cord-323551-22v2hn3v.txt === reduce.pl bib === id = cord-322524-bq9ok8h1 author = Belongia, Edward A title = Clinical Features, Severity, and Incidence of RSV Illness During 12 Consecutive Seasons in a Community Cohort of Adults ≥60 Years Old date = 2018-11-27 pages = extension = .txt mime = text/plain words = 5184 sentences = 285 flesch = 45 summary = Studies conducted in the 1980s and 1990s first identified RSV as a cause of acute respiratory illness in a variety of adult populations, including older adults, working-age adults, hospitalized patients, and residents of long-term care facilities [5] [6] [7] [8] [9] . A 6-season study of adults ≥50 years old with predominantly outpatient acute respiratory illness found that RSV was the third most common viral pathogen (after influenza and human rhinovirus) [19] . The objective of this study was to describe the clinical characteristics, severity, clinical outcomes, and long-term incidence of medically attended RSV illness in a community cohort of adults ≥60 years of age from the 2004-2005 through 2015-2016 influenza seasons. Seasonal incidence of medically attended respiratory syncytial virus infection in a community cohort of adults ≥50 years old cache = ./cache/cord-322524-bq9ok8h1.txt txt = ./txt/cord-322524-bq9ok8h1.txt === reduce.pl bib === id = cord-324432-k0g3r1lw author = Maykowski, Philip title = Seasonality and clinical impact of human parainfluenza viruses date = 2018-08-29 pages = extension = .txt mime = text/plain words = 2340 sentences = 123 flesch = 41 summary = PATIENTS/METHODS: This retrospective study was performed from January 2013 to December 2015 in children and adults with HPIV, detected by multiplex reverse transcription polymerase chain reaction, participating in a community surveillance study of acute respiratory infections (ARIs) in New York City and patients admitted to a tertiary care center in the same neighborhood. The community cohort was derived from the Mobile Surveillance for Acute Respiratory Infections (ARIs) and Influenza-like Illness (ILI) in the Community (MoSAIC) study, a 5-year community-based surveillance ordinal logistic regression demonstrated that increased severity of illness was significantly associated with HPIV-4 and chronic cardiovascular and respiratory conditions in children and with age ≥65 years and chronic respiratory conditions in adults. epidemiology, parainfluenza, respiratory, seasonality, viruses F I G U R E 1 Flowcharts depicting the overall number of respiratory viral panel (RVP) tests ordered which yielded the final number of human parainfluenza virus (HPIV) types in the community cohort (1A) and in hospitalized patients (1B) study in New York City (NYC) that includes 250 households annually. cache = ./cache/cord-324432-k0g3r1lw.txt txt = ./txt/cord-324432-k0g3r1lw.txt === reduce.pl bib === id = cord-319877-izn315hb author = de Wit, Emmie title = SARS and MERS: recent insights into emerging coronaviruses date = 2016-06-27 pages = extension = .txt mime = text/plain words = 9387 sentences = 424 flesch = 43 summary = Scientific advancements since the 2002–2003 severe acute respiratory syndrome coronavirus (SARS-CoV) pandemic allowed for rapid progress in our understanding of the epidemiology and pathogenesis of MERS-CoV and the development of therapeutics. The downregulation of ACE2 results in the excessive production of angiotensin II by the related enzyme ACE, and it has been suggested that the stimulation of type 1a angiotensin II receptor and Middle East respiratory syndrome coronavirus (MERS-CoV) encode two large polyproteins, pp1a and pp1ab, which are proteolytically cleaved into 16 non-structural proteins (nsps), including papain-like protease (PLpro), 3C-like protease (3CLpro), RNA-dependent RNA polymerase (RdRp), helicase (Hel) and exonuclease (ExoN). Both severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) have developed mechanisms to interfere with these signalling pathways, as shown; these subversion strategies involve both structural proteins (membrane (M) and nucleocapsid (N)) and non-structural proteins (nsp1, nsp3b, nsp4a, nsp4b, nsp5, nsp6 and papain-like protease (PLpro); indicated in the figure by just their nsp numbers and letters). cache = ./cache/cord-319877-izn315hb.txt txt = ./txt/cord-319877-izn315hb.txt === reduce.pl bib === id = cord-324601-s3rgxtg6 author = Mhimbira, F. title = Prevalence and clinical significance of respiratory viruses and bacteria detected in tuberculosis patients compared to household contact controls in Tanzania: a cohort study date = 2019-01-31 pages = extension = .txt mime = text/plain words = 3260 sentences = 156 flesch = 43 summary = title: Prevalence and clinical significance of respiratory viruses and bacteria detected in tuberculosis patients compared to household contact controls in Tanzania: a cohort study We therefore studied the prevalence of respiratory pathogens in TB patients and household contact controls, and assessed the associations between both respiratory viruses and bacterial pathogens and the clinical presentation of TB patients who were prospectively recruited in an area of Dar es Salaam (Tanzania) with a high TB burden. Logistic regression models adjusting for age, sex, and HIV infection were used to assess the associations between respiratory pathogens and clinical presentations of TB at the time of recruitment among TB patients, with the following outcome variables: severe TB score (score of 6) versus mild (score of 1e5), high sputum bacterial load (sputum AFB smear microscopy of 2þ) versus low bacterial load, and presence versus absence of lung infiltrations and cavitations (chest x-ray findings). cache = ./cache/cord-324601-s3rgxtg6.txt txt = ./txt/cord-324601-s3rgxtg6.txt === reduce.pl bib === id = cord-325635-don9qjpz author = Turner, Paul title = Respiratory virus surveillance in hospitalised pneumonia patients on the Thailand-Myanmar border date = 2013-09-16 pages = extension = .txt mime = text/plain words = 4302 sentences = 236 flesch = 47 summary = Using global population data for 2005, for children under the age of five years, it was estimated that RSV was responsible for over 30 million episodes of lower respiratory tract infections (LRTI), with~3 million of these requiring hospital admission, and 66,000-199,000 deaths [7] . In 2007, the US Centers for Disease Control and Prevention (CDC) and the Shoklo Malaria Research Unit (SMRU) established a respiratory virus surveillance programme in the Burmese refugee population living in Maela camp, Northwest Thailand. Laboratory-enhanced surveillance has documented the contribution of respiratory viruses to 708 hospitalised clinical pneumonia episodes occurring in a crowded refugee camp on the Thailand-Myanmar border during April 2009 to September 2011. The results are broadly consistent with a similar surveillance programme conducted in two Kenyan refugee camps [22] , where 51.3% patients with severe acute respiratory infection (SARI) had at least one of adenovirus, hMPV, influenza A/B, parainfluenza virus 1-3, or RSV detected. cache = ./cache/cord-325635-don9qjpz.txt txt = ./txt/cord-325635-don9qjpz.txt === reduce.pl bib === id = cord-325783-pqonn0as author = Nicholls, John M title = Lung pathology of fatal severe acute respiratory syndrome date = 2003-05-24 pages = extension = .txt mime = text/plain words = 4022 sentences = 250 flesch = 49 summary = Methods Post-mortem tissue samples from six patients who died from SARS in February and March, 2003 , and an open lung biopsy from one of these patients were studied by histology and virology. Methods Post-mortem tissue samples from six patients who died from SARS in February and March, 2003 , and an open lung biopsy from one of these patients were studied by histology and virology. Since Nov 1, 2002 , an outbreak of severe acute respiratory syndrome (SARS) has affected 33 countries in five continents, with 7053 reported cases and 506 deaths at the time of writing. The case definition was fever (temperature 38°C or higher), cough or shortness of breath, new pulmonary infiltrates on chest radiograph, and either a history of exposure to a patient with SARS or a lack of response to empirical antimicrobial coverage for typical and atypical pneumonia (beta-lactams and macrolides, fluoroquinolones or tetracyclines). cache = ./cache/cord-325783-pqonn0as.txt txt = ./txt/cord-325783-pqonn0as.txt === reduce.pl bib === id = cord-324786-8k81jetq author = Chang, Anne B title = Antibiotics for bronchiectasis exacerbations in children: rationale and study protocol for a randomised placebo-controlled trial date = 2012-08-31 pages = extension = .txt mime = text/plain words = 5672 sentences = 298 flesch = 43 summary = Our study tests the hypothesis that both oral azithromycin and amoxicillin-clavulanic acid are superior to placebo at improving resolution rates of respiratory exacerbations by day 14 in children with bronchiectasis unrelated to cystic fibrosis. Our multicentre, double-blind RCT is designed to determine if azithromycin and amoxicillin-clavulanic acid, compared with placebo, improve symptom resolution on day 14 in children with acute respiratory exacerbations. Early and effective management of bronchiectasis exacerbations in children may lead to reduced hospitalisations, better quality of life (QOL) and improved future adult lung function. Our study tests the primary hypothesis that both oral azithromycin and amoxicillin-clavulanic acid are superior to placebo in improving the resolution rate of respiratory exacerbations by day 14 in children with non-CF bronchiectasis. We are conducting a multicentre, parallel group, double-blind placebo RCT (with concealed allocation) to assess the impact of treatment with antibiotics (azithromycin or amoxicillinclavulanic acid) in children with an exacerbation of bronchiectasis. cache = ./cache/cord-324786-8k81jetq.txt txt = ./txt/cord-324786-8k81jetq.txt === reduce.pl bib === id = cord-315598-qwh72inx author = Mendoza, Jose Luis Accini title = ACTUALIZACION DE LA DECLARACIÓN DE CONSENSO EN MEDICINA CRITICA PARA LA ATENCIÓN MULTIDISCIPLINARIA DEL PACIENTE CON SOSPECHA O CONFIRMACIÓN DIAGNÓSTICA DE COVID-19 date = 2020-10-06 pages = extension = .txt mime = text/plain words = 69640 sentences = 6489 flesch = 54 summary = De otorgarse un Consentimiento Informado amplio, éste debería ser única y exclusivamente para los procesos asociados con COVID-19".(71) AMCI ® Se recomienda considerar la transición del cuidado intensivo al cuidado paliativo en todo paciente con sospecha o diagnóstico de COVID-19 sin mejoría a pesar de las intervenciones óptimas, con empeoramiento progresivo de su pronóstico vital y ante un evidente deterioro; aplicando medidas generales en control de síntomas ( Manejo de secreciones -Tratamiento del dolor -Tratamiento de la disnea -Sedación paliativa), así como apoyo espiritual, siempre acompañando al paciente y nunca abandonarlo en el final de la vida. En cuanto hace referencia a la situación actual de pandemia por SARS-CoV-2 y compromiso pulmonar; Wu y cols, en Marzo de 2.020 realizaron un estudio retrospectivo de 201 pacientes con COVID-19 en China; para aquellos pacientes que desarrollaron SDRA, el tratamiento con metilprednisolona estuvo asociado con una disminución del riesgo de muerte (23/50 [46%] con esteroides vs 21/34 [62%] sin esteroides; HR, 0.38 [IC 95%, 0.20-0.72]), con las limitaciones de los estudios retrospectivo, de un solo centro, con un limitado número de pacientes (400). cache = ./cache/cord-315598-qwh72inx.txt txt = ./txt/cord-315598-qwh72inx.txt === reduce.pl bib === id = cord-324898-bjxpuqhr author = Lazzeri, Marta title = How Italian respiratory physiotherapists have faced and are facing the coronavirus disease 2019 pandemic date = 2020-08-03 pages = extension = .txt mime = text/plain words = 1620 sentences = 73 flesch = 34 summary = Where present, respiratory physiotherapists (RPh) made a great contribution by working together with other health professionals in assisting patients, providing "quick basic training sessions" about respiratory care for non-specialist healthcare professionals, locating and assessing all kinds of equipment (ventilators, interfaces, oxygen delivery systems, among others) to assist patients with respiratory failure and implementing early intervention with those patients in healthier conditions. Despite the absolute novelty of the pathology and the lack of scientific evidence, based on the available knowledge of physiopathology and respiratory care strategies, in collaboration with other scientific societies (Associazione Italiana Fisioterapisti -AIFI-, Associazione Italiana Pneumologi Ospedalieri -AIPO-, Società Italiana Pneumologia -SIP-, European Respiratory Society-ERS-), documents have been published in open-access journals and platform aimed to promote safe use of personal protective equipment (PPE) and to support the decision process in the management of COVID-19 patients in the acute and postacute phases [1] [2] [3] [4] . cache = ./cache/cord-324898-bjxpuqhr.txt txt = ./txt/cord-324898-bjxpuqhr.txt === reduce.pl bib === id = cord-324775-3x5os79m author = Crowe, J.E. title = Human Respiratory Viruses date = 2008-07-30 pages = extension = .txt mime = text/plain words = 5716 sentences = 300 flesch = 43 summary = Respiratory syncytial virus (RSV) is the most common pathogen, with hMPV, PIV-3, influenza viruses, and rhinoviruses accounting for the majority of the remainder of acute viral respiratory infections. Respiratory syncytial virus (RSV), parainfluenza viruses (PIVs), adenoviruses, and influenza viruses were identified initially as the most common causes of serious lower respiratory tract disease in infants and children. These patients also suffer more frequent and more severe disease including mortality with common respiratory viruses, including RSV, hMPV, PIV, influenza viruses, rhinoviruses, and adenoviruses. Enterovirus infections occur most commonly in the summer months in temperate areas, which differs from the season of many of the other most common respiratory viruses such as paramyxoviruses and influenza virus. Humans generally do not develop lifelong immunity to reinfection with these viruses; rather, specific immunity protects against severe and lower respiratory tract disease. Humans generally do not develop lifelong immunity to reinfection with these viruses; rather, specific immunity protects against severe and lower respiratory tract disease. cache = ./cache/cord-324775-3x5os79m.txt txt = ./txt/cord-324775-3x5os79m.txt === reduce.pl bib === id = cord-324843-r43u7sld author = Kockuzu, Esra title = Comprehensive Analysis of Severe Viral Infections of Respiratory Tract admitted to PICUs during the Winter Season in Turkey date = 2019-06-17 pages = extension = .txt mime = text/plain words = 3747 sentences = 239 flesch = 51 summary = OBJECTIVES: To analyze the course of seasonal viral infections of respiratory tract in patients hospitalized in pediatric intensive care units (PICU) of 16 centers in Turkey. The critical pH value related with mortality was ≤7.10, and critical PCO(2) ≥60 mm Hg. CONCLUSION: Our findings demonstrate that patients with neurological symptoms, tachycardia, hypoxia, hypotension, acidosis, impaired liver, and renal function at the time of admission exhibit more severe mortal progressions. By presenting the analyzed data of 302 PICU admissions, current study reveals severity of viral respiratory tract infections and release tips for handling them. 7 This retrospective observational study was conducted in order to analyze the course of seasonal viral infections of respiratory tract in patients hospitalized in PICUs of 16 centers representing the whole country. Viral respiratory tract infections constitute significant proportion of patients admitted to PICUs in winter, and these patients require advanced intensive care support with high mortality and morbidity rates. cache = ./cache/cord-324843-r43u7sld.txt txt = ./txt/cord-324843-r43u7sld.txt === reduce.pl bib === id = cord-327264-j0efi5vc author = Waterer, Grant title = Respiratory infections in the Asia‐Pacific region date = 2017-05-24 pages = extension = .txt mime = text/plain words = 557 sentences = 33 flesch = 52 summary = Lower respiratory tract infections remain the number one cause of death in the developing world. 1 In the developed world, lower respiratory tract infections are still the fifth leading cause of death. As well as host factors, it is the speed of adaptation of the pathogens that makes it most likely that we will not conquer death from respiratory infection any time soon. While some progress has been made in reducing pneumococcal disease with the newer conjugate vaccines, 2 there is evidence that the speed of adaptation (as measured by the proportion of strains not covered by the vaccines) is increasing. In this series on respiratory infections in Respirology, many of the above-mentioned challenges will be covered including the burden of disease due to respiratory pathogens (both acute and long-term), drug-resistant pathogens and newly emerging pathogens. cache = ./cache/cord-327264-j0efi5vc.txt txt = ./txt/cord-327264-j0efi5vc.txt === reduce.pl bib === id = cord-325611-tu1bn4hu author = Pérez-Sautu, Unai title = Target-independent high-throughput sequencing methods provide evidence that already known human viral pathogens play a main role in respiratory infections with unexplained etiology date = 2019-07-23 pages = extension = .txt mime = text/plain words = 5285 sentences = 259 flesch = 41 summary = We systematically collected samples from a prospective cohort of pediatric patients with respiratory infections, that returned negative results by validated molecular RT–PCR assays, and studied them with a target-independent, high-throughput sequencing-based approach. In this report, we performed a systematic study of respiratory specimens collected from a carefully characterized and highly representative, prospective cohort of pediatric cases suffering unexplained ARI, and we compared the rate of detection of pathogens by utilizing validated molecular assays, and a comprehensive sequence-independent, high-throughput sequencing-based analysis. In order to assess for the clinical relevance of the viral identifications made by HTS in the specimens collected from the unexplained cases of respiratory infections, a second cohort of age-matched healthy individuals from the same epidemiologic environment was also studied with the same methodology. Respiratory viral pathogens identified by target-agnostic HTS analysis and confirmed by contig-specific molecular assays in the respiratory specimens from the cases of respiratory infection and from the control group. cache = ./cache/cord-325611-tu1bn4hu.txt txt = ./txt/cord-325611-tu1bn4hu.txt === reduce.pl bib === id = cord-327493-v2iatbol author = Kwon, Hyo Jin title = Clinical manifestations of respiratory adenoviral infection among hospitalized children in Korea date = 2013-08-05 pages = extension = .txt mime = text/plain words = 2820 sentences = 190 flesch = 41 summary = BACKGROUND: The objective of our study was to understand the epidemiological and clinical features of respiratory adenoviral infections among children at a single institution over the course of several years. CONCLUSION: Our study demonstrates that respiratory adenovirus infections are an important cause of hospitalization in young children, and contribute to a significant morbidity. The study was performed to more fully characterize the epidemiological pattern, clinical features and complications associated with hospitalization for adenoviral infection in Korean children. Adenovirus was associated with a wide variety of diagnoses, ranging from upper respiratory tract infections (URTI) to severe pneumonia and encephalitis ( Table 1 ). 22 reported that 70% of hospitalized children with adenoviral infection had pneumonia, while our results revealed a significant proportion of patients (45.4%) with URTI. Lower respiratory tract infections due to adenovirus in hospitalized Korean children: epidemiology, clinical features, and prognosis cache = ./cache/cord-327493-v2iatbol.txt txt = ./txt/cord-327493-v2iatbol.txt === reduce.pl bib === id = cord-325830-mrtpihc7 author = Nelson, Philipp P. title = Current and Future Point-of-Care Tests for Emerging and New Respiratory Viruses and Future Perspectives date = 2020-04-29 pages = extension = .txt mime = text/plain words = 4974 sentences = 273 flesch = 46 summary = In this review, we summarize recently published characteristics of POCTs and discuss their implications for the treatment of RTIs. The second key aspect of this work is a description of new and innovative diagnostic techniques, ranging from biosensors to novel portable and current lab-based nucleic acid amplification methods with the potential future use in point-of-care settings. In this review, we summarize recently published characteristics of POCTs and discuss their implications for the treatment of RTIs. The second key aspect of this work is a description of new and innovative diagnostic techniques, ranging from biosensors to novel portable and current lab-based nucleic acid amplification methods with the potential future use in point-of-care settings. cache = ./cache/cord-325830-mrtpihc7.txt txt = ./txt/cord-325830-mrtpihc7.txt === reduce.pl bib === id = cord-326122-5m1727m1 author = Wishaupt, Jérôme O. title = PCR testing for Paediatric Acute Respiratory Tract Infections date = 2014-08-04 pages = extension = .txt mime = text/plain words = 4910 sentences = 259 flesch = 41 summary = The Pediatric Infectious Disease Society (PIDS) and the Infectious Diseases Society of America (IDSA) recommend in their guideline 'Community-Acquired Pneumonia (CAP) in Infants and Children' the use of sensitive and specific tests for the rapid diagnosis of influenza virus and other respiratory viruses in the evaluation of children older than three months of age with CAP [19] . In another recent retrospective study of 177 children with ARI in a general hospital, antibiotic management was not influenced after detecting a viral respiratory pathogen, although the authors state that routine testing of common respiratory pathogens could lead to a better understanding of their role in disease in children with respiratory symptoms [38] . Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children cache = ./cache/cord-326122-5m1727m1.txt txt = ./txt/cord-326122-5m1727m1.txt === reduce.pl bib === id = cord-324950-ux7shvji author = Saade, Georges title = Coinfections and their molecular consequences in the porcine respiratory tract date = 2020-06-16 pages = extension = .txt mime = text/plain words = 11744 sentences = 522 flesch = 36 summary = In pigs, the term "Porcine Respiratory Disease Complex" (PRDC) is often used to describe coinfections involving viruses such as swine Influenza A Virus (swIAV), Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), and Porcine CircoVirus type 2 (PCV2) as well as bacteria like Actinobacillus pleuropneumoniae, Mycoplasma hyopneumoniae and Bordetella bronchiseptica. The outcome of any coinfection or superinfection can be affected by the interactions taking place between the infectious agents, the nature of the cell/host, adverse environmental and management conditions, intestinal and respiratory microbiomes, and the triggered immune response-innate and adaptive-developed afterwards [2, 3] . It is well-known that viral infections can induce an ideal environment for a bacterial superinfection through different mechanisms such as the destruction of the epithelial barrier, the over-expression of the receptors involved in the bacterial adhesion to the cells, and the alteration of the host immune response [1, 2, 94, 95] . cache = ./cache/cord-324950-ux7shvji.txt txt = ./txt/cord-324950-ux7shvji.txt === reduce.pl bib === id = cord-328086-ji2emajn author = Zhou, Jie‐ying title = Human bocavirus and human metapneumovirus in hospitalized children with lower respiratory tract illness in Changsha, China date = 2018-01-11 pages = extension = .txt mime = text/plain words = 2099 sentences = 142 flesch = 48 summary = BACKGROUND: Lower respiratory tract illness is a major cause of morbidity and mortality in children worldwide, however, information about the epidemiological and clinical characteristics of LRTIs caused by HMPV and HBoV in China is limited. OBJECTIVES: Human bocavirus (HBoV) and human metapneumovirus (HMPV) are two important viruses for children with lower respiratory tract infections (LRTI). Clinical disease and viral load in children infected with respiratory syncytial virus or human metapneumovirus Clinical characteristics and viral load of respiratory syncytial virus and human metapneumovirus in children hospitaled for acute lower respiratory tract infection High viral load of human bocavirus correlates with duration of wheezing in children with severe lower respiratory tract infection High prevalence of human bocavirus detected in young children with severe acute lower respiratory tract disease by use of a standard PCR protocol and a novel real-time PCR protocol Clinical significance of different virus load of human bocavirus in patients with lower respiratory tract infection cache = ./cache/cord-328086-ji2emajn.txt txt = ./txt/cord-328086-ji2emajn.txt === reduce.pl bib === id = cord-326004-wg47sd06 author = Wilson, Patrick T title = Respiratory Pathogens in Children 1 Month to 5 Years of Age Presenting With Undifferentiated Acute Respiratory Distress in 2 District-Level Hospitals in Ghana date = 2018-09-03 pages = extension = .txt mime = text/plain words = 2193 sentences = 103 flesch = 48 summary = A recently conducted prospective randomized controlled trial at 2 district-level hospitals in Ghana revealed that the use of continuous positive airway pressure (CPAP) reduces the allcause mortality rate in children <1 year old who presented with undifferentiated acute respiratory distress [3] . In that study, nasopharyngeal swabs were collected from the children at the time of presentation and tested for common pediatric respiratory pathogens; the goal was to decrease the knowledge gap regarding the incidence of respiratory pathogens that affect children <5 years of age in low-and middle-income countries. In this report, we describe the respiratory pathogens detected in children aged 1 month to 5 years who presented to 1 of 2 district-level hospitals in Ghana with undifferentiated acute respiratory distress. Despite the limitations of this study, our results show that viral respiratory pathogens were frequent among children aged 1 month to 5 years who presented with acute respiratory distress to 1 of 2 district-level hospitals in Ghana. cache = ./cache/cord-326004-wg47sd06.txt txt = ./txt/cord-326004-wg47sd06.txt === reduce.pl bib === id = cord-327685-fymfqvp3 author = Channappanavar, Rudragouda title = Pathogenic human coronavirus infections: causes and consequences of cytokine storm and immunopathology date = 2017-05-02 pages = extension = .txt mime = text/plain words = 5834 sentences = 288 flesch = 33 summary = In contrast, highly pathogenic hCoVs such as severe acute respiratory syndrome CoV (SARS-CoV) and Middle East respiratory syndrome CoV (MERS-CoV) predominantly infect lower airways and cause fatal pneumonia. Severe pneumonia caused by pathogenic hCoVs is often associated with rapid virus replication, massive inflammatory cell infiltration and elevated pro-inflammatory cytokine/chemokine responses resulting in acute lung injury (ALI), and acute respiratory distress syndrome (ARDS). Although there is no direct evidence for the involvement of pro-inflammatory cytokines and chemokines in lung pathology during SARS and MERS, correlative evidence from patients with severe disease suggests a role for hyper-inflammatory responses in hCoV pathogenesis. Infection of non-human primates (NHPs) with SARS-CoV induced a dysregulated immune response resulting in increased disease severity in aged but not young NHPs, despite similar viral titers in the airways [67] . T cell responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-infected mice cache = ./cache/cord-327685-fymfqvp3.txt txt = ./txt/cord-327685-fymfqvp3.txt === reduce.pl bib === id = cord-329877-vish6v8e author = Lapinsky, Stephen E. title = ICU management of severe acute respiratory syndrome date = 2003-05-09 pages = extension = .txt mime = text/plain words = 2639 sentences = 149 flesch = 45 summary = BACKGROUND: Severe acute respiratory syndrome (SARS) is a contagious viral illness first recognized in late 2002. Severe acute respiratory syndrome (SARS) is a viral illness characterized by a syndrome of fever and respiratory symptoms that can progress to respiratory failure and death. This review describes the current state of knowledge of SARS, with particular reference to the management of the critically ill patient and the safety and protection of the ICU staff. Case definitions of SARS are currently based on the presence of epidemiological risk factors (close contact with SARS cases or travel to SARS "affected" areas) along with a combination of fever and respiratory symptoms, with or without hypoxia and/or chest radiographic changes [3] . Other high-risk procedures include obtaining nasopharyngeal swabs, bag-mask ventilation, intubation, suctioning, chest physiotherapy in nonintubated patients, nebulized drug therapy, noninvasive ventilation, and extubation (see Table 1 ). cache = ./cache/cord-329877-vish6v8e.txt txt = ./txt/cord-329877-vish6v8e.txt === reduce.pl bib === id = cord-328742-r4ht266w author = Heo, Jung Yeon title = Molecular Epidemiology of Human Adenovirus–Associated Febrile Respiratory Illness in Soldiers, South Korea(1) date = 2018-07-17 pages = extension = .txt mime = text/plain words = 3073 sentences = 165 flesch = 44 summary = During January 2013–April 2014, we subjected nasopharyngeal specimens collected from patients with acute febrile respiratory illness in a military hospital to PCR testing to detect 12 respiratory viruses and sequence a partial hexon gene for human adenovirus (HAdV) molecular typing. During January 2013-April 2014, we subjected nasopharyngeal specimens collected from patients with acute febrile respiratory illness in a military hospital to PCR testing to detect 12 respiratory viruses and sequence a partial hexon gene for human adenovirus (HAdV) molecular typing. HAdV is most prevalent in patients with acute lower respiratory tract infection and is the most common cause of pneumonia among military personnel in South Korea (12) . Thus, our study aimed to investigate the epidemiology of HAdV infections and to compare the clinical characteristics by type of HAdVs in soldiers in South Korea via hospital-based surveillance on viral respiratory infections. cache = ./cache/cord-328742-r4ht266w.txt txt = ./txt/cord-328742-r4ht266w.txt === reduce.pl bib === id = cord-333355-ykmp4ven author = Kuchar, E. title = Pathophysiology of Clinical Symptoms in Acute Viral Respiratory Tract Infections date = 2015-03-19 pages = extension = .txt mime = text/plain words = 6665 sentences = 370 flesch = 46 summary = In this article we discuss the pathophysiology of common symptoms of acute viral respiratory infections (e.g., sneezing, nasal discharge, sore throat, cough, muscle pains, malaise, and mood changes). The development of sneezing before coughing in patients with a common cold may be partly explained by the involvement of the upper airways first and the infection subsequent spread to the lower respiratory tract (Eccles 2005) . We focused on the most significant symptoms of acute viral respiratory infections: sneezing, nasal discharge and obstruction, sore throat, coughing, muscle pains, malaise and mood changes, fever, and febrile seizures in children. Macrophages play a key role in triggering an acute phase response with the production of cytokines (Beutler 2003) , while the release of proinflammatory cytokines and other mediators cause upper respiratory tract infection symptoms (Eccles 2000a, b) . cache = ./cache/cord-333355-ykmp4ven.txt txt = ./txt/cord-333355-ykmp4ven.txt === reduce.pl bib === id = cord-330343-p7a8chn4 author = Kelly-Cirino, Cassandra title = An updated roadmap for MERS-CoV research and product development: focus on diagnostics date = 2019-02-01 pages = extension = .txt mime = text/plain words = 5812 sentences = 274 flesch = 40 summary = ► Diagnostic research and development (R&D) needs to include point-of-care testing options, syndromic panels for differential diagnosis, a greater understanding of viral and antibody kinetics, improved access to clinical specimens, and establishment of international reference standards. Diagnostics play a central role in the early detection and control of outbreaks and can enable a more nuanced understanding of the disease kinetics and risk factors for the Middle East respiratory syndrome-coronavirus (MERS-CoV), one of the high-priority pathogens identified by the WHO. Diagnostics play a central role in the early detection and control of outbreaks and can enable a more nuanced understanding of the disease kinetics and risk factors for the Middle East respiratory syndrome-coronavirus (MERS-CoV), one of the high-priority pathogens identified by the WHO. In this review we identified sources for molecular and serological diagnostic tests used in MERS-CoV detection, case management and outbreak investigations, as well as surveillance for humans and animals (camels), and summarised the performance of currently available tests, diagnostic needs, and associated challenges for diagnostic test development and implementation. cache = ./cache/cord-330343-p7a8chn4.txt txt = ./txt/cord-330343-p7a8chn4.txt === reduce.pl bib === id = cord-326163-u8nh8cr3 author = van Benten, Inesz J. title = RSV‐induced bronchiolitis but not upper respiratory tract infection is accompanied by an increased nasal IL‐18 response date = 2003-08-18 pages = extension = .txt mime = text/plain words = 4379 sentences = 231 flesch = 46 summary = The aim of this study was to investigate potential differences in the local nasal immune response between bronchiolitis and upper respiratory tract infection induced by respiratory syncytial virus (RSV). This study investigated whether differences could be observed on the cellular level between the nasal immune responses of infants with RSV-induced bronchiolitis and RSV-induced upper respiratory tract infection. During the acute phase of bronchiolitis as well as during upper respiratory tract infection, there was a marked increase in the numbers of macrophages (CD68positive cells) in nasal brush samples compared with convalescent samples (Fig. 1A) . Most importantly, this study showed a striking difference in cytokine responses between both types of infection, i.e., an increase in the number of IL-18 positive cells in nasal brush samples during bronchiolitis. cache = ./cache/cord-326163-u8nh8cr3.txt txt = ./txt/cord-326163-u8nh8cr3.txt === reduce.pl bib === id = cord-330919-dep3v1pt author = Whyte, Claire S title = Fibrinolytic abnormalities in acute respiratory distress syndrome (ARDS) and versatility of thrombolytic drugs to treat COVID‐19 date = 2020-04-23 pages = extension = .txt mime = text/plain words = 4254 sentences = 251 flesch = 36 summary = The global pandemic of coronavirus disease 2019 (COVID‐19) is associated with the development of acute respiratory distress syndrome (ARDS), which requires ventilation in critically ill patients. Tissue factor (TF) is exposed on damaged alveolar endothelial cells and on the surface of leukocytes promoting fibrin deposition, while significantly elevated levels of plasminogen activator inhibitor 1 (PAI‐1) from lung epithelium and endothelial cells create a hypofibrinolytic state. In severe cases, patients with COVID-19 develop a type of acute respiratory distress syndrome (ARDS), sepsis and multiorgan failure. However, the principal fibrinolytic inhibitor described in the pathogenesis of ARDS is plasminogen activator inhibitor 1 (PAI-1), which is known to be elevated in severe acute respiratory syndrome coronavirus (SARS-CoV) and ALI [11, 61] . Tissue Plasminogen Activator (tPA) as a Novel Treatment for Refractory COVID-19 Associated Acute Respiratory Distress Syndrome (ARDS)? Activator (tPA) Treatment for COVID-19 Associated Acute Respiratory Distress Syndrome (ARDS): A Case Series cache = ./cache/cord-330919-dep3v1pt.txt txt = ./txt/cord-330919-dep3v1pt.txt === reduce.pl bib === id = cord-332055-lrpfzsog author = DeVos, Elizabeth title = Approach to Adult Patients with Acute Dyspnea date = 2015-11-27 pages = extension = .txt mime = text/plain words = 4415 sentences = 271 flesch = 45 summary = National and world organizations define asthma "by the history of respiratory symptoms such as wheeze, shortness of breath, chest tightness and cough that vary over time and in intensity, together with variable expiratory airflow limitation." 12 The reversibility of airflow obstruction is the hallmark distinguishing asthma from other obstructive respiratory disorders. In contrast, chronic obstructive pulmonary disease (COPD)/ emphysema is defined as "persistent airflow limitation that is usually progressive and associated with enhanced chronic inflammatory responses in the airways and the lungs." 12 These patients also frequently wheeze, but may have a different course of acute and chronic disease. Rapid evaluation by lung-cardiac inferior vena cava (LCI) integrated ultrasound for differentiating heart failure from pulmonary disease as the cause of acute dyspnea in the emergency setting Clinical policy: critical issues in the evaluation and management of adult patients presenting to the emergency department with acute heart failure syndromes cache = ./cache/cord-332055-lrpfzsog.txt txt = ./txt/cord-332055-lrpfzsog.txt === reduce.pl bib === id = cord-330079-pdaowkop author = Xu, Lin title = Surveillance and Genome Analysis of Human Bocavirus in Patients with Respiratory Infection in Guangzhou, China date = 2012-09-11 pages = extension = .txt mime = text/plain words = 4469 sentences = 205 flesch = 50 summary = To investigate the epidemiological and genetic variation of HBoV in Guangzhou, South China, we screened 3460 throat swab samples from 1686 children and 1774 adults with acute respiratory infection symptoms for HBoV between March 2010 and February 2011, and analyzed the complete genome sequence of 2 HBoV strains. In our current study, we screened throat swab specimens from patients with acute respiratory tract infection symptoms for HBoV and other common respiratory viruses over a 12-month period using polymerase chain reaction (PCR) methods, and in addition, the molecular phylogeny and complete genome sequences of 2 HBoV strains were also analyzed. Of the 3460 samples collected from patients with respiratory tract infection symptoms and signs enrolled in the study during the period between March 2010 and February 2011, detection for 7 viruses, namely, Influenza, PIV, RSV, HMPV, HCoV, AdV and HBoV, showed that 1275 (36.8%) were found positive for one single virus and 112 (3.2%) were infected by more than one virus. cache = ./cache/cord-330079-pdaowkop.txt txt = ./txt/cord-330079-pdaowkop.txt === reduce.pl bib === id = cord-329306-p5wmqmvj author = Kim, Kiwook title = Rhinovirus Associated Severe Respiratory Failure in Immunocompetent Adult Patient date = 2014-09-30 pages = extension = .txt mime = text/plain words = 1015 sentences = 64 flesch = 38 summary = Rhinovirus infection is typically associated with the common cold and has rarely been reported as a cause of severe pneumonia in immunocompetent adults. Rhinovirus infection can extend to lower respiratory tract in children [4] [5] [6] or immunocompromised hosts 7, 8 , but is generally not concerned as singular cause of severe pneumonia, especially in immunocompetent adults. Although technical advances have allowed for increased detection of viral pneumonia, viral infections other than influenza are generally not considered as causes of severe respiratory tract infection in immunocompetent hosts, because viral clearance usually occurs rapidly in healthy individuals. Therefore, it is still believed that severe viral pneumonia caused by frequently exposed rhinovirus could hardly occurs in immunocompetent adults. On the contrary, our relatively young immunocompetent patient suffered severe rhinovirus pneumonia without bacterial co-infection, which was confirmed by BAL fluid analysis, and not by the nasopharyngeal specimen. Rhinovirus associated with severe lower respiratory tract infections in children cache = ./cache/cord-329306-p5wmqmvj.txt txt = ./txt/cord-329306-p5wmqmvj.txt === reduce.pl bib === id = cord-336335-spap39b7 author = Silva, Denise R title = Respiratory viral infections and effects of meteorological parameters and air pollution in adults with respiratory symptoms admitted to the emergency room date = 2013-08-26 pages = extension = .txt mime = text/plain words = 4176 sentences = 244 flesch = 47 summary = OBJECTIVES: The objectives of this study were to determine the number of emergency visits for influenza-like illness (ILI) and severe acute respiratory infection (SARI) and to evaluate the association between ILI/SARI, RVI prevalence, and meteorological factors/air pollution, in the city of Porto Alegre, Brazil, from November 2008 to October 2010. The correlations among meteorological variables, air pollution, ILI/SARI cases, and respiratory viruses demonstrated the relevance of climate factors as significant underlying contributors to the prevalence of RVI. The aims of this study were to determine the number of emergency room visits for influenza-like illness (ILI) and severe acute respiratory infection (SARI) and to evaluate the association between ILI/SARI frequency, respiratory virus prevalence, and meteorological factors/air pollution, especially in adult population, in a humid subtropical climate. The data were analyzed using time-series analysis, through a generalized linear model (GLM) to examine the association between ILI or SARI and air pollution/meteorological variables, using logistic regression. cache = ./cache/cord-336335-spap39b7.txt txt = ./txt/cord-336335-spap39b7.txt === reduce.pl bib === id = cord-328829-yywxmioq author = Boixeda, Ramon title = Microbiological study of patients hospitalized for acute exacerbation of chronic obstructive pulmonary disease (AE-COPD) and the usefulness of analytical and clinical parameters in its identification (VIRAE study) date = 2012-05-25 pages = extension = .txt mime = text/plain words = 3823 sentences = 207 flesch = 41 summary = title: Microbiological study of patients hospitalized for acute exacerbation of chronic obstructive pulmonary disease (AE-COPD) and the usefulness of analytical and clinical parameters in its identification (VIRAE study) The etiology of the respiratory infection was studied by conventional sputum, paired serology tests for atypical bacteria, and viral diagnostic techniques (immunochromatography, immunofluorescence, cell culture, and molecular biology techniques). The aims of our study were to identify the etiology of respiratory infections in patients hospitalized for AE-COPD using different diagnostic tests and to evaluate the usefulness of the clinical and analytical parameters of the diagnostic process. Identification was made based on the respiratory infection and dyspnea admission diagnoses from the International Statistical Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) 19,20 (491, 492, 493, 496, 518.81, 464, 465, 466, 519.11, 786 .0), excluding the patients who had a known cause of respiratory failure that was different from infectious exacerbation (heart failure, pulmonary thromboembolism, pneumonia). cache = ./cache/cord-328829-yywxmioq.txt txt = ./txt/cord-328829-yywxmioq.txt === reduce.pl bib === id = cord-329263-o5e2go23 author = Kaplan, Nasser M. title = Molecular epidemiology and disease severity of respiratory syncytial virus in relation to other potential pathogens in children hospitalized with acute respiratory infection in Jordan date = 2007-11-26 pages = extension = .txt mime = text/plain words = 4170 sentences = 238 flesch = 51 summary = title: Molecular epidemiology and disease severity of respiratory syncytial virus in relation to other potential pathogens in children hospitalized with acute respiratory infection in Jordan Human respiratory syncytial virus (HRSV) is the major viral cause of acute lower respiratory tract infections in children. Human respiratory syncytial virus (HRSV) is the leading viral cause of acute respiratory infection in infants and young children in terms of prevalence and effect [Shay et al., 2001] . We also compared the disease severity of HRSV subgroups A and B and their associated genotypes in hospitalized Jordanian children set in the context of other potential respiratory pathogens. A total of 72/326 (22%) patients had no pathogens detected by PCR (Table I) , but 254 (78%) had at least one potential respiratory pathogen detected which consisted of 140/ 326 (43%) HRSV, 116/312 (37%) adenoviruses, 57/312 (18%) HBoV, 36/325 (11%) rhinovirus, 14/312 (4.5%) Chlamydia spp., 8/326 (2.5%) HMPV, 4/325 (1.2%) human coronavirus NL63, and 2/323 (0.6%) influenza A virus. cache = ./cache/cord-329263-o5e2go23.txt txt = ./txt/cord-329263-o5e2go23.txt === reduce.pl bib === id = cord-331228-wbd0s4fo author = Shehata, Mahmoud M. title = Middle East respiratory syndrome coronavirus: a comprehensive review date = 2016-01-20 pages = extension = .txt mime = text/plain words = 7512 sentences = 372 flesch = 46 summary = authors: Shehata, Mahmoud M.; Gomaa, Mokhtar R.; Ali, Mohamed A.; Kayali, Ghazi Role of the spike glycoprotein of human Middle East respiratory syndrome coronavirus (MERS-CoV) in virus entry and syncytia formation Middle East respiratory syndrome coronavirus (MERS-CoV)-Saudi Arabia Epidemiological, demographic, and clinical characteristics of 47 cases of Middle East respiratory syndrome coronavirus disease from Saudi Arabia: a descriptive study First cases of Middle East respiratory syndrome coronavirus (MERS-CoV) infections in France, investigations and implications for the prevention of human-to-human transmission Clinical features and viral diagnosis of two cases of infection with Middle East respiratory syndrome coronavirus: a report of nosocomial transmission Middle East respiratory syndrome coronavirus infection in dromedary camels in Saudi Arabia cache = ./cache/cord-331228-wbd0s4fo.txt txt = ./txt/cord-331228-wbd0s4fo.txt === reduce.pl bib === id = cord-331288-elnwn7l5 author = Grützmacher, Kim title = Human quarantine: Toward reducing infectious pressure on chimpanzees at the Taï Chimpanzee Project, Côte d'Ivoire date = 2017-01-17 pages = extension = .txt mime = text/plain words = 3690 sentences = 171 flesch = 44 summary = This study investigates the incidence of respiratory symptoms and human respiratory viruses in humans at a human‐great ape interface, the Taï Chimpanzee Project (TCP) in Côte d'Ivoire, and consequently, the effectiveness of a 5‐day quarantine designed to reduce the risk of potential exposure to human respiratory pathogens. This study investigates the incidence of respiratory symptoms and human respiratory viruses in humans at a human-great ape interface, the Taï Chimpanzee Project (TCP) in Côte d'Ivoire, and consequently, the effectiveness of a 5-day quarantine designed to reduce the risk of potential exposure to human respiratory pathogens. Furthermore, the risk of potential exposure to human pathogens is assessed by testing sick humans to detect common human respiratory viruses they brought to the habituation site, and by randomly testing apparently healthy humans in the beginning and at the end of quarantine to assess the possibility of excreting HRSV and HMPV, the two most relevant viruses for wild great apes. cache = ./cache/cord-331288-elnwn7l5.txt txt = ./txt/cord-331288-elnwn7l5.txt === reduce.pl bib === id = cord-325353-tx6s4ggu author = Restori, Katherine H. title = Neonatal Immunity, Respiratory Virus Infections, and the Development of Asthma date = 2018-06-04 pages = extension = .txt mime = text/plain words = 13653 sentences = 618 flesch = 42 summary = The goals of this review are (1) to outline the differences between the neonatal and adult immune systems and (2) to present murine and human data that support the hypothesis that early-life interactions between the immune system and respiratory viruses can create a lung environment conducive to the development of asthma. Because RSV, influenza, and RVs cause a large proportion of respiratorytract infections in neonates, we will focus primarily on these three pathogens as models to better understand how early-life infection and antiviral immune responses might contribute to the subsequent development of asthma. The addition of RSV infection of airway epithelial cells with production of the type-2 innate cytokines, IL-33 (138) , TSLP (123) , and IL-25 (128) , would, therefore, be predicted to create an even more exaggerated type-2-biased microenvironment in the lung with activation of other immune cells (e.g., M2 macrophages, DCs, and/or ILC2 cells) and the development of AHR. cache = ./cache/cord-325353-tx6s4ggu.txt txt = ./txt/cord-325353-tx6s4ggu.txt === reduce.pl bib === id = cord-328501-mbwgi56x author = Pang, Junxiong title = Risk factors for febrile respiratory illness and mono-viral infections in a semi-closed military environment: a case-control study date = 2015-07-25 pages = extension = .txt mime = text/plain words = 5767 sentences = 275 flesch = 46 summary = title: Risk factors for febrile respiratory illness and mono-viral infections in a semi-closed military environment: a case-control study CONCLUSION: Increasing age, smoker, recruit-camp, stay-out personnel with ill household members and stay-in personnel with ill bunkmates were independent risk factors of FRI in a semi-closed military environment. Previous documented risk factors of FRI in other countries included body mass index equal or greater than 25 kg/m 2 , previous respiratory tract infections [30] , overcrowding and closed units [29, [31] [32] [33] , presence of sand and dust storms, extreme temperature changes [34, 35] , smoking [36] , female, Navy service, poor latrine facilities, increasing age and higher rank [37] . Increasing age, smokers, recruit camp, stay-out personnel with ill household members and stay-in personnel with ill bunkmates were independent risk factors of FRI in a semi-closed military setting. Outbreak of febrile respiratory illness associated with adenovirus 11a infection in a Singapore military training cAMP cache = ./cache/cord-328501-mbwgi56x.txt txt = ./txt/cord-328501-mbwgi56x.txt === reduce.pl bib === id = cord-331520-o9e4qqn4 author = Kistler, Christine E. title = The Winter Respiratory Viral Season During the COVID-19 Pandemic date = 2020-10-26 pages = extension = .txt mime = text/plain words = 2724 sentences = 168 flesch = 44 summary = The winter respiratory virus season always poses challenges for long-term care settings; this winter, SARS-CoV-2 will compound the usual viral infection challenges. This special article discusses unique considerations that COVID-19 brings to the health and well-being of residents and staff in nursing homes and other long-term care settings this winter. Before the COVID-19 pandemic, influenza was the most concerning viral respiratory infection 27 for nursing home (NH) residents, with outbreaks requiring both treatment and prophylaxis, and 28 even causing some buildings to close to outsiders for brief periods of time. In 39 this special article, we discuss unique challenges that COVID-19 will bring to the health and 40 well-being of residents and staff in long-term care settings this winter. The winter respiratory virus season always poses challenges for long-term care settings, and 307 those challenges will be exacerbated with the second wave of COVID-19; as such, they present 308 numerous implications for practice, policy, and research. cache = ./cache/cord-331520-o9e4qqn4.txt txt = ./txt/cord-331520-o9e4qqn4.txt === reduce.pl bib === id = cord-331973-avjw4kx1 author = Das, Shubhagata title = Laboratory Diagnosis of Respiratory Tract Infections in Children – the State of the Art date = 2018-10-18 pages = extension = .txt mime = text/plain words = 5141 sentences = 228 flesch = 34 summary = Serological tests can successfully identify antibodies to most respiratory pathogens such as RSV, adenovirus, influenza A and B, parainfluenza 1-3 virus, etc., and can detect mixed infections from hospitalized children suffering from acute respiratory infections, with the exception of infants for whom an antibody response is usually undetected (Hall et al., 1991; Chkhaidze et al., 2006) . FA testing, in addition to RT-PCR, is useful for epidemiological studies as it increases the probability of identifying acute viral infections and has been used for accurate assessment of respiratory viruses other than influenza in children (Sawatwong et al., 2012; Feikin et al., 2013; Zhang et al., 2017) . Most of the studies evaluating the clinical performance of these assays have reported high sensitivity (87-100%) and specificity (>98%) for detecting influenza A/B and RSV in pediatric and adult patients (Bell et al., 2014; Nie et al., 2014; Popowitch and Miller, 2015; Gibson et al., 2017; Ling et al., 2018) . cache = ./cache/cord-331973-avjw4kx1.txt txt = ./txt/cord-331973-avjw4kx1.txt === reduce.pl bib === id = cord-335116-c83xyev5 author = Proença-Módena, José Luiz title = Respiratory viruses are continuously detected in children with chronic tonsillitis throughout the year date = 2014-07-21 pages = extension = .txt mime = text/plain words = 3637 sentences = 175 flesch = 38 summary = Methods: The fluctuations of respiratory virus detection were compared to the major climatic variables during a two-year period using adenoids and palatine tonsils from 172 children with adenotonsillar hypertrophy and clinical evidence of obstructive sleep apnoea syndrome or recurrent adenotonsillitis, without symptoms of acute respiratory infection (ARI), by TaqMan real-time PCR. Methods: The fluctuations of respiratory virus detection were compared to the major climatic variables during a two-year period using adenoids and palatine tonsils from 172 children with adenotonsillar hypertrophy and clinical evidence of obstructive sleep apnoea syndrome or recurrent adenotonsillitis, without symptoms of acute respiratory infection (ARI), by TaqMan real-time PCR. We have previously reported high rates of detection of respiratory virus genomes in tonsils and adenoids from patients with chronic adenotonsillar diseases, suggesting a significant association of viruses, particularly picornaviruses, with severe tonsillar hypertrophy [3] . cache = ./cache/cord-335116-c83xyev5.txt txt = ./txt/cord-335116-c83xyev5.txt === reduce.pl bib === id = cord-335567-ssnvr6nj author = Berry, Michael title = Identification of New Respiratory Viruses in the New Millennium date = 2015-03-06 pages = extension = .txt mime = text/plain words = 7477 sentences = 379 flesch = 40 summary = In 2001, this led to the discovery of human metapneumovirus (hMPV) and soon following that the outbreak of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) promoted an increased interest in coronavirology and the latter discovery of human coronavirus (HCoV) NL63 and HCoV-HKU1. Middle East Respiratory Syndrome coronavirus (MERS-CoV) represents the most recent outbreak of a completely novel respiratory virus, which occurred in Saudi Arabia in 2012 and presents a significant threat to human health. In recent years six new human respiratory viruses have been reported including human metapneumovirus (hMPV) [16] , bocavirus and four new human coronaviruses including Severe Acute Respiratory Syndrome coronavirus (SARS-CoV), human coronavirus NL63 (HCoV-NL63), HCoV-HKU1 and Middle East Respiratory Syndrome coronavirus (MERS-CoV). Evidence of a novel human coronavirus that is associated with respiratory tract disease in infants and young children Genetic variability of human coronavirus OC43-, 229E-, and NL63-like strains and their association with lower respiratory tract infections of hospitalized infants and immunocompromised patients cache = ./cache/cord-335567-ssnvr6nj.txt txt = ./txt/cord-335567-ssnvr6nj.txt === reduce.pl bib === id = cord-337747-7sb03moe author = Lagare, Adamou title = Molecular detection of respiratory pathogens among children aged younger than 5 years hospitalized with febrile acute respiratory infections: A prospective hospital‐based observational study in Niamey, Niger date = 2019-10-11 pages = extension = .txt mime = text/plain words = 2647 sentences = 140 flesch = 43 summary = title: Molecular detection of respiratory pathogens among children aged younger than 5 years hospitalized with febrile acute respiratory infections: A prospective hospital‐based observational study in Niamey, Niger This study aims to describe viral and bacterial infections among children aged younger than 5 years hospitalized with febrile ARI at two hospitals in Niamey, Niger's capital city, and the reported clinical procedures. 14 This study aims to describe the viral and bacterial infections among children aged younger than 5 years hospitalized with febrile ARI at two national hospitals of Niamey, the capital city of Niger, and the reported clinical procedures. In this 1-year prospective study, both viral and bacterial pathogens were detected in high proportion among hospitalized children aged younger than 5 years with febrile ARI in Niamey, Niger. Viral and bacterial etiology of severe acute respiratory illness among children < 5 years of age without influenza in Niger cache = ./cache/cord-337747-7sb03moe.txt txt = ./txt/cord-337747-7sb03moe.txt === reduce.pl bib === id = cord-332926-8hdkpkgz author = Meissner, H. Cody title = Bronchiolitis date = 2017-07-18 pages = extension = .txt mime = text/plain words = 3934 sentences = 246 flesch = 35 summary = During seasonal outbreaks of bronchiolitis from November through March in North America, respiratory syncytial virus (RSV) is identified as the etiologic agent in up to 80% of hospitalized children 7 (Table 33 .1). Unlike other respiratory viral infections, exposure to passive household tobacco smoke has not been associated with an increased risk of RSV hospitalization on a consistent basis. Most infants with bronchiolitis can be managed at home with supportive care, but concerns regarding increasing respiratory effort, apnea, or inability to feed adequately may precipitate hospitalization of a young child. Approximately 30% to 40% of RSV-infected infants experience progression of disease to the lower respiratory tract. Technical report: updated guidance for palivizumab prophylaxis among infants and young children at increased risk of hospitalization for respiratory syncytial virus infection Technical report: updated guidance for palivizumab prophylaxis among infants and young children at increased risk of hospitalization for respiratory syncytial virus infection cache = ./cache/cord-332926-8hdkpkgz.txt txt = ./txt/cord-332926-8hdkpkgz.txt === reduce.pl bib === id = cord-336420-1a2u9p4t author = Söderman, Martina title = Frequent Respiratory Viral Infections in Children with Febrile Neutropenia - A Prospective Follow-Up Study date = 2016-06-16 pages = extension = .txt mime = text/plain words = 4200 sentences = 208 flesch = 46 summary = title: Frequent Respiratory Viral Infections in Children with Febrile Neutropenia A Prospective Follow-Up Study Advances in molecular methods have increased the sensitivity of viral diagnostics tests, with recent studies reporting the detection of respiratory viruses in the nasopharynx in 44-57% of childhood febrile neutropenia episodes using real-time polymerase chain reaction (PCR) [3] [4] [5] 12] . Viral nucleic acids were extracted from the NPA with a MagAttract Virus Mini M48 kit (Qiagen, Sollentuna, Sweden) and analyzed with in-house real-time PCRs for the following 16 viruses: adenovirus (HAdV); bocavirus (HBoV); coronaviruses NL63/OC43/229E/HKU1 (HCoV); enterovirus (EV); influenza virus A, including A(H1N1)pdm09 and B (Flu); metapneumovirus (HMPV); parainfluenza viruses 1-3 (PIV); respiratory syncytial virus (RSV) and rhinovirus (RV) [19] . These results support the theory holding that there is a causal relationship between respiratory viral infections and episodes of febrile neutropenia, but proving this theory will require more longitudinal studies with asymptomatic neutropenic control cohorts. cache = ./cache/cord-336420-1a2u9p4t.txt txt = ./txt/cord-336420-1a2u9p4t.txt === reduce.pl bib === id = cord-335055-gzuug3p5 author = Kwiyolecha, Elizabeth title = Patterns of viral pathogens causing upper respiratory tract infections among symptomatic children in Mwanza, Tanzania date = 2020-10-28 pages = extension = .txt mime = text/plain words = 3311 sentences = 196 flesch = 45 summary = title: Patterns of viral pathogens causing upper respiratory tract infections among symptomatic children in Mwanza, Tanzania Therefore, there is a paramount need to establish information on the common etiologies of RTIs in Tanzania, the information that can stimulate further studies and possible control interventions including introduction of cheap and reliable methods to detect these pathogens in clinical settings. In addition due to increased use of antibiotic without a support of a diagnostic test in the treatment of URTI as observed in number of previous studies [11] [12] [13] , make the availability of epidemiological data on the patterns of etiology of URTI of paramount important. A cross sectional hospital based study involving 339 children aged 1-59 months presenting with RTI symptoms was conducted from October 2017 to February 2018 in the city of Mwanza, Tanzania. A previous study 33 , documented Rhinovirus to cause up to 25-85% of the upper respiratory tract infections. cache = ./cache/cord-335055-gzuug3p5.txt txt = ./txt/cord-335055-gzuug3p5.txt === reduce.pl bib === id = cord-337137-0ey40gzw author = Lo, Anthony WI title = How the SARS coronavirus causes disease: host or organism? date = 2005-12-17 pages = extension = .txt mime = text/plain words = 5201 sentences = 289 flesch = 45 summary = Published by John Wiley & Sons, Ltd. Severe acute respiratory syndrome (SARS) is a new viral disease caused by a novel coronavirus, SARS-CoV ( Figure 1 ) [1, 2] . Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for pathogenesis and virus transmission pathways Tissue and cellular tropism of the coronavirus associated with severe acute respiratory syndrome: an in-situ hybridization study of fatal cases Detection of severe acute respiratory syndrome-associated coronavirus in pneumocytes of the lung Immunohistochemical, in situ hybridization, and ultrastructural localization of SARS-associated coronavirus in lung of a fatal case of severe acute respiratory syndrome in Taiwan Retroviruses pseudotyped with the severe acute respiratory syndrome coronavirus spike protein efficiently infect cells expressing angiotensin-converting enzyme 2 The severe acute respiratory syndrome coronavirus 3a protein up-regulates expression of fibrinogen in lung epithelial cells Autoantibodies against human epithelial cells and endothelial cells after severe acute respiratory syndrome (SARS)-associated coronavirus infection cache = ./cache/cord-337137-0ey40gzw.txt txt = ./txt/cord-337137-0ey40gzw.txt === reduce.pl bib === id = cord-332361-pdoln3nr author = Khor, Chee-Sieng title = Epidemiology and seasonality of respiratory viral infections in hospitalized children in Kuala Lumpur, Malaysia: a retrospective study of 27 years date = 2012-03-20 pages = extension = .txt mime = text/plain words = 3806 sentences = 222 flesch = 45 summary = title: Epidemiology and seasonality of respiratory viral infections in hospitalized children in Kuala Lumpur, Malaysia: a retrospective study of 27 years CONCLUSION: Viral RTIs, particularly due to RSV, are commonly detected in respiratory samples from hospitalized children in Kuala Lumpur, Malaysia. In this study, we describe etiological agents, demographic details of patients, and seasonality (including association with meteorological factors) due to viral RTIs in a teaching hospital in Kuala Lumpur, over the last 27 years. Our findings support a previous local study carried out over a year, which showed that RSV was the most commonly detected respiratory virus, followed by parainfluenza viruses, influenza viruses and adenovirus [7] . Respiratory viral infections due to RSV, parainfluenza viruses, influenza viruses and adenovirus are significant causes of morbidity in hospitalized children in Kuala Lumpur, and are likely to be underdiagnosed. cache = ./cache/cord-332361-pdoln3nr.txt txt = ./txt/cord-332361-pdoln3nr.txt === reduce.pl bib === id = cord-339039-6gyo9rya author = Bonvehí, Pablo E. title = Transmission and Control of Respiratory Viral Infections in the Healthcare Setting date = 2018-04-30 pages = extension = .txt mime = text/plain words = 4737 sentences = 248 flesch = 37 summary = The purpose of this review is to describe the most frequent and relevant nosocomial viral respiratory infections, their mechanisms of transmission and the infection control measures to prevent their spread in the healthcare setting. RECENT FINDINGS: Although most mechanisms of transmission and control measures of nosocomial viral infections are already known, improved diagnostic tools allow better characterization of these infections and also lead to the discovery of new viruses such as the coronavirus, which is the cause of the Middle East Respiratory Syndrome, or the human bocavirus. Influenza virus can be transmitted through infectious droplets eliminated by patients when coughing or sneezing, or through direct contact with surfaces contaminated by respiratory secretions from symptomatic infected subjects (Table 1 ) [32] . Preventive measures to avoid adenovirus nosocomial infections include patient cohorting, reduction of visitors and contact and droplet precautions, along with the exclusion of infected healthcare workers from clinical duties (Table 2 ) [13, 36] . cache = ./cache/cord-339039-6gyo9rya.txt txt = ./txt/cord-339039-6gyo9rya.txt === reduce.pl bib === id = cord-333868-qrnsmhws author = Rothman, Richard E. title = Respiratory Hygiene in the Emergency Department date = 2006-08-23 pages = extension = .txt mime = text/plain words = 7437 sentences = 362 flesch = 35 summary = These agents are relatively uncommon, however, in most US EDs, and as recently as 2003, the Centers for Disease Control and Prevention (CDC) reported that health care facility environments are rarely implicated in respiratory pathogen transmission (except in cases of immunocompromised patients). All health care facilities should have policies and procedures in place for respiratory infection control practice with specific operational plans for handling a large influx of potentially infectious patients in the event of a significant outbreak. 3, 5, 16, 17, 39 Underscoring this is the findings from one epidemiologic outbreak of SARS in Toronto that found that 36% of new infections in the hospital occurred in health care workers, with the highest rates in those working in EDs and ICUs. 5 Both the World Health Organization and the CDC provide general recommendations for handling of patients with suspected respiratory infections that include having triage staff adhere to proper hand hygiene procedures and donning face masks and eye protection. cache = ./cache/cord-333868-qrnsmhws.txt txt = ./txt/cord-333868-qrnsmhws.txt === reduce.pl bib === id = cord-336562-5qmzne98 author = Auten, Richard title = Pediatric pulmonology year in review 2016: Part 2 date = 2017-04-25 pages = extension = .txt mime = text/plain words = 2535 sentences = 134 flesch = 40 summary = The ability to obtain tidal breathing measurements may lead to new insights into changes in chest and abdominal motion in pediatric respiratory disease. 47 Acute viral bronchiolitis, due to RSV and other pathogens, continues to have a major impact worldwide on childhood mortality and hospital admissions, 51 is associated with subsequent asthma and allergy risk, 52 and could be increasing in incidence. 57 Flores et al 58 conducted a randomized clinical trial comparing 3% hypertonic saline to normal saline in previously healthy infants hospitalized with mild-to-moderate acute viral bronchiolitis. Thus, the study does not support the use of nebulized hypertonic saline over normal saline in therapy of hospitalized children with mild-to-moderate acute viral bronchiolitis. Association between trafficrelated air pollution and asthma in preschool children in a national Japanese nested case-control study Changes in lung function measured by spirometry and the forced oscillation technique in cystic fibrosis patients undergoing treatment for respiratory tract exacerbation cache = ./cache/cord-336562-5qmzne98.txt txt = ./txt/cord-336562-5qmzne98.txt === reduce.pl bib === id = cord-333286-lr32e0w4 author = Lehtoranta, Liisa title = Role of Probiotics in Stimulating the Immune System in Viral Respiratory Tract Infections: A Narrative Review date = 2020-10-16 pages = extension = .txt mime = text/plain words = 6768 sentences = 338 flesch = 35 summary = We searched PubMed, Google Scholar, and Web of Knowledge for pre-clinical and clinical studies investigating the effect of probiotics on respiratory virus infections, immune response, and the course of upper and lower respiratory tract illness. Similar effects have been demonstrated in several mouse studies with the ability to reduce virus titers in lung tissues and modulation of antiviral and pro-inflammatory gene expression before and after viral infection. The upregulation of IFN response seems to prime cells for better resistance against virus infection as probiotics were shown effective in inhibiting the replication of various respiratory viruses, including influenza viruses and RSV. Similar effects have been demonstrated in mice with the ability of the probiotics to reduce virus titers in lung tissues and to modulate antiviral and pro-inflammatory gene expression before and after viral infection. Similar effects have been demonstrated in mice with the ability of the probiotics to reduce virus titers in lung tissues and to modulate antiviral and pro-inflammatory gene expression before and after viral infection. cache = ./cache/cord-333286-lr32e0w4.txt txt = ./txt/cord-333286-lr32e0w4.txt === reduce.pl bib === id = cord-335505-s013j5ex author = Zhang, Chen title = Viral Etiology and Clinical Profiles of Children with Severe Acute Respiratory Infections in China date = 2013-08-22 pages = extension = .txt mime = text/plain words = 3186 sentences = 173 flesch = 44 summary = BACKGROUND: No comprehensive analysis is available on the viral etiology and clinical characterization among children with severe acute respiratory infection (SARI) in China during 2009 H1N1 pandemic and post-pandemic period. The RVP Fast assay simultaneously detects the following viruses: respiratory syncytial virus (RSV); influenza(IFV) A (H1, H3, and H5) and B viruses; parainfluenza viruse (PIV) 1, 2, 3, and 4; human metapneumovirus (hMPV); adenovirus(ADV); piconavirus(PIC) which includes enterovirus (EV) and rhinovirus (RV); human coronaviruse(HCoV) NL63, HKU1, 229E, and OC43; and human bocavirus(BoCA). To find the reason that causes severe infection, we performed complete comparison between VSARI patients and the SARI, including clinical signs, number of viral target, gender, and age(Table 3, Figure 2B ). To find the association between virus infection and clinical signs in SARI, binary logistic regression was performed between 4 commonly diagnosed respiratory abnormality, including anhelation, respiratory failure, heart failure and pleural effusion, and the viral target detected by xTAG® RVP FAST. cache = ./cache/cord-335505-s013j5ex.txt txt = ./txt/cord-335505-s013j5ex.txt === reduce.pl bib === id = cord-336743-udokbcki author = Lilitsis, Emmanouil title = Inspiratory effort and breathing pattern change in response to varying the assist level: a physiological study date = 2020-06-10 pages = extension = .txt mime = text/plain words = 3436 sentences = 165 flesch = 46 summary = Setting the level of ventilator assist in everyday practice relies mostly on the clinical estimation of inspiratory effort, as indicated by the breathing pattern -tidal volume (VT) and respiratory rate (RR)-and clinical signs of respiratory distress (Boles et al., 2007; Hansen-Flaschen, 2000; Hess, 2001; Ray et al., 2006) . The aim of this study was to 1) characterize the responses of respiratory drive, respiratory effort, and breathing pattern to changing levels of ventilatory assist in critically ill patients and 2) assess if changes in respiratory rate may indicate changes in respiratory drive and effort. To this end, during proportional assist ventilation with adjustable gain factors (PAV+), noninvasive measurements of respiratory drive, effort (as indicated by inspiratory muscle pressure) were obtained at different levels of assist, using a validated prototype monitor (PVI) (Kondili et al., 2010; Younes et al., 2007) . cache = ./cache/cord-336743-udokbcki.txt txt = ./txt/cord-336743-udokbcki.txt === reduce.pl bib === id = cord-340104-6n0sn5lk author = Fagbo, Shamsudeen F. title = Acute viral respiratory infections among children in MERS‐endemic Riyadh, Saudi Arabia, 2012–2013 date = 2016-07-29 pages = extension = .txt mime = text/plain words = 3325 sentences = 194 flesch = 50 summary = This large study population determined the burden of respiratory viruses associated with ARI in children over a 2-year period a multiplex molecular testing platform. With over 60% of 2235 children testing positive for respiratory viruses, more infections were detected than previous studies [Akhter et al., 2009; Al Hajjar et al., 2011; Alanazi et al., 2013; Bukhari and Elhazmi, 2013] . This high rate was significantly different from that obtained in the present 2-year study (23% detection for RSV in children positive for respiratory viruses), as well as others [Alanazi et al., 2013; Amer et al., 2015] . Viruses associated with respiratory tract infections in children attending to the emergency room, king abdulaziz medical city, riyadh, Saudi Arabia Viral agents causing acute lower respiratory tract infections in hospitalized children at a tertiary care center in Saudi Arabia cache = ./cache/cord-340104-6n0sn5lk.txt txt = ./txt/cord-340104-6n0sn5lk.txt === reduce.pl bib === id = cord-342314-nx0a3nvd author = Gebru, Mu’uz title = Aerobic bacteriological studies on the respiratory tracts of apparently healthy and pneumonic camels (Camelus dromedaries) in selected districts of Afar Region, Ethiopia date = 2017-11-16 pages = extension = .txt mime = text/plain words = 5042 sentences = 284 flesch = 51 summary = title: Aerobic bacteriological studies on the respiratory tracts of apparently healthy and pneumonic camels (Camelus dromedaries) in selected districts of Afar Region, Ethiopia A cross-sectional study was conducted to isolate and identify bacterial species from the respiratory tract of apparently healthy and pneumonic camels in Asayita and Dubti woredas in the Afar Region, Ethiopia. There was a statistically significant association between the health status of the camels as well as the anatomical site studied with the isolation rates of the major respiratory pathogens (p < 0.05). Therefore, the present study was conducted to determine comparatively the bacterial species associated with camels with and without pneumonic lungs, identify the Streptococci spp. Besides, there was a statistically significant difference between pneumonic and apparently healthy camels with the isolation rate of the major respiratory pathogens (except B. The pathogenic bacteria isolated during the present study period are comparable to those previously reported from the respiratory tract of apparently healthy camels (Ahmed and Musa 2015) . cache = ./cache/cord-342314-nx0a3nvd.txt txt = ./txt/cord-342314-nx0a3nvd.txt === reduce.pl bib === id = cord-343074-dsubeaso author = Lee, Wan‐Ji title = Molecular epidemiology of a post‐influenza pandemic outbreak of acute respiratory infections in Korea caused by human adenovirus type 3 date = 2014-06-01 pages = extension = .txt mime = text/plain words = 3530 sentences = 183 flesch = 46 summary = title: Molecular epidemiology of a post‐influenza pandemic outbreak of acute respiratory infections in Korea caused by human adenovirus type 3 An outbreak of upper respiratory tract infections associated with human adenovirus (HAdV) occurred on a national scale in Korea from September to December 2010, following a major H1N1 influenza pandemic. To determine the principal cause of the outbreak, direct polymerase chain reaction (PCR) amplification followed by sequence analysis targeting parts of the hexon gene of HAdV was performed. Serotypes of 1,007 PCR‐diagnosed HAdV‐positive samples from patients with an acute upper respiratory tract illness were determined and epidemiological characteristics including major aged group and clinical symptoms were analyzed. Epidemiological and molecular data presented in this study confirmed that the outbreak in 2010 was not associated with genetic alterations causing a change in the pathology of the major causative agent, HAdV-3, nor with multiple infections with other respiratory viruses. cache = ./cache/cord-343074-dsubeaso.txt txt = ./txt/cord-343074-dsubeaso.txt === reduce.pl bib === id = cord-337562-pkejb0a9 author = Bialasiewicz, Seweryn title = Merkel Cell Polyomavirus DNA in Respiratory Specimens from Children and Adults date = 2009-03-17 pages = extension = .txt mime = text/plain words = 1738 sentences = 91 flesch = 55 summary = Merkel cell polyomavirus (MCPyV) DNA was detected in 7 (1.3%) of 526 respiratory tract samples from patients in Australia with upper or lower respiratory tract symptoms. Merkel cell polyomavirus (MCPyV) DNA was detected in 7 (1.3%) of 526 respiratory tract samples from patients in Australia with upper or lower respiratory tract symptoms. I n the past 2 years, several previously unknown human polyomaviruses (PyVs) have been identifi ed: KI virus (KIPyV) (1) and WU virus (WUPyV) (2) from respiratory samples, and more recently, Merkel cell polyomavirus (MCPyV), most commonly from Merkel cell carcinoma tissue (3) . The presence of MCPyV in samples positive by real-time PCR was then confi rmed by using partial large T antigen (LT3) and major capsid protein (VP1) conventional MCPyV detection PCR assays of Feng et al. Sequence data from positive specimens indicate that MCPyV found in respiratory secretions is similar to the viruses identifi ed within Merkel cell carcinomas. cache = ./cache/cord-337562-pkejb0a9.txt txt = ./txt/cord-337562-pkejb0a9.txt === reduce.pl bib === id = cord-339009-wcoch07b author = File, Thomas M. title = Severe Acute Respiratory Syndrome: Pertinent Clinical Characteristics and Therapy date = 2012-08-23 pages = extension = .txt mime = text/plain words = 6023 sentences = 324 flesch = 50 summary = Because the causative agent of SARS is • one or more clinical findings of respiratory illness (e.g. cough, contagious, preventative measures focus on avoidance of exposhortness of breath, difficulty in breathing, or hypoxia) sure, and infection control strategies for suspected patients and • travel within 10 days of onset of symptoms to an area with contacts. [12] Of the reported cases was updated to include laboratory criteria for evidence of infection 64% were from China, 19% from Hong Kong, 8% from Taiwan, with the SARS-associated coronavirus (SARS-CoV). Algorithm for evaluating and managing patients requiring hospitalization for radiographically confirmed pneumonia, in the absence of person-toperson transmission of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) anywhere in the world. cache = ./cache/cord-339009-wcoch07b.txt txt = ./txt/cord-339009-wcoch07b.txt === reduce.pl bib === id = cord-333026-9f6ecg30 author = Kompanikova, J. title = Microbiologic Methods in the Diagnostics of Upper Respiratory Tract Pathogens date = 2017-03-03 pages = extension = .txt mime = text/plain words = 1784 sentences = 100 flesch = 49 summary = Blood samples were simultaneously examined by the enzyme-linked immunosorbent assay (ELISA) and by the FilmArray Respiratory Panel for eight different pathogens in a total of 15 tests performed in nasopharyngeal swabs. Nonetheless, since most repiratory tract infections are viral in origin and there is no treatment available, the diagnosis provided by the FilmArray Panel does not provide any additional clinical benefit and thus should be used only whenever necessary on the individual basis. This method allows for identification of 21 different respiratory pathogens from a nasopharyngeal swab, 18 of viral etiology and three of bacterial origin (Idaho Technology 2007). The laboratory costs to run one examination with different methods showed that the FilmArray multiplex PCR respiratory panel is more expensive than the ELISA, HIT, and the cultivation. Since most URIs are viral in origin and there is no treatment available, the diagnosis provided by the FilmArray panel is not always necessary and the method should be used on an individual basis when clinically justified. cache = ./cache/cord-333026-9f6ecg30.txt txt = ./txt/cord-333026-9f6ecg30.txt === reduce.pl bib === id = cord-342476-0rupk21u author = van Rijn, Anneloes L. title = The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease date = 2019-10-24 pages = extension = .txt mime = text/plain words = 4036 sentences = 220 flesch = 44 summary = The sensitivity, specificity and predictive values of mNGS were calculated based on 24 PCR positive and 1120 PCR negative target results of 88 samples and the normalized read counts (Table 5 ). The following markers were tested for potential associations with clinical severity of exacerbation (exacerbation severity, self-reported exacerbation severity), length of exacerbation and a decrease/increase in FEV 1 (control visit compared to baseline): mNGS pathogen positive versus negative exacerbation (qPCR targets), the number of normalized reads (log, cutoff of �5normalized reads) for the different target viruses (species level). The Shannon diversity scores for bacteriophages (normalized reads, cut-off of �5normalized reads) were comparable for COPD exacerbations of viral aetiology in PCR positive versus negative patients (Fig 5) . In this study, the respiratory virome in patients with COPD exacerbations was analysed with both mNGS and qPCR, and combined with clinical data. cache = ./cache/cord-342476-0rupk21u.txt txt = ./txt/cord-342476-0rupk21u.txt === reduce.pl bib === id = cord-339852-9rq7zzqs author = Theamboonlers, Apiradee title = Human Coronavirus Infection among Children with Acute Lower Respiratory Tract Infection in Thailand date = 2006-11-30 pages = extension = .txt mime = text/plain words = 2949 sentences = 169 flesch = 50 summary = In addition, we performed this study in order to delineate the prevalence, the potential clinical impacts and evaluation of the genetic characterization of this pathogen in young children who presented with acute lower respiratory tract infections (ALRI). In this study we applied molecular biology techniques to identify hCoV in nasopharyngeal secretions (NPs) for the study on the prevalence of molecular characterization and clinical correlation of coronavirus infections in hospitalized infants and young children with acute lower respiratory tract infection (ALRI). In this study, we have identifi ed human coronavirus hCoV-OC43 and hCoV-229E infection in infants and young children presenting with ALRI. hCoV-229E and hCoV-OC43 have previously been proven responsible for infecting people of all age groups and causing severe lower respiratory tract infection primarily in frail patients such as young children and elderly individuals [17] [18] [19] . The clinical features associated with coronavirus infection appear to be similar to those observed with other respiratory viruses, such as RSV, parainfl uenza virus and human metapneumovirus. cache = ./cache/cord-339852-9rq7zzqs.txt txt = ./txt/cord-339852-9rq7zzqs.txt === reduce.pl bib === id = cord-342133-khrljehj author = Principi, Nicola title = Bocavirus Infection in Otherwise Healthy Children with Respiratory Disease date = 2015-08-12 pages = extension = .txt mime = text/plain words = 5116 sentences = 243 flesch = 49 summary = To evaluate the role of human bocavirus (hBoV) as a causative agent of respiratory disease, the importance of the viral load in respiratory disease type and severity and the pathogenicity of the different hBoV species, we studied all hBoV-positive nasopharyngeal samples collected from children who attended an emergency room for a respiratory tract infection during three winters (2009–2010, 2011–2012, and 2013–2014). To evaluate the circulation of the different hBoV types and the possible relationships between viral load, virus genetic characteristics, and the severity of infection, nasopharyngeal swabs were collected from otherwise healthy children attending the emergency room of the Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Italy, due to a respiratory tract infection arising between November 1 and March 31 during 3 winters (2009-2010, 2011-2012, and 2013-2014) . Single detection of human bocavirus 1 with a high viral load in severe respiratory tract infections in previously healthy children cache = ./cache/cord-342133-khrljehj.txt txt = ./txt/cord-342133-khrljehj.txt === reduce.pl bib === id = cord-339386-sxyeuiw1 author = McIntosh, Kenneth title = 157 Coronaviruses, Including Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) date = 2015-12-31 pages = extension = .txt mime = text/plain words = 8499 sentences = 482 flesch = 49 summary = The virus was quickly identified as a new CoV most closely related to several bat CoVs. 6 This report was followed by a number of other reports identifying a total of 537 infected individuals, all of whom had acute respiratory symptoms, severe in most, and fatal in 145 (as of May 11, 2014) . 6 Between then and May 2014, a total of 537 cases occurred, all infected by this virus, now termed the Middle East respiratory syndrome coronavirus (MERS-CoV). In response to the global spread and associated severe disease, the World Health Organization coordinated a rapid and effective control program that included isolation of cases, careful attention to contact, droplet and airborne infection control procedures, quarantine of exposed persons in some settings, and efforts to control spread between countries through travel advisories and travel alerts. cache = ./cache/cord-339386-sxyeuiw1.txt txt = ./txt/cord-339386-sxyeuiw1.txt === reduce.pl bib === id = cord-339869-euikj8fv author = Cebey-López, Miriam title = Does Viral Co-Infection Influence the Severity of Acute Respiratory Infection in Children? date = 2016-04-20 pages = extension = .txt mime = text/plain words = 3325 sentences = 201 flesch = 40 summary = However, bacterial superinfection was associated with increased severity (OR: 4.356; P-value = 0.005), PICU admission (OR: 3.342; P-value = 0.006), higher clinical score (1.988; P-value = 0.002) respiratory support requirement (OR: 7.484; P-value < 0.001) and longer hospital length of stay (OR: 1.468; P-value < 0.001). However, bacterial superinfection was associated with increased severity (OR: 4.356; P-value = 0.005), PICU admission (OR: 3.342; P-value = 0.006), higher clinical score (1.988; P-value = 0.002) respiratory Introduction Molecular techniques including polymerase chain reaction (PCR) have increased the sensitivity of detection for common and emerging respiratory viruses, and often reveal the presence of more than one pathogen in respiratory patients. Our study aims to analyze the relationship between viral or bacterial co-infection detected by molecular methods, and the clinical phenotype of children admitted to hospital with lower tract acute respiratory infections (LT-ARI). PICU admission, disease severity according to different scales, need for respiratory support, and length of hospital stay followed a similar pattern in viral mono-versus co-infected children. cache = ./cache/cord-339869-euikj8fv.txt txt = ./txt/cord-339869-euikj8fv.txt === reduce.pl bib === id = cord-340811-w4x4falm author = Frizzelli, Annalisa title = What happens to people’s lungs when they get coronavirus disease 2019? date = 2020-05-11 pages = extension = .txt mime = text/plain words = 1779 sentences = 106 flesch = 46 summary = Search terms include novel coronavirus pneumonia, severe acute respiratory syndrome coronavirus 2, coronavirus and ventilation. Interestingly, patients with COVID-19 pneumonia may present an atypical form of ARDS characterized by a dissociation between their relatively preserved lung mechanics and the severity of hypoxemia (23) . Oxygen therapy should be considered immediately when patients affected by severe acute respiratory infection have the following conditions: hypoxemia (PaO2 <60 mmHg or SpO 2 <93% when breathing air); respiratory distress (respiratory frequency> 24 times/min); hypotension (systolic blood pressure <100 mmHg) (24) . Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study cache = ./cache/cord-340811-w4x4falm.txt txt = ./txt/cord-340811-w4x4falm.txt === reduce.pl bib === id = cord-340280-m1j6v33y author = Jeon, Jae‐Hyun title = Incidence and seasonality of respiratory viruses causing acute respiratory infections in the Northern United Arab Emirates date = 2019-04-07 pages = extension = .txt mime = text/plain words = 2983 sentences = 179 flesch = 47 summary = OBJECTIVES: This study was designed to describe the molecular epidemiology and seasonality of acute respiratory infection (ARI)‐related respiratory viruses in the United Arab Emirates (UAE). 1, 5, 9 Contrary to the accumulating knowledge of ARIs in temperate regions, epidemiological research on acute respiratory viral illness in tropical and subtropical areas is limited, although the epidemiological diversity, according to local climate and latitude, has been well studied. 14 Our study was designed to describe the molecular epidemiology of ARI-related respiratory viruses, including the seasonality of the viruses in the northern UAE for over 2 years. 2, 24, 25 FLU was the most common respiratory virus in all age groups, and the positivity rate was 20.0%, which is similar to previous data reported from studies in Oman. 7,34 However, our data suggest that in the UAE, like in other temperate countries, a diverse set of respiratory viruses contribute to the ARI cases that compel patients to visit medical facilities, because of their severity. cache = ./cache/cord-340280-m1j6v33y.txt txt = ./txt/cord-340280-m1j6v33y.txt === reduce.pl bib === id = cord-343365-4y9fedcr author = Chang, Christopher title = Unmet Needs in Respiratory Diseases: “You Can’t Know Where You Are Going Until You Know Where You Have Been”—Anonymous date = 2013-11-30 pages = extension = .txt mime = text/plain words = 7295 sentences = 407 flesch = 50 summary = The promise of gene therapy as a cure for the disease has fizzled out, and while new antimicrobials and other pharmaceuticals promise improved longevity and better quality of life, the average life span of a patient with cystic fibrosis is still at about 35 years. Several significant challenge areas include the diagnosis and treatment of certain specific infectious lung diseases, including viral lower respiratory infections caused by respiratory syncytial virus, rhinovirus, metapneumovirus, coronovirus, and enterovirus. The search for a vaccine for respiratory syncytial virus (RSV) has been ongoing for many years, but like the previous case of gene therapy in cystic fibrosis, this also has been a challenge to achieve. The current global strategies for the development of an RSV vaccine now target four areas: infants <6 months of age; infants >6 months of age and young children; pregnant women for whom passive immunization can be implemented; and the elderly, in whom RSV can also have significant morbidity [52] [53] [54] . cache = ./cache/cord-343365-4y9fedcr.txt txt = ./txt/cord-343365-4y9fedcr.txt === reduce.pl bib === id = cord-342993-deuytbml author = Maffey, Alberto F. title = Viruses and atypical bacteria associated with asthma exacerbations in hospitalized children date = 2010-05-06 pages = extension = .txt mime = text/plain words = 3285 sentences = 167 flesch = 47 summary = 3 Various viral agents, including the respiratory syncytial virus (HRSV), influenza A and B (FLUAV and FLUBV), parainfluenza (HPIV), adenovirus (HAdV), rhinovirus (HRV), enterovirus (HEV), coronavirus (HCoV), and the recently described metapneumovirus (HMPV) 4 and bocavirus (HBoV) 5 have been detected in patients presenting with asthma exacerbation. [10] [11] We performed a cross-sectional study to determine by means of immunofluorescence assay (IFA) and molecular techniques the prevalence of traditional and newly described respiratory viruses and atypical bacteria in children hospitalized due to an acute asthma exacerbation in Buenos Aires, a temperate southern hemisphere city. [30] [31] In conclusion, the present study confirms the high prevalence of respiratory viruses in hospitalized children with an acute asthma exacerbation, highlights the importance both of HRSV and HRV in all age groups, and describes their seasonal pattern in a temperate Southern Hemisphere location. cache = ./cache/cord-342993-deuytbml.txt txt = ./txt/cord-342993-deuytbml.txt === reduce.pl bib === id = cord-342915-r9kv67we author = Hayden, Frederick G. title = Advances in antivirals for non‐influenza respiratory virus infections date = 2013-11-01 pages = extension = .txt mime = text/plain words = 5748 sentences = 281 flesch = 33 summary = Most of the treatment data regarding antivirals for non-influenza respiratory viruses have been derived from observational studies in immunocompromised hosts, and sometimes, infants, but recent randomized, controlled trials in specific target populations have helped to address the potential value of antiviral interventions. 12, [17] [18] [19] In addition, systematic reviews of the observational reports concluded that the common use of multiple agents in combination, varying dose regimens, paucity of studies with systematic data collection, complications from immunosuppressive therapy, and the lack of randomized, controlled trials meant that existing data were inconclusive with regard to putative antivirals and thus inadequate to determine appropriate management of SARS infections. In addition, one approved agent for selected parasitic infections, oral nitazoxanide, may have interferon-inducing properties, is inhibitory for various respiratory viruses including influenza and a canine CoV in vitro, 32 and has shown promising dose-related activity in a phase 2, placebo-controlled, randomized trial in treating uncomplicated influenza 33 Consequently, nitazoxanide would be an interesting agent to test alone and in combination with other antivirals for CoV infections. cache = ./cache/cord-342915-r9kv67we.txt txt = ./txt/cord-342915-r9kv67we.txt === reduce.pl bib === id = cord-343042-9mue4eiv author = Bertozzi, Giuseppe title = Mistrial or Misdiagnosis: The Importance of Autopsy and Histopathological Examination in Cases of Sudden Infant Bronchiolitis-Related Death date = 2020-05-27 pages = extension = .txt mime = text/plain words = 2451 sentences = 117 flesch = 38 summary = Following these complaints, the autopsy was performed, and subsequent histological examinations revealed the presence of typical and pathognomonic histological findings of acute viral bronchiolitis, whose morphological appearance is poorly reported in the literature. For all these reasons, the autopsy, either clinical or medicolegal, is mandatory in cases of sudden unexpected infant death to manage claim requests because only the histological examinations performed on samples collected during the autopsy can reveal the real cause of death. In fact, in the reported case studies, histopathologic diagnostics identified pathognomonic signs of acute bronchiolitis characterized by edema, congestion, leukocytic infiltration in the bronchiolar wall, leukocytes in the peribronchial interstitial pulmonary space, allowing the identification of the exact cause of death. The analysis of the presented cases shows that the autopsy is mandatory in SUID occurrence, in which the absence of anamnestic data and/or acute clinical signs does not allow to identify the cause of death. cache = ./cache/cord-343042-9mue4eiv.txt txt = ./txt/cord-343042-9mue4eiv.txt === reduce.pl bib === id = cord-345211-4ivqlsgt author = Murdoch, David R. title = How recent advances in molecular tests could impact the diagnosis of pneumonia date = 2016-03-07 pages = extension = .txt mime = text/plain words = 5994 sentences = 295 flesch = 35 summary = Guidelines for the management of community-acquired pneumonia in children are even more restrictive, again recommending that tests should mainly be used on patients with severe disease, with a focus on blood cultures and detection of respiratory viruses [11, 12] . While not exactly new (polymerase chain reaction (PCR) assays for respiratory pathogens have been around for over 20 years), the widespread adoption of nucleic acid detection tests (NATs) by diagnostic laboratories has been relatively slow. The NATs that are most widely used in diagnostic laboratories are those that detect potential pneumonia pathogens that are not part of the normal flora, namely respiratory viruses and selected non-colonizing bacteria. Quantitative multiplex PCR has been used to determine the etiology of community-acquired pneumonia in adults using cutoffs developed for interpretation of culture results from lower respiratory tract specimens [85, 86] . cache = ./cache/cord-345211-4ivqlsgt.txt txt = ./txt/cord-345211-4ivqlsgt.txt === reduce.pl bib === id = cord-343050-1pfqgvie author = Huang, Qiu Sue title = Southern Hemisphere Influenza and Vaccine Effectiveness Research and Surveillance date = 2015-06-09 pages = extension = .txt mime = text/plain words = 6054 sentences = 281 flesch = 29 summary = The results during the first 2 years (2012-2013) provided scientific evidence to (a) support a change to NZ's vaccination policy for young children due to high influenza hospitalizations in these children; (b) contribute to the revision of the World Health Organization's case definition for severe acute respiratory illness for global influenza surveillance; and (c) contribute in part to vaccine strain selection using vaccine effectiveness assessment in the prevention of influenza-related consultations and hospitalizations. Over 5 years, we hope this project will shed more light on the burden of influenza and other respiratory pathogens in our study population and subgroups and estimate key epidemiologic parameters such as relative rates of infection, clinical disease, general practice visits and hospitalizations as well as risk factors for illness, effectiveness of vaccination, mechanisms of immunity and monitoring for new influenza viruses with pandemic potential such as A(H7N9) and other emerging viruses (e.g. MERS-CoV) and provide a framework for timely assessment of severity which is essential in an event of emergence of these pathogens. cache = ./cache/cord-343050-1pfqgvie.txt txt = ./txt/cord-343050-1pfqgvie.txt === reduce.pl bib === id = cord-342649-ysossker author = Scagnolari, Carolina title = Evaluation of viral load in infants hospitalized with bronchiolitis caused by respiratory syncytial virus date = 2012-03-10 pages = extension = .txt mime = text/plain words = 3759 sentences = 161 flesch = 42 summary = The relationship between viral load, disease severity and antiviral immune activation in infants suffering from respiratory syncytial virus (RSV)-associated bronchiolitis has not been well identified. The main objective of this study was to determine the existence of a correlation between RSV load and disease severity and also between different clinical markers and mRNA levels of the interferon stimulated gene (ISG)56 in infants hospitalized for bronchiolitis. Results indicated that viral load was positively related to the clinical severity of bronchiolitis, the length of hospital stay, the levels of glycemia and the relative gene expression of ISG56, whereas an inverse correlation was observed with the levels of hemoglobin. In the framework of a study aimed at understanding the pathogenesis of RSV infection and at further characterizing viral and host factors involved in determining the severity of bronchiolitis, we addressed whether any diVerences in RSV-RNA levels in the airway tracts of infants with bronchiolitis might explain the broad clinical spectrum of RSVassociated bronchiolitis. cache = ./cache/cord-342649-ysossker.txt txt = ./txt/cord-342649-ysossker.txt === reduce.pl bib === id = cord-341765-ml6eo8r3 author = Widhidewi, Ni Wayan title = Identification of viral etiology of acute respiratory tract infections in children and adults in Tabanan, Bali, Indonesia date = 2020-03-25 pages = extension = .txt mime = text/plain words = 2740 sentences = 153 flesch = 45 summary = title: Identification of viral etiology of acute respiratory tract infections in children and adults in Tabanan, Bali, Indonesia This study was based on utilizing molecular techniques targeting a panel of 11 endemic and emerging respiratory viral pathogens including zoonotic viruses in a cohort of children and adults presenting at Tabanan General Hospital, Bali, with acute respiratory illness, from January to November 2017. In this study, throat swab specimens were collected from patients with respiratory symptoms to identify viral etiological agents of ARTI. Singleplex PCR assays were used for detection of a panel of respiratory viruses using family-level primers for Paramyxoviridae, Herpesviridae, Coronaviridae, Hantaviridae, Adenoviridae, Arenaviridae; genus-level primers for Enterovirus, Henipavirus, Influenza A virus, Bocavirus; and Pneumovirinae sub-family primer including respiratory syncytial virus (RSV) and human metapneumovirus (HMPV). In addition to the influenza virus routinely screened in ARTI studies, other viral agents associated with severity like Herpesviridae, Enterovirus and RSV should be screened in respiratory illnesses. cache = ./cache/cord-341765-ml6eo8r3.txt txt = ./txt/cord-341765-ml6eo8r3.txt === reduce.pl bib === id = cord-345472-qrddwebe author = Sebina, Ismail title = The Contribution of Neutrophils to the Pathogenesis of RSV Bronchiolitis date = 2020-07-27 pages = extension = .txt mime = text/plain words = 8184 sentences = 411 flesch = 28 summary = A vaccine against respiratory syncytial virus (RSV), the leading cause of viral bronchiolitis in infancy, remains elusive, and hence new therapeutic modalities are needed to limit disease severity. (1), degranulation (2), respiratory oxygen species (ROS) production (3), and the release of neutrophil extracellular traps (NETosis) (4) are associated with increased lung inflammation, systemic fever, mucus hypersecretion, airway obstruction, and epithelial cell death. Excessive neutrophil-derived inflammatory cytokine production (1), degranulation (2), respiratory oxygen species (ROS) production (3), and the release of neutrophil extracellular traps (NETosis) (4) are associated with increased lung inflammation, systemic fever, mucus hypersecretion, airway obstruction, and epithelial cell death. Unlike wild-type (WT) control mice, plasmacytoid dendritic cell (pDC)-depleted, Toll-like receptor (TLR)7-deficient, or interferon regulatory factor (IRF)7-deficient neonatal mice develop severe pathology, characterised by increased neutrophilia and lung inflammation in response to acute PVM infection [80] [81] [82] . cache = ./cache/cord-345472-qrddwebe.txt txt = ./txt/cord-345472-qrddwebe.txt === reduce.pl bib === id = cord-343390-y903mxcj author = Hoppe, Ingrid Bortolin Affonso Lux title = Bovine respiratory syncytial virus seroprevalence and risk factors in non-vaccinated dairy cattle herds in Brazil date = 2018-06-27 pages = extension = .txt mime = text/plain words = 2917 sentences = 165 flesch = 53 summary = title: Bovine respiratory syncytial virus seroprevalence and risk factors in non-vaccinated dairy cattle herds in Brazil This study aimed to characterize the epidemiology of BRSV infection in dairy cattle herds of São Paulo State, Brazil, using serological and risk factors analyses. The analysis of risk factors indicated that the age group and the occurrence of coinfection with bovine herpesvirus 1 (BoHV-1) and bovine viral diarrhea virus 1 (BVDV-1) should be associated with a higher prevalence of BRSV, while natural suckling was considered a protective factor. Due to this, the current study aimed to determine antibody prevalence against BRSV and investigate some risk factors associated with BRSV seroprevalence in herds of an important milk producing region in São Paulo State, Brazil. Bovine respiratory syncytial virus seroprevalence and risk factors in endemic dairy cattle herds Prevalence of and risk factors for bovine respiratory syncytial virus (BRSV) infection in non-vaccinated dairy and dual-purpose cattle herds in Ecuador cache = ./cache/cord-343390-y903mxcj.txt txt = ./txt/cord-343390-y903mxcj.txt === reduce.pl bib === id = cord-342853-n3e6yawi author = Naghipour, Mohammadreza title = Human bocavirus in Iranian children with acute respiratory infections date = 2007-03-26 pages = extension = .txt mime = text/plain words = 2115 sentences = 121 flesch = 53 summary = Human bocavirus (HBoV), a virus discovered in Sweden in 2005, has been associated with acute respiratory infections in young children and subsequent reports suggest that HBoV may have a worldwide distribution. This report describes the frequency and clinical presentation of HBoV in 261 Iranian children<5 years old with acute respiratory infections attending two regional hospitals in Rasht, Iran in the winter of 2003–2004. Human bocavirus (HBoV) was first described in 2005 [Allander et al., 2005] and it was suggested that the virus might be a cause of acute respiratory infections. Children less than 5 years of age with acute respiratory infections of less than 7 days duration attending the outpatient department or being admitted to hospital from Saturday to Thursday were enrolled after informed parental consent. Given the high frequency of HBoV in Iran, this virus might play a significant role as a cause of acute respiratory infections in children. cache = ./cache/cord-342853-n3e6yawi.txt txt = ./txt/cord-342853-n3e6yawi.txt === reduce.pl bib === id = cord-347255-fl9lur4h author = May, Larissa title = Rapid Multiplex Testing for Upper Respiratory Pathogens in the Emergency Department: A Randomized Controlled Trial date = 2019-11-05 pages = extension = .txt mime = text/plain words = 4057 sentences = 181 flesch = 40 summary = Secondary outcomes included the proportion of patients with a respiratory pathogen identified by the FilmArray Respiratory Panel test or any other upper respiratory pathogen diagnostic test ordered by the physician; the proportion of patients with a laboratory-confirmed influenza diagnosis; the proportion of patients receiving appropriate anti-influenza treatment or prescription in the ED by an emergency medicine clinician (composite rate of anti-influenza treatment in positive patients and nonuse of anti-influenza treatment in negative patients); the proportion of patients discharged home from the ED vs hospital admission; the proportion of patients with all-cause or respiratory illness-related repeat ED visit, hospital or ICU admission, or death within 30 days; clinician adherence to guidelines for the treatment of patients with influenza (recommendations for use of antivirals only); length of ED stay; length of hospital stay; time to influenza test results; and time to other respiratory pathogen test results. Thus, we conducted a randomized clinical trial of the FilmArray RP vs usual care in ED patients with signs or symptoms of upper respiratory infection or influenza-like illness. cache = ./cache/cord-347255-fl9lur4h.txt txt = ./txt/cord-347255-fl9lur4h.txt === reduce.pl bib === id = cord-347465-yu6oj30v author = Kurskaya, Olga title = Viral etiology of acute respiratory infections in hospitalized children in Novosibirsk City, Russia (2013 – 2017) date = 2018-09-18 pages = extension = .txt mime = text/plain words = 3383 sentences = 194 flesch = 45 summary = METHODS: We tested nasal and throat swabs of 1560 children with upper or lower respiratory infection for main respiratory viruses (influenza viruses A and B, parainfluenza virus types 1–4, respiratory syncytial virus, metapneumovirus, four human coronaviruses, rhinovirus, adenovirus and bocavirus) using a RT-PCR Kit. RESULTS: We detected 1128 (72.3%) samples were positive for at least one virus. We detected significant decrease of the respiratory syncytial virus-infection incidence in children with increasing age, while the reverse relationship was observed for influenza viruses. We detected significant decrease of the respiratory syncytial virus-infection incidence in children with increasing age, while the reverse relationship was observed for influenza viruses. In conclusion, in our study we investigated the etiological structure of acute respiratory viral infections in hospitalized children in Novosibirsk, Russia, and evaluated age and seasonal distribution of the various respiratory viruses. cache = ./cache/cord-347465-yu6oj30v.txt txt = ./txt/cord-347465-yu6oj30v.txt === reduce.pl bib === id = cord-344889-1y4ieamp author = Cameron, Robert J. title = Virus infection in exacerbations of chronic obstructive pulmonary disease requiring ventilation date = 2006-05-24 pages = extension = .txt mime = text/plain words = 4309 sentences = 242 flesch = 46 summary = OBJECTIVES: We aimed to characterise and quantify the incidence of common infectious agents in acute exacerbations of chronic obstructive pulmonary disease (COPD) requiring ventilation, with a focus on respiratory viruses. Abstract Objectives: We aimed to characterise and quantify the incidence of common infectious agents in acute exacerbations of chronic obstructive pulmonary disease (COPD) requiring ventilation, with a focus on respiratory viruses. Of these, influenza types A and B (Inf A, B), parainfluenza types 1, 2 and 3 (Para 1, 2, 3), rhinovirus (RV), adenovirus (AV), respiratory syncytial virus (RSV), coronavirus (CoV) [11, 12] and, less commonly, human metapneumovirus (hMPV) [13] , and enterovirus (EV) [14, 15] have been shown to play significant roles in airway infections. A probable virus pathogen was found in 46 cases (43%) and a probable bacterial aetiology was found in 25 cases (23%) in this study of ventilated COPD exacerbation patients. cache = ./cache/cord-344889-1y4ieamp.txt txt = ./txt/cord-344889-1y4ieamp.txt === reduce.pl bib === id = cord-343325-cbrly7f5 author = Denault, André Y. title = A proposed lung ultrasound and phenotypic algorithm for the care of COVID-19 patients with acute respiratory failure date = 2020-05-21 pages = extension = .txt mime = text/plain words = 4025 sentences = 255 flesch = 45 summary = title: A proposed lung ultrasound and phenotypic algorithm for the care of COVID-19 patients with acute respiratory failure We propose a management algorithm that combines the respiratory rate and oxygenation index with bedside lung ultrasound examination and monitoring that could help determine earlier the requirement for intubation and other surveillance of COVID-19 patients with respiratory failure. His phenotype changed from an H-type to an (D) L-type (courtesy of Dr. Emmanuel Charbonney and Dr. Lawrence Leroux) Lung ultrasound in COVID-19 respiratory failure therapy with a high-flow nasal cannula (HFNC) with an increased fraction of inspired oxygen (F I O 2 ). 51 Lung ultrasound can also impact clinical decision-making in patients with acute respiratory failure 52, 53 and provide comprehensive monitoring of regional lung aeration changes that could be used to predict response to prone positioning with improved right (Figs 6 and 7) [54] [55] [56] or higher positive end-expiratory pressure strategy. cache = ./cache/cord-343325-cbrly7f5.txt txt = ./txt/cord-343325-cbrly7f5.txt === reduce.pl bib === id = cord-344271-5aynmdsk author = de Souza Luna, Luciano Kleber title = Spectrum of Viruses and Atypical Bacteria in Intercontinental Air Travelers with Symptoms of Acute Respiratory Infection date = 2007-03-01 pages = extension = .txt mime = text/plain words = 2304 sentences = 147 flesch = 54 summary = title: Spectrum of Viruses and Atypical Bacteria in Intercontinental Air Travelers with Symptoms of Acute Respiratory Infection Using sensitive polymerase chain reactions, we studied the spectrum of atypical bacteria and respiratory viruses in travelers fulfilling the case definition of severe acute respiratory syndrome. These assays were used to determine a point prevalence of the full spectrum of respiratory viruses and atypical bacteria in SARS-compatible patients. Inf and PIV were clearly the most prevalent agents in flight patients, at 14.2% and 15.5%, respectively, without significant differences between age groups (1-way analysis of variance [ANOVA], 95% significance level). Baseline data on the prevalence of respiratory viruses and atypical bacteria after air travel are not currently available. It cannot be told whether the high prevalence and diversity of respiratory viruses seen in our study is specific to patients with recent intercontinental air travel. cache = ./cache/cord-344271-5aynmdsk.txt txt = ./txt/cord-344271-5aynmdsk.txt === reduce.pl bib === id = cord-347509-2ysw9a0a author = Aronen, Matti title = Virus Etiology of Airway Illness in Elderly Adults date = 2016-06-20 pages = extension = .txt mime = text/plain words = 1759 sentences = 111 flesch = 47 summary = 1, 2 Susceptibility to respiratory viral infections may be important especially in older age, but the viral etiology and clinical significance of respiratory illnesses in elderly adults is poorly documented. [2] [3] [4] The aims of this study were to investigate the presence of viruses in elderly adults and to assess the association between viral infection and respiratory illness and between viral infection and chronic illness in individuals with an illness that requires hospitalization. 10 The current study shows that there is an association between respiratory virus detection and weight in elderly adults. 3, 4 The objective of the current study was to assess what older adults with cancer know about their diagnosis and treatment and to identify factors associated with the completeness of this information. cache = ./cache/cord-347509-2ysw9a0a.txt txt = ./txt/cord-347509-2ysw9a0a.txt === reduce.pl bib === id = cord-346290-my8ow5ee author = Nelson, Philipp P. title = Respiratory Viral Pathogens date = 2020-05-28 pages = extension = .txt mime = text/plain words = 4160 sentences = 238 flesch = 42 summary = Respiratory viruses are responsible for a variety of clinical syndromes including the common cold, acute otitis media, laryngitis, sinusitis, pneumonia, bronchiolitis, influenza-like illness, and exacerbations of asthma and chronic obstructive pulmonary disease. Treatment modalities include over-the-counter and non-specific remedies along with a small number of specific antiviral medications such as the influenza neuraminidase inhibitors or palivizumab against respiratory syncytial virus. Viruses of the family of Pneumoviridae form enveloped, spherical or filamentous virions with 100-200 nm in diameter, which contain a single, linear, negative-sense RNA genome. Human bocavirus 1 (HBoV1), a member of the species Primate bocaparvovirus 1, in the genus Bocaparvovirus and the subfamily of Parvovirinae, is strongly associated with upper and lower respiratory tract infections in young children. The common cold is a rather benign clinical entity, which may however be complicated by secondary bacterial infections, otitis media, sinusitis, pneumonia, and asthma exacerbations; severe courses of disease and death may occur in young children and immunocompromised patients. cache = ./cache/cord-346290-my8ow5ee.txt txt = ./txt/cord-346290-my8ow5ee.txt === reduce.pl bib === id = cord-349279-wbb7h2zu author = Walker, Gregory J. title = Viruses associated with acute respiratory infection in a community‐based cohort of healthy New Zealand children date = 2019-05-07 pages = extension = .txt mime = text/plain words = 2767 sentences = 155 flesch = 46 summary = The rates of infection and community epidemiology of respiratory viruses in healthy children needs further definition to assist interpretation of molecular diagnostic assays in this population. The most commonly detected viruses in samples collected during ARI were HRV (52.8%), HCoV (11.0%), parainfluenza virus (PIF) (6.0%), IFV (4.5%), RSV (3.8%), and HMPV (3.5%). Detection of any virus and codetection of viruses were both significantly associated with swabs collected during ARI episodes. While their corresponding risk ratios are not considered significant, the number of detections of these viruses is relatively small, and a larger analysis would be required to rule out the clinical significance of detecting HRV-B, AdV and HBoV in ARIs. The effect of viral coinfection on respiratory disease severity in children has not been well established. New molecular virus detection methods and their clinical value in lower respiratory tract infections in children Viruses associated with acute respiratory infection in a community-based cohort of healthy New Zealand children cache = ./cache/cord-349279-wbb7h2zu.txt txt = ./txt/cord-349279-wbb7h2zu.txt === reduce.pl bib === id = cord-347246-0vofftmj author = Everitt, J I title = Infectious diseases of the upper respiratory tract: implications for toxicology studies. date = 1990-04-17 pages = extension = .txt mime = text/plain words = 3572 sentences = 190 flesch = 28 summary = This paper reviews several important infectious diseases of the upper airway of rats and mice and discusses the potential influence of these conditions on the results of toxicology studies. All three agents cause significant rodent respiratory disease, with lesions in the upper airways, including the nasal passages. Although there are many excellent descriptive studies ofthe histogenesis of Sendai virus-induced lesions within the lower respiratory tract, few pathology reports include a description of lesions in the nasal cavity and upper airway. Although numerous bacteria can infect the upper airway of the rat and mouse, they are not generally prevalent in well-conducted toxicology studies begun with animals free of adventitious murine pathogens and maintained with modern methods of laboratory animal husbandry. A variety of important microbial pathogens including viruses, mycoplasmas, bacteria, and fungi infect the upper respiratory tract of the mouse and rat and result in significant pathologic alterations. cache = ./cache/cord-347246-0vofftmj.txt txt = ./txt/cord-347246-0vofftmj.txt === reduce.pl bib === id = cord-346673-kyc1wks5 author = NICKBAKHSH, S. title = Extensive multiplex PCR diagnostics reveal new insights into the epidemiology of viral respiratory infections date = 2016-03-02 pages = extension = .txt mime = text/plain words = 5415 sentences = 237 flesch = 41 summary = In particular, our study shows that (i) human coronavirus infections are more common during influenza seasons and in co-infections than previously recognized, (ii) factors associated with co-infection differ from those associated with viral infection overall, (iii) virus prevalence has increased over time especially in infants aged <1 year, and (iv) viral infection risk is greater in the post-2009 pandemic era, likely reflecting a widespread change in the viral population that warrants further investigation. We analysed diagnostic data generated by NHSGGC using multiplex PCR from 2005 to 2013 with the following objectives: (i) to describe testing and virus prevalence trends, (ii) to examine temporal and patient subgroup distributions for each individual virus, and (iii) to compare factors associated with overall viral infection and co-infection using statistical modelling, in order to provide robust and timely estimates of who is most at risk of viral-associated respiratory illness, and when, within a major urban UK population. cache = ./cache/cord-346673-kyc1wks5.txt txt = ./txt/cord-346673-kyc1wks5.txt === reduce.pl bib === id = cord-348490-dqabq6d8 author = Maeder, Muriel N. title = Sickle-cell disease in febrile children living in a rural village of Madagascar and association with malaria and respiratory infections date = 2016-12-01 pages = extension = .txt mime = text/plain words = 4287 sentences = 210 flesch = 49 summary = title: Sickle-cell disease in febrile children living in a rural village of Madagascar and association with malaria and respiratory infections From May 2011 to November 2013, a cross-sectional study was conducted in the rural village of Ampasimanjeva in the south east cost of Madagascar aiming to identify blood-borne protein biomarkers that can differentiate the causes of unexplained acute febrile illness in children. Our study shows that prevalence of SCD was 2.4% and that of SCT 23.8% among children aged 2-59 months presenting with fever and living in high endemic area for malaria. However, among the 23 viral and atypical bacteria pathogens studied, there was no statistical difference in prevalence between the three groups for 20 of them and include HRV the most common respiratory virus detected or influenza virus A (H1N1)/ pdm09 known to increase disease severity in children with SCD [29] . cache = ./cache/cord-348490-dqabq6d8.txt txt = ./txt/cord-348490-dqabq6d8.txt === reduce.pl bib === id = cord-349226-xzlc1pni author = Khatiwada, Saroj title = Lung microbiome and coronavirus disease 2019 (COVID-19): possible link and implications date = 2020-08-05 pages = extension = .txt mime = text/plain words = 4312 sentences = 231 flesch = 35 summary = To date there is no direct evidence from human or animal studies on the role of lung microbiome in modifying COVID-19 disease; however, related studies support that microbiome can play an essential role in developing immunity against viral infections. The COVID-19 disease is caused by a virus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which emerged in Wuhan, China at the end of 2019 [4] . The COVID-19 disease begins with the invasion of lungs by SARS-CoV-2 virus, and the major complications that develop subsequently are related to lung infection and immune response generation, therefore, lung microbiome might play an important role from initiation to the progression of this disease [16] . The SARS-CoV-2 viral infection occurs amid the local environment of diverse microbiota; therefore, it is apparent that lung microbiota can have an impact on the initiation, development, and progression of the COVID-19 disease. cache = ./cache/cord-349226-xzlc1pni.txt txt = ./txt/cord-349226-xzlc1pni.txt === reduce.pl bib === id = cord-346253-0mnsm6s4 author = Ahanchian, Hamid title = Respiratory viral infections in children with asthma: do they matter and can we prevent them? date = 2012-09-13 pages = extension = .txt mime = text/plain words = 7744 sentences = 399 flesch = 35 summary = HRV are the most common viral agents [33] ; Other respiratory tract viruses detected in children with an asthma exacerbation include RSV, influenza, coronavirus, hMPV, parainfluenza virus, adenovirus, and bocavirus [34] [35] [36] . Beside importance for bone health, vitamin D plays an important role in adequate function of both the innate and adaptive immune systems including development of dendritic cells and regulatory T lymphocytes [151, 152] production of antimicrobial proteins by airway epithelium [153] , modifying the effect of intestinal flora on inflammatory disorders [107] , and modulation of the inflammatory response to viral infections [154] . In a recent study of 48 children from five to 18 years of age, with newly diagnosed asthma, vitamin D supplementation during the northern hemisphere winter months (September to July) prevented declining serum concentrations of 25(OH) D and reduced the risk of asthma exacerbation triggered by acute respiratory tract infections [161] . cache = ./cache/cord-346253-0mnsm6s4.txt txt = ./txt/cord-346253-0mnsm6s4.txt === reduce.pl bib === id = cord-346096-aml84iv1 author = Bailey, Emily S. title = Molecular surveillance of respiratory viruses with bioaerosol sampling in an airport date = 2018-09-17 pages = extension = .txt mime = text/plain words = 2503 sentences = 131 flesch = 46 summary = These results suggest the feasibility of employing bioaerosol surveillance techniques in public transportation areas, such as airports, as a noninvasive way to detect and characterize novel respiratory viruses. In this pilot study, we studied bioaerosol samples collected in Raleigh Durham International Airport for molecular evidence of respiratory viruses. Although not the focus of our study, we did not detect viable viruses using culture analysis associated with positive aerosol samples at RDU airport. In this pilot aerosol study, we conducted surveillance for human and zoonotic respiratory viruses in an airport setting over a period of nine weeks from January to March 2018. Despite these limitations, the results of this study suggest that aerosol sampling is a useful technique for respiratory virus surveillance in high traffic and crowded areas such as airports. cache = ./cache/cord-346096-aml84iv1.txt txt = ./txt/cord-346096-aml84iv1.txt === reduce.pl bib === id = cord-347262-q88g1561 author = Schutzer‐Weissmann, J. title = Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection risk during elective peri‐operative care: a narrative review date = 2020-07-11 pages = extension = .txt mime = text/plain words = 4753 sentences = 279 flesch = 39 summary = Whilst none of these were anaesthetists or intensivists, 53/1718 (3.1%) healthcare workers performing or involved in tracheal intubation of patients with confirmed or suspected COVID-19 subsequently reported laboratory-confirmed SARS-CoV-2 infection [4] . Here, we review the evidence from SARS and contemporaneous data from COVID-19 to inform assessment and management of the risk of SARS-CoV-2 transmission to healthcare workers involved in elective peri-operative care. The WHO list of aerosol-generating procedures is based on epidemiological evidence of transmission to healthcare workers caring for SARS patients [30, [36] [37] [38] [39] [40] [41] [42] [43] [44] . The studies upon which the WHO list of aerosol-generating procedures is based do not provide any direct evidence that tracheal intubation itself increases the risk of SARS transmission. Aerosol Generating Procedures and Risk of Transmission of Acute Respiratory Infections to Healthcare Workers: A Systematic Review cache = ./cache/cord-347262-q88g1561.txt txt = ./txt/cord-347262-q88g1561.txt === reduce.pl bib === id = cord-346887-dl0wc4u2 author = Cho, Hye Jung title = Respiratory viruses in neonates hospitalized with acute lower respiratory tract infections date = 2012-12-11 pages = extension = .txt mime = text/plain words = 3073 sentences = 193 flesch = 53 summary = The aims of this study were to determine the overall distribution of respiratory viruses in neonates hospitalized with acute lower respiratory tract infectiosns (ALRI) and to describe the clinical characteristics of RSV infections in these neonates. In addition to respiratory syncytial virus (RSV), human rhinovirus (hRV), human parainfluenza virus (hPIV), and human metapneumovirus (hMPV) have been found to be major causes of acute lower respiratory tract infections (ALRI) in infants and young children. 1, 13 One study based on hospitalized children with ALRI in Korea reported that RSV (33.2%) was the most common virus among 13 respiratory viruses and was followed by hRV (19.1%), influenza virus (16.9%), hMPV (15.4%), and hPIV (8.3%). In the present study a significantly higher proportion of the RSV group obtained infections from neonatal day-care centers. FLIP-2 Study: Risk factors linked to respiratory syncytial virus infection requiring hospitalization in premature infants born in Spain at a gestational age of 32 to 35 weeks cache = ./cache/cord-346887-dl0wc4u2.txt txt = ./txt/cord-346887-dl0wc4u2.txt === reduce.pl bib === id = cord-349287-mwj2qby4 author = Mackay, Ian M. title = MERS coronavirus: diagnostics, epidemiology and transmission date = 2015-12-22 pages = extension = .txt mime = text/plain words = 14290 sentences = 671 flesch = 51 summary = The first known cases of Middle East respiratory syndrome (MERS), associated with infection by a novel coronavirus (CoV), occurred in 2012 in Jordan but were reported retrospectively. Most human cases of MERS have been linked to lapses in infection prevention and control (IPC) in healthcare settings, with approximately 20 % of all virus detections reported among healthcare workers (HCWs) and higher exposures in those with occupations that bring them into close contact with camels. Since asymptomatic zoonoses have been posited [72] , an absence of antibodies to MERS-CoV among some humans who have regular and close contact with camels may reflect the rarity of actively infected animals at butcheries, a limited transmission risk associated with slaughtering DCs [70] , a pre-existing cross-protective immune status or some other factor(s) resulting in a low risk of disease and concurrent seroconversion developing after exposure in this group. First cases of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infections in France, investigations and implications for the prevention of human-tohuman transmission cache = ./cache/cord-349287-mwj2qby4.txt txt = ./txt/cord-349287-mwj2qby4.txt === reduce.pl bib === id = cord-349606-lup6tm2s author = Biill Primo, Osvaldo Vinícius title = Detection of Respiratory Viruses in Nasopharyngeal Swab and Adenoid Tissue from Children Submitted to Adenoidectomy: Pre- and Postoperative Analysis date = 2014-02-17 pages = extension = .txt mime = text/plain words = 2793 sentences = 157 flesch = 45 summary = Methods A prospective observational study was conducted in 36 patients under 12 years of age with upper airway lymphoid hypertrophy who were undergoing adenoidectomy, in which various respiratory viruses were investigated using real-time polymerase chain reaction in adenoid tissue and nasopharyngeal secretions collected preoperatively and 30 days postoperatively. Methods A prospective observational study was conducted in 36 patients under 12 years of age with upper airway lymphoid hypertrophy who were undergoing adenoidectomy, in which various respiratory viruses were investigated using realtime polymerase chain reaction in adenoid tissue and nasopharyngeal secretions collected preoperatively and 30 days postoperatively. Several respiratory viruses (influenza A and B; parainfluenza 1, 2, 3, and 4; rhinovirus; respiratory syncytial virus; human bocavirus; coronaviruses; and metapneumovirus) were investigated by quantitative real-time polymerase chain reaction (q-PCR) in adenoid tissue removed surgically and nasal swab specimens collected preoperatively and at 1 month postoperative follow-up visit. cache = ./cache/cord-349606-lup6tm2s.txt txt = ./txt/cord-349606-lup6tm2s.txt === reduce.pl bib === id = cord-346539-kxnrf5g5 author = Riggioni, Carmen title = A compendium answering 150 questions on COVID‐19 and SARS‐CoV‐2 date = 2020-06-14 pages = extension = .txt mime = text/plain words = 15760 sentences = 1112 flesch = 48 summary = This paper answers pressing questions, formulated by young clinicians and scientists, on SARS‐CoV‐2, COVID‐19 and allergy, focusing on the following topics: virology, immunology, diagnosis, management of patients with allergic disease and asthma, treatment, clinical trials, drug discovery, vaccine development and epidemiology. The first cases of the coronavirus disease 2019 (COVID19) , caused by the novel severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2), were reported in China in December 2019 1 and rapidly led to pandemic. 40, 41 A seroconversion study in COVID-19 patients has found and association between disease severity and SARS-CoV-2-specific IgA levels. Mesenchymal stem cell therapy may potentiate the low IFN-I and -III levels and moderate IFN-stimulated gene response reported in SARS-CoV-2-infected ferrets and COVID-19 patients. Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial cache = ./cache/cord-346539-kxnrf5g5.txt txt = ./txt/cord-346539-kxnrf5g5.txt === reduce.pl bib === id = cord-349956-h4i2t2cr author = Hoang, Van-Thuan title = The dynamics and interactions of respiratory pathogen carriage among French pilgrims during the 2018 Hajj date = 2019-11-21 pages = extension = .txt mime = text/plain words = 4851 sentences = 260 flesch = 44 summary = We conducted this study to describe the dynamics of the acquisition of respiratory pathogens, their potential interactions and risk factors for possible lower respiratory tract infection symptoms (LRTI) among French pilgrims during the 2018 Hajj. showed that human rhinovirus (HRV) and influenza viruses were the most common viral respiratory pathogens isolated from ill Hajj pilgrims [6] . Unadjusted associations between respiratory pathogen carriage with multiples factors: sociodemographic characteristics (gender, ≥60 years), chronic respiratory disease, BMI classification, smoking status; individual preventive measures (vaccination against influenza, vaccination against IPD, use of a face mask, hand washing, disinfectant gel and disposable handkerchiefs); antibiotic intake 10 days before each sample; respiratory virus or bacteria and dual carriage were analysed by univariable analysis. aureus carriage increase and the initial wave of respiratory symptoms, suggests that this pathogen association was responsible for the RTIs that affected most pilgrims soon after arriving in Mecca. cache = ./cache/cord-349956-h4i2t2cr.txt txt = ./txt/cord-349956-h4i2t2cr.txt === reduce.pl bib === id = cord-350928-vj5qlzpj author = Arnott, Alicia title = Human bocavirus amongst an all‐ages population hospitalised with acute lower respiratory infections in Cambodia date = 2012-04-25 pages = extension = .txt mime = text/plain words = 4315 sentences = 317 flesch = 55 summary = Objectives To investigate the prevalence and genetic diversity of HBoV amongst hospitalized patients with acute lower respiratory infection (ALRI) in Cambodia. In patients where HBoV is the only virus detected, the clinical symptoms reported are similar to those occurring as a result of infection with respiratory syncytial virus (RSV) and human metapneumovirus (HMPV), including bronchiolitis, bronchitis, pneumonia and exacerbation of asthma. 20 Here, we report the findings of the first study investigating the prevalence, seasonality, clinical characteristics and the molecular epidemiology of HBoV in amongst an all-ages population of patients hospitalized for acute lower respiratory illness (ALRI) in Cambodia over 3 consecutive years. 5 In this study, ALRI patient samples were screened for HBoV infection using a highly sensitive multiplex PCR assay previously shown to have a lower limit of detection of 4 copies of HBoV DNA ⁄ ll of viral transport medium. cache = ./cache/cord-350928-vj5qlzpj.txt txt = ./txt/cord-350928-vj5qlzpj.txt === reduce.pl bib === id = cord-351008-p0n1fdxw author = Monge, Susana title = Ambulance dispatch calls attributable to influenza A and other common respiratory viruses in the Netherlands (2014‐2016) date = 2020-05-14 pages = extension = .txt mime = text/plain words = 3080 sentences = 166 flesch = 45 summary = We evaluated whether ambulance dispatch calls of highest urgency reflect the circulation of influenza A virus, influenza B virus, respiratory syncytial virus (RSV), rhinovirus, adenovirus, coronavirus, parainfluenzavirus and human metapneumovirus (hMPV). Specifically, we evaluated the association of syndromes compatible with respiratory infections in ambulance dispatches with trends in detections of influenza A, influenza B, RSV, rhinovirus, adenovirus, coronavirus, parainfluenza and human metapneumovirus (hMPV). Calls with triage codes that were potentially compatible with respiratory infections (Table 1) year, and hMPV (4%) and influenza A (1%) mainly during the winter peaks. Because of its ability to capture variations in respiratory virus circulation, ambulance dispatch data might be useful to signal events and to monitor the respiratory season as a whole, specifically reflecting severe infections and thus complementing existing surveillance systems. Use of ambulance dispatch calls for surveillance of severe acute respiratory infections Ambulance dispatch calls attributable to influenza A and other common respiratory viruses in the Netherlands cache = ./cache/cord-351008-p0n1fdxw.txt txt = ./txt/cord-351008-p0n1fdxw.txt === reduce.pl bib === id = cord-349560-8n65rgfz author = Kleines, Michael title = WU Polyomavirus (WUPyV): A Recently Detected Virus Causing Respiratory Disease? date = 2009-11-04 pages = extension = .txt mime = text/plain words = 4053 sentences = 230 flesch = 45 summary = The WU polyomavirus (WUPyV) is a novel member of the family Polyomaviridae recently detected in respiratory tract specimens by shotgun sequencing. Creer and co-workers [1] identified at least one potential pathogen in 69% of specimens from adults suffering from lower respiratory tract infections (LRTI, 63% contained viruses, 26% contained bacteria) still leaving a significant diagnostic gap to be filled with so far unidentified pathogenic microorganisms. For this reason, detection of virus-specific antibodies by complement fixation assays, enzyme linked immunosorbent assays (ELISA), or immunofluorescence assays (IFA), all of which are available for established respiratory viruses, is inappropriate for the identification of the etiologic agent causing an acute respiratory tract infection, but useful for retrospective or epidemiological studies. Following the discovery of WUPyV in Australia, the virus was detected in specimens from patients with respiratory tract disease on all continents suggesting a worldwide distribution [10, [29] [30] [31] . cache = ./cache/cord-349560-8n65rgfz.txt txt = ./txt/cord-349560-8n65rgfz.txt === reduce.pl bib === id = cord-354918-129inbwq author = Kotsimbos, T. title = Respiratory infectious disease: complacency with empiricism in the age of molecular science. We can do better! date = 2007-06-04 pages = extension = .txt mime = text/plain words = 2102 sentences = 100 flesch = 32 summary = A few home truths (i) Viral infections are an important cause of respiratory infection and yet a specific diagnosis is rarely made, (ii) few antiviral therapies exist and when they do -such as in the case of influenza -they are either underused or overused because of diagnostic inefficiencies, (iii) our approach to using antibacterial agents is guided by 'what should reasonably be covered' or 'what organisms are being missed' rather than a treatment regimen targeted for a particular organism, (iv) in association with diagnostic uncertainty, we do not make sufficient allowances for immunocompromised states or overexuberant immune responses to respiratory infectious disease (RID) and (v) current antibiotic guidelines encourage an approach of increasingly covering all potential organisms depending on the severity of illness. Our current reliance on empirical antibiotic strategies to cover 'likely bacterial pathogens' as set out in numerous guidelines is unavoidable in the short term given the current diagnostic limitations for respiratory infection syndromes. cache = ./cache/cord-354918-129inbwq.txt txt = ./txt/cord-354918-129inbwq.txt === reduce.pl bib === id = cord-351323-cbejbm5v author = Roy Mukherjee, Tapasi title = Spectrum of respiratory viruses circulating in eastern India: Prospective surveillance among patients with influenza‐like illness during 2010–2011 date = 2013-06-13 pages = extension = .txt mime = text/plain words = 3277 sentences = 168 flesch = 41 summary = The samples were tested further for influenza C virus, parainfluenza viruses 1–4, human rhinovirus, metapneumovirus and respiratory syncytial virus by conventional RT‐ PCR. Hence the information on epidemiology and clinical features of respiratory virus infection in India is based entirely on research studies and the disease burden or seasonal prevalence of respiratory viruses remains largely undefined. This study initiated to complete the information on circulating respiratory viruses among patients attending the outpatients departments of different hospitals with acute respiratory infections in the eastern region of India during 2010 through 2011. Comparative evaluation of real-time PCR and conventional RT-PCR during 2 year surveillance for influenza and respiratory syncytial virus among children with acute respiratory infections in Kolkata, India, reveals a distinct seasonality of infection Prevalence of respiratory syncytial virus group B genotype BA-IV strains among children with acute respiratory tract infection in Kolkata, Eastern India cache = ./cache/cord-351323-cbejbm5v.txt txt = ./txt/cord-351323-cbejbm5v.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-351046-yq7287k9 author = Schubert, Gena title = How Much Drool Is Too Much?() date = 2019-12-13 pages = extension = .txt mime = text/plain words = 3232 sentences = 199 flesch = 46 summary = There is a broad differential for a patient with respiratory failure, and careful physical examination and history are imperative to reduce morbidity and prevent mortality. There is a broad differential for a patient with respiratory failure, and careful physical examination and history are imperative to reduce morbidity and prevent mortality. The initial vital signs on his third ED presentation were as follows: temperature 36.7°C, heart rate 130 beats per minute, respiratory rate 30 breaths per minute, pulse oximetry 99%, and blood pressure of 113/81 mm Hg. On examination, the patient was awake and calm in his mother's arms with no acute distress. The differential for a patient presenting to the ED with acute respiratory distress is broad and includes infection, ingestion, trauma, envenomation, muscular disorders, and autoimmune etiologies. Scorpion envenomation often presents with respiratory distress along with increased drooling, abnormal eye movements, muscle twitching, and agitation. 13, 14 The treatment for myasthenia gravis begins with respiratory support including intubation or noninvasive ventilation. cache = ./cache/cord-351046-yq7287k9.txt txt = ./txt/cord-351046-yq7287k9.txt === reduce.pl bib === id = cord-351990-aham72b9 author = Radin, Jennifer M. title = Epidemiology of Pathogen-Specific Respiratory Infections among Three US Populations date = 2014-12-30 pages = extension = .txt mime = text/plain words = 4511 sentences = 220 flesch = 43 summary = METHODS: Febrile respiratory illness (FRI) and severe acute respiratory infection (SARI) surveillance was conducted from October 2011 through March 2013 among three US populations: civilians near the US–Mexico border, Department of Defense (DoD) beneficiaries, and military recruits. Recruits with rhinovirus had higher percentages of pneumonia, cough, shortness of breath, congestion, cough, less fever and longer time to seeking care and were more likely to be male compared to those in the no/unknown pathogen group. This study aimed to describe characteristics associated with specific respiratory pathogens, as well as the etiology, seasonality, and coinfection rates among three US populations: military recruits, Department of Defense (DoD) beneficiaries, and civilians living near the US-Mexico border. Additionally, the following demographic and clinical signs and symptoms were collected from each FRI and SARI case: sex, age, study population, month of illness, pneumonia, sore throat, cough, nausea, shortness of breath, congestion, pink eye, body ache, headache, temperature, number of days of symptoms before seeking care, and date of seeking care. cache = ./cache/cord-351990-aham72b9.txt txt = ./txt/cord-351990-aham72b9.txt === reduce.pl bib === id = cord-353698-gj8sx3zy author = Bibiano-Guillen, C. title = Adapted Diving Mask (ADM) device as respiratory support with oxygen output during COVID-19 pandemic date = 2020-10-28 pages = extension = .txt mime = text/plain words = 3320 sentences = 198 flesch = 52 summary = title: Adapted Diving Mask (ADM) device as respiratory support with oxygen output during COVID-19 pandemic The most extended therapeutic approach for COVID-19 is based on two main strategies [10] [11] [12] [13] : pharmacological treatment directed toward several physiological targets (viremia, immunological reactions, prothrombotic reactions) and hemodynamic and respiratory support with positive end-expiratory pressure (PEEP) in addition to mechanical ventilation. A descriptive case series study of twenty-five patients with acute respiratory syndrome secondary to SARS-CoV2 infection was performed at a Spanish center, Hospital Universitario Infanta Leonor of Madrid, between March 30 and April 18, 2020. Table 4 shows the different variables used to analyze the improvement in the intervention and the mean value of all oxygen saturation measurements for all days that ADM therapy was used in those patients who prolonged its time of use. cache = ./cache/cord-353698-gj8sx3zy.txt txt = ./txt/cord-353698-gj8sx3zy.txt === reduce.pl bib === id = cord-352222-zq9o66i4 author = Rajatonirina, Soatiana title = Outcome Risk Factors during Respiratory Infections in a Paediatric Ward in Antananarivo, Madagascar 2010–2012 date = 2013-09-12 pages = extension = .txt mime = text/plain words = 4137 sentences = 245 flesch = 46 summary = BACKGROUND: Acute respiratory infections are a leading cause of infectious disease-related morbidity, hospitalisation and mortality among children worldwide, and particularly in developing countries. MATERIALS AND METHODS: We conducted a prospective study in a paediatric ward in Antananarivo from November 2010 to July 2012 including patients under 5 years old suffering from respiratory infections. CONCLUSION: Co-mordidity, low-income and age under 6 months increase the risk of severe outcome for children infected by numerous respiratory pathogens. Our study aimed to evaluate the risk factors associated with the evolution and outcome of respiratory illnesses in patients aged under 5 years old hospitalised in one of the four main public hospitals in Antananarivo. In our study, Streptococcus pneumoniae was the most common bacterial pathogen as in other studies of hospitalised patients with acute respiratory illness, and Haemophilus influenzae type B was the next most frequent [16] [17] [18] [19] . cache = ./cache/cord-352222-zq9o66i4.txt txt = ./txt/cord-352222-zq9o66i4.txt === reduce.pl bib === id = cord-353308-e4s8el0s author = Parashar, Umesh D title = Severe acute respiratory syndrome: review and lessons of the 2003 outbreak date = 2004-05-20 pages = extension = .txt mime = text/plain words = 4499 sentences = 224 flesch = 45 summary = This dramatic chain of transmission brought to the world's attention this new respiratory disease, called severe acute respiratory syndrome (SARS), and clearly illustrated the potential for SARS to spread extensively from a single infected person and to rapidly disseminate globally through air travel. Diarrhoea has been reported at presentation in approximately 25% of patients, although this symptom was observed in as many as 73% of all patients affected by an outbreak at an apartment complex in Hong Kong that is believed to have resulted from fecal-oral/respiratory transmission of SARS-CoV. [53] [54] [55] [56] Given that profuse watery diarrhoea is seen in a significant proportion of patients and SARS-CoV can be shed in large quantities in stool, faeces remain a possible source of virus and fecal-oral or fecal-respiratory spread are the leading hypotheses for a large outbreak affecting more than 300 people at an apartment complex in Hong Kong. Fatal severe acute respiratory syndrome is associated with multiorgan involvement by coronavirus (SARS-CoV) cache = ./cache/cord-353308-e4s8el0s.txt txt = ./txt/cord-353308-e4s8el0s.txt === reduce.pl bib === id = cord-352684-4o623x3n author = Tan, M. Y. title = Bocavirus infection following paediatric liver transplantation date = 2016-10-23 pages = extension = .txt mime = text/plain words = 1628 sentences = 109 flesch = 50 summary = We report HBoV infection in a child post‐liver transplantation, who presented with persistent fever and mild tachypnea, 3 weeks after a successful transplant. She had episodes of prolonged fever even after her collections were drained, and a respiratory multiplex (PCR-based test) to look for viruses, from nasopharyngeal aspirates, was negative (3 weeks prior to transplant). 4 However, in recent years, it has been emerged that HBoV alone is pathogenic and can cause disease in immunocompetent children, most commonly presenting with respiratory symptoms, such as wheeze and bronchiolitis. 8 There are a few reports of HBoV infections in immunocompromised hosts wherein they have caused respiratory or diarrhoeal illness, and rarely even life-threatening conditions in the stem cell transplant population. 9 HBoV has also been shown to cause disseminated illness in a child, post-stem cell transplant. 11 There are no reports of HBoV-associated respiratory infections in children after liver transplantation. cache = ./cache/cord-352684-4o623x3n.txt txt = ./txt/cord-352684-4o623x3n.txt === reduce.pl bib === id = cord-355165-xc6ythgp author = van den Wijngaard, Cees title = Validation of Syndromic Surveillance for Respiratory Pathogen Activity date = 2008-06-17 pages = extension = .txt mime = text/plain words = 4561 sentences = 224 flesch = 42 summary = We defi ned syndrome data as data in health-related registries that refl ect infectious disease activity without identifying causative pathogen(s) or focusing on pathogenspecifi c symptoms (such as routine surveillance data for infl uenza-like illness [11] or surveillance of acute fl accid paralysis for polio [12] ). Six registries were selected ( Table 1 ) that collected data on work absenteeism, general practice (GP) consultations, prescription medications dispensed by pharmacies, diagnostic test requests (laboratory submissions) (13), hospital diagnoses, and deaths. As a reference for the syndrome data, we included specifi c pathogen counts for 1999-2004 from the following sources: 1) Weekly Sentinel Surveillance System of the Dutch Working Group on Clinical Virology (which covers 38%-73% of the population of the Netherlands [14] respiratory disease-related counts of Streptococcus pneumoniae (data in 2003-2004 were interpolated for 2 laboratories during short periods of missing data; total coverage 24%); and 3) national mandatory notifi cations of pertussis. cache = ./cache/cord-355165-xc6ythgp.txt txt = ./txt/cord-355165-xc6ythgp.txt === reduce.pl bib === id = cord-353786-284qn075 author = Chen, Zhi-Min title = Diagnosis and treatment recommendations for pediatric respiratory infection caused by the 2019 novel coronavirus date = 2020-02-05 pages = extension = .txt mime = text/plain words = 3521 sentences = 224 flesch = 47 summary = title: Diagnosis and treatment recommendations for pediatric respiratory infection caused by the 2019 novel coronavirus At the onset of the disease, infected children mainly present with fever, fatigue and cough, which may be accompanied by nasal congestion, runny nose, expectoration, diarrhea, headache, etc. 2. Children with a history of contacting patients with fever or respiratory symptoms who have a travel or residence history in Wuhan City and neighboring areas, or in other areas with persistent local transmission within 14 days prior to disease onset. 3. Children with a history of contacting confirmed or suspected cases infected with 2019-nCoV within 14 days prior to disease onset. 4. Children who are related with a cluster outbreak: in addition to this patient, there are other patients with fever or respiratory symptoms, including suspected or confirmed cases infected with 2019-nCoV. Most of the cases have normal or decreased white blood cell counts, while severely infected children show reduced level of lymphocyte count. cache = ./cache/cord-353786-284qn075.txt txt = ./txt/cord-353786-284qn075.txt ===== Reducing email addresses cord-003798-nki2sasr cord-024188-d7tnku8z cord-253502-v2hh3w3r cord-005646-xhx9pzhj cord-283399-iz4l9i0d cord-285557-my16g91c cord-289139-5ljqnc39 cord-302111-kg0dmgq0 cord-294155-94skyx5f cord-306315-vt2e0crh cord-313749-f2ct57em cord-323009-frej2qmb Creating transaction Updating adr table ===== Reducing keywords cord-005774-7z6uyn6p cord-000285-7p3b6tyf cord-003798-nki2sasr cord-007176-61e9obb3 cord-016070-e9ix35x3 cord-000877-usz7pnvu cord-003488-pfzy8p5v cord-002227-x1ddi8wg cord-007234-hcpa8ej5 cord-016990-ot1wi3xi cord-002590-24o2viv3 cord-004397-ypli7wtu cord-011095-79ce5900 cord-020267-0axms5fp cord-018302-lmly43rd cord-023728-fgcldn4e cord-016451-k8m2xz0e cord-018319-tylkbh4h cord-017107-sg8n12hs cord-016499-5iqpl23p 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score: 43 nouns: patients; infection; virus; children; infections; viruses; disease; study; influenza; tract; pneumonia; lung; cells; syndrome; studies; cases; treatment; coronavirus; age; cell; detection; years; asthma; risk; symptoms; infants; time; results; data; illness; group; samples; response; days; care; analysis; bronchiolitis; use; pathogens; adults; diagnosis; type; therapy; role; blood; protein; mortality; hospital; rhinovirus; rate verbs: using; associated; including; showing; causing; increased; detect; finding; induced; reported; following; occurred; identify; infecting; develop; compared; based; required; reduce; suggests; hospitalized; observed; performed; provided; result; considered; led; describes; seen; related; determined; presented; remaining; treated; tested; involved; demonstrated; obtained; known; collected; evaluated; acquired; affecting; needed; making; indicates; decrease; given; improve; confirm adjectives: respiratory; viral; acute; clinical; human; severe; syncytial; high; pulmonary; lower; common; positive; immune; bacterial; different; specific; significant; first; important; new; higher; non; upper; early; chronic; similar; low; several; many; young; molecular; available; inflammatory; infectious; present; negative; diagnostic; single; possible; large; novel; antiviral; pediatric; epithelial; major; multiple; healthy; recent; normal; small adverbs: also; however; well; significantly; often; frequently; therefore; respectively; even; usually; previously; especially; particularly; less; commonly; recently; highly; still; generally; approximately; currently; mainly; relatively; clinically; least; first; furthermore; critically; later; newly; moreover; potentially; now; rapidly; primarily; typically; probably; worldwide; prior; rather; yet; directly; finally; together; statistically; alone; much; early; almost; widely pronouns: it; we; their; our; they; its; i; them; one; he; she; us; his; her; itself; your; you; themselves; my; me; him; mg; hadv-4; ours; himself; mrnas; pdcs; em; oneself; ya; thee; stat1; ourselves; nsp10; clustalx; y903mxcj; wupyv; unintentionallya; u; tv/; tnfrt; thr399ile; t; s; rsv; p~; pyrsvac-183; p.dligh]cine; ol!guria; nsp15 proper nouns: RSV; SARS; PCR; CoV; MERS; el; RNA; COVID-19; ARDS; A; HRV; East; Middle; ICU; Fig; los; HBoV; China; RT; C; parainfluenza; PRRSV; CoV-2; B; con; IFN; Human; mg; Coronavirus; T; Respiratory; Health; RV; Influenza; para; Table; H1N1; metapneumovirus; COPD; United; II; del; HCoV; un; ARI; •; States; S.; Disease; PIV keywords: respiratory; infection; rsv; virus; sars; patient; pcr; child; mers; covid-19; disease; acute; study; cell; asthma; viral; pneumonia; lung; human; hrv; east; bronchiolitis; middle; ards; severe; rna; ifn; copd; infant; ari; syndrome; sari; pulmonary; influenza; coronavirus; case; prrsv; icu; hrsv; cause; vaccine; result; porcine; oc43; hmpv; hbov; hajj; cov; china; treatment one topic; one dimension: respiratory file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095417/ titles(s): Infant lung function testing in the intensive care unit three topics; one dimension: respiratory; lung; patients file(s): https://api.elsevier.com/content/article/pii/B9780124158474000598, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7271179/, https://www.sciencedirect.com/science/article/pii/S0122726220300859?v=s5 titles(s): Respiratory Virus Vaccines | Respiratory System, Mediastinum, and Pleurae | ACTUALIZACION DE LA DECLARACIÓN DE CONSENSO EN MEDICINA CRITICA PARA LA ATENCIÓN MULTIDISCIPLINARIA DEL PACIENTE CON SOSPECHA O CONFIRMACIÓN DIAGNÓSTICA DE COVID-19 five topics; three dimensions: respiratory children infections; respiratory virus infection; patients respiratory lung; pneumonia pulmonary lung; en el con file(s): https://www.ncbi.nlm.nih.gov/pubmed/28122603/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7112677/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095534/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7271179/, https://www.sciencedirect.com/science/article/pii/S0122726220300859?v=s5 titles(s): A protocol for a systematic literature review: comparing the impact of seasonal and meteorological parameters on acute respiratory infections in Indigenous and non-Indigenous peoples | Understanding the mechanisms of viral induced asthma: New therapeutic directions | 8th European Congress of Intensive Care Medicine Athens - Greece, October 18–22, 1995 Abstracts | Respiratory System, Mediastinum, and Pleurae | ACTUALIZACION DE LA DECLARACIÓN DE CONSENSO EN MEDICINA CRITICA PARA LA ATENCIÓN MULTIDISCIPLINARIA DEL PACIENTE CON SOSPECHA O CONFIRMACIÓN DIAGNÓSTICA DE COVID-19 Type: cord title: keyword-respiratory-cord date: 2021-05-25 time: 16:15 username: emorgan patron: Eric Morgan email: emorgan@nd.edu input: keywords:respiratory ==== make-pages.sh htm files ==== make-pages.sh complex files ==== make-pages.sh named enities ==== making bibliographics id: cord-022084-hap7flng author: ARRUDA, EURICO title: Respiratory Tract Viral Infections date: 2009-05-15 words: 19181.0 sentences: 1041.0 pages: flesch: 43.0 cache: ./cache/cord-022084-hap7flng.txt txt: ./txt/cord-022084-hap7flng.txt summary: The Centers for Disease Control and Prevention (CDC) recommends the immunization of persons aged 50 years and older; residents of nursing homes; children and adults with chronic cardiovascular or pulmonary disease, including asthma; persons chronically ill with diabetes mellitus, renal dysfunction, or hemoglobinopathies; immunosuppressed patients including those with HIV infection; children and adolescents on chronic aspirin therapy who may develop postinfluenza Reye'' s syndrome; women who will be pregnant during the influenza season; children aged 6 to 23 months; those who can transmit influenza to persons at high risk, such as health-care workers and household contacts of those at high risk including children 0 to 23 months of age; crew members of cruise ships; providers of essential services; and unimmunized travelers to areas where influenza may be circulating, including the tropics, the southern hemisphere between April and September, and those traveling in large organized tourist groups. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152450/ doi: 10.1016/b978-0-443-06668-9.50064-8 id: cord-000877-usz7pnvu author: Abdel-Moneim, Ahmed S. title: Detection of Bocavirus in Children Suffering from Acute Respiratory Tract Infections in Saudi Arabia date: 2013-01-30 words: 1826.0 sentences: 101.0 pages: flesch: 51.0 cache: ./cache/cord-000877-usz7pnvu.txt txt: ./txt/cord-000877-usz7pnvu.txt summary: title: Detection of Bocavirus in Children Suffering from Acute Respiratory Tract Infections in Saudi Arabia Swabs samples from 80 children with respiratory tract infections were examined for the presence of HBoV. Human bocavirus (HBoV) was first found in children with acute respiratory tract infections in 2005 [1] . The current study aims to screen the epidemiological status and molecular phylogeny of HBoV isolates prevailing in pediatric patients with respiratory infection in Saudi Arabia. The current study investigated the prevalence of HBoV in patients suffering from respiratory tract infections in Saudi Arabia. Furthermore, the phylogenetic analysis results of three selected sequences showed that the Saudi HBoV1 strains obtained from respiratory samples belonged to group I human bocaviruses (Fig. 1) . Detection of human bocavirus in Japanese children with lower respiratory tract infections Frequent detection of viral coinfection in children hospitalized with acute respiratory tract infection using a real-time polymerase chain reaction abstract: Human bocavirus (HBoV) was recently discovered in children with respiratory distress and/or diarrhea. To our knowledge, no previous study has reported the existence of bocavirus in Saudi Arabia. Swabs samples from 80 children with respiratory tract infections were examined for the presence of HBoV. Real-time polymerase chain reaction was used as a sensitive method to detect the HBoV. Direct gene sequencing was used to determine the genotype of the detected virus isolates. HBoV was detected in 22.5% of the examined patients. The NP1 partial gene sequence from all patients showed that the circulated strains were related to HBoV-1 genotype. Most of HBoV infected patients showed evidence of mixed coinfection with other viral pathogens. The current study clearly demonstrated that genetically conserved HBoV1 circulates in Saudi Arabia. Interestingly, most of the HBoV1 infected cases were associated with high rates of co-infections with other viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3559585/ doi: 10.1371/journal.pone.0055500 id: cord-291217-fpte1q9m author: Adams, Madeleine title: Management of bronchiolitis date: 2009-05-13 words: 3536.0 sentences: 153.0 pages: flesch: 32.0 cache: ./cache/cord-291217-fpte1q9m.txt txt: ./txt/cord-291217-fpte1q9m.txt summary: The most recent Cochrane review of 22 trials involving 1428 infants with bronchiolitis who received inhaled bronchodilators (including β 2 agonists, ipratropium and adrenergic agents) reported a significant improvement in overall average clinical score, but had no effect on either pulse oximetry measurements or on risk of hospitalization. However, a recent placebo-controlled study of montelukast in 53 infants with a first episode of bronchiolitis demonstrated absence of benefit, with no significant differences in length of hospitalization, clinical severity score, or inflammatory mediators between the two groups. Fluids (either enteral or parenteral) and oxygen are the mainstays, although cpap or mechanical ventilation are effective for respiratory failure • there is no role for bronchodilators, corticosteroids, antiviral agents, physiotherapy, nebulized dnase or antibiotics, but nebulized 3% hypertonic saline administered with a bronchodilator may decrease length of stay in hospital abstract: Bronchiolitis is the commonest cause of hospital admission in infancy. Severity varies from mild and self-limiting through to respiratory failure requiring intensive care and ventilation. Many viruses cause bronchiolitis, the commonest being respiratory syncytial virus (RSV). Supportive care is the mainstay of treatment, with emphasis on fluid replacement and oxygen therapy. Agents with evidence of no benefit in acute bronchiolitis include β(2) agonists, ipratropium, montelukast, corticosteroids, antiviral agents such as ribavirin or RSV immunoglobulin, physiotherapy, nebulized deoxyribonuclease or antibiotics. It is possible that nebulized epinephrine has a small short-term effect, and that nebulized 3% hypertonic saline administered with a bronchodilator may decrease length of stay in hospital. Preventative strategies such as RSV immunoglobulin or the anti-RSV monoclonal antibody palivizumab can decrease disease severity. url: https://api.elsevier.com/content/article/pii/S175172220900050X doi: 10.1016/j.paed.2009.03.001 id: cord-346253-0mnsm6s4 author: Ahanchian, Hamid title: Respiratory viral infections in children with asthma: do they matter and can we prevent them? date: 2012-09-13 words: 7744.0 sentences: 399.0 pages: flesch: 35.0 cache: ./cache/cord-346253-0mnsm6s4.txt txt: ./txt/cord-346253-0mnsm6s4.txt summary: HRV are the most common viral agents [33] ; Other respiratory tract viruses detected in children with an asthma exacerbation include RSV, influenza, coronavirus, hMPV, parainfluenza virus, adenovirus, and bocavirus [34] [35] [36] . Beside importance for bone health, vitamin D plays an important role in adequate function of both the innate and adaptive immune systems including development of dendritic cells and regulatory T lymphocytes [151, 152] production of antimicrobial proteins by airway epithelium [153] , modifying the effect of intestinal flora on inflammatory disorders [107] , and modulation of the inflammatory response to viral infections [154] . In a recent study of 48 children from five to 18 years of age, with newly diagnosed asthma, vitamin D supplementation during the northern hemisphere winter months (September to July) prevented declining serum concentrations of 25(OH) D and reduced the risk of asthma exacerbation triggered by acute respiratory tract infections [161] . abstract: BACKGROUND: Asthma is a major public health problem with a huge social and economic burden affecting 300 million people worldwide. Viral respiratory infections are the major cause of acute asthma exacerbations and may contribute to asthma inception in high risk young children with susceptible genetic background. Acute exacerbations are associated with decreased lung growth or accelerated loss of lung function and, as such, add substantially to both the cost and morbidity associated with asthma. DISCUSSION: While the importance of preventing viral infection is well established, preventive strategies have not been well explored. Good personal hygiene, hand-washing and avoidance of cigarette smoke are likely to reduce respiratory viral infections. Eating a healthy balanced diet, active probiotic supplements and bacterial-derived products, such as OM-85, may reduce recurrent infections in susceptible children. There are no practical anti-viral therapies currently available that are suitable for widespread use. SUMMARY: Hand hygiene is the best measure to prevent the common cold. A healthy balanced diet, active probiotic supplements and immunostimulant OM-85 may reduce recurrent infections in asthmatic children. url: https://doi.org/10.1186/1471-2431-12-147 doi: 10.1186/1471-2431-12-147 id: cord-262673-j2ot35lt author: Ahmed-Hassan, Hanaa title: Innate Immune Responses to Highly Pathogenic Coronaviruses and Other Significant Respiratory Viral Infections date: 2020-08-18 words: 8591.0 sentences: 472.0 pages: flesch: 41.0 cache: ./cache/cord-262673-j2ot35lt.txt txt: ./txt/cord-262673-j2ot35lt.txt summary: Furthermore, respiratory epithelial cells and lung macrophages are capable of secreting a broad range of chemokines like IL-8, Macrophage inflammatory protein-1 (MIP-1), RANTES and cytokines including TNF-α, IL-6, IL-1β that influence the types of immune cells being recruited to the area in response to acute viral infections (177, 178) . Both Influenza and SARS virus can induce acute lung injury (ALI) which is accompanied by high levels of C5a, leading to the influx and activation of innate immune cells (199) (Figure 1) . Innate immune response of human alveolar type II cells infected with severe acute respiratory syndrome-coronavirus Middle East respiratory syndrome coronavirus shows poor replication but significant induction of antiviral responses in human monocytederived macrophages and dendritic cells Dynamic innate immune responses of human bronchial epithelial cells to severe acute respiratory syndrome-associated coronavirus infection Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells abstract: The new pandemic virus SARS-CoV-2 emerged in China and spread around the world in <3 months, infecting millions of people, and causing countries to shut down public life and businesses. Nearly all nations were unprepared for this pandemic with healthcare systems stretched to their limits due to the lack of an effective vaccine and treatment. Infection with SARS-CoV-2 can lead to Coronavirus disease 2019 (COVID-19). COVID-19 is respiratory disease that can result in a cytokine storm with stark differences in morbidity and mortality between younger and older patient populations. Details regarding mechanisms of viral entry via the respiratory system and immune system correlates of protection or pathogenesis have not been fully elucidated. Here, we provide an overview of the innate immune responses in the lung to the coronaviruses MERS-CoV, SARS-CoV, and SARS-CoV-2. This review provides insight into key innate immune mechanisms that will aid in the development of therapeutics and preventive vaccines for SARS-CoV-2 infection. url: https://doi.org/10.3389/fimmu.2020.01979 doi: 10.3389/fimmu.2020.01979 id: cord-257073-dm80bxnd author: Akmatov, Manas K. title: E-mail-based symptomatic surveillance combined with self-collection of nasal swabs: a new tool for acute respiratory infection epidemiology date: 2011-08-17 words: 3515.0 sentences: 177.0 pages: flesch: 46.0 cache: ./cache/cord-257073-dm80bxnd.txt txt: ./txt/cord-257073-dm80bxnd.txt summary: OBJECTIVE: We examined the feasibility of combining communication by e-mail and self-collection of nasal swabs for the prospective detection of acute respiratory infections in a non-medical setting. Conclusions: Combining e-mail-based symptomatic surveillance with nasal self-swabbing promises to be a powerful tool for the real-time identification of incident cases of acute respiratory infections and the associated pathogens in population-based studies. Conclusions: Combining e-mail-based symptomatic surveillance with nasal self-swabbing promises to be a powerful tool for the real-time identification of incident cases of acute respiratory infections and the associated pathogens in population-based studies. We tested the feasibility of combining real-time symptomatic surveillance with nasal self-swabbing for the prospective collection of epidemiologic and virological data on acute respiratory infections. Combining e-mail-based active symptomatic surveillance with self-collection of nasal swabs ensured prospective, accurate collection of data on incident episodes of acute respiratory infections and timely sample collection for the detection of respiratory pathogens. abstract: OBJECTIVE: We examined the feasibility of combining communication by e-mail and self-collection of nasal swabs for the prospective detection of acute respiratory infections in a non-medical setting. METHODS: The study was conducted among a convenience sample of employees (n = 53) at a research institution (December 2009–April 2010). Real-time data on the occurrence of acute respiratory symptoms and a nasal self-swab were collected prospectively, with automated weekly e-mails as a reminder mechanism. Reverse transcription polymerase chain reaction (RT-PCR) was used to detect respiratory viral pathogens in the swabs. RESULTS: Fifty-one out of 53 participants completed the study. The study design was well accepted. Thirty (∼57%) participants reported at least one episode of acute respiratory infection and returned the nasal swab during the study period (eight participants reported two episodes). The majority had no difficulties taking the self-swab and preferred this to swabbing by study personnel. Most participants obtained and returned the swabs within the recommended time. Viral respiratory pathogens were detected in 19 of 38 swabs (50%), with coronaviruses 229E/NL63 and OC43 and rhinoviruses A and B constituting 17 positive swabs (89%). CONCLUSIONS: Combining e-mail-based symptomatic surveillance with nasal self-swabbing promises to be a powerful tool for the real-time identification of incident cases of acute respiratory infections and the associated pathogens in population-based studies. url: https://api.elsevier.com/content/article/pii/S120197121100155X doi: 10.1016/j.ijid.2011.07.005 id: cord-277276-j2qzhvzi author: Al-Ayed, Mohamed S. title: Viral etiology of respiratory infections in children in southwestern Saudi Arabia using multiplex reverse-transcriptase polymerase chain reaction date: 2014 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: To investigate 15 respiratory viruses in children with acute respiratory tract infections (ARTIs) using multiplex reverse-transcriptase polymerase chain reaction (RT-PCR), and to analyze the clinical and epidemiological features of these viruses. METHODS: In a cross-sectional study, 135 children, ≤5 years of age who presented with ARTIs in Najran Maternity and Children Hospital, Najran, Saudi Arabia between October 2012 and July 2013 were included. The clinical and sociodemographic data, and the laboratory results were recorded using a standardized questionnaire. Two nasopharyngeal swabs were collected from each child: one for bacteriological examination, and the second for viral detection using multiplex RT-PCR. RESULTS: A single viral pathogen was detected in 76 patients, viral coinfections in 9, and mixed viral and bacterial pathogens in 15. Respiratory syncytial virus was isolated in 33 patients, human rhinovirus (hRV) in 22, adenovirus (AdV) in 19, human metapneumovirus in 13, influenza virus in 10, parainfluenza virus in 7, human corona virus (hCoV) in 4, and human bocavirus in one. CONCLUSION: Respiratory syncytial virus, hRV, and AdV were the most frequent viruses, accounting for more than two-thirds of the cases. Other viruses, such as MPV, hCoV NL63, and hCoV OC43, may play a role in pediatric ARTIs. Of significance is the potential use of multiplex RT-PCR to provide epidemiological and virological data for early detection of the emergence of novel respiratory viruses in the era of the Middle East respiratory syndrome coronavirus. url: https://www.ncbi.nlm.nih.gov/pubmed/25399211/ doi: nan id: cord-310508-zgqbfmzl author: Alavi-Moghaddam, Mostafa title: A Novel Coronavirus Outbreak from Wuhan City in China, Rapid Need for Emergency Departments Preparedness and Response; a Letter to Editor date: 2020-02-02 words: 1243.0 sentences: 69.0 pages: flesch: 44.0 cache: ./cache/cord-310508-zgqbfmzl.txt txt: ./txt/cord-310508-zgqbfmzl.txt summary: This report to World Health Organization (WHO), raised global public health concern because this is the third coronavirus âȂŞassociated acute respiratory illness outbreak. Clinical care of patients with suspected 2019-nCoV should focus on early recognition, immediate isolation (separation), implementation of appropriate infection prevention and control (IPC) measures and provision optimized supportive care. Both the health care worker (HCW) and the suspected case of acute respiratory illness (ALI) should wear a medical mask and the patient should better be directed to a separate area, an isolation room if available. At the time being, emergency preparedness and response for providing appropriate care to the patients suspected to coronavirus-associated acute respiratory illness (abovementioned plans) should be developed and implemented in the emergency departments, as the frontline of treating human infections of 2019-nCov in the hospitals. Clinical management of severe acute respiratory infection when novel coronavirus (2019-nCoV) infection is suspected: interim guidance abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32185368/ doi: nan id: cord-291639-hioh2s35 author: Alfredo, Potena title: Pathophysiology of viral-induced exacerbations of COPD date: 2007-12-17 words: 4434.0 sentences: 205.0 pages: flesch: 34.0 cache: ./cache/cord-291639-hioh2s35.txt txt: ./txt/cord-291639-hioh2s35.txt summary: Many epidemiological and clinical studies have suggested a role for respiratory viral infections in the natural history of chronic obstructive pulmonary disease (COPD), particularly during their exacerbations highlighting the need for development of effective vaccines and/or treatment for these viruses. In this review we will provide an overview of the relationship between respiratory virus infection and the molecular mechanisms involved in the activation of airway infl ammation in COPD exacerbations. It has been postulated that bacterial colonization could contribute to increased susceptibility to viral infection in COPD patients for example by increasing ICAM-1 expression in bronchial epithelial cells either directly or through induced infl ammation (Sajjan et al 2006) . Despite growing clinical evidence for a role of respiratory viral infections in the pathogenesis of COPD exacerbations, the precise mechanisms of respiratory virus-induced airway infl ammation and of host defenses against respiratory viruses are poorly understood (Johnston 2005) . abstract: Inflammation of the lower airways is a central feature of chronic obstructive pulmonary disease (COPD). Inflammatory responses are associated with an increased expression of a cascade of proteins including cytokines, chemokines, growth factors, enzymes, adhesion molecules and receptors. In most cases the increased expression of these proteins is the result of enhanced gene transcription: many of these genes are not expressed in normal cells under resting conditions but they are induced in the inflammatory process in a cell-specific manner. Transcription factors regulate the expression of many pro-inflammatory genes and play a key role in the pathogenesis of airway inflammation. Many studies have suggested a role for viral infections as a causative agent of COPD exacerbations. In this review we will focus our attention on the relationship between common respiratory viral infections and the molecular and inflammatory mechanisms that lead to COPD exacerbation. url: https://www.ncbi.nlm.nih.gov/pubmed/18268922/ doi: nan id: cord-260457-m1jbpo5l author: Allander, Tobias title: Human Bocavirus and Acute Wheezing in Children date: 2007-04-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: 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-321851-ku4z34lu author: Alosaimi, Bandar title: MERS-CoV infection is associated with downregulation of genes encoding Th1 and Th2 cytokines/chemokines and elevated inflammatory innate immune response in the lower respiratory tract date: 2020-02-29 words: 5619.0 sentences: 299.0 pages: flesch: 45.0 cache: ./cache/cord-321851-ku4z34lu.txt txt: ./txt/cord-321851-ku4z34lu.txt summary: Our results showed a downregulation of Th2, inadequate (partial) Th1 immune response and high expression levels of inflammatory cytokines IL-1α and IL-1β and the neutrophil chemoattractant chemokine IL-8 (CXCL8) in the lower respiratory tract of MERS-CoV infected patients. The lower respiratory tract samples from MERS-CoV infected patients and healthy non-infected controls were used to quantify expression levels of the main 12 human pro-inflammatory cytokines and chemokines (IL-1α, IL-1β, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12, IL-17A, IFN-γ, TNF-α, and GM-CSF). A side-by-side analysis of the data derived from the RT 2 -PCR profiling of pulmonary Th1/Th2 responses showed that genes encoding Th1 and Th2-related cytokines and chemokines were largely downregulated in the lower respiratory tract of MERS-CoV infected patients. Therefore, the high expression of inflammatory cytokines and downregulation of the Th1 and Th2 immune responses in the lower respiratory tracts of MERS-CoV infected patients may contribute to a more severe infection, higher case fatality, lung inflammation, and immunopathology. abstract: Abstract MERS-CoV, a highly pathogenic virus in humans, is associated with high morbidity and case fatality. Inflammatory responses have a significant impact on MERS-CoV pathogenesis and disease outcome. However, CD4+ T-cell induced immune responses during acute MERS-CoV infection are barely detectable, with potent inhibition of effector T cells and downregulation of antigen presentation. The local pulmonary immune response, particularly the Th1 and Th2-related immune response during acute severe MERS-CoV infection is not fully understood. In this study, we offer the first insights into the pulmonary gene expression profile of Th1 and Th2-related cytokines/chemokines (Th1 & Th2 responses) during acute MERS-CoV infection using RT2 Profiler PCR Arrays. We also quantified the expression level of primary inflammatory cytokines/chemokines. Our results showed a downregulation of Th2, inadequate (partial) Th1 immune response and high expression levels of inflammatory cytokines IL-1α and IL-1β and the neutrophil chemoattractant chemokine IL-8 (CXCL8) in the lower respiratory tract of MERS-CoV infected patients. Moreover, we identified a high viral load in all included patients. We also observed a correlation between inflammatory cytokines, Th1, and Th2 downregulation and the case fatality rate. Th1 and Th2 response downregulation, high expression of inflammatory cytokines, and high viral load may contribute to lung inflammation, severe infection, the evolution of pneumonia and ARDS, and a higher case fatality rate. Further study of the molecular mechanisms underlying the Th1 and Th2 regulatory pathways will be vital for active vaccine development and the identification of novel therapeutic strategies. url: https://doi.org/10.1016/j.cyto.2019.154895 doi: 10.1016/j.cyto.2019.154895 id: cord-292828-29jbf9ik author: Alsaleh, Asma N title: Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control date: 2014-01-09 words: 3915.0 sentences: 185.0 pages: flesch: 45.0 cache: ./cache/cord-292828-29jbf9ik.txt txt: ./txt/cord-292828-29jbf9ik.txt summary: title: Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control We therefore investigated the impact of sample collection quality and the presence of visible mould in samples upon respiratory virus detection by real-time polymerase chain reaction (PCR) assays. Quality control measures, including monitoring human DNA loads using ERV3 as a marker for epithelial cell components in samples should be undertaken to optimize the validity of real-time PCR results for respiratory virus investigations in community-based studies. Importantly, when using highly sensitive polymerase chain reaction (PCR) assays the detection rates for respiratory viruses are similar in both anterior nasal swab specimens and samples collected by the more traditional method of nasopharyngeal aspiration [18, 19] . The ORChID project is an ongoing comprehensive community-based study using PCR assays to detect respiratory viruses in anterior nasal swab specimens taken weekly by parents from their infants throughout the first 2-years of life. abstract: BACKGROUND: Carefully conducted, community-based, longitudinal studies are required to gain further understanding of the nature and timing of respiratory viruses causing infections in the population. However, such studies pose unique challenges for field specimen collection, including as we have observed the appearance of mould in some nasal swab specimens. We therefore investigated the impact of sample collection quality and the presence of visible mould in samples upon respiratory virus detection by real-time polymerase chain reaction (PCR) assays. METHODS: Anterior nasal swab samples were collected from infants participating in an ongoing community-based, longitudinal, dynamic birth cohort study. The samples were first collected from each infant shortly after birth and weekly thereafter. They were then mailed to the laboratory where they were catalogued, stored at -80°C and later screened by PCR for 17 respiratory viruses. The quality of specimen collection was assessed by screening for human deoxyribonucleic acid (DNA) using endogenous retrovirus 3 (ERV3). The impact of ERV3 load upon respiratory virus detection and the impact of visible mould observed in a subset of swabs reaching the laboratory upon both ERV3 loads and respiratory virus detection was determined. RESULTS: In total, 4933 nasal swabs were received in the laboratory. ERV3 load in nasal swabs was associated with respiratory virus detection. Reduced respiratory virus detection (odds ratio 0.35; 95% confidence interval 0.27-0.44) was observed in samples where the ERV3 could not be identified. Mould was associated with increased time of samples reaching the laboratory and reduced ERV3 loads and respiratory virus detection. CONCLUSION: Suboptimal sample collection and high levels of visible mould can impact negatively upon sample quality. Quality control measures, including monitoring human DNA loads using ERV3 as a marker for epithelial cell components in samples should be undertaken to optimize the validity of real-time PCR results for respiratory virus investigations in community-based studies. url: https://doi.org/10.1186/1471-2334-14-15 doi: 10.1186/1471-2334-14-15 id: cord-017140-k4lzwfge author: Andersen, Bjørg Marit title: Protection of Upper Respiratory Tract, Mouth and Eyes date: 2018-09-25 words: 6161.0 sentences: 412.0 pages: flesch: 59.0 cache: ./cache/cord-017140-k4lzwfge.txt txt: ./txt/cord-017140-k4lzwfge.txt summary: • Patient with suspected contagious respiratory infection-during transport, examination, treatment, etc.; use a face mask-also on the patient-to protect others and the environment from contamination. Department management is responsible for training, use and control of face masks, respirators and eye protection and that the equipment and written guidelines are available [5] . P3 mask is used by the surgical team and during all sterile procedures: in the case of operative treatment of patients with special types of airborne infection such as tuberculosis, etc., see above. However, surgical masks are not approved as protection against airborne infections: [5, 14, 24, 25] "Harmful microorganisms (bacteria, viruses, fungi) or components of microorganisms (e.g. endotoxins) may occur in air, either in dust, smoke or aerosols, or even finer distributed as droplet nuclei where all liquid has dried in. Transmission of microbes via small particles and droplet nuclei from influenza patients is not adequately controlled by the use of surgical mask [50] [51] [52] . abstract: Pathogenic bacteria and viruses may invade via upper and lower respiratory tract and via eye mucosa. When an infected person coughs or sneezes heavily, small, invisible droplets with the infective agent may reach a good distance from the source. By using the right form of protection at the right time, infection and disease are prevented. The present chapter is focused on the protection against airborne infections. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121627/ doi: 10.1007/978-3-319-99921-0_13 id: cord-306450-sh2mrhoq author: Appak, Özgür title: Viral respiratory infections diagnosed by multiplex polymerase chain reaction in pediatric patients date: 2019-01-03 words: 1742.0 sentences: 99.0 pages: flesch: 52.0 cache: ./cache/cord-306450-sh2mrhoq.txt txt: ./txt/cord-306450-sh2mrhoq.txt summary: The aim of this study was to investigate the respiratory viruses in children admitted to a university hospital with acute respiratory tract infection during the last 8 years by a multiplex polymerase chain reaction (PCR) assay. where coinfections were the most frequent cause of the respiratory infections in the studied group and followed by RV/EV and influenza A/B, respectively ( Figure 1B ). In our study, the age relation was significant for RSV and HMPV which were detected in 89% (260 of 292) and 81% (84 of 104) of children under 5 years, respectively. Similar to RSV, HMPV infections were frequently seen in winter and spring months as it was the case in our study while 90% of the HMPV cases were detected between January and April. Epidemiologic analysis of respiratory viral infections mainly in hospitalized children and adults in Midwest University Medical Center after the implementation of a 14-virus multiplex nucleic acid amplification test abstract: Syndromic diagnosis by multiplex nucleic acid amplification tests is the most practical approach to respiratory tract infections since the symptoms are rarely agent‐specific. The aim of this study was to investigate the respiratory viruses in children admitted to a university hospital with acute respiratory tract infection during the last 8 years by a multiplex polymerase chain reaction (PCR) assay. A total of 3162 respiratory samples collected from children between April 2011 and April 2018 tested by a multiplex real‐time PCR assay. Two different commercial assays were used during the study period, "AusDiagnostics/Respiratory Pathogens 12 (AusDiagnostics)" used between April 2011 and December 2015, which changed to "Fast Track Diagnostics/Respiratory Pathogens 21 (Fast Track Diagnostics)" after January 2016 to cover more viruses. Nucleic acid extraction was done by EZ1 Advanced XL platform (QIAGEN). Respiratory pathogens detected in 1857 of the 3162 (58.7%) samples. The most prevalent viruses during the 8‐year period were rhinovirus/enterovirus (RV/EV; 36.2%), respiratory syncytial virus (RSV; 19%), and influenza virus A/B (14.7%). Rhinovirus was the main contributor to the RV/EV group as shown by the assay used during the 2016‐2018 period. RV/EV and adenoviruses detected throughout the year. Influenza virus was most frequently detected during January to March when both RSV and metapneumovirus were also in circulation. The coinfection percentage was 10.2%. Rhinovirus was the most common virus in coinfections while RSV plus rhinovirus/enterovirus were the most frequent combination. RSV and metapneumovirus showed a similar seasonal distribution to the influenza virus, which made it necessary to use a virological diagnostic assay during the influenza season. url: https://doi.org/10.1002/jmv.25379 doi: 10.1002/jmv.25379 id: cord-265445-bazcczdj author: Arias-Bravo, Guisselle title: Overnutrition in Infants Is Associated With High Level of Leptin, Viral Coinfection and Increased Severity of Respiratory Infections: A Cross-Sectional Study date: 2020-02-18 words: 4565.0 sentences: 257.0 pages: flesch: 50.0 cache: ./cache/cord-265445-bazcczdj.txt txt: ./txt/cord-265445-bazcczdj.txt summary: title: Overnutrition in Infants Is Associated With High Level of Leptin, Viral Coinfection and Increased Severity of Respiratory Infections: A Cross-Sectional Study Objective: To investigate the relationship of overnutrition (obese and overweight) with severity of illness in children hospitalized with acute lower respiratory infections (ALRIs), frequency of viral coinfections and leptin levels. However, the empirical evidence needed to estimate the impact of overnutrition (including overweight and obese conditions) on the severity of viral respiratory infections in children is still lacking (10) . Hence, the objective of this study was to estimate the relationship of overnutrition on severity of illness in infants (aged between 0 and 5 months) and children (aged between 6 and 24 months) hospitalized with ALRIs. Moreover, frequency of viral coinfection, RSV viral load and levels of leptin according to nutritional status were evaluated. abstract: Objective: To investigate the relationship of overnutrition (obese and overweight) with severity of illness in children hospitalized with acute lower respiratory infections (ALRIs), frequency of viral coinfections and leptin levels. Methods: We studied 124 children <2 years old that were hospitalized for ALRI. Nutritional status was calculated by z-scores according to weight-for-age z-scores, length or height-for-age z-scores, and weight-for-height z-scores. Nasopharyngeal aspirates (NPAs) were obtained and viral respiratory pathogens were identified using reverse transcription polymerase chain reactions (RT-PCR). Respiratory syncytial virus (RSV) load was assessed using quantitative RT-PCR. NPA and plasma leptin level were measured. Clinical data and nutritional status were recorded, and patients were followed up until hospital discharge. Viral coinfection was defined as the presence of two or more viruses detected in the same respiratory sample. Severity of illness was determined by length of hospitalization and duration of oxygen therapy. Results: Children with overnutrition showed a greater frequency of viral coinfection than those with normal weight (71% obese vs. 37% normal weight p = 0.013; 68% overweight vs. 37% normal weight p = 0.004). A lower RSV load was found in obese (5.91 log(10) copies/mL) and overweight children (6.49 log(10) copies/mL) compared to normal weight children (8.06 log(10) copies/mL; p = 0.021 in both cases). In multivariate analysis, obese, and overweight infants <6 months old were associated with longer hospital stays (RR = 1.68; CI: 1.30–2.15 and obese: RR = 1.68; CI: 1.01–2.71, respectively) as well as a greater duration of oxygen therapy (RR = 1.80; IC: 1.41–2.29 and obese: RR = 1.91; CI: 1.15–3.15, respectively). Obese children <6 months showed higher plasma leptin level than normal weight children (7.58 vs. 5.12 ng/μl; p <0.046). Conclusions: In infants younger than 6 months, overnutrition condition was related to increased severity of infections and high plasma leptin level. Also, children with overnutrition showed a greater frequency of viral coinfection and low RSV viral load compared to normal weights children. These findings further contribute to the already existent evidence supporting the importance of overnutrition prevention in pediatric populations. url: https://www.ncbi.nlm.nih.gov/pubmed/32133330/ doi: 10.3389/fped.2020.00044 id: cord-350928-vj5qlzpj author: Arnott, Alicia title: Human bocavirus amongst an all‐ages population hospitalised with acute lower respiratory infections in Cambodia date: 2012-04-25 words: 4315.0 sentences: 317.0 pages: flesch: 55.0 cache: ./cache/cord-350928-vj5qlzpj.txt txt: ./txt/cord-350928-vj5qlzpj.txt summary: Objectives To investigate the prevalence and genetic diversity of HBoV amongst hospitalized patients with acute lower respiratory infection (ALRI) in Cambodia. In patients where HBoV is the only virus detected, the clinical symptoms reported are similar to those occurring as a result of infection with respiratory syncytial virus (RSV) and human metapneumovirus (HMPV), including bronchiolitis, bronchitis, pneumonia and exacerbation of asthma. 20 Here, we report the findings of the first study investigating the prevalence, seasonality, clinical characteristics and the molecular epidemiology of HBoV in amongst an all-ages population of patients hospitalized for acute lower respiratory illness (ALRI) in Cambodia over 3 consecutive years. 5 In this study, ALRI patient samples were screened for HBoV infection using a highly sensitive multiplex PCR assay previously shown to have a lower limit of detection of 4 copies of HBoV DNA ⁄ ll of viral transport medium. abstract: Please cite this paper as: Arnott et al. (2013) Human bocavirus amongst an all‐ages population hospitalised with acute lower respiratory infections in Cambodia. Influenza and Other Respiratory Viruses 7(2) 201–210. Background Human bocavirus (HBoV) is a novel parvovirus that is associated with respiratory and gastrointestinal tract disease. Objectives To investigate the prevalence and genetic diversity of HBoV amongst hospitalized patients with acute lower respiratory infection (ALRI) in Cambodia. Study Design Samples were collected from 2773 patients of all ages hospitalised with symptoms of ALRI between 2007 and 2009. All samples were screened by multiplex RT‐PCR/PCR for 18 respiratory viruses. All samples positive for HBoV were sequenced and included in this study. Results Of the samples tested, 43 (1·5%) were positive for HBoV. The incidence of HBoV did not vary between the consecutive seasons investigated, and HBoV infections were detected year‐round. The incidence of HBoV infection was highest in patients aged <2 years, with pneumonia or bronchopneumonia the most common clinical diagnosis, regardless of age. A total of 19 patients (44%) were co‐infected with HBoV and an additional respiratory pathogen. All isolates were classified as HBoV type 1 (HBoV‐1). High conservation between Cambodian NP1 and V1V2 gene sequences was observed. Conclusions Human bocavirus infection can result in serious illness, however is frequently detected in the context of viral co‐infection. Specific studies are required to further understand the true pathogenesis of HBoV in the context of severe respiratory illness. url: https://www.ncbi.nlm.nih.gov/pubmed/22531100/ doi: 10.1111/j.1750-2659.2012.00369.x id: cord-347509-2ysw9a0a author: Aronen, Matti title: Virus Etiology of Airway Illness in Elderly Adults date: 2016-06-20 words: 1759.0 sentences: 111.0 pages: flesch: 47.0 cache: ./cache/cord-347509-2ysw9a0a.txt txt: ./txt/cord-347509-2ysw9a0a.txt summary: 1, 2 Susceptibility to respiratory viral infections may be important especially in older age, but the viral etiology and clinical significance of respiratory illnesses in elderly adults is poorly documented. [2] [3] [4] The aims of this study were to investigate the presence of viruses in elderly adults and to assess the association between viral infection and respiratory illness and between viral infection and chronic illness in individuals with an illness that requires hospitalization. 10 The current study shows that there is an association between respiratory virus detection and weight in elderly adults. 3, 4 The objective of the current study was to assess what older adults with cancer know about their diagnosis and treatment and to identify factors associated with the completeness of this information. abstract: nan url: https://doi.org/10.1111/jgs.14175 doi: 10.1111/jgs.14175 id: cord-275166-qduf08kp author: Assane, Dieng title: Viral and Bacterial Etiologies of Acute Respiratory Infections Among Children Under 5 Years in Senegal date: 2018-02-13 words: 1877.0 sentences: 119.0 pages: flesch: 44.0 cache: ./cache/cord-275166-qduf08kp.txt txt: ./txt/cord-275166-qduf08kp.txt summary: Adenovirus was the most prevalent virus (50%; n = 81), followed by influenza virus (45.68%, n = 74), rhinovirus (40.12%; n = 65), enterovirus (25.31%; n = 41), and respiratory syncytial virus (16.05%; n = 26), whereas Streptococcus pneumoniae (17%; n = 29), Moraxella catarrhalis (15.43%; n = 25), and Haemophilus influenzae (8.02%; n = 13) were the most commonly isolated bacteria. Respiratory tract infections (RTIs) such as acute otitis media, sinusitis, bronchitis, and community-acquired pneumonia are a leading cause of infectious disease-related morbidity, hospitalization, and mortality among children worldwide, particularly in low-income countries. 1 According to World Health Organization (WHO), the prevalence of hospitalized children under 5 years with acute respiratory infections (ARIs) is estimated to be 20% and 90% of those were due to pneumonia. 4, 5 However, primary infections with viral pathogens can predispose to secondary bacterial infections, and the most frequently isolated bacteria in ARIs include Streptococcus pneumonia and Haemophilus influenzae. abstract: Acute respiratory infections (ARIs) are the leading cause of infectious disease–related morbidity, hospitalization, and morbidity among children worldwide. This study aimed to assess the viral and bacterial causes of ARI morbidity and mortality in children under 5 years in Senegal. Nasopharyngeal samples were collected from children under 5 years who had ARI. Viruses and bacteria were identified using multiplex real-time reverse transcription-polymerase chain reaction and conventional biochemical techniques, respectively. Adenovirus was the most prevalent virus (50%; n = 81), followed by influenza virus (45.68%, n = 74), rhinovirus (40.12%; n = 65), enterovirus (25.31%; n = 41), and respiratory syncytial virus (16.05%; n = 26), whereas Streptococcus pneumoniae (17%; n = 29), Moraxella catarrhalis (15.43%; n = 25), and Haemophilus influenzae (8.02%; n = 13) were the most commonly isolated bacteria. Virus pathogens seem more likely to be more prevalent in our settings and were often associated with bacteria and S. pneumoniae (6%; 16) coinfection. url: https://doi.org/10.1177/1178636118758651 doi: 10.1177/1178636118758651 id: cord-336562-5qmzne98 author: Auten, Richard title: Pediatric pulmonology year in review 2016: Part 2 date: 2017-04-25 words: 2535.0 sentences: 134.0 pages: flesch: 40.0 cache: ./cache/cord-336562-5qmzne98.txt txt: ./txt/cord-336562-5qmzne98.txt summary: The ability to obtain tidal breathing measurements may lead to new insights into changes in chest and abdominal motion in pediatric respiratory disease. 47 Acute viral bronchiolitis, due to RSV and other pathogens, continues to have a major impact worldwide on childhood mortality and hospital admissions, 51 is associated with subsequent asthma and allergy risk, 52 and could be increasing in incidence. 57 Flores et al 58 conducted a randomized clinical trial comparing 3% hypertonic saline to normal saline in previously healthy infants hospitalized with mild-to-moderate acute viral bronchiolitis. Thus, the study does not support the use of nebulized hypertonic saline over normal saline in therapy of hospitalized children with mild-to-moderate acute viral bronchiolitis. Association between trafficrelated air pollution and asthma in preschool children in a national Japanese nested case-control study Changes in lung function measured by spirometry and the forced oscillation technique in cystic fibrosis patients undergoing treatment for respiratory tract exacerbation abstract: Pediatric Pulmonology continues to publish research and clinical topics related to the entire range of children's respiratory disorders. As we have done annually in recent years, we here summarize some of the past year's publications in our major topic areas, as well as selected literature in these areas from other core journals relevant to our discipline. This review (Part 2) covers selected articles on neonatology, asthma, physiology and lung function testing, and infectious diseases. url: https://doi.org/10.1002/ppul.23719 doi: 10.1002/ppul.23719 id: cord-261598-w2tyongu author: Babady, N Esther title: The FilmArray® respiratory panel: an automated, broadly multiplexed molecular test for the rapid and accurate detection of respiratory pathogens date: 2014-01-09 words: 6030.0 sentences: 293.0 pages: flesch: 39.0 cache: ./cache/cord-261598-w2tyongu.txt txt: ./txt/cord-261598-w2tyongu.txt summary: The FilmArray Respiratory Panel (RP) (BioFire Diagnostics, Inc., Salt Lake City, UT, USA) is the first multiplex molecular panel cleared by the US FDA for the detection of both bacterial and viral respiratory pathogens in nasopharygeal swabs. The FilmArray Respiratory Panel (RP) (BioFire Diagnostics, Inc., Salt Lake City, UT, USA) is the first multiplex molecular panel cleared by the US FDA for the detection of both bacterial and viral respiratory pathogens in nasopharygeal swabs. Although the infection usually remains limited to the upper respiratory tract in most patients, complications due to influenza viruses have been reported in HSCT and SOT patients, especially lung transplant recipients [18, 22, 23] . In 2008, the FDA cleared the first broadly multiplexed molecular assay, the xTAG Ò respiratory viral panel ( Two studies have evaluated the performance of the eSensor RVP compared to other multiplex respiratory panels including the FilmArray RP, the xTAG RVP and the xTAG RVP FAST and to laboratory developed tests [58, 59] . abstract: The FilmArray Respiratory Panel (RP) (BioFire(™) Diagnostics, Inc., Salt Lake City, UT, USA) is the first multiplex molecular panel cleared by the US FDA for the detection of both bacterial and viral respiratory pathogens in nasopharygeal swabs. The FilmArray RP targets 20 pathogens including 17 viruses and subtypes and three bacteria, and is performed with minimal sample manipulation. The FilmArray RP has a fully automated sample-to-answer workflow with a turn-around-time of approximately 1 h. The reported sensitivity and specificity of the assay ranges from 80 to 100 and 100%, respectively, with the sensitivity for the adenovirus as low as 46%. A new version of the FilmArray RP assay (version 1.7) with improved sensitivity for the adenovirus was released in 2013. The performance characteristics and simplified workflow have allowed its implementation in a wide range of laboratories. The FilmArray RP has changed the diagnostic landscape and will have a significant impact on the care of patients with respiratory tract infection. url: https://doi.org/10.1586/14737159.2013.848794 doi: 10.1586/14737159.2013.848794 id: cord-318229-29cgwivt author: Baier, Claas title: Molecular characteristics and successful management of a respiratory syncytial virus outbreak among pediatric patients with hemato-oncological disease date: 2018-02-13 words: 5698.0 sentences: 309.0 pages: flesch: 47.0 cache: ./cache/cord-318229-29cgwivt.txt txt: ./txt/cord-318229-29cgwivt.txt summary: An outbreak case is a patient with a positive RSV laboratory testing in samples from the upper or lower respiratory tract and a definite or possible nosocomial onset. Considering bed and room occupancy on the ward during the outbreak, direct patient to patient transmission (e.g. via droplets or contaminated surfaces) in cases 1 and 2 as well as 3 and 4 seemed epidemiologically possible as each pair was accommodated in the same room before samples were tested positive for RSV. Overlying sequence information from different quasispecies detected in the samples are highlighted in a box measures, in particular single room accommodation for contact patients (quarantine), suspension of all social activities, and surgical masks for all HCWs and visitors at any time, addressed the postulated RSV transmission pathways during this outbreak. Outbreak of respiratory syncytial virus (RSV) infection in immunocompromised adults on a hematology ward abstract: BACKGROUND: Respiratory syncytial virus (RSV) is responsible for upper and lower respiratory tract infection in adults and children. Especially immunocompromised patients are at high risk for a severe course of infection, and mortality is increased. Moreover RSV can spread in healthcare settings and can cause outbreaks. Herein we demonstrate the successful control and characteristics of a RSV outbreak that included 8 patients in our Department of Pediatric Hematology and Oncology. METHODS: We performed an epidemiologic investigation and a molecular analysis of the outbreak strains. Moreover we present the outbreak control bundle and our concept for RSV screening in the winter season. RESULTS: RSV A and B strains caused the outbreak. RSV B strains affected 3 patients, 2 of whom were co-infected with RSV A. Exactly this RSV A strain was detected in another 5 patients. Our multimodal infection control bundle including prophylactic RSV screening was able to rapidly stop the outbreak. CONCLUSION: An infection control bundle in RSV outbreaks should address all potential transmission pathways. In pediatric settings the restriction of social activities might have a temporal negative impact on quality of life but helps to limit transmission opportunities. Molecular analysis allows better understanding of RSV outbreaks and, if done in a timely manner, might be helpful for guidance of infection control measures. url: https://www.ncbi.nlm.nih.gov/pubmed/29449938/ doi: 10.1186/s13756-018-0316-2 id: cord-346096-aml84iv1 author: Bailey, Emily S. title: Molecular surveillance of respiratory viruses with bioaerosol sampling in an airport date: 2018-09-17 words: 2503.0 sentences: 131.0 pages: flesch: 46.0 cache: ./cache/cord-346096-aml84iv1.txt txt: ./txt/cord-346096-aml84iv1.txt summary: These results suggest the feasibility of employing bioaerosol surveillance techniques in public transportation areas, such as airports, as a noninvasive way to detect and characterize novel respiratory viruses. In this pilot study, we studied bioaerosol samples collected in Raleigh Durham International Airport for molecular evidence of respiratory viruses. Although not the focus of our study, we did not detect viable viruses using culture analysis associated with positive aerosol samples at RDU airport. In this pilot aerosol study, we conducted surveillance for human and zoonotic respiratory viruses in an airport setting over a period of nine weeks from January to March 2018. Despite these limitations, the results of this study suggest that aerosol sampling is a useful technique for respiratory virus surveillance in high traffic and crowded areas such as airports. abstract: Recognizing that crowded, high-traffic airports and airplanes have been implicated in respiratory disease transmission, we partnered with administrators of Raleigh Durham International Airport (RDU) in conducting a pilot study of aerosol surveillance for respiratory viruses at RDU. From January to March 2018 we used NIOSH 2-stage samplers to collect 150 min aerosol samples in crowded areas at RDU. Four (17%) of the 24 samples were positive for known respiratory pathogens including influenza D virus and adenovirus. These results suggest the feasibility of employing bioaerosol surveillance techniques in public transportation areas, such as airports, as a noninvasive way to detect and characterize novel respiratory viruses. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s40794-018-0071-7) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s40794-018-0071-7 doi: 10.1186/s40794-018-0071-7 id: cord-255901-nl9k8uwd author: Barasheed, Osamah title: Uptake and effectiveness of facemask against respiratory infections at mass gatherings: a systematic review date: 2016-03-29 words: 4522.0 sentences: 256.0 pages: flesch: 50.0 cache: ./cache/cord-255901-nl9k8uwd.txt txt: ./txt/cord-255901-nl9k8uwd.txt summary: Studies conducted in community or health care settings found facemasks to be generally effective against influenza-like illness (ILI) or even against severe acute respiratory syndrome (SARS) but its effectiveness against respiratory infections at MGs remains unknown. 15, 17 A review of non-pharmaceutical interventions against respiratory tract infections among Hajj pilgrims presented data on the uptake of facemask and acknowledged that compliance was generally poor, but did not evaluate its effectiveness during Hajj. A few studies showed that providing educational session on protective measures against respiratory infections (including facemask) before Hajj was associated with significantly higher uptake of facemasks among pilgrims. 68 Focused studies are required to investigate factors influencing facemask compliance among attendees of Hajj and other MGs. In this systematic review, pooled data of facemask effectiveness showed that participants who used facemask during Hajj are about 20% less likely to suffer from respiratory infections compared to those who do not use it. abstract: OBJECTIVES: The risk of acquisition and transmission of respiratory infections is high among attendees of mass gatherings (MGs). Currently used interventions have limitations yet the role of facemask in preventing those infections at MG has not been systematically reviewed. We have conducted a systematic review to synthesise evidence about the uptake and effectiveness of facemask against respiratory infections in MGs. METHODS: A comprehensive literature search was conducted according to the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines using major electronic databases such as, Medline, EMBASE, SCOPUS and CINAHL. RESULTS: Of 25 studies included, the pooled sample size was 12710 participants from 55 countries aged 11 to 89 years, 37% were female. The overall uptake of facemask ranged from 0.02% to 92.8% with an average of about 50%. Only 13 studies examined the effectiveness of facemask, and their pooled estimate revealed significant protectiveness against respiratory infections (relative risk [RR] = 0.89, 95% CI: 0.84-0.94, p < 0.01), but the study end points varied widely. CONCLUSION: A modest proportion of attendees of MGs use facemask, the practice is more widespread among health care workers. Facemask use seems to be beneficial against certain respiratory infections at MGs but its effectiveness against specific infection remains unproven. url: https://api.elsevier.com/content/article/pii/S1201971216310104 doi: 10.1016/j.ijid.2016.03.023 id: cord-276927-rxudwp2v author: Barbas, Carmen Sílvia Valente title: Goal-Oriented Respiratory Management for Critically Ill Patients with Acute Respiratory Distress Syndrome date: 2012-08-23 words: 7991.0 sentences: 374.0 pages: flesch: 35.0 cache: ./cache/cord-276927-rxudwp2v.txt txt: ./txt/cord-276927-rxudwp2v.txt summary: Rapid administration of antibiotics and resuscitative measures in case of sepsis and septic shock associated with protective ventilatory strategies and early short-term paralysis associated with differential ventilatory techniques (recruitment maneuvers with adequate positive end-expiratory pressure titration, prone position, and new extracorporeal membrane oxygenation techniques) in severe ARDS can help improve its prognosis. Incorporation of modified risk factors such as acute increase of respiratory rate, presence of tachypnea, detection of pulse oximeter desaturation, increased necessity of oxygen supplementation, presence of low pH, acidosis, or hypoxemia in an arterial blood gas sample in clinical practice can improve the clinicians'' ability to perform early diagnosis and prompt therapeutic intervention in ARDS [17] . abstract: This paper, based on relevant literature articles and the authors' clinical experience, presents a goal-oriented respiratory management for critically ill patients with acute respiratory distress syndrome (ARDS) that can help improve clinicians' ability to care for these patients. Early recognition of ARDS modified risk factors and avoidance of aggravating factors during hospital stay such as nonprotective mechanical ventilation, multiple blood products transfusions, positive fluid balance, ventilator-associated pneumonia, and gastric aspiration can help decrease its incidence. An early extensive clinical, laboratory, and imaging evaluation of “at risk patients” allows a correct diagnosis of ARDS, assessment of comorbidities, and calculation of prognostic indices, so that a careful treatment can be planned. Rapid administration of antibiotics and resuscitative measures in case of sepsis and septic shock associated with protective ventilatory strategies and early short-term paralysis associated with differential ventilatory techniques (recruitment maneuvers with adequate positive end-expiratory pressure titration, prone position, and new extracorporeal membrane oxygenation techniques) in severe ARDS can help improve its prognosis. Revaluation of ARDS patients on the third day of evolution (Sequential Organ Failure Assessment (SOFA), biomarkers and response to infection therapy) allows changes in the initial treatment plans and can help decrease ARDS mortality. url: https://doi.org/10.1155/2012/952168 doi: 10.1155/2012/952168 id: cord-256065-zz2907h0 author: Barral-Arca, Ruth title: A Meta-Analysis of Multiple Whole Blood Gene Expression Data Unveils a Diagnostic Host-Response Transcript Signature for Respiratory Syncytial Virus date: 2020-03-06 words: 5643.0 sentences: 285.0 pages: flesch: 44.0 cache: ./cache/cord-256065-zz2907h0.txt txt: ./txt/cord-256065-zz2907h0.txt summary: title: A Meta-Analysis of Multiple Whole Blood Gene Expression Data Unveils a Diagnostic Host-Response Transcript Signature for Respiratory Syncytial Virus We meta-analyzed seven transcriptome microarray studies from the public Gene Expression Omnibus (GEO) repository containing a total of 922 samples, including RSV, healthy controls, coronaviruses, enteroviruses, influenzas, rhinoviruses, and coinfections, from both adult and pediatric patients. RSV additionally induced over-representation of differential expressed pattern recognition receptor genes as compared to healthy controls (Table S3 ): (i) Toll-like receptors (TLR) cascades (R-HSA-168898; adjusted p-value = 1.23 × 10 −3 ), including TLR3 (R-HSA-168164; adjusted p-value = 2.45 × 10 −2 ), which are specialized in the recognition of conserved molecular features of different pathogens such as bacteria, viruses, fungi, and parasites; and (ii) C-type lectin receptors (R-HSA-5621481; adjusted p-value = 5.12 × 10 −6 ), capable of sensing glycans present in viral pathogens to activate antiviral immune responses such as phagocytosis, cytokine production, antigen processing and presentation, and subsequent T cell activation. abstract: Respiratory syncytial virus (RSV) is one of the major causes of acute lower respiratory tract infection worldwide. The absence of a commercial vaccine and the limited success of current therapeutic strategies against RSV make further research necessary. We used a multi-cohort analysis approach to investigate host transcriptomic biomarkers and shed further light on the molecular mechanism underlying RSV-host interactions. We meta-analyzed seven transcriptome microarray studies from the public Gene Expression Omnibus (GEO) repository containing a total of 922 samples, including RSV, healthy controls, coronaviruses, enteroviruses, influenzas, rhinoviruses, and coinfections, from both adult and pediatric patients. We identified > 1500 genes differentially expressed when comparing the transcriptomes of RSV-infected patients against healthy controls. Functional enrichment analysis showed several pathways significantly altered, including immunologic response mediated by RSV infection, pattern recognition receptors, cell cycle, and olfactory signaling. In addition, we identified a minimal 17-transcript host signature specific for RSV infection by comparing transcriptomic profiles against other respiratory viruses. These multi-genic signatures might help to investigate future drug targets against RSV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32155831/ doi: 10.3390/ijms21051831 id: cord-320286-9tumplp3 author: Bastien, Nathalie title: Human Bocavirus Infection, Canada date: 2006-05-17 words: 1425.0 sentences: 85.0 pages: flesch: 59.0 cache: ./cache/cord-320286-9tumplp3.txt txt: ./txt/cord-320286-9tumplp3.txt summary: The virus was identified in clinical specimens from infants and children with respiratory tract illness. All specimens were negative for influenza viruses A and B; parainfluenza viruses 1, 2, and 3; adenovirus; and respiratory syncytial virus (RSV) by direct or indirect fluorescence assays or virus isolation and for human metapneumovirus (HMPV) by reverse transcription-polymerase chain reaction. Although a causal relationship still needs to be demonstrated by including a control group of healthy persons, detection of HBoV in respiratory tract specimens from patients with undiagnosed ARI suggests that this virus may be associated with respiratory illness. Most (89%) hospitalizations were in persons <5 years of age, which suggests that HBoV may cause more severe respiratory illness in infants and children, similar to disease caused by RSV (4, 5) , HMPV (6,7), human coronavirus NL63 (8) (9) (10) (11) (12) (13) (14) , and human coronavirus 229E (15) . abstract: Human Bocavirus was detected in 18 (1.5%) of 1,209 respiratory specimens collected in 2003 and 2004 in Canada. The main symptoms of affected patients were cough (78%), fever (67%), and sore throat (44%). Nine patients were hospitalized; of these, 8 (89%) were <5 years of age. url: https://www.ncbi.nlm.nih.gov/pubmed/16704852/ doi: 10.3201/eid1205.051424 id: cord-322524-bq9ok8h1 author: Belongia, Edward A title: Clinical Features, Severity, and Incidence of RSV Illness During 12 Consecutive Seasons in a Community Cohort of Adults ≥60 Years Old date: 2018-11-27 words: 5184.0 sentences: 285.0 pages: flesch: 45.0 cache: ./cache/cord-322524-bq9ok8h1.txt txt: ./txt/cord-322524-bq9ok8h1.txt summary: Studies conducted in the 1980s and 1990s first identified RSV as a cause of acute respiratory illness in a variety of adult populations, including older adults, working-age adults, hospitalized patients, and residents of long-term care facilities [5] [6] [7] [8] [9] . A 6-season study of adults ≥50 years old with predominantly outpatient acute respiratory illness found that RSV was the third most common viral pathogen (after influenza and human rhinovirus) [19] . The objective of this study was to describe the clinical characteristics, severity, clinical outcomes, and long-term incidence of medically attended RSV illness in a community cohort of adults ≥60 years of age from the 2004-2005 through 2015-2016 influenza seasons. Seasonal incidence of medically attended respiratory syncytial virus infection in a community cohort of adults ≥50 years old abstract: BACKGROUND: The epidemiology and burden of respiratory syncytial virus (RSV) illness are not well defined in older adults. METHODS: Adults ≥60 years old seeking outpatient care for acute respiratory illness were recruited from 2004–2005 through 2015–2016 during the winter seasons. RSV was identified from respiratory swabs by multiplex polymerase chain reaction. Clinical characteristics and outcomes were ascertained by interview and medical record abstraction. The incidence of medically attended RSV was estimated for each seasonal cohort. RESULTS: RSV was identified in 243 (11%) of 2257 enrollments (241 of 1832 individuals), including 121 RSV type A and 122 RSV type B. The RSV clinical outcome was serious in 47 (19%), moderate in 155 (64%), and mild in 41 (17%). Serious outcomes included hospital admission (n = 29), emergency department visit (n = 13), and pneumonia (n = 23) and were associated with lower respiratory tract symptoms during the enrollment visit. Moderate outcomes included receipt of a new antibiotic prescription (n = 144; 59%), bronchodilator/nebulizer (n = 45; 19%), or systemic corticosteroids (n = 28; 12%). The relative risk of a serious outcome was significantly increased in persons aged ≥75 years (vs 60–64 years) and in those with chronic obstructive pulmonary disease or congestive heart failure. The average seasonal incidence was 139 cases/10 000, and it was significantly higher in persons with cardiopulmonary disease compared with others (rate ratio, 1.89; 95% confidence interval, 1.44–2.48). CONCLUSIONS: RSV causes substantial outpatient illness with lower respiratory tract involvement. Serious outcomes are common in older patients and those with cardiopulmonary disease. url: https://www.ncbi.nlm.nih.gov/pubmed/30619907/ doi: 10.1093/ofid/ofy316 id: cord-272143-6ej3eibd author: Benavides‐Nieto, Marta title: The role of respiratory viruses in children with humoral immunodeficiency on immunoglobulin replacement therapy date: 2018-12-21 words: 1875.0 sentences: 133.0 pages: flesch: 40.0 cache: ./cache/cord-272143-6ej3eibd.txt txt: ./txt/cord-272143-6ej3eibd.txt summary: We have evaluated these infections in children with humoral immunodeficiencies who required immunoglobulin replacement therapy, considering their relationship with symptoms, lung function, bacterial co‐infection, and outcomes. CONCLUSIONS: In our experience, viral respiratory tract infections can cause significant respiratory symptoms and impaired lung function, in children with HID, despite immunoglobulin replacement therapy. Children with severe T-cell immunodeficiencies present impaired clearance of respiratory viruses, and pulmonary complications of viral infections are leading causes of morbidity and mortality in this group of patients. 1 However, the role of respiratory viruses in children with other types of primary immunodeficiency (PID), mainly those with humoral immunodeficiencies (HID) or diseases of immune dysregulation, has hardly been studied. 2, 7 We report, to the best of our knowledge, the first study that analyses respiratory viruses in pediatric patients with predominantly antibody deficiency who required IRT, considering their relationship with clinical symptoms and pulmonary function, bacterial co-infection, treatment and outcomes. abstract: BACKGROUND: The role of viruses in children with respiratory tract infections and humoral immunodeficiencies has hardly been studied. We have evaluated these infections in children with humoral immunodeficiencies who required immunoglobulin replacement therapy, considering their relationship with symptoms, lung function, bacterial co‐infection, and outcomes. METHODS: We conducted a prospective case‐control study during a 1‐year period, including children with humoral immunodeficiencies receiving immunoglobulin replacement therapy. For each patient, at least one healthy family member was included. Respiratory samples for viral detection were taken every 1‐3 months, and in case of respiratory tract infections. Symptoms questionnaires were filled biweekly. Spirometry and sputum culture were performed in every episode. RESULTS: Sixty‐six episodes were analyzed in 14 patients (median age 12 years; IQR 7‐17), identifying 18 respiratory viruses (27.3%), being rhinovirus the most frequently isolated one (12/18; 66%). Positive viral episodes were associated with clinical symptoms (89% vs 43%), more frequent antibiotic treatment (44% vs 15%) or hospital admission (22% vs 0%) than negative ones. Patients with positive viral detection showed impaired lung function, with lower FEV1 and FVC values. CONCLUSIONS: In our experience, viral respiratory tract infections can cause significant respiratory symptoms and impaired lung function, in children with HID, despite immunoglobulin replacement therapy. These patients could benefit from the monitoring of viral infections, as these may be a gateway for ongoing lung damage. url: https://www.ncbi.nlm.nih.gov/pubmed/30575324/ doi: 10.1002/ppul.24214 id: cord-275605-mbiojk39 author: Benkouiten, Samir title: Clinical respiratory infections and pneumonia during the Hajj pilgrimage: A systematic review date: 2018-12-04 words: 5812.0 sentences: 282.0 pages: flesch: 46.0 cache: ./cache/cord-275605-mbiojk39.txt txt: ./txt/cord-275605-mbiojk39.txt summary: METHOD: The MEDLINE/PubMed and Scopus databases were searched for all relevant papers published prior to February 2018 that evaluated the prevalence of clinical symptoms of respiratory infections, including pneumonia, among Hajj pilgrims, as well as their influenza and pneumococcal vaccination status. We carried out a systematic review of cohort and hospital studies that reported the prevalence of clinical symptoms of respiratory infections and pneumonia among pilgrims during the Hajj, and both their influenza and pneumococcal vaccination status, with the aim to provide data allowing the investigation of the impact of this large mass-gathering event on public health policies and services and to identify potential targets for preventive measures. For inclusion, the article had to meet the following criteria: (1) Original study involving Hajj pilgrims; (2) detailed description of the study population, including influenza and pneumococcal vaccination status when available; (3) clinical or self-reported respiratory symptoms and diseases. abstract: BACKGROUND: The Islamic Hajj pilgrimage to Mecca is one of the world's largest annual mass gatherings. Inevitable overcrowding during the pilgrims' stay greatly increases the risk of acquiring and spreading infectious diseases, especially respiratory diseases. METHOD: The MEDLINE/PubMed and Scopus databases were searched for all relevant papers published prior to February 2018 that evaluated the prevalence of clinical symptoms of respiratory infections, including pneumonia, among Hajj pilgrims, as well as their influenza and pneumococcal vaccination status. RESULTS: A total of 61 papers were included in the review. Both cohort- and hospital-based studies provide complementary data, and both are therefore necessary to provide a complete picture of the total burden of respiratory diseases during the Hajj. Respiratory symptoms have been common among Hajj pilgrims over the last 15 years. In cohorts of pilgrims, cough ranged from 1.9% to 91.5%. However, the prevalence rates of the most common symptoms (cough, sore throat, and subjective fever) of influenza-like illness (ILI) varied widely across the included studies. These studies have shown variable results, with overall rates of ILI ranging from 8% to 78.2%. These differences might result from differences in study design, study period, and rates of vaccination against seasonal influenza that ranged from 1.1% to 100% among study participants. Moreover, the definition of ILI was inconsistent across studies. In hospitalized Hajj pilgrims, the prevalence of pneumonia, that remains a major concern in critically ill patients, ranged from 0.2% to 54.8%. CONCLUSIONS: Large multinational follow-up studies are recommended for clinic-based syndromic surveillance, in conjunction with microbiological surveillance. Matched cohorts ensure better comparability across studies. However, study design and data collection procedures should be standardized to facilitate reporting and to achieve comparability between studies. Furthermore, the definition of ILI, and of most common symptoms used to define respiratory infections (e.g., upper respiratory tract infection), need to be precisely defined and consistently used. Future studies need to address potential effect of influenza and pneumococcal vaccine in the context of the Hajj pilgrimage. url: https://doi.org/10.1016/j.tmaid.2018.12.002 doi: 10.1016/j.tmaid.2018.12.002 id: cord-285557-my16g91c author: Berger, A. title: Severe acute respiratory syndrome (SARS)—paradigm of an emerging viral infection date: 2004-01-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract An acute and often severe respiratory illness emerged in southern China in late 2002 and rapidly spread to different areas of the Far East as well as several countries around the globe. When the outbreak of this apparently novel infectious disease termed severe acute respiratory syndrome (SARS) came to an end in July 2003, it had caused over 8000 probable cases worldwide and more than 700 deaths. Starting in March 2003, the World Health Organization (WHO) organised an unprecedented international effort by leading laboratories working together to find the causative agent. Little more than one week later, three research groups from this WHO-coordinated network simultaneously found evidence of a hitherto unknown coronavirus in SARS patients, using different approaches. After Koch’s postulates had been fulfilled, WHO officially declared on 16 April 2003 that this virus never before seen in humans is the cause of SARS. Ever since, progress around SARS-associated coronavirus (SARS-CoV) has been swift. Within weeks of the first isolate being obtained, its complete genome was sequenced. Diagnostic tests based on the detection of SARS-CoV RNA were developed and made available freely and widely; nevertheless the SARS case definition still remains based on clinical and epidemiological criteria. The agent’s environmental stability, methods suitable for inactivation and disinfection, and potential antiviral compounds have been studied, and development of vaccines and immunotherapeutics is ongoing. Despite its grave consequences in humanitarian, political and economic terms, SARS may serve as an example of how much can be achieved through a well-coordinated international approach, combining the latest technological advances of molecular virology with more “traditional” techniques carried out to an excellent standard. url: https://www.ncbi.nlm.nih.gov/pubmed/14675864/ doi: 10.1016/j.jcv.2003.09.011 id: cord-335567-ssnvr6nj author: Berry, Michael title: Identification of New Respiratory Viruses in the New Millennium date: 2015-03-06 words: 7477.0 sentences: 379.0 pages: flesch: 40.0 cache: ./cache/cord-335567-ssnvr6nj.txt txt: ./txt/cord-335567-ssnvr6nj.txt summary: In 2001, this led to the discovery of human metapneumovirus (hMPV) and soon following that the outbreak of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) promoted an increased interest in coronavirology and the latter discovery of human coronavirus (HCoV) NL63 and HCoV-HKU1. Middle East Respiratory Syndrome coronavirus (MERS-CoV) represents the most recent outbreak of a completely novel respiratory virus, which occurred in Saudi Arabia in 2012 and presents a significant threat to human health. In recent years six new human respiratory viruses have been reported including human metapneumovirus (hMPV) [16] , bocavirus and four new human coronaviruses including Severe Acute Respiratory Syndrome coronavirus (SARS-CoV), human coronavirus NL63 (HCoV-NL63), HCoV-HKU1 and Middle East Respiratory Syndrome coronavirus (MERS-CoV). Evidence of a novel human coronavirus that is associated with respiratory tract disease in infants and young children Genetic variability of human coronavirus OC43-, 229E-, and NL63-like strains and their association with lower respiratory tract infections of hospitalized infants and immunocompromised patients abstract: The rapid advancement of molecular tools in the past 15 years has allowed for the retrospective discovery of several new respiratory viruses as well as the characterization of novel emergent strains. The inability to characterize the etiological origins of respiratory conditions, particularly in children, led several researchers to pursue the discovery of the underlying etiology of disease. In 2001, this led to the discovery of human metapneumovirus (hMPV) and soon following that the outbreak of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) promoted an increased interest in coronavirology and the latter discovery of human coronavirus (HCoV) NL63 and HCoV-HKU1. Human bocavirus, with its four separate lineages, discovered in 2005, has been linked to acute respiratory tract infections and gastrointestinal complications. Middle East Respiratory Syndrome coronavirus (MERS-CoV) represents the most recent outbreak of a completely novel respiratory virus, which occurred in Saudi Arabia in 2012 and presents a significant threat to human health. This review will detail the most current clinical and epidemiological findings to all respiratory viruses discovered since 2001. url: https://doi.org/10.3390/v7030996 doi: 10.3390/v7030996 id: cord-343042-9mue4eiv author: Bertozzi, Giuseppe title: Mistrial or Misdiagnosis: The Importance of Autopsy and Histopathological Examination in Cases of Sudden Infant Bronchiolitis-Related Death date: 2020-05-27 words: 2451.0 sentences: 117.0 pages: flesch: 38.0 cache: ./cache/cord-343042-9mue4eiv.txt txt: ./txt/cord-343042-9mue4eiv.txt summary: Following these complaints, the autopsy was performed, and subsequent histological examinations revealed the presence of typical and pathognomonic histological findings of acute viral bronchiolitis, whose morphological appearance is poorly reported in the literature. For all these reasons, the autopsy, either clinical or medicolegal, is mandatory in cases of sudden unexpected infant death to manage claim requests because only the histological examinations performed on samples collected during the autopsy can reveal the real cause of death. In fact, in the reported case studies, histopathologic diagnostics identified pathognomonic signs of acute bronchiolitis characterized by edema, congestion, leukocytic infiltration in the bronchiolar wall, leukocytes in the peribronchial interstitial pulmonary space, allowing the identification of the exact cause of death. The analysis of the presented cases shows that the autopsy is mandatory in SUID occurrence, in which the absence of anamnestic data and/or acute clinical signs does not allow to identify the cause of death. abstract: Pediatrics, among all the branches of medicine, is a sector not particularly affected by a high number of claims. Nevertheless, the economic value of the compensation is significantly high, for example, in cases of children who suffered multiple disabilities following perinatal lesions with a long life expectancy. In Italy, most of the claims for compensation concern surgical pathologies and infections. Among these latter, the dominant role is taken by respiratory tract infections. In this context, the purpose of this manuscript is to present a case series of infant deaths in different emergency-related facilities (ambulances, emergency rooms) denounced by relatives. Following these complaints, the autopsy was performed, and subsequent histological examinations revealed the presence of typical and pathognomonic histological findings of acute viral bronchiolitis, whose morphological appearance is poorly reported in the literature. The analysis of these cases made it possible to highlight the following conclusions: the main problems in diagnosing sudden death causes, especially in childhood, are the rapidity of death and the scarce correlation between the preexistent diseases and of the cause of death itself. For all these reasons, the autopsy, either clinical or medicolegal, is mandatory in cases of sudden unexpected infant death to manage claim requests because only the histological examinations performed on samples collected during the autopsy can reveal the real cause of death. url: https://doi.org/10.3389/fped.2020.00229 doi: 10.3389/fped.2020.00229 id: cord-000602-z5p3a64x author: Bhat, Niranjan title: Use and Evaluation of Molecular Diagnostics for Pneumonia Etiology Studies date: 2012-03-08 words: 3608.0 sentences: 165.0 pages: flesch: 26.0 cache: ./cache/cord-000602-z5p3a64x.txt txt: ./txt/cord-000602-z5p3a64x.txt summary: Although our final molecular diagnostic platform was ultimately selected on the basis of operational and strategic considerations determined by the specific context of PERCH, our review highlighted several conceptual and practical challenges in respiratory diagnostics that have broader relevance for the performance and interpretation of pneumonia research studies. Although our final molecular diagnostic platform was ultimately selected on the basis of operational and strategic considerations determined by the specific context of PERCH, our review highlighted several conceptual and practical challenges in respiratory diagnostics that have broader relevance for the performance and interpretation of pneumonia research studies. The specific research-related demands of PERCH added to these constraints, requiring that our diagnostic strategy must exclude any prior assumptions regarding the likely importance of specific pathogens; must include a full range of respiratory tract specimens, including upper respiratory swab or aspirate, induced sputum, lung aspirate, bronchoalveolar lavage, and pleural fluid; must be comprehensive, yet realistic; must appropriately balance the demands of accuracy and efficiency; must account for both clinical and research ethical issues; and must be feasible for use and support at all participating field sites. abstract: Comprehensive microbiological testing will be a core function of the Pneumonia Etiology Research for Child Health (PERCH) project. The development stage of PERCH provided the time and resources necessary for us to conduct a comprehensive review of the current state of respiratory diagnostics. These efforts allowed us to articulate the unique requirements of PERCH, establish that molecular methods would be central to our testing strategy, and focus on a short list of candidate platforms. This process also highlighted critical challenges in the general design and interpretation of diagnostic evaluation studies, particularly in the field of respiratory infections. Although our final molecular diagnostic platform was ultimately selected on the basis of operational and strategic considerations determined by the specific context of PERCH, our review highlighted several conceptual and practical challenges in respiratory diagnostics that have broader relevance for the performance and interpretation of pneumonia research studies. url: https://academic.oup.com/cid/article-pdf/54/suppl_2/S153/20938419/cir1060.pdf doi: 10.1093/cid/cir1060 id: cord-337562-pkejb0a9 author: Bialasiewicz, Seweryn title: Merkel Cell Polyomavirus DNA in Respiratory Specimens from Children and Adults date: 2009-03-17 words: 1738.0 sentences: 91.0 pages: flesch: 55.0 cache: ./cache/cord-337562-pkejb0a9.txt txt: ./txt/cord-337562-pkejb0a9.txt summary: Merkel cell polyomavirus (MCPyV) DNA was detected in 7 (1.3%) of 526 respiratory tract samples from patients in Australia with upper or lower respiratory tract symptoms. Merkel cell polyomavirus (MCPyV) DNA was detected in 7 (1.3%) of 526 respiratory tract samples from patients in Australia with upper or lower respiratory tract symptoms. I n the past 2 years, several previously unknown human polyomaviruses (PyVs) have been identifi ed: KI virus (KIPyV) (1) and WU virus (WUPyV) (2) from respiratory samples, and more recently, Merkel cell polyomavirus (MCPyV), most commonly from Merkel cell carcinoma tissue (3) . The presence of MCPyV in samples positive by real-time PCR was then confi rmed by using partial large T antigen (LT3) and major capsid protein (VP1) conventional MCPyV detection PCR assays of Feng et al. Sequence data from positive specimens indicate that MCPyV found in respiratory secretions is similar to the viruses identifi ed within Merkel cell carcinomas. abstract: Merkel cell polyomavirus (MCPyV) DNA was detected in 7 (1.3%) of 526 respiratory tract samples from patients in Australia with upper or lower respiratory tract symptoms. Partial T antigen and major capsid protein sequences of MCPyV identified in respiratory secretions showed high homology (99%–100%) to those found in Merkel cell carcinoma. url: https://doi.org/10.3201/eid1503.081067 doi: 10.3201/eid1503.081067 id: cord-353698-gj8sx3zy author: Bibiano-Guillen, C. title: Adapted Diving Mask (ADM) device as respiratory support with oxygen output during COVID-19 pandemic date: 2020-10-28 words: 3320.0 sentences: 198.0 pages: flesch: 52.0 cache: ./cache/cord-353698-gj8sx3zy.txt txt: ./txt/cord-353698-gj8sx3zy.txt summary: title: Adapted Diving Mask (ADM) device as respiratory support with oxygen output during COVID-19 pandemic The most extended therapeutic approach for COVID-19 is based on two main strategies [10] [11] [12] [13] : pharmacological treatment directed toward several physiological targets (viremia, immunological reactions, prothrombotic reactions) and hemodynamic and respiratory support with positive end-expiratory pressure (PEEP) in addition to mechanical ventilation. A descriptive case series study of twenty-five patients with acute respiratory syndrome secondary to SARS-CoV2 infection was performed at a Spanish center, Hospital Universitario Infanta Leonor of Madrid, between March 30 and April 18, 2020. Table 4 shows the different variables used to analyze the improvement in the intervention and the mean value of all oxygen saturation measurements for all days that ADM therapy was used in those patients who prolonged its time of use. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0735675720309396?v=s5 doi: 10.1016/j.ajem.2020.10.043 id: cord-349606-lup6tm2s author: Biill Primo, Osvaldo Vinícius title: Detection of Respiratory Viruses in Nasopharyngeal Swab and Adenoid Tissue from Children Submitted to Adenoidectomy: Pre- and Postoperative Analysis date: 2014-02-17 words: 2793.0 sentences: 157.0 pages: flesch: 45.0 cache: ./cache/cord-349606-lup6tm2s.txt txt: ./txt/cord-349606-lup6tm2s.txt summary: Methods A prospective observational study was conducted in 36 patients under 12 years of age with upper airway lymphoid hypertrophy who were undergoing adenoidectomy, in which various respiratory viruses were investigated using real-time polymerase chain reaction in adenoid tissue and nasopharyngeal secretions collected preoperatively and 30 days postoperatively. Methods A prospective observational study was conducted in 36 patients under 12 years of age with upper airway lymphoid hypertrophy who were undergoing adenoidectomy, in which various respiratory viruses were investigated using realtime polymerase chain reaction in adenoid tissue and nasopharyngeal secretions collected preoperatively and 30 days postoperatively. Several respiratory viruses (influenza A and B; parainfluenza 1, 2, 3, and 4; rhinovirus; respiratory syncytial virus; human bocavirus; coronaviruses; and metapneumovirus) were investigated by quantitative real-time polymerase chain reaction (q-PCR) in adenoid tissue removed surgically and nasal swab specimens collected preoperatively and at 1 month postoperative follow-up visit. abstract: Introduction The presence of respiratory viruses in lymphoid tissues of the nasopharynx and oropharynx and its impact on recurrent infections and hypertrophy of these tissues are not yet fully understood. Objective To identify and determine the prevalence of major respiratory viruses in nasopharyngeal secretions and adenoid tissue pre- and postoperatively of children undergoing adenoidectomy. Methods A prospective observational study was conducted in 36 patients under 12 years of age with upper airway lymphoid hypertrophy who were undergoing adenoidectomy, in which various respiratory viruses were investigated using real-time polymerase chain reaction in adenoid tissue and nasopharyngeal secretions collected preoperatively and 30 days postoperatively. Results At least 1 viral agent was isolated in any of the samples collected in 58.3% of children and 25.9% of total samples. Respiratory viruses were identified in 33.8% of preoperative nasopharyngeal specimens and in 19.8% of postoperative secretion. Of the 21 patients with positive results for any respiratory virus, 6 (28.6%) had more than 1 virus. Considering all 36 respiratory viruses found, the main agent isolated was rhinovirus (27.8%), followed by bocavirus (22.2%). Conclusion The virus found more frequently in all samples was rhinovirus. After removal of adenoid tissue, there was a decrease in the prevalence of the virus contained in nasopharyngeal secretion 30 days after surgery. url: https://doi.org/10.1055/s-0034-1368135 doi: 10.1055/s-0034-1368135 id: cord-281051-i229xv0o author: Bishop-Williams, Katherine E. title: A protocol for a systematic literature review: comparing the impact of seasonal and meteorological parameters on acute respiratory infections in Indigenous and non-Indigenous peoples date: 2017-01-26 words: 6404.0 sentences: 366.0 pages: flesch: 44.0 cache: ./cache/cord-281051-i229xv0o.txt txt: ./txt/cord-281051-i229xv0o.txt summary: This protocol outlines our process for conducting a systematic review to investigate whether associations between ARI and seasonal or meteorological parameters differ between Indigenous and non-Indigenous groups residing in the same geographical region. This paper outlines a protocol for conducting a systematic review to investigate whether associations between ARI and seasonal or meteorological parameters differ between Indigenous and non-Indigenous groups residing in the same geographical region. This research builds from the United Nations Declaration of the Rights of Indigenous Peoples [13] understanding of the term Indigenous peoples, which states that an Indigenous person self-identifies as Indigenous; has historical continuity Table 1 Inclusion and exclusion criteria for a systematic literature review investigating the impact of seasonal and meteorological parameters on acute respiratory infection (ARI) in Indigenous and non-Indigenous peoples abstract: BACKGROUND: Acute respiratory infections (ARI) are a leading cause of morbidity and mortality globally, and are often linked to seasonal and/or meteorological conditions. Globally, Indigenous peoples may experience a different burden of ARI compared to non-Indigenous peoples. This protocol outlines our process for conducting a systematic review to investigate whether associations between ARI and seasonal or meteorological parameters differ between Indigenous and non-Indigenous groups residing in the same geographical region. METHODOLOGY: A search string will be used to search PubMed(®), CAB Abstracts/CAB Direct(©), and Science Citation Index(®) aggregator databases. Articles will be screened using inclusion/exclusion criteria applied first at the title and abstract level, and then at the full article level by two independent reviewers. Articles maintained after full article screening will undergo risk of bias assessment and data will be extracted. Heterogeneity tests, meta-analysis, and forest and funnel plots will be used to synthesize the results of eligible studies. DISCUSSION AND REGISTRATION: This protocol paper describes our systematic review methods to identify and analyze relevant ARI, season, and meteorological literature with robust reporting. The results are intended to improve our understanding of potential associations between seasonal and meteorological parameters and ARI and, if identified, whether this association varies by place, population, or other characteristics. The protocol is registered in the PROSPERO database (#38051). ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13643-016-0399-x) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/28122603/ doi: 10.1186/s13643-016-0399-x id: cord-328829-yywxmioq author: Boixeda, Ramon title: Microbiological study of patients hospitalized for acute exacerbation of chronic obstructive pulmonary disease (AE-COPD) and the usefulness of analytical and clinical parameters in its identification (VIRAE study) date: 2012-05-25 words: 3823.0 sentences: 207.0 pages: flesch: 41.0 cache: ./cache/cord-328829-yywxmioq.txt txt: ./txt/cord-328829-yywxmioq.txt summary: title: Microbiological study of patients hospitalized for acute exacerbation of chronic obstructive pulmonary disease (AE-COPD) and the usefulness of analytical and clinical parameters in its identification (VIRAE study) The etiology of the respiratory infection was studied by conventional sputum, paired serology tests for atypical bacteria, and viral diagnostic techniques (immunochromatography, immunofluorescence, cell culture, and molecular biology techniques). The aims of our study were to identify the etiology of respiratory infections in patients hospitalized for AE-COPD using different diagnostic tests and to evaluate the usefulness of the clinical and analytical parameters of the diagnostic process. Identification was made based on the respiratory infection and dyspnea admission diagnoses from the International Statistical Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) 19,20 (491, 492, 493, 496, 518.81, 464, 465, 466, 519.11, 786 .0), excluding the patients who had a known cause of respiratory failure that was different from infectious exacerbation (heart failure, pulmonary thromboembolism, pneumonia). abstract: PURPOSE: Respiratory infection is the most common cause for acute exacerbation of chronic obstructive pulmonary disease (AE-COPD). The aim of this work was to study the etiology of the respiratory infection in order to assess the usefulness of the clinical and analytical parameters used for COPD identification. PATIENTS AND METHODS: We included 132 patients over a period of 2 years. The etiology of the respiratory infection was studied by conventional sputum, paired serology tests for atypical bacteria, and viral diagnostic techniques (immunochromatography, immunofluorescence, cell culture, and molecular biology techniques). We grouped the patients into four groups based on the pathogens isolated (bacterial versus. viral, known etiology versus unknown etiology) and compared the groups. RESULTS: A pathogen was identified in 48 patients. The pathogen was identified through sputum culture in 34 patients, seroconversion in three patients, and a positive result from viral techniques in 14 patients. No significant differences in identifying etiology were observed in the clinical and analytical parameters within the different groups. The most cost-effective tests were the sputum test and the polymerase chain reaction. CONCLUSION: Based on our experience, clinical and analytical parameters are not useful for the etiological identification of COPD exacerbations. Diagnosing COPD exacerbation is difficult, with the conventional sputum test for bacterial etiology and molecular biology techniques for viral etiology providing the most profitability. Further studies are necessary to identify respiratory syndromes or analytical parameters that can be used to identify the etiology of new AE-COPD cases without the laborious diagnostic techniques. url: https://www.ncbi.nlm.nih.gov/pubmed/22745532/ doi: 10.2147/copd.s30568 id: cord-281916-v6u5mr2i author: Bonnin, Paul title: Study and interest of cellular load in respiratory samples for the optimization of molecular virological diagnosis in clinical practice date: 2016-08-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Respiratory viral diagnosis of upper respiratory tract infections has largely developed through multiplex molecular techniques. Although the sensitivity of different types of upper respiratory tract samples seems to be correlated to the number of sampled cells, this link remains largely unexplored. METHODS: Our study included 800 upper respiratory tract specimens of which 400 negative and 400 positive for viral detection in multiplex PCR. All samples were selected and matched for age in these 2 groups. For the positive group, samples were selected for the detected viral species. RESULTS: Among the factors influencing the cellularity were the type of sample (p < 0.0001); patient age (p < 0.001); viral positive or negative nature of the sample (p = 0.002); and, for the positive samples, the number of viral targets detected (0.004 < p < 0.049) and viral species. CONCLUSION: The cellular load of upper respiratory samples is multifactorial and occurs for many in the sensitivity of molecular detection. However it was not possible to determine a minimum cellularity threshold allowing molecular viral detection. The differences according to the type of virus remain to be studied on a larger scale. url: https://doi.org/10.1186/s12879-016-1730-9 doi: 10.1186/s12879-016-1730-9 id: cord-339039-6gyo9rya author: Bonvehí, Pablo E. title: Transmission and Control of Respiratory Viral Infections in the Healthcare Setting date: 2018-04-30 words: 4737.0 sentences: 248.0 pages: flesch: 37.0 cache: ./cache/cord-339039-6gyo9rya.txt txt: ./txt/cord-339039-6gyo9rya.txt summary: The purpose of this review is to describe the most frequent and relevant nosocomial viral respiratory infections, their mechanisms of transmission and the infection control measures to prevent their spread in the healthcare setting. RECENT FINDINGS: Although most mechanisms of transmission and control measures of nosocomial viral infections are already known, improved diagnostic tools allow better characterization of these infections and also lead to the discovery of new viruses such as the coronavirus, which is the cause of the Middle East Respiratory Syndrome, or the human bocavirus. Influenza virus can be transmitted through infectious droplets eliminated by patients when coughing or sneezing, or through direct contact with surfaces contaminated by respiratory secretions from symptomatic infected subjects (Table 1 ) [32] . Preventive measures to avoid adenovirus nosocomial infections include patient cohorting, reduction of visitors and contact and droplet precautions, along with the exclusion of infected healthcare workers from clinical duties (Table 2 ) [13, 36] . abstract: PURPOSE OF THE REVIEW: Viral respiratory infections have been recognized as a cause of severe illness in immunocompromised and non-immunocompromised hosts. This acknowledgement is a consequence of improvement in diagnosis and better understanding of transmission. Available vaccines and antiviral drugs for prophylaxis and treatment have been developed accordingly. Viral respiratory pathogens are increasingly recognized as nosocomial pathogens as well. The purpose of this review is to describe the most frequent and relevant nosocomial viral respiratory infections, their mechanisms of transmission and the infection control measures to prevent their spread in the healthcare setting. RECENT FINDINGS: Although most mechanisms of transmission and control measures of nosocomial viral infections are already known, improved diagnostic tools allow better characterization of these infections and also lead to the discovery of new viruses such as the coronavirus, which is the cause of the Middle East Respiratory Syndrome, or the human bocavirus. Also, the ability to understand better the impact, dissemination and prevention of these viruses, allows us to improve the measures to prevent these infections. SUMMARY: Healthcare viral respiratory infections increase patient morbidity. Each virus has a different mechanism of transmission; therefore, early detection and prompt implementation of infection control measures are very important in order to avoid their transmission in the hospital setting. url: https://www.ncbi.nlm.nih.gov/pubmed/32226322/ doi: 10.1007/s40506-018-0163-y id: cord-284332-p4c1fneh author: Bosma, Karen J. title: Pharmacotherapy for Prevention and Treatment of Acute Respiratory Distress Syndrome: Current and Experimental Approaches date: 2012-09-19 words: 14516.0 sentences: 721.0 pages: flesch: 37.0 cache: ./cache/cord-284332-p4c1fneh.txt txt: ./txt/cord-284332-p4c1fneh.txt summary: [47] Although both of these studies were conducted prior to the 1994 AECC definition, ARDS was strictly defined in the aforementioned studies, including a PaO 2 /FiO 2 ratio <150 or intrapulmonary shunt >20% in patients requiring mechanical ventilation and who had diffuse infiltrates on chest radiograph without clinical evidence of heart failure as pulmonary arterial occlusion pressures were <18 mmHg. Building on the results of these two studies, Sinuff and colleagues [48] developed practice guidelines for prophylactic ketoconazole use, and tested the implementation and efficacy of these guidelines in two ICUs (one control and one active comparator). [119] A phase II study enrolling 98 patients with ALI compared an antioxidant enteral feeding formula containing eicosapentaenoic acid, g-linolenic acid and antioxidant vitamins with placebo, and observed improved oxygenation, reduced pulmonary inflammation, fewer days of mechanical ventilation and fewer non-pulmonary organ failures in the treatment arm, although there was no difference in mortality between this approach and the control group. abstract: The acute respiratory distress syndrome (ARDS) arises from direct and indirect injury to the lungs and results in a life-threatening form of respiratory failure in a heterogeneous, critically ill patient population. Critical care technologies used to support patients with ARDS, including strategies for mechanical ventilation, have resulted in improved outcomes in the last decade. However, there is still a need for effective pharmacotherapies to treat ARDS, as mortality rates remain high. To date, no single pharmacotherapy has proven effective in decreasing mortality in adult patients with ARDS, although exogenous surfactant replacement has been shown to reduce mortality in the paediatric population with ARDS from direct causes. Several promising therapies are currently being investigated in preclinical and clinical trials for treatment of ARDS in its acute and subacute, exudative phases. These include exogenous surfactant therapy, β(2)-adrenergic receptor agonists, antioxidants, immunomodulating agents and HMG-CoA reductase inhibitors (statins). Recent research has also focused on prevention of acute lung injury and acute respiratory distress in patients at risk. Drugs such as captopril, rosiglitazone and incyclinide (COL-3), a tetracycline derivative, have shown promising results in animal models, but have not yet been tested clinically. Further research is needed to discover therapies to treat ARDS in its late, fibroproliferative phase. Given the vast number of negative clinical trials to date, it is unlikely that a single pharmacotherapy will effectively treat all patients with ARDS from differing causes. Future randomized controlled trials should target specific, more homogeneous subgroups of patients for single or combination therapy. url: https://www.ncbi.nlm.nih.gov/pubmed/20568833/ doi: 10.2165/10898570-000000000-00000 id: cord-259997-8f8di4eu author: Botti, Chiara title: Characterization of respiratory infection viruses in hospitalized children from Naples province in Southern Italy date: 2018-04-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Most acute respiratory infections (ARIs) in children are due to viral etiology, and represent an important cause of mortality and morbidity in children <5 years old in developing countries. The pathogens that cause ARIs vary geographically and by season, and viruses serve a major role. In the present study, the distribution of the seven respiratory viruses that are more prevalent in Southern European countries were retrospectively analyzed in a Southern Italy Hospital, that centralizes pediatric diseases from the Naples province. Viruses were categorized by a FilmArray Respiratory Panel, and demonstrated no substantial differences in sex, age and seasonal viruses distribution. However, all the investigated viruses had a higher detection rate in the surrounding municipalities than in the metropolitan area of Naples. In recent years, the association between air pollution and respiratory infections has become an increasing public health concern. The data in this study support this association in the surrounding areas of Naples extensively contaminated by environmental toxic agents. In these areas, characterization of the epidemiology of ARIs is required to implement a prevention and control program. url: https://www.ncbi.nlm.nih.gov/pubmed/29805499/ doi: 10.3892/etm.2018.6061 id: cord-268038-9jjpc1a2 author: Boukhvalova, M title: Treatment with novel RSV Ig RI-002 controls viral replication and reduces pulmonary damage in immunocompromised Sigmodon hispidus date: 2015-09-14 words: 4354.0 sentences: 230.0 pages: flesch: 37.0 cache: ./cache/cord-268038-9jjpc1a2.txt txt: ./txt/cord-268038-9jjpc1a2.txt summary: These results indicate the potential of RI-002 to improve outcome of RSV infection in immunocompromised subjects not only by controlling viral replication, but also by reducing damage to lung parenchyma and epithelial airway lining, but further studies are needed. In this case, treatment with a drug that has strong antiviral activity may have a higher therapeutic efficacy in immunosuppressed patients compared with immunocompetent individuals infected with RSV because of the reduction in pulmonary damage caused by excessive viral replication. Although normal cotton rats treated with saline cleared RSV by day 10 post infection, immunosuppressed saline-treated animals had~6 log 10 PFU of virus in their lungs and noses at that time. To determine whether RI-002 has an effect on pulmonary pathology associated with prolonged RSV replication in immunosuppressed animals, lung tissue was collected for histopathology analysis on day 10 post infection. abstract: Respiratory syncytial virus (RSV) is a significant cause of bronchiolitis and pneumonia in several high health risk populations, including infants, elderly and immunocompromised individuals. Mortality in hematopoietic stem cell transplant recipients with lower respiratory tract RSV infection can exceed 80%. It has been shown that RSV replication in immunosuppressed individuals is significantly prolonged, but the contribution of pulmonary damage, if any, to the pathogenesis of RSV disease in this susceptible population is not known. In this work, we tested RI-002, a novel standardized Ig formulation containing a high level of RSV-neutralizing Ab, for its ability to control RSV infection in immunocompromised cotton rats Sigmodon hispidus. Animals immunosuppressed by repeat cyclophosphamide injections were infected with RSV and treated with RI-002. Prolonged RSV replication, characteristic of immunosuppressed cotton rats, was inhibited by RI-002 administration. Ab treatment reduced detection of systemic dissemination of viral RNA. Importantly, pulmonary interstitial inflammation and epithelial hyperplasia that were significantly elevated in immunosuppressed animals were reduced by RI-002 administration. These results indicate the potential of RI-002 to improve outcome of RSV infection in immunocompromised subjects not only by controlling viral replication, but also by reducing damage to lung parenchyma and epithelial airway lining, but further studies are needed. url: https://doi.org/10.1038/bmt.2015.212 doi: 10.1038/bmt.2015.212 id: cord-023712-nptuuixw author: Bower, John title: Bronchiolitis date: 2014-10-31 words: 5404.0 sentences: 307.0 pages: flesch: 41.0 cache: ./cache/cord-023712-nptuuixw.txt txt: ./txt/cord-023712-nptuuixw.txt summary: 12 Influenza A and B viruses frequently cause lower respiratory tract disease among children younger than 2 years of age, but the proportion manifesting as bronchiolitis is less than that observed with RSV. Although rapid diagnostic testing is generally unnecessary, it may be useful at times for implementing appropriate infection control, monitoring seasonal patterns of respiratory pathogens, restricting antimicrobial use, or providing confirmation of the diagnosis in children with unusual clinical presentations or severe disease. Timely diagnosis of specific viral respiratory pathogens may occasionally be necessary to guide specific antiviral therapy in children with high-risk conditions or severe illness with influenza or RSV. Although the risk of respiratory failure is relatively low for most children with RSV bronchiolitis, a small number of severely affected infants will require assisted ventilation in most intensive care units each year. Comparison of risk factors for human metapneumovirus and respiratory syncytial virus disease severity in young children abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173511/ doi: 10.1016/b978-1-4557-4801-3.00068-0 id: cord-023728-fgcldn4e author: Bower, John title: Croup in Children (Acute Laryngotracheobronchitis) date: 2014-10-31 words: 3887.0 sentences: 232.0 pages: flesch: 53.0 cache: ./cache/cord-023728-fgcldn4e.txt txt: ./txt/cord-023728-fgcldn4e.txt summary: The term croup now generally refers to an acute respiratory tract illness characterized by a distinctive barking cough, hoarseness, and inspiratory stridor in a young child, usually between 6 months and 3 years old. From 1979 to 1997, croup cases associated with parainfluenza viruses, estimated from the National Hospital Discharge Survey, showed that the number of admissions among children younger than 5 years decreased by approximately one third. 14 The human coronaviruses (hCoV) have been identified in up to 7% of young children with acute respiratory tract infections, with the NL63 strain most often associated with croup. Although abrupt onset of stridor at night may be the initial indication of illness, most children have a prodrome of mild upper respiratory tract signs of rhinorrhea, cough, and sometimes fever 12 to 48 hours before the onset of the distinctive "rough and stridulous" cough of croup. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173542/ doi: 10.1016/b978-1-4557-4801-3.00061-8 id: cord-257171-kp2huia0 author: Brand, Kim H. title: Use of MMP‐8 and MMP‐9 to assess disease severity in children with viral lower respiratory tract infections date: 2012-07-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Matrix metalloproteinases (MMPs) play an important role in respiratory inflammatory diseases, such as asthma and chronic obstructive pulmonary disease. It was hypothesized that MMP‐8 and MMP‐9 may function as biological markers to assess disease severity in viral lower respiratory tract infections in children. MMP‐8 and MMP‐9 mRNA expression levels in peripheral blood mononuclear cells (PBMCs) and granulocytes obtained in both the acute and recovery phase from 153 children with mild, moderate, and severe viral lower respiratory tract infections were determined using real‐time PCR. In addition, MMP‐8 and MMP‐9 concentrations in blood and nasopharyngeal specimens were determined during acute mild, moderate, and severe infection, and after recovery using ELISA. Furthermore, PBMCs and neutrophils obtained from healthy volunteers were stimulated with RSV, LPS (TLR4 agonist), and Pam3Cys (TLR2 agonist) in vitro. Disease severity of viral lower respiratory tract infections in children is associated with increased expression levels of the MMP‐8 and MMP‐9 genes in both PBMCs and granulocytes. On the contrary, in vitro experiments showed that MMP‐8 and MMP‐9 mRNA and protein expression in PBMCs and granulocytes is not induced by stimulation with RSV, the most frequent detected virus in young children with viral lower respiratory tract infections. These data indicate that expression levels of the MMP‐8 and MMP‐9 genes in both PBMCs and neutrophils are associated with viral lower respiratory tract infections disease severity. These observations justify future validation in independent prospective study cohorts of the usefulness of MMP‐8 and MMP‐9 as potential markers for disease severity in viral respiratory infections. J. Med. Virol. 84:1471–1480, 2012. © 2012 Wiley Periodicals, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/22825827/ doi: 10.1002/jmv.23301 id: cord-296836-aizquh16 author: Brenner, Hermann title: Vitamin D Insufficiency and Deficiency and Mortality from Respiratory Diseases in a Cohort of Older Adults: Potential for Limiting the Death Toll during and beyond the COVID-19 Pandemic? date: 2020-08-18 words: 4435.0 sentences: 192.0 pages: flesch: 39.0 cache: ./cache/cord-296836-aizquh16.txt txt: ./txt/cord-296836-aizquh16.txt summary: We assessed the prevalence of vitamin D insufficiency and deficiency, defined by 25-hydroxyvitamin D (25(OH)D) blood levels of 30–50 and <30 nmol/L, respectively, and their association with mortality from respiratory diseases during 15 years of follow-up in a cohort of 9548 adults aged 50–75 years from Saarland, Germany. Vitamin D insufficiency and deficiency are common and account for a large proportion of respiratory disease mortality in older adults, supporting the hypothesis that vitamin D(3) supplementation could be helpful to limit the burden of the COVID-19 pandemic, particularly among women. We previously assessed the prevalence of vitamin D insufficiency and deficiency and their association with all-cause mortality and mortality from cardiovascular, cancer and respiratory diseases during a mean follow-up of 9.5 years in a cohort of 9548 adults aged 50-75 years from Saarland, Germany [4] [5] [6] [7] [8] . abstract: The COVID-19 pandemic goes along with increased mortality from acute respiratory disease. It has been suggested that vitamin D(3) supplementation might help to reduce respiratory disease mortality. We assessed the prevalence of vitamin D insufficiency and deficiency, defined by 25-hydroxyvitamin D (25(OH)D) blood levels of 30–50 and <30 nmol/L, respectively, and their association with mortality from respiratory diseases during 15 years of follow-up in a cohort of 9548 adults aged 50–75 years from Saarland, Germany. Vitamin D insufficiency and deficiency were common (44% and 15%, respectively). Compared to those with sufficient vitamin D status, participants with vitamin D insufficiency and deficiency had strongly increased respiratory mortality, with adjusted hazard ratios (95% confidence intervals) of 2.1 (1.3–3.2) and 3.0 (1.8–5.2) overall, 4.3 (1.3–14.4) and 8.5 (2.4–30.1) among women, and 1.9 (1.1–3.2) and 2.3 (1.1–4.4) among men. Overall, 41% (95% confidence interval: 20–58%) of respiratory disease mortality was statistically attributable to vitamin D insufficiency or deficiency. Vitamin D insufficiency and deficiency are common and account for a large proportion of respiratory disease mortality in older adults, supporting the hypothesis that vitamin D(3) supplementation could be helpful to limit the burden of the COVID-19 pandemic, particularly among women. url: https://www.ncbi.nlm.nih.gov/pubmed/32824839/ doi: 10.3390/nu12082488 id: cord-301254-093yih5n author: Brittain-Long, Robin title: Prospective evaluation of a novel multiplex real-time PCR assay for detection of fifteen respiratory pathogens—Duration of symptoms significantly affects detection rate date: 2010-01-18 words: 2860.0 sentences: 160.0 pages: flesch: 48.0 cache: ./cache/cord-301254-093yih5n.txt txt: ./txt/cord-301254-093yih5n.txt summary: OBJECTIVES: The aim of the present study was to evaluate the diagnostic performance and clinical use of a novel multiplex PCR method in adults with community-acquired respiratory viral infection, and the impact of duration of symptoms on detection rates. CONCLUSIONS: Duration of symptoms significantly affects the detection rate of respiratory pathogens by multiplex real-time PCR in nasopharyngeal swab samples from adult patients with respiratory infections. The aim of the present study was to evaluate the diagnostic performance and clinical use of a novel multiplex PCR method in adults with community-acquired respiratory viral infection, and the impact of duration of symptoms on detection rates. All patients still positive for the same agent on follow-up had a higher Ct-value (corresponding to a lower Table 2 Follow-up (10 ± 2 days after initial visit) test result from analysis with real-time PCR of nasopharyngeal/throat swab specimens. abstract: BACKGROUND: Nucleic acid amplification techniques have improved the diagnostic possibilities in respiratory tract infections, although their clinical applicability is not yet fully defined. We have evaluated a multiplex real-time PCR method for the detection of 13 respiratory viruses and 2 bacteria (Mycoplasma and Chlamydophila) in a clinical setting. OBJECTIVES: The aim of the present study was to evaluate the diagnostic performance and clinical use of a novel multiplex PCR method in adults with community-acquired respiratory viral infection, and the impact of duration of symptoms on detection rates. STUDY DESIGN: Nasopharyngeal swab samples were prospectively collected from 209 adult outpatients with respiratory infections and 100 asymptomatic controls. RESULTS: An infectious agent was identified in 43% of samples from patients and 2% of asymptomatic controls. The detection rate was significantly higher in samples from patients with a duration of symptoms of 6 days or less (51%) than in samples from patients with a duration of symptoms of 7 days or more (30%, p < 0.01). For human corona viruses, and influenza virus A and B there was a correlation between the amount of virus in each patient sample as measured Ct values and duration of symptoms. CONCLUSIONS: Duration of symptoms significantly affects the detection rate of respiratory pathogens by multiplex real-time PCR in nasopharyngeal swab samples from adult patients with respiratory infections. Our finding should be taken into account when using these tests in clinical practise. url: https://www.ncbi.nlm.nih.gov/pubmed/20080440/ doi: 10.1016/j.jcv.2009.12.010 id: cord-313749-f2ct57em author: Brittain-Long, Robin title: Multiplex real-time PCR for detection of respiratory tract infections date: 2007-12-26 words: 1566.0 sentences: 94.0 pages: flesch: 50.0 cache: ./cache/cord-313749-f2ct57em.txt txt: ./txt/cord-313749-f2ct57em.txt summary: title: Multiplex real-time PCR for detection of respiratory tract infections STUDY DESIGN: An assay targeting influenza virus A (IfA) and B (IfB), parainfluenza 1-3 (PIV), human metapneumovirus (MPV), respiratory syncytial virus (RSV), rhinovirus (RV), enterovirus (EV), adenovirus (AdV), human coronaviruses (229E, OC43, NL63), M. We developed a real-time PCR procedure, based on automated specimen extraction and multiplex amplification, at a relatively low cost (D 33). We believe that a combination of low cost, high accuracy and prompt result delivery is the key to achieving a wide clinical use of molecular diagnostics of respiratory infections. Further studies of respiratory infection aetiologies in different patient categories, and of the clinical utility of this and similar multiplex assays, need to be carried out. Real-time RT-PCR detection of 12 respiratory viral infections in four triplex reactions Rapid and sensitive method using multiplex real-time PCR for diagnosis of infections by influenza A and influenza B viruses, respiratory syncytial virus, and parainfluenza viruses 1, 2, 3, and 4 abstract: BACKGROUND: Broad diagnostics of respiratory infection by molecular assays has not yet won acceptance due to technical difficulties and high costs. OBJECTIVES: To evaluate clinical applicability of multiplex real-time PCR. STUDY DESIGN: An assay targeting influenza virus A (IfA) and B (IfB), parainfluenza 1-3 (PIV), human metapneumovirus (MPV), respiratory syncytial virus (RSV), rhinovirus (RV), enterovirus (EV), adenovirus (AdV), human coronaviruses (229E, OC43, NL63), M. pneumoniae and Ch. pneumoniae was developed and run daily on consecutive clinical nasopharyngeal swab samples. RESULTS: An etiology was identified in 48% of the 954 samples, with IfA in 25%, RV in 20%, MPV in 10% and M. pneumoniae in 10% of the positive. By a rational procedure costs could be reduced and the customer price set relatively low (€33 per sample). CONCLUSION: Streamlined testing and cost limitation is achievable and probably critical for implementation of a broad molecular diagnostics of respiratory infections. url: https://api.elsevier.com/content/article/pii/S1386653207003940 doi: 10.1016/j.jcv.2007.10.029 id: cord-267274-3ygl3stc author: Britton, Philip N title: COVID-19 public health measures and respiratory syncytial virus date: 2020-09-18 words: 1038.0 sentences: 56.0 pages: flesch: 47.0 cache: ./cache/cord-267274-3ygl3stc.txt txt: ./txt/cord-267274-3ygl3stc.txt summary: We analysed three separate datasets from the SCHN electronic records from Jan 1, 2015, to June 30, 2020, in children younger than 16 years: (1) laboratory tests for respiratory syncytial virus by PCR; (2) hospital admissions for bronchiolitis coded by the ICD-10 Australian Modification (J21.0, J21.1, J21.8, and J21.9); and (3) emergency department attendances for acute respiratory illness coded by the Systematised Nomenclature of Medicine Clinical Terminology (appendix p 4). We observed concurrent lower frequencies of respiratory syncytial virus (A and B) detection, admission to hospital for bronchiolitis, and emergency department attendance for acute respiratory illnesses (appendix p 1) in 2020 compared with preceding years. The small uptick in emergency department attendances and bronchiolitis admissions in June, 2020 (appendix p 1) was not associated with increased respiratory syncytial virus detections. abstract: nan url: https://api.elsevier.com/content/article/pii/S2352464220303072 doi: 10.1016/s2352-4642(20)30307-2 id: cord-315339-dcui85lw author: Broadbent, Andrew J. title: Respiratory Virus Vaccines date: 2015-03-13 words: 28246.0 sentences: 1270.0 pages: flesch: 39.0 cache: ./cache/cord-315339-dcui85lw.txt txt: ./txt/cord-315339-dcui85lw.txt summary: Although neutralizing antibodies directed against the HA globular head are highly efficient at preventing and clearing influenza virus infection, they can also FIGURE 3 In the memory phase, migratory lung DCs capture viral antigen retained on follicular DCs (FDCs) in tertiary lymphoid organs and present it to specific T cells in the respiratory draining lymph nodes. This explains why passively transferred IgG is effective at preventing severe disease from respiratory infections in experimental animals and why serum IgG antibodies are the main correlate of protection for parentally administered inactivated influenza vaccines in humans (Section Respiratory Virus Vaccines). Nasal administration of influenza vaccine with type I IFN was effective at inducing serum antigen-specific IgG2a and mucosal IgA antibody responses and at providing full protection against influenza virus challenge (Proietti et al., 2002) . abstract: This chapter reviews the main viral pathogens of the respiratory tract, the immune responses they induce, currently available vaccines, and vaccines that are in development to control them. The main viruses responsible for acute respiratory infection in people include respiratory syncytial, influenza, human parainfluenza, human metapneumo-, human rhino-, corona-, and adenoviruses. Licensed vaccines are available only for influenza virus, with vaccines against the other pathogens either in clinical trials or in preclinical stages of development. The majority of studies evaluating respiratory virus vaccines measure serum antibody responses, because, although both cellular and humoral responses contribute to the clearance of a primary infection, neutralizing antibodies are known to protect against secondary infection. Humoral responses can be readily detected after vaccination with inactivated or subunit vaccines; however, fewer individuals seroconvert after vaccination with live vaccines. Alternative immune mechanisms such as mucosal antibody responses are probably responsible for protection by live attenuated vaccines, and immune correlates of protection are under investigation. url: https://api.elsevier.com/content/article/pii/B9780124158474000598 doi: 10.1016/b978-0-12-415847-4.00059-8 id: cord-295074-fsbp4fky author: Broor, Shobha title: Rates of respiratory virus-associated hospitalization in children aged <5 years in rural northern India date: 2013-11-21 words: 3902.0 sentences: 177.0 pages: flesch: 33.0 cache: ./cache/cord-295074-fsbp4fky.txt txt: ./txt/cord-295074-fsbp4fky.txt summary: Rates of respiratory virus-associated hospitalization in children aged <5 years in rural northern India Introduction Acute respiratory infections are recognized as an important cause of mortality, hospitalization, and healthcare utilization in young children globally. 17e20 Using data from population-based surveillance of approximately 9500 children for hospitalizations for acute medical illness in rural northern India and concomitant testing for respiratory viruses by real-time reverse transcription polymerase chain reaction (rRT-PCR), we estimate the incidence of respiratory virus-associated hospitalizations among children aged <5 years. Incidences were also calculated for children aged <6 months for RSV and influenza since maternal immunization with RSV and Among the 98 children with respiratory virus-associated illness, history of fever (82%) and cough (69%) were the most commonly reported symptoms. RSV and influenza viruses circulated with clearly defined but different seasonality and were infrequently detected among children without fever or respiratory symptoms or signs, similar to prior studies. abstract: OBJECTIVES: Though respiratory viruses are thought to cause substantial morbidity globally in children aged <5 years, the incidence of severe respiratory virus infections in children is unknown in India where 20% of the world's children live. METHODS: During August 2009–July 2011, prospective population-based surveillance was conducted for hospitalizations of children aged <5 years in a rural community in Haryana State. Clinical data and respiratory specimens were collected. Swabs were tested by RT-PCR for influenza and parainfluenza viruses, respiratory syncytial virus (RSV), human metapneumovirus, coronaviruses, and adenovirus. Average annual hospitalization incidence was calculated using census data and adjusted for hospitalizations reported to occur at non-study hospitals according to a comunity healthcare utilization survey. RESULTS: Of 245 hospitalized children, respiratory viruses were detected among 98 (40%), of whom 92 (94%) had fever or respiratory symptoms. RSV accounted for the highest virus-associated hospitalization incidence (34.6/10,000, 95% CI 26.3–44.7) and 20% of hospitalizations. There were 11.8/10,000 (95% CI 7.9–18.4) influenza-associated hospitalizations (7% of hospitalizations). RSV and influenza virus detection peaked in winter (November–February) and rainy seasons (July), respectively. CONCLUSION: Respiratory viruses were associated with a substantial proportion of hospitalizations among young children in a rural Indian community. Public health research and prevention in India should consider targeting RSV and influenza in young children. url: https://doi.org/10.1016/j.jinf.2013.11.005 doi: 10.1016/j.jinf.2013.11.005 id: cord-022337-f3a349cb author: Busse, William W. title: Infections date: 2007-05-09 words: 7599.0 sentences: 391.0 pages: flesch: 40.0 cache: ./cache/cord-022337-f3a349cb.txt txt: ./txt/cord-022337-f3a349cb.txt summary: There is also evidence that the viruses which cause wheezing with respiratory tract infections may be age dependent; for example, infants wheeze with RSV while older children have exacerbations of asthma with rhinovirus.^^ To extend these observations. However, as already discussed, the increased frequency of LARs to antigen was still noted 4 weeks after the viral infection, suggesting that a viral respiratory infection has a greater, and possibly more lasting, effect on factors that participate in the development of LARs. Virus-associated airway hyperresponsiveness is a multifactorial process involving a complex interplay of IgE-dependent reactions, epithelial activation or damage, autonomic nervous system dysfunction and, of particular interest and relevance to our discussion, enhanced allergic inflammation."^^ In IgE-mediated reactions, the tissue response, be it the skin, nose or airway, is influenced by I g E sensitization of mast cells and basophils, release of bronchospastic and inflammatory mediators from sensitized cells, and the response of the target organ, which in asthma is bronchial smooth muscle. abstract: Wheezing with respiratory infections is extremely common in early childhood. It is estimated that the prevalence of wheezing during the first five years of life varies from 30–60%. In the majority of children who experience wheezing with respiratory infections, these episodes of wheezing become less frequent as the child grows older. However, determining whether the initial episode of wheezing with a viral respiratory illness is an important factor in the eventual development of asthma is an important question. Although a significant body of information suggests an association between respiratory tract illnesses in early life and the later development of airway dysfunction, this relationship is difficult to establish and indicates the complexity of factors that surround the development of bronchial hyperresponsiveness and eventual expression of asthma. A similarly important issue to resolve is the relationship between respiratory infections and the pathogenesis of airway hyperresponsiveness. It is apparent that viral, not bacterial, upper respiratory infections (URIs) trigger asthma attacks. With the use of more sensitive techniques to identify respiratory viruses, the relationship between respiratory infections, particularly viral URIs, and asthma has become even more convincing and important. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155587/ doi: 10.1016/b978-012079027-2/50112-x id: cord-257220-fe2sacjj author: Butler, J. E. title: Porcine reproductive and respiratory syndrome (PRRS): an immune dysregulatory pandemic date: 2014-07-01 words: 19650.0 sentences: 994.0 pages: flesch: 44.0 cache: ./cache/cord-257220-fe2sacjj.txt txt: ./txt/cord-257220-fe2sacjj.txt summary: LDV elevates IgG levels in mice with little production of virus-specific antibodies [11, 21] , which is almost identical to what is seen in isolator piglets infected with PRRSV [22] (''''The effect of age, rearing, complement and the role of mucosal immunity'''' section). Polyclonal activation of B cells occurs in lymphoid organs from porcine reproductive and respiratory syndrome virus (PRRSV)-induced pigs The presence of alpha interferon at the time of infection alters the innate and adaptive immune responses to porcine reproductive and respiratory syndrome virus Interferon type I response in porcine reproductive and respiratory syndrome virus-infected MARC-145 cells Antigen-specific B cell responses to porcine reproductive and respiratory syndrome virus infection Antibody production and blastogenesis response in pigs experimentally infected with porcine reproductive and respiratory syndrome virus Neutralizing antibody responses of pigs infected with natural GP5 N-glycan mutants of porcine reproductive and respiratory syndrome virus abstract: Porcine reproductive and respiratory disease syndrome (PRRS) is a viral pandemic that especially affects neonates within the “critical window” of immunological development. PRRS was recognized in 1987 and within a few years became pandemic causing an estimated yearly $600,000 economic loss in the USA with comparative losses in most other countries. The causative agent is a single-stranded, positive-sense enveloped arterivirus (PRRSV) that infects macrophages and plasmacytoid dendritic cells. Despite the discovery of PRRSV in 1991 and the publication of >2,000 articles, the control of PRRS is problematic. Despite the large volume of literature on this disease, the cellular and molecular mechanisms describing how PRRSV dysregulates the host immune system are poorly understood. We know that PRRSV suppresses innate immunity and causes abnormal B cell proliferation and repertoire development, often lymphopenia and thymic atrophy. The PRRSV genome is highly diverse, rapidly evolving but amenable to the generation of many mutants and chimeric viruses for experimental studies. PRRSV only replicates in swine which adds to the experimental difficulty since no inbred well-defined animal models are available. In this article, we summarize current knowledge and apply it toward developing a series of provocative and testable hypotheses to explain how PRRSV immunomodulates the porcine immune system with the goal of adding new perspectives on this disease. url: https://www.ncbi.nlm.nih.gov/pubmed/24981123/ doi: 10.1007/s12026-014-8549-5 id: cord-272179-wvw5mmy3 author: Calderaro, Adriana title: Human respiratory viruses, including SARS-CoV-2, circulating in the winter season 2019-2020 in Parma, Northern Italy date: 2020-10-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: This study aimed to determine the prevalence of respiratory virus infections, including SARS-CoV-2, during December 2019 – March 2020, in a tertiary care hospital-based survey in Parma (Northern Italy). METHODS: A total of 906 biological samples of respiratory tract were analyzed by both conventional (including culture) and molecular assays targeting SARS-CoV-2 and the other respiratory viruses nucleic acids. RESULTS: 474 samples (52.3%) were positive for at least one virus for a total of 583 viruses detected. Single infections were detected in 380 (80.2%) samples and mixed infections were detected in 94 (19.8%). RSV (138/583: 23.7%) and RV (130/583: 22.3%) were the most common viruses identified, followed by SARS-CoV2 (82/583: 14.1%). RSV predominates until February with 129 detections and drastically decreases in March to 9 detections. SARS-CoV-2 absent in our area until February 26, in just over a month reached 82 detections. SARS-CoV-2 was found in mixed infections only in 3 cases all observed in children younger than one year old. CONCLUSIONS: This study showed a completely different trend between SARS-CoV-2 and the "common" respiratory viruses that have seen children most affected without distinction of sex, as opposed to SARS-CoV-2 that have seen adult males the most infected. url: https://api.elsevier.com/content/article/pii/S1201971220321895 doi: 10.1016/j.ijid.2020.09.1473 id: cord-258139-x4js9vqe author: Callan, Robert J title: Biosecurity and bovine respiratory disease date: 2005-03-04 words: 7688.0 sentences: 405.0 pages: flesch: 37.0 cache: ./cache/cord-258139-x4js9vqe.txt txt: ./txt/cord-258139-x4js9vqe.txt summary: Alternatively, when the causative pathogens are endemic in a population and individual susceptibility is dependent on numerous interrelated factors, the management of animal resistance and risk factors may be proportionally more important for disease prevention than biosecurity practices. The authors emphasize five areas of biosecurity management that should be more rigorously applied for the reduction of respiratory disease prevalence in cattle, including (1) strategic vaccination, (2) calf biosecurity, (3) housing ventilation, (4) commingling and animal contact, and (5) bovine viral diarrhea virus control. Airborne pathogen concentration is a function of many factors, including animal type, housing system, stocking rate, bedding, humidity, dust particle density and size, and finally, elimination through ventilation. Because the pathogens involved in bovine respiratory disease are enzootic in the general cattle population, biosecurity practices aimed at the complete elimination of exposure are currently impractical. Because the pathogens involved in bovine respiratory disease are enzootic in the general cattle population, biosecurity practices aimed at the complete elimination of exposure are currently impractical. abstract: Although biosecurity practices play a role in minimizing respiratory disease in cattle, they must be used in combination with other management strategies that address the many other risk factors. Because the pathogens involved in bovine respiratory disease are enzootic in the general cattle population, biosecurity practices aimed at the complete elimination of exposure are currently impractical. Several animal husbandry and production management practices can be used to minimize pathogen shedding, exposure, and transmission within a given population, however. Various combinations of these control measures can be applied to individual farms to help decrease the morbidity and mortality attributed to respiratory disease. url: https://api.elsevier.com/content/article/pii/S074907200200004X doi: 10.1016/s0749-0720(02)00004-x id: cord-020700-iko8gy1e author: Calvo, Cristina title: Respiratory viral infections in a cohort of children during the first year of life and their role in the development of wheezing() date: 2017-07-06 words: 3945.0 sentences: 228.0 pages: flesch: 53.0 cache: ./cache/cord-020700-iko8gy1e.txt txt: ./txt/cord-020700-iko8gy1e.txt summary: INTRODUCTION: It is known that infants with viral respiratory infections severe enough to require hospital admission have a high risk of developing recurrent wheezing. The main aim of this study was to analyse symptomatic and asymptomatic respiratory viral infections during the first year of life in a cohort of infants, recruited at birth, and the development of recurrent wheezing. The objective of our prospective study was to analyse asymptomatic and symptomatic infections of varying severity in a cohort of newborns during the first year of life and assess their role in the development of recurrent wheezing. We defined ''''first detected viral infection'''' as PCR detecting a respiratory virus in a sample for the first time in the life of a child, whether the infection was asymptomatic, symptomatic and managed at the outpatient level, or symptomatic and requiring hospital admission. abstract: INTRODUCTION: It is known that infants with viral respiratory infections severe enough to require hospital admission have a high risk of developing recurrent wheezing. Few data have been published on unselected populations. The main aim of this study was to analyse symptomatic and asymptomatic respiratory viral infections during the first year of life in a cohort of infants, recruited at birth, and the development of recurrent wheezing. PATIENTS AND METHODS: A total of 302 newborns were recruited. A nasopharyngeal aspirate was taken when the patients had a respiratory infection, as well as in the visits for vaccination at 2, 4, 6, and 12 months. RT-nested PCR assays were performed to detect 16 viruses. RESULTS: A total of 1293 samples were analysed (1005 healthy controls and 288 respiratory infections). Samples taken during routine check-ups were positive in 30.8% of cases, while those with respiratory infection were positive in 77.8%, P < .001 (OR: 3, 95% CI: 2.4–3.8). A total of 239 (79%) infants had at least 1 positive respiratory viral infection detected. The most frequent virus (71%) was rhinovirus (RV). Recurrent wheezing was found in 27 (11%) children during their first year of life (1.2 episodes, SD 2.9). Recurrent wheezing was present in 58.3% of patients admitted to hospital during their first viral infection, vs. 8.6% of infants when the first infection was mild or who had asymptomatic viral detection, P < .001 (OR: 2.18; 95% CI: 1.05–4.5). CONCLUSIONS: In our series, severe respiratory infections leading to hospitalisation in the first months of life are risk factors for developing wheezing, but not in the case of mild RV infections. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7146761/ doi: 10.1016/j.anpede.2016.08.008 id: cord-001070-zlzag6a8 author: Camargo, C.N. title: Human rhinovirus infections in symptomatic and asymptomatic subjects date: 2012-06-01 words: 630.0 sentences: 47.0 pages: flesch: 38.0 cache: ./cache/cord-001070-zlzag6a8.txt txt: ./txt/cord-001070-zlzag6a8.txt summary: The role of rhinovirus asymptomatic infections in the transmission among close contacts subjects is unknown. We investigated HRV infections rates on selected populations of a pair of one child and one family member, health care workers (HCW), and immunocompromised patients with and without respiratory symptoms from June to September. One hundred and eleven health care workers (HCW) from São Paulo Hospital, 36 pairs of one child and one family member and 8 blood marrow transplanted hospitalized patients (BMT). Influenza and rhinovirus infections among health-care workers Acute Respiratory Infection and Influenza-Like Illness Viral Etiologies in Brazilian Adults Use of polymerase chain reaction for diagnosis of picornavirus infection in subjects with and without respiratory symptoms Rhinovirus transmission within families with children: Insidence of symptomatic and assymptomatic infections Viral respiratory infections in hospitalized and community control children in Alaska Frequent detection of respiratory viruses in adult recipients of stem cell transplants with the use of real-time polymerase chain reaction, compared with viral culture abstract: The role of rhinovirus asymptomatic infections in the transmission among close contacts subjects is unknown. We tested health care workers, a pair of one child and a family member and immunocompromised patients (n =191). HRV were detected on 22.9% symptomatic and 3.6% asymptomatic cases suggesting lower transmission among contacts. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3769032/ doi: 10.1590/s1517-838220120004000049 id: cord-344889-1y4ieamp author: Cameron, Robert J. title: Virus infection in exacerbations of chronic obstructive pulmonary disease requiring ventilation date: 2006-05-24 words: 4309.0 sentences: 242.0 pages: flesch: 46.0 cache: ./cache/cord-344889-1y4ieamp.txt txt: ./txt/cord-344889-1y4ieamp.txt summary: OBJECTIVES: We aimed to characterise and quantify the incidence of common infectious agents in acute exacerbations of chronic obstructive pulmonary disease (COPD) requiring ventilation, with a focus on respiratory viruses. Abstract Objectives: We aimed to characterise and quantify the incidence of common infectious agents in acute exacerbations of chronic obstructive pulmonary disease (COPD) requiring ventilation, with a focus on respiratory viruses. Of these, influenza types A and B (Inf A, B), parainfluenza types 1, 2 and 3 (Para 1, 2, 3), rhinovirus (RV), adenovirus (AV), respiratory syncytial virus (RSV), coronavirus (CoV) [11, 12] and, less commonly, human metapneumovirus (hMPV) [13] , and enterovirus (EV) [14, 15] have been shown to play significant roles in airway infections. A probable virus pathogen was found in 46 cases (43%) and a probable bacterial aetiology was found in 25 cases (23%) in this study of ventilated COPD exacerbation patients. abstract: OBJECTIVES: We aimed to characterise and quantify the incidence of common infectious agents in acute exacerbations of chronic obstructive pulmonary disease (COPD) requiring ventilation, with a focus on respiratory viruses. DESIGN: An epidemiological study conducted over 3 years. SETTING: A 12-bed intensive care unit (ICU). PARTICIPANTS: ICU patients over 45 years of age with a primary diagnosis of COPD exacerbation requiring non-invasive ventilation (NIV) or ventilation via endotracheal tube (ETT). MATERIALS AND METHODS: Nasopharyngeal aspirates (NPA) and posterior pharyngeal swabs (PS) were tested for viruses with immunofluorescence assay (IFA), virus culture (VC) and polymerase chain reaction (PCR). Paired virus and atypical pneumonia serology assays were taken. Blood, sputum and endotracheal aspirates were cultured for bacteria. RESULTS: 107 episodes in 105 patients were recorded. Twenty-three (21%) died within 28 days. A probable infectious aetiology was found in 69 patient episodes (64%). A virus was identified in 46 cases (43%), being the sole organism in 35 cases (33%) and part of a mixed infection in 11 cases (10%). A probable bacterial aetiology was found in 25 cases (23%). There was no statistically significant difference in clinical characteristics or outcomes between the group with virus infections and that without. CONCLUSION: Forty-six (43%) of the patients with COPD exacerbation requiring mechanical ventilation had a probable viral pathogen. Prodromal, clinical and outcome parameters did not distinguish virus from non-virus illness. PCR was the most sensitive whilst virus culture was the least of virus assays. ELECTRONIC SUPPLEMENTARY MATERIAL: The electronic reference of this article is http://dx.doi.org/10.1007/s00134-006-0202-x. The online full-text version of this article includes electronic supplementary material. This material is available to authorised users and can be accessed by means of the ESM button beneath the abstract or in the structured full-text article. To cite or link to this article you can use the above reference. url: https://www.ncbi.nlm.nih.gov/pubmed/16791664/ doi: 10.1007/s00134-006-0202-x id: cord-254265-8i86c8kt author: Camps, Marta title: Prevalence of human metapneumovirus among hospitalized children younger than 1 year in Catalonia, Spain date: 2008-06-12 words: 4567.0 sentences: 227.0 pages: flesch: 42.0 cache: ./cache/cord-254265-8i86c8kt.txt txt: ./txt/cord-254265-8i86c8kt.txt summary: In 67/99 children (67%) at least one viral pathogen was identified, the viruses detected most frequently were respiratory syncytial virus (35%), human metapneumovirus (25%) and rhinovirus (19%). The aim of the present study was to describe the role of human metapneumovirus and other common respiratory viruses including: influenza virus A, B, and C, parainfluenza 1-4 viruses, adenoviruses, respiratory syncytial virus A and B, rhinovirus, coronavirus 229E and OC43 and enterovirus as bronchiolitis, and bronchopneumonia pathogens among hospitalized children younger than 1 year, taking into account that in this age group respiratory viruses are the main etiological agents of lower respiratory tract infections [Shay et al., 1999; Smyth and Openshaw, 2006; Bush and Thomson, 2007] . Detection of human metapneumovirus RNA sequences in nasopharyngeal aspirates of young French children with acute bronchiolitis by real-time reverse transcriptase PCR and phylogenetic analysis abstract: Human metapneumovirus was discovered recently respiratory virus implicated in both upper and lower respiratory tract infection. In children, the clinical symptoms of human metapneumovirus are similar to those produced by respiratory syncytial virus, ranging from mild to severe diseases such as bronchiolitis and pneumonia. The aim of the present study was to describe the prevalence of human metapneumovirus and other common respiratory viruses among admitted to hospital infants. From January 2006 to June 2006, 99 nasopharyngeal aspirates were collected from hospitalized children younger than 12 months in order to study respiratory viruses. Human metapneumovirus detection was performed by cell culture and two RT‐PCR targeting on polymerase and fusion genes. The latter gene was used for phylogenetic analysis. In 67/99 children (67%) at least one viral pathogen was identified, the viruses detected most frequently were respiratory syncytial virus (35%), human metapneumovirus (25%) and rhinovirus (19%). The results obtained in this study, show that: (1) human metapneumovirus is one of the most important viruses among children less than 12 months; (2) children infected with human metapneumovirus were significantly older than those infected by respiratory syncytial virus; (3) human metapneumovirus was associated more frequently with pneumonia whereas respiratory syncytial virus was only detected in patients with bronchiolitis; (4) there was a clear epidemiological succession pattern with only a small overlap among the viruses detected most frequently; (5) all human metapneumovirus samples were clustered within sublineage A2. J. Med. Virol. 80:1452–1460, 2008. © 2008 Wiley‐Liss, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/18551601/ doi: 10.1002/jmv.21209 id: cord-339869-euikj8fv author: Cebey-López, Miriam title: Does Viral Co-Infection Influence the Severity of Acute Respiratory Infection in Children? date: 2016-04-20 words: 3325.0 sentences: 201.0 pages: flesch: 40.0 cache: ./cache/cord-339869-euikj8fv.txt txt: ./txt/cord-339869-euikj8fv.txt summary: However, bacterial superinfection was associated with increased severity (OR: 4.356; P-value = 0.005), PICU admission (OR: 3.342; P-value = 0.006), higher clinical score (1.988; P-value = 0.002) respiratory support requirement (OR: 7.484; P-value < 0.001) and longer hospital length of stay (OR: 1.468; P-value < 0.001). However, bacterial superinfection was associated with increased severity (OR: 4.356; P-value = 0.005), PICU admission (OR: 3.342; P-value = 0.006), higher clinical score (1.988; P-value = 0.002) respiratory Introduction Molecular techniques including polymerase chain reaction (PCR) have increased the sensitivity of detection for common and emerging respiratory viruses, and often reveal the presence of more than one pathogen in respiratory patients. Our study aims to analyze the relationship between viral or bacterial co-infection detected by molecular methods, and the clinical phenotype of children admitted to hospital with lower tract acute respiratory infections (LT-ARI). PICU admission, disease severity according to different scales, need for respiratory support, and length of hospital stay followed a similar pattern in viral mono-versus co-infected children. abstract: BACKGROUND: Multiple viruses are often detected in children with respiratory infection but the significance of co-infection in pathogenesis, severity and outcome is unclear. OBJECTIVES: To correlate the presence of viral co-infection with clinical phenotype in children admitted with acute respiratory infections (ARI). METHODS: We collected detailed clinical information on severity for children admitted with ARI as part of a Spanish prospective multicenter study (GENDRES network) between 2011–2013. A nested polymerase chain reaction (PCR) approach was used to detect respiratory viruses in respiratory secretions. Findings were compared to an independent cohort collected in the UK. RESULTS: 204 children were recruited in the main cohort and 97 in the replication cohort. The number of detected viruses did not correlate with any markers of severity. However, bacterial superinfection was associated with increased severity (OR: 4.356; P-value = 0.005), PICU admission (OR: 3.342; P-value = 0.006), higher clinical score (1.988; P-value = 0.002) respiratory support requirement (OR: 7.484; P-value < 0.001) and longer hospital length of stay (OR: 1.468; P-value < 0.001). In addition, pneumococcal vaccination was found to be a protective factor in terms of degree of respiratory distress (OR: 2.917; P-value = 0.035), PICU admission (OR: 0.301; P-value = 0.011), lower clinical score (-1.499; P-value = 0.021) respiratory support requirement (OR: 0.324; P-value = 0.016) and oxygen necessity (OR: 0.328; P-value = 0.001). All these findings were replicated in the UK cohort. CONCLUSION: The presence of more than one virus in hospitalized children with ARI is very frequent but it does not seem to have a major clinical impact in terms of severity. However bacterial superinfection increases the severity of the disease course. On the contrary, pneumococcal vaccination plays a protective role. url: https://www.ncbi.nlm.nih.gov/pubmed/27096199/ doi: 10.1371/journal.pone.0152481 id: cord-303322-d69o3z8d author: Chang, Anne B title: Randomized placebo-controlled trial on azithromycin to reduce the morbidity of bronchiolitis in Indigenous Australian infants: rationale and protocol date: 2011-04-14 words: 5403.0 sentences: 287.0 pages: flesch: 37.0 cache: ./cache/cord-303322-d69o3z8d.txt txt: ./txt/cord-303322-d69o3z8d.txt summary: Our randomised, placebo-controlled trial of azithromycin in Indigenous infants hospitalised with bronchiolitis is designed to determine whether it can reduce short-term (and potentially long-term) morbidity from respiratory illness in Australian Indigenous infants who are at high risk of developing chronic respiratory illness. Indigenous infants (aged ≤ 24-months, expected number = 200) admitted to one of two regional hospitals (Darwin, Northern Territory and Townsville, Queensland) with a clinical diagnosis of bronchiolitis and fulfilling inclusion criteria are randomised (allocation concealed) to either azithromycin (30 mg/kg/dose) or placebo administered once weekly for three doses. Indigenous infants (aged ≤ 24-months, expected number = 200) admitted to one of two regional hospitals (Darwin, Northern Territory and Townsville, Queensland) with a clinical diagnosis of bronchiolitis and fulfilling inclusion criteria are randomised (allocation concealed) to either azithromycin (30 mg/kg/dose) or placebo administered once weekly for three doses. abstract: BACKGROUND: Acute lower respiratory infections are the commonest cause of morbidity and potentially preventable mortality in Indigenous infants. Infancy is also a critical time for post-natal lung growth and development. Severe or repeated lower airway injury in very young children likely increases the likelihood of chronic pulmonary disorders later in life. Globally, bronchiolitis is the most common form of acute lower respiratory infections during infancy. Compared with non-Indigenous Australian infants, Indigenous infants have greater bacterial density in their upper airways and more severe bronchiolitis episodes. Our study tests the hypothesis that the anti-microbial and anti-inflammatory properties of azithromycin, improve the clinical outcomes of Indigenous Australian infants hospitalised with bronchiolitis. METHODS: We are conducting a dual centre, randomised, double-blind, placebo-controlled, parallel group trial in northern Australia. Indigenous infants (aged ≤ 24-months, expected number = 200) admitted to one of two regional hospitals (Darwin, Northern Territory and Townsville, Queensland) with a clinical diagnosis of bronchiolitis and fulfilling inclusion criteria are randomised (allocation concealed) to either azithromycin (30 mg/kg/dose) or placebo administered once weekly for three doses. Clinical data are recorded twice daily and nasopharyngeal swab are collected at enrolment and at the time of discharge from hospital. Primary outcomes are 'length of oxygen requirement' and 'duration of stay,' the latter based upon being judged as 'ready for respiratory discharge'. The main secondary outcome is readmission for a respiratory illness within 6-months of leaving hospital. Descriptive virological and bacteriological (including development of antibiotic resistance) data from nasopharyngeal samples will also be reported. DISCUSSION: Two published studies, both involving different patient populations and settings, as well as different macrolide antibiotics and treatment duration, have produced conflicting results. Our randomised, placebo-controlled trial of azithromycin in Indigenous infants hospitalised with bronchiolitis is designed to determine whether it can reduce short-term (and potentially long-term) morbidity from respiratory illness in Australian Indigenous infants who are at high risk of developing chronic respiratory illness. If azithromycin is efficacious in reducing the morbidly of Indigenous infants hospitalised with bronchiolitis, the intervention would lead to improved short term (and possibly long term) health benefits. TRIAL REGISTRATION: Australia and New Zealand Clinical Trials Register (ANZCTR): ACTRN12610000326099 url: https://doi.org/10.1186/1745-6215-12-94 doi: 10.1186/1745-6215-12-94 id: cord-324786-8k81jetq author: Chang, Anne B title: Antibiotics for bronchiectasis exacerbations in children: rationale and study protocol for a randomised placebo-controlled trial date: 2012-08-31 words: 5672.0 sentences: 298.0 pages: flesch: 43.0 cache: ./cache/cord-324786-8k81jetq.txt txt: ./txt/cord-324786-8k81jetq.txt summary: Our study tests the hypothesis that both oral azithromycin and amoxicillin-clavulanic acid are superior to placebo at improving resolution rates of respiratory exacerbations by day 14 in children with bronchiectasis unrelated to cystic fibrosis. Our multicentre, double-blind RCT is designed to determine if azithromycin and amoxicillin-clavulanic acid, compared with placebo, improve symptom resolution on day 14 in children with acute respiratory exacerbations. Early and effective management of bronchiectasis exacerbations in children may lead to reduced hospitalisations, better quality of life (QOL) and improved future adult lung function. Our study tests the primary hypothesis that both oral azithromycin and amoxicillin-clavulanic acid are superior to placebo in improving the resolution rate of respiratory exacerbations by day 14 in children with non-CF bronchiectasis. We are conducting a multicentre, parallel group, double-blind placebo RCT (with concealed allocation) to assess the impact of treatment with antibiotics (azithromycin or amoxicillinclavulanic acid) in children with an exacerbation of bronchiectasis. abstract: BACKGROUND: Despite bronchiectasis being increasingly recognised as an important cause of chronic respiratory morbidity in both indigenous and non-indigenous settings globally, high quality evidence to inform management is scarce. It is assumed that antibiotics are efficacious for all bronchiectasis exacerbations, but not all practitioners agree. Inadequately treated exacerbations may risk lung function deterioration. Our study tests the hypothesis that both oral azithromycin and amoxicillin-clavulanic acid are superior to placebo at improving resolution rates of respiratory exacerbations by day 14 in children with bronchiectasis unrelated to cystic fibrosis. METHODS: We are conducting a bronchiectasis exacerbation study (BEST), which is a multicentre, randomised, double-blind, double-dummy, placebo-controlled, parallel group trial, in five centres (Brisbane, Perth, Darwin, Melbourne, Auckland). In the component of BEST presented here, 189 children fulfilling inclusion criteria are randomised (allocation-concealed) to receive amoxicillin-clavulanic acid (22.5 mg/kg twice daily) with placebo-azithromycin; azithromycin (5 mg/kg daily) with placebo-amoxicillin-clavulanic acid; or placebo-azithromycin with placebo-amoxicillin-clavulanic acid for 14 days. Clinical data and a paediatric cough-specific quality of life score are obtained at baseline, at the start and resolution of exacerbations, and at day 14. In most children, blood and deep nasal swabs are also collected at the same time points. The primary outcome is the proportion of children whose exacerbations have resolved at day 14. The main secondary outcome is the paediatric cough-specific quality of life score. Other outcomes are time to next exacerbation; requirement for hospitalisation; duration of exacerbation; and spirometry data. Descriptive viral and bacteriological data from nasal samples and blood markers will also be reported. DISCUSSION: Effective, evidence-based management of exacerbations in people with bronchiectasis is clinically important. Yet, there are few randomised controlled trials (RCTs) in the neglected area of non-cystic fibrosis bronchiectasis. Indeed, no published RCTs addressing the treatment of bronchiectasis exacerbations in children exist. Our multicentre, double-blind RCT is designed to determine if azithromycin and amoxicillin-clavulanic acid, compared with placebo, improve symptom resolution on day 14 in children with acute respiratory exacerbations. Our planned assessment of the predictors of antibiotic response, the role of antibiotic-resistant respiratory pathogens, and whether early treatment with antibiotics affects duration and time to the next exacerbation, are also all novel. TRIAL REGISTRATION: Australia and New Zealand Clinical Trials Register (ANZCTR) number ACTRN12612000011886. url: https://doi.org/10.1186/1745-6215-13-156 doi: 10.1186/1745-6215-13-156 id: cord-343365-4y9fedcr author: Chang, Christopher title: Unmet Needs in Respiratory Diseases: “You Can’t Know Where You Are Going Until You Know Where You Have Been”—Anonymous date: 2013-11-30 words: 7295.0 sentences: 407.0 pages: flesch: 50.0 cache: ./cache/cord-343365-4y9fedcr.txt txt: ./txt/cord-343365-4y9fedcr.txt summary: The promise of gene therapy as a cure for the disease has fizzled out, and while new antimicrobials and other pharmaceuticals promise improved longevity and better quality of life, the average life span of a patient with cystic fibrosis is still at about 35 years. Several significant challenge areas include the diagnosis and treatment of certain specific infectious lung diseases, including viral lower respiratory infections caused by respiratory syncytial virus, rhinovirus, metapneumovirus, coronovirus, and enterovirus. The search for a vaccine for respiratory syncytial virus (RSV) has been ongoing for many years, but like the previous case of gene therapy in cystic fibrosis, this also has been a challenge to achieve. The current global strategies for the development of an RSV vaccine now target four areas: infants <6 months of age; infants >6 months of age and young children; pregnant women for whom passive immunization can be implemented; and the elderly, in whom RSV can also have significant morbidity [52] [53] [54] . abstract: The care of patients with respiratory diseases has improved vastly in the past 50 years. In spite of that, there are still massive challenges that have not been resolved. Although the incidence of tuberculosis has decreased in the developed world, it is still a significant public health problem in the rest of the world. There are still over 2 million deaths annually from tuberculosis, with most of these occurring in the developing world. Even with the development of new pharmaceuticals to treat tuberculosis, there is no indication that the disease will be eradicated. Respiratory syncytial virus, severe acute respiratory syndrome, and pertussis are other respiratory infectious diseases with special problems of their own, from vaccine development to vaccine coverage. Asthma, one of the most common chronic diseases in children, still accounts for significant mortality and morbidity, as well as high health care costs worldwide. Even in developed countries such as the USA, there are over 4,000 deaths per year. Severe asthma presents a special problem, but the question is whether there can be one treatment pathway for all patients with severe asthma. Severe asthma is a heterogeneous disease with many phenotypes and endotypes. The gene for cystic fibrosis was discovered over 24 years ago. The promise of gene therapy as a cure for the disease has fizzled out, and while new antimicrobials and other pharmaceuticals promise improved longevity and better quality of life, the average life span of a patient with cystic fibrosis is still at about 35 years. What are the prospects for gene therapy in the twenty-first century? Autoimmune diseases of the lung pose a different set of challenges, including the development of biomarkers to diagnose and monitor the disease and biological modulators to treat the disease. url: https://www.ncbi.nlm.nih.gov/pubmed/24293395/ doi: 10.1007/s12016-013-8399-2 id: cord-327685-fymfqvp3 author: Channappanavar, Rudragouda title: Pathogenic human coronavirus infections: causes and consequences of cytokine storm and immunopathology date: 2017-05-02 words: 5834.0 sentences: 288.0 pages: flesch: 33.0 cache: ./cache/cord-327685-fymfqvp3.txt txt: ./txt/cord-327685-fymfqvp3.txt summary: In contrast, highly pathogenic hCoVs such as severe acute respiratory syndrome CoV (SARS-CoV) and Middle East respiratory syndrome CoV (MERS-CoV) predominantly infect lower airways and cause fatal pneumonia. Severe pneumonia caused by pathogenic hCoVs is often associated with rapid virus replication, massive inflammatory cell infiltration and elevated pro-inflammatory cytokine/chemokine responses resulting in acute lung injury (ALI), and acute respiratory distress syndrome (ARDS). Although there is no direct evidence for the involvement of pro-inflammatory cytokines and chemokines in lung pathology during SARS and MERS, correlative evidence from patients with severe disease suggests a role for hyper-inflammatory responses in hCoV pathogenesis. Infection of non-human primates (NHPs) with SARS-CoV induced a dysregulated immune response resulting in increased disease severity in aged but not young NHPs, despite similar viral titers in the airways [67] . T cell responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-infected mice abstract: Human coronaviruses (hCoVs) can be divided into low pathogenic and highly pathogenic coronaviruses. The low pathogenic CoVs infect the upper respiratory tract and cause mild, cold-like respiratory illness. In contrast, highly pathogenic hCoVs such as severe acute respiratory syndrome CoV (SARS-CoV) and Middle East respiratory syndrome CoV (MERS-CoV) predominantly infect lower airways and cause fatal pneumonia. Severe pneumonia caused by pathogenic hCoVs is often associated with rapid virus replication, massive inflammatory cell infiltration and elevated pro-inflammatory cytokine/chemokine responses resulting in acute lung injury (ALI), and acute respiratory distress syndrome (ARDS). Recent studies in experimentally infected animal strongly suggest a crucial role for virus-induced immunopathological events in causing fatal pneumonia after hCoV infections. Here we review the current understanding of how a dysregulated immune response may cause lung immunopathology leading to deleterious clinical manifestations after pathogenic hCoV infections. url: https://www.ncbi.nlm.nih.gov/pubmed/28466096/ doi: 10.1007/s00281-017-0629-x id: cord-268324-86a0n0dc author: Charitos, Ioannis A title: Special features of SARS-CoV-2 in daily practice date: 2020-09-26 words: 6117.0 sentences: 279.0 pages: flesch: 42.0 cache: ./cache/cord-268324-86a0n0dc.txt txt: ./txt/cord-268324-86a0n0dc.txt summary: The severe acute respiratory syndrome-coronavirus-2 (commonly known as SARS-CoV-2) is a novel coronavirus (designated as 2019-nCoV), which was isolated for the first time after the Chinese health authorities reported a cluster of pneumonia cases in Wuhan, China in December 2019. The clinical picture of critical patients with severe inflammatory-induced lung disease and with sepsis or septic shock needing intensive care support and mechanical ventilation is characterized by a wide range of signs and symptoms of life-threatening multiorgan dysfunction or failure, including dyspnoea, tachypnoea (respiratory rate of > 30/min), tachycardia, chest pain or tightness, hypoxemia, virus-induced distributive shock, cardiac dysfunction, elevations in multiple inflammatory cytokines, renal impairment with oliguria, altered mental status, functional alterations of organs expressed as laboratory data of hyperbilirubinemia, acidosis [serum lactate level > 2 mmol/L (18 mg/dL)], coagulopathy, and thrombocytopenia. abstract: The severe acute respiratory syndrome-coronavirus-2 (commonly known as SARS-CoV-2) is a novel coronavirus (designated as 2019-nCoV), which was isolated for the first time after the Chinese health authorities reported a cluster of pneumonia cases in Wuhan, China in December 2019. Optimal management of the Coronavirus Disease-2019 disease is evolving quickly and treatment guidelines, based on scientific evidence and experts’ opinions with clinical experience, are constantly being updated. On January 30, 2020, the World Health Organization declared the SARS-CoV-2 outbreak as a "Public Health Emergency of International Concern". The total lack of immune protection brought about a severe spread of the contagion all over the world. For this reason, diagnostic tools, patient management and therapeutic approaches have been tested along the way, in the desperate race to break free from the widespread infection and its fatal respiratory complications. Current medical knowledge and research on severe and critical patients’ management and experimental treatments are still evolving, but several protocols on minimizing risk of infection among the general population, patients and healthcare workers have been approved and diffused by International Health Authorities. url: https://www.ncbi.nlm.nih.gov/pubmed/33024749/ doi: 10.12998/wjcc.v8.i18.3920 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-018319-tylkbh4h author: Chemaly, Roy F. title: Respiratory Viruses date: 2011-01-04 words: 8852.0 sentences: 467.0 pages: flesch: 37.0 cache: ./cache/cord-018319-tylkbh4h.txt txt: ./txt/cord-018319-tylkbh4h.txt summary: Historically, the most common causes of respiratory infections in cancer patients were thought to be opportunistic bacteria and fungi, but newer diagnostic methods have revealed that respiratory viruses can cause serious morbidity and mortality in such patients, including leukemia patients and hematopoietic stem cell transplant (HSCT) recipients. Many viruses are known to cause respiratory tract infections, but the most common in hospitalized cancer patients are influenza viruses, respiratory syncytial virus (RSV), and parainfluenza viruses (PIV) [1, 2] . Although the combination of ribavirin and intravenous immunoglobulin (IVIG) or palivizumab has not been evaluated in a randomized trial, it is sometimes used in severely ill patients with RSV pneumonia, especially HSCT recipients, given that they have high mortality rates from this infection [3, 11, 14] . However, because other viruses can produce the same syndrome and influenza infection can produce other respiratory syndromes, a confirmatory test detecting the virus or viral antigens in nasal washes, throat swabs, respiratory tract secretions, or bronchoalveolar lavage specimens is needed in sporadic cases and in immunocompromised patients. abstract: The respiratory viruses as a group are the most common cause of an acute infectious illness in developed societies. The immunocompromised state of many cancer patients constitutes the basis for the frequent failure of the host to promote a normal and rapid recovery from an acute respiratory viral infection and results in a more severe and prolonged infection that causes significant morbidity and mortality in these patients. Those respiratory viruses that are most prevalent and most prone to produce lower respiratory illnesses and pneumonia in healthy hosts, RSV, influenza viruses, and parainfluenza viruses, are those most likely to cause severe illness and pneumonia leading to hospitalization in immunocompromised persons. However, viruses less prone to produce a lower respiratory illness but that are highly prevalent, such as rhinoviruses, may frequently be associated with severe illness. The limited availability of antivirals and vaccines for the acute respiratory viruses means that these infections will continue to be important for many years and dictate a need for utilizing infection control procedures as much as possible, particularly in hospitals and institutions, so as to minimize spread. Efforts to develop specific vaccines are important as their use could prevent as well as reduce exposure of cancer patients to these viruses. Development of specific antivirals is important for use in immunocompromised patients as normal recovery mechanisms may be seriously impaired. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123165/ doi: 10.1007/978-1-60761-644-3_32 id: cord-283604-fqc9jp0l author: Chen, Meng title: Adenoviruses Associated with Acute Respiratory Diseases Reported in Beijing from 2011 to 2013 date: 2015-03-27 words: 3060.0 sentences: 127.0 pages: flesch: 39.0 cache: ./cache/cord-283604-fqc9jp0l.txt txt: ./txt/cord-283604-fqc9jp0l.txt summary: To identify the types of human adenoviruses (HAdVs) causing respiratory illness in Beijing, a sentinel surveillance project on the viral aetiology of acute respiratory infection was initiated in 2011. The comparison results of the penton base, hexon, and fiber gene sequences of the Beijing HAdV-3, HAdV-4, HAdV-7, and HAdV-55 strains in this study and those from the GenBank database indicated significant spatial and temporal conservation and stability of sequences within the genome; however, the phylogenetic relationship indicated that both strain BJ04 and strain BJ09 isolated in 2012 and 2013, respectively, may have recombined between HAdV-1 genome and HAdV-2 genome within species HAdV-C, indicating intraspecies recombination. The comparison results of the penton base, hexon, and fiber gene sequences between the Beijing HAdV-3, HAdV-4, HAdV-7, and HAdV-55 strains in this study and the strains from the GenBank database indicated significant conservation and stability of the sequences within the genome across time and space. abstract: BACKGROUND: Adenovirus is one of the most common causes of viral acute respiratory infections. To identify the types of human adenoviruses (HAdVs) causing respiratory illness in Beijing, a sentinel surveillance project on the viral aetiology of acute respiratory infection was initiated in 2011. PRINCIPAL FINDINGS: Through the surveillance project, 4617 cases of respiratory infections were identified during 2011-2013. Throat swabs (pharynx and tonsil secretions) were collected from all the patients, and 15 different respiratory viruses were screened by multiplex one-step PCR method. 45 were identified as adenovirus-positive from sporadic and outbreak cases of respiratory infection by a multiplex one-step RT-PCR method, and a total of 21 adenovirus isolates were obtained. Five HAdV types among three species, including HAdV-3 (species HAdV-B), HAdV-4 (species HAdV-E), HAdV-7 (species HAdV-B), HAdV-55 (species HAdV-B), and an undefined HAdV type (species HAdV-C) were identified. The comparison results of the penton base, hexon, and fiber gene sequences of the Beijing HAdV-3, HAdV-4, HAdV-7, and HAdV-55 strains in this study and those from the GenBank database indicated significant spatial and temporal conservation and stability of sequences within the genome; however, the phylogenetic relationship indicated that both strain BJ04 and strain BJ09 isolated in 2012 and 2013, respectively, may have recombined between HAdV-1 genome and HAdV-2 genome within species HAdV-C, indicating intraspecies recombination. CONCLUSIONS: This study confirmed that at least 5 HAdV types including HAdV-3, HAdV-4, HAdV-7, HAdV-55 and an undefined HAdV type were co-circulating and were the causative agents of respiratory tract infections in recent years in Beijing. HAdV-3, HAdV-4, HAdV-7, and HAdV-55 showed the apparent stability of the genomes, while intraspecies recombination was identified in strain BJ04 and BJ09. The recombinants carrying penton base gene of HAdV-1 as well as hexon and fiber genes of HAdV-2 might be a novel type of HAdV worthy of further study. url: https://www.ncbi.nlm.nih.gov/pubmed/25816320/ doi: 10.1371/journal.pone.0121375 id: cord-278935-3lgud7l8 author: Chen, Zheng‐Rong title: Clinical and epidemiological profiles of lower respiratory tract infection in hospitalized children due to human bocavirus in a subtropical area of China date: 2014-04-30 words: 4779.0 sentences: 236.0 pages: flesch: 47.0 cache: ./cache/cord-278935-3lgud7l8.txt txt: ./txt/cord-278935-3lgud7l8.txt summary: title: Clinical and epidemiological profiles of lower respiratory tract infection in hospitalized children due to human bocavirus in a subtropical area of China Furthermore, epidemiological data shows that HBoV is present year-round with different incidence rates from 2.2% to 19% in children with lower respiratory tract infection [Manning et al., 2006; Weissbrich et al., 2006; Allander et al., 2007; Canducci et al., 2008] . The purpose of this study was to ascertain the frequency, seasonal, and clinical characteristics in hospitalized children with lower respiratory tract infection and evaluate the effects of meteorological factors on the incidence of HBoV in a subtropical region of China. Based on the data from this study, HBoV was the third most common pathogen after RSV and Mycoplasma pneumoniae with an incidence of 6.6% in all hospitalized children with lower respiratory tract infection in Suzhou area. abstract: Lower respiratory tract infection is a major cause of morbidity and mortality in children. Human bocavirus (HBoV) is confirmed to have an association with pediatric lower respiratory tract infection. Seasonal and meteorological factors may play a key role in the epidemiology of HBoV. The purpose of this study was to ascertain the frequency, season, and clinical characteristics of hospitalized children with HBoV infection. In addition, an evaluation of the effects of meteorological factors on the incidence of HBoV in a subtropical area in China will be conducted. Children were <14 years in age and hospitalized for lower respiratory tract infection between January 1, 2009 and December 31, 2012 in the Respiratory Disease Department at the Children's Hospital affiliated to Soochow University. Multi‐pathogens were detected in nasopharyngeal aspirate samples. The association between HBoV activity and regional meteorological conditions was analyzed. The average incidence of HBoV infection was 6.6% (502/7,626). Of the 502 HBoV positive children, the median age was 13 months (range 1–156 months). The HBoV infection rate was highest among the 7–12 months groups (12.9%, 163/1,267). Seasonal distribution of HBoV was noted during June to November, especially during the summer season (June to August). HBoV activity was associated with temperature and humidity although the lag effect between temperature and HBoV activity observed. HBoV is one of the most common viral pathogens in children with lower respiratory tract infection. HBoV infection occurs throughout the year with a peak during the summer. Temperature and humidity may affect the incidence of HBoV. J. Med. Virol. 86:2154–2162, 2014. © 2014 Wiley Periodicals, Inc. url: https://doi.org/10.1002/jmv.23952 doi: 10.1002/jmv.23952 id: cord-353786-284qn075 author: Chen, Zhi-Min title: Diagnosis and treatment recommendations for pediatric respiratory infection caused by the 2019 novel coronavirus date: 2020-02-05 words: 3521.0 sentences: 224.0 pages: flesch: 47.0 cache: ./cache/cord-353786-284qn075.txt txt: ./txt/cord-353786-284qn075.txt summary: title: Diagnosis and treatment recommendations for pediatric respiratory infection caused by the 2019 novel coronavirus At the onset of the disease, infected children mainly present with fever, fatigue and cough, which may be accompanied by nasal congestion, runny nose, expectoration, diarrhea, headache, etc. 2. Children with a history of contacting patients with fever or respiratory symptoms who have a travel or residence history in Wuhan City and neighboring areas, or in other areas with persistent local transmission within 14 days prior to disease onset. 3. Children with a history of contacting confirmed or suspected cases infected with 2019-nCoV within 14 days prior to disease onset. 4. Children who are related with a cluster outbreak: in addition to this patient, there are other patients with fever or respiratory symptoms, including suspected or confirmed cases infected with 2019-nCoV. Most of the cases have normal or decreased white blood cell counts, while severely infected children show reduced level of lymphocyte count. abstract: Since December 2019, an epidemic caused by novel coronavirus (2019-nCoV) infection has occurred unexpectedly in China. As of 8 pm, 31 January 2020, more than 20 pediatric cases have been reported in China. Of these cases, ten patients were identified in Zhejiang Province, with an age of onset ranging from 112 days to 17 years. Following the latest National recommendations for diagnosis and treatment of pneumonia caused by 2019-nCoV (the 4th edition) and current status of clinical practice in Zhejiang Province, recommendations for the diagnosis and treatment of respiratory infection caused by 2019-nCoV for children were drafted by the National Clinical Research Center for Child Health, the National Children’s Regional Medical Center, Children’s Hospital, Zhejiang University School of Medicine to further standardize the protocol for diagnosis and treatment of respiratory infection in children caused by 2019-nCoV. url: https://doi.org/10.1007/s12519-020-00345-5 doi: 10.1007/s12519-020-00345-5 id: cord-016451-k8m2xz0e author: Chertow, Daniel S. title: Influenza, Measles, SARS, MERS, and Smallpox date: 2020-01-03 words: 6141.0 sentences: 365.0 pages: flesch: 41.0 cache: ./cache/cord-016451-k8m2xz0e.txt txt: ./txt/cord-016451-k8m2xz0e.txt summary: Influenza, measles, SARS, MERS, and smallpox illnesses are caused by highly infectious viral pathogens that induce critical illness. Measles infects and disrupts tissues throughout the body; however, severe disease is primarily due to lower respiratory tract and neurological complications [72] . Global epidemiology of avian influenza A H5N1 virus infection in humans, 1997-2015: a systematic review of individual case data Transmission of Middle East respiratory syndrome coronavirus infections in healthcare settings Viral shedding and antibody response in 37 patients with Middle East respiratory syndrome coronavirus infection Viral RNA in blood as indicator of severe outcome in Middle East respiratory syndrome coronavirus infection Clinical features and viral diagnosis of two cases of infection with Middle East respiratory syndrome coronavirus: a report of nosocomial transmission Clinical course and outcomes of critically ill patients with Middle East respiratory syndrome coronavirus infection abstract: Influenza, measles, SARS, MERS, and smallpox illnesses are caused by highly infectious viral pathogens that induce critical illness. These biologically diverse viruses enter and replicate within host cells triggering viral- and host-mediated damage that results in pneumonia and multiorgan failure in severe cases. Early case identification and strict infection control limit healthcare transmission. Vaccination allowed smallpox eradication and limits global measles and seasonal influenza mortality. While SARS-coronavirus (CoV) is no longer circulating, MERS-CoV and zoonotic influenza viruses, with pandemic potential, remain persistent threats. Supportive critical care is the mainstay of treatment for severe disease due to these viral infections. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120728/ doi: 10.1007/978-3-030-33803-9_5 id: cord-264255-q5izs39f author: Chieochansin, Thaweesak title: Human bocavirus (HBoV) in Thailand: Clinical manifestations in a hospitalized pediatric patient and molecular virus characterization date: 2007-12-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVE: Human bocavirus (HBoV), a novel virus, which based on molecular analysis has been associated with respiratory tract diseases in infants and children have recently been studied worldwide. To determine prevalence, clinical features and perform phylogenetic analysis in HBoV infected Thai pediatric patients. METHODS: HBoV was detected from 302 nasopharyngeal (NP) suctions of pediatric patients with acute lower respiratory tract illness and sequenced applying molecular techniques. RESULTS: The incidence of HBoV infection in pediatric patients amounted to 6.62% with 40% co-infected with other respiratory viruses. There were no clinical specific manifestations for HBoV; however, fever and productive cough were commonly found. Generalized rales and wheezing were detected in most of the patients as well as perihilar infiltrates. The alignment and phylogenetic analysis of partial VP1 genes showed minor variations. CONCLUSION: Our results indicated that HBoV can be detected in nasopharyngeal aspirate specimens from infants and children with acute lower respiratory tract illness. url: https://www.ncbi.nlm.nih.gov/pubmed/18164764/ doi: 10.1016/j.jinf.2007.11.006 id: cord-017897-mbwm0ytg author: Chiumello, Davide title: The Acute Respiratory Distress Syndrome: Diagnosis and Management date: 2018-10-01 words: 4825.0 sentences: 215.0 pages: flesch: 35.0 cache: ./cache/cord-017897-mbwm0ytg.txt txt: ./txt/cord-017897-mbwm0ytg.txt summary: In order to guarantee a better patient adaptation to the ventilator, to reduce the oxygen consumption related to the respiratory muscle activity and to guarantee a protective transpulmonary pressure, the use of neuromuscular blockers is accepted in clinical practice [49] . The indications for the prone positioning have changed over time: once it was used to improve arterial oxygenation in the most severe forms of respiratory failure [53, 54] ; while nowadays it aims to achieve a more homogeneous distribution of stress and strain within the lung parenchyma, acting in synergy with the remaining therapies and protecting against the ventilator induced lung injury [55] . Lung recruitability is better estimated according to the Berlin definition of acute respiratory distress syndrome at standard 5 cm H2O rather than higher positive end-expiratory pressure: a retrospective cohort study Ventilation strategy using low tidal volumes, recruitment maneuvers, and high positive end-expiratory pressure for acute lung injury and acute respiratory distress syndrome: a randomized controlled trial abstract: Acute respiratory distress syndrome (ARDS) is characterized by a new acute onset of hypoxemia secondary to a pulmonary edema of non-cardiogenic origin, bilateral lung opacities and reduction in respiratory system compliance after an insult direct or indirect to lungs. Its first description was in 1970s, and then several shared definitions tried to describe this clinical entity; the last one, known as Berlin definition, brought an improvement in predictive ability for mortality. In the present chapter, the diagnostic workup of the syndrome will be presented with particular attention to microbiological investigations which represent a milestone in the diagnostic process and to imaging techniques such as CT scan and lung ultrasound. Despite the treatment is mainly based on supportive strategies, attention should be applied to assure adequate respiratory gas exchange while minimizing the risk of ventilator-induced lung injury (VILI) onset. Therefore will be described several therapeutic approaches to ARDS, including noninvasive mechanical ventilation (NIMV), high-flow nasal cannulas (HFNC) and invasive ventilation with particular emphasis to risks and benefits of mechanical ventilation, PEEP optimization and lung protective ventilation strategies. Rescue techniques, such as permissive hypercapnia, prone positioning, neuromuscular blockade, inhaled vasodilators, corticosteroids, recruitment maneuvers and extracorporeal life support, will also be reviewed. Finally, the chapter will deal with the mechanical ventilation weaning process with particular emphasis on extrapulmonary factors such as neurologic, diaphragmatic or cardiovascular alterations which can lead to weaning failure. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122583/ doi: 10.1007/978-3-319-94189-9_11 id: cord-346887-dl0wc4u2 author: Cho, Hye Jung title: Respiratory viruses in neonates hospitalized with acute lower respiratory tract infections date: 2012-12-11 words: 3073.0 sentences: 193.0 pages: flesch: 53.0 cache: ./cache/cord-346887-dl0wc4u2.txt txt: ./txt/cord-346887-dl0wc4u2.txt summary: The aims of this study were to determine the overall distribution of respiratory viruses in neonates hospitalized with acute lower respiratory tract infectiosns (ALRI) and to describe the clinical characteristics of RSV infections in these neonates. In addition to respiratory syncytial virus (RSV), human rhinovirus (hRV), human parainfluenza virus (hPIV), and human metapneumovirus (hMPV) have been found to be major causes of acute lower respiratory tract infections (ALRI) in infants and young children. 1, 13 One study based on hospitalized children with ALRI in Korea reported that RSV (33.2%) was the most common virus among 13 respiratory viruses and was followed by hRV (19.1%), influenza virus (16.9%), hMPV (15.4%), and hPIV (8.3%). In the present study a significantly higher proportion of the RSV group obtained infections from neonatal day-care centers. FLIP-2 Study: Risk factors linked to respiratory syncytial virus infection requiring hospitalization in premature infants born in Spain at a gestational age of 32 to 35 weeks abstract: BACKGROUND: The burden of respiratory syncytial virus (RSV) in neonates has not been clearly studied. The aims of this study were to determine the overall distribution of respiratory viruses in neonates hospitalized with acute lower respiratory tract infectiosns (ALRI) and to describe the clinical characteristics of RSV infections in these neonates. METHODS: From January 2009 through May 2010, neonates aged <1 month who were hospitalized with ALRI and did not have underlying disease were included in the study. Viruses were identified on multiplex reverse transcription polymerase chain reaction using nasal swab samples. Clinical variables were evaluated between the RSV and non‐RSV infection groups. RESULTS: Of the 108 infants included in the study, 46 (42.6%) had RSV; human rhinovirus (18.5%), human parainfluenza virus 3 (7.5%), and human metapneumovirus (3.7%) were the next most common infections. Codetections accounted for 8.3% of the cases. Crowding increased the risk of RSV infection compared to the non‐RSV group (OR, 16.5; P = 0.001). The RSV group had a greater incidence of dyspnea (P = 0.027), pneumonia (P < 0.001), requirement for oxygen (P < 0.001), and prolonged hospitalization (P = 0.011) than the non‐RSV group. CONCLUSIONS: RSV was the most common viral etiology in neonates without underlying diseases who were hospitalized with ALRI. The disease severity of RSV infection was worse than that of other detected viral infections. Strict prevention strategies should be considered in overcrowded situations. url: https://www.ncbi.nlm.nih.gov/pubmed/22978535/ doi: 10.1111/j.1442-200x.2012.03727.x id: cord-253148-3t4o27xp author: Chow, Brian D.W. title: Evidence of human bocavirus circulating in children and adults, Cleveland, Ohio date: 2008-09-19 words: 2700.0 sentences: 200.0 pages: flesch: 50.0 cache: ./cache/cord-253148-3t4o27xp.txt txt: ./txt/cord-253148-3t4o27xp.txt summary: STUDY DESIGN: From October 2005 through October 2006, we screened respiratory samples from children and adults negative for common respiratory pathogens for HBoV by PCR. CONCLUSIONS: HBoV circulates in Cleveland, OH, in children and adults with similar frequencies, and can warrant hospitalization and intensive care. We sought to further define the clinical and epidemiologic characteristics of HBoV in adult and pediatric patients in Cleveland, OH. Isolates positive for HBoV were screened for common respiratory viruses by RT-PCR with published primer sets. Forty samples (2.2%) tested positive for HBoV by PCR: 36 (90%) pediatric patients and 4 (10%) adult patients. Of pediatric patients who screened positive for HBoV, 27 (84.4%) were admitted to the hospital, including 9 (28.1%) who required intensive care. However, this report suggests that clinical disease associated with HBoV alone may be severe enough to require admission to the hospital in both adults and children and to the intensive care unit in children. abstract: BACKGROUND: Viral respiratory illness is a major cause of morbidity and mortality. The human bocavirus (HBoV) is a recently recognized parvovirus isolated from human respiratory secretions. OBJECTIVES: To define the clinical and epidemiologic characteristics in adult and pediatric patients with evidence of HBoV. STUDY DESIGN: From October 2005 through October 2006, we screened respiratory samples from children and adults negative for common respiratory pathogens for HBoV by PCR. Demographic and clinical characteristics were obtained from medical records of HBoV positive individuals. RESULTS: Of 2075 samples screened, 1826 (88.0%) represented distinct respiratory events: 1539 (84.3%) were pediatric (<18 years), and 273 (15.0%) adult (≥18 years). Forty (2.2%) patients had HBoV: 36 (2.3%) children and 4 (1.5%) adults. HBoV positive children had history of prematurity (31.3%) and cardiac disease (18.8%). Adults had underlying pulmonary (100%) and cardiac (50%) disease. Twenty-seven children (84.4%) were hospitalized; 9 (28.1%) required intensive care. All adults were hospitalized; none required intensive care. Nosocomial acquisition likely occurred in 3 patients. CONCLUSIONS: HBoV circulates in Cleveland, OH, in children and adults with similar frequencies, and can warrant hospitalization and intensive care. Further study would clarify our understanding of this newly recognized human pathogen. url: https://www.ncbi.nlm.nih.gov/pubmed/18805051/ doi: 10.1016/j.jcv.2008.07.009 id: cord-253223-us0ey8dq author: Chow, Brian D.W. title: The Human Bocaviruses: A Review and Discussion of Their Role in Infection date: 2009-11-03 words: 5912.0 sentences: 401.0 pages: flesch: 49.0 cache: ./cache/cord-253223-us0ey8dq.txt txt: ./txt/cord-253223-us0ey8dq.txt summary: [38] [39] [40] [42] [43] [44] In a recent casecontrol study on acute gastroenteritis, Arthur and colleagues 13 examined stool specimens for potential pathogens, including all three species of human bocavirus. The large percentage of coinfections associated with human bocavirus infections suggests that evaluation for further pathogens should be undertaken for any patient diagnosed with HBoV-1. Human bocavirus infection in children with respiratory tract disease Human bocavirus detection in nasopharyngeal aspirates of children without clinical symptoms of respiratory infection Detection of human bocavirus in Japanese children with lower respiratory tract infections High prevalence of human bocavirus detected in young children with severe acute lower respiratory tract disease by use of a standard PCR protocol and a novel real-time PCR protocol Human bocavirus DNA detected by quantitative real-time PCR in two children hospitalized for lower respiratory tract infection abstract: Respiratory tract infections are a leading cause of morbidity and mortality worldwide. The human bocavirus (HBoV) is a newly recognized human parvovirus first reported in 2005. Since its discovery, this virus has been associated with upper and lower respiratory tract disease and gastroenteritis worldwide. This article is a comprehensive review of what is known about HBoV. It includes an evaluation of diagnostic modalities, symptoms occurring in affected patients, and a discussion as to whether HBoV is responsible for identified clinical manifestations. The article reviews the incidence and effect of coinfection and updates on related members (HBoV-2 and HBoV-3) recently reported. Understanding of respiratory viruses such as HBoV remains vitally important to the health of adult and pediatric patients. url: https://api.elsevier.com/content/article/pii/S0272271209000596 doi: 10.1016/j.cll.2009.07.010 id: cord-311275-ysr9nqun author: Chuaychoo, Benjamas title: Clinical manifestations and outcomes of respiratory syncytial virus infection in adult hospitalized patients date: 2019-07-03 words: 3164.0 sentences: 199.0 pages: flesch: 41.0 cache: ./cache/cord-311275-ysr9nqun.txt txt: ./txt/cord-311275-ysr9nqun.txt summary: There were a few data of adult hospitalized patients with RSV infection, with high complications, in Thailand; [3, 12, 13] however, additional clinical data are required for planning patient management and also disease prevention in this region. RSV, respiratory syncytial virus; ARI, acute respiratory illness; COPD, chronic obstructive pulmonary disease; HAP, hospital-acquired pneumonia; VAP, ventilator-associated pneumonia. The pre-existing coronary arterial disease (CAD) was the risk factor of overall cardiovascular complications in hospitalized adult patients with RSV infection with odds ratio 6.18, (95% CI 1.18-32.5), p = 0.03, adjusted for age, sex, HT, DLP, DM, pre-existing CHF, arrhythmia, and VHD. The prospective study of all adult hospitalized patients with acute respiratory illness should be conducted to determine the prevalence, clinical manifestations, and outcomes of the virus. Most of the adult hospitalized patients with RSV infections aged ≥ 50 years old and had pre-existing cardiopulmonary diseases, hematologic malignancy, immunocompromised hosts, and DM. abstract: BACKGROUND: Respiratory syncytial virus (RSV) is an important virus found in adult hospitalized patients. OBJECTIVES: To study the clinical outcomes of hospitalized patients aged ≥ 15 years and diagnosed with RSV infection. STUDY DESIGN: Both retrospective and prospective cohort studies were conducted at a university hospital between May 2014 and December 2015. Results: RSV was detected in 86 of 1562(5.5%) adult hospitalized patients suspected of respiratory viral infection. Sixty-nine patients were included in the study. RSV was detected by RT-PCR (82.6%), IFA (10.1%), and both RT-PCR and IFA (7.3%). Most patients (87.0%) were aged ≥ 50 years. Cardiovascular diseases, pulmonary diseases, immunocompromised hosts, and diabetes were the major comorbidities. The common manifestations were cough (92.8%), dyspnea (91.3%), sputum production (87.0%), tachypnea (75.4%), wheezing (73.9%), and fever (71.0%). Fifty- five patients (79.7%) were diagnosed with pneumonia. Hypoxemia (SpO2 ≤ 92%) was found in 53.6% patients. Twenty-five of 69(36.2%) patients developed respiratory failure and required ventilatory support. Cardiovascular complications were found in 24.6% of patients. Congestive heart failure, acute myocardial infarction (MI), new atrial fibrillation, and supraventricular tachycardia were found in 9(13.0%), 7(10.1%), 4(5.8%), and 3(4.3%) of 69 patients, respectively. Overall mortality was 15.9%. Pneumonia (81.8%) and acute MI (18.2%) were the major causes of death. CONCLUSIONS: Most adult hospitalized patients with RSV infection were of advanced age and had comorbidities. Cardiopulmonary complications were the major causes of death. Management and prevention of RSV infection in these vulnerable groups are necessary. url: https://doi.org/10.1016/j.jcv.2019.07.001 doi: 10.1016/j.jcv.2019.07.001 id: cord-294933-oc2glu4a author: Cinesi Gómez, César title: Clinical consensus recommendations regarding non-invasive respiratory support in the adult patient with acute respiratory failure secondary to SARS-CoV-2 infection date: 2020-06-19 words: 5643.0 sentences: 337.0 pages: flesch: 45.0 cache: ./cache/cord-294933-oc2glu4a.txt txt: ./txt/cord-294933-oc2glu4a.txt summary: The document provides clinical recommendations for the noninvasive respiratory support (noninvasive ventilation, high flow oxygen therapy with nasal cannula) in any patient with suspected or confirmed presentation of COVID-19 with acute respiratory failure. The document provides clinical recommendations for the noninvasive respiratory support (noninvasive ventilation, high flow oxygen therapy with nasal cannula) in any patient with suspected or confirmed presentation of COVID-19 with acute respiratory failure. The present document has been developed by consensus among the scientific societies involved in acute respiratory failure in adult patients, and seeks to provide a more detailed description of the recommendations on the use of non-invasive respiratory support (NIRS) in the management of acute respiratory failure (ARF) secondary to infection by the newly emergent SARS-CoV-2 coronavirus, which causes so-called COVID-19 disease, as a complement to the information emitted by the Spanish Ministry of Health, Consumer Affairs and Social Wellbeing (Ministerio de Sanidad, Consumo y Bienestar Social [MSC]), 1,2 which is frequently updated and establishes a series of general recommendations. abstract: Abstract Coronavirus disease 2019 (COVID-19) is a respiratory tract infection caused by a newly emergent coronavirus, that was first recognized in Wuhan, China, in December 2019. Currently, the World Health Organization (WHO) has defined the infection as a global pandemic and there is a health and social emergency for the management of this new infection. While most people with COVID-19 develop only mild or uncomplicated illness, approximately 14% develop severe disease that requires hospitalization and oxygen support, and 5% require admission to an intensive care unit. In severe cases, COVID-19 can be complicated by the acute respiratory distress syndrome (ARDS), sepsis and septic shock, and multiorgan failure. This consensus document has been prepared on evidence-informed guidelines developed by a multidisciplinary panel of health care providers from four Spanish scientific societies (Spanish Society of Intensive Care Medicine [SEMICYUC], Spanish Society of Pulmonologists [SEPAR], Spanish Society of Emergency [SEMES], Spanish Society of Anesthesiology, Reanimation, and Pain [SEDAR]) with experience in the clinical management of patients with COVID-19 and other viral infections, including SARS, as well as sepsis and ARDS. The document provides clinical recommendations for the noninvasive respiratory support (noninvasive ventilation, high flow oxygen therapy with nasal cannula) in any patient with suspected or confirmed presentation of COVID-19 with acute respiratory failure. This consensus guidance should serve as a foundation for optimized supportive care to ensure the best possible chance for survival and to allow for reliable comparison of investigational therapeutic interventions as part of randomized controlled trials. url: https://www.sciencedirect.com/science/article/pii/S217357272030120X doi: 10.1016/j.medine.2020.03.002 id: cord-023509-tvqpv6fp author: Corrin, Bryan title: Occupational, environmental and iatrogenic lung disease date: 2011-03-02 words: 42576.0 sentences: 2457.0 pages: flesch: 45.0 cache: ./cache/cord-023509-tvqpv6fp.txt txt: ./txt/cord-023509-tvqpv6fp.txt summary: As a general rule, exposure to silica dust extends over many years, often 20 or more, before the symptoms of silicosis first appear: by the time the disease becomes overt clinically, much irreparable damage has been inflicted on the lungs. Confusingly, the term ''acute silicosis'' has since been applied to a further effect of heavy dust exposure in tunnellers, sand blasters and silica flour workers, namely pulmonary alveolar lipoproteinosis (see below), 71, 72 whilst the terms ''accelerated silicosis'' or ''cellular phase silicosis'' have been substituted for ''acute silicosis'' in referring to the rapid development of early cellular lesions. Asbestosis is defined as diffuse interstitial fibrosis of the lung caused by exposure to asbestos dust. The finely divided fume of several metals is highly toxic to the lungs and capable of producing severe acute and chronic damage to both the conductive airways and the alveoli, resulting in acute tracheobronchitis and bronchiolitis, diffuse alveolar damage, obliterative bronchiolitis and pulmonary fibrosis. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7170212/ doi: 10.1016/b978-0-7020-3369-8.00007-0 id: cord-277327-il8uaavn author: Couch, MD, Robert B. title: Respiratory Viral Infections in Immunocompetent and Immunocompromised Persons date: 1997-03-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The acute respiratory illnesses are the most common type of acute illness in the United States today. The respiratory viruses—which include influenza viruses, parainfluenza viruses, respiratory syncytial virus (RSV), rhinoviruses, coronaviruses, and adenoviruses—cause the majority of these illnesses. Some of these viruses cause illness throughout the year, whereas others are most common in winter. All population groups experience these infections and illnesses. As the number of elderly persons and those with underlying disease increases, awareness is growing that these common infections can have serious consequences. This has recently been emphasized for immunocompromised persons. At the M.D. Anderson Cancer Center (MDACC), infection surveillance of mostly hospitalized adults with leukemia or a recent bone marrow transplant yielded a respiratory virus from 181 of 668 (27.1%) respiratory illness episodes. In descending order of frequency, infections with RSV, rhinoviruses, influenza viruses, parainfluenza viruses, and adenoviruses were detected in each of three surveillance years. High frequencies of nosocomial acquisition occurred, as has been noted in prior reports. Similarly, persistence of infection and high frequencies of pneumonia and death among infected patients occurred, which have also been noted earlier. At MDACC, pneumonia occurred in 58–78% of infected patients, and 22–44% died. The role of the virus infection in many cases of pneumonia is uncertain, but death from pure viral pneumonia is well documented. A number of immune deficiencies in this patient population and options for control of these infections have been described that can, respectively, account for the medical problem and provide ways to approach prevention and treatment. url: https://www.ncbi.nlm.nih.gov/pubmed/10868136/ doi: 10.1016/s0002-9343(97)00003-x id: cord-258366-fu9b446y author: Couto, Carla R. title: Fighting Misconceptions to Improve Compliance with Influenza Vaccination among Health Care Workers: An Educational Project date: 2012-02-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The compliance with influenza vaccination is poor among health care workers (HCWs) due to misconceptions about safety and effectiveness of influenza vaccine. We proposed an educational prospective study to demonstrate to HCWs that influenza vaccine is safe and that other respiratory viruses (RV) are the cause of respiratory symptoms in the months following influenza vaccination. 398 HCWs were surveyed for adverse events (AE) occurring within 48 h of vaccination. AE were reported by 30% of the HCWs. No severe AE was observed. A subset of 337 HCWs was followed up during four months, twice a week, for the detection of respiratory symptoms. RV was diagnosed by direct immunofluorescent assay (DFA) and real time PCR in symptomatic HCWs. Influenza A was detected in five episodes of respiratory symptoms (5.3%) and other RV in 26 (27.9%) episodes. The incidence density of influenza and other RV was 4.3 and 10.8 episodes per 100 HCW-month, respectively. The educational nature of the present study may persuade HCWs to develop a more positive attitude to influenza vaccination. url: https://doi.org/10.1371/journal.pone.0030670 doi: 10.1371/journal.pone.0030670 id: cord-284372-v95fzp8n author: Coyle, Peter V title: A touchdown nucleic acid amplification protocol as an alternative to culture backup for immunofluorescence in the routine diagnosis of acute viral respiratory tract infections date: 2004-10-25 words: 4717.0 sentences: 224.0 pages: flesch: 43.0 cache: ./cache/cord-284372-v95fzp8n.txt txt: ./txt/cord-284372-v95fzp8n.txt summary: title: A touchdown nucleic acid amplification protocol as an alternative to culture backup for immunofluorescence in the routine diagnosis of acute viral respiratory tract infections To overcome this problem we developed a diagnostic molecular strip which combined a generic nested touchdown protocol with in-house primer master-mixes that could recognise 12 common respiratory viruses. CONCLUSIONS: The touchdown protocol with pre-dispensed primer master-mixes was suitable for replacing virus culture for the diagnosis of respiratory viruses which were negative by immunofluorescence. To test the feasibility of its routine use we needed to clinically validate its performance in a routine setting on specimens tested in parallel with our standard immunofluorescence protocol for the diagnosis of acute virus respiratory infections. In conclusion the use of the touchdown protocol with pre-dispensed and quality checked primer master-mixes was suitable for replacing virus culture for the diagnosis of respiratory viruses for immunofluorescence negative specimens. abstract: BACKGROUND: Immunofluorescence and virus culture are the main methods used to diagnose acute respiratory virus infections. Diagnosing these infections using nucleic acid amplification presents technical challenges, one of which is facilitating the different optimal annealing temperatures needed for each virus. To overcome this problem we developed a diagnostic molecular strip which combined a generic nested touchdown protocol with in-house primer master-mixes that could recognise 12 common respiratory viruses. RESULTS: Over an 18 month period a total of 222 specimens were tested by both immunofluorescence and the molecular strip. The specimens came from 103 males (median age 3.5 y), 80 females (median age 9 y) and 5 quality assurance scheme specimens. Viruses were recovered from a number of specimen types including broncho-alveolar lavage, nasopharyngeal secretions, sputa, post-mortem lung tissue and combined throat and nasal swabs. Viral detection by IF was poor in sputa and respiratory swabs. A total of 99 viruses were detected in the study from 79 patients and 4 quality control specimens: 31 by immunofluorescence and 99 using the molecular strip. The strip consistently out-performed immunofluorescence with no loss of diagnostic specificity. CONCLUSIONS: The touchdown protocol with pre-dispensed primer master-mixes was suitable for replacing virus culture for the diagnosis of respiratory viruses which were negative by immunofluorescence. Results by immunofluorescence were available after an average of 4–12 hours while molecular strip results were available within 24 hours, considerably faster than viral culture. The combined strip and touchdown protocol proved to be a convenient and reliable method of testing for multiple viruses in a routine setting. url: https://www.ncbi.nlm.nih.gov/pubmed/15504232/ doi: 10.1186/1471-2180-4-41 id: cord-324775-3x5os79m author: Crowe, J.E. title: Human Respiratory Viruses date: 2008-07-30 words: 5716.0 sentences: 300.0 pages: flesch: 43.0 cache: ./cache/cord-324775-3x5os79m.txt txt: ./txt/cord-324775-3x5os79m.txt summary: Respiratory syncytial virus (RSV) is the most common pathogen, with hMPV, PIV-3, influenza viruses, and rhinoviruses accounting for the majority of the remainder of acute viral respiratory infections. Respiratory syncytial virus (RSV), parainfluenza viruses (PIVs), adenoviruses, and influenza viruses were identified initially as the most common causes of serious lower respiratory tract disease in infants and children. These patients also suffer more frequent and more severe disease including mortality with common respiratory viruses, including RSV, hMPV, PIV, influenza viruses, rhinoviruses, and adenoviruses. Enterovirus infections occur most commonly in the summer months in temperate areas, which differs from the season of many of the other most common respiratory viruses such as paramyxoviruses and influenza virus. Humans generally do not develop lifelong immunity to reinfection with these viruses; rather, specific immunity protects against severe and lower respiratory tract disease. Humans generally do not develop lifelong immunity to reinfection with these viruses; rather, specific immunity protects against severe and lower respiratory tract disease. abstract: Viruses are the leading causes of acute lower respiratory-tract infection in infancy. Respiratory syncytial virus (RSV) is the most common pathogen, with hMPV, PIV-3, influenza viruses, and rhinoviruses accounting for the majority of the remainder of acute viral respiratory infections. Humans generally do not develop lifelong immunity to reinfection with these viruses; rather, specific immunity protects against severe and lower respiratory-tract disease. url: https://api.elsevier.com/content/article/pii/B978012374410400488X doi: 10.1016/b978-012374410-4.00488-x id: cord-017364-d9zmdm23 author: Crowe, James E. title: Paramyxoviruses: Respiratory Syncytial Virus and Human Metapneumovirus date: 2014-02-27 words: 18331.0 sentences: 897.0 pages: flesch: 37.0 cache: ./cache/cord-017364-d9zmdm23.txt txt: ./txt/cord-017364-d9zmdm23.txt summary: A virus causing a similar cytopathic effect in cultured cells was recovered from infants with respiratory illness shortly after, and studies of human antibodies in the serum of infants and children indicated that infection was common early in life [ 1 , 2 ] . Higher titers of virus in respiratory secretions usually are associated with increased severity of disease, in prospective studies of natural infection [ 114 ] or of clinical vaccine trials [ 115 ] . Most epidemiologic studies of MPV in children show that the virus is the second leading cause of lower respiratory infection after RSV. Acute lower respiratory tract infections by human metapneumovirus in children in Southwest China: a 2-year study The impact of infection with human metapneumovirus and other respiratory viruses in young infants and children at high risk for severe pulmonary disease Comparison of risk factors for human metapneumovirus and respiratory syncytial virus disease severity in young children abstract: Human respiratory syncytial virus (RSV) and human metapneumovirus (MPV) are members of the family Paramyxoviridae of the Mononegavirales order, comprising the nonsegmented negative-strand RNA viruses. Paramyxoviridae has two subfamilies: Paramyxovirinae, which includes the parainfluenza viruses 1–4 and measles and mumps viruses, and Pneumovirinae, which includes RSV and MPV. Pneumovirinae has two genera: Pneumovirus, which includes human RSV, bovine respiratory syncytial virus, and pneumonia virus of mice, and Metapneumovirus, which includes human MPV and avian metapneumovirus, sometimes called avian pneumovirus. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121911/ doi: 10.1007/978-1-4899-7448-8_26 id: cord-003488-pfzy8p5v author: Cruces, Pablo title: Respiratory mechanics in infants with severe bronchiolitis on controlled mechanical ventilation date: 2017-10-06 words: 3697.0 sentences: 229.0 pages: flesch: 46.0 cache: ./cache/cord-003488-pfzy8p5v.txt txt: ./txt/cord-003488-pfzy8p5v.txt summary: Bronchiolitis is usually a self-limited disease, but some children may develop respiratory failure with increased work of breathing (WOB), hypoxemia and hypercarbia requiring mechanical ventilation (MV) in addition to usual supportive measures [7, 8] . These findings may seem unexpected and contradictory with the current understanding of severe bronchiolitis as a primarily obstructive airway disease with an increase in Abbreviations: mo months old, PF ratio PaO 2 /FIO 2 ratio, OI oxygenation index, PIM 2 Pediatric index of mortality 2, RSV respiratory syncytial virus, PNB preterm newborn, HMD hyaline membrane disease a Viral Studies were negative, but pneumococcal superinfection was diagnosed expiratory resistance, but they are supported by the observation done over a half century ago by Krieger et al. Correlation between respiratory system compliance and expiratory airway resistance measured in children on mechanical ventilation due to severe bronchiolitis. abstract: BACKGROUND: Analysis of respiratory mechanics during mechanical ventilation (MV) is able to estimate resistive, elastic and inertial components of the working pressure of the respiratory system. Our aim was to discriminate the components of the working pressure of the respiratory system in infants on MV with severe bronchiolitis admitted to two PICU’s. METHODS: Infants younger than 1 year old with acute respiratory failure caused by severe bronchiolitis underwent neuromuscular blockade, tracheal intubation and volume controlled MV. Shortly after intubation studies of pulmonary mechanics were performed using inspiratory and expiratory breath hold. The maximum inspiratory and expiratory flow (QI and QE) as well as peak inspiratory (PIP), plateau (PPL) and total expiratory pressures (tPEEP) were measured. Inspiratory and expiratory resistances (RawI and RawE) and Time Constants (K(TI) and K(TE)) were calculated. RESULTS: We included 16 patients, of median age 2.5 (1–5.8) months. Bronchiolitis due to respiratory syncytial virus was the main etiology (93.8%) and 31.3% had comorbidities. Measured respiratory pressures were PIP 29 (26–31), PPL 24 (20–26), tPEEP 9 [8–11] cmH2O. Elastic component of the working pressure was significantly higher than resistive and both higher than threshold (tPEEP – PEEP) (P < 0.01). QI was significantly lower than QE [5 (4.27–6.75) v/s 16.5 (12–23.8) L/min. RawI and RawE were 38.8 (32–53) and 40.5 (22–55) cmH2O/L/s; K(TI) and K(TE) [0.18 (0.12–0.30) v/s 0.18 (0.13–0.22) s], and K(TI):K(TE) ratio was 1:1.04 (1:0.59–1.42). CONCLUSIONS: Analysis of respiratory mechanics of infants with severe bronchiolitis receiving MV shows that the elastic component of the working pressure of the respiratory system is the most important. The elastic and resistive components in conjunction with flow profile are characteristic of restrictive diseases. A better understanding of lung mechanics in this group of patients may lead to change the traditional ventilatory approach to severe bronchiolitis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12890-017-0475-6) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6389183/ doi: 10.1186/s12890-017-0475-6 id: cord-284858-hrljsc8l author: Cui, Shu-Juan title: Co-infection cases of human common respiratory viruses in Beijing, 2010–2012 date: 2013-02-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/23453410/ doi: 10.1016/j.bjid.2012.08.026 id: cord-021894-lq8yr710 author: Cunningham, Steve title: Bronchiolitis date: 2018-03-13 words: 6536.0 sentences: 351.0 pages: flesch: 39.0 cache: ./cache/cord-021894-lq8yr710.txt txt: ./txt/cord-021894-lq8yr710.txt summary: Globally there are an estimated 33.8 million cases of RSV lower respiratory tract infection each year in children under 5 years of age, resulting in 3.4 million admissions to the hospital and 66 to 199 thousand deaths (with the majority in low-and middle-income countries). 42, 43 Severity of disease is associated with both infant risk factors (including lack of adaptive T cell response), 26,44 but also RSV virus specific factors (viral antigen load and direct cytotoxic effects). Respiratory syncytial virus genomic load and disease severity among children hospitalized with bronchiolitis: multicenter cohort studies in the United States and Finland Respiratory syncytial virus load, viral dynamics, and disease severity in previously healthy naturally infected children The risk of mortality among young children hospitalized for severe respiratory syncytial virus infection High incidence of pulmonary bacterial co-infection in children with severe respiratory syncytial virus (RSV) bronchiolitis abstract: Acute viral bronchiolitis is a common viral lower respiratory tract infection in young children. Most typically caused by respiratory syncytial virus in 70% of cases, the condition lasts for 4 to 7 days, with a prolonged cough in many. Children with comorbidity, particularly those born prematurely or with significant congenital heart disease, are at risk of more severe disease. Nasal obstruction progresses over 3 to 4 days to difficulty with feeding and increased work of breathing with hypoxemia. Crackles and/or wheeze may be auscultated. Apnoea may be a presenting sign in those less than 3 months of age. Viral load is highest at peak of symptoms and in those with more severe disease. Approximately 2% to 3% of all children are admitted to hospital with bronchiolitis. The differential diagnosis may include bacterial pneumonia, congenital lesions of the lung or heart, or an interstitial lung disease. There are no effective treatments, and admission is for feeding support (by nasogastric or intravenous fluids) or treatment of hypoxemia. Critical care support is required for some infants experiencing respiratory failure, though mortality rates remain unchanged. Practice within and between countries varies significantly and alignment of practice is a common goal of guidelines. Vaccines for RSV are in advanced development, as are several antiviral therapies for RSV. In most children, acute symptoms improve within 5 to 7 days and cough by 2 weeks. Recurrent wheeze is common following acute bronchiolitis and a good association with a diagnosis of asthma in childhood. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152174/ doi: 10.1016/b978-0-323-44887-1.00024-9 id: cord-302111-kg0dmgq0 author: Darden, Dijoia B. title: The Clinical Presentation and Immunology of Viral Pneumonia and Implications for Management of Coronavirus Disease 2019 date: 2020-04-29 words: 4492.0 sentences: 257.0 pages: flesch: 34.0 cache: ./cache/cord-302111-kg0dmgq0.txt txt: ./txt/cord-302111-kg0dmgq0.txt summary: Given the rapidly emerging pandemic associated with the novel severe acute respiratory syndrome coronavirus 2 causing coronavirus disease 2019, it is important to review the clinical presentation and immunologic changes associated with viral pneumonia. Given the rapidly emerging pandemic associated with the novel severe acute respiratory syndrome coronavirus 2 causing coronavirus disease 2019, it is important to review the clinical presentation and immunologic changes associated with viral pneumonia. Key Words: coronavirus; immunology; influenza virus; severe acute respiratory syndrome; viral pneumonia P neumonia is the leading infectious cause of hospitalization among adults and children in the United States (1) . Given the rapid spread of this virus and its association with severe pulmonary disease, the purpose of this review is to provide an overview of the presentation and immunology of viral pneumonia, principles of early management, and application to COVID-19. abstract: This review will briefly examine the clinical presentation and important immunology of viral pneumonia with a focus on severe acute respiratory syndrome coronavirus 2 (coronavirus disease 2019). DATA SOURCES, STUDY SELECTION, DATA EXTRACTION, AND DATA SYNTHESIS: The most relevant, original and review literature were assessed for inclusion in this review. Sources included the Centers for Disease Control and Prevention, World Health Organization, and PubMed. CONCLUSIONS: Pneumonia is a leading cause of hospitalization and death worldwide, with viral etiologies being very common. Given the rapidly emerging pandemic associated with the novel severe acute respiratory syndrome coronavirus 2 causing coronavirus disease 2019, it is important to review the clinical presentation and immunologic changes associated with viral pneumonia. Symptoms of viral pneumonia include common respiratory tract infection symptoms of cough, fever, and shortness of breath. Immunologic changes include up-regulation of airway pro-inflammatory cytokines and pathogen- and damage-associated molecular patterns contributing to cytokine and genomic changes. Coronavirus disease 2019 clinical presentation is typical of viral pneumonia with an increased prevalence of early pulmonary infiltrates and lymphopenia. Principles of early coronavirus disease 2019 management and isolation as well as potential therapeutic approaches to the emerging pandemic are discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/32426751/ doi: 10.1097/cce.0000000000000109 id: cord-331973-avjw4kx1 author: Das, Shubhagata title: Laboratory Diagnosis of Respiratory Tract Infections in Children – the State of the Art date: 2018-10-18 words: 5141.0 sentences: 228.0 pages: flesch: 34.0 cache: ./cache/cord-331973-avjw4kx1.txt txt: ./txt/cord-331973-avjw4kx1.txt summary: Serological tests can successfully identify antibodies to most respiratory pathogens such as RSV, adenovirus, influenza A and B, parainfluenza 1-3 virus, etc., and can detect mixed infections from hospitalized children suffering from acute respiratory infections, with the exception of infants for whom an antibody response is usually undetected (Hall et al., 1991; Chkhaidze et al., 2006) . FA testing, in addition to RT-PCR, is useful for epidemiological studies as it increases the probability of identifying acute viral infections and has been used for accurate assessment of respiratory viruses other than influenza in children (Sawatwong et al., 2012; Feikin et al., 2013; Zhang et al., 2017) . Most of the studies evaluating the clinical performance of these assays have reported high sensitivity (87-100%) and specificity (>98%) for detecting influenza A/B and RSV in pediatric and adult patients (Bell et al., 2014; Nie et al., 2014; Popowitch and Miller, 2015; Gibson et al., 2017; Ling et al., 2018) . abstract: In the pediatric population, respiratory infections are the most common cause of physician visits. Although many respiratory illnesses are self-limiting viral infections that resolve with time and supportive care, it can be critical to identify the causative pathogen at an early stage of the disease in order to implement effective antimicrobial therapy and infection control. Over the last few years, diagnostics for respiratory infections have evolved substantially, with the development of novel assays and the availability of updated tests for newer strains of pathogens. Newer laboratory methods are rapid, highly sensitive and specific, and are gradually replacing the conventional gold standards, although the clinical utility of these assays is still under evaluation. This article reviews the current laboratory methods available for testing for respiratory pathogens and discusses the advantages and disadvantages of each approach. url: https://doi.org/10.3389/fmicb.2018.02478 doi: 10.3389/fmicb.2018.02478 id: cord-299379-ch7a39d6 author: De Conto, Flora title: Epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in Northern Italy() date: 2019-01-17 words: 4005.0 sentences: 274.0 pages: flesch: 56.0 cache: ./cache/cord-299379-ch7a39d6.txt txt: ./txt/cord-299379-ch7a39d6.txt summary: title: Epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in Northern Italy() The viral etiology of ARTIs was investigated over 3 years (October 2012–September 2015) in 2575 children in Parma, Italy, using indirect immunofluorescent staining of respiratory samples for viral antigens, cell culture, and molecular assays. The simultaneous use of different diagnostic tools allowed us to identify a putative viral etiology in half the children examined and to provide an estimate of the epidemiology and seasonality of respiratory viruses associated with ARTIs. Acute respiratory tract infections (ARTIs) are a persistent public health problem (Lu et al., 2013) . This three-year (October 2012-September 2015) hospital-based survey in Parma (Northern Italy) aimed to determine the prevalence of respiratory virus infections, their seasonality, and any patterns of mixed infections in children with ARTIs by using indirect immunofluorescent staining of respiratory samples for viral antigens, cell culture, and molecular assays. abstract: Acute respiratory tract infections (ARTIs) are among the leading causes of morbidity and mortality in children. The viral etiology of ARTIs was investigated over 3 years (October 2012–September 2015) in 2575 children in Parma, Italy, using indirect immunofluorescent staining of respiratory samples for viral antigens, cell culture, and molecular assays. Respiratory viruses were detected in 1299 cases (50.44%); 1037 (79.83%) were single infections and 262 (20.17%) mixed infections. The highest infection incidence was in children aged >6 months to ≤3 years (57.36%). Human respiratory syncytial virus (27.12%) and human adenovirus (23.58%) were the most common viruses identified. The virus detection rate decreased significantly between the first and third epidemic season (53.9% vs. 43.05%, P < 0.0001). The simultaneous use of different diagnostic tools allowed us to identify a putative viral etiology in half the children examined and to provide an estimate of the epidemiology and seasonality of respiratory viruses associated with ARTIs. url: https://doi.org/10.1016/j.diagmicrobio.2019.01.008 doi: 10.1016/j.diagmicrobio.2019.01.008 id: cord-332055-lrpfzsog author: DeVos, Elizabeth title: Approach to Adult Patients with Acute Dyspnea date: 2015-11-27 words: 4415.0 sentences: 271.0 pages: flesch: 45.0 cache: ./cache/cord-332055-lrpfzsog.txt txt: ./txt/cord-332055-lrpfzsog.txt summary: National and world organizations define asthma "by the history of respiratory symptoms such as wheeze, shortness of breath, chest tightness and cough that vary over time and in intensity, together with variable expiratory airflow limitation." 12 The reversibility of airflow obstruction is the hallmark distinguishing asthma from other obstructive respiratory disorders. In contrast, chronic obstructive pulmonary disease (COPD)/ emphysema is defined as "persistent airflow limitation that is usually progressive and associated with enhanced chronic inflammatory responses in the airways and the lungs." 12 These patients also frequently wheeze, but may have a different course of acute and chronic disease. Rapid evaluation by lung-cardiac inferior vena cava (LCI) integrated ultrasound for differentiating heart failure from pulmonary disease as the cause of acute dyspnea in the emergency setting Clinical policy: critical issues in the evaluation and management of adult patients presenting to the emergency department with acute heart failure syndromes abstract: Undifferentiated patients in respiratory distress require immediate attention in the emergency department. Using a thorough history and clinical examination, clinicians can determine the most likely causes of dyspnea. Understanding the pathophysiology of the most common diseases contributing to dyspnea guides rational testing and informed, expedited treatment decisions. url: https://www.sciencedirect.com/science/article/pii/S0733862715000747 doi: 10.1016/j.emc.2015.08.008 id: cord-260750-utbuj5iz author: Dear, Jonathan D. title: Bacterial Pneumonia in Dogs and Cats date: 2013-11-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Bacterial pneumonia is a common clinical diagnosis in dogs but seems to occur less commonly in cats. Underlying causes include viral infection, aspiration injury, and foreign body inhalation. Identification of the organisms involved in disease, appropriate use of antibiotics and adjunct therapy, and control of risk factors for pneumonia improve management. url: https://www.ncbi.nlm.nih.gov/pubmed/24268339/ doi: 10.1016/j.cvsm.2013.09.003 id: cord-343325-cbrly7f5 author: Denault, André Y. title: A proposed lung ultrasound and phenotypic algorithm for the care of COVID-19 patients with acute respiratory failure date: 2020-05-21 words: 4025.0 sentences: 255.0 pages: flesch: 45.0 cache: ./cache/cord-343325-cbrly7f5.txt txt: ./txt/cord-343325-cbrly7f5.txt summary: title: A proposed lung ultrasound and phenotypic algorithm for the care of COVID-19 patients with acute respiratory failure We propose a management algorithm that combines the respiratory rate and oxygenation index with bedside lung ultrasound examination and monitoring that could help determine earlier the requirement for intubation and other surveillance of COVID-19 patients with respiratory failure. His phenotype changed from an H-type to an (D) L-type (courtesy of Dr. Emmanuel Charbonney and Dr. Lawrence Leroux) Lung ultrasound in COVID-19 respiratory failure therapy with a high-flow nasal cannula (HFNC) with an increased fraction of inspired oxygen (F I O 2 ). 51 Lung ultrasound can also impact clinical decision-making in patients with acute respiratory failure 52, 53 and provide comprehensive monitoring of regional lung aeration changes that could be used to predict response to prone positioning with improved right (Figs 6 and 7) [54] [55] [56] or higher positive end-expiratory pressure strategy. abstract: Pulmonary complications are the most common clinical manifestations of coronavirus disease (COVID-19). From recent clinical observation, two phenotypes have emerged: a low elastance or L-type and a high elastance or H-type. Clinical presentation, pathophysiology, pulmonary mechanics, radiological and ultrasound findings of these two phenotypes are different. Consequently, the therapeutic approach also varies between the two. We propose a management algorithm that combines the respiratory rate and oxygenation index with bedside lung ultrasound examination and monitoring that could help determine earlier the requirement for intubation and other surveillance of COVID-19 patients with respiratory failure. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12630-020-01704-6) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s12630-020-01704-6 doi: 10.1007/s12630-020-01704-6 id: cord-308201-lavcsqov author: Desforges, Marc title: Human Coronaviruses and Other Respiratory Viruses: Underestimated Opportunistic Pathogens of the Central Nervous System? date: 2019-12-20 words: 8470.0 sentences: 473.0 pages: flesch: 36.0 cache: ./cache/cord-308201-lavcsqov.txt txt: ./txt/cord-308201-lavcsqov.txt summary: Viruses infecting human CNS cells could then cause different types of encephalopathy, including encephalitis, and long-term neurological diseases. Even though no clear cause and effect link has ever been made with the onset of human neurological diseases, their neuropathogenicity is being increasingly recognized in humans, as several recent reports associated cases of encephalitis [244] , acute flaccid paralysis [271] and other neurological symptoms, including possible complications of HCoV infection such as Guillain-Barré syndrome or ADEM [249, [272] [273] [274] [275] [276] [277] [278] [279] . Like for several other respiratory viruses, accumulating evidence now indicate that HCoV are neuroinvasive in humans and we hypothesize that these recognized respiratory pathogens are potentially neurovirulent as well, as they could participate in short-and long-term neurological disorders either as a result of inadequate host immune responses and/or viral propagation in the CNS, which directly induces damage to resident cells. abstract: Respiratory viruses infect the human upper respiratory tract, mostly causing mild diseases. However, in vulnerable populations, such as newborns, infants, the elderly and immune-compromised individuals, these opportunistic pathogens can also affect the lower respiratory tract, causing a more severe disease (e.g., pneumonia). Respiratory viruses can also exacerbate asthma and lead to various types of respiratory distress syndromes. Furthermore, as they can adapt fast and cross the species barrier, some of these pathogens, like influenza A and SARS-CoV, have occasionally caused epidemics or pandemics, and were associated with more serious clinical diseases and even mortality. For a few decades now, data reported in the scientific literature has also demonstrated that several respiratory viruses have neuroinvasive capacities, since they can spread from the respiratory tract to the central nervous system (CNS). Viruses infecting human CNS cells could then cause different types of encephalopathy, including encephalitis, and long-term neurological diseases. Like other well-recognized neuroinvasive human viruses, respiratory viruses may damage the CNS as a result of misdirected host immune responses that could be associated with autoimmunity in susceptible individuals (virus-induced neuro-immunopathology) and/or viral replication, which directly causes damage to CNS cells (virus-induced neuropathology). The etiological agent of several neurological disorders remains unidentified. Opportunistic human respiratory pathogens could be associated with the triggering or the exacerbation of these disorders whose etiology remains poorly understood. Herein, we present a global portrait of some of the most prevalent or emerging human respiratory viruses that have been associated with possible pathogenic processes in CNS infection, with a special emphasis on human coronaviruses. url: https://doi.org/10.3390/v12010014 doi: 10.3390/v12010014 id: cord-267973-uvz7kavu author: Do, Lien Anh Ha title: Respiratory Syncytial Virus and Other Viral Infections among Children under Two Years Old in Southern Vietnam 2009-2010: Clinical Characteristics and Disease Severity date: 2016-08-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Despite a high burden of respiratory syncytial virus (RSV) infections among children, data on demographic and clinical characteristics of RSV are scarce in low and middle income countries. This study aims to describe the viral etiologies, the demographic, epidemiological, and clinical characteristics of children under two years of age who were hospitalized with a lower respiratory tract infections (LRTI), focusing on RSV (prevalence, seasonality, subgroups, viral load) and its association with disease severity. METHODS: A prospective study among children under two years of age, hospitalized with LRTI was conducted in two referral pediatric hospitals in Ho Chi Minh City, Vietnam, from May 2009 to December 2010. Socio-demographic, clinical data and nasopharyngeal swabs were collected on enrolment and discharge. Multiplex real-time RT-PCR (13 viruses) and quantitative RSV RT-PCR were used to identify viral pathogens, RSV load and subgroups. RESULTS: Among 632 cases, 48% were RSV positive. RSV infections occurred at younger age than three other leading viral infections i.e rhinovirus (RV), metapneumovirus (MPV), parainfluenza virus (PIV-3) and were significantly more frequent in the first 6 months of life. Clinical severity score of RSV infection was significantly higher than PIV-3 but not for RV or MPV. In multivariate analysis, RV infection was significantly associated with severity while RSV infection was not. Among RSV infections, neither viral load nor viral co-infections were significantly associated with severity. Young age and having fever at admission were significantly associated with both RSV and LRTI severity. A shift in RSV subgroup predominance was observed during two consecutive rainy seasons but was not associated with severity. CONCLUSION: We report etiologies, the epidemiological and clinical characteristics of LRTI among hospitalized children under two years of age and risk factors of RSV and LRTI severity. url: https://doi.org/10.1371/journal.pone.0160606 doi: 10.1371/journal.pone.0160606 id: cord-048197-9785vg6d author: Domachowske, Joseph B title: Gene expression in epithelial cells in response to pneumovirus infection date: 2001-05-11 words: 4688.0 sentences: 193.0 pages: flesch: 34.0 cache: ./cache/cord-048197-9785vg6d.txt txt: ./txt/cord-048197-9785vg6d.txt summary: The respiratory epithelial target cells respond to viral infection with specific alterations in gene expression, including production of chemoattractant cytokines, adhesion molecules, elements that are related to the apoptosis response, and others that remain incompletely understood. The transcription factor NF-IL-6 is also produced in response to RSV infection [13] , and participates in a co-operative manner with NF-κB in the regulation of IL-8 gene expression [11] , although later studies suggest that activator protein-1 may function preferentially in this role [14] . Again, as part of our systematic study of gene expression in response to pneumovirus infection, we found that human respiratory epithelial cells respond to RSV infection with increased expression of the cytoskeletal protein cytokeratin-17 [36] . Inhibiton of viral replication reverses respiratory syncytial virus-induced NF-κ κB activation and interleukin-8 gene expression in A549 cells Respiratory syncytial virus infection induces expression of the anti-apoptosis gene IEX-1L in human respiratory epithelial cells abstract: Respiratory syncytial virus (RSV) and pneumonia virus of mice (PVM) are viruses of the family Paramyxoviridae, subfamily pneumovirus, which cause clinically important respiratory infections in humans and rodents, respectively. The respiratory epithelial target cells respond to viral infection with specific alterations in gene expression, including production of chemoattractant cytokines, adhesion molecules, elements that are related to the apoptosis response, and others that remain incompletely understood. Here we review our current understanding of these mucosal responses and discuss several genomic approaches, including differential display reverse transcription-polymerase chain reaction (PCR) and gene array strategies, that will permit us to unravel the nature of these responses in a more complete and systematic manner. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59580/ doi: 10.1186/rr61 id: cord-289050-9w7ks01n author: Donoso, Alejandro F. title: Fatal hemorrhagic pneumonia caused by human metapneumovirus in an immunocompetent child date: 2008-08-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/18937761/ doi: 10.1111/j.1442-200x.2008.02673.x id: cord-261756-4lybl57r author: Dubert, Marie title: Late viral or bacterial respiratory infections in lung transplanted patients: impact on respiratory function date: 2020-02-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Respiratory infections are a major threat for lung recipients. We aimed to compare with a monocentric study the impact of late viral and bacterial respiratory infections on the graft function. METHODS: Patients, who survived 6 months or more following lung transplantation that took place between 2009 and 2014, were classified into three groups: a viral infection group (VIG) (without any respiratory bacteria), a bacterial infection group (BIG) (with or without any respiratory viruses), and a control group (CG) (no documented infection). Chronic lung allograft dysfunction (CLAD) and acute rejection were analysed 6 months after the inclusion in the study. RESULTS: Among 99 included lung recipients, 57 (58%) had at least one positive virological respiratory sample during the study period. Patients were classified as follows: 38 in the VIG, 25 in the BIG (among which 19 co-infections with a virus) and 36 in the CG. The BIG presented a higher initial deterioration in lung function (p = 0.05) than the VIG. But 6 months after the infection, only the VIG presented a median decrease of forced expiratory volume in 1 s; − 35 mL (IQR; − 340; + 80) in the VIG, + 140 mL (+ 60;+ 330) in the BIG and + 10 (− 84;+ 160) in the CG, p < 0.01. Acute rejection was more frequent in the VIG (n = 12 (32%)), than the BIG (n = 6 (24%)) and CG (n = 3 (8%)), p < 0.05, despite presenting no more CLAD (p = 0.21). CONCLUSIONS: Despite a less severe initial presentation, single viral respiratory infections seem to lead to a greater deterioration in lung function, and to more acute rejection, than bacterial infections. url: https://www.ncbi.nlm.nih.gov/pubmed/32093612/ doi: 10.1186/s12879-020-4877-3 id: cord-048447-chz8luni author: Duffett, Mark title: Surfactant therapy for acute respiratory failure in children: a systematic review and meta-analysis date: 2007-06-15 words: 3996.0 sentences: 215.0 pages: flesch: 38.0 cache: ./cache/cord-048447-chz8luni.txt txt: ./txt/cord-048447-chz8luni.txt summary: The primary objective of the systematic review is to assess the effect of the administration of pulmonary surfactant compared with no therapy or with placebo on all-cause mortality (at or before hospital discharge) in mechanically ventilated children with acute respiratory failure. We used the following characteristics to assess the methodologic quality: allocation concealment (sealed envelopes or central randomization were considered adequate), blinding (which of the trial personnel and caregivers were blinded, and the methods used to ensure blinding), completeness of followup (assessed by the number of patients randomized for whom there were no outcomes), similarity of the groups at baseline (with respect to known prognostic factors: age, aetiology, severity of illness as measured by the Pediatric Risk of Mortality score, and immunosuppression), whether a standard or recommended strategy for mechanical ventilation was used, and whether a priori criteria for the use of co-interventions were used. abstract: INTRODUCTION: Exogenous surfactant is used to treat acute respiratory failure in children, although the benefits and harms in this setting are not clear. The objective of the present systematic review is to assess the effect of exogenous pulmonary surfactant on all-cause mortality in children mechanically ventilated for acute respiratory failure. METHODS: We searched the MEDLINE, EMBASE, CINAHL and Ovid Healthstar databases, the bibliographies of included trials and review articles, conference proceedings and trial registries. We included prospective, randomized, controlled trials of pulmonary surfactant that enrolled intubated and mechanically ventilated children with acute respiratory failure. We excluded trials that exclusively enrolled neonates or patients with asthma. Two reviewers independently rated trials for inclusion, extracted data and assessed the methodologic quality. We quantitatively pooled the results of trials, where suitable, using a random effects model. RESULTS: Six trials randomizing 314 patients were included. Surfactant use reduced mortality (relative risk = 0.7, 95% confidence interval = 0.4 to 0.97, P = 0.04), was associated with increased ventilator-free days (weighted mean difference = 2.5 days, 95% confidence interval = 0.3 to 4.6 days, P = 0.02) and reduced the duration of ventilation (weighted mean difference = 2.3 days, 95% confidence interval = 0.1 to 4.4 days, P = 0.04). CONCLUSION: Surfactant use decreased mortality, was associated with more ventilator-free days and reduced the duration of ventilation. No serious adverse events were reported. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2206432/ doi: 10.1186/cc5944 id: cord-303299-p15irs4e author: Dzien, Alexander title: Will the COVID-19 pandemic slow down in the Northern hemisphere by the onset of summer? An epidemiological hypothesis date: 2020-06-23 words: 1263.0 sentences: 70.0 pages: flesch: 51.0 cache: ./cache/cord-303299-p15irs4e.txt txt: ./txt/cord-303299-p15irs4e.txt summary: The infection caused by the human corona virus COVID-19 (SARS-CoV2) resulted in a worldwide pandemic affecting several million people and causing severe disease and fatality mostly based on virus mediated lung failure [1, 2] . However, epidemics with respiratory virus such as not only influenza but also human corona viruses are prevalent in the Northern hemisphere over several months during the cold season and then disappear whereas influenza remains prevalent in tropical regions throughout the whole year [5] [6] [7] . The grey lines indicate seasons where no specific pandemic respiratory infections are recorded. If COVID-19 would behave similar to other respiratory viruses causing respiratory infections including human corona viruses which peak during winter time and early spring, there is hope that the COVID-19 pandemic can be slowed down by this seasonal trend [7, 9] . However, pandemics with new viruses such as the influenza H1N1v can circulate independent of typical respiratory viral seasons throughout the whole year [10] . abstract: The COVID-19 pandemic has affected most countries of the world. As corona viruses are highly prevalent in the cold season, the question remains whether or not the pandemic will improve with increasing temperatures in the Northern hemisphere. We use data from a primary care registry of almost 15,000 patients over 20 years to retrieve information on viral respiratory infection outbreaks. Our analysis suggests that the severity of the pandemic will be softened by the seasonal change to summer. url: https://www.ncbi.nlm.nih.gov/pubmed/32578052/ doi: 10.1007/s15010-020-01460-1 id: cord-257244-gryp0khc author: Edwards, M. R. title: The potential of anti‐infectives and immunomodulators as therapies for asthma and asthma exacerbations date: 2017-08-10 words: 5746.0 sentences: 317.0 pages: flesch: 37.0 cache: ./cache/cord-257244-gryp0khc.txt txt: ./txt/cord-257244-gryp0khc.txt summary: Despite these important associations, the use of antiinfectives (antibiotics, antivirals, antifungals, vaccines) that specifically target known pathogens, or drugs that are based on or exploit microbe-host receptor interactions (toll-like receptor agonists, bacterial lysates) or are immunomodulators (vitamin D), and/or may work in part by altering our associated microbiology (probiotics) are, with the exception of severe asthma, seldom considered in asthma treatment, prevention and guidelines. Overall, antibiotic use is associated with asthma risk rather than protection at most stages of human development, including pregnancy, 10, 11 early life 12 and childhood, 13 although why this is so is a subject widely debated. 10 In retrospective studies, the association between antibiotic use and increased risk of asthma or wheezing in children is further confused due to the potential of reverse causation. Inhibiting virus replication through interfering with viral enzymes active within cells poses additional problems in drug discovery; however, several useful inhibitors for respiratory tract viruses have found their way into phase I/II clinical trials. abstract: Asthma is responsible for approximately 25,000 deaths annually in Europe despite available medicines that maintain asthma control and reduce asthma exacerbations. Better treatments are urgently needed for the control of chronic asthma and reduction in asthma exacerbations, the major cause of asthma mortality. Much research spanning >20 years shows a strong association between microorganisms including pathogens in asthma onset, severity and exacerbation, yet with the exception of antibiotics, few treatments are available that specifically target the offending pathogens. Recent insights into the microbiome suggest that modulating commensal organisms within the gut or lung may also be a possible way to treat/prevent asthma. The European Academy of Allergy & Clinical Immunology Task Force on Anti‐infectives in Asthma was initiated to investigate the potential of anti‐infectives and immunomodulators in asthma. This review provides a concise summary of the current literature and aimed to identify and address key questions that concern the use of anti‐infectives and both microbe‐ and host‐based immunomodulators and their feasibility for use in asthma. url: https://www.ncbi.nlm.nih.gov/pubmed/28722755/ doi: 10.1111/all.13257 id: cord-306411-dutbxfl4 author: Eifan, Saleh A. title: Respiratory Tract Viral Infections and Coinfections Identified by Anyplex™ II RV16 Detection Kit in Pediatric Patients at a Riyadh Tertiary Care Hospital date: 2017-11-21 words: 2641.0 sentences: 132.0 pages: flesch: 38.0 cache: ./cache/cord-306411-dutbxfl4.txt txt: ./txt/cord-306411-dutbxfl4.txt summary: title: Respiratory Tract Viral Infections and Coinfections Identified by Anyplex™ II RV16 Detection Kit in Pediatric Patients at a Riyadh Tertiary Care Hospital This retrospective cohort study aimed to determine the etiological agents responsible for respiratory tract infections by Anyplex II RV16 detection kit (RV16, Seegene), involving 2266 pediatric patients with respiratory infections admitted to the Department of Pediatrics at King Abdul-Aziz Medical City, Ministry of National Guard, Riyadh, from July 2014 to June 2015. Different studies reported the detection of viruses like human respiratory syncytial virus A (RSV A), human respiratory syncytial virus B (RSV B), human adenovirus (AdV), Human metapneumovirus (HMPV), human coronavirus, and human parainfluenza virus (PIV). This study aimed to determine the distribution of 16 different viruses causing respiratory infections in children, by using RV16, and to compare data on demographic characteristics, symptoms, and single infections or coinfections. abstract: Respiratory infections are caused by an array of viruses, and limited information is available about viral coexistence, comparative symptoms, and the burden of illness. This retrospective cohort study aimed to determine the etiological agents responsible for respiratory tract infections by Anyplex II RV16 detection kit (RV16, Seegene), involving 2266 pediatric patients with respiratory infections admitted to the Department of Pediatrics at King Abdul-Aziz Medical City, Ministry of National Guard, Riyadh, from July 2014 to June 2015. The most frequent respiratory infections were recorded in the 1 to 5 year age group (44.7%). Rhinovirus (32.5%), Adenovirus (16.9%), and Respiratory syncytial virus (RSV) B (10.4%) were most common. In single viral infections, Rhinovirus (41.2%), Metapneumovirus (15.3%), and Bocavirus (13.7%) were most frequent. In multiple viral infections, Rhinovirus (36.7%), Adenovirus (35.2%), Bocavirus (11.2), RSV B (7.8%), and RSV A (6.7%) were most frequent. No significant difference was observed in clinical presentations; however, rhinorrhea and hypodynamia were significantly associated with viral respiratory infections. Most respiratory viral pathogens peaked during December, January, March, and April. Rhinovirus, Adenovirus, and Bocavirus circulations were detected throughout the year. Winter peaks were recorded for Rhinovirus, RSV B, Adenovirus, and RSV A, whereas the Metapneumovirus, and the Bocavirus peaked in March and April. These findings enhance understanding of viral etiology and distribution to improve respiratory infection management and treatment. url: https://www.ncbi.nlm.nih.gov/pubmed/29359144/ doi: 10.1155/2017/1928795 id: cord-321284-0y69n1ea author: El Kholy, A. A. title: The use of multiplex PCR for the diagnosis of viral severe acute respiratory infection in children: a high rate of co-detection during the winter season date: 2016-06-10 words: 3345.0 sentences: 175.0 pages: flesch: 46.0 cache: ./cache/cord-321284-0y69n1ea.txt txt: ./txt/cord-321284-0y69n1ea.txt summary: title: The use of multiplex PCR for the diagnosis of viral severe acute respiratory infection in children: a high rate of co-detection during the winter season This study confirms the high rate of detection of viral nucleic acids by multiplex PCR among hospitalized children admitted with SARI, as well as the high rate of co-detection of multiple viruses. Forty healthy age-matched asymptomatic children with no history of a recent respiratory tract infection during the previous 2 weeks, who were not admitted to the hospital, and who do not have any chronic underlying illness were included as a control group. This study confirms the high rate of detection of viral nucleic acids by multiplex PCR) among hospitalized children admitted with severe acute respiratory infection, as well as the high rate of detection of multiple viruses. abstract: Respiratory tract infection is a major cause of hospitalization in children. Although most such infections are viral in origin, it is difficult to differentiate bacterial and viral infections, as the clinical symptoms are similar. Multiplex polymerase chain reaction (PCR) methods allow testing for multiple pathogens simultaneously and are, therefore, gaining interest. This prospective case-control study was conducted from October 2013 to February 2014. Nasopharyngeal (NP) and oropharyngeal (throat) swabs were obtained from children admitted with severe acute respiratory infection (SARI) at a tertiary hospital. A control group of 40 asymptomatic children was included. Testing for 16 viruses was done by real-time multiplex PCR. Multiplex PCR detected a viral pathogen in 159/177 (89.9 %) patients admitted with SARI. There was a high rate of co-infection (46.9 %). Dual detections were observed in 64 (36.2 %), triple detections in 17 (9.6 %), and quadruple detections in 2 (1.1 %) of 177 samples. Seventy-eight patients required intensive care unit (ICU) admission, of whom 28 (35.8 %) had co-infection with multiple viruses. AdV, HBoV, HRV, HEV, and HCoV-OC43 were also detected among asymptomatic children. This study confirms the high rate of detection of viral nucleic acids by multiplex PCR among hospitalized children admitted with SARI, as well as the high rate of co-detection of multiple viruses. AdV, HBoV, HRV, HEV, and HCoV-OC43 were also detected in asymptomatic children, resulting in challenges in clinical interpretation. Studies are required to provide quantitative conclusions that will facilitate clinical interpretation and application of the results in the clinical setting. url: https://doi.org/10.1007/s10096-016-2698-5 doi: 10.1007/s10096-016-2698-5 id: cord-306315-vt2e0crh author: Elabbadi, Alexandre title: Respiratory virus-associated infections in HIV-infected adults admitted to the intensive care unit for acute respiratory failure: a 6-year bicenter retrospective study (HIV-VIR study) date: 2020-09-14 words: 4734.0 sentences: 244.0 pages: flesch: 36.0 cache: ./cache/cord-306315-vt2e0crh.txt txt: ./txt/cord-306315-vt2e0crh.txt summary: CONCLUSIONS: Viruses are frequently identified in the respiratory tract of HIV-infected patients with acute respiratory failure that requires ICU admission, but with a non-viral copathogen in two-thirds of cases. Indeed, using nucleic acid amplification test such as multiplex polymerase chain reaction (mPCR), these pathogens have been shown highly prevalent (20-56%) in large cohorts of adult patients admitted to the ICU for all-cause ARF [7, 8] , community-acquired pneumonia [9, 10] , hospitalacquired pneumonia [11] , acute exacerbation of COPD [12, 13] , and asthma [14] , compared to asymptomatic adults [15, 16] . We investigated whether a respiratory virus-associated infection Table 2 Causative diagnosis of acute respiratory failure in 123 HIV-infected patients admitted to the ICU Data are presented as number (%). Viruses are frequently identified in the respiratory tract of HIV-infected patients with ARF that required ICU admission, but with a non-viral copathogen in two-thirds of cases. abstract: INTRODUCTION: Acute respiratory failure is the main reason for admission to the intensive care unit (ICU) in HIV-infected adults. There is little data about the epidemiology of respiratory viruses in this population. METHODS: HIV-infected adults admitted to two intensive care units over a 6-year period for an acute respiratory failure and explored for respiratory viruses with multiplex polymerase chain reaction (mPCR) were retrospectively selected. Objectives were to describe the prevalence of respiratory viruses, coinfections with non-viral pathogens, and hospital outcome. RESULTS: A total of 123 episodes were included. An HIV infection was newly diagnosed in 9% of cases and 72% of the population were on antiretroviral therapy. Real-time mPCR tests identified at least one respiratory virus in the respiratory tract of 33 (27%) patients, but with a non-viral copathogen in two-thirds of cases. Rhinovirus was predominant, documented in 15 patients, followed by Influenza and Respiratory Syncytial Viruses (both n = 6). The prevalence of respiratory virus-associated infection did not vary along with the level of the CD4 T-cell deficiency, except for Rhinovirus which was more prevalent in patients with a CD4 lymphocyte count below 200 cells/µL (n = 13 (20%) vs. n = 2 (4%), p < 0.01). In multivariate analysis, respiratory virus-associated infection was not associated with a worse prognosis. CONCLUSIONS: Viruses are frequently identified in the respiratory tract of HIV-infected patients with acute respiratory failure that requires ICU admission, but with a non-viral copathogen in two-thirds of cases. Rhinovirus is the predominant viral specie; its prevalence is highest in patients with a CD4 lymphocyte count below 200 cells/µL. url: https://doi.org/10.1186/s13613-020-00738-9 doi: 10.1186/s13613-020-00738-9 id: cord-286443-t0asknzu author: Emerson, Julia title: Home Self-Collection of Nasal Swabs for Diagnosis of Acute Respiratory Virus Infections in Children With Cystic Fibrosis date: 2013-07-14 words: 4006.0 sentences: 185.0 pages: flesch: 45.0 cache: ./cache/cord-286443-t0asknzu.txt txt: ./txt/cord-286443-t0asknzu.txt summary: title: Home Self-Collection of Nasal Swabs for Diagnosis of Acute Respiratory Virus Infections in Children With Cystic Fibrosis In the current study, we investigated the feasibility of home self-collection of NS in children with CF experiencing onset of new respiratory illness, with samples mailed to a central laboratory for respiratory virus detection by real-time PCR. If respiratory illness with onset of symptoms in the previous 7 days was present at a clinic visit, subjects were first asked to blow their nose to remove mucus that might inhibit PCR, and paired swabs were obtained as follows: a deep nasal (mid-turbinate) sample was collected by research staff, by first measuring from the opening of one naris to the nasal bridge, and then inserting a standard flexible nasopharyngeal flocked nylon swab (Copan Diagnostics Inc, Murrieta, CA; catalog No. 503CS01) until mild resistance was encountered, approximately one-half to two-thirds the length of the nose. abstract: BACKGROUND: Understanding the importance of respiratory viruses in children with cystic fibrosis (CF) has been limited because of challenges using clinic- or hospital-based diagnostic testing. We conducted a pilot study to assess feasibility of home self- (or parent-) collection of nasal swabs (NS). METHODS: Cystic fibrosis patients aged 6–18 years with new respiratory illness participated. In clinic, a deep nasal flocked swab was collected by research staff and compared with an anterior foam NS obtained after instillation of saline spray. At home, up to 2 self-collections of paired foam NS (with and without saline) were collected and mailed for real-time polymerase chain reaction (PCR) testing. RESULTS: Paired swabs were collected from 28 patients: 18 sets in clinic (deep nasal vs saline foam NS) and 43 sets at home (saline vs dry foam NS) with 9 (50%) and 35 (81%) virus detections, respectively. Home-collected NS were obtained closer to illness onset, with a mean difference in symptom days of −2.3 between home and clinic collections (95% confidence interval [CI] −3.5, −1.2; P < .001). Rhinovirus comprised 73% of virus detections; the difference in mean PCR cycle threshold values for rhinovirus between swabs collected at home versus clinic was −3.8 (95% CI −6.8, −0.9; P = .014), indicating significantly higher viral load for home-collected swabs. CONCLUSIONS: Home-collected foam NS had a higher positivity rate compared with clinic-collected swabs, likely because collection was closer to illness onset. Home self-collection is feasible and well tolerated for timely respiratory virus diagnosis and provides a novel approach for clinical diagnostics and surveillance of respiratory virus infections among CF patients. url: http://europepmc.org/articles/pmc3869469?pdf=render doi: 10.1093/jpids/pit039 id: cord-255011-7oqfod62 author: Erles, Kerstin title: Canine Respiratory Coronavirus: An Emerging Pathogen in the Canine Infectious Respiratory Disease Complex date: 2008-05-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Infectious respiratory disease in dogs is a constant challenge because of the involvement of several pathogens and environmental factors. Canine respiratory coronavirus (CRCoV) is a new coronavirus of dogs, which is widespread in North America, Japan, and several European countries. CRCoV has been associated with respiratory disease, particularly in kenneled dog populations. The virus is genetically and antigenically distinct from enteric canine coronavirus; therefore, specific tests are required for diagnosis. url: https://www.ncbi.nlm.nih.gov/pubmed/18501280/ doi: 10.1016/j.cvsm.2008.02.008 id: cord-306278-c4q4la5c author: Esposito, Susanna title: Epidemiology and Clinical Characteristics of Respiratory Infections Due to Adenovirus in Children Living in Milan, Italy, during 2013 and 2014 date: 2016-04-05 words: 4660.0 sentences: 220.0 pages: flesch: 48.0 cache: ./cache/cord-306278-c4q4la5c.txt txt: ./txt/cord-306278-c4q4la5c.txt summary: To evaluate the predominant human adenovirus (HAdV) species and types associated with pediatric respiratory infections, nasopharyngeal swabs were collected from otherwise healthy children attending an emergency room in Milan, Italy, due to a respiratory tract infection from January 1 to February 28 of two subsequent years, 2013 and 2014. To evaluate the circulation of the different HAdV types and the possible relationship between viral load, viral genetic characteristics, and the severity of infection, nasopharyngeal swabs were collected from otherwise healthy children consecutively attending the Emergency Room of the Fondazione IRCCS Ca'' Granda Ospedale Maggiore Policlinico, University of Milan, Italy, due to a respiratory tract infection. However, further studies are needed to identify the potential pathogenetic role of the different species and types of HAdV and the importance of viral load in the severity of infection. abstract: To evaluate the predominant human adenovirus (HAdV) species and types associated with pediatric respiratory infections, nasopharyngeal swabs were collected from otherwise healthy children attending an emergency room in Milan, Italy, due to a respiratory tract infection from January 1 to February 28 of two subsequent years, 2013 and 2014. The HAdVs were detected using a respiratory virus panel fast assay (xTAG RVP FAST v2) and with a HAdV-specific real-time polymerase chain reaction; their nucleotides were sequenced, and they were tested for positive selection. Among 307 nasopharyngeal samples, 61 (19.9%) tested positive for HAdV. HAdV was the only virus detected in 31/61 (50.8%) cases, whereas it was found in association with one other virus in 25 (41.0%) cases and with two or more viruses in 5 (8.2%) cases. Human Enterovirus/human rhinovirus and respiratory syncytial virus were the most common co-infecting viral agents and were found in 12 (19.7%) and 7 (11.5%) samples, respectively. Overall, the HAdV strain sequences analyzed were highly conserved. In comparison to HAdV-negative children, those infected with HAdV had a reduced frequency of lower respiratory tract involvement (36.1% vs 55.2%; p = 0.007), wheezing (0.0% vs 12.5%; p = 0.004), and hospitalization (27.9% vs 56.1%; p<0.001). Antibiotic therapy and white blood cell counts were more frequently prescribed (91.9% vs 57.1%; p = 0.04) and higher (17,244 ± 7,737 vs 9,565 ± 3,211 cells/μL; p = 0.04), respectively, in children infected by HAdV-C than among those infected by HAdV-B. On the contrary, those infected by HAdV-B had more frequently lower respiratory tract involvement (57.1% vs 29.7%) but difference did not reach statistical significant (p = 0.21). Children with high viral load were absent from child care attendance for a longer period of time (14.5 ± 7.5 vs 5.5 ± 3.2 days; p = 0.002) and had higher C reactive protein levels (41.3 ± 78.5 vs 5.4 ± 9.6 μg/dL; p = 0.03). This study has shown that HAdV infections are diagnosed more commonly than usually thought and that HAdVs are stable infectious agents that do not frequently cause severe diseases. A trend toward more complex disease in cases due to HAdV species C and in those with higher viral load was demonstrated. However, further studies are needed to clarify factors contributing to disease severity to understand how to develop adequate preventive and therapeutic measures. url: https://www.ncbi.nlm.nih.gov/pubmed/27045588/ doi: 10.1371/journal.pone.0152375 id: cord-320950-x02zp349 author: Esposito, Susanna title: Multiplex Platforms for the Identification of Respiratory Pathogens: Are They Useful in Pediatric Clinical Practice? date: 2019-06-04 words: 5863.0 sentences: 267.0 pages: flesch: 41.0 cache: ./cache/cord-320950-x02zp349.txt txt: ./txt/cord-320950-x02zp349.txt summary: A systematic review and meta-analysis (Huang et al., 2018) of studies on the accuracy of FA-RP, Nanosphere Verigene RV+ test (Hologic, 2018; Luminex, 2018) Gen-Probe Prodesse assays (Hologic, 2018) in the detection of IV A, IV B virus, RSV, hMPV, and AV showed that all of these assays had high diagnostic accuracy, with an area under the receiver operating characteristic curve (AUROC) equal to or >0.98 for all tested viruses. In a study involving 46 children aged 6-36 months with bocavirus infection, it was shown that in 22% of cases, the virus persisted in the respiratory secretions for more than 30 days, despite the rapid disappearance of clinical manifestations (Wagner et al., 2016) . In conclusion, multiplex platforms, despite significantly increasing the possibility to detect which pathogens are present in the respiratory secretions of a child with a respiratory infection, do not offer any advantage in comparison to tradition diagnostic tests regarding the identification of the true etiologic agent of the disease. abstract: Respiratory tract infections (RTIs) are extremely common especially in the first year of life. Knowledge of the etiology of a RTI is essential to facilitate the appropriate management and the implementation of the most effective control measures. This perspective explains why laboratory methods that can identify pathogens in respiratory secretions have been developed over the course of many years. High-complexity multiplex panel assays that can simultaneously detect up to 20 viruses and up to four bacteria within a few hours have been marketed. However, are these platforms actually useful in pediatric clinical practice? In this manuscript, we showed that these platforms appear to be particularly important for epidemiological studies and clinical research. On the contrary, their routine use in pediatric clinical practice remains debatable. They can be used only in the hospital as they require specific equipment and laboratory technicians with considerable knowledge, training, and experience. Moreover, despite more sensitive and specific than other tests routinely used for respiratory pathogen identification, they do not offer significantly advantage for detection of the true etiology of a respiratory disease. Furthermore, knowledge of which virus is the cause of a respiratory disease is not useful from a therapeutic point of view unless influenza virus or respiratory syncytial virus are the infecting agents as effective drugs are available only for these pathogens. On the other hand, multiplex platforms can be justified in the presence of severe clinical manifestations, and in immunocompromised patients for whom specific treatment option can be available, particularly when they can be used simultaneously with platforms that allow identification of antimicrobial resistance to commonly used drugs. It is highly likely that these platforms, particularly those with high sensitivity and specificity and with low turnaround time, will become essential when new drugs effective and safe against most of the respiratory viruses will be available. Further studies on how to differentiate carriers from patients with true disease, as well as studies on the implications of coinfections and identification of antimicrobial resistance, are warranted. url: https://doi.org/10.3389/fcimb.2019.00196 doi: 10.3389/fcimb.2019.00196 id: cord-347246-0vofftmj author: Everitt, J I title: Infectious diseases of the upper respiratory tract: implications for toxicology studies. date: 1990-04-17 words: 3572.0 sentences: 190.0 pages: flesch: 28.0 cache: ./cache/cord-347246-0vofftmj.txt txt: ./txt/cord-347246-0vofftmj.txt summary: This paper reviews several important infectious diseases of the upper airway of rats and mice and discusses the potential influence of these conditions on the results of toxicology studies. All three agents cause significant rodent respiratory disease, with lesions in the upper airways, including the nasal passages. Although there are many excellent descriptive studies ofthe histogenesis of Sendai virus-induced lesions within the lower respiratory tract, few pathology reports include a description of lesions in the nasal cavity and upper airway. Although numerous bacteria can infect the upper airway of the rat and mouse, they are not generally prevalent in well-conducted toxicology studies begun with animals free of adventitious murine pathogens and maintained with modern methods of laboratory animal husbandry. A variety of important microbial pathogens including viruses, mycoplasmas, bacteria, and fungi infect the upper respiratory tract of the mouse and rat and result in significant pathologic alterations. abstract: The consequences of adventitious infectious agents upon the interpretation of toxicology studies performed in rats and mice are incompletely understood. Several prevalent murine pathogens cause alterations of the respiratory system that can confuse the assessment of chemically induced airway injury. In some instances the pathogenesis of infection with these agents has been relatively well studied in the lower respiratory tract. However, there are few well-controlled studies that have examined the upper respiratory region, which result in interpretive problems for toxicologic pathologists. The conduct and interpretation of both short-term and chronic rodent bioassays can be compromised by both the clinical and subclinical manifestations of infectious diseases. This paper reviews several important infectious diseases of the upper airway of rats and mice and discusses the potential influence of these conditions on the results of toxicology studies. url: https://www.ncbi.nlm.nih.gov/pubmed/2200664/ doi: nan id: cord-340104-6n0sn5lk author: Fagbo, Shamsudeen F. title: Acute viral respiratory infections among children in MERS‐endemic Riyadh, Saudi Arabia, 2012–2013 date: 2016-07-29 words: 3325.0 sentences: 194.0 pages: flesch: 50.0 cache: ./cache/cord-340104-6n0sn5lk.txt txt: ./txt/cord-340104-6n0sn5lk.txt summary: This large study population determined the burden of respiratory viruses associated with ARI in children over a 2-year period a multiplex molecular testing platform. With over 60% of 2235 children testing positive for respiratory viruses, more infections were detected than previous studies [Akhter et al., 2009; Al Hajjar et al., 2011; Alanazi et al., 2013; Bukhari and Elhazmi, 2013] . This high rate was significantly different from that obtained in the present 2-year study (23% detection for RSV in children positive for respiratory viruses), as well as others [Alanazi et al., 2013; Amer et al., 2015] . Viruses associated with respiratory tract infections in children attending to the emergency room, king abdulaziz medical city, riyadh, Saudi Arabia Viral agents causing acute lower respiratory tract infections in hospitalized children at a tertiary care center in Saudi Arabia abstract: The emergence of the Middle East Respiratory Syndrome (MERS) in Saudi Arabia has intensified focus on Acute Respiratory Infections [ARIs]. This study sought to identify respiratory viruses (RVs) associated with ARIs in children presenting at a tertiary hospital. Children (aged ≤13) presenting with ARI between January 2012 and December 2013 tested for 15 RVs using the Seeplex(R) RV15 kit were retrospectively included. Epidemiological data was retrieved from patient records. Of the 2235 children tested, 61.5% were ≤1 year with a male: female ratio of 3:2. Viruses were detected in 1364 (61.02%) children, 233 (10.4%) having dual infections: these viruses include respiratory syncytial virus (RSV) (24%), human rhinovirus (hRV) (19.7%), adenovirus (5.7%), influenza virus (5.3%), and parainfluenzavirus‐3 (4.6%). Children, aged 9–11 months, were most infected (60.9%). Lower respiratory tract infections (55.4%) were significantly more than upper respiratory tract infection (45.3%) (P < 0.001). Seasonal variation of RV was directly and inversely proportional to relative humidity and temperature, respectively, for non MERS coronaviruses (NL63, 229E, and OC43). The study confirms community‐acquired RV associated with ARI in children and suggests modulating roles for abiotic factors in RV epidemiology. However, community‐based studies are needed to elucidate how these factors locally influence RV epidemiology. J. Med. Virol. 89:195–201, 2017. © 2016 Wiley Periodicals, Inc. url: https://doi.org/10.1002/jmv.24632 doi: 10.1002/jmv.24632 id: cord-009860-qebenhxz author: Falsey, Ann R. title: Viral Respiratory Infections in the Institutionalized Elderly: Clinical and Epidemiologic Findings date: 2015-04-27 words: 3461.0 sentences: 220.0 pages: flesch: 52.0 cache: ./cache/cord-009860-qebenhxz.txt txt: ./txt/cord-009860-qebenhxz.txt summary: Serologic evidence of infection with respiratory syncytial virus (RSV) and parainfluenza were determined by enzyme immunoassay (EIA), and influenza by hemagglutination‐inhibition assay and EIA. This is despite the fact that each year many residents of nursing homes become ill with respiratory infections not proven to be influenza, either by culture or serology. The purpose of this study was to identify all common respiratory viruses which cause symptomatic dsease during the winter months in nursing home patients, by utilizing both viral cultures and serology, and to assess their clinical impact. Subjects Between December 11, 1989 and March 13, 1990 , the head nurse on each floor identified residents who had signs or symptoms of acute respiratory illness including nasal congestion, pharyngitis, cough, wheezing, or respiratory difficulty with or without fever. The groups of viruses responsible for most acute respiratory infections are rhinovirus, coronavirus, influenza, RSV, parainfluenza, and adeno~irus.~ An attempt was made to diagnose each of these pathogens, with the exception of coronavirus, utilizing either culture, serology, or both. abstract: OBJECTIVE: To prospectively evaluate the incidence and impact of viral respiratory infection in the institutionalized elderly during a winter season. DESIGN: Prospective descriptive study, without intervention. METHOD: Patients with respiratory illnesses were evaluated by a directed history and physical examination. Nasopharyngeal secretions for viral culture were obtained, and acute and convalescent serum samples were obtained for analysis. Serologic evidence of infection with respiratory syncytial virus (RSV) and parainfluenza were determined by enzyme immunoassay (EIA), and influenza by hemagglutination‐inhibition assay and EIA. SETTING: A 591‐bed nursing home. PARTICIPANTS: Residents with signs or symptoms of acute respiratory illness (nasal congestion, pharyngitis, cough, wheezing, or respiratory difficulty) were eligible for study. RESULTS: A viral etiology was documented in 62 out of 149 illnesses (42%). RSV was the most common virus associated with illness; it was documented in 27% of respiratory illnesses, followed by rhinovirus (9%), parainfluenza (6%), and influenza (1%). RSV was associated with significantly more severe disease when compared with rhinovirus. Clustering of specific viral infections occurred, suggesting nosocomial transmission. CONCLUSIONS: Viruses are an important cause of acute respiratory infections in the institutionalized elderly during the winter months. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7166501/ doi: 10.1111/j.1532-5415.1992.tb01929.x id: cord-292871-vgposxom author: Falsey, Ann R. title: The “Common Cold” in Frail Older Persons: Impact of Rhinovirus and Coronavirus in a Senior Daycare Center date: 2015-04-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVE: To evaluate the incidence and impact of rhino‐virus and Coronavirus infections in older persons attending daycare. DESIGN: Prospective descriptive study. SETTING: Three senior daycare centers in Rochester, New York. PATIENTS: Frail older persons and staff members of the daycare centers who developed signs or symptoms of an acute respiratory illness MEASUREMENTS: Demographic, medical, and physical findings were recorded on subjects at baseline and during respiratory illness. Nasopharyngeal specimens for viral culture as well as acute and convalescent sera for Coronavirus 229E enzyme immunoassay (EIA) were obtained for all illnesses. RESULTS: During the 44 months of study, 352 older persons experienced 522 illnesses. Thirty‐five (7%) of 522 cultures were positive for rhinovirus and 37 (8%) of 451 serologies were positive for Coronavirus 229E infection. The clinical syndromes associated with rhinovirus and Coronavirus infection were similar and characterized by nasal congestion, cough, and constitutional symptoms. No patient died or was hospitalized, but approximately 50% had evidence of lower respiratory tract involvement. The average illness lasted 14 days. During the same period, 113 staff developed 338 respiratory illnesses. Eight percent were identified as Coronavirus and 9% as rhinovirus. Cough, sputum production, and constitutional symptoms were significantly more common among older persons. CONCLUSIONS: Rhinovirus and Coronavirus 229E are common causes of moderately debilitating acute respiratory illnesses among older persons attending daycare. url: https://www.ncbi.nlm.nih.gov/pubmed/9180664/ doi: 10.1111/j.1532-5415.1997.tb01474.x id: cord-314841-b5l6epy3 author: Falsey, Ann Regina title: Respiratory viral infections date: 2019-08-15 words: 6006.0 sentences: 300.0 pages: flesch: 32.0 cache: ./cache/cord-314841-b5l6epy3.txt txt: ./txt/cord-314841-b5l6epy3.txt summary: Analysis of the host transcriptional response during respiratory viral infection using in-vitro, animal models and natural and experimental human challenge have furthered the understanding of the mechanisms and predictors of severe disease and may identify potential therapeutic targets to prevent and ameliorate illness. In addition to sensitive and rapid diagnostic testing, new molecular techniques allow an understanding of viral evolution, mechanisms and predictors of severe disease, interrogation of vaccine responses, improved bacterial and viral diagnostics and associations of viral infections with non-respiratory medical events. A number of candidate genes influencing respiratory virus susceptibility have been identified in animal and human studies and involve host virus interactions, innate immune signaling, interferon related pathways and cytokine responses (Table 1) [49] [50] [51] [69] [70] [71] [72] [73] [74] [75] . In addition, two compartments, the respiratory epithelium and blood can be sampled in human studies and interrogated using different viruses or viral strains to develop gene signatures for prognosis, as indicators of severity and to identify potential therapeutic targets. abstract: Molecular analysis of respiratory viruses and the host response to both infection and vaccination have transformed our understanding of these ubiquitous pathogens. Polymerase chain reaction for the rapid and accurate diagnosis of viral infections has led to a better understanding of the epidemiology and impact of many common respiratory viruses and resulted in better patient care. Over the past decade a number of new respiratory viruses including human metapneumovirus and new coronaviruses have been discovered using molecular techniques such as random primer amplification, pan-viral array and next generation sequencing. Analysis of the host transcriptional response during respiratory viral infection using in-vitro, animal models and natural and experimental human challenge have furthered the understanding of the mechanisms and predictors of severe disease and may identify potential therapeutic targets to prevent and ameliorate illness. url: https://www.sciencedirect.com/science/article/pii/B9780128014967000095 doi: 10.1016/b978-0-12-801496-7.00009-5 id: cord-301011-xbuqd0j5 author: Felten-Barentsz, Karin M title: Recommendations for Hospital-Based Physical Therapists Managing Patients With COVID-19 date: 2020-06-18 words: 3952.0 sentences: 259.0 pages: flesch: 39.0 cache: ./cache/cord-301011-xbuqd0j5.txt txt: ./txt/cord-301011-xbuqd0j5.txt summary: In line with international initiatives, this article aims to provide guidance and detailed recommendations for hospital-based physical therapists managing patients hospitalized with COVID-19 through a national approach in the Netherlands. A working group conducted a purposive scan of the literature and drafted initial recommendations based on the knowledge of symptoms in patients with COVID-19, and current practice for physical therapist management for patients hospitalized with lung disease and patients admitted to the intensive care unit (ICU). 12 In line with this international study 12 and the consensus statement of Italian respiratory therapists 13 we aim to provide guidance and detailed recommendations for hospital-based physical therapists managing patients hospitalized with COVID-19 through a national approach in the Netherlands. Physical therapist management for patients hospitalized with COVID-19 comprises elements of respiratory support and active mobilization. Physical therapist management for patients hospitalized with COVID-19 comprises elements of respiratory support and active mobilization. abstract: OBJECTIVE: The COVID-19 pandemic is rapidly evolving and has led to increased numbers of hospitalizations worldwide. Hospitalized patients with COVID-19 experience a variety of symptoms, including fever, muscle pain, tiredness, cough, and difficulty breathing. Elderly people and those with underlying health conditions are considered to be more at risk of developing severe symptoms and have a higher risk of physical deconditioning during their hospital stay. Physical therapists have an important role in supporting hospitalized patients with COVID-19 but also need to be aware of challenges when treating these patients. In line with international initiatives, this article aims to provide guidance and detailed recommendations for hospital-based physical therapists managing patients hospitalized with COVID-19 through a national approach in the Netherlands. METHODS: A pragmatic approach was used. A working group conducted a purposive scan of the literature and drafted initial recommendations based on the knowledge of symptoms in patients with COVID-19, and current practice for physical therapist management for patients hospitalized with lung disease and patients admitted to the intensive care unit (ICU). An expert group of hospital-based physical therapists in the Netherlands provided feedback on the recommendations, which were finalized when consensus was reached among the members of the working group. RESULTS: The recommendations include safety recommendations, treatment recommendations, discharge recommendations, and staffing recommendations. Treatment recommendations address 2 phases of hospitalization: when patients are critically ill and admitted to the ICU, and when patients are severely ill and admitted to the COVID ward. Physical therapist management for patients hospitalized with COVID-19 comprises elements of respiratory support and active mobilization. Respiratory support includes breathing control, thoracic expansion exercises, airway clearance techniques, and respiratory muscle strength training. Recommendations toward active mobilization include bed mobility activities, active range-of-motion exercises, active (−assisted) limb exercises, activities-of-daily-living training, transfer training, cycle ergometer, pre-gait exercises, and ambulation. url: https://www.ncbi.nlm.nih.gov/pubmed/32556323/ doi: 10.1093/ptj/pzaa114 id: cord-292261-gh9cifjr author: Feng, Fan title: Qigong for the Prevention, Treatment, and Rehabilitation of COVID-19 Infection in Older Adults date: 2020-05-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The elderly are at high risk of contracting respiratory infectious diseases, including COVID-19 infection. The recent pandemic has the potential to cause significant physical and mental damage in older adults. Similarly to other mind-body exercises in Traditional Chinese medicine, Qigong features regulation of breath rhythm and pattern, body movement and posture, and meditation. Given these traits, Qigong has the potential to play a role in the prevention, treatment, and rehabilitation of respiratory infections, such as COVID-19. Potential mechanisms of action include stress reduction, emotion regulation, strengthening of respiratory muscles, reduction of inflammation, and enhanced immune function. Three forms of Qigong; abdominal breathing, Ba Duan Jin and Liu Zi Jue, all of which are gentle, smooth, and simple for the elderly to practice, are recommended in this context. url: https://www.ncbi.nlm.nih.gov/pubmed/32425471/ doi: 10.1016/j.jagp.2020.05.012 id: cord-294568-12eyo13f author: Fernandes-Matano, Larissa title: Prevalence of non-influenza respiratory viruses in acute respiratory infection cases in Mexico date: 2017-05-03 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Acute respiratory infections are the leading cause of morbidity and mortality worldwide. Although a viral aetiological agent is estimated to be involved in up to 80% of cases, the majority of these agents have never been specifically identified. Since 2009, diagnostic and surveillance efforts for influenza virus have been applied worldwide. However, insufficient epidemiological information is available for the many other respiratory viruses that can cause Acute respiratory infections. METHODS: This study evaluated the presence of 14 non-influenza respiratory viruses in 872 pharyngeal exudate samples using RT-qPCR. All samples met the operational definition of a probable case of an influenza-like illness or severe acute respiratory infection and had a previous negative result for influenza by RT-qPCR. RESULTS: The presence of at least one non-influenza virus was observed in 312 samples (35.8%). The most frequent viruses were rhinovirus (RV; 33.0%), human respiratory syncytial virus (HRSV; 30.8%) and human metapneumovirus (HMPV; 10.6%). A total of 56 cases of co-infection (17.9%) caused by 2, 3, or 4 viruses were identified. Approximately 62.5% of all positive cases were in children under 9 years of age. CONCLUSION: In this study, we identified 13 non-influenza respiratory viruses that could occur in any season of the year. This study provides evidence for the prevalence and seasonality of a wide range of respiratory viruses that circulate in Mexico and constitute a risk for the population. Additionally, our data suggest that including these tests more widely in the diagnostic algorithm for influenza may reduce the use of unnecessary antibiotics, reduce the hospitalisation time, and enrich national epidemiological data with respect to the infections caused by these viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/28467515/ doi: 10.1371/journal.pone.0176298 id: cord-339009-wcoch07b author: File, Thomas M. title: Severe Acute Respiratory Syndrome: Pertinent Clinical Characteristics and Therapy date: 2012-08-23 words: 6023.0 sentences: 324.0 pages: flesch: 50.0 cache: ./cache/cord-339009-wcoch07b.txt txt: ./txt/cord-339009-wcoch07b.txt summary: Because the causative agent of SARS is • one or more clinical findings of respiratory illness (e.g. cough, contagious, preventative measures focus on avoidance of exposhortness of breath, difficulty in breathing, or hypoxia) sure, and infection control strategies for suspected patients and • travel within 10 days of onset of symptoms to an area with contacts. [12] Of the reported cases was updated to include laboratory criteria for evidence of infection 64% were from China, 19% from Hong Kong, 8% from Taiwan, with the SARS-associated coronavirus (SARS-CoV). Algorithm for evaluating and managing patients requiring hospitalization for radiographically confirmed pneumonia, in the absence of person-toperson transmission of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) anywhere in the world. abstract: Severe acute respiratory syndrome (SARS) is a newly emerged infection that is caused by a previously unrecognized virus–a novel coronavirus designated as SARS-associated coronavirus (SARS-CoV). From November 2002 to July 2003 the cumulative number of worldwide cases was >8000, with a mortality rate of close to 10%. The mortality has been higher in older patients and those with co-morbidities. SARS has been defined using clinical and epidemiological criteria and cases are considered laboratory-confirmed if SARS coronavirus is isolated, if antibody to SARS coronavirus is detected, or a polymerase chain reaction test by appropriate criteria is positive. At the time of writing (24 May 2004), no specific therapy has been recommended. A variety of treatments have been attempted, but there are no controlled data. Most patients have been treated throughout the illness with broad-spectrum antimicrobials, supplemental oxygen, intravenous fluids, and other supportive measures. Transmission of SARS is facilitated by close contact with patients with symptomatic infection. The majority of cases have been reported among healthcare providers and family members of SARS patients. Since SARS-CoV is contagious, measures for prevention center on avoidance of exposure, and infection control strategies for suspected cases and contacts. This includes standard precautions (hand hygiene), contact precautions (gowns, goggles, gloves) and airborne precautions (negative pressure rooms and high efficiency masks). In light of reports of new cases identified during the winter of 2003–4 in China, it seems possible that SARS will be an important cause of pneumonia in the future, and the screening of outpatients at risk for SARS may become part of the pneumonia evaluation. url: https://www.ncbi.nlm.nih.gov/pubmed/15813661/ doi: 10.2165/00151829-200504020-00003 id: cord-314190-fvdock94 author: Florin, Todd A title: Viral bronchiolitis date: 2017-01-01 words: 7584.0 sentences: 404.0 pages: flesch: 38.0 cache: ./cache/cord-314190-fvdock94.txt txt: ./txt/cord-314190-fvdock94.txt summary: The evidence and guideline recommendations consistently support a clinical diagnosis with the limited role for diagnostic testing for children presenting with the typical clinical syndrome of viral upper respiratory infection progressing to the lower respiratory tract. 24, 25, 27, 29, 30 Studies have investigated whether severity of illness, as measured by need for hospital admission, length of hospital stay, intensive care unit admission, repeated emergency department visits, and apnoea, is associated with specifi c viral infections or co-infections, but the evidence is confl icting. Recent studies suggest that higher respiratory syncytial virus genomic load, measured using quantitative PCR, might be associated with increased length of stay, use of respiratory support, and need for intensive care, in addition to recurrent wheezing, compared with lower viral loads. Systematic literature review assessing tobacco smoke exposure as a risk factor for serious respiratory syncytial virus disease among infants and young children abstract: Viral bronchiolitis is a common clinical syndrome affecting infants and young children. Concern about its associated morbidity and cost has led to a large body of research that has been summarised in systematic reviews and integrated into clinical practice guidelines in several countries. The evidence and guideline recommendations consistently support a clinical diagnosis with the limited role for diagnostic testing for children presenting with the typical clinical syndrome of viral upper respiratory infection progressing to the lower respiratory tract. Management is largely supportive, focusing on maintaining oxygenation and hydration of the patient. Evidence suggests no benefit from bronchodilator or corticosteroid use in infants with a first episode of bronchiolitis. Evidence for other treatments such as hypertonic saline is evolving but not clearly defined yet. For infants with severe disease, the insufficient available data suggest a role for high-flow nasal cannula and continuous positive airway pressure use in a monitored setting to prevent respiratory failure. url: https://doi.org/10.1016/s0140-6736(16)30951-5 doi: 10.1016/s0140-6736(16)30951-5 id: cord-017784-4r3fpmlb author: Foccillo, Giampiero title: The Infections Causing Acute Respiratory Failure in Elderly Patients date: 2019-08-06 words: 3573.0 sentences: 170.0 pages: flesch: 31.0 cache: ./cache/cord-017784-4r3fpmlb.txt txt: ./txt/cord-017784-4r3fpmlb.txt summary: Severe community-acquired pneumonia and acute exacerbations of chronic obstructive pulmonary disease (AECOPD) are causes of acute respiratory failure (ARF) in elderly patients. This process termed immunosenescence or immune dysregulation, together changes in lung function who occur with advancing age, play a critical role in the manifestation of age-related pulmonary diseases such as infections (i.e., pneumonia), chronic obstructive pulmonary disease (COPD), and increased the risk for develop sepsis [1] . Triggering causes of ARF in advanced aged patients are especially acute heart decompensation, severe community-acquired pneumonia (CAP), acute exacerbations of COPD (AECOPD), and pulmonary embolism. Lower respiratory tract infections, including pneumonia and exacerbation of chronic obstructive pulmonary disease, are among the most common causes of ARF in elderly people and the most important cause of hospitalization. Antibiotic therapy and treatment failure in patients hospitalized for acute exacerbations of chronic obstructive pulmonary disease abstract: The immune system of older individuals declines with advancing age (“immunosenescence”) increasing susceptibility to infection, as well as to an increased risk of a worse outcome. Severe community-acquired pneumonia and acute exacerbations of chronic obstructive pulmonary disease (AECOPD) are causes of acute respiratory failure (ARF) in elderly patients. Non-invasive mechanical ventilation (NIV) is effective in the treatment of patients with ARF, above all in case of AECOPD. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122443/ doi: 10.1007/978-3-030-26664-6_5 id: cord-016020-awanrm9u author: Fox, Julie D. title: Respiratory Pathogens date: 2007 words: 4603.0 sentences: 220.0 pages: flesch: 30.0 cache: ./cache/cord-016020-awanrm9u.txt txt: ./txt/cord-016020-awanrm9u.txt summary: In addition, despite the well-recognized association of viral infections with upper and lower respiratory tract infections, the current diagnostic virology procedures do not provide an answer rapidly enough to with parainfluenza virus type 4, human coronaviruses, rhinoviruses, and some enteroviruses would not ordinarily be identified without RNA detection methods. Published diagnostic methods for detection of respiratory pathogen DNA or RNA directly from clinical specimens utilize target amplification procedures such as polymerase chain reaction (PCR) or nucleic acid sequence-based amplification (NASBA).Although direct detection methods based on nucleic acid hybridization would be theoretically possible, the amount of target nucleic acid in specimens may be minimal and such methods would lack sensitivity compared to amplification methods, unless the organism was propagated before analysis. Thus, the molecular amplification procedures reported for direct detection of respiratory pathogens in clinical samples include PCR (e.g., Reference 19 and Figure 41 assays have utilized bacterial ribosomal RNA (rRNA; e.g., Reference 22 ). abstract: Respiratory tract infections are among the most common presenting complaints of patients in both hospital and community settings. They are a considerable burden in terms of both patient morbidity and public health interventions. Laboratory diagnosis of respiratory tract infections should provide guidance in therapy and prognosis, as well as useful epidemiological information reflecting trends in the community. Understanding and monitoring such trends facilitates early recognition of new infectious agents in a population. A summary of the common viruses and bacteria causing respiratory tract infections and their clinical relevance is given in Tables 41–1 and 41–2, respectively. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120168/ doi: 10.1007/978-0-387-33227-7_41 id: cord-253145-1fbj1rdv author: Fox, Julie D. title: Nucleic acid amplification tests for detection of respiratory viruses date: 2007-10-31 words: 5391.0 sentences: 270.0 pages: flesch: 40.0 cache: ./cache/cord-253145-1fbj1rdv.txt txt: ./txt/cord-253145-1fbj1rdv.txt summary: Assays based on nucleic acid amplification and detection can be designed against a broad range of respiratory viruses and have been particularly useful for detection of recently identified viruses such as human metapneumovirus and coronaviruses NL63 and HKU1. Use of NATs allows assessment of the impact of a wider array of potential pathogens on respiratory infections than previously possible and target-specific (multiplex) approaches have proved feasible for enhanced broadspectrum respiratory virus diagnosis. Many feasibility studies have confirmed that NATs improve detection of potential pathogens from lower respiratory tract specimens as well as from respiratory swabs even where alternative methods such as DFA and culture are available (Hibbitts and Fox, 2002; Moore et al., 2004; Lee et al., 2006) . If individual NATs are utilized, multiple infections are identified frequently but use of real-time multiplex reactions may lead to competition between amplification and detection Table 1 Enhanced detection of respiratory viruses using NATs abstract: Abstract Nucleic acid amplification tests (NATs) are increasingly being used for diagnosis of respiratory virus infections. The most familiar formats use DNA or RNA target amplification methods for enhanced sensitivity above culture and antigen-based procedures. Although gel and plate-hybridisation methods are still utilised for analysis of amplified products, detection using “real-time” methods which do not require handling of amplified products are favoured in many laboratories. Assays based on nucleic acid amplification and detection can be designed against a broad range of respiratory viruses and have been particularly useful for detection of recently identified viruses such as human metapneumovirus and coronaviruses NL63 and HKU1. However, the wide range of potential pathogens which can cause similar respiratory symptomology and disease makes application of individual diagnostic assays based on detection of DNA and RNA both complex and expensive. One way to resolve this potential problem is to undertake multiplexed nucleic acid amplification reactions with analysis of amplified products by suspension microarray. The Respiratory Virus Panel (RVP) from Luminex Molecular Diagnostics is one example of such an approach which could be made available to diagnostic and public health laboratories for broad spectrum respiratory virus detection. url: https://www.sciencedirect.com/science/article/pii/S1386653207700057 doi: 10.1016/s1386-6532(07)70005-7 id: cord-283910-k10j5dzd author: Fretzayas, Andrew title: Etiology and clinical features of viral bronchiolitis in infancy date: 2017-05-04 words: 4685.0 sentences: 260.0 pages: flesch: 43.0 cache: ./cache/cord-283910-k10j5dzd.txt txt: ./txt/cord-283910-k10j5dzd.txt summary: Recent advances in laboratory diagnostic methods confer to the identifi cation of different viruses as etiologic pathogens of bronchiolitis, although respiratory syncytial virus (RSV) remains the main culprit The aim of this review was to present the clinical picture of bronchiolitis as a whole entity irrespective of the virology as well as in relation to the particular viral parthogens that are incriminated as etiological factors. We searched the databases with the following key words: viral bronchiolitis, clinical features, definition, epidemiology, etiology, guidelines, severity score, adenovirus, bocavirus, coronavirus, influenza, metapneumovirus, parainfluenza, respiratory synchytial virus, and rhinovirus. In 2006 American Academy of Pediatrics (AAP) published a clinical practice guideline for bronchiolitis, [3] that was updated in 2014 [4] according to which bronchiolitis is "a constellation of signs and symptoms including children younger than 2 years including a viral upper respiratory tract prodrome followed by increased respiratory effort and wheezing". abstract: BACKGROUND: Bronchiolitis is a common lower respiratory tract infection in infancy. The aim of this review is to present the clinical profile of viral bronchiolitis, the different culprit viruses and the disease severity in relation to the viral etiology. DATA SOURCES: Databases including PubMed and Google Scholar were searched for articles about the clinical features of bronchiolitis and its viral etiology. The most relevant articles to the scope of this review were analyzed. RESULTS: Currently there are two main definitions for bronchiolitis which are not identical, the European definition and the American one. The most common viral pathogen that causes bronchiolitis is respiratory syncytial virus which was identified in 1955; now many other viruses have been implicated in the etiology of bronchiolitis such as rhinovirus, adenovirus, metapneumovirus, and bocavirus. Several studies have attempted to investigate the correlation of bronchiolitis severity with the type of detected virus or viruses. However, the results were not consitent. CONCLUSIONS: For the time being, the diagnosis of bronchiolitis remains clinical. The isolation of the responsible respiratory pathogens does not seem to confer to the prognosis of the disease severity. url: https://www.ncbi.nlm.nih.gov/pubmed/28470580/ doi: 10.1007/s12519-017-0031-8 id: cord-017499-51yy7y9n author: Freye, Enno title: Mechanism of Action of Opioids and Clinical Effects date: 2008 words: 24955.0 sentences: 1278.0 pages: flesch: 45.0 cache: ./cache/cord-017499-51yy7y9n.txt txt: ./txt/cord-017499-51yy7y9n.txt summary: Thus, -selective opioids like morphine, fentanyl and sufentanil, due to the high density of binding sites, mediate their main action within the brain stem and the midbrain. This sterospecificity of opiate action supports the concept of selective receptor binding to a site, which is able to distinguish in "handedness or goodness of fit" of an opioid molecule maximal response induced by administration of the active agent. On the other hand mixed agonist/antagonists, such as pentazocine, nalorphine, levallorphan, nalbuphine and butorphanol, demonstrate characteristics, which enable them to displace a pure agonist at the receptor site (antagonistic effect), but at the same time when administered by themselves, they induce opioid related effects such as analgesia and respiratory depression (agonistic effects; Table II-7) . However, a less potent opioid like codeine or tramadol, even when given in dosages higher than their therapeutic margin, will not induce a clinically relevant respiratory depressive effect ( Figure II-34) . abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122075/ doi: 10.1007/978-1-4020-5947-6_2 id: cord-340811-w4x4falm author: Frizzelli, Annalisa title: What happens to people’s lungs when they get coronavirus disease 2019? date: 2020-05-11 words: 1779.0 sentences: 106.0 pages: flesch: 46.0 cache: ./cache/cord-340811-w4x4falm.txt txt: ./txt/cord-340811-w4x4falm.txt summary: Search terms include novel coronavirus pneumonia, severe acute respiratory syndrome coronavirus 2, coronavirus and ventilation. Interestingly, patients with COVID-19 pneumonia may present an atypical form of ARDS characterized by a dissociation between their relatively preserved lung mechanics and the severity of hypoxemia (23) . Oxygen therapy should be considered immediately when patients affected by severe acute respiratory infection have the following conditions: hypoxemia (PaO2 <60 mmHg or SpO 2 <93% when breathing air); respiratory distress (respiratory frequency> 24 times/min); hypotension (systolic blood pressure <100 mmHg) (24) . Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study abstract: The novel coronavirus SARS-CoV-2 was first identified in Wuhan in December 2019 as cause of the consequent novel coronavirus disease 2019 (COVID-19). The virus has since spread worldwide. The clinical presentation following human infection ranges from a mild upper respiratory tract infection to severe acute respiratory distress syndrome and sepsis. We reviewed literature using Pubmed to identify relevant English-language articles published until April 15, 2020. Search terms include novel coronavirus pneumonia, severe acute respiratory syndrome coronavirus 2, coronavirus and ventilation. We summarized what SARS-CoV-2 infection means for the lungs. (www.actabiomedica.it) url: https://www.ncbi.nlm.nih.gov/pubmed/32420938/ doi: 10.23750/abm.v91i2.9574 id: cord-323551-22v2hn3v author: Galanti, M. title: Rates of asymptomatic respiratory virus infection across age groups date: 2019-04-15 words: 3120.0 sentences: 152.0 pages: flesch: 39.0 cache: ./cache/cord-323551-22v2hn3v.txt txt: ./txt/cord-323551-22v2hn3v.txt summary: We enrolled 214 individuals at multiple New York City locations and tested weekly for respiratory viral pathogens, irrespective of symptom status, from fall 2016 to spring 2018. Here, we document rates of asymptomatic respiratory virus infection through a large-scale community study across multiple age groups. For the entire duration of the study, participants provided a daily report rating nine respiratory illness-related symptoms (fever, chills, muscle pain, watery eyes, runny nose, sneezing, sore throat, cough, chest pain), which were recorded on a Likert scale (0 = none, 1 = mild, 2 = moderate, 3 = severe). Pairwise comparisons between single infections and coinfections across all eight definitions showed that testing positive for multiple viruses was not associated with more severe symptoms. Figure 3 shows that while children were most frequently infected with a respiratory virus (they presented with the highest number of viral shedding events per season), they recorded (as reported by their parents) the lowest symptom scores on average. abstract: Respiratory viral infections are a leading cause of disease worldwide. A variety of respiratory viruses produce infections in humans with effects ranging from asymptomatic to life-treathening. Standard surveillance systems typically only target severe infections (ED outpatients, hospitalisations, deaths) and fail to track asymptomatic or mild infections. Here we performed a large-scale community study across multiple age groups to assess the pathogenicity of 18 respiratory viruses. We enrolled 214 individuals at multiple New York City locations and tested weekly for respiratory viral pathogens, irrespective of symptom status, from fall 2016 to spring 2018. We combined these test results with participant-provided daily records of cold and flu symptoms and used this information to characterise symptom severity by virus and age category. Asymptomatic infection rates exceeded 70% for most viruses, excepting influenza and human metapneumovirus, which produced significantly more severe outcomes. Symptoms were negatively associated with infection frequency, with children displaying the lowest score among age groups. Upper respiratory manifestations were most common for all viruses, whereas systemic effects were less typical. These findings indicate a high burden of asymptomatic respiratory virus infection exists in the general population. url: https://doi.org/10.1017/s0950268819000505 doi: 10.1017/s0950268819000505 id: cord-316956-nnqi0dj1 author: Gamiño‐Arroyo, Ana E. title: Epidemiology and clinical characteristics of respiratory syncytial virus infections among children and adults in Mexico date: 2016-08-18 words: 2497.0 sentences: 138.0 pages: flesch: 45.0 cache: ./cache/cord-316956-nnqi0dj1.txt txt: ./txt/cord-316956-nnqi0dj1.txt summary: title: Epidemiology and clinical characteristics of respiratory syncytial virus infections among children and adults in Mexico Respiratory syncytial virus (RSV) is the major infectious cause of lower respiratory tract illness in infants and young children around the world. 11 In the present study, 570 cases of RSV infection identified during four epidemic years in Mexico were evaluated to clarify the epidemiology of this infection and to assess the possible variations in demographic and clinical characteristics according to viral groups. 6 In this report, we analyzed the characteristics of 570 patients (399 children and 171 adults) with confirmed RSV infection included in the study during a 4-year period. Epidemiological and clinical data of hospitalizations associated with respiratory syncytial virus infection in children under 5 years of age in Spain: FIVE multicenter study Epidemiology and clinical characteristics of respiratory syncytial virus infections among children and adults in Mexico abstract: BACKGROUND: Respiratory syncytial virus (RSV) is a leading etiological agent of acute respiratory tract infections and hospitalizations in children. However, little information is available regarding RSV infections in Latin American countries, particularly among adult patients. OBJECTIVE: To describe the epidemiology of RSV infection and to analyze the factors associated with severe infections in children and adults in Mexico. METHODS: Patients ≥1 month old, who presented with an influenza‐like illness (ILI) to six hospitals in Mexico, were eligible for participation in the study. Multiplex reverse‐transcriptase polymerase chain reaction identified viral pathogens in nasal swabs from 5629 episodes of ILI. Patients in whom RSV was detected were included in this report. RESULTS: Respiratory syncytial virus was detected in 399 children and 171 adults. RSV A was detected in 413 cases and RSV B in 163, including six patients who had coinfection with both subtypes; 414 (72.6%) patients required hospital admission, including 96 (16.8%) patients that required admission to the intensive care unit. Coinfection with one or more respiratory pathogens other than RSV was detected in 159 cases. Young age (in children) and older age (in adults) as well as the presence of some underlying conditions were associated with more severe disease. CONCLUSIONS: This study confirms that RSV is an important respiratory pathogen in children in Mexico. In addition, a substantial number of cases in adults were also detected highlighting the relevance of this virus in all ages. It is important to identify subjects at high risk of complications who may benefit from current or future preventive interventions. url: https://doi.org/10.1111/irv.12414 doi: 10.1111/irv.12414 id: cord-299952-xvtt8fz8 author: Gao, LuLu title: A randomized controlled trial of low-dose recombinant human interferons α-2b nasal spray to prevent acute viral respiratory infections in military recruits date: 2010-06-17 words: 4447.0 sentences: 224.0 pages: flesch: 50.0 cache: ./cache/cord-299952-xvtt8fz8.txt txt: ./txt/cord-299952-xvtt8fz8.txt summary: title: A randomized controlled trial of low-dose recombinant human interferons α-2b nasal spray to prevent acute viral respiratory infections in military recruits To assess the efficacy and safety of a low-dose recombinant human interferon α-2b (rIFNα-2b) nasal spray in preventing acute viral respiratory infections in military population, we performed this randomized controlled trial. To evaluate the efficacy and safety of this new nasal spray in preventing acute respiratory infections in military population, we performed this randomized, placebo-controlled, double-blind trial. In summary, this randomized controlled trial suggested that the recombinant human interferon ␣-2b nasal spray can be used to prevent common acute viral respiratory infections caused by Flu-A, Flu-B, PIV1-3 and ADV and was generally well tolerated among military recruits. The efficacy of preventing viral respiratory infections by the rIFN␣-2b nasal spray should be evaluated further in different population groups, such as children and the elderly, and more samples should be involved in the further study. abstract: The military population has a high disease burden of acute viral respiratory infections in China. To assess the efficacy and safety of a low-dose recombinant human interferon α-2b (rIFNα-2b) nasal spray in preventing acute viral respiratory infections in military population, we performed this randomized controlled trial. The results showed that application of the rIFNα-2b nasal spray had the benefits in prevention of infections caused by influenza A virus, influenza B virus parainfluenza viruses 1–3 and adenovirus species B. However, no benefit was seen in preventing respiratory syncytial virus. No severe adverse events were reported. Therefore, the rIFNα-2b nasal spray was effective and well tolerated for preventing common viral respiratory infections in the military recruits. url: https://doi.org/10.1016/j.vaccine.2010.03.062 doi: 10.1016/j.vaccine.2010.03.062 id: cord-269437-0pvqvhqs author: Gastañaduy, Paul A. title: Update: Severe Respiratory Illness Associated with Middle East Respiratory Syndrome Coronavirus (MERS-CoV) — Worldwide, 2012–2013 date: 2013-06-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: CDC continues to work in consultation with the World Health Organization (WHO) and other partners to better understand the public health risk posed by the Middle East Respiratory Syndrome Coronavirus (MERS-CoV), formerly known as novel coronavirus, which was first reported to cause human infection in September 2012. The continued reporting of new cases indicates that there is an ongoing risk for transmission to humans in the area of the Arabian Peninsula. New reports of cases outside the region raise concerns about importation to other geographic areas. Nosocomial outbreaks with transmission to health-care personnel highlight the importance of infection control procedures. Recent data suggest that mild respiratory illness might be part of the clinical spectrum of MERS-CoV infection, and presentations might not initially include respiratory symptoms. In addition, patients with comorbidities or immunosuppression might be at increased risk for infection, severe disease, or both. Importantly, the incubation period might be longer than previously estimated. Finally, lower respiratory tract specimens (e.g., sputum, bronchoalveolar lavage, bronchial wash, or tracheal aspirate) should be collected in addition to nasopharyngeal sampling for evaluation of patients under investigation. An Emergency Use Authorization (EUA) was recently issued by the Food and Drug Administration (FDA) to allow for expanded availability of diagnostic testing in the United States. url: https://www.ncbi.nlm.nih.gov/pubmed/23760190/ doi: nan id: cord-342314-nx0a3nvd author: Gebru, Mu’uz title: Aerobic bacteriological studies on the respiratory tracts of apparently healthy and pneumonic camels (Camelus dromedaries) in selected districts of Afar Region, Ethiopia date: 2017-11-16 words: 5042.0 sentences: 284.0 pages: flesch: 51.0 cache: ./cache/cord-342314-nx0a3nvd.txt txt: ./txt/cord-342314-nx0a3nvd.txt summary: title: Aerobic bacteriological studies on the respiratory tracts of apparently healthy and pneumonic camels (Camelus dromedaries) in selected districts of Afar Region, Ethiopia A cross-sectional study was conducted to isolate and identify bacterial species from the respiratory tract of apparently healthy and pneumonic camels in Asayita and Dubti woredas in the Afar Region, Ethiopia. There was a statistically significant association between the health status of the camels as well as the anatomical site studied with the isolation rates of the major respiratory pathogens (p < 0.05). Therefore, the present study was conducted to determine comparatively the bacterial species associated with camels with and without pneumonic lungs, identify the Streptococci spp. Besides, there was a statistically significant difference between pneumonic and apparently healthy camels with the isolation rate of the major respiratory pathogens (except B. The pathogenic bacteria isolated during the present study period are comparable to those previously reported from the respiratory tract of apparently healthy camels (Ahmed and Musa 2015) . abstract: A cross-sectional study was conducted to isolate and identify bacterial species from the respiratory tract of apparently healthy and pneumonic camels in Asayita and Dubti woredas in the Afar Region, Ethiopia. From a total of 74 lung tissue and 74 tracheal swab samples Staphylococcus aureus, 16.3%, Streptococcus equi subsp. equi, 13.0%, and Pasteurella multocida, 10.9%, were dominant isolates from pneumonic lungs; Escherichia coli, 12.7%, Proteus species, 10.9%, and Klebsiella pneumoniae, 9.1%, were the majority in the normal lungs. The majority of the isolates colonized both anatomical sites investigated. There was a statistically significant association between the health status of the camels as well as the anatomical site studied with the isolation rates of the major respiratory pathogens (p < 0.05). Furthermore, the isolates were susceptible to norfloxacin, streptomycin, and gentamicin but resistant to ampicillin and tetracycline on in vitro test. Further studies on the pathogenicity of the major isolates are recommended. url: https://doi.org/10.1007/s11250-017-1476-4 doi: 10.1007/s11250-017-1476-4 id: cord-252037-rj61mzqj author: Gerna, G. title: Changing circulation rate of human metapneumovirus strains and types among hospitalized pediatric patients during three consecutive winter-spring seasons date: 2005-06-28 words: 2203.0 sentences: 116.0 pages: flesch: 44.0 cache: ./cache/cord-252037-rj61mzqj.txt txt: ./txt/cord-252037-rj61mzqj.txt summary: In this study, we examined: i) the circulation rate of hMPV among the other respiratory viruses during 3 consecutive winter-spring seasons; ii) the relative circulation of the 2 types and the 4 subtypes of hMPV during the same 3-year period; iii) the relative impact of hMPV as compared to hRSV in determining admission to the hospital of infants with acute respiratory infections. The relative distribution of different respiratory viruses causing severe infections requiring admission to the hospital of infants and young children in three consecutive winter-spring seasons from 2001 through 2004 is reported in Table 2 Within the aliquot of patients found positive for some respiratory virus, no difference in the circulation rate was observed for respiratory virus infections caused by influenzavirus B, hPIVs, hAdVs, hCoVs, and coinfections along the three years studied. abstract: From 2001 through 2004, 808 pediatric patients admitted to hospital because of acute respiratory infections were examined for presence of respiratory viruses by either direct fluorescent staining using monoclonal antibodies or RT-PCR during three consecutive winter-spring seasons. On the whole, 336 (42%) patients were detected as positive for one or more respiratory viruses. The most widely circulating virus was human respiratory syncytial virus (hRSV) infecting 50% of positive patients, followed by human metapneumovirus (hMPV) found in 13% of patients, and then by influenza virus type A, human parainfluenzaviruses and coinfections. Significant variations in the circulation rate of hRSV, hMPV and influenzavirus type A were observed during the individual seasons. In addition, the circulation rates of the different types of hMPV changed yearly. In 2001–2002 and 2002–2003 hMPV circulated at a significant lower proportion than hRSV, while in 2003–2004 the circulation rates of the two viruses were closer. In conclusion, the 4 hMPV subtypes circulated yearly in Northern Italy flanking hRSV as major respiratory pathogens in the infantile patient population. url: https://www.ncbi.nlm.nih.gov/pubmed/15986171/ doi: 10.1007/s00705-005-0581-2 id: cord-262366-cmjnb0al author: Gerna, Giuseppe title: Genetic variability of human coronavirus OC43‐, 229E‐, and NL63‐like strains and their association with lower respiratory tract infections of hospitalized infants and immunocompromised patients date: 2006-05-23 words: 5857.0 sentences: 304.0 pages: flesch: 51.0 cache: ./cache/cord-262366-cmjnb0al.txt txt: ./txt/cord-262366-cmjnb0al.txt summary: title: Genetic variability of human coronavirus OC43‐, 229E‐, and NL63‐like strains and their association with lower respiratory tract infections of hospitalized infants and immunocompromised patients In the winter–spring seasons 2003–2004 and 2004–2005, 47 (5.7%) patients with acute respiratory infection associated with human coronavirus (hCoV) 229E‐, NL63‐, and OC43‐like strains were identified among 823 (597 immunocompetent and 226 immunocompromised) patients admitted to hospital with acute respiratory syndromes. © 2006 Wiley‐Liss, Inc. In the winter-spring seasons 2003-2004 and 2004-2005, 47 (5.7%) patients with acute respiratory infection associated with human coronavirus (hCoV) 229E-, NL63-, and OC43-like strains were identified among 823 (597 immunocompetent and 226 immunocompromised) patients admitted to hospital with acute respiratory syndromes. abstract: In the winter–spring seasons 2003–2004 and 2004–2005, 47 (5.7%) patients with acute respiratory infection associated with human coronavirus (hCoV) 229E‐, NL63‐, and OC43‐like strains were identified among 823 (597 immunocompetent and 226 immunocompromised) patients admitted to hospital with acute respiratory syndromes. Viral infections were diagnosed by either immunological (monoclonal antibodies) or molecular (RT‐PCR) methods. Each of two sets of primer pairs developed for detection of all CoVs (panCoV) failed to detect 15 of the 53 (28.3%) hCoV strains identified. On the other hand, all hCoV strains could be detected by using type‐specific primers targeting genes 1ab and N. The HuH‐7 cell line was found to be susceptible to isolation and identification of OC43‐ and 229E‐like strains. Overall, hCoV infection was caused by OC43‐like, 229E‐like, and NL63‐like strains in 25 (53.2%), 10 (21.3%), and 9 (19.1%) patients, respectively. In addition, three patients (6.4%) were infected by untypeable hCoV strains. NL63‐like strains were not found to circulate in 2003–2004, and 229E‐like strains did not circulate in 2004–2005, while OC43‐like strains were detected in both seasons. The monthly distribution reached a peak during January through March. Lower predominated over upper respiratory tract infections in each age group. In addition, hCoV infections interested only immunocompetent infants and young children during the first year of life, while all adults were immunocompromised patients. Coinfections of hCoVs and other respiratory viruses (mostly interesting the first year of life) were observed in 14 of the 47 (29.8%) patients and were associated with severe respiratory syndromes more frequently than hCoV single infections (P = 0.002). In conclusion, the use of multiple primer sets targeting different genes is recommended for diagnosis of all types of hCoV infection. In addition, the detection of still untypeable hCoV strains suggests that the number of hCoVs involved in human pathology might further increase. Finally, hCoVs should be screened routinely for in both infants and immunocompromised patients with acute respiratory infection. J. Med. Virol. 78:938–949, 2006. © 2006 Wiley‐Liss, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/16721849/ doi: 10.1002/jmv.20645 id: cord-280857-0o1ikwks author: Goligher, Ewan C. title: Clinical strategies for implementing lung and diaphragm-protective ventilation: avoiding insufficient and excessive effort date: 2020-11-02 words: 6146.0 sentences: 274.0 pages: flesch: 25.0 cache: ./cache/cord-280857-0o1ikwks.txt txt: ./txt/cord-280857-0o1ikwks.txt summary: This review summarizes practical strategies for achieving lung and diaphragm-protective targets at the bedside, focusing on inspiratory and expiratory ventilator settings, monitoring of inspiratory effort or respiratory drive, management of dyssynchrony, and sedation considerations. Several strategies can be used to facilitate lung and diaphragm protective ventilation, including modulation of ventilator inspiratory and expiratory assist, drugs that modify respiratory drive and/or effort, extracorporeal CO 2 removal (ECCO 2 R) and electrical stimulation of the respiratory muscles, as shown in Fig. 2 . [7] also showed that higher ECCO 2 R support reduced P 0.1 , respiratory muscle effort, and transpulmonary pressure in spontaneously breathing patients recovering from severe ARDS [74] . These preliminary findings suggest that partial neuromuscular blockade could be a feasible approach to achieving lung and diaphragm-protective ventilation targets in patients with high respiratory effort. abstract: Mechanical ventilation may have adverse effects on both the lung and the diaphragm. Injury to the lung is mediated by excessive mechanical stress and strain, whereas the diaphragm develops atrophy as a consequence of low respiratory effort and injury in case of excessive effort. The lung and diaphragm-protective mechanical ventilation approach aims to protect both organs simultaneously whenever possible. This review summarizes practical strategies for achieving lung and diaphragm-protective targets at the bedside, focusing on inspiratory and expiratory ventilator settings, monitoring of inspiratory effort or respiratory drive, management of dyssynchrony, and sedation considerations. A number of potential future adjunctive strategies including extracorporeal CO(2) removal, partial neuromuscular blockade, and neuromuscular stimulation are also discussed. While clinical trials to confirm the benefit of these approaches are awaited, clinicians should become familiar with assessing and managing patients’ respiratory effort, based on existing physiological principles. To protect the lung and the diaphragm, ventilation and sedation might be applied to avoid excessively weak or very strong respiratory efforts and patient-ventilator dysynchrony. url: https://doi.org/10.1007/s00134-020-06288-9 doi: 10.1007/s00134-020-06288-9 id: cord-320107-wels9wt7 author: Gottlieb, Jens title: Community-Acquired Respiratory Viruses date: 2018-03-26 words: 3659.0 sentences: 220.0 pages: flesch: 40.0 cache: ./cache/cord-320107-wels9wt7.txt txt: ./txt/cord-320107-wels9wt7.txt summary: Resolution of respiratory virus infection requires not only the elimination of the Keywords ► lung transplantation ► community-acquired respiratory viruses ► ribavirin ► bronchiolitis obliterns syndrome The incidence of community-acquired respiratory viruses (CARVs) is $15 cases per 100 patient-years after lung transplantation (LTx). The incidence of community-acquired respiratory viruses (CARVs) is $15 cases per 100 patient-years after lung transplantation (LTx). 8 In contrast to the nonimmunosuppressed host, CARV infection usually leads to more severe illness in the lung transplanted recipient with a higher incidence of respiratory failure. ALN-RSV01 for prevention of bronchiolitis obliterans syndrome after respiratory syncytial virus infection in lung transplant recipients Incidence and outcomes of respiratory viral infections in lung transplant recipients: a prospective study Upper and lower respiratory tract viral infections and acute graft rejection in lung transplant recipients Community-acquired respiratory viral infections in lung transplant recipients: a single season cohort study abstract: The incidence of community-acquired respiratory viruses (CARVs) is ∼15 cases per 100 patient-years after lung transplantation (LTx). Paramyxoviruses account for almost 50% of the cases of CARV infection in LTx. Most patients will be symptomatic with a mean decline of 15 to 20% in forced expiratory volume in 1 second. The attributable death rate is low in recent years 15 to 25% CARV infected LTx patients will develop chronic lung allograft dysfunction within a year after CARV infection. This risk seems to be increased in comparison to the noninfected LTx recipient. Detection rate of CARV dependent on clinical awareness, sampling, and diagnostic method with nucleic acid testing by polymerase chain reaction in bronchoalveolar lavage is the gold standard after LTx. There is no approved treatment for paramyxoviruses, most centers use ribavirin by various routes. Toxicity of systemic ribavirin is of concern and some patients will have contraindication to this treatment modality. Treatment may reduce the risk to develop chronic lung allograft dysfunction and respiratory failure. Agents under development are inhibiting viral attachment and use silencing mechanisms of viral replication. url: https://www.ncbi.nlm.nih.gov/pubmed/29579772/ doi: 10.1055/s-0037-1615799 id: cord-259422-5ex12eun author: Graat, Judith M title: A prospective, community-based study on virologic assessment among elderly people with and without symptoms of acute respiratory infection date: 2003-12-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND AND OBJECTIVE: Community-based elderly studies concerning microbiology of acute respiratory infections are scarce. Data on subclinical infections are even totally absent, although asymptomatic persons might act as a source of respiratory infections. METHODS: In a 1-year community-based study, we prospectively investigated the possible virologic cause of acute respiratory infections in 107 symptomatic case episodes and 91 symptom-free control periods. Participants, persons ⩾60 years, reported daily the presence of respiratory symptoms in a diary. Virologic assessment was performed by polymerase chain reaction (PCR) and serology. RESULTS: In 58% of the case episodes a pathogen was demonstrated, the most common being rhinoviruses (32%), coronaviruses (17%), and influenzaviruses (7%). The odds ratio for demonstrating a virus in cases with symptoms vs. controls without symptoms was 30.0 (95% confidence interval 10.2–87.6). In 4% of the symptom-free control periods a virus was detected. CONCLUSION: This study supports the importance of rhinovirus infections in community-dwelling elderly persons, whereas asymptomatic elderly persons can also harbor pathogens as detected by PCR, and thus might be a source of infection for their environment. url: https://www.ncbi.nlm.nih.gov/pubmed/14680673/ doi: 10.1016/s0895-4356(03)00171-9 id: cord-022082-1dq623oe author: Greaves, Peter title: Respiratory Tract date: 2007-09-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The chapter describes different aspects of the respiratory tract. In preclinical safety studies, pathologies of the respiratory system can be a result of an intercurrent disease or can be induced by systemically administered drugs. Intranasal or inhalation modes of therapy pose particular challenges in terms of the formulations and technologies required to administer a drug. A complex technology is developed to support the assessment of adverse effects of inhaled substances in rodent and nonrodent species, and the extrapolation of experimental findings to humans. The nasal chambers are the structures that are first to be subjected to the effects of inhaled substances, whether microorganisms or chemical substances. In rodents, the relatively small size of the nose and nasal sinuses facilitates a histological examination. Findings show that infectious agents cause inflammation in the nose and nasal sinuses, and this may be associated with inflammation in the conjunctiva, the middle ear, and the oral cavity. It has been observed that a particular response of the rodent nasal mucosa to some irritant substances, including pharmaceutical agents, is the formation of rounded eosinophilic inclusions in the cytoplasm of sustentacular cells of the olfactory epithelium, and to a lesser extent in respiratory and glandular epithelial cells. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152448/ doi: 10.1016/b978-044452771-4/50007-9 id: cord-267436-mivxm8oh author: Groneberg, David A title: Treatment and vaccines for severe acute respiratory syndrome date: 2005-03-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The causative agent of severe acute respiratory syndrome (SARS), which affected over 8000 individuals worldwide and was responsible for over 700 deaths in the 2002–2003 outbreak, is a coronavirus that was unknown before the outbreak. Although many different treatments were used during the outbreak, none were implemented in a controlled fashion. Thus, the optimal treatment for SARS is unknown. Since the outbreak, much work has been done testing new agents against SARS using in-vitro methods and animal models. In addition, global research efforts have focused on the development of vaccines against SARS. Efforts should be made to evaluate the most promising treatments and vaccines in controlled clinical trials, should another SARS outbreak occur. url: https://api.elsevier.com/content/article/pii/S1473309905013071 doi: 10.1016/s1473-3099(05)01307-1 id: cord-331288-elnwn7l5 author: Grützmacher, Kim title: Human quarantine: Toward reducing infectious pressure on chimpanzees at the Taï Chimpanzee Project, Côte d''Ivoire date: 2017-01-17 words: 3690.0 sentences: 171.0 pages: flesch: 44.0 cache: ./cache/cord-331288-elnwn7l5.txt txt: ./txt/cord-331288-elnwn7l5.txt summary: This study investigates the incidence of respiratory symptoms and human respiratory viruses in humans at a human‐great ape interface, the Taï Chimpanzee Project (TCP) in Côte d''Ivoire, and consequently, the effectiveness of a 5‐day quarantine designed to reduce the risk of potential exposure to human respiratory pathogens. This study investigates the incidence of respiratory symptoms and human respiratory viruses in humans at a human-great ape interface, the Taï Chimpanzee Project (TCP) in Côte d''Ivoire, and consequently, the effectiveness of a 5-day quarantine designed to reduce the risk of potential exposure to human respiratory pathogens. Furthermore, the risk of potential exposure to human pathogens is assessed by testing sick humans to detect common human respiratory viruses they brought to the habituation site, and by randomly testing apparently healthy humans in the beginning and at the end of quarantine to assess the possibility of excreting HRSV and HMPV, the two most relevant viruses for wild great apes. abstract: Due to their genetic relatedness, great apes are highly susceptible to common human respiratory pathogens. Although most respiratory pathogens, such as human respiratory syncytial virus (HRSV) and human metapneumovirus (HMPV), rarely cause severe disease in healthy human adults, they are associated with considerable morbidity and mortality in wild great apes habituated to humans for research or tourism. To prevent pathogen transmission, most great ape projects have established a set of hygiene measures ranging from keeping a specific distance, to the use of surgical masks and establishment of quarantines. This study investigates the incidence of respiratory symptoms and human respiratory viruses in humans at a human‐great ape interface, the Taï Chimpanzee Project (TCP) in Côte d'Ivoire, and consequently, the effectiveness of a 5‐day quarantine designed to reduce the risk of potential exposure to human respiratory pathogens. To assess the impact of quarantine as a preventative measure, we monitored the quarantine process and tested 262 throat swabs for respiratory viruses, collected during quarantine over a period of 1 year. Although only 1 subject tested positive for a respiratory virus (HRSV), 17 subjects developed symptoms of infection while in quarantine and were subsequently kept from approaching the chimpanzees, preventing potential exposure in 18 cases. Our results suggest that quarantine—in combination with monitoring for symptoms—is effective in reducing the risk of potential pathogen exposure. This research contributes to our understanding of how endangered great apes can be protected from human‐borne infectious disease. url: https://doi.org/10.1002/ajp.22619 doi: 10.1002/ajp.22619 id: cord-319675-mwy3t1ny author: Gu, Li title: Sustained Viremia and High Viral Load in Respiratory Tract Secretions Are Predictors for Death in Immunocompetent Adults with Adenovirus Pneumonia date: 2016-08-17 words: 3081.0 sentences: 164.0 pages: flesch: 56.0 cache: ./cache/cord-319675-mwy3t1ny.txt txt: ./txt/cord-319675-mwy3t1ny.txt summary: At admission (on day 5–7 after illness onset), the patients in fatal cases presented higher initial viral loads in respiratory tract secretions (8.578 ± 2.115 vs 6.263 ± 1.225 Log(10) copies/ml, p = 0.023). Our results suggest that a higher initial viral load (10 8 copy/ml) in the respiratory tract samples on day 5-7 after disease onset is a predictor for fatal clinical outcome. In one case, as shown in Fig 2, even though the patient presented with a higher viral load (10 8.32 copies / ml) in tracheal aspiration, which may be associated fatal outcome, his clinical manifestation recovered gradually with a downward trend in the viral load in respiratory tract and whole blood samples. A higher initial viral load (10 8 copy/ml) in the respiratory tract on day 5-7 after disease onset and sustained viremia for 2 weeks or more may be associated with fatal clinical outcomes. abstract: The predictors for fatal adenovirus (AdV) pneumonia among immunocompetent adults are unclear. Laboratory-confirmed, hospitalized AdV pneumonia adults were prospectively enrolled in Beijing Chao-Yang hospital from March to June 2013. Clinical data and serial whole blood and respiratory tract secretions from such patients were collected. Quantitative real-time polymerase chain reaction was performed to quantify the viral load. A total of 14 AdV pneumonia cases were consecutively enrolled, and four of them were fatal. Ten cases were caused by AdV-55, three by AdV-7 and one by AdV-3. There were no differences in age, gender or underlying diseases between the patients in the fatal cases and surviving cases. At admission (on day 5–7 after illness onset), the patients in fatal cases presented higher initial viral loads in respiratory tract secretions (8.578 ± 2.115 vs 6.263 ± 1.225 Log(10) copies/ml, p = 0.023). All patients in fatal cases presented with viremia on day 12–14 (100% vs 66.7%, p = 0.017). A higher initial viral load in the respiratory tract and sustained viremia (more than 2 weeks) may be predictors for fatal clinical outcomes. url: https://doi.org/10.1371/journal.pone.0160777 doi: 10.1371/journal.pone.0160777 id: cord-000285-7p3b6tyf author: HARTERT, Tina V. title: The Tennessee Children''s Respiratory Initiative: Objectives, design and recruitment results of a prospective cohort study investigating infant viral respiratory illness and the development of asthma and allergic diseases date: 2010-04-08 words: 3846.0 sentences: 169.0 pages: flesch: 38.0 cache: ./cache/cord-000285-7p3b6tyf.txt txt: ./txt/cord-000285-7p3b6tyf.txt summary: The primary goals of the study are: (i) to investigate both the acute and the long-term health consequences of varying severity and aetiology of clinically significant viral respiratory tract infections on the outcomes of allergic rhinitis (AR) and early childhood asthma; and (ii) to identify the potentially modifiable factors that define children who are at greatest risk of developing asthma following infant respiratory viral infection. Thus, we designed the prospective TCRI to establish a base for the evaluation of both the risks and benefits of documented significant infant viral respiratory infection of varying severity and aetiology and other environmental exposures on childhood atopy outcomes and to establish a biospecimen repository for analyses including biomarker testing and genotyping. The TCRI is a prospective cohort of mother-infant dyads enrolled in a longitudinal investigation of the relationship of infant viral respiratory infection severity and aetiology and the interaction of other risk factors on the development of childhood asthma and allergic diseases. abstract: Background and objective: The ‘attack rate’ of asthma following viral lower respiratory tract infections (LRTI) is about 3–4 fold higher than that of the general population; however, the majority of children who develop viral LRTI during infancy do not develop asthma, and asthma incidence has been observed to continuously decrease with age. Thus, we do not understand how viral LRTI either predispose or serve as a marker of children to develop asthma. The Tennessee Children's Respiratory Initiative has been established as a longitudinal prospective investigation of infants and their biological mothers. The primary goals are to investigate both the acute and the long‐term health consequences of varying severity and aetiology of clinically significant viral respiratory tract infections on early childhood outcomes. Methods: Over four respiratory viral seasons, 2004–2008, term, non‐low birth weight previously healthy infants and their biological mothers were enrolled during an infant's acute viral respiratory illness. Longitudinal follow up to age 6 years is ongoing. Results: This report describes the study objectives, design and recruitment results of the over 650 families enrolled in this longitudinal investigation. The Tennessee Children's Respiratory Initiative is additionally unique because it is designed in parallel with a large retrospective birth cohort of over 95 000 mother–infant dyads with similar objectives to investigate the role of respiratory viral infection severity and aetiology in the development of asthma. Conclusions: Future reports from this cohort will help to clarify the complex relationship between infant respiratory viral infection severity, aetiology, atopic predisposition and the subsequent development of early childhood asthma and atopic diseases. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2992986/ doi: 10.1111/j.1440-1843.2010.01743.x id: cord-018408-ttae193b author: Haddad, Imad Y. title: Pneumonia and Empyema date: 2008-11-15 words: 6160.0 sentences: 345.0 pages: flesch: 33.0 cache: ./cache/cord-018408-ttae193b.txt txt: ./txt/cord-018408-ttae193b.txt summary: Second, patients with genetic or acquired immune defi ciency commonly develop severe pneumonia with opportunistic infections that usually do not infect healthy children. These immunocompromised patients commonly have been given chemo-radiotherapy for cancer or are receiving immune-suppressive agents to prevent rejection episodes following solid organ and hematopoietic stem cell transplantation. The pathogens that commonly produce CAP or VAP, such as Streptococcus pneumoniae, Gram-negative bacilli, and Staphylococcus aureus, are relatively virulent bacteria so that only a small inoculum is required and the aspiration is usually subtle. Bacterial organisms recovered from tracheal secretions obtained through an endotracheal tube may or may not refl ect the causative agent(s) responsible for lower respiratory tract infection. In addition, recipients of solid organ and hematopoietic stem cell transplantation (HSCT) are frequently given life-long treatment with immunosuppressive agents designed to prevent graft rejection or graft-versus-host disease. Early-onset nosocomial pneumonia and VAP are commonly caused by antibiotic-sensitive, community-acquired organisms (e.g., Strep. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123273/ doi: 10.1007/978-1-84800-925-7_17 id: cord-253761-wjm8ju3v author: Haidopoulou, Katerina title: Human bocavirus infections in hospitalized Greek children date: 2010-03-09 words: 2012.0 sentences: 114.0 pages: flesch: 52.0 cache: ./cache/cord-253761-wjm8ju3v.txt txt: ./txt/cord-253761-wjm8ju3v.txt summary: To define the epidemiological profile and the clinical characteristics associated with HBoV infection in a population of children hospitalized with respiratory tract infection. MATERIAL AND METHODS: During a one-year period throat swab samples were collected from 370 previously healthy children, aged 14 days to 13 years, admitted to two different paediatric wards because of respiratory tract infection. The aim of the present study was to define the epidemiological profile and the clinical characteristics associated with HBoV in hospitalized children with respiratory tract infection (RTI) in Greece. One may argue that the fact that HBoV is prevalent in samples from patients with respiratory tract infection does not guarantee a causative role for the symptoms, especially when -as in this case -it is frequently detected in combination with other respiratory viruses of known pathogenic potential. Human bocavirus infection in young children in the United States: molecular epidemiological profile and clinical characteristics of a newly emerging respiratory virus abstract: INTRODUCTION: The epidemiology of human bocavirus (HBoV) infections has not been described in Greece, a south-eastern European country. To define the epidemiological profile and the clinical characteristics associated with HBoV infection in a population of children hospitalized with respiratory tract infection. MATERIAL AND METHODS: During a one-year period throat swab samples were collected from 370 previously healthy children, aged 14 days to 13 years, admitted to two different paediatric wards because of respiratory tract infection. Samples were tested for HBoV by PCR amplifying a part of the NS1 gene. RESULTS: Human bocavirus was detected in 12 children (3.2%). Four of the 12 cases were co-infections, 3 of them with influenza A and 1 with coronavirus OC43. Cases were observed only during the cold months. The mean age of children was 1.8 years (range 2 months to 4 years). The most common symptoms were fever, cough and various degrees of respiratory distress. All children were clinically diagnosed as having lower respiratory tract infections, mainly pneumonia and acute laryngotracheobronchitis, and recovered uneventfully. CONCLUSIONS: HBoV infections occur in Greece mostly among very young children. They accounted for 3.2% of children hospitalized with acute respiratory disease. Cases were observed only in late autumn to early spring. url: https://doi.org/10.5114/aoms.2010.13515 doi: 10.5114/aoms.2010.13515 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-005774-7z6uyn6p author: Hammer, J. title: Infant lung function testing in the intensive care unit date: 1995 words: 5005.0 sentences: 232.0 pages: flesch: 45.0 cache: ./cache/cord-005774-7z6uyn6p.txt txt: ./txt/cord-005774-7z6uyn6p.txt summary: This review will focus on techniques which are used to measure thoracoabdominal asynchrony, tidal breathing flow-volume loops, small airway function (forced expiratory maneuvers), respiratory mechanics and lung volumes in critically ill infants and children. In 1989, Shannon [49] proposed in this Journal that the minimum physiological information needed for the intelligent use of mechanical ventilation (particularly if lower airway and/or pulmonary parenchymal disease was apparent) required the measurement of at least 4 variables: i) arterial partial pressure of carbon dioxide; ii) arterial oxygen saturation; iii) the mechanical time constant of the lung and iv) FRC. In 1989, Shannon [49] proposed in this Journal that the minimum physiological information needed for the intelligent use of mechanical ventilation (particularly if lower airway and/or pulmonary parenchymal disease was apparent) required the measurement of at least 4 variables: i) arterial partial pressure of carbon dioxide; ii) arterial oxygen saturation; iii) the mechanical time constant of the lung and iv) FRC. abstract: As a result of the previous shortage of tools to assess objectively the overall physiological status of the respiratory system in infants and young children, it has been difficult to measure the degree of physiological disorder or the response to therapy in respiratory diseases such as BPD, the pediatric version of ARDS, bronchiolitis, pneumonia, asthma and croup in this patient population. The newborn — four-year old child is particularly difficult to study because of their lack of cooperation and size. The recent progress in computer technology made pulmonary function testing available for this age range and opened up new possibilities for monitoring changes in disease processes affecting the respiratory system. This may improve medical management of infants and children with lung and heart diseases in particular. In 1989, Shannon [49] proposed in this Journal that the minimum physiological information needed for the intelligent use of mechanical ventilation (particularly if lower airway and/or pulmonary parenchymal disease was apparent) required the measurement of at least 4 variables: i) arterial partial pressure of carbon dioxide; ii) arterial oxygen saturation; iii) the mechanical time constant of the lung and iv) FRC. In many circumstances, arterial CO(2) is approximated by alveolar (end-tidal) CO(2) and the arterial oxygen saturation is obtained from pulse oximetry accurately if perfusion is adequate. The mechanical time constant and FRC are easily measured by the techniques described above and together provide important information concerning appropriate ventilator settings for a given disease. The described techniques bring new insights and awareness, but also new responsibilities in the management of infants and children with respiratory compromise. Not all of these techniques need to be applied to all infants in the ICU. Not all the assumptions upon which some of the techniques we have described are based will prove true. Any such methods which do not withstand solid scientific testing must be quickly discarded and replaced with better and (hopefully) easier methods. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095417/ doi: 10.1007/bf01704742 id: cord-271669-dkg6229j author: Han, Seung Beom title: Respiratory Viral Infections in Children and Adolescents with Hematological Malignancies date: 2019-01-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Despite the introduction of a polymerase chain reaction (PCR) test for the diagnosis of respiratory viral infection (RVI), guidance on the application of this test and the management of RVI in immunocompromised children is lacking. This study evaluated the clinical characteristics of RVI and established strategies for the PCR test in children and adolescents with hematological malignancies. METHODS: This study included children and adolescents with underlying hematological malignancies and respiratory symptoms, in whom a multiplex PCR test was performed. Patients in whom RVI was identified and not identified were categorized into Groups I and II, respectively. Group I was sub-divided into patients with upper and lower respiratory infections. The medical records of the enrolled patients were retrospectively reviewed. RESULTS: A total of 93 respiratory illnesses were included. Group I included 46 (49.5%) cases of RVI, including 31 (67.4%) upper and 15 (32.6%) lower respiratory infections. Rhinovirus (37.0%) was the most common viral pathogen. Significantly more patients in Group I had community-acquired respiratory illnesses (p=0.003) and complained of rhinorrhea (p<0.001) and sputum (p=0.008) than those in Group II. In Group I, significantly more patients with lower respiratory infections had uncontrolled underlying malignancies (p=0.038) and received re-induction or palliative chemotherapy (p=0.006) than those with upper respiratory infections. CONCLUSIONS: A multiplex PCR test should be considered for RVI diagnosis in immunocompromised children and adolescents with respiratory symptoms, especially in those with rhinorrhea or sputum prominent over a cough. The early application of the PCR test in patients with uncontrolled underlying malignancies may improve outcomes. url: https://doi.org/10.4084/mjhid.2019.006 doi: 10.4084/mjhid.2019.006 id: cord-286337-qk90xb3a author: Hanada, Shigeo title: Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia date: 2018-11-16 words: 9806.0 sentences: 436.0 pages: flesch: 22.0 cache: ./cache/cord-286337-qk90xb3a.txt txt: ./txt/cord-286337-qk90xb3a.txt summary: While the effects of these alterations on risk of secondary bacterial pneumonia have not been studied, potential mechanisms by which these changes might modulate susceptibility to secondary bacterial infections include alterations in the nature and magnitude of the immune response in the host (microbiome on host effects) and facilitating growth of pathogens in the absence of normal commensals (inter-microbial effects). Given the effects of viruses on enhancing bacterial adherence to the epithelium (86) (87) (88) , it is perhaps not surprising that multiple studies of human subjects as well as in animal models have shown that viral infections are associated with increased colonization by potentially pathogenic bacteria (known as "pathobionts"). Another study of patients with 2009 pandemic H1N1 influenza infection revealed that the predominant phyla of the upper respiratory tract (nasal and nasopharyngeal samples) in patients harboring pandemic H1N1 were Actinobacteria, Firmicutes, and Proteobacteria although normal controls were not included; however, the authors suggested that flu is associated with an expansion of Proteobacteria (109) which is generally less abundant in healthy hosts. abstract: Influenza and other respiratory viral infections are the most common type of acute respiratory infection. Viral infections predispose patients to secondary bacterial infections, which often have a more severe clinical course. The mechanisms underlying post-viral bacterial infections are complex, and include multifactorial processes mediated by interactions between viruses, bacteria, and the host immune system. Studies over the past 15 years have demonstrated that unique microbial communities reside on the mucosal surfaces of the gastrointestinal tract and the respiratory tract, which have both direct and indirect effects on host defense against viral infections. In addition, antiviral immune responses induced by acute respiratory infections such as influenza are associated with changes in microbial composition and function (“dysbiosis”) in the respiratory and gastrointestinal tract, which in turn may alter subsequent immune function against secondary bacterial infection or alter the dynamics of inter-microbial interactions, thereby enhancing the proliferation of potentially pathogenic bacterial species. In this review, we summarize the literature on the interactions between host microbial communities and host defense, and how influenza, and other acute respiratory viral infections disrupt these interactions, thereby contributing to the pathogenesis of secondary bacterial infections. url: https://doi.org/10.3389/fimmu.2018.02640 doi: 10.3389/fimmu.2018.02640 id: cord-007417-az8xd66p author: Hansbro, Nicole G. title: Understanding the mechanisms of viral induced asthma: New therapeutic directions date: 2008-01-29 words: 29677.0 sentences: 1459.0 pages: flesch: 41.0 cache: ./cache/cord-007417-az8xd66p.txt txt: ./txt/cord-007417-az8xd66p.txt summary: Whether an infection induces disease depends on viral (type (E.g. RSV, RV)), host (genetic susceptibility, age, immune responses) and environmental (allergen exposure, season) factors. With respect to allergy RSV infection might only trigger defective immunity in genetically susceptible individuals or that allergic inflammatory and immune responses may promote the influx of virus-specific cells into the airways increasing inflammation and AHR (Schwarze et al., 1999c) . Nevertheless most studies suggest that Th1 responses may result in viral clearance and mild symptoms whereas an aberrant bias towards a Th2 phenotype may lead to more intense RSV-induced disease and promote the development of asthma . Animal models have been used to determine if RSV can induce the development of asthma by triggering pro-asthmatic immune responses that lead to variable airflow obstruction and airway inflammation. Further studies are required to elucidate the links between infection, immune responses and susceptibility to chronic respiratory diseases and why some individuals but not others develop persistent wheeze and asthma. abstract: Asthma is a common and debilitating disease that has substantially increased in prevalence in Western Societies in the last 2 decades. Respiratory tract infections by respiratory syncytial virus (RSV) and rhinovirus (RV) are widely implicated as common causes of the induction and exacerbation of asthma. These infections in early life are associated with the induction of wheeze that may progress to the development of asthma. Infections may also promote airway inflammation and enhance T helper type 2 lymphocyte (Th2 cell) responses that result in exacerbations of established asthma. The mechanisms of how RSV and RV induce and exacerbate asthma are currently being elucidated by clinical studies, in vitro work with human cells and animal models of disease. This research has led to many potential therapeutic strategies and, although none are yet part of clinical practise, they show much promise for the prevention and treatment of viral disease and subsequent asthma. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7112677/ doi: 10.1016/j.pharmthera.2007.11.002 id: cord-007030-mewo9w43 author: Hashim, Suhana title: The prevalence and preventive measures of the respiratory illness among Malaysian pilgrims in 2013 hajj season date: 2016-02-08 words: 3903.0 sentences: 237.0 pages: flesch: 55.0 cache: ./cache/cord-007030-mewo9w43.txt txt: ./txt/cord-007030-mewo9w43.txt summary: The purpose of this study is to determine the prevalence of respiratory illness and its associated factors among Malaysian hajj pilgrims in 2013 and to describe its preventive measures. Malaysian hajj pilgrims with previous experience of hajj (OR 0.24; 95% CI 0.10–0.56) or umrah (OR 0.19; 95% CI 0.07–0.52) and those who have practiced good hand hygiene (OR 0.35; 95% CI 0.16–0.79) were found to be significantly associated with lower risk of having respiratory illness. All preventive measures which include hand hygiene, wearing face masks and influenza vaccination must be practiced together as bundle of care to reduce respiratory illness effectively. Data based on the social demographic, co-morbid illness, smoking habits, symptoms of respiratory illness, history of contact with respiratory ill patients, previous experience of hajj or umrah, the practice of preventive measures, influenza and pneumococcal vaccination and supplement intake against respiratory illness were obtained by a self-administered proforma. abstract: Background. Respiratory illness continues to exert a burden on hajj pilgrims in Makkah. The purpose of this study is to determine the prevalence of respiratory illness and its associated factors among Malaysian hajj pilgrims in 2013 and to describe its preventive measures. Methods. A cross-sectional study was conducted in Makkah and Malaysia during the 2013 hajj season. A self-administered proforma on social demographics, previous experience of hajj or umrah, smoking habits, co-morbid illness and practices of preventive measures against respiratory illness were obtained. Results. A total of 468 proforma were analysed. The prevalence of the respiratory illness was 93.4% with a subset of 78.2% fulfilled the criteria for influenza-like illness (ILI). Most of them (77.8%) had a respiratory illness of <2 weeks duration. Approximately 61.8% were administered antibiotics but only 2.1% of them had been hospitalized. Most of them acquired the infection after a brief stay at Arafat (81.2%). Vaccination coverages for influenza virus and pneumococcal disease were quite high, 65.2% and 59.4%, respectively. For other preventive measures practices, only 31.8% of them practiced good hand hygiene, ∼82.9% of pilgrims used surgical face masks, N95 face masks, dry towels, wet towels or veils as their face masks. Nearly one-half of the respondents (44.4%) took vitamins as their food supplement. Malaysian hajj pilgrims with previous experience of hajj (OR 0.24; 95% CI 0.10–0.56) or umrah (OR 0.19; 95% CI 0.07–0.52) and those who have practiced good hand hygiene (OR 0.35; 95% CI 0.16–0.79) were found to be significantly associated with lower risk of having respiratory illness. Otherwise, pilgrims who had contact with those with respiratory illness (OR 2.61; 95% CI 1.12–6.09) was associated with higher risk. Conclusions. The prevalence of respiratory illness remains high among Malaysian hajj pilgrims despite having some practices of preventive measures. All preventive measures which include hand hygiene, wearing face masks and influenza vaccination must be practiced together as bundle of care to reduce respiratory illness effectively. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107508/ doi: 10.1093/jtm/tav019 id: cord-282303-idh7io9v author: Hassan, Md. Zakiul title: Contamination of hospital surfaces with respiratory pathogens in Bangladesh date: 2019-10-28 words: 4158.0 sentences: 203.0 pages: flesch: 39.0 cache: ./cache/cord-282303-idh7io9v.txt txt: ./txt/cord-282303-idh7io9v.txt summary: With limited infection control practices in overcrowded Bangladeshi hospitals, surfaces may play an important role in the transmission of respiratory pathogens in hospital wards and pose a serious risk of infection for patients, health care workers, caregivers and visitors. With limited infection control practices in overcrowded Bangladeshi hospitals, surfaces may play an important role in the transmission of respiratory pathogens in hospital wards and pose a serious risk of infection for patients, health care workers, caregivers and visitors. Respiratory viral and bacterial pathogens, including Staphylococcus aureus, Streptococcus pyogenes, influenza viruses, respiratory syncytial virus, adenovirus, rhinoviruses and novel coronavirus strains, can survive on hospital surfaces for days, weeks or even months. This study identified that hospital surfaces in these Bangladeshi hospitals, were frequently contaminated with respiratory pathogens and pose a potential threat for fomite-borne transmission of respiratory infections to patients, healthcare workers and family caregivers. abstract: With limited infection control practices in overcrowded Bangladeshi hospitals, surfaces may play an important role in the transmission of respiratory pathogens in hospital wards and pose a serious risk of infection for patients, health care workers, caregivers and visitors. In this study, we aimed to identify if surfaces near hospitalized patients with respiratory infections were contaminated with respiratory pathogens and to identify which surfaces were most commonly contaminated. Between September-November 2013, we collected respiratory (nasopharyngeal and oropharyngeal) swabs from patients hospitalized with respiratory illness in adult medicine and paediatric medicine wards at two public tertiary care hospitals in Bangladesh. We collected surface swabs from up to five surfaces near each case-patient including: the wall, bed rail, bed sheet, clinical file, and multipurpose towel used for care giving purposes. We tested swabs using real-time multiplex PCR for 19 viral and 12 bacterial pathogens. Case-patients with at least one pathogen detected had corresponding surface swabs tested for those same pathogens. Of 104 patients tested, 79 had a laboratory-confirmed respiratory pathogen. Of the 287 swabs collected from surfaces near these patients, 133 (46%) had evidence of contamination with at least one pathogen. The most commonly contaminated surfaces were the bed sheet and the towel. Sixty-two percent of patients with a laboratory-confirmed respiratory pathgen (49/79) had detectable viral or bacterial nucleic acid on at least one surface. Klebsiella pneumoniae was the most frequently detected pathogen on both respiratory swabs (32%, 33/104) and on surfaces near patients positive for this organism (97%, 32/33). Surfaces near patients hospitalized with respiratory infections were frequently contaminated by pathogens, with Klebsiella pneumoniae being most common, highlighting the potential for transmission of respiratory pathogens via surfaces. Efforts to introduce routine cleaning in wards may be a feasible strategy to improve infection control, given that severe space constraints prohibit cohorting patients with respiratory illness. url: https://doi.org/10.1371/journal.pone.0224065 doi: 10.1371/journal.pone.0224065 id: cord-301988-cevv81h3 author: Hassoun, Ali title: Seasonal variation of respiratory pathogen colonization in asymptomatic health care professionals: A single-center, cross-sectional, 2-season observational study date: 2015-08-01 words: 3067.0 sentences: 169.0 pages: flesch: 40.0 cache: ./cache/cord-301988-cevv81h3.txt txt: ./txt/cord-301988-cevv81h3.txt summary: BACKGROUND: The purpose of this study was to determine the seasonal variance of potentially pathogenic bacterial and viral organisms in nasopharyngeal specimens obtained from asymptomatic health care professionals (HCPs) during the 2014 winter and summer months. Although asymptomatic HCPs certainly harbor a number of different potentially infectious agents, future studies are needed to determine whether colonized pathogens are transmitted or initiate infection in at-risk patient populations. Here, we describe the frequency and seasonal variation of bacterial and viral detections in asymptomatic health care professionals (HCPs) during the winter and summer months of 2014. 4 By elucidating changes in pathogen colonization rates in asymptomatic HCPs during different time periods in the year, health care organizations can monitor which potentially pathogenic agents are most prevalent in carriers in a health care setting and observe correlations with infection levels in at-risk hospitalized patients. abstract: BACKGROUND: The purpose of this study was to determine the seasonal variance of potentially pathogenic bacterial and viral organisms in nasopharyngeal specimens obtained from asymptomatic health care professionals (HCPs) during the 2014 winter and summer months. METHODS: Nasopharyngeal specimens from 100 HCPs were collected from Huntsville Hospital (Huntsville, AL) during the winter and from 100 HCPs during the summer. All subjects were tested for 22 viruses and 19 bacteria using Target Enriched Multiplex Polymerase Chain Reaction. Both seasonal cohorts were composed of students, nurses, physicians, and residents. RESULTS: Of the 100 HCPs tested during the winter, 34 subjects were colonized with at least 1 bacterium, and 11 tested positive for at least 1 virus. Methicillin-resistant Staphylococcus aureus (MRSA), Moraxella catarrhalis, and coronavirus were the most frequently detected potentially infectious agents. Of the 100 HCPs tested during the summer, 37 tested positive for at least 1 bacterium, and 4 tested positive for a viral agent. The most prevalent bacteria were MRSA and Klebsiella pneumonia. CONCLUSION: Nasopharyngeal carriage among asymptomatic HCPs was common, but the frequency and presence of potential pathogens varied with each season. Understanding the colonization and infection potential of upper respiratory organisms is important, particularly for viruses. Although asymptomatic HCPs certainly harbor a number of different potentially infectious agents, future studies are needed to determine whether colonized pathogens are transmitted or initiate infection in at-risk patient populations. url: https://www.ncbi.nlm.nih.gov/pubmed/26052103/ doi: 10.1016/j.ajic.2015.04.195 id: cord-342915-r9kv67we author: Hayden, Frederick G. title: Advances in antivirals for non‐influenza respiratory virus infections date: 2013-11-01 words: 5748.0 sentences: 281.0 pages: flesch: 33.0 cache: ./cache/cord-342915-r9kv67we.txt txt: ./txt/cord-342915-r9kv67we.txt summary: Most of the treatment data regarding antivirals for non-influenza respiratory viruses have been derived from observational studies in immunocompromised hosts, and sometimes, infants, but recent randomized, controlled trials in specific target populations have helped to address the potential value of antiviral interventions. 12, [17] [18] [19] In addition, systematic reviews of the observational reports concluded that the common use of multiple agents in combination, varying dose regimens, paucity of studies with systematic data collection, complications from immunosuppressive therapy, and the lack of randomized, controlled trials meant that existing data were inconclusive with regard to putative antivirals and thus inadequate to determine appropriate management of SARS infections. In addition, one approved agent for selected parasitic infections, oral nitazoxanide, may have interferon-inducing properties, is inhibitory for various respiratory viruses including influenza and a canine CoV in vitro, 32 and has shown promising dose-related activity in a phase 2, placebo-controlled, randomized trial in treating uncomplicated influenza 33 Consequently, nitazoxanide would be an interesting agent to test alone and in combination with other antivirals for CoV infections. abstract: Progress in the development of antivirals for non‐influenza respiratory viruses has been slow with the result that many unmet medical needs and few approved agents currently exist. This commentary selectively reviews examples of where specific agents have provided promising clinical benefits in selected target populations and also considers potential therapeutics for emerging threats like the SARS and Middle East respiratory syndrome coronaviruses. Recent studies have provided encouraging results in treating respiratory syncytial virus infections in lung transplant recipients, serious parainfluenza virus and adenovirus infections in immunocompromised hosts, and rhinovirus colds in outpatient asthmatics. While additional studies are needed to confirm the efficacy and safety of the specific agents tested, these observations offer the opportunity to expand therapeutic studies to other patient populations. url: https://www.ncbi.nlm.nih.gov/pubmed/24215380/ doi: 10.1111/irv.12173 id: cord-307261-0a3iztns author: Hayden, Randall T. title: Comparison of two broadly multiplexed PCR systems for viral detection in clinical respiratory tract specimens from immunocompromised children date: 2012-01-30 words: 4052.0 sentences: 206.0 pages: flesch: 48.0 cache: ./cache/cord-307261-0a3iztns.txt txt: ./txt/cord-307261-0a3iztns.txt summary: title: Comparison of two broadly multiplexed PCR systems for viral detection in clinical respiratory tract specimens from immunocompromised children Samples were de-identified and assayed in parallel using two different, broadly multiplexed PCR systems: ResPlex™ II Panel v2.0 (ResPlex), Qiagen, Hilden, Germany and FilmArray(®) Respiratory Panel (FilmArray), Idaho Technology Inc., Salt Lake City, UT. Two broadly multiplexed PCR systems were compared to each other and to a panel of laboratory developed tests for the detection of respiratory viral pathogens in clinical respiratory tract specimens from pediatric immunocompromised children. FilmArray detected viral targets: adenovirus, bocavirus, coronavirus 229E, HKU1, NL63, OC43, enterovirus, hMPV, human rhinovirus, influenza virus types A and B, parainfluenza viruses 1, 2, 3 and 4, and RSV. The current study, to our knowledge, is the first reported that compares the FilmArray with the ResPlex II v2.0 for the direct detection of viral agents in clinical respiratory tract specimens from immunocompromised children. abstract: BACKGROUND: The detection of viral respiratory tract infections has evolved greatly with the development of PCR based commercial systems capable of simultaneously detecting a wide variety of pathogens. OBJECTIVES: Evaluate the relative performance of two commercial broad range systems for the detection of viral agents in clinical respiratory tract specimens from immunocompromised children. STUDY DESIGN: A total of 176 patient samples were included in the analysis, representing only the first sample collected for each patient, and excluding failed reactions. Samples were de-identified and assayed in parallel using two different, broadly multiplexed PCR systems: ResPlex™ II Panel v2.0 (ResPlex), Qiagen, Hilden, Germany and FilmArray(®) Respiratory Panel (FilmArray), Idaho Technology Inc., Salt Lake City, UT. Method comparison was based upon pair-wise concordance of results according to patient age, viral target and number of targets detected. RESULTS: The two systems showed an overall concordance, by patient, of 83.8% (p = 0.0001). FilmArray detected at least one target in 68.8% of samples, while ResPlex detected at least one target in 56.8%. ResPlex failed to detect 20.7% of FilmArray positives, and FilmArray failed to detect 4% of ResPlex positives. The relative performance of each system (including which system detected a higher number of positive samples) varied when stratified by target viral pathogen. CONCLUSIONS: Broadly multiplexed PCR is an effective means of detecting large numbers of clinically relevant respiratory viral pathogens. url: https://www.sciencedirect.com/science/article/pii/S1386653211005531 doi: 10.1016/j.jcv.2011.12.020 id: cord-286924-zk7hzcla author: Haytoğlu, Zeliha title: Bocavirus Viremia and Hepatitis in an Immunocompetent Child date: 2017-05-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: So far, many studies have shown that Human Bocavirus ( HBoV) is the main pathogen of the respiratory tract. Until now, there is no study that proves the association between HBoV and hepatitis. HBoV viremia/DNAemia has been associated closely with acute primary infection and moderate-to-severe illness but, more detailed clinical data about HBoV dissemination are still unavailable. CASE REPORT: Here we report a 2-years-5-months-old girl suffering from respiratory distress and heptitis followed in our intensive care unit. HBoV was detected in our patients nose and throat swabs concurrent with whole blood sample by positive polymerase chain reactions. After a through investigation no causative agent other than HBoV viremia was found. CONCLUSION: Human Bocavirus viremia with high viral loads may be associated with hepatitis. url: https://www.ncbi.nlm.nih.gov/pubmed/28443581/ doi: 10.4274/balkanmedj.2015.1492 id: cord-006261-yw5k8qkz author: Heath, Gregory W. title: Exercise and Upper Respiratory Tract Infections: Is There a Relationship? date: 2012-10-23 words: 6209.0 sentences: 329.0 pages: flesch: 44.0 cache: ./cache/cord-006261-yw5k8qkz.txt txt: ./txt/cord-006261-yw5k8qkz.txt summary: Few studies have investigated the common belief that moderate physical activity is beneficial in decreasing risk of respiratory tract infections and improving immune function. Laboratory and clinical studies suggest that changes in immune parameters associated with heavy train ing lead to adverse health effects, particularly an increase in the incidence or severity of upper respiratory tract infections. During this time, the women in the exercise group experienced fewer upper respiratory tract infection symptom days, improved cardiorespiratory fitness, and increased natural killer cell numbers compared with their sedentary controls. This study indicates that intensity of exercise may playa role, and that moderate activity may actually improve immune function and associated upper respiratory tract infection symptoms. Clinical studies examining the effects of moderate levels of physical activity have shown possible enhanced immune responses with a concomitant impact on the length and severity of an upper respiratory tract infection. The effects of moderate exercise training on natural killer cells and acute upper respiratory tract infections abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7100814/ doi: 10.2165/00007256-199214060-00003 id: cord-267003-k7eo2c26 author: Hendaus, Mohamed A title: Virus-induced secondary bacterial infection: a concise review date: 2015-08-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Respiratory diseases are a very common source of morbidity and mortality among children. Health care providers often face a dilemma when encountering a febrile infant or child with respiratory tract infection. The reason expressed by many clinicians is the trouble to confirm whether the fever is caused by a virus or a bacterium. The aim of this review is to update the current evidence on the virus-induced bacterial infection. We present several clinical as well in vitro studies that support the correlation between virus and secondary bacterial infections. In addition, we discuss the pathophysiology and prevention modes of the virus–bacterium coexistence. A search of the PubMed and MEDLINE databases was carried out for published articles covering bacterial infections associated with respiratory viruses. This review should provide clinicians with a comprehensive idea of the range of bacterial and viral coinfections or secondary infections that could present with viral respiratory illness. url: https://www.ncbi.nlm.nih.gov/pubmed/26345407/ doi: 10.2147/tcrm.s87789 id: cord-328742-r4ht266w author: Heo, Jung Yeon title: Molecular Epidemiology of Human Adenovirus–Associated Febrile Respiratory Illness in Soldiers, South Korea(1) date: 2018-07-17 words: 3073.0 sentences: 165.0 pages: flesch: 44.0 cache: ./cache/cord-328742-r4ht266w.txt txt: ./txt/cord-328742-r4ht266w.txt summary: During January 2013–April 2014, we subjected nasopharyngeal specimens collected from patients with acute febrile respiratory illness in a military hospital to PCR testing to detect 12 respiratory viruses and sequence a partial hexon gene for human adenovirus (HAdV) molecular typing. During January 2013-April 2014, we subjected nasopharyngeal specimens collected from patients with acute febrile respiratory illness in a military hospital to PCR testing to detect 12 respiratory viruses and sequence a partial hexon gene for human adenovirus (HAdV) molecular typing. HAdV is most prevalent in patients with acute lower respiratory tract infection and is the most common cause of pneumonia among military personnel in South Korea (12) . Thus, our study aimed to investigate the epidemiology of HAdV infections and to compare the clinical characteristics by type of HAdVs in soldiers in South Korea via hospital-based surveillance on viral respiratory infections. abstract: During January 2013–April 2014, we subjected nasopharyngeal specimens collected from patients with acute febrile respiratory illness in a military hospital to PCR testing to detect 12 respiratory viruses and sequence a partial hexon gene for human adenovirus (HAdV) molecular typing. We analyzed the epidemiologic characteristics of HAdV infections and compared clinical characteristics of HAdV types. Among the 305 patients with acute febrile respiratory illness, we detected respiratory viruses in 139 (45.6%) patients; HAdV was the most prevalent virus (69 cases). Of the 40 adenoviruses identified based on type, HAdV-55 (29 cases) was the most prevalent, followed by HAdV-4 (9 cases). HAdV-55 was common in patients with pneumonia (odds ratio 2.17; 95% CI 0.48–9.86) and hospitalized patients (odds ratio 5.21; 95% CI 1.06–25.50). In soldiers with HAdV infection in Korea, HAdV-55 was the most prevalent type and might be associated with severe clinical outcomes. url: https://www.ncbi.nlm.nih.gov/pubmed/29912713/ doi: 10.3201/eid2407.171222 id: cord-019100-rce6kyu4 author: Heymann, Peter W. title: VIRUS-INDUCED WHEEZING IN CHILDREN: Respiratory Syncytial Virus (RSV) and Rhinovirus date: 1998-02-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The strong association between infantile wheezing and respiratory tract infections caused by the respiratory syncytial virus (RSV) has been well established. In studies of older children, rhinovirus becomes the major virus associated with asthma. These relationships are outlined in the box on page 36. In the past, this relationship was more difficult to appreciate, because rhinovirus does not always grow well in culture. In addition, the linkage between asthma and atopy during childhood has raised the question whether viral infections alone can precipitate exacerbations of asthma. Use of the polymerase chain reaction (PCR) to measure viral nucleic acid material has provided the opportunity to study virus-induced wheezing among children in greater detail, and investigations of experimental rhinovirus infections in adults have demonstrated how this virus can augment both the early and late phase manifestations of airway hyperreactivity. This article reviews recent advances that have enhanced our understanding of virus-induced wheezing, along with new information indicating that interactions between viral infections and allergic inflammation may be critical to the pathogenesis of acute symptoms. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7125794/ doi: 10.1016/s0889-8561(05)70345-3 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-299835-92karhpl author: Ho, Khek Y. title: Mild Illness Associated with Severe Acute Respiratory Syndrome Coronavirus Infection: Lessons from a Prospective Seroepidemiologic Study of Health-Care Workers in a Teaching Hospital in Singapore date: 2004-02-17 words: 3524.0 sentences: 163.0 pages: flesch: 52.0 cache: ./cache/cord-299835-92karhpl.txt txt: ./txt/cord-299835-92karhpl.txt summary: title: Mild Illness Associated with Severe Acute Respiratory Syndrome Coronavirus Infection: Lessons from a Prospective Seroepidemiologic Study of Health-Care Workers in a Teaching Hospital in Singapore Participating HCWs completed a questionnaire and provided paired serum samples, which were analyzed by 2 different laboratories blinded to clinical data, by use of an enzyme-linked immunosorbent assay based on a protocol developed by the Centers for Disease Control and Prevention and a dot-blot immunoassay, with confirmation by a viral neutralization assay. Of the 372 HCWs participating in the present study, 8 were found to have positive antibodies to the SARS coronavirus in both samples by use of both test methods, and 6 had pneumonia and had been hospitalized for either probable or suspected SARS infection, whereas 2 had fever but did not have changes on chest radiographs. abstract: Background. Severe acute respiratory syndrome (SARS) is a newly recognized infectious disease that has recently emerged in East Asia and North America. Although the clinical features of acute infection have been well described, mildly symptomatic or asymptomatic infections have not been well characterized. Objective. To assess the spectrum of illness in health-care workers (HCWs). Methods. A prospective seroepidemiologic cohort study was conducted on 372 HCWs in a large teaching hospital in Singapore who were both exposed and not exposed to patients with SARS. Participating HCWs completed a questionnaire and provided paired serum samples, which were analyzed by 2 different laboratories blinded to clinical data, by use of an enzyme-linked immunosorbent assay based on a protocol developed by the Centers for Disease Control and Prevention and a dot-blot immunoassay, with confirmation by a viral neutralization assay. Results. A total of 21 patients with SARS were treated at our hospital. They were associated with transmission to 14 staff members, patients, and visitors in our hospital. Of the 372 HCWs participating in the present study, 8 were found to have positive antibodies to the SARS coronavirus in both samples by use of both test methods, and 6 had pneumonia and had been hospitalized for either probable or suspected SARS infection, whereas 2 had fever but did not have changes on chest radiographs. All seropositive HCWs had been exposed either directly or indirectly to patients with SARS. No asymptomatic, nonexposed staff members were found to be seropositive. There was a trend towards protection for HCWs who, while fully protected, had had contact with patients with SARS. Conclusions. Although the majority of cases of SARS are associated with pneumonia, a small number of mildly symptomatic individuals do seroconvert. HCWs who are exposed to patients with SARS can be infected with SARS, regardless of the intensity of exposure. This has implications for surveillance and infection control planning, in the event that SARS returns next winter. url: https://www.ncbi.nlm.nih.gov/pubmed/14767817/ doi: 10.1086/381558 id: cord-349956-h4i2t2cr author: Hoang, Van-Thuan title: The dynamics and interactions of respiratory pathogen carriage among French pilgrims during the 2018 Hajj date: 2019-11-21 words: 4851.0 sentences: 260.0 pages: flesch: 44.0 cache: ./cache/cord-349956-h4i2t2cr.txt txt: ./txt/cord-349956-h4i2t2cr.txt summary: We conducted this study to describe the dynamics of the acquisition of respiratory pathogens, their potential interactions and risk factors for possible lower respiratory tract infection symptoms (LRTI) among French pilgrims during the 2018 Hajj. showed that human rhinovirus (HRV) and influenza viruses were the most common viral respiratory pathogens isolated from ill Hajj pilgrims [6] . Unadjusted associations between respiratory pathogen carriage with multiples factors: sociodemographic characteristics (gender, ≥60 years), chronic respiratory disease, BMI classification, smoking status; individual preventive measures (vaccination against influenza, vaccination against IPD, use of a face mask, hand washing, disinfectant gel and disposable handkerchiefs); antibiotic intake 10 days before each sample; respiratory virus or bacteria and dual carriage were analysed by univariable analysis. aureus carriage increase and the initial wave of respiratory symptoms, suggests that this pathogen association was responsible for the RTIs that affected most pilgrims soon after arriving in Mecca. abstract: We conducted this study to describe the dynamics of the acquisition of respiratory pathogens, their potential interactions and risk factors for possible lower respiratory tract infection symptoms (LRTI) among French pilgrims during the 2018 Hajj. Each participant underwent four successive systematic nasopharyngeal swabs before and during their stay in Saudi Arabia. Carriage of the main respiratory pathogens was assessed by PCR. 121 pilgrims were included and 93.4% reported respiratory symptoms during the study period. The acquisition of rhinovirus, coronaviruses and Staphylococcus aureus occurred soon after arrival in Saudi Arabia and rates decreased gradually after days 5 and 6. In contrast, Streptococcus pneumoniae and Klebsiella pneumoniae carriage increased progressively until the end of the stay in Saudi Arabia. Haemophilus influenzae and Moraxella catarrhalis carriage increased starting around days 12 and 13, following an initial clearance. Influenza viruses were rarely isolated. We observed an independent positive mutual association between S. aureus and rhinovirus carriage and between H. influenzae and M. catarrhalis carriage. Dual carriage of H. influenzae and M. catarrhalis was strongly associated with S. pneumoniae carriage (OR = 6.22). Finally, our model showed that M. catarrhalis carriage was negatively associated with K. pneumoniae carriage. Chronic respiratory disease was associated with symptoms of LRTI. K. pneumoniae, M. catarrhalis-S. aureus and H. influenzae-rhinovirus dual carriage was associated with LRTI symptoms. Our data suggest that RTIs at the Hajj are a result of complex interactions between a number of respiratory viruses and bacteria. url: https://www.ncbi.nlm.nih.gov/pubmed/31749410/ doi: 10.1080/22221751.2019.1693247 id: cord-289282-4oz6r7op author: Hon, Kam Lun title: Overview: The history and pediatric perspectives of severe acute respiratory syndromes: Novel or just like SARS date: 2020-06-01 words: 3558.0 sentences: 269.0 pages: flesch: 58.0 cache: ./cache/cord-289282-4oz6r7op.txt txt: ./txt/cord-289282-4oz6r7op.txt summary: title: Overview: The history and pediatric perspectives of severe acute respiratory syndromes: Novel or just like SARS The WHO coined the acronym SARS (severe acute respiratory syndrome) and subsequently the causative virus as SARS‐CoV. Clinical presentations and outcome of severe acute respiratory syndrome in children Clinical features, diagnosis, treatment and short-term outcome of severe acute respiratory syndrome (SARS) in children Severe acute respiratory syndrome (SARS) in children: epidemiology, presentation and management Screening for Middle East respiratory syndrome coronavirus infection in hospital patients and their healthcare worker and family contacts: a prospective descriptive study Middle East respiratory syndrome coronavirus in pediatrics: a report of seven cases from Saudi Arabia The epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (COVID-19) in China Comparative analysis of eleven healthcare-associated outbreaks of Middle East respiratory syndrome coronavirus (Mers-Cov) from 2015 to 2017 Overview: The history and pediatric perspectives of severe acute respiratory syndromes: Novel or just like SARS abstract: Many respiratory viral infections such as influenza and measles result in severe acute respiratory symptoms and epidemics. In the spring of 2003, an epidemic of coronavirus pneumonia spread from Guangzhou to Hong Kong and subsequently to the rest of the world. The WHO coined the acronym SARS (severe acute respiratory syndrome) and subsequently the causative virus as SARS‐CoV. In the summer of 2012, epidemic of pneumonia occurred again in Saudi Arabia which was subsequently found to be caused by another novel coronavirus. WHO coined the term MERS (Middle East respiratory syndrome) to denote the Middle East origin of the novel virus (MERS‐CoV). In the winter of 2019, another outbreak of pneumonia occurred in Wuhan, China which rapidly spread globally. Yet another novel coronavirus was identified as the culprit and has been named SARS‐CoV‐2 due to its similarities with SARS‐CoV, and the disease as coronavirus disease‐2019. This overview aims to compare and contrast the similarities and differences of these three major episodes of coronavirus outbreak, and conclude that they are essentially the same viral respiratory syndromes caused by similar strains of coronavirus with different names. Coronaviruses have caused major epidemics and outbreaks worldwide in the last two decades. From an epidemiological perspective, they are remarkably similar in the mode of spread by droplets. Special focus is placed on the pediatric aspects, which carry less morbidity and mortality in all three entities. url: https://doi.org/10.1002/ppul.24810 doi: 10.1002/ppul.24810 id: cord-343390-y903mxcj author: Hoppe, Ingrid Bortolin Affonso Lux title: Bovine respiratory syncytial virus seroprevalence and risk factors in non-vaccinated dairy cattle herds in Brazil date: 2018-06-27 words: 2917.0 sentences: 165.0 pages: flesch: 53.0 cache: ./cache/cord-343390-y903mxcj.txt txt: ./txt/cord-343390-y903mxcj.txt summary: title: Bovine respiratory syncytial virus seroprevalence and risk factors in non-vaccinated dairy cattle herds in Brazil This study aimed to characterize the epidemiology of BRSV infection in dairy cattle herds of São Paulo State, Brazil, using serological and risk factors analyses. The analysis of risk factors indicated that the age group and the occurrence of coinfection with bovine herpesvirus 1 (BoHV-1) and bovine viral diarrhea virus 1 (BVDV-1) should be associated with a higher prevalence of BRSV, while natural suckling was considered a protective factor. Due to this, the current study aimed to determine antibody prevalence against BRSV and investigate some risk factors associated with BRSV seroprevalence in herds of an important milk producing region in São Paulo State, Brazil. Bovine respiratory syncytial virus seroprevalence and risk factors in endemic dairy cattle herds Prevalence of and risk factors for bovine respiratory syncytial virus (BRSV) infection in non-vaccinated dairy and dual-purpose cattle herds in Ecuador abstract: BACKGROUND: The cattle industry is one of the most important Brazilian agribusiness sectors and is a strong contributor to the national economy. Annually about 44.6 million calves are bred, which makes the optimal management of these animals extremely important. Several diseases can affect the initial stages of the bovine production chain, being the bovine respiratory syncytial virus (BRSV) one of the most relevant pathogens. This study aimed to characterize the epidemiology of BRSV infection in dairy cattle herds of São Paulo State, Brazil, using serological and risk factors analyses. For that, 1243 blood samples were collected of animals from 26 farms and a questionnaire about possible risk factors for BRSV prevalence was performed. The obtained blood sera were analyzed using virus neutralization test (VNT). RESULTS: VNT results showed high BRSV prevalence in dairy cattle herds, reaching 79.5% of seropositivity. The BRSV seroprevalence among studied farms ranged from 40 to 100%. The analysis of risk factors indicated that the age group and the occurrence of coinfection with bovine herpesvirus 1 (BoHV-1) and bovine viral diarrhea virus 1 (BVDV-1) should be associated with a higher prevalence of BRSV, while natural suckling was considered a protective factor. CONCLUSIONS: The study showed that adult animals over 1 year old are an important risk factor for the high seroprevalence of BRSV in herds. The high BRSV prevalence associated with BoHV-1 and BVDV-1 suggests that biosecurity measures should be applied in order to reduce viral dissemination. Additionally, the natural suckling may be an important management to protect calves from high BRSV seroprevalence. url: https://doi.org/10.1186/s12917-018-1535-8 doi: 10.1186/s12917-018-1535-8 id: cord-270947-6e5cw2q9 author: Huang, H.-S. title: Multiplex PCR system for the rapid diagnosis of respiratory virus infection: systematic review and meta-analysis date: 2017-12-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: To provide a summary of evidence for the diagnostic accuracies of three multiplex PCR systems (mPCRs)—BioFire FilmArray RP (FilmArray), Nanosphere Verigene RV+ test (Verigene RV+) and Hologic Gen-Probe Prodesse assays—on the detection of viral respiratory infections. METHODS: A comprehensive search up to 1 July 2017 was conducted on Medline and Embase for studies that utilized FilmArray, Verigene RV+ and Prodesse for diagnosis of viral respiratory infections. A summary of diagnostic accuracies for the following five viruses were calculated: influenza A virus (FluA), influenza B virus, respiratory syncytial virus, human metapneumovirus and adenovirus. Hierarchical summary receiver operating curves were used for estimating the viral detection performance per assay. RESULTS: Twenty studies of 5510 patient samples were eligible for analysis. Multiplex PCRs demonstrated high diagnostic accuracy, with area under the receiver operating characteristic curve (AUROC) equal to or more than 0.98 for all the above viruses except for adenovirus (AUROC 0.89). FilmArray, Verigene RV+ and ProFlu+ (the only Prodesse assay with enough data) demonstrated a summary sensitivity for FluA of 0.911 (95% confidence interval, 0.848–0.949), 0.949 (95% confidence interval, 0.882–0.979) and 0.954 (95% confidence interval, 0.871–0.985), respectively. The three mPCRs were comparable in terms of detection of FluA. CONCLUSIONS: Point estimates calculated from eligible studies showed that the three mPCRs (FilmArray, Verigene RV+ and ProFlu+) are highly accurate and may provide important diagnostic information for early identification of respiratory virus infections. In patients with low pretest probability for FluA, these three mPCRs can predict a low possibility of infection and may justify withholding empirical antiviral treatments. url: https://www.ncbi.nlm.nih.gov/pubmed/29208560/ doi: 10.1016/j.cmi.2017.11.018 id: cord-343050-1pfqgvie author: Huang, Qiu Sue title: Southern Hemisphere Influenza and Vaccine Effectiveness Research and Surveillance date: 2015-06-09 words: 6054.0 sentences: 281.0 pages: flesch: 29.0 cache: ./cache/cord-343050-1pfqgvie.txt txt: ./txt/cord-343050-1pfqgvie.txt summary: The results during the first 2 years (2012-2013) provided scientific evidence to (a) support a change to NZ''s vaccination policy for young children due to high influenza hospitalizations in these children; (b) contribute to the revision of the World Health Organization''s case definition for severe acute respiratory illness for global influenza surveillance; and (c) contribute in part to vaccine strain selection using vaccine effectiveness assessment in the prevention of influenza-related consultations and hospitalizations. Over 5 years, we hope this project will shed more light on the burden of influenza and other respiratory pathogens in our study population and subgroups and estimate key epidemiologic parameters such as relative rates of infection, clinical disease, general practice visits and hospitalizations as well as risk factors for illness, effectiveness of vaccination, mechanisms of immunity and monitoring for new influenza viruses with pandemic potential such as A(H7N9) and other emerging viruses (e.g. MERS-CoV) and provide a framework for timely assessment of severity which is essential in an event of emergence of these pathogens. abstract: The 2009 influenza A(H1N1)pdm09 pandemic highlighted the need for improved scientific knowledge to support better pandemic preparedness and seasonal influenza control. The Southern Hemisphere Influenza and Vaccine Effectiveness Research and Surveillance (SHIVERS) project, a 5-year (2012–2016) multiagency and multidisciplinary collaboration, aimed to measure disease burden, epidemiology, aetiology, risk factors, immunology, effectiveness of vaccination and other prevention strategies for influenza and other respiratory infectious diseases of public health importance. Two active, prospective, population-based surveillance systems were established for monitoring influenza and other respiratory pathogens among those hospitalized patients with acute respiratory illness and those enrolled patients seeking consultations at sentinel general practices. In 2015, a sero-epidemiological study will use a sample of patients from the same practices. These data will provide a full picture of the disease burden and risk factors from asymptomatic infections to severe hospitalized disease and deaths and related economic burden. The results during the first 2 years (2012–2013) provided scientific evidence to (a) support a change to NZ's vaccination policy for young children due to high influenza hospitalizations in these children; (b) contribute to the revision of the World Health Organization's case definition for severe acute respiratory illness for global influenza surveillance; and (c) contribute in part to vaccine strain selection using vaccine effectiveness assessment in the prevention of influenza-related consultations and hospitalizations. In summary, SHIVERS provides valuable international platforms for supporting seasonal influenza control and pandemic preparedness, and responding to other emerging/endemic respiratory-related infections. url: https://www.ncbi.nlm.nih.gov/pubmed/25912617/ doi: 10.1111/irv.12315 id: cord-024183-1mrdjc39 author: Hutchison, Alastair A. title: The Respiratory System date: 2013-10-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: This chapter addresses upper airway physiology for the pediatric intensivist, focusing on functions that affect ventilation, with an emphasis on laryngeal physiology and control in breathing. Effective control of breathing ensures that the airway is protected, maintains volume homeostasis, and provides ventilation. Upper airway structures are effectors for all of these functions that affect the entire airway. Nasal functions include air conditioning and protective reflexes that can be exaggerated and involve circulatory changes. Oral cavity and pharyngeal patency enable airflow and feeding, but during sleep pharyngeal closure can result in apnea. Coordination of breathing with sucking and nutritive swallowing alters during development, while nonnutritive swallowing at all ages limits aspiration. Laryngeal functions in breathing include protection of the subglottic airway, active maintenance of its absolute volume, and control of tidal flow patterns. These are vital functions for normal lung growth in fetal life and during rapid adaptations to breathing challenges from birth through adulthood. Active central control of breathing focuses on the coordination of laryngeal and diaphragmatic activities, which adapts according to the integration of central and peripheral inputs. For the intensivist, knowledge of upper airway physiology can be applied to improve respiratory support. In a second part the mechanical properties of the respiratory system as a critical component of the chain of events that result in translation of the output of the respiratory rhythm generator to ventilation are described. A comprehensive understanding of respiratory mechanics is essential to the delivery of optimized and individualized mechanical ventilation. The basic elements of respiratory mechanics will be described and developmental changes in the airways, lungs, and chest wall that impact on measurement of respiratory mechanics with advancing postnatal age are reviewed. This will be follwowed by two sections, the first on respiratory mechanics in various neonatal pathologies and the second in pediatric pathologies. The latter can be classified in three categories. First, restrictive diseases may be of pulmonary origin, such as chronic interstitial lung diseases or acute lung injury/acute respiratory distress syndrome, which are usually associated with reduced lung compliance. Restrictive diseases may also be due to chest wall abnormalities such as obesity or scoliosis (idiopathic or secondary to neuromuscular diseases), which are associated with a reduction in chest wall compliance. Second, obstructive diseases are represented by asthma and wheezing disorders, cystic fibrosis, long term sequelae of neonatal lung disease and bronchiolitis obliterans following hematopoietic stem cell transplantation. Obstructive diseases are defined by a reduced FEV1/VC ratio. Third, neuromuscular diseases, mainly represented by DMD and SMA, are associated with a decrease in vital capacity linked to respiratory muscle weakness that is better detected by PImax, PEmax and SNIP measurements. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7193717/ doi: 10.1007/978-3-642-01219-8_4 id: cord-007176-61e9obb3 author: Jackson, George Gee title: Viroses Causing Common Respiratory Infections in Man. III. Respiratory Syncytial Viroses and Coronavimses date: 1973-11-17 words: 4090.0 sentences: 299.0 pages: flesch: 50.0 cache: ./cache/cord-007176-61e9obb3.txt txt: ./txt/cord-007176-61e9obb3.txt summary: RS virus was estimated, from sucrose density gradient centrifugation studies, to be 90-120 nm in diameter [2] ; viral particles in infected cells measured 65 nm by electron microscopy. All adults tested possessed detectable levels of neutralizing antibody to RS virus before challenge, but the titer of naturally acquired antibody had no significant effect on subsequent RS infection of volunteers and was poorly correlated with development of mild clinical illnesses. The neutralization test is more sensitive than CF when serum from infants is used, but rises in neutralizing antibody have been detected in only half of the virus-positive infections in this age group. Virus structures were detected 6-8 hr later [17] .· Infection of WI-38 cells with strain 229E resulted in a reorganization of the cytoplasm, as determined by electron microscopy. Respiratory syncytial virus infection in adult volunteers. Respiratory syncytial virus infection in adult volunteers. Morphology and development of respiratory syncytial virus in cell culture abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7109772/ doi: 10.1093/infdis/128.5.674 id: cord-256827-tht5h1tu author: Jain, Neemisha title: Upper respiratory tract infections date: 2001 words: 2740.0 sentences: 201.0 pages: flesch: 43.0 cache: ./cache/cord-256827-tht5h1tu.txt txt: ./txt/cord-256827-tht5h1tu.txt summary: Common cold is caused by viruses in most circumstances and does not require antimicrobial agent unless it is complicated by acute otitis media with effusion, tonsillitis, sinusitis, and lower respiratory tract infection. Five to six days after initiation of treatment, cephalexin and placebo groups did not differ in the presence of nasal discharge, incidence of complications, or parental opinion of benefit of medicationY Cough occurs in 60-80% of common cold and does not suggest a bacterial etiology. n Even in uncomplicated viral upper respiratory infection, as occurs in common cold, there is inflammation and congestion of both the nasal and the sinus mucosa. Persistence of signs and symptoms of upper respiratory infection i.e. rhinorrhea or cough for more than 10-14 days is a pointer towards sinusitis. abstract: Acute respiratory infections accounts for 20–40% of outpatient and 12–35% of inpatient attendance in a general hospital. Upper respiratory tract infections including nasopharyngitis, pharyngitis, tonsillitis and otitis media constitute 87.5% of the total episodes of respiratory infections. The vast majority of acute upper respiratory tract infections are caused by viruses. Common cold is caused by viruses in most circumstances and does not require antimicrobial agent unless it is complicated by acute otitis media with effusion, tonsillitis, sinusitis, and lower respiratory tract infection. Sinusitis is commonly associated with common cold. Most instances of rhinosinusitis are viral and therefore, resolve spontaneously without antimicrobial therapy. The most common bacterial agents causing sinusitis areS. pneumoniae, H. influenzae, M. catarrhalis,S. aureus andS. pyogenes. Amoxycillin is antibacterial of choice. The alternative drugs are cefaclor or cephalexin. The latter becomes first line if sinusitis is recurrent or chronic. Acute pharyngitis is commonly caused by viruses and does not need antibiotics. About 15% of the episodes may be due to Group A beta hemolytic streptococcus (GABS). Early initiation of antibiotics in pharyngitis due to GABS can prevent complications such as acute rheumatic fever. The drug of choice is penicillin for 10–14 days. The alternative medications include oral cephalosporins (cefaclor, cephalexin), amoxicillin or macrolides. url: https://www.ncbi.nlm.nih.gov/pubmed/11838568/ doi: 10.1007/bf02722930 id: cord-322657-q4aeood2 author: Jartti, Tuomas title: Respiratory Picornaviruses and Respiratory Syncytial Virus as Causative Agents of Acute Expiratory Wheezing in Children date: 2004-06-17 words: 3169.0 sentences: 177.0 pages: flesch: 45.0 cache: ./cache/cord-322657-q4aeood2.txt txt: ./txt/cord-322657-q4aeood2.txt summary: We studied the viral etiology of acute expiratory wheezing (bronchiolitis, acute asthma) in 293 hospitalized children in a 2-year prospective study in Finland. To prevent and treat acute expiratory wheezing illnesses in children, efforts should be focused on RSV, enterovirus, and rhinovirus infections. The purpose of the study was to investigate the role of 11 respiratory viruses in children hospitalized for acute expiratory wheezing. The supernatants of cell cultures exhibiting a cytopathogenic effect were further studied by antigen detection for adenovirus; influenza A and B viruses; parainfluenza virus types 1, 2, and 3; and RSV or by reverse transcription (RT)-PCR for enterovirus-es and rhinovirus. First, respiratory virus infection was detected in up to 90% of hospitalized children with acute expiratory wheezing. In conclusion, this study showed that acute expiratory wheezing necessitating hospitalization was most often associated with RSV, enterovirus, and rhinovirus infections. abstract: We studied the viral etiology of acute expiratory wheezing (bronchiolitis, acute asthma) in 293 hospitalized children in a 2-year prospective study in Finland. A potential causative viral agent was detected in 88% of the cases. Eleven different viruses were represented. Respiratory syncytial virus (RSV) (27%), enteroviruses (25%), rhinovirus (24%), and nontypable rhino/enterovirus (16%) were found most frequently. In infants, RSV was found in 54% and respiratory picornaviruses (rhinovirus and enteroviruses) in 42% of the cases. In older children, respiratory picornaviruses dominated (65% of children ages 1-2 years and 82% of children ages >3 years). Human metapneumovirus was detected in 4% of all children and in 11% of infants. To prevent and treat acute expiratory wheezing illnesses in children, efforts should be focused on RSV, enterovirus, and rhinovirus infections. url: https://www.ncbi.nlm.nih.gov/pubmed/15207063/ doi: 10.3201/eid1006.030629 id: cord-006325-3no74e74 author: Jeannoël, M. title: Microorganisms associated with respiratory syncytial virus pneumonia in the adult population date: 2018-10-23 words: 1955.0 sentences: 108.0 pages: flesch: 39.0 cache: ./cache/cord-006325-3no74e74.txt txt: ./txt/cord-006325-3no74e74.txt summary: A more severe outcome was observed for RSV-bacteria-associated pneumonia compared with RSV pneumonia: length of stay was significantly longer (16 days vs 10 days) and ICU hospitalization more frequent (66.7% vs 21.0%) (p < 0.05). In conclusion, we did not observe major differences in the epidemiology of bacterial superinfections in RSV-positive pneumonia compared to reports on post-influenza pneumonia. RSV and bacteria coinfection was statistically associated with a more severe outcome than RSV-positive pneumonia as length of stay was significantly longer (16 days vs 10 days) and ICU hospitalization more frequent (66.7% vs 21.0%) (p < 0.05). It is probably due to the systematic testing strategy associated to a Species distribution of pathogenic bacteria involved in RSV-positive pneumonia (CAP) and hospital-acquired pneumonia (HAP) sampling bias toward influenza-like illness. Clinical characteristics and outcome of respiratory syncytial virus infection among adults hospitalized with influenza-like illness in France abstract: Respiratory syncytial virus (RSV) has been recognized as responsible for severe respiratory illness in adults, especially in the elderly. While pneumonia is commonly observed during RSV infection, the burden and epidemiology of bacterial superinfection is poorly understood. The aim of this study was to identify microorganisms associated with RSV-positive pneumonia in adults. A retrospective study was conducted during three consecutive winters (October to April 2013–2016) in the University Hospital of Lyon, France. During RSV circulation periods, a systematic RSV screening was performed by reverse-transcription PCR on all respiratory samples collected from adults. Records of RSV-positive patients were subsequently analyzed to identify radiologically confirmed pneumonia cases. Bacteria were identified by standard bacteriology cultures or urinary antigen screening and classified as potentially causative of pneumonia if quantification was above the specific threshold as defined by the European Manual of Clinical Microbiology. Overall, 14,792 adult respiratory samples were screened for RSV detection by PCR. In total, 292 had a positive RSV detection (2.0%) among which 89 presented with pneumonia including 27 bacterial superinfections (9.3%) with Streptococcus pneumonia, Haemophilus influenza, Staphylococcus aureus, Pseudomonas aeruginosa, and Moraxella catarrhalis. Most patients were elderly (55.6%) and patients with comorbidities (77.8%). A more severe outcome was observed for RSV-bacteria-associated pneumonia compared with RSV pneumonia: length of stay was significantly longer (16 days vs 10 days) and ICU hospitalization more frequent (66.7% vs 21.0%) (p < 0.05). In conclusion, we did not observe major differences in the epidemiology of bacterial superinfections in RSV-positive pneumonia compared to reports on post-influenza pneumonia. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101617/ doi: 10.1007/s10096-018-3407-3 id: cord-295189-bz3gi15h author: Jennings, Lance C. title: Respiratory viruses in airline travellers with influenza symptoms: Results of an airport screening study date: 2015-03-14 words: 3264.0 sentences: 166.0 pages: flesch: 48.0 cache: ./cache/cord-295189-bz3gi15h.txt txt: ./txt/cord-295189-bz3gi15h.txt summary: STUDY DESIGN: Data were collected from travellers arriving at Christchurch International Airport, New Zealand, during the winter 2008, via a symptom questionnaire, temperature testing, and respiratory sampling. CONCLUSIONS: The high prevalence of respiratory virus infections caused by viruses other than influenza in this study, many with overlapping symptotology to influenza, has important implications for any screening strategies for the prediction of influenza in airline travellers. In a 2008 study, we sought to assess the prevalence of influenza infection in symptomatic and asymptomatic arriving international airline travellers and whether using a symptom-screening questionnaire and temperature measurement could reliably predict seasonal influenza infection [16] . The high prevalence of respiratory virus infections caused by viruses other than influenza in this study, many with overlapping symptoms to influenza, has important implications for any screening strategy for the prediction of influenza in airline travellers. abstract: BACKGROUND: There is very little known about the prevalence and distribution of respiratory viruses, other than influenza, in international air travellers and whether symptom screening would aid in the prediction of which travellers are more likely to be infected with specific respiratory viruses. OBJECTIVES: In this study, we investigate whether, the use of a respiratory symptom screening tool at the border would aid in predicting which travellers are more likely to be infected with specific respiratory viruses. STUDY DESIGN: Data were collected from travellers arriving at Christchurch International Airport, New Zealand, during the winter 2008, via a symptom questionnaire, temperature testing, and respiratory sampling. RESULTS: Respiratory viruses were detected in 342 (26.0%) of 1313 samples obtained from 2714 symptomatic travellers. The most frequently identified viruses were rhinoviruses (128), enteroviruses (77) and influenza B (48). The most frequently reported symptoms were stuffy or runny nose (60%), cough (47%), sore throat (27%) and sneezing (24%). Influenza B infections were associated with the highest number of symptoms (mean of 3.4) followed by rhinoviruses (mean of 2.2) and enteroviruses (mean of 1.9). The positive predictive value (PPV) of any symptom for any respiratory virus infection was low at 26%. CONCLUSIONS: The high prevalence of respiratory virus infections caused by viruses other than influenza in this study, many with overlapping symptotology to influenza, has important implications for any screening strategies for the prediction of influenza in airline travellers. url: https://www.ncbi.nlm.nih.gov/pubmed/25959149/ doi: 10.1016/j.jcv.2015.03.011 id: cord-340280-m1j6v33y author: Jeon, Jae‐Hyun title: Incidence and seasonality of respiratory viruses causing acute respiratory infections in the Northern United Arab Emirates date: 2019-04-07 words: 2983.0 sentences: 179.0 pages: flesch: 47.0 cache: ./cache/cord-340280-m1j6v33y.txt txt: ./txt/cord-340280-m1j6v33y.txt summary: OBJECTIVES: This study was designed to describe the molecular epidemiology and seasonality of acute respiratory infection (ARI)‐related respiratory viruses in the United Arab Emirates (UAE). 1, 5, 9 Contrary to the accumulating knowledge of ARIs in temperate regions, epidemiological research on acute respiratory viral illness in tropical and subtropical areas is limited, although the epidemiological diversity, according to local climate and latitude, has been well studied. 14 Our study was designed to describe the molecular epidemiology of ARI-related respiratory viruses, including the seasonality of the viruses in the northern UAE for over 2 years. 2, 24, 25 FLU was the most common respiratory virus in all age groups, and the positivity rate was 20.0%, which is similar to previous data reported from studies in Oman. 7,34 However, our data suggest that in the UAE, like in other temperate countries, a diverse set of respiratory viruses contribute to the ARI cases that compel patients to visit medical facilities, because of their severity. abstract: BACKGROUND: The data on the seasonality of respiratory viruses helps to ensure the optimal vaccination period and to monitor the possible outbreaks of variant type. OBJECTIVES: This study was designed to describe the molecular epidemiology and seasonality of acute respiratory infection (ARI)‐related respiratory viruses in the United Arab Emirates (UAE). METHODS: Both upper and lower respiratory specimens were collected for the analysis from all the patients who visited the Sheikh Khalifa Specialty Hospital (SKSH) with ARI for over 2 years. The multiplex real‐time reverse transcription polymerase chain reaction (rRT‐PCR) test was used to detect respiratory viruses, which include human adenovirus, influenza virus (FLU) A and B, respiratory syncytial virus, parainfluenza viruses, human rhinovirus (HRV), human metapneumovirus, human enterovirus, human coronavirus, and human bocavirus. RESULTS: A total of 1,362 respiratory samples were collected from 733 (53.8%) male and 629 (46.2%) female patients with ARI who visited the SKSH between November 2015 and February 2018. The rRT‐PCR test revealed an overall positivity rate of 37.2% (507/1362). The positive rate increased during winter; it was highest in December and lowest in September. FLU was the most frequently detected virus (273/1362 [20.0%]), followed by human rhinovirus (146/1362 [10.7%]). The FLU positivity rate showed two peaks, which occurred in August and December. The peak‐to‐low ratio for FLU was 2.26 (95% confidence interval: 1.52‐3.35). CONCLUSIONS: The pattern of FLU in the UAE parallels to that of temperate countries. The trend of the small peak of FLU in the summer suggests a possibility of semi‐seasonal pattern in the UAE. url: https://doi.org/10.1002/jmv.25464 doi: 10.1002/jmv.25464 id: cord-274127-12x5cc8i author: Jeong, Ji Hun title: Comparison of sputum and nasopharyngeal swabs for detection of respiratory viruses date: 2014-05-06 words: 2721.0 sentences: 148.0 pages: flesch: 49.0 cache: ./cache/cord-274127-12x5cc8i.txt txt: ./txt/cord-274127-12x5cc8i.txt summary: Paired specimens of nasopharyngeal swabs and sputum were obtained from 154 subjects, and RNA was extracted and tested for 16 different respiratory viruses using the Anyplex II RV16 Detection kit (Seegene, Seoul, Korea). The detection rates of respiratory viruses from sputum samples were significantly higher than those from nasopharyngeal swabs in adults using real‐time multiplex RT‐PCR. The aim of this study was to compare the detection rates of respiratory viruses in paired nasopharyngeal swabs and sputum samples from adult patients with respiratory symptoms using multiplex real-time RT-PCR. The present study found that the overall detection rate from sputum samples in adults was significantly higher than from nasopharyngeal swabs using multiplex real-time RT-PCR. In conclusion, the detection rates of respiratory viruses from sputum samples are significantly higher than those from nasopharyngeal swabs in adults using multiple real-time RT-PCR. abstract: Diagnostic tests for respiratory viral infections use traditionally either nasopharyngeal washes or swabs. Sputum is representative of the lower respiratory tract but is used rarely for viral testing. The aim of this study was to compare the detection rates of respiratory viruses from nasopharyngeal swabs and sputum using a multiplex real‐time reverse transcription‐polymerase chain reaction (RT‐PCR). Adults who were admitted or presented to the clinics of Gil Medical Center with acute respiratory symptoms were recruited from 1 November 2012 to 31 March 2013. Paired specimens of nasopharyngeal swabs and sputum were obtained from 154 subjects, and RNA was extracted and tested for 16 different respiratory viruses using the Anyplex II RV16 Detection kit (Seegene, Seoul, Korea). The positive rate was 53% (81/154) for nasopharyngeal swabs and 68% (105/154) for sputum (P < 0.001). One hundred thirty‐four viruses were identified for 107 illnesses. Influenza A virus, RSV A, HRV, coronavirus OC43, and adenovirus were detected more frequently in sputum samples than in nasopharyngeal swabs (P < 0.001). Importantly, 12 of 44 (27%) influenza A infections and 11 of 27 (41%) RSV infections were positive in only sputum samples. The detection rates of respiratory viruses from sputum samples were significantly higher than those from nasopharyngeal swabs in adults using real‐time multiplex RT‐PCR. These findings suggest that sputum would benefit for the detection of respiratory viruses by nucleic acid amplification tests (NAATs) in patients who produce sputum. Further studies are needed to establish standardized RNA extraction methods from sputum samples. J. Med. Virol. 86:2122–2127, 2014. © 2014 Wiley Periodicals, Inc. url: https://doi.org/10.1002/jmv.23937 doi: 10.1002/jmv.23937 id: cord-225826-bwghyhqx author: Jiang, Zheng title: Combining Visible Light and Infrared Imaging for Efficient Detection of Respiratory Infections such as COVID-19 on Portable Device date: 2020-04-15 words: 4812.0 sentences: 276.0 pages: flesch: 56.0 cache: ./cache/cord-225826-bwghyhqx.txt txt: ./txt/cord-225826-bwghyhqx.txt summary: In this work, we perform the health screening through the combination of the RGB and thermal videos obtained from the dual-mode camera and deep learning architecture.We first accomplish a respiratory data capture technique for people wearing masks by using face recognition. In this study, we develop a portable and intelligent health screening device that uses thermal imaging to extract respiration data from masked people which is then used to do the health screening classification via deep learning architecture. After extracting breathing data from the video obtained from the thermal camera, a deep learning neural network is performed to work on the classification between healthy and abnormal respiration conditions. First, we combine the face recognition technology with dual-mode imaging to accomplish a respiratory data extraction method for people wearing masks, which is quite essential for current situation. Finally, we use a bidirectional GRU neural network with attention mechanism (BiGRU-AT) model to work on the classification task with the input respiration data. abstract: Coronavirus Disease 2019 (COVID-19) has become a serious global epidemic in the past few months and caused huge loss to human society worldwide. For such a large-scale epidemic, early detection and isolation of potential virus carriers is essential to curb the spread of the epidemic. Recent studies have shown that one important feature of COVID-19 is the abnormal respiratory status caused by viral infections. During the epidemic, many people tend to wear masks to reduce the risk of getting sick. Therefore, in this paper, we propose a portable non-contact method to screen the health condition of people wearing masks through analysis of the respiratory characteristics. The device mainly consists of a FLIR one thermal camera and an Android phone. This may help identify those potential patients of COVID-19 under practical scenarios such as pre-inspection in schools and hospitals. In this work, we perform the health screening through the combination of the RGB and thermal videos obtained from the dual-mode camera and deep learning architecture.We first accomplish a respiratory data capture technique for people wearing masks by using face recognition. Then, a bidirectional GRU neural network with attention mechanism is applied to the respiratory data to obtain the health screening result. The results of validation experiments show that our model can identify the health status on respiratory with the accuracy of 83.7% on the real-world dataset. The abnormal respiratory data and part of normal respiratory data are collected from Ruijin Hospital Affiliated to The Shanghai Jiao Tong University Medical School. Other normal respiratory data are obtained from healthy people around our researchers. This work demonstrates that the proposed portable and intelligent health screening device can be used as a pre-scan method for respiratory infections, which may help fight the current COVID-19 epidemic. url: https://arxiv.org/pdf/2004.06912v1.pdf doi: nan id: cord-304876-txaoz7oh author: Jordan, Paul C title: Nucleosides for the treatment of respiratory RNA virus infections date: 2018-03-21 words: 10962.0 sentences: 654.0 pages: flesch: 46.0 cache: ./cache/cord-304876-txaoz7oh.txt txt: ./txt/cord-304876-txaoz7oh.txt summary: 42 Viral polymerase: An important molecular target for antiviral therapy Nucleoside analogs represent one of the dominant classes of antiviral agents due to their widespread use against the common chronic infections caused by human immunodeficiency virus (HIV), hepatitis B virus, and herpesviruses. 43 After being metabolized by host kinases to their triphosphate form, antiviral nucleotides compete with natural nucleoside triphosphates (NTPs) to bind to the active site of viral polymerases and alter DNA or RNA synthesis. 122 However, the results summarized here indicate that nucleoside analogs targeting the viral RNA polymerase of rhinovirus, EV71, and other enteroviruses have the potential to be efficacious in preclinical animal models, providing a rationale to conduct human studies with safer molecules sharing the same mode of action. Structure and functional analysis of the RNA-and viral phosphoprotein-binding domain of respiratory syncytial virus M2-1 protein abstract: Influenza virus, respiratory syncytial virus, human metapneumovirus, parainfluenza virus, coronaviruses, and rhinoviruses are among the most common viruses causing mild seasonal colds. These RNA viruses can also cause lower respiratory tract infections leading to bronchiolitis and pneumonia. Young children, the elderly, and patients with compromised cardiac, pulmonary, or immune systems are at greatest risk for serious disease associated with these RNA virus respiratory infections. In addition, swine and avian influenza viruses, together with severe acute respiratory syndrome-associated and Middle Eastern respiratory syndrome coronaviruses, represent significant pandemic threats to the general population. In this review, we describe the current medical need resulting from respiratory infections caused by RNA viruses, which justifies drug discovery efforts to identify new therapeutic agents. The RNA polymerase of respiratory viruses represents an attractive target for nucleoside and nucleotide analogs acting as inhibitors of RNA chain synthesis. Here, we present the molecular, biochemical, and structural fundamentals of the polymerase of the four major families of RNA respiratory viruses: Orthomyxoviridae, Pneumoviridae/Paramyxoviridae, Coronaviridae, and Picornaviridae. We summarize past and current efforts to develop nucleoside and nucleotide analogs as antiviral agents against respiratory virus infections. This includes molecules with very broad antiviral spectrum such as ribavirin and T-705 (favipiravir), and others targeting more specifically one or a few virus families. Recent advances in our understanding of the structure(s) and function(s) of respiratory virus polymerases will likely support the discovery and development of novel nucleoside analogs. url: https://www.ncbi.nlm.nih.gov/pubmed/29562753/ doi: 10.1177/2040206618764483 id: cord-329263-o5e2go23 author: Kaplan, Nasser M. title: Molecular epidemiology and disease severity of respiratory syncytial virus in relation to other potential pathogens in children hospitalized with acute respiratory infection in Jordan date: 2007-11-26 words: 4170.0 sentences: 238.0 pages: flesch: 51.0 cache: ./cache/cord-329263-o5e2go23.txt txt: ./txt/cord-329263-o5e2go23.txt summary: title: Molecular epidemiology and disease severity of respiratory syncytial virus in relation to other potential pathogens in children hospitalized with acute respiratory infection in Jordan Human respiratory syncytial virus (HRSV) is the major viral cause of acute lower respiratory tract infections in children. Human respiratory syncytial virus (HRSV) is the leading viral cause of acute respiratory infection in infants and young children in terms of prevalence and effect [Shay et al., 2001] . We also compared the disease severity of HRSV subgroups A and B and their associated genotypes in hospitalized Jordanian children set in the context of other potential respiratory pathogens. A total of 72/326 (22%) patients had no pathogens detected by PCR (Table I) , but 254 (78%) had at least one potential respiratory pathogen detected which consisted of 140/ 326 (43%) HRSV, 116/312 (37%) adenoviruses, 57/312 (18%) HBoV, 36/325 (11%) rhinovirus, 14/312 (4.5%) Chlamydia spp., 8/326 (2.5%) HMPV, 4/325 (1.2%) human coronavirus NL63, and 2/323 (0.6%) influenza A virus. abstract: Human respiratory syncytial virus (HRSV) is the major viral cause of acute lower respiratory tract infections in children. Few data about the molecular epidemiology of respiratory syncytial virus in developing countries, such as Jordan, are available. The frequency and severity of infections caused by HRSV were assessed in hospitalized Jordanian children <5 years of age compared with other potential etiological agents. Overall a potential pathogen was detected in 78% (254/326) of the children. HRSV was detected in 43% (140/326) of the nasopharyngeal aspirates. HRSV was found more frequently during the winter (January/February), being less frequent or negligible by spring (March/April). Analysis of 135 HRSV‐positive strains using restriction fragment length polymorphism showed that 94 (70%) belonged to subgroup A, and 41 (30%) to subgroup B. There were also two cases of mixed genotypic infection. Only four of the six previously described N genotypes were detected with NP4 predominating. There were no associations between subgroup or N‐genogroup and disease severity. HRSV was significantly associated with more severe acute respiratory infection and the median age of children with HRSV was lower than for those without. Next in order of frequency were adenovirus (116/312: 37%), human bocavirus (57/312: 18%), rhinovirus (36/325: 11%), Chlamydia spp. (14/312: 4.5%), human metapneumovirus (8/326: 2.5%), human coronavirus NL63 (4/325: 1.2%), and influenza A virus (2/323: 0.6%). Influenza B; parainfluenza viruses 1–4, human coronavirus HKU1 and Mycoplasma pneumoniae were not detected. J. Med. Virol. 80:168–174, 2008. © 2007 Wiley‐Liss, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/18041044/ doi: 10.1002/jmv.21067 id: cord-262347-ejhz9rra author: Kappes, Matthew A. title: PRRSV structure, replication and recombination: Origin of phenotype and genotype diversity date: 2015-03-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Porcine reproductive and respiratory disease virus (PRRSV) has the intrinsic ability to adapt and evolve. After 25 years of study, this persistent pathogen has continued to frustrate efforts to eliminate infection of herds through vaccination or other elimination strategies. The purpose of this review is to summarize the research on the virion structure, replication and recombination properties of PRRSV that have led to the extraordinary phenotype and genotype diversity that exists worldwide. url: https://doi.org/10.1016/j.virol.2015.02.012 doi: 10.1016/j.virol.2015.02.012 id: cord-330343-p7a8chn4 author: Kelly-Cirino, Cassandra title: An updated roadmap for MERS-CoV research and product development: focus on diagnostics date: 2019-02-01 words: 5812.0 sentences: 274.0 pages: flesch: 40.0 cache: ./cache/cord-330343-p7a8chn4.txt txt: ./txt/cord-330343-p7a8chn4.txt summary: ► Diagnostic research and development (R&D) needs to include point-of-care testing options, syndromic panels for differential diagnosis, a greater understanding of viral and antibody kinetics, improved access to clinical specimens, and establishment of international reference standards. Diagnostics play a central role in the early detection and control of outbreaks and can enable a more nuanced understanding of the disease kinetics and risk factors for the Middle East respiratory syndrome-coronavirus (MERS-CoV), one of the high-priority pathogens identified by the WHO. Diagnostics play a central role in the early detection and control of outbreaks and can enable a more nuanced understanding of the disease kinetics and risk factors for the Middle East respiratory syndrome-coronavirus (MERS-CoV), one of the high-priority pathogens identified by the WHO. In this review we identified sources for molecular and serological diagnostic tests used in MERS-CoV detection, case management and outbreak investigations, as well as surveillance for humans and animals (camels), and summarised the performance of currently available tests, diagnostic needs, and associated challenges for diagnostic test development and implementation. abstract: Diagnostics play a central role in the early detection and control of outbreaks and can enable a more nuanced understanding of the disease kinetics and risk factors for the Middle East respiratory syndrome-coronavirus (MERS-CoV), one of the high-priority pathogens identified by the WHO. In this review we identified sources for molecular and serological diagnostic tests used in MERS-CoV detection, case management and outbreak investigations, as well as surveillance for humans and animals (camels), and summarised the performance of currently available tests, diagnostic needs, and associated challenges for diagnostic test development and implementation. A more detailed understanding of the kinetics of infection of MERS-CoV is needed in order to optimise the use of existing assays. Notably, MERS-CoV point-of-care tests are needed in order to optimise supportive care and to minimise transmission risk. However, for new test development, sourcing clinical material continues to be a major challenge to achieving assay validation. Harmonisation and standardisation of laboratory methods are essential for surveillance and for a rapid and effective international response to emerging diseases. Routine external quality assessment, along with well-characterised and up-to-date proficiency panels, would provide insight into MERS-CoV diagnostic performance worldwide. A defined set of Target Product Profiles for diagnostic technologies will be developed by WHO to address these gaps in MERS-CoV outbreak management. url: https://doi.org/10.1136/bmjgh-2018-001105 doi: 10.1136/bmjgh-2018-001105 id: cord-010368-plpghewn author: Kenmoe, Sebastien title: Association of early viral lower respiratory infections and subsequent development of atopy, a systematic review and meta-analysis of cohort studies date: 2020-04-24 words: 3924.0 sentences: 204.0 pages: flesch: 44.0 cache: ./cache/cord-010368-plpghewn.txt txt: ./txt/cord-010368-plpghewn.txt summary: Although not confirmed in all studies with a symmetric distribution of the 23 confounding factors investigated, the overall analyses showed that there was a relationship between childhood viral LRTI at < 5 years and serum test diagnosed-atopy (OR = 2.0, [95% CI = 1.0–4.1]), allergic rhinoconjunctivitis (OR = 1.7, [95% CI = 1.1–2.9]), hyperreactivity diagnosed by serum tests with food (OR = 5.3, [1.7–16.7]) or inhaled allergens (OR = 4.2, [95% CI = 2.1–8.5]), or furred animals (OR = 0.6, [95% CI = 0.5–0.9]). The purpose of this systematic review and meta-analysis of Long-term sEquelAe of lower Respiratory tract infections iN Early childhood (A LEARNED study) was to investigate the association between viral LRTI at <5 years and the atopy development at > 2 years. Pérez-Yarza in a systematic review including children younger than 3 years with HRSV respiratory infection from 1985 to 2006 also suggested controversial findings about the subsequent risk of allergic sensitization development defined by positive skin or serum tests specific for common allergens [11] . abstract: INTRODUCTION: Existing evidence on the relationship between childhood lower respiratory tract infections (LRTI) and the subsequent atopy development is controversial. We aimed to investigate an association between viral LRTI at <5 years and the development of atopy at > 2 years. METHODS: We conducted a search at Embase, Pubmed, Web of Science, and Global Index Medicus. We collected data from the included articles. We estimated the odds ratio and the 95% confidence intervals with a random effect model. We determined factors associated with atopy development after childhood LRTI using univariate and multivariate meta-regression analyses. We recorded this systematic review at PROSPERO with the number CRD42018116955. RESULTS: We included 24 studies. There was no relationship between viral LRTI at <5 years and skin prick test-diagnosed-atopy (OR = 1.2, [95% CI = 0.7–2.0]), unknown diagnosed-atopy (OR = 0.7, [95% CI = 0.4–1.3]), atopic dermatitis (OR = 1.2, [95% CI = 0.9–1.6]), hyperreactivity to pollen (OR = 0.8, [95% CI = 0.3–2.7]), food (OR = 0.8, [95% CI = 0.3–2.5]), or house dust mite (OR = 1.1, [95% CI = 0.6–2.2]). Although not confirmed in all studies with a symmetric distribution of the 23 confounding factors investigated, the overall analyses showed that there was a relationship between childhood viral LRTI at < 5 years and serum test diagnosed-atopy (OR = 2.0, [95% CI = 1.0–4.1]), allergic rhinoconjunctivitis (OR = 1.7, [95% CI = 1.1–2.9]), hyperreactivity diagnosed by serum tests with food (OR = 5.3, [1.7–16.7]) or inhaled allergens (OR = 4.2, [95% CI = 2.1–8.5]), or furred animals (OR = 0.6, [95% CI = 0.5–0.9]). CONCLUSION: These results suggest that there is no association between viral LRTI at < 5 years and the majority of categories of atopy studied during this work. These results, however, are not confirmed for the remaining categories of atopy and more particularly those diagnosed by serum tests. There is a real need to develop more accurate atopy diagnostic tools. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7182231/ doi: 10.1371/journal.pone.0231816 id: cord-293354-55nawxos author: Kenmoe, Sebastien title: Viral etiology of severe acute respiratory infections in hospitalized children in Cameroon, 2011–2013 date: 2016-05-09 words: 3714.0 sentences: 238.0 pages: flesch: 50.0 cache: ./cache/cord-293354-55nawxos.txt txt: ./txt/cord-293354-55nawxos.txt summary: title: Viral etiology of severe acute respiratory infections in hospitalized children in Cameroon, 2011–2013 This study was conducted to gain new insights into the timeliness of virus circulation and viral etiology among children aged ≤15 years, hospitalized for SARI. hBoV occurred intermittently all over the study period, while the prevalence of remaining viral etiologies was low, ranging from 0 to 5 positive samples per month for each virus, numbers which appeared insufficient to allow for the description of seasonal patterns. Viral etiology of hospitalized acute lower respiratory infections in children under 5 years of age -a systematic review and meta-analysis Viral etiology of acute lower respiratory tract infections in hospitalized young children in Northern Taiwan Frequent detection of viral coinfection in children hospitalized with acute respiratory tract infection using a real-time polymerase chain reaction Epidemiology and seasonality of respiratory viral infections in hospitalized children in Kuala Lumpur, Malaysia: a retrospective study of 27 years abstract: BACKGROUND: Severe acute respiratory illness (SARI) is recognized as an important cause of morbidity, mortality, and hospitalization among children in developing countries. Little is known, however, in tropical countries like Cameroon about the cause and seasonality of respiratory infections, especially in hospitalized settings. Objectives: Our study investigates the viral etiology and seasonality of SARI in hospitalized children in Yaounde, Cameroon. METHODS: Prospective clinic surveillance was conducted to identify hospitalized children aged ≤15 years presenting with respiratory symptoms ≤5‐day duration. Demographic and clinical data, and respiratory specimens were collected. Nasopharyngeal samples were tested for 17 respiratory viruses using a multiplex polymerase chain reaction. The viral distribution and demographic data were statistically analyzed. RESULTS: From September 2011 through September 2013, 347 children aged ≤15 years were enrolled. At least one virus was identified in each of 65·4% children, of which 29·5% were coinfections; 27·3% were positive for human adenovirus (hAdV), 13·2% for human respiratory syncytial virus (hRSV), 11·5% for rhinovirus/enterovirus (RV/EV), 10·6% for human bocavirus (hBoV), 9·8% for influenza virus (Inf), 6·6% for human parainfluenza virus (hPIV), 5·7% for human coronavirus (hCoV), and 2·3% for human metapneumovirus (hMPV). While hRSV showed seasonal patterns, hAdV and RV/EV were detected throughout the year and no evident temporal patterns were observed for the remaining viruses. CONCLUSION: Respiratory viruses were associated with a high burden of hospitalizations among children in Cameroon. Nevertheless, additional studies evaluating asymptomatic Cameroonian children will be important in understanding the relationship between viral carriage and disease. url: https://www.ncbi.nlm.nih.gov/pubmed/27012372/ doi: 10.1111/irv.12391 id: cord-294544-iutcduix author: Kesson, Alison M. title: Respiratory virus infections date: 2007-09-06 words: 6057.0 sentences: 297.0 pages: flesch: 38.0 cache: ./cache/cord-294544-iutcduix.txt txt: ./txt/cord-294544-iutcduix.txt summary: 1 This has enabled the identification of many viruses, including those commonly causing respiratory infections -influenza, RSV, PIV 1-4, adenoviruses, measles, enteroviruses, rhinoviruses, VZV, CMV and HSV. 3 After 24-72 h of culture, using pooled or single fluorescein isothiocyanate (FITC)-labelled monoclonal antibodies directed against influenza A and B, RSV, parainfluenza 1-3 and adenoviruses, rapid identification of a respiratory virus infection can be established. Diagnosis of rhinovirus infection rarely requires laboratory testing but virus isolation, detection of viral RNA by RT-PCR, antigen detection by DIF in cells from respiratory secretions or detection of a fourfold rise in antibody titres by neutralization test or EIA can be performed if required. Diagnosis of the specific cause of an acute pneumonia due to a particular viral agent is complicated by difficulty in obtaining appropriate lower respiratory tract samples for culture and in isolating or detecting certain pathogens, and additionally by the frequent asymptomatic shedding of some viruses, e.g. herpes simplex virus or adenoviruses. abstract: The respiratory tract is a frequent site of infection with a wide range of viruses. Each family of viruses can cause differing clinical syndromes depending on the age of the patient and the immune response. As a corollary, different clinical syndromes can be caused by different families of viruses. url: https://www.sciencedirect.com/science/article/pii/S1526054207000668 doi: 10.1016/j.prrv.2007.07.003 id: cord-349226-xzlc1pni author: Khatiwada, Saroj title: Lung microbiome and coronavirus disease 2019 (COVID-19): possible link and implications date: 2020-08-05 words: 4312.0 sentences: 231.0 pages: flesch: 35.0 cache: ./cache/cord-349226-xzlc1pni.txt txt: ./txt/cord-349226-xzlc1pni.txt summary: To date there is no direct evidence from human or animal studies on the role of lung microbiome in modifying COVID-19 disease; however, related studies support that microbiome can play an essential role in developing immunity against viral infections. The COVID-19 disease is caused by a virus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which emerged in Wuhan, China at the end of 2019 [4] . The COVID-19 disease begins with the invasion of lungs by SARS-CoV-2 virus, and the major complications that develop subsequently are related to lung infection and immune response generation, therefore, lung microbiome might play an important role from initiation to the progression of this disease [16] . The SARS-CoV-2 viral infection occurs amid the local environment of diverse microbiota; therefore, it is apparent that lung microbiota can have an impact on the initiation, development, and progression of the COVID-19 disease. abstract: Coronavirus disease 2019 (COVID-19) is a rapidly emerging disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The disease begins as an infection of lungs, which is self-limiting in the majority of infections; however, some develop severe respiratory distress and organ failures. Lung microbiome, though neglected previously have received interest recently because of its association with several respiratory diseases and immunity. Lung microbiome can modify the risk and consequences of COVID-19 disease by activating an innate and adaptive immune response. In this review, we examine the current evidence on COVID-19 disease and lung microbiome, and how lung microbiome can affect SARS-CoV-2 infection and the outcomes of this disease. To date there is no direct evidence from human or animal studies on the role of lung microbiome in modifying COVID-19 disease; however, related studies support that microbiome can play an essential role in developing immunity against viral infections. Future studies need to be undertaken to find the relationship between lung microbiome and COVID-19 disease. url: https://doi.org/10.1016/j.humic.2020.100073 doi: 10.1016/j.humic.2020.100073 id: cord-332361-pdoln3nr author: Khor, Chee-Sieng title: Epidemiology and seasonality of respiratory viral infections in hospitalized children in Kuala Lumpur, Malaysia: a retrospective study of 27 years date: 2012-03-20 words: 3806.0 sentences: 222.0 pages: flesch: 45.0 cache: ./cache/cord-332361-pdoln3nr.txt txt: ./txt/cord-332361-pdoln3nr.txt summary: title: Epidemiology and seasonality of respiratory viral infections in hospitalized children in Kuala Lumpur, Malaysia: a retrospective study of 27 years CONCLUSION: Viral RTIs, particularly due to RSV, are commonly detected in respiratory samples from hospitalized children in Kuala Lumpur, Malaysia. In this study, we describe etiological agents, demographic details of patients, and seasonality (including association with meteorological factors) due to viral RTIs in a teaching hospital in Kuala Lumpur, over the last 27 years. Our findings support a previous local study carried out over a year, which showed that RSV was the most commonly detected respiratory virus, followed by parainfluenza viruses, influenza viruses and adenovirus [7] . Respiratory viral infections due to RSV, parainfluenza viruses, influenza viruses and adenovirus are significant causes of morbidity in hospitalized children in Kuala Lumpur, and are likely to be underdiagnosed. abstract: BACKGROUND: Viral respiratory tract infections (RTI) are relatively understudied in Southeast Asian tropical countries. In temperate countries, seasonal activity of respiratory viruses has been reported, particularly in association with temperature, while inconsistent correlation of respiratory viral activity with humidity and rain is found in tropical countries. A retrospective study was performed from 1982-2008 to investigate the viral etiology of children (≤ 5 years old) admitted with RTI in a tertiary hospital in Kuala Lumpur, Malaysia. METHODS: A total of 10269 respiratory samples from all children ≤ 5 years old received at the hospital's diagnostic virology laboratory between 1982-2008 were included in the study. Immunofluorescence staining (for respiratory syncytial virus (RSV), influenza A and B, parainfluenza types 1-3, and adenovirus) and virus isolation were performed. The yearly hospitalization rates and annual patterns of laboratory-confirmed viral RTIs were determined. Univariate ANOVA was used to analyse the demographic parameters of cases. Multiple regression and Spearman's rank correlation were used to analyse the correlation between RSV cases and meteorological parameters. RESULTS: A total of 2708 cases were laboratory-confirmed using immunofluorescence assays and viral cultures, with the most commonly detected being RSV (1913, 70.6%), parainfluenza viruses (357, 13.2%), influenza viruses (297, 11.0%), and adenovirus (141, 5.2%). Children infected with RSV were significantly younger, and children infected with influenza viruses were significantly older. The four main viruses caused disease throughout the year, with a seasonal peak observed for RSV in September-December. Monthly RSV cases were directly correlated with rain days, and inversely correlated with relative humidity and temperature. CONCLUSION: Viral RTIs, particularly due to RSV, are commonly detected in respiratory samples from hospitalized children in Kuala Lumpur, Malaysia. As in temperate countries, RSV infection in tropical Malaysia also caused seasonal yearly epidemics, and this has implications for prophylaxis and vaccination programmes. url: https://www.ncbi.nlm.nih.gov/pubmed/22429933/ doi: 10.1186/1471-2431-12-32 id: cord-329306-p5wmqmvj author: Kim, Kiwook title: Rhinovirus Associated Severe Respiratory Failure in Immunocompetent Adult Patient date: 2014-09-30 words: 1015.0 sentences: 64.0 pages: flesch: 38.0 cache: ./cache/cord-329306-p5wmqmvj.txt txt: ./txt/cord-329306-p5wmqmvj.txt summary: Rhinovirus infection is typically associated with the common cold and has rarely been reported as a cause of severe pneumonia in immunocompetent adults. Rhinovirus infection can extend to lower respiratory tract in children [4] [5] [6] or immunocompromised hosts 7, 8 , but is generally not concerned as singular cause of severe pneumonia, especially in immunocompetent adults. Although technical advances have allowed for increased detection of viral pneumonia, viral infections other than influenza are generally not considered as causes of severe respiratory tract infection in immunocompetent hosts, because viral clearance usually occurs rapidly in healthy individuals. Therefore, it is still believed that severe viral pneumonia caused by frequently exposed rhinovirus could hardly occurs in immunocompetent adults. On the contrary, our relatively young immunocompetent patient suffered severe rhinovirus pneumonia without bacterial co-infection, which was confirmed by BAL fluid analysis, and not by the nasopharyngeal specimen. Rhinovirus associated with severe lower respiratory tract infections in children abstract: Rhinovirus infection is typically associated with the common cold and has rarely been reported as a cause of severe pneumonia in immunocompetent adults. A 55-year-old previous healthy woman, who consumed half a bottle of alcohol daily, presented with respiratory failure after one week of upper respiratory infection symptoms. Radiography revealed bilateral, diffuse ground glass opacity with patchy consolidation in the whole lung field; bronchoalveolar lavage fluid analysis indicated that rhinovirus was the causative organism. After five days of conservative support, the symptoms and radiographic findings began to improve. We report this rare case of rhinovirus pneumonia in an otherwise healthy host along with a review of references. url: https://doi.org/10.4046/trd.2014.77.3.132 doi: 10.4046/trd.2014.77.3.132 id: cord-331520-o9e4qqn4 author: Kistler, Christine E. title: The Winter Respiratory Viral Season During the COVID-19 Pandemic date: 2020-10-26 words: 2724.0 sentences: 168.0 pages: flesch: 44.0 cache: ./cache/cord-331520-o9e4qqn4.txt txt: ./txt/cord-331520-o9e4qqn4.txt summary: The winter respiratory virus season always poses challenges for long-term care settings; this winter, SARS-CoV-2 will compound the usual viral infection challenges. This special article discusses unique considerations that COVID-19 brings to the health and well-being of residents and staff in nursing homes and other long-term care settings this winter. Before the COVID-19 pandemic, influenza was the most concerning viral respiratory infection 27 for nursing home (NH) residents, with outbreaks requiring both treatment and prophylaxis, and 28 even causing some buildings to close to outsiders for brief periods of time. In 39 this special article, we discuss unique challenges that COVID-19 will bring to the health and 40 well-being of residents and staff in long-term care settings this winter. The winter respiratory virus season always poses challenges for long-term care settings, and 307 those challenges will be exacerbated with the second wave of COVID-19; as such, they present 308 numerous implications for practice, policy, and research. abstract: The winter respiratory virus season always poses challenges for long-term care settings; this winter, SARS-CoV-2 will compound the usual viral infection challenges. This special article discusses unique considerations that COVID-19 brings to the health and well-being of residents and staff in nursing homes and other long-term care settings this winter. Specific topics include preventing the spread of respiratory viruses, promoting immunization, and the diagnosis and treatment of suspected respiratory infection. Policy-relevant issues are discussed, including whether to mandate influenza immunization for staff, the availability and use of personal protective equipment, supporting staff if they become ill, and the distribution of a COVID-19 vaccine when it becomes available. Research is applicable in all of these areas, including regarding the use of emerging electronic decision support tools. If there is a positive side to this year’s winter respiratory virus season, it is that staff, residents, family members, and clinicians will be especially vigilant about potential infection. url: https://api.elsevier.com/content/article/pii/S1525861020309221 doi: 10.1016/j.jamda.2020.10.030 id: cord-349560-8n65rgfz author: Kleines, Michael title: WU Polyomavirus (WUPyV): A Recently Detected Virus Causing Respiratory Disease? date: 2009-11-04 words: 4053.0 sentences: 230.0 pages: flesch: 45.0 cache: ./cache/cord-349560-8n65rgfz.txt txt: ./txt/cord-349560-8n65rgfz.txt summary: The WU polyomavirus (WUPyV) is a novel member of the family Polyomaviridae recently detected in respiratory tract specimens by shotgun sequencing. Creer and co-workers [1] identified at least one potential pathogen in 69% of specimens from adults suffering from lower respiratory tract infections (LRTI, 63% contained viruses, 26% contained bacteria) still leaving a significant diagnostic gap to be filled with so far unidentified pathogenic microorganisms. For this reason, detection of virus-specific antibodies by complement fixation assays, enzyme linked immunosorbent assays (ELISA), or immunofluorescence assays (IFA), all of which are available for established respiratory viruses, is inappropriate for the identification of the etiologic agent causing an acute respiratory tract infection, but useful for retrospective or epidemiological studies. Following the discovery of WUPyV in Australia, the virus was detected in specimens from patients with respiratory tract disease on all continents suggesting a worldwide distribution [10, [29] [30] [31] . abstract: The WU polyomavirus (WUPyV) is a novel member of the family Polyomaviridae recently detected in respiratory tract specimens by shotgun sequencing. Intriguingly, viral genome has been detected in 0.4% to 11.5% of respiratory tract specimens from children with respiratory disease. The levels of co-infection with established respiratory viruses were in the range between 30.8% and 91.7%. Moreover, some studies report detection of WUPyV in stool or serum. So far, WUPyV infections can not be distinguished from other viral infections by means of clinical symptoms. Respiratory tract disease like pneumonia or bronchitis is frequently observed in patients harbouring WUPyV. Detection of viremia suggests systemic infections. However, the available data do not prove WUPyV to be a human pathogen. Further investigations are necessary. url: https://doi.org/10.3390/v1030678 doi: 10.3390/v1030678 id: cord-312615-q333qgps author: Knobbe, Rebecca B title: Pathogens Causing Respiratory Tract Infections in Children Less Than 5 Years of Age in Senegal date: 2019-12-30 words: 4466.0 sentences: 284.0 pages: flesch: 51.0 cache: ./cache/cord-312615-q333qgps.txt txt: ./txt/cord-312615-q333qgps.txt summary: The aim of this study was to identity the various respiratory pathogens causing acute respiratory tract infections in children below 5 years of age visiting a sub-urban primary care clinic in Senegal. CONCLUSIONS: This case-control study in a primary care setting in sub-Saharan Africa found influenza virus A and B, RSV, and S pneumoniae to be the main causes of acute respiratory tract infections in children below 5 years of age. Therefore, the aim of this case-control study was to investigate the prevalence of the different viruses and bacteria colonizing the airways and their association with the occurrence of ARTIs and severity of disease in children less than 5 years of age, visiting a sub-urban primary care clinic in Dakar, Senegal. This case-control study investigates the prevalence of the different viruses and bacteria colonizing the airways and their 6 Microbiology Insights association with the occurrence of ARTIs in children visiting a sub-urban primary care clinic in Senegal. abstract: INTRODUCTION: While acute respiratory tract infections are the main cause of paediatric mortality and morbidity worldwide, pathogen patterns shift due to factors such as hygiene, vaccinations, and antibiotic resistance. Knowledge about current cause of respiratory infections is lacking, particularly in low- and middle-income countries. The aim of this study was to identity the various respiratory pathogens causing acute respiratory tract infections in children below 5 years of age visiting a sub-urban primary care clinic in Senegal. METHODS: A case-control study was performed in September and October 2018. Oropharyngeal swabs were collected from cases; infants with fever and respiratory symptoms, and controls; children involved in the vaccination programme. Viral identification was conducted by polymerase chain reaction for 21 different viruses; bacteria were identified by culture studies. Associations between microorganisms, acute respiratory infection and severity of disease were calculated by multivariate regression adjusting for confounders such as age, sex, and living area. RESULTS: Overall, 102 cases and 96 controls were included. Microorganisms were detected in 90.1% of cases and 53.7% of controls (P < .001). Influenza virus A (including H1N1), influenza virus B, respiratory syncytial virus (RSV), and Streptococcus pneumoniae were independently associated with acute respiratory tract infections. Co-detection of two or more pathogens was present in 49.5% of cases; 31.7% of cases had a pneumonia and 90.2% was treated with antibiotics. CONCLUSIONS: This case-control study in a primary care setting in sub-Saharan Africa found influenza virus A and B, RSV, and S pneumoniae to be the main causes of acute respiratory tract infections in children below 5 years of age. We recommend evaluation of antibiotics prescription behaviour in this setting. url: https://doi.org/10.1177/1178636119890885 doi: 10.1177/1178636119890885 id: cord-270258-9vgpphiu author: Ko, Jae-Hoon title: Predictive factors for pneumonia development and progression to respiratory failure in MERS-CoV infected patients date: 2016-08-09 words: 3460.0 sentences: 171.0 pages: flesch: 43.0 cache: ./cache/cord-270258-9vgpphiu.txt txt: ./txt/cord-270258-9vgpphiu.txt summary: To identify factors which can predict pneumonia development and progression to respiratory failure at the early course of the disease, we evaluated MERS-CoV infected patients managed in a tertiary care center during the 2015 MERS outbreak in Korea. To identify factors which can predict pneumonia development and progression to respiratory failure at the early course of the disease, we reviewed the electronic medical records of who were diagnosed with MERS-CoV infection and admitted at Samsung Medical Center, a 1950 tertiary care university hospital which managed the largest number of MERS-CoV infected patients as a single center during the 2015 Korean MERS outbreak. The present analysis of predictive factors for pneumonia development and progression to respiratory failure using variables obtained by day 3 of symptom onset could be conducted owing to the observation of entire clinical course of the disease from the exposure to MERS-CoV. abstract: BACKGROUND: After the 2015 Middle East respiratory syndrome (MERS) outbreak in Korea, prediction of pneumonia development and progression to respiratory failure was emphasized in control of MERS outbreak. METHODS: MERS-CoV infected patients who were managed in a tertiary care center during the 2015 Korean MERS outbreak were reviewed. To analyze predictive factors for pneumonia development and progression to respiratory failure, we evaluated clinical variables measured within three days from symptom onset. RESULTS: A total of 45 patients were included in the study: 13 patients (28.9%) did not develop pneumonia, 19 developed pneumonia without respiratory failure (42.2%), and 13 progressed to respiratory failures (28.9%). The identified predictive factors for pneumonia development included age ≥45 years, fever ≥37.5 °C, thrombocytopenia, lymphopenia, CRP ≥ 2 mg/dL, and a threshold cycle value of PCR less than 28.5. For respiratory failure, the indicators included male, hypertension, low albumin concentration, thrombocytopenia, lymphopenia, and CRP ≥ 4 mg/dL (all P < 0.05). With ≥ two predictive factors for pneumonia development, 100% of patients developed pneumonia. Patients lacking the predictive factors did not progress to respiratory failure. CONCLUSION: For successful control of MERS outbreak, MERS-CoV infected patients with ≥ two predictive factors should be intensively managed from the initial presentation. url: https://api.elsevier.com/content/article/pii/S0163445316302092 doi: 10.1016/j.jinf.2016.08.005 id: cord-151024-qe7c2uks author: Koca, Caglar title: Molecular Communication Theoretical Modeling and Analysis of SARS-CoV2 Transmission in Human Respiratory System date: 2020-11-07 words: 5622.0 sentences: 353.0 pages: flesch: 56.0 cache: ./cache/cord-151024-qe7c2uks.txt txt: ./txt/cord-151024-qe7c2uks.txt summary: We further provide the impulse response of SARS-CoV2-ACE2 receptor binding event to determine the proportion of the virus population reaching different regions of the respiratory tract. These results are especially important to understand the effect of SARS-CoV2 on the different human populations at different ages who have different mucus flow rates and ACE2 receptor concentrations in the different regions of the respiratory tract. • Determining impulse response of SARS-CoV2 infection process for the first time in literature • Calculating ACE2 receptor densities in the different regions of the respiratory tract: Based on the available data on surface parameters, we calculate ACE2 receptor density crudely. Due to the cylindrical symmetry assumption, we can make a longitudinal Upon entering the mucus and periciliary layer, viruses use their viral S-spike proteins to bind to ACE2 receptors on host cell surfaces [43] . abstract: Severe Acute Respiratory Syndrome-CoronaVirus 2 (SARS-CoV2) caused the ongoing pandemic. This pandemic devastated the world by killing more than a million people, as of October 2020. It is imperative to understand the transmission dynamics of SARS-CoV2 so that novel and interdisciplinary prevention, diagnostic, and therapeutic techniques could be developed. In this work, we model and analyze the transmission of SARS-CoV2 through the human respiratory tract from a molecular communication perspective. We consider that virus diffusion occurs in the mucus layer so that the shape of the tract does not have a significant effect on the transmission. Hence, this model reduces the inherent complexity of the human respiratory system. We further provide the impulse response of SARS-CoV2-ACE2 receptor binding event to determine the proportion of the virus population reaching different regions of the respiratory tract. Our findings confirm the results in the experimental literature on higher mucus flow rate causing virus migration to the lower respiratory tract. These results are especially important to understand the effect of SARS-CoV2 on the different human populations at different ages who have different mucus flow rates and ACE2 receptor concentrations in the different regions of the respiratory tract. url: https://arxiv.org/pdf/2011.05154v1.pdf doi: nan id: cord-324843-r43u7sld author: Kockuzu, Esra title: Comprehensive Analysis of Severe Viral Infections of Respiratory Tract admitted to PICUs during the Winter Season in Turkey date: 2019-06-17 words: 3747.0 sentences: 239.0 pages: flesch: 51.0 cache: ./cache/cord-324843-r43u7sld.txt txt: ./txt/cord-324843-r43u7sld.txt summary: OBJECTIVES: To analyze the course of seasonal viral infections of respiratory tract in patients hospitalized in pediatric intensive care units (PICU) of 16 centers in Turkey. The critical pH value related with mortality was ≤7.10, and critical PCO(2) ≥60 mm Hg. CONCLUSION: Our findings demonstrate that patients with neurological symptoms, tachycardia, hypoxia, hypotension, acidosis, impaired liver, and renal function at the time of admission exhibit more severe mortal progressions. By presenting the analyzed data of 302 PICU admissions, current study reveals severity of viral respiratory tract infections and release tips for handling them. 7 This retrospective observational study was conducted in order to analyze the course of seasonal viral infections of respiratory tract in patients hospitalized in PICUs of 16 centers representing the whole country. Viral respiratory tract infections constitute significant proportion of patients admitted to PICUs in winter, and these patients require advanced intensive care support with high mortality and morbidity rates. abstract: OBJECTIVES: To analyze the course of seasonal viral infections of respiratory tract in patients hospitalized in pediatric intensive care units (PICU) of 16 centers in Turkey. MATERIALS AND METHODS: It is a retrospective, observational, and multicenter study conducted in 16 tertiary PICUs in Turkey includes a total of 302 children with viral cause in the nasal swab which required PICU admission with no interventions. RESULTS: Median age of patients was 12 months. Respiratory syncytial virus (RSV) was more common in patients over one year of age whereas influenza, human Bocavirus in patients above a year of age was more common (p <0.05). Clinical presentations influencing mortality were neurologic symptoms, tachycardia, hypoxia, hypotension, elevated lactate, and acidosis. The critical pH value related with mortality was ≤7.10, and critical PCO(2) ≥60 mm Hg. CONCLUSION: Our findings demonstrate that patients with neurological symptoms, tachycardia, hypoxia, hypotension, acidosis, impaired liver, and renal function at the time of admission exhibit more severe mortal progressions. Presence of acidosis and multiorgan failure was found to be predictor for mortality. Knowledge of clinical presentation and age-related variations among seasonal viruses may give a clue about severe course and prognosis. By presenting the analyzed data of 302 PICU admissions, current study reveals severity of viral respiratory tract infections and release tips for handling them. HOW TO CITE THIS ARTICLE: Kockuzu E, Bayrakcı B, Kesici S, Cıtak A, Karapınar K, Emeksiz S, et al. Comprehensive Analysis of Severe Viral Infections of Respiratory Tract admitted to PICUs During the Winter Season in Turkey. Indian J Crit Care Med 2019;23(6):263–269. url: https://doi.org/10.5005/jp-journals-10071-23177 doi: 10.5005/jp-journals-10071-23177 id: cord-333026-9f6ecg30 author: Kompanikova, J. title: Microbiologic Methods in the Diagnostics of Upper Respiratory Tract Pathogens date: 2017-03-03 words: 1784.0 sentences: 100.0 pages: flesch: 49.0 cache: ./cache/cord-333026-9f6ecg30.txt txt: ./txt/cord-333026-9f6ecg30.txt summary: Blood samples were simultaneously examined by the enzyme-linked immunosorbent assay (ELISA) and by the FilmArray Respiratory Panel for eight different pathogens in a total of 15 tests performed in nasopharyngeal swabs. Nonetheless, since most repiratory tract infections are viral in origin and there is no treatment available, the diagnosis provided by the FilmArray Panel does not provide any additional clinical benefit and thus should be used only whenever necessary on the individual basis. This method allows for identification of 21 different respiratory pathogens from a nasopharyngeal swab, 18 of viral etiology and three of bacterial origin (Idaho Technology 2007). The laboratory costs to run one examination with different methods showed that the FilmArray multiplex PCR respiratory panel is more expensive than the ELISA, HIT, and the cultivation. Since most URIs are viral in origin and there is no treatment available, the diagnosis provided by the FilmArray panel is not always necessary and the method should be used on an individual basis when clinically justified. abstract: Upper respiratory tract infection (URI) is a nonspecific term used to describe acute infections involving the nose, paranasal sinuses, pharynx, and larynx above the vocal cords. The aim of this study was to provide a summary of the most common pathogens of URI and to compare advantages and disadvantages of traditional and new rapid microbiological tests used to identify them. Blood samples were simultaneously examined by the enzyme-linked immunosorbent assay (ELISA) and by the FilmArray Respiratory Panel for eight different pathogens in a total of 15 tests performed in nasopharyngeal swabs. The ELISA method is unable to identify the pathologic agent until the host’s immune system elicits a response. The method is readily available in many laboratories at a low cost, which puts less strain on economic resources. The FilmArray(®) Panel, on the other hand, is more expensive, but it is fast and exact in the identification of a broad spectrum etiologic agents. Nonetheless, since most repiratory tract infections are viral in origin and there is no treatment available, the diagnosis provided by the FilmArray Panel does not provide any additional clinical benefit and thus should be used only whenever necessary on the individual basis. url: https://doi.org/10.1007/5584_2017_10 doi: 10.1007/5584_2017_10 id: cord-354918-129inbwq author: Kotsimbos, T. title: Respiratory infectious disease: complacency with empiricism in the age of molecular science. We can do better! date: 2007-06-04 words: 2102.0 sentences: 100.0 pages: flesch: 32.0 cache: ./cache/cord-354918-129inbwq.txt txt: ./txt/cord-354918-129inbwq.txt summary: A few home truths (i) Viral infections are an important cause of respiratory infection and yet a specific diagnosis is rarely made, (ii) few antiviral therapies exist and when they do -such as in the case of influenza -they are either underused or overused because of diagnostic inefficiencies, (iii) our approach to using antibacterial agents is guided by ''what should reasonably be covered'' or ''what organisms are being missed'' rather than a treatment regimen targeted for a particular organism, (iv) in association with diagnostic uncertainty, we do not make sufficient allowances for immunocompromised states or overexuberant immune responses to respiratory infectious disease (RID) and (v) current antibiotic guidelines encourage an approach of increasingly covering all potential organisms depending on the severity of illness. Our current reliance on empirical antibiotic strategies to cover ''likely bacterial pathogens'' as set out in numerous guidelines is unavoidable in the short term given the current diagnostic limitations for respiratory infection syndromes. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/17547721/ doi: 10.1111/j.1445-5994.2007.01424.x id: cord-333355-ykmp4ven author: Kuchar, E. title: Pathophysiology of Clinical Symptoms in Acute Viral Respiratory Tract Infections date: 2015-03-19 words: 6665.0 sentences: 370.0 pages: flesch: 46.0 cache: ./cache/cord-333355-ykmp4ven.txt txt: ./txt/cord-333355-ykmp4ven.txt summary: In this article we discuss the pathophysiology of common symptoms of acute viral respiratory infections (e.g., sneezing, nasal discharge, sore throat, cough, muscle pains, malaise, and mood changes). The development of sneezing before coughing in patients with a common cold may be partly explained by the involvement of the upper airways first and the infection subsequent spread to the lower respiratory tract (Eccles 2005) . We focused on the most significant symptoms of acute viral respiratory infections: sneezing, nasal discharge and obstruction, sore throat, coughing, muscle pains, malaise and mood changes, fever, and febrile seizures in children. Macrophages play a key role in triggering an acute phase response with the production of cytokines (Beutler 2003) , while the release of proinflammatory cytokines and other mediators cause upper respiratory tract infection symptoms (Eccles 2000a, b) . abstract: In this article we discuss the pathophysiology of common symptoms of acute viral respiratory infections (e.g., sneezing, nasal discharge, sore throat, cough, muscle pains, malaise, and mood changes). Since clinical symptoms are not sufficient to determine the etiology of viral respiratory tract infections, we believe that the host defense mechanisms are critical for the symptomatology. Consequently, this review of literature is focused on the pathophysiology of respiratory symptoms regardless of their etiology. We assume that despite a high prevalence of symptoms of respiratory infection, their pathogenesis is not widely known. A better understanding of the symptoms’ pathogenesis could improve the quality of care for patients with respiratory tract infections. url: https://doi.org/10.1007/5584_2015_110 doi: 10.1007/5584_2015_110 id: cord-129086-ra2njvcz author: Kumar, Sanjay title: The perspective of fluid flow behavior of respiratory droplets and aerosols through the facemasks in context of SARS-CoV-2 date: 2020-10-10 words: 8130.0 sentences: 466.0 pages: flesch: 52.0 cache: ./cache/cord-129086-ra2njvcz.txt txt: ./txt/cord-129086-ra2njvcz.txt summary: However, in more recent times, the focus has shifted towards the theoretical investigations of fluid flow mechanisms involved in the virus-laden particles prevention by facemasks. 44 While these experimental studies are essential for the broad characterization and design evaluation of respiratory facemasks, further theoretical and numerical methods and algorithm-based investigations provide a better insight into the facemask''s fluid flow dynamics and the droplet leakage through the facemask openings. The computational fluid flow models have shown their potentials in an improved prediction of the spreading of respiratory virus-laden droplets and aerosols, sensitive to the ambient environment, and crucial to the public health responses. The results revealed that the small droplets travel a larger distance and remain suspended in the air for a longer time under the influence of airflow, supporting the mandatory use of facemasks to prevent the virus. In recent years, the respiratory droplets flow behavior through the facemasks has typically well-predicted using the computational fluid dynamics (CFD) techniques. abstract: In the unfortunate event of current ongoing pandemic COVID-19, where vaccination development is still at the initial stage, several preventive control measures such as social distancing, hand-hygiene, and personal protective equipment have been recommended by health professionals and organizations. Among them, the safe wearing of facemasks has played a vital role in reducing the likelihood and severity of infectious respiratory disease transmission. The reported research in facemasks has covered many of their material types, fabrication techniques, mechanism characterization, and application aspects. However, in more recent times, the focus has shifted towards the theoretical investigations of fluid flow mechanisms involved in the virus-laden particles prevention by facemasks. This exciting research domain aims to address the complex fluid transport that led to designing a facemask with a better performance. This review paper discusses the recent updates on fluid flow dynamics through the facemasks. Key design aspects such as thermal comfort and flow resistance are discussed. Furthermore, the recent progress in the investigations on the efficacy of facemasks for prevention of COVID 19 spread and the impact of wearing facemasks are presented. Finally, the potential research directions for analyzing the fluid flow behavior are highlighted. url: https://arxiv.org/pdf/2010.06385v1.pdf doi: nan id: cord-347465-yu6oj30v author: Kurskaya, Olga title: Viral etiology of acute respiratory infections in hospitalized children in Novosibirsk City, Russia (2013 – 2017) date: 2018-09-18 words: 3383.0 sentences: 194.0 pages: flesch: 45.0 cache: ./cache/cord-347465-yu6oj30v.txt txt: ./txt/cord-347465-yu6oj30v.txt summary: METHODS: We tested nasal and throat swabs of 1560 children with upper or lower respiratory infection for main respiratory viruses (influenza viruses A and B, parainfluenza virus types 1–4, respiratory syncytial virus, metapneumovirus, four human coronaviruses, rhinovirus, adenovirus and bocavirus) using a RT-PCR Kit. RESULTS: We detected 1128 (72.3%) samples were positive for at least one virus. We detected significant decrease of the respiratory syncytial virus-infection incidence in children with increasing age, while the reverse relationship was observed for influenza viruses. We detected significant decrease of the respiratory syncytial virus-infection incidence in children with increasing age, while the reverse relationship was observed for influenza viruses. In conclusion, in our study we investigated the etiological structure of acute respiratory viral infections in hospitalized children in Novosibirsk, Russia, and evaluated age and seasonal distribution of the various respiratory viruses. abstract: BACKGROUND: Acute respiratory infections (ARIs) cause a considerable morbidity and mortality worldwide especially in children. However, there are few studies of the etiological structure of ARIs in Russia. In this work, we analyzed the etiology of ARIs in children (0–15 years old) admitted to Novosibirsk Children’s Municipal Clinical Hospital in 2013–2017. METHODS: We tested nasal and throat swabs of 1560 children with upper or lower respiratory infection for main respiratory viruses (influenza viruses A and B, parainfluenza virus types 1–4, respiratory syncytial virus, metapneumovirus, four human coronaviruses, rhinovirus, adenovirus and bocavirus) using a RT-PCR Kit. RESULTS: We detected 1128 (72.3%) samples were positive for at least one virus. The most frequently detected pathogens were respiratory syncytial virus (358/1560, 23.0%), influenza virus (344/1560, 22.1%), and rhinovirus (235/1560, 15.1%). Viral co-infections were found in 163 out of the 1128 (14.5%) positive samples. We detected significant decrease of the respiratory syncytial virus-infection incidence in children with increasing age, while the reverse relationship was observed for influenza viruses. CONCLUSIONS: We evaluated the distribution of respiratory viruses in children with ARIs and showed the prevalence of respiratory syncytial virus and influenza virus in the etiological structure of infections. This study is important for the improvement and optimization of diagnostic tactics, control and prevention of the respiratory viral infections. url: https://www.ncbi.nlm.nih.gov/pubmed/30226876/ doi: 10.1371/journal.pone.0200117 id: cord-263764-2ewz8ok4 author: Kutter, Jasmin S title: Transmission routes of respiratory viruses among humans date: 2018-01-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Respiratory tract infections can be caused by a wide variety of viruses. Airborne transmission via droplets and aerosols enables some of these viruses to spread efficiently among humans, causing outbreaks that are difficult to control. Many outbreaks have been investigated retrospectively to study the possible routes of inter-human virus transmission. The results of these studies are often inconclusive and at the same time data from controlled experiments is sparse. Therefore, fundamental knowledge on transmission routes that could be used to improve intervention strategies is still missing. We here present an overview of the available data from experimental and observational studies on the transmission routes of respiratory viruses between humans, identify knowledge gaps, and discuss how the available knowledge is currently implemented in isolation guidelines in health care settings. url: https://doi.org/10.1016/j.coviro.2018.01.001 doi: 10.1016/j.coviro.2018.01.001 id: cord-335055-gzuug3p5 author: Kwiyolecha, Elizabeth title: Patterns of viral pathogens causing upper respiratory tract infections among symptomatic children in Mwanza, Tanzania date: 2020-10-28 words: 3311.0 sentences: 196.0 pages: flesch: 45.0 cache: ./cache/cord-335055-gzuug3p5.txt txt: ./txt/cord-335055-gzuug3p5.txt summary: title: Patterns of viral pathogens causing upper respiratory tract infections among symptomatic children in Mwanza, Tanzania Therefore, there is a paramount need to establish information on the common etiologies of RTIs in Tanzania, the information that can stimulate further studies and possible control interventions including introduction of cheap and reliable methods to detect these pathogens in clinical settings. In addition due to increased use of antibiotic without a support of a diagnostic test in the treatment of URTI as observed in number of previous studies [11] [12] [13] , make the availability of epidemiological data on the patterns of etiology of URTI of paramount important. A cross sectional hospital based study involving 339 children aged 1-59 months presenting with RTI symptoms was conducted from October 2017 to February 2018 in the city of Mwanza, Tanzania. A previous study 33 , documented Rhinovirus to cause up to 25-85% of the upper respiratory tract infections. abstract: Upper-respiratory tract infections (URTI) are the leading causes of childhood morbidities. This study investigated etiologies and patterns of URTI among children in Mwanza, Tanzania. A cross-sectional study involving 339 children was conducted between October-2017 and February-2018. Children with features suggestive of URTI such as nasal congestion, dry cough, painful swallowing and nasal discharge with/without fever were enrolled. Pathogens were detected from nasopharyngeal and ear-swabs by multiplex-PCR and culture respectively. Full blood count and C-reactive protein analysis were also done. The median age was 16 (IQR: 8–34) months. Majority (82.3%) had fever and nasal-congestion (65.5%). Rhinitis (55.9%) was the commonest diagnosis followed by pharyngitis (19.5%). Viruses were isolated in 46% of children, the commonest being Rhinoviruses (23.9%). Nineteen percent of children had more than 2 viruses; Rhinovirus and Enterovirus being the commonest combination. The commonest bacteria isolated from ears were Staphylococcus aureus and Pseudomonas aeruginosa. Children with viral pathogens had significantly right shift of lymphocytes (73%—sensitivity). Majority (257/339) of children were symptoms free on eighth day. Viruses are the commonest cause of URTI with Rhinitis being the common diagnosis. Rapid diagnostic assays for URTI pathogens are urgently needed in low-income countries to reduce unnecessary antibiotic prescriptions which is associated with antibiotic resistance. url: https://doi.org/10.1038/s41598-020-74555-2 doi: 10.1038/s41598-020-74555-2 id: cord-321756-a7eh4dkb author: Kwofie, Theophilus B title: Respiratory viruses in children hospitalized for acute lower respiratory tract infection in Ghana date: 2012-04-10 words: 3675.0 sentences: 204.0 pages: flesch: 48.0 cache: ./cache/cord-321756-a7eh4dkb.txt txt: ./txt/cord-321756-a7eh4dkb.txt summary: The study was done to identify viruses associated with acute lower respiratory tract infection among children less than 5 years. Majority of acute lower respiratory tract infections (ALRTI) in developed countries have been reported to be often due to viral pathogens of which most common are RSV, PIV, influenza viruses, Adv, human Coronaviruses and Bocaviruses [5] [6] [7] . This study was done to determine the burden of respiratory viruses among children hospitalized at the Komfo Anokye Teaching Hospital for acute lower respiratory illness using the Real Time Polymerase Chain Reaction (RT-PCR). The overall prevalence is comparable to previous studies done in other developing countries [24] and the predominance of RSV is in accordance with the assertion that this virus is the single most frequent lower respiratory tract pathogen in infants and young children worldwide [25] [26] [27] . abstract: BACKGROUND: Acute respiratory tract infections are one of the major causes of morbidity and mortality among young children in developing countries. Information on the viral aetiology of acute respiratory infections in developing countries is very limited. The study was done to identify viruses associated with acute lower respiratory tract infection among children less than 5 years. METHOD: Nasopharyngeal samples and blood cultures were collected from children less than 5 years who have been hospitalized for acute lower respiratory tract infection. Viruses and bacteria were identified using Reverse Transcriptase Real-Time Polymerase Chain Reaction and conventional biochemical techniques. RESULTS: Out of 128 patients recruited, 33(25.88%%, 95%CI: 18.5% to 34.2%) were positive for one or more viruses. Respiratory Syncytial Virus (RSV) was detected in 18(14.1%, 95%CI: 8.5% to 21.3%) patients followed by Adenoviruses (AdV) in 13(10.2%, 95%CI: 5.5% to 16.7%), Parainfluenza (PIV type: 1, 2, 3) in 4(3.1%, 95%CI: 0.9% to 7.8%) and influenza B viruses in 1(0.8%, 95%CI: 0.0 to 4.3). Concomitant viral and bacterial co-infection occurred in two patients. There were no detectable significant differences in the clinical signs, symptoms and severity for the various pathogens isolated. A total of 61.1% (22/36) of positive viruses were detected during the rainy season and Respiratory Syncytial Virus was the most predominant. CONCLUSION: The study has demonstrated an important burden of respiratory viruses as major causes of childhood acute respiratory infection in a tertiary health institution in Ghana. The data addresses a need for more studies on viral associated respiratory tract infection. url: https://doi.org/10.1186/1743-422x-9-78 doi: 10.1186/1743-422x-9-78 id: cord-327493-v2iatbol author: Kwon, Hyo Jin title: Clinical manifestations of respiratory adenoviral infection among hospitalized children in Korea date: 2013-08-05 words: 2820.0 sentences: 190.0 pages: flesch: 41.0 cache: ./cache/cord-327493-v2iatbol.txt txt: ./txt/cord-327493-v2iatbol.txt summary: BACKGROUND: The objective of our study was to understand the epidemiological and clinical features of respiratory adenoviral infections among children at a single institution over the course of several years. CONCLUSION: Our study demonstrates that respiratory adenovirus infections are an important cause of hospitalization in young children, and contribute to a significant morbidity. The study was performed to more fully characterize the epidemiological pattern, clinical features and complications associated with hospitalization for adenoviral infection in Korean children. Adenovirus was associated with a wide variety of diagnoses, ranging from upper respiratory tract infections (URTI) to severe pneumonia and encephalitis ( Table 1 ). 22 reported that 70% of hospitalized children with adenoviral infection had pneumonia, while our results revealed a significant proportion of patients (45.4%) with URTI. Lower respiratory tract infections due to adenovirus in hospitalized Korean children: epidemiology, clinical features, and prognosis abstract: BACKGROUND: The objective of our study was to understand the epidemiological and clinical features of respiratory adenoviral infections among children at a single institution over the course of several years. METHODS: From January 2005 to April 2009, 1836 children (≤15 years old) who had been admitted to Korea University Ansan Hospital were tested for acute respiratory infection. The patients who were positive for an adenovirus infection were enrolled in this study, and their medical records were retrospectively reviewed. RESULTS: Adenoviruses were isolated from 310 patients. The male to female ratio was 1.6:1 and mean age was 32 ± 24 months. Children under 5 years of age had the highest prevalence. In 2007, adenovirus infections occurred endemically throughout the year. The clinical diagnoses were primarily upper respiratory tract infections (45.4%), lower respiratory tract infections (48.1%), and neurologic disease (5.2%). Associated symptoms, signs and laboratory findings included fever (91.9%), cough (83.9%), pharyngeal injection (62.3%), rale (32.6%) and elevated C‐reactive protein (93.9%). The most common radiologic findings were perihilar and peribronchial infiltrates (42.6%). Co‐infections were observed in 29 cases. The mean durations of hospitalization and fever were 6.2 ± 6.5 and 4.8 ± 3.1 days, respectively. The lengths of hospitalization were similar for patients admitted for upper respiratory tract infections with severe morbidity and those admitted for lower respiratory tract infections. No children in the study died. CONCLUSION: Our study demonstrates that respiratory adenovirus infections are an important cause of hospitalization in young children, and contribute to a significant morbidity. url: https://www.ncbi.nlm.nih.gov/pubmed/23566140/ doi: 10.1111/ped.12108 id: cord-296605-p67twx7a author: LAU, Arthur Chun-Wing title: Management of Critically Ill Patients with Severe Acute Respiratory Syndrome (SARS) date: 2004-03-10 words: 4846.0 sentences: 247.0 pages: flesch: 38.0 cache: ./cache/cord-296605-p67twx7a.txt txt: ./txt/cord-296605-p67twx7a.txt summary: title: Management of Critically Ill Patients with Severe Acute Respiratory Syndrome (SARS) Most SARS patients would require high flow oxygen supplementation, 20–30% required intensive care unit (ICU) or high dependency care, and 13–26% developed acute respiratory distress syndrome (ARDS). The management of critically ill SARS patients requires timely institution of pharmacotherapy where applicable and supportive treatment (oxygen therapy, noninvasive and invasive ventilation). More than onethird of all the SARS patients required high flow oxygen therapy [4] , 20-30% required intensive care unit (ICU) admission or high dependency care, and 13-26% developed acute respiratory distress syndrome (ARDS) [5, 6] . Description and clinical treatment of an early outbreak of severe acute respiratory syndrome (SARS) in Guangzhou, PR China Evaluation of non-invasive positive pressure ventilation in treatment for patients with severe acute respiratory syndrome Clinical observation of non-invasive positive pressure ventilation (NIPPV) in the treatment of severe acute respiratory syndrome (SARS) abstract: Severe acute respiratory syndrome (SARS) is frequently complicated with acute respiratory failure. In this article, we aim to focus on the management of the subgroup of SARS patients who are critically ill. Most SARS patients would require high flow oxygen supplementation, 20–30% required intensive care unit (ICU) or high dependency care, and 13–26% developed acute respiratory distress syndrome (ARDS). In some of these patients, the clinical course can progress relentlessly to septic shock and/or multiple organ dysfunction syndrome (MODS). The management of critically ill SARS patients requires timely institution of pharmacotherapy where applicable and supportive treatment (oxygen therapy, noninvasive and invasive ventilation). Superimposed bacterial and other opportunistic infections are common, especially in those treated with mechanical ventilation. Subcutaneous emphysema, pneumothoraces and pneumomediastinum may arise spontaneously or as a result of positive ventilatory assistance. Older age is a consistently a poor prognostic factor. Appropriate use of personal protection equipment and adherence to infection control measures is mandatory for effective infection control. Much of the knowledge about the clinical aspects of SARS is based on retrospective observational data and randomized-controlled trials are required for confirmation. Physicians and scientists all over the world should collaborate to study this condition which may potentially threaten human existence. url: https://www.ncbi.nlm.nih.gov/pubmed/15912185/ doi: nan id: cord-274749-ji91qq9q author: Lagare, Adamou title: Viral and bacterial etiology of severe acute respiratory illness among children < 5 years of age without influenza in Niger date: 2015-11-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Globally, pneumonia is the leading cause of morbidity and mortality in children, with the highest burden experienced in sub-Saharan Africa and Asia. However, there is a dearth of information on the etiology of severe acute respiratory illness (SARI) in Africa, including Niger. METHODS: We implemented a retrospective study as part of national influenza sentinel surveillance in Niger. We randomly selected a sample of nasopharyngeal specimens collected from children <5 years of age hospitalized with SARI from January 2010 through December 2012 in Niger. The samples were selected from individuals that tested negative by real-time reverse transcription polymerase chain reaction (rRT-PCR) for influenza A and B virus. The samples were analyzed using the Fast Track Diagnostic Respiratory Pathogens 21plus Kit (BioMérieux, Luxemburg), which detects 23 respiratory pathogens including 18 viral and 5 bacterial agents. RESULTS: Among the 160 samples tested, 138 (86 %) tested positive for at least one viral or bacterial pathogen; in 22 (16 %) sample, only one pathogen was detected. We detected at least one respiratory virus in 126 (78 %) samples and at least one bacterium in 102 (64 %) samples. Respiratory syncytial virus (56/160; 35 %), rhinovirus (47/160; 29 %) and parainfluenza virus (39/160; 24 %) were the most common viral pathogens detected. Among bacterial pathogens, Streptococcus pneumoniae (90/160; 56 %) and Haemophilus influenzae type b (20/160; 12 %) predominated. CONCLUSIONS: The high prevalence of certain viral and bacterial pathogens among children <5 years of age with SARI highlights the need for continued and expanded surveillance in Niger. url: https://doi.org/10.1186/s12879-015-1251-y doi: 10.1186/s12879-015-1251-y id: cord-337747-7sb03moe author: Lagare, Adamou title: Molecular detection of respiratory pathogens among children aged younger than 5 years hospitalized with febrile acute respiratory infections: A prospective hospital‐based observational study in Niamey, Niger date: 2019-10-11 words: 2647.0 sentences: 140.0 pages: flesch: 43.0 cache: ./cache/cord-337747-7sb03moe.txt txt: ./txt/cord-337747-7sb03moe.txt summary: title: Molecular detection of respiratory pathogens among children aged younger than 5 years hospitalized with febrile acute respiratory infections: A prospective hospital‐based observational study in Niamey, Niger This study aims to describe viral and bacterial infections among children aged younger than 5 years hospitalized with febrile ARI at two hospitals in Niamey, Niger''s capital city, and the reported clinical procedures. 14 This study aims to describe the viral and bacterial infections among children aged younger than 5 years hospitalized with febrile ARI at two national hospitals of Niamey, the capital city of Niger, and the reported clinical procedures. In this 1-year prospective study, both viral and bacterial pathogens were detected in high proportion among hospitalized children aged younger than 5 years with febrile ARI in Niamey, Niger. Viral and bacterial etiology of severe acute respiratory illness among children < 5 years of age without influenza in Niger abstract: BACKGROUND AND AIMS: In Niger, acute respiratory infections (ARIs) are the second most common cause of death in children aged younger than 5 years. However, the etiology of ARI is poorly understood in the country. This study aims to describe viral and bacterial infections among children aged younger than 5 years hospitalized with febrile ARI at two hospitals in Niamey, Niger's capital city, and the reported clinical procedures. METHODS: We conducted a prospective study among children aged younger than 5 years hospitalized with febrile ARI at two national hospitals in Niamey between January and December 2015. Clinical presentation and procedures during admission were documented using a standardized case investigation form. Nasopharyngeal specimens collected from each patient were tested for a panel of respiratory viruses and bacteria using the Fast Track Diagnostic 21 Plus kit. RESULTS: We enrolled and tested 638 children aged younger than 5 years, of whom 411 (64.4%) were aged younger than 1 year, and 15 (2.4%) died during the study period. Overall, 496/638 (77.7%) specimens tested positive for at least one respiratory virus or bacterium; of these, 195 (39.3%) tested positive for respiratory viruses, 126 (25.4%) tested positive for respiratory bacteria, and 175 (35.3%) tested positive for both respiratory viruses and bacteria. The predominant viruses detected were respiratory syncytial virus (RSV) (149/638; 23.3%), human parainfluenza virus (HPIV) types 1 to 4 (78/638; 12.2%), human rhinovirus (HRV) (62/638; 9.4%), human adenovirus (HAV) (60/638; 9.4%), and influenza virus (INF) (52/638; 8.1%). Streptococcus pneumoniae (249/638; 39.0%) was the most frequently detected bacterium, followed by Staphylococcus aureus (112/638; 12.2%) and Haemophilus influenzae type B (16/638; 2.5%). Chest X‐rays were performed at the discretion of the attending physician on 301 (47.2%) case patients. Of these patients, 231 (76.7%) had abnormal radiological findings. A total of 135/638 (21.2%) and 572/638 (89.7%) children received antibiotic treatment prior to admission and during admission, respectively. CONCLUSION: A high proportion of respiratory viruses was detected among children aged younger than 5 years with febrile ARI, raising concerns about excessive use of antibiotics in Niger. url: https://doi.org/10.1002/hsr2.137 doi: 10.1002/hsr2.137 id: cord-261908-olcuq6tm author: Lai, Ka-Man title: Propagation of Respiratory Aerosols by the Vuvuzela date: 2011-05-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Vuvuzelas, the plastic blowing horns used by sports fans, recently achieved international recognition during the FIFA World Cup soccer tournament in South Africa. We hypothesised that vuvuzelas might facilitate the generation and dissemination of respiratory aerosols. To investigate the quantity and size of aerosols emitted when the instrument is played, eight healthy volunteers were asked to blow a vuvuzela. For each individual the concentration of particles in expelled air was measured using a six channel laser particle counter and the duration of blowing and velocity of air leaving the vuvuzela were recorded. To allow comparison with other activities undertaken at sports events each individual was also asked to shout and the measurements were repeated while using a paper cone to confine the exhaled air. Triplicate measurements were taken for each individual. The mean peak particle counts were 658×10(3) per litre for the vuvuzela and 3.7×10(3) per litre for shouting, representing a mean log(10) difference of 2.20 (95% CI: 2.03,2.36; p<0.001). The majority (>97%) of particles captured from either the vuvuzela or shouting were between 0.5 and 5 microns in diameter. Mean peak airflows recorded for the vuvuzela and shouting were 6.1 and 1.8 litres per second respectively. We conclude that plastic blowing horns (vuvuzelas) have the capacity to propel extremely large numbers of aerosols into the atmosphere of a size able to penetrate the lower lung. Some respiratory pathogens are spread via contaminated aerosols emitted by infected persons. Further investigation is required to assess the potential of the vuvuzela to contribute to the transmission of aerosol borne diseases. We recommend, as a precautionary measure, that people with respiratory infections should be advised not to blow their vuvuzela in enclosed spaces and where there is a risk of infecting others. url: https://doi.org/10.1371/journal.pone.0020086 doi: 10.1371/journal.pone.0020086 id: cord-003917-bswndfvk author: Lalle, Eleonora title: Pulmonary Involvement during the Ebola Virus Disease date: 2019-08-24 words: 5545.0 sentences: 245.0 pages: flesch: 40.0 cache: ./cache/cord-003917-bswndfvk.txt txt: ./txt/cord-003917-bswndfvk.txt summary: Filoviruses have become a worldwide public health concern, especially during the 2013–2016 Western Africa Ebola virus disease (EVD) outbreak—the largest outbreak, both by number of cases and geographical extension, recorded so far in medical history. During the 2013–2016 Western Africa outbreak, Ebola virus (EBOV) was detected in the lung of infected patients suggesting a role in lung pathogenesis. However, new evidences collected during the recent 2013-2016 Ebola outbreak hypothesized shedding of the virus in the lung and identified viral replication markers in sputum samples collected from EBOV infected patients [14] . However, new evidences collected during the recent 2013-2016 Ebola outbreak hypothesized shedding of the virus in the lung and identified viral replication markers in sputum samples collected from EBOV infected patients [14] . Interestingly, evidence collected in animal studies, in the epidemiological analysis of transmission chains, and in the most recent Ebola outbreaks suggests that EBOV may be able to cause primary pulmonary infection. abstract: Filoviruses have become a worldwide public health concern, especially during the 2013–2016 Western Africa Ebola virus disease (EVD) outbreak—the largest outbreak, both by number of cases and geographical extension, recorded so far in medical history. EVD is associated with pathologies in several organs, including the liver, kidney, and lung. During the 2013–2016 Western Africa outbreak, Ebola virus (EBOV) was detected in the lung of infected patients suggesting a role in lung pathogenesis. However, little is known about lung pathogenesis and the controversial issue of aerosol transmission in EVD. This review highlights the pulmonary involvement in EVD, with a special focus on the new data emerging from the 2013–2016 Ebola outbreak. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6784166/ doi: 10.3390/v11090780 id: cord-329877-vish6v8e author: Lapinsky, Stephen E. title: ICU management of severe acute respiratory syndrome date: 2003-05-09 words: 2639.0 sentences: 149.0 pages: flesch: 45.0 cache: ./cache/cord-329877-vish6v8e.txt txt: ./txt/cord-329877-vish6v8e.txt summary: BACKGROUND: Severe acute respiratory syndrome (SARS) is a contagious viral illness first recognized in late 2002. Severe acute respiratory syndrome (SARS) is a viral illness characterized by a syndrome of fever and respiratory symptoms that can progress to respiratory failure and death. This review describes the current state of knowledge of SARS, with particular reference to the management of the critically ill patient and the safety and protection of the ICU staff. Case definitions of SARS are currently based on the presence of epidemiological risk factors (close contact with SARS cases or travel to SARS "affected" areas) along with a combination of fever and respiratory symptoms, with or without hypoxia and/or chest radiographic changes [3] . Other high-risk procedures include obtaining nasopharyngeal swabs, bag-mask ventilation, intubation, suctioning, chest physiotherapy in nonintubated patients, nebulized drug therapy, noninvasive ventilation, and extubation (see Table 1 ). abstract: BACKGROUND: Severe acute respiratory syndrome (SARS) is a contagious viral illness first recognized in late 2002. It has now been documented in 26 countries worldwide, with significant outbreaks in China, Hong Kong, Singapore, and Toronto. Research into identifying the etiological agent, evaluating modes of disease transmission, and treatment options is currently ongoing. DISCUSSION: The disease can produce a severe bilateral pneumonia, with progressive hypoxemia. Up to 20% of patients require mechanical ventilatory support, with a fatal outcome occurring in about 5% of cases. CONCLUSIONS: We review the current knowledge about this disease, with particular emphasis on ICU management and infection control precautions to prevent disease transmission. ELECTRONIC SUPPLEMENTARY MATERIAL: Supplementary material is available if you access this article at http://dx.doi.org/10.1007/s00134-003-1821-0. On that page (frame on the left side) a link takes you directly to the supplementary material. url: https://doi.org/10.1007/s00134-003-1821-0 doi: 10.1007/s00134-003-1821-0 id: cord-263749-bbhh5xb1 author: Larenas-Linnemann, Désirée title: Enhancing innate immunity against virus in times of COVID-19: trying to untangle facts from fictions date: 2020-10-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Introduction In the light of the current COVID-19 pandemic, during which the world is confronted with a new, highly contagious virus that suppresses innate immunity as one of its initial virulence mechanisms, thus escaping from the first-line human defense mechanisms, enhancing innate immunity seems a good preventive strategy. Methods Without the intention to write an official systematic review, but more to give an overview of possible strategies, in this review article we discuss several interventions that might stimulate innate immunity and thus our defense against (viral) respiratory tract infections. Some of these interventions can also stimulate the adaptive T- and B-cell responses, but our main focus is on the innate part of immunity. We divide the reviewed interventions in: 1) lifestyle related (exercise, >7 hours sleep, forest walking, meditation/mindfulness, vitamin supplementation); 2) Non-specific immune stimulants (letting fever advance, bacterial vaccines, probiotics, dialyzable leukocyte extract, pidotimod) and 3) specific vaccines with heterologous effect (BCG vaccine, mumps-measles-rubeola vaccine, i.e.). Results For each of these interventions we briefly comment on their definition, possible mechanisms and evidence of clinical efficacy or lack of it, especially focusing on respiratory tract infections, viral infections and eventually a reduced mortality in severe respiratory infections in the intensive care unit. At the end a summary table demonstrates the best trials supporting (or not) clinical evidence. Conclusion Several interventions have some degree of evidence for enhancing the innate immune response and thus conveying possible benefit, but specific trials in COVID-19 should be conducted to support solid recommendations. url: https://www.ncbi.nlm.nih.gov/pubmed/33072240/ doi: 10.1016/j.waojou.2020.100476 id: cord-287156-3plpi6i9 author: Lassandro, Giuseppe title: Children in Coronaviruses’ Wonderland: What Clinicians Need to Know date: 2020-07-01 words: 8021.0 sentences: 535.0 pages: flesch: 43.0 cache: ./cache/cord-287156-3plpi6i9.txt txt: ./txt/cord-287156-3plpi6i9.txt summary: Among the seven coronaviruses that affect humans (SARS)-CoV, the Middle East respiratory syndrome (MERS)-CoV, and the most recent coronavirus disease 2019 (COVID-19) represent potential life-threatening diseases worldwide. Children appear to be less susceptible to develop severe clinical disease and present usually with mild and aspecific symptoms similar to other respiratory infections typical of childhood. 8, 9 Additionally, three HCoVs responsible for outbreaks involving high case fatality rates have been detected in humans in the last two decades: the severe acute respiratory syndrome (SARS)-CoV, the Middle East respiratory syndrome (MERS)-CoV and the new coronavirus disease 2019 (COVID-19) ( Table 1) . Principal features of severe acute respiratory syndrome (SARS)-CoV, the Middle East respiratory syndrome (MERS)-CoV and the most recent coronavirus disease 2019 (COVID19) . Clinical features and viral diagnosis of two cases of infection with Middle East Respiratory Syndrome coronavirus: a report of nosocomial transmission abstract: Human coronaviruses (HCoVs) commonly cause mild upper-respiratory tract illnesses but can lead to more severe and diffusive diseases. A variety of signs and symptoms may be present, and infections can range in severity from the common cold and sore throat to more serious laryngeal or tracheal infections, bronchitis, and pneumonia. Among the seven coronaviruses that affect humans (SARS)-CoV, the Middle East respiratory syndrome (MERS)-CoV, and the most recent coronavirus disease 2019 (COVID-19) represent potential life-threatening diseases worldwide. In adults, they may cause severe pneumonia that evolves in respiratory distress syndrome and multiorgan failure with a high mortality rate. Children appear to be less susceptible to develop severe clinical disease and present usually with mild and aspecific symptoms similar to other respiratory infections typical of childhood. However, some children, such as infants, adolescents, or those with underlying diseases may be more at-risk categories and require greater caution from clinicians. Available data on pediatric coronavirus infections are rare and scattered in the literature. The purpose of this review is to provide to clinicians a complete and updated panel useful to recognize and characterize the broad spectrum of clinical manifestations of coronavirus infections in the pediatric age. url: https://www.ncbi.nlm.nih.gov/pubmed/32670520/ doi: 10.4084/mjhid.2020.042 id: cord-324898-bjxpuqhr author: Lazzeri, Marta title: How Italian respiratory physiotherapists have faced and are facing the coronavirus disease 2019 pandemic date: 2020-08-03 words: 1620.0 sentences: 73.0 pages: flesch: 34.0 cache: ./cache/cord-324898-bjxpuqhr.txt txt: ./txt/cord-324898-bjxpuqhr.txt summary: Where present, respiratory physiotherapists (RPh) made a great contribution by working together with other health professionals in assisting patients, providing "quick basic training sessions" about respiratory care for non-specialist healthcare professionals, locating and assessing all kinds of equipment (ventilators, interfaces, oxygen delivery systems, among others) to assist patients with respiratory failure and implementing early intervention with those patients in healthier conditions. Despite the absolute novelty of the pathology and the lack of scientific evidence, based on the available knowledge of physiopathology and respiratory care strategies, in collaboration with other scientific societies (Associazione Italiana Fisioterapisti -AIFI-, Associazione Italiana Pneumologi Ospedalieri -AIPO-, Società Italiana Pneumologia -SIP-, European Respiratory Society-ERS-), documents have been published in open-access journals and platform aimed to promote safe use of personal protective equipment (PPE) and to support the decision process in the management of COVID-19 patients in the acute and postacute phases [1] [2] [3] [4] . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32765900/ doi: 10.1186/s40945-020-00086-8 id: cord-264059-jf4j00bp author: Lee, Chien-Chang title: Combining Procalcitonin and Rapid Multiplex Respiratory Virus Testing for Antibiotic Stewardship in Older Adult Patients With Severe Acute Respiratory Infection date: 2019-11-30 words: 4611.0 sentences: 251.0 pages: flesch: 36.0 cache: ./cache/cord-264059-jf4j00bp.txt txt: ./txt/cord-264059-jf4j00bp.txt summary: 3 Initial studies demonstrated that such POC multiplex PCR systems identified previously under-evaluated viral or atypical infections in ED dyspneic patients, and the additional information on rapid respiratory infection testing may also change the physician''s antibiotic-prescribing behavior, enabling more timely and appropriate treatment. In this study, we aimed to assess the impact of implementing a diagnostic algorithm that combines rapid respiratory viral surveillance and PCT tests on older patients presenting to the ED with severe acute respiratory illness. This prospective cohort study reports the clinical impact of rapid molecular diagnosis of respiratory pathogens in conjunction with PCT testing on older adult patients presenting to the ED with severe acute respiratory illness. The findings of our study support the use of rapid multiplex PCR respiratory panels in conjunction with the PCT test for early diagnosis of respiratory viral infection and to inform optimizing antibiotic use in older adult patients presenting to the ED with severe acute respiratory illness. abstract: OBJECTIVES: Virus infection is underevaluated in older adults with severe acute respiratory infections (SARIs). We aimed to evaluate the clinical impact of combining point-of-care molecular viral test and serum procalcitonin (PCT) level for antibiotic stewardship in the emergency department (ED). DESIGN: A prospective twin-center cohort study was conducted between January 2017 and March 2018. SETTING AND PARTICIPANTS: Older adult patients who presented to the ED with SARIs received a rapid molecular test for 17 respiratory viruses and a PCT test. MEASURES: To evaluate the clinical impact, we compared the outcomes of SARI patients between the experimental cohort and a propensity score–matched historical cohort. The primary outcome was the proportion of antibiotics discontinuation or de-escalation in the ED. The secondary outcomes included duration of intravenous antibiotics, length of hospital stay, and mortality. RESULTS: A total of 676 patients were included, of which 169 patients were in the experimental group and 507 patients were in the control group. More than one-fourth (27.9%) of the patients in the experimental group tested positive for virus. Compared with controls, the experimental group had a significantly higher proportion of antibiotics discontinuation or de-escalation in the ED (26.0% vs 16.1%, P = .007), neuraminidase inhibitor uses (8.9% vs 0.6%, P < .001), and shorter duration of intravenous antibiotics (10.0 vs 14.5 days, P < .001). CONCLUSIONS AND IMPLICATIONS: Combining rapid viral surveillance and PCT test is a useful strategy for early detection of potential viral epidemics and antibiotic stewardship. Clustered viral respiratory infections in a nursing home is common. Patients transferred from nursing homes to ED may benefit from this approach. url: https://www.ncbi.nlm.nih.gov/pubmed/31791902/ doi: 10.1016/j.jamda.2019.09.020 id: cord-303606-ypkia5x1 author: Lee, So-lun title: Is respiratory viral infection really an important trigger of asthma exacerbations in children? date: 2011-03-30 words: 3525.0 sentences: 179.0 pages: flesch: 46.0 cache: ./cache/cord-303606-ypkia5x1.txt txt: ./txt/cord-303606-ypkia5x1.txt summary: We performed a prospective cohort study from September 2003 to December 2004 to delineate attributing the effect of different respiratory viral infections including newly discovered ones to asthma exacerbations in children in Hong Kong. Plausible explanations for much lower virus detection rate than previously reported include improved personal hygiene and precautionary measures taken during respiratory tract infections in the immediate post-severe acute respiratory syndrome period together with a significant contribution of other adverse factors like environmental air pollution. Plausible explanations for much lower virus detection rate than previously reported include improved personal hygiene and precautionary measures taken during respiratory tract infections in the immediate post-severe acute respiratory syndrome period together with a significant contribution of other adverse factors like environmental air pollution. Thus, we carried out a prospective study to delineate the current role of different viral respiratory tract infections including newly discovered respiratory viruses in asthma exacerbation in children in our locality. abstract: We performed a prospective cohort study from September 2003 to December 2004 to delineate attributing the effect of different respiratory viral infections including newly discovered ones to asthma exacerbations in children in Hong Kong. One hundred and fourteen children aged 6–14 years with chronic stable asthma and on regular inhaled steroid were monitored for respiratory symptoms over a full calendar year from recruitment. They would attend the study clinic if peak expiratory flow rate decreased to below 80% of their baselines, if they met a predefined symptom score, or if parents subjectively felt them developing a cold. Virological diagnosis using virus culture, antigen detection, and polymerase chain reaction methods on nasal swab specimens would be attempted for all these visits irrespective of triggers. Physician diagnosed outcome of each episode was documented. Three hundred and five episodes of respiratory illnesses were captured in the cohort. Nasal specimens were available in 166 episodes, 92 of which were diagnosed as asthma exacerbations, and 74 non-asthma related episodes. Respiratory viruses were detected in 61 of 166 episodes (36.7%). There was no significant difference in virus detection rate between asthma exacerbations (32 out of 97 episodes, 34.8%) and non-asthma respiratory illnesses (29 out of 79 episodes, 39.2%). Although newly discovered respiratory viruses were identified in these episodes, rhinovirus was the commonest organism associated with both asthma exacerbations and non-asthma related episodes. Plausible explanations for much lower virus detection rate than previously reported include improved personal hygiene and precautionary measures taken during respiratory tract infections in the immediate post-severe acute respiratory syndrome period together with a significant contribution of other adverse factors like environmental air pollution. We conclude that not all viral infections in children with asthma lead to an asthma exacerbation and the attributing effect of different triggers of asthma exacerbations in children vary across different time periods and across different localities. url: https://www.ncbi.nlm.nih.gov/pubmed/21448631/ doi: 10.1007/s00431-011-1446-1 id: cord-343074-dsubeaso author: Lee, Wan‐Ji title: Molecular epidemiology of a post‐influenza pandemic outbreak of acute respiratory infections in Korea caused by human adenovirus type 3 date: 2014-06-01 words: 3530.0 sentences: 183.0 pages: flesch: 46.0 cache: ./cache/cord-343074-dsubeaso.txt txt: ./txt/cord-343074-dsubeaso.txt summary: title: Molecular epidemiology of a post‐influenza pandemic outbreak of acute respiratory infections in Korea caused by human adenovirus type 3 An outbreak of upper respiratory tract infections associated with human adenovirus (HAdV) occurred on a national scale in Korea from September to December 2010, following a major H1N1 influenza pandemic. To determine the principal cause of the outbreak, direct polymerase chain reaction (PCR) amplification followed by sequence analysis targeting parts of the hexon gene of HAdV was performed. Serotypes of 1,007 PCR‐diagnosed HAdV‐positive samples from patients with an acute upper respiratory tract illness were determined and epidemiological characteristics including major aged group and clinical symptoms were analyzed. Epidemiological and molecular data presented in this study confirmed that the outbreak in 2010 was not associated with genetic alterations causing a change in the pathology of the major causative agent, HAdV-3, nor with multiple infections with other respiratory viruses. abstract: An outbreak of upper respiratory tract infections associated with human adenovirus (HAdV) occurred on a national scale in Korea from September to December 2010, following a major H1N1 influenza pandemic. Data from the Korea Influenza and Respiratory Surveillance System (KINRESS) showed an unusually high positive rate accounting for up to 20% of all diagnosed cases. To determine the principal cause of the outbreak, direct polymerase chain reaction (PCR) amplification followed by sequence analysis targeting parts of the hexon gene of HAdV was performed. Serotypes of 1,007 PCR‐diagnosed HAdV‐positive samples from patients with an acute upper respiratory tract illness were determined and epidemiological characteristics including major aged group and clinical symptoms were analyzed. The principal symptom of HAdV infections was fever and the vulnerable aged group was 1–5 years old. Based on sequence analysis, HAdV‐3 was the predominant serotype in the outbreak, with an incidence of 74.3%. From the beginning of 2010 until May, the major serotypes were HAdV‐1, 2, and 5 (70–100%) in any given period. However, an outbreak dominated by HAdV‐3 started between July and August and peaked in September. Phylogenetic analysis revealed that there was no genetic variation in HAdV‐3. The results demonstrated that an outbreak of upper respiratory illness followed by H1N1 influenza pandemic in Korea was caused mainly by emerged HAdV‐3. J. Med. Virol. 87: 10–17, 2015. © 2014 Wiley Periodicals, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/24889391/ doi: 10.1002/jmv.23984 id: cord-333286-lr32e0w4 author: Lehtoranta, Liisa title: Role of Probiotics in Stimulating the Immune System in Viral Respiratory Tract Infections: A Narrative Review date: 2020-10-16 words: 6768.0 sentences: 338.0 pages: flesch: 35.0 cache: ./cache/cord-333286-lr32e0w4.txt txt: ./txt/cord-333286-lr32e0w4.txt summary: We searched PubMed, Google Scholar, and Web of Knowledge for pre-clinical and clinical studies investigating the effect of probiotics on respiratory virus infections, immune response, and the course of upper and lower respiratory tract illness. Similar effects have been demonstrated in several mouse studies with the ability to reduce virus titers in lung tissues and modulation of antiviral and pro-inflammatory gene expression before and after viral infection. The upregulation of IFN response seems to prime cells for better resistance against virus infection as probiotics were shown effective in inhibiting the replication of various respiratory viruses, including influenza viruses and RSV. Similar effects have been demonstrated in mice with the ability of the probiotics to reduce virus titers in lung tissues and to modulate antiviral and pro-inflammatory gene expression before and after viral infection. Similar effects have been demonstrated in mice with the ability of the probiotics to reduce virus titers in lung tissues and to modulate antiviral and pro-inflammatory gene expression before and after viral infection. abstract: Viral respiratory tract infection (RTI) is the most frequent cause of infectious illnesses including the common cold. Pharmacological solutions for treating or preventing viral RTIs are so far limited and thus several self-care products are available in the market. Some dietary supplements such as probiotics have been shown to modulate immune system function and their role in reducing the risk and the course of RTIs has been investigated extensively within the past decade. However, the mechanism of action and the efficacy of probiotics against viral RTIs remains unclear. We searched PubMed, Google Scholar, and Web of Knowledge for pre-clinical and clinical studies investigating the effect of probiotics on respiratory virus infections, immune response, and the course of upper and lower respiratory tract illness. The literature summarized in this narrative review points out that specific probiotic strains seem effective in pre-clinical models, through stimulating the immune system and inhibiting viral replication. Clinical studies indicate variable efficacy on upper respiratory illnesses and lack proof of diagnosed viral infections. However, meta-analyses of clinical studies indicate that probiotics could be beneficial in upper respiratory illnesses without specific etiology. Further studies aiming at discovering the mechanisms of action of probiotics and clinical efficacy are warranted. url: https://doi.org/10.3390/nu12103163 doi: 10.3390/nu12103163 id: cord-265380-2gs34xcw author: Leist, Sarah R. title: Genetically Engineering a Susceptible Mouse Model for MERS-CoV-Induced Acute Respiratory Distress Syndrome date: 2019-09-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Since 2012, monthly cases of Middle East respiratory syndrome coronavirus (MERS-CoV) continue to cause severe respiratory disease that is fatal in ~35% of diagnosed individuals. The ongoing threat to global public health and the need for novel therapeutic countermeasures have driven the development of animal models that can reproducibly replicate the pathology associated with MERS-CoV in human infections. The inability of MERS-CoV to replicate in the respiratory tracts of mice, hamsters, and ferrets stymied initial attempts to generate small animal models. Identification of human dipeptidyl peptidase IV (hDPP4) as the receptor for MERS-CoV infection opened the door for genetic engineering of mice. Precise molecular engineering of mouse DPP4 (mDPP4) with clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology maintained inherent expression profiles, and limited MERS-CoV susceptibility to tissues that naturally express mDPP4, notably the lower respiratory tract wherein MERS-CoV elicits severe pulmonary pathology. Here, we describe the generation of the 288–330(+/+) MERS-CoV mouse model in which mice were made susceptible to MERS-CoV by modifying two amino acids on mDPP4 (A288 and T330), and the use of adaptive evolution to generate novel MERS-CoV isolates that cause fatal respiratory disease. The 288–330(+/+) mice are currently being used to evaluate novel drug, antibody, and vaccine therapeutic countermeasures for MERS-CoV. The chapter starts with a historical perspective on the emergence of MERS-CoV and animal models evaluated for MERS-CoV pathogenesis, and then outlines the development of the 288–330(+/+) mouse model, assays for assessing a MERS-CoV pulmonary infection in a mouse model, and describes some of the challenges associated with using genetically engineered mice. url: https://www.ncbi.nlm.nih.gov/pubmed/31883094/ doi: 10.1007/978-1-0716-0211-9_12 id: cord-258336-zs04l3s0 author: Leotte, Jaqueline title: Impact and seasonality of human rhinovirus infection in hospitalized patients for two consecutive years date: 2017-06-30 words: 3254.0 sentences: 180.0 pages: flesch: 46.0 cache: ./cache/cord-258336-zs04l3s0.txt txt: ./txt/cord-258336-zs04l3s0.txt summary: Abstract Objectives To report epidemiological features, clinical characteristics, and outcomes of human rhinovirus (HRV) infections in comparison with other community acquired respiratory virus (CRV) infections in patients hospitalized for two consecutive years. The present study reports the epidemiological features, clinical characteristics, and outcomes of HRV infections in comparison with other CRV infections in patients hospitalized in a referral hospital in Southern Brazil, for two consecutive years. Patients hospitalized at an academic tertiary care center in Southern Brazil from whom respiratory samples were collected and sent for investigation, or who were diagnosed with SARI in 2012 or 2013, were included in the study. The medical records and influenza notification forms of patients with detectable respiratory virus were reviewed, focusing on epidemiology, clinical manifestation, outcome, laboratory findings, and diagnosis of SARI. In conclusion, HRV has a high prevalence in the hospitalized children and was present in cases of severe disease, including death. abstract: Abstract Objectives To report epidemiological features, clinical characteristics, and outcomes of human rhinovirus (HRV) infections in comparison with other community acquired respiratory virus (CRV) infections in patients hospitalized for two consecutive years. Methods This was a cross-sectional study. Clinical, epidemiological, and laboratory data of patients hospitalized with acute respiratory syndrome in a tertiary care hospital from 2012 to 2013 were reviewed. Results HRV was the most common CRV observed (36%, 162/444) and was present in the majority of viral co-detections (69%, 88/128), mainly in association with human enterovirus (45%). Most HRV-infected patients were younger than 2 years (57%). Overall, patients infected with HRV had a lower frequency of severe acute respiratory infection than those infected with other CRVs (60% and 84%, respectively, p =0.006), but had more comorbidities (40% and 27%, respectively; p =0.043). However, in the adjusted analysis this association was not significant. The mortality rate within the HRV group was 3%. Detection of HRV was more prevalent during autumn and winter, with a moderately negative correlation between viral infection frequency and temperature (r =−0.636, p <0.001) but no correlation with rainfall (r =−0.036, p =0.866). Conclusion HRV is usually detected in hospitalized children with respiratory infections and is often present in viral co-detections. Comorbidities are closely associated with HRV infections. These infections show seasonal variation, with predominance during colder seasons. url: https://www.ncbi.nlm.nih.gov/pubmed/27916571/ doi: 10.1016/j.jped.2016.07.004 id: cord-253502-v2hh3w3r author: Leung, C.W. title: Clinical picture, diagnosis, treatment and outcome of severe acute respiratory syndrome (SARS) in children date: 2004-11-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Children are susceptible to infection by SARS-associated coronavirus (SARS-CoV) but the clinical picture of SARS is milder than in adults. Teenagers resemble adults in presentation and disease progression and may develop severe illness requiring intensive care and assisted ventilation. Fever, malaise, cough, coryza, chills or rigor, sputum production, headache, myalgia, leucopaenia, lymphopaenia, thrombocytopaenia, mildly prolonged activated partial thromboplastin times and elevated lactate dehydrogenase levels are common presenting features. Radiographic findings are non-specific but high-resolution computed tomography of the thorax in clinically suspected cases may be an early diagnostic aid when initial chest radiographs appear normal. The improved reverse transcription-polymerase chain reaction (RT-PCR) assays are critical in the early diagnosis of SARS, with sensitivity approaching 80% in the first 3 days of illness when performed on nasopharyngeal aspirates, the preferred specimens. Absence of seroconversion to SARS-CoV beyond 28 days from disease onset generally excludes the diagnosis. The best treatment strategy for SARS among children remains to be determined. No case fatality has been reported in children and the short- to medium-term outcome appears to be good. The importance of continued monitoring for any long-term complications due to the disease or its empiric treatment, cannot be overemphasised. url: https://www.sciencedirect.com/science/article/pii/S152605420400079X doi: 10.1016/j.prrv.2004.07.010 id: cord-282533-w6kl74c8 author: Li, Jin title: Rapid detection of respiratory organisms with the FilmArray respiratory panel in a large children’s hospital in China date: 2018-10-11 words: 3378.0 sentences: 174.0 pages: flesch: 44.0 cache: ./cache/cord-282533-w6kl74c8.txt txt: ./txt/cord-282533-w6kl74c8.txt summary: METHODS: Nasopharyngeal swab or sputum specimens were collected from children aged 19 days to 15 years who were admitted to a hospital in Shanghai and diagnosed with RTIs. The specimens were tested with the FilmArray Respiratory Panel, a multiplex PCR assay that detects 16 viruses, Mycoplasma pneumoniae (M. CONCLUSIONS: FilmArray RP allows the rapid simultaneous detection of a wide number of respiratory organisms, with limited hands-on time, in Chinese pediatric patients with RTIs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-018-3429-6) contains supplementary material, which is available to authorized users. The aim of this study was to evaluate the application of FilmArray RP for the detection of respiratory organisms, and to provide information about the seasonality and prevalence of these organisms in pediatric patients with RTIs in a large children''s hospital in China. abstract: BACKGROUND: Respiratory tract infections (RTIs) are the most common illness in children, and rapid diagnosis is required for the optimal management of RTIs, especially severe infections. METHODS: Nasopharyngeal swab or sputum specimens were collected from children aged 19 days to 15 years who were admitted to a hospital in Shanghai and diagnosed with RTIs. The specimens were tested with the FilmArray Respiratory Panel, a multiplex PCR assay that detects 16 viruses, Mycoplasma pneumoniae (M. pneumoniae), Bordetella pertussis (B. pertussis) and Chlamydophila pneumoniae (C. pneumoniae). RESULTS: Among the 775 children studied, 626 (80.8%, 626/775) tested positive for at least one organism, and multiple organisms were detected in 198 (25.5%). Rhinoviruses/enteroviruses (25.5%, 198/775) were detected most often, followed by respiratory syncytial virus (19.5%, 151/775), parainfluenza virus 3 (14.8%, 115/775), influenza A or B (10.9%), adenovirus (10.8%), M. pneumoniae (10.6%) and B. pertussis (6.3%). The prevalence of organisms differed by age, and most of the viruses were more common in winter. Of the 140 children suspected of having pertussis, 35.0% (49/140) tested positive for B. pertussis. CONCLUSIONS: FilmArray RP allows the rapid simultaneous detection of a wide number of respiratory organisms, with limited hands-on time, in Chinese pediatric patients with RTIs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-018-3429-6) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12879-018-3429-6 doi: 10.1186/s12879-018-3429-6 id: cord-002227-x1ddi8wg author: Li, Wanli title: Emergency treatment and nursing of children with severe pneumonia complicated by heart failure and respiratory failure: 10 case reports date: 2016-07-29 words: 4023.0 sentences: 204.0 pages: flesch: 40.0 cache: ./cache/cord-002227-x1ddi8wg.txt txt: ./txt/cord-002227-x1ddi8wg.txt summary: In the process of nursing children with severe pneumonia, intensive care was provided, including condition assessment and diagnosis, close observation of disease, keeping the airway unblocked, rational oxygen therapy, prevention and treatment of respiratory and circulatory failure, support of vital organs, complications, and health education. As a result, severe pneumonia produces corresponding clinical symptoms, such as respiratory failure, heart failure, toxic encephalopathy and intestinal paralysis, which endanger the lives of children in the short term, and is the first cause of death of pediatric inpatients (6, 7) . Type I respiratory failure also refers to the coexistence of hypoxemia and hypercapnia, impairment of ventilatory function and gas exchange functions, severe lung lesion, obstruction of trachea and bronchia caused by sticky secretions, blood change of PaO 2 <60 mmHg, and PaCO 2 >50 mmHg. Main clinical manifestations of children patients with type I pneumonia with respiratory failure include, poor mental state or dysphoria, polypnea, cyanosis of lips, dyspnea, nasal flaring and three depression signs. abstract: Pneumonia refers to lung inflammation caused by different pathogens or other factors, and is a common pediatric disease occurring in infants and young children. It is closely related to the anatomical and physiological characteristics of infants and young children and is more frequent during winter and spring, or sudden changes in temperature. Pneumonia is a serious disease that poses a threat to children's health and its morbidity and mortality rank first, accounting for 24.5–65.2% of pediatric inpatients. Due to juvenile age, severe illness and rapid changes, children often suffer acute heart failure, respiratory failure and even toxic encephalopathy at the same time. The concurrence in different stages of the process of emergency treatment tends to relapse, which directly places the lives of these children at risk. Severe pneumonia constitutes one of the main causes of infant mortality. In the process of nursing children with severe pneumonia, intensive care was provided, including condition assessment and diagnosis, close observation of disease, keeping the airway unblocked, rational oxygen therapy, prevention and treatment of respiratory and circulatory failure, support of vital organs, complications, and health education. The inflammatory response was proactively controlled, to prevent suffocation and reduce mortality. In summary, positive and effective nursing can promote the rehabilitation of children patients, which can be reinforced with adequate communication with the parents and/or caretakers. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5038202/ doi: 10.3892/etm.2016.3558 id: cord-272538-gclrtie7 author: Li, Xuechao title: Viral etiologies and epidemiology of patients with acute respiratory infections based on sentinel hospitals in Gansu Province, Northwest China, 2011‐2015 date: 2018-02-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Understanding etiological role and epidemiological profile is needed to improve clinical management and prevention of acute respiratory infections (ARIs). A 5‐year prospective study about active surveillance for outpatients and inpatients with ARIs was conducted in Gansu province, China, from January 2011 to November 2015. Respiratory specimens were collected from patients and tested for eight respiratory viruses using polymerase chain reaction (PCR) or reverse transcription polymerase chain reaction (RT‐PCR). In this study, 2768 eligible patients with median age of 43 years were enrolled including pneumonia (1368, 49.2%), bronchitis (435, 15.7%), upper respiratory tract infection or URTI (250, 9.0%), and unclassified ARI (715, 25.8%). Overall, 29.2% (808/2768) were positive for any one of eight viruses, of whom 130 cases were identified with two or more viruses. Human rhinovirus (HRV) showed the highest detection rate (8.6%), followed by influenza virus (Flu, 7.3%), respiratory syncytial virus (RSV, 6.1%), human coronavirus (hCoV, 4.3%), human parainfluenza (PIV, 4.0%), adenovirus (ADV, 2.1%), human metapneumovirus (hMPV, 1.6%), and human bocavirus (hBoV, 0.7%). Compared with URTI, RSV was more likely identified in pneumonia (χ(2) = 12.720, P < 0.001) and hCoV was more commonly associated with bronchitis than pneumonia (χ(2) = 15.019, P < 0.001). In patients aged less than 5 years, RSV showed the highest detection rate and hCoV was the most frequent virus detected in adults and elderly. The clear epidemical seasons were observed in HRV, Flu, and hCoV infections. These findings could serve as a reference for local health authorities in drawing up further plans to prevent and control ARIs associated with viral etiologies. url: https://www.ncbi.nlm.nih.gov/pubmed/29388679/ doi: 10.1002/jmv.25040 id: cord-251986-ajlpb9li author: Li, Yan‐Chao title: The neuroinvasive potential of SARS‐CoV2 may play a role in the respiratory failure of COVID‐19 patients date: 2020-03-11 words: 2250.0 sentences: 125.0 pages: flesch: 47.0 cache: ./cache/cord-251986-ajlpb9li.txt txt: ./txt/cord-251986-ajlpb9li.txt summary: This virus shares highly homological sequence with SARS‐CoV, and causes acute, highly lethal pneumonia coronavirus disease 2019 (COVID‐19) with clinical symptoms similar to those reported for SARS‐CoV and MERS‐CoV. A growing body of evidence shows that neurotropism is one common feature of CoVs. 1, [9] [10] [11] [12] Therefore, it is urgent to make clear whether SARS-CoV-2 can gain access to the central nervous system (CNS) and induce neuronal injury leading to the acute respiratory distress. Mechanisms of host defense following severe acute respiratory syndrome-coronavirus (SARS-CoV) pulmonary infection of mice Exploring the pathogenesis of severe acute respiratory syndrome (SARS): the tissue distribution of the coronavirus (SARS-CoV) and its putative receptor, angiotensin-converting enzyme 2 (ACE2) Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for pathogenesis and virus transmission pathways Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients abstract: Following the severe acute respiratory syndrome coronavirus (SARS‐CoV) and Middle East respiratory syndrome coronavirus (MERS‐CoV), another highly pathogenic coronavirus named SARS‐CoV‐2 (previously known as 2019‐nCoV) emerged in December 2019 in Wuhan, China, and rapidly spreads around the world. This virus shares highly homological sequence with SARS‐CoV, and causes acute, highly lethal pneumonia coronavirus disease 2019 (COVID‐19) with clinical symptoms similar to those reported for SARS‐CoV and MERS‐CoV. The most characteristic symptom of patients with COVID‐19 is respiratory distress, and most of the patients admitted to the intensive care could not breathe spontaneously. Additionally, some patients with COVID‐19 also showed neurologic signs, such as headache, nausea, and vomiting. Increasing evidence shows that coronaviruses are not always confined to the respiratory tract and that they may also invade the central nervous system inducing neurological diseases. The infection of SARS‐CoV has been reported in the brains from both patients and experimental animals, where the brainstem was heavily infected. Furthermore, some coronaviruses have been demonstrated able to spread via a synapse‐connected route to the medullary cardiorespiratory center from the mechanoreceptors and chemoreceptors in the lung and lower respiratory airways. Considering the high similarity between SARS‐CoV and SARS‐CoV2, it remains to make clear whether the potential invasion of SARS‐CoV2 is partially responsible for the acute respiratory failure of patients with COVID‐19. Awareness of this may have a guiding significance for the prevention and treatment of the SARS‐CoV‐2‐induced respiratory failure. url: https://doi.org/10.1002/jmv.25728 doi: 10.1002/jmv.25728 id: cord-262623-lmf2h6oc author: Light, R. Bruce title: Plagues in the ICU: A Brief History of Community-Acquired Epidemic and Endemic Transmissible Infections Leading to Intensive Care Admission date: 2009-01-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The ability to diagnose and treat infectious diseases and handle infectious disease outbreaks continues to improve. For the most part, the major plagues of antiquity remain historical footnotes, yet, despite many advances, there is clear evidence that major pandemic illness is always just one outbreak away. In addition to the HIV pandemic, the smaller epidemic outbreaks of Legionnaire's disease, hantavirus pulmonary syndrome, and severe acute respiratory syndrome, among many others, points out the potential risk associated with a lack of preplanning and preparedness. Although pandemic influenza is at the top of the list when discussing possible future major infectious disease outbreaks, the truth is that the identity of the next major pandemic pathogen cannot be predicted with any accuracy. We can only hope that general preparedness and the lessons learned from previous outbreaks suffice. url: https://www.ncbi.nlm.nih.gov/pubmed/19268795/ doi: 10.1016/j.ccc.2008.11.002 id: cord-336743-udokbcki author: Lilitsis, Emmanouil title: Inspiratory effort and breathing pattern change in response to varying the assist level: a physiological study date: 2020-06-10 words: 3436.0 sentences: 165.0 pages: flesch: 46.0 cache: ./cache/cord-336743-udokbcki.txt txt: ./txt/cord-336743-udokbcki.txt summary: Setting the level of ventilator assist in everyday practice relies mostly on the clinical estimation of inspiratory effort, as indicated by the breathing pattern -tidal volume (VT) and respiratory rate (RR)-and clinical signs of respiratory distress (Boles et al., 2007; Hansen-Flaschen, 2000; Hess, 2001; Ray et al., 2006) . The aim of this study was to 1) characterize the responses of respiratory drive, respiratory effort, and breathing pattern to changing levels of ventilatory assist in critically ill patients and 2) assess if changes in respiratory rate may indicate changes in respiratory drive and effort. To this end, during proportional assist ventilation with adjustable gain factors (PAV+), noninvasive measurements of respiratory drive, effort (as indicated by inspiratory muscle pressure) were obtained at different levels of assist, using a validated prototype monitor (PVI) (Kondili et al., 2010; Younes et al., 2007) . abstract: AIM: To describe the response of breathing pattern and inspiratory effort upon changes in assist level and to assesss if changes in respiratory rate may indicate changes in respiratory muscle effort. METHODS: Prospective study of 82 patients ventilated on proportional assist ventilation (PAV+). At three levels of assist (20%-50%-80%), patients’ inspiratory effort and breathing pattern were evaluated using a validated prototype monitor. RESULTS: Independent of the assist level, a wide range of respiratory rates (16-35br/min) was observed when patients’ effort was within the accepted range. Changing the assist level resulted in paired changes in inspiratory effort and rate of the same tendency (increase or decrease) in all but four patients. Increasing the level in assist resulted in a 31% (8-44%) decrease in inspiratory effort and a 10% (0-18%) decrease in respiratory rate. The change in respiratory rate upon the change in assist correlated modestly with the change in the effort (R = 0.5). CONCLUSION: Changing assist level results in changes in both respiratory rate and effort in the same direction, with change in effort being greater than that of respiratory rate. Yet, neither the magnitude of respiratory rate change nor the resulting absolute value may reliably predict the level of effort after a change in assist. url: https://api.elsevier.com/content/article/pii/S1569904820301324 doi: 10.1016/j.resp.2020.103474 id: cord-266516-0ure8256 author: Lim, Tow Keang title: Pneumonia in the tropics date: 2017-08-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Pneumonia in the tropics poses a heavy disease burden. The complex interplay of climate change, human migration influences and socio‐economic factors lead to changing patterns of respiratory infections in tropical climate but also increasingly in temperate countries. Tropical and poorer countries, especially South East Asia, also bear the brunt of the global tuberculosis (TB) pandemic, accounting for almost one‐third of the burden. But, as human migration patterns evolve, we expect to see more TB cases in higher income as well as temperate countries, and rise in infections like scrub typhus from ecotourism activities. Fuelled by the ease of air travel, novel zoonotic infections originating from the tropics have led to global respiratory pandemics. As such, clinicians worldwide should be aware of these new conditions as well as classical tropical bacterial pneumonias such as melioidosis. Rarer entities such as co‐infections of leptospirosis and chikungunya or dengue will need careful consideration as well. In this review, we highlight aetiologies of pneumonia seen more commonly in the tropics compared with temperate regions, their disease burden, variable clinical presentations as well as impact on healthcare delivery. url: https://www.ncbi.nlm.nih.gov/pubmed/28763150/ doi: 10.1111/resp.13137 id: cord-315037-lmur80te author: Lin, Chien-Yu title: Increased Detection of Viruses in Children with Respiratory Tract Infection Using PCR date: 2020-01-15 words: 4190.0 sentences: 241.0 pages: flesch: 42.0 cache: ./cache/cord-315037-lmur80te.txt txt: ./txt/cord-315037-lmur80te.txt summary: We performed a multiplex real-time polymerase chain reaction (PCR) to investigate the viral etiology in pediatric patients and compared the detection rates with those determined using traditional antigen tests and virus cultures. This study aims to detect respiratory viruses in children using PCR and to compare the detection power of this technique against that when using traditional antigen tests and virus cultures. For children with respiratory symptoms and with a clinical suspicion of virus infection, a test for RSV antigen test, human parainfluenza virus (PIV) type 3 antigen test, viral PCR for enterovirus, or viral cultures was prescribed by the judgment of pediatricians. The following multiplex PCR assays were performed for each sample to detect RNA/DNA of 15 respiratory viruses, including RSV A or B, FluA, FluB, human enterovirus (EV), MPV, human parainfluenza virus types 1-4, human rhinovirus (RV), coronavirus OC43/NL63/229E, human adenovirus (ADV), and human bocavirus (Boca). The present study demonstrates that PCR has higher detectability for respiratory viruses compared to traditional antigen tests and viral cultures. abstract: Respiratory viruses are a common cause of respiratory tract infection (RTI), particularly in neonates and children. Rapid and accurate diagnosis of viral infections could improve clinical outcomes and reduce the use of antibiotics and treatment sessions. Advances in diagnostic technology contribute to the accurate detection of viruses. We performed a multiplex real-time polymerase chain reaction (PCR) to investigate the viral etiology in pediatric patients and compared the detection rates with those determined using traditional antigen tests and virus cultures. Fifteen respiratory viruses were included in our investigation: respiratory syncytial virus A/B (RSV), influenza virus A (FluA) and influenza virus B (FluB), human metapneumovirus (MPV), enterovirus (EV), human parainfluenza virus (PIV) types 1–4, human rhinovirus (RV), human coronavirus OC43, NL63, and 229E, human adenovirus (ADV), and human bocavirus (Boca). In total, 474 specimens were collected and tested. Respiratory viruses were detected more frequently by PCR (357, 75.3%) than they were by traditional tests (229, 49.3%). The leading pathogens were RSV (113, 23.8%), RV (72, 15.2%), PIV3 (53, 11.2%), FluA (51, 10.8%), and ADV (48, 10.1%). For children younger than 5 years, RSV and RV were most prevalent; for children older than 5 years, FluA and ADV were the most frequently detected. Of the specimens, 25.8% (92/357) were coinfected with two or more viruses. RV, Boca, PIV2, FluB, and PIV4 had higher rates of coinfection; MPV and PIV1 had the lowest rates of coinfection (9.1% and 5.3%). To conclude, the detection power of PCR was better than that of traditional antigen tests and virus cultures when considering the detection of respiratory viruses. RSV and RV were the leading viral pathogens identified in the respiratory specimens. One-quarter of the positive specimens were coinfected with two or more viruses. In the future, further application of PCR may contribute to the rapid and accurate diagnosis of respiratory viruses and could improve patient outcomes. url: https://www.ncbi.nlm.nih.gov/pubmed/31952364/ doi: 10.3390/ijerph17020564 id: cord-312741-0au4nctt author: Lin, Panpan title: Coronavirus in human diseases: Mechanisms and advances in clinical treatment date: 2020-10-01 words: 14665.0 sentences: 840.0 pages: flesch: 42.0 cache: ./cache/cord-312741-0au4nctt.txt txt: ./txt/cord-312741-0au4nctt.txt summary: 160, 161 Once the PAMPs from invaded viruses are detected, RIG-I and MDA5 interact with the mitochondrial antiviral signaling protein (MAVs) that is a mitochondrial membrane-bound F I G U R E 2 Escape mechanisms of innate immune response of SARS-CoV and MERS-CoV adaptor molecule, followed by the activation of several kinase complexes and multiple subsequent transcription factors (IRF3, IRF7, and NF-κB). Antiviral peptides analogous derived from these regions exhibited inhibition to the spike protein-mediated cell-cell fusion and viral entry in viruses such as SARS-CoV, MERS-CoV, as well as HCoV-229E. Receptor-binding domain of severe acute respiratory syndrome coronavirus spike protein contains multiple conformation-dependent epitopes that induce highly potent neutralizing antibodies Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry Evidence that TMPRSS2 activates the severe acute respiratory syndrome coronavirus spike protein for membrane fusion and reduces viral control by the humoral immune response Inhibition of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infectivity by peptides analogous to the viral spike protein abstract: Coronaviruses (CoVs), a subfamily of coronavirinae, are a panel of single‐stranded RNA virus. Human coronavirus (HCoV) strains (HCoV‐229E, HCoV‐OC43, HCoV‐HKU1, HCoV‐NL63) usually cause mild upper respiratory diseases and are believed to be harmless. However, other HCoVs, associated with severe acute respiratory syndrome, Middle East respiratory syndrome, and COVID‐19, have been identified as important pathogens due to their potent infectivity and lethality worldwide. Moreover, currently, no effective antiviral drugs treatments are available so far. In this review, we summarize the biological characters of HCoVs, their association with human diseases, and current therapeutic options for the three severe HCoVs. We also highlight the discussion about novel treatment strategies for HCoVs infections. url: https://www.ncbi.nlm.nih.gov/pubmed/33173860/ doi: 10.1002/mco2.26 id: cord-007796-zggk0x2q author: Lindemans, Caroline A. title: The Immune Response to Viral Lower Respiratory Tract Infection date: 2005 words: 9767.0 sentences: 518.0 pages: flesch: 38.0 cache: ./cache/cord-007796-zggk0x2q.txt txt: ./txt/cord-007796-zggk0x2q.txt summary: In respect to the role of viruses in the pathogenesis of acute and chronic airway disease in children, it is of utmost importance that we gain a proper understanding of the underlying mechanisms involved in order to design effective therapeutic and preventive strategies. Epithelial cells are key regulators of the innate immune response against viral infections (Garofalo and Haeberle, 2000) , producing a number of inflammatory mediators in response to RSV infection. In summary, in RSV lower respiratory tract infections, cytotoxic CD8ϩ T-cells are involved in viral clearance while the humoral response is required for the protection against reinfection. The innate immune defense to viral respiratory tract infections consists of the mucosal layer, type 1 interferons, activated phagocytes, and NK-cells. A key question is whether the association with the development of asthma is merely an expression of increased susceptibility to both asthma and RSV-induced lower respiratory tract infections or whether true causality is involved. abstract: Viruses are responsible for the majority of respiratory infections in childhood,causing considerable morbidity and mortality. It is estimated that in the United States approximately $ 652 million per year is spent on medical costs for respiratory syncytial virus (RSV) related disease alone (Paramore et al., 2004). Viruses cause a variety of respiratory diseases in children from the common cold to life-threatening pneumonia and bronchiolitis. The host reacts to a viral infection with a combination of innate and adaptive immune mechanisms, usually resulting in the clearance of the virus and clinical recovery. However, there is an accumulating evidence for a number of viral infections that the host immune response actually enhances disease in the course of clearing virus from the infected organs. Interestingly, the effectiveness of the immune response seems to be dependent on the age and probably genetic background of the child. This has important implications for treatment as well as vaccine development. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123507/ doi: 10.1007/0-387-25342-4_4 id: cord-274763-i6e3g3te author: Liu, Wen-Kuan title: Epidemiology of HBoV1 infection and relationship with meteorological conditions in hospitalized pediatric patients with acute respiratory illness: a 7-year study in a subtropical region date: 2018-07-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Human bocavirus 1 (HBoV1) is an important cause of acute respiratory illness (ARI), yet the epidemiology and effect of meteorological conditions on infection is not fully understood. To investigate the distribution of HBoV1 and determine the effect of meteorological conditions, hospitalized pediatric patients were studied in a subtropical region of China. METHODS: Samples from 11,399 hospitalized pediatric patients (≤14 years old), with ARI were tested for HBoV1 and other common respiratory pathogens using real-time PCR, between July 2009 and June 2016. In addition, local meteorological data were collected. RESULTS: Of the 11,399 patients tested, 5606 (49.2%) were positive for at least one respiratory pathogen. Two hundred forty-eight of 11,399 (2.2%) were positive for HBoV1 infection. Co-infection was common in HBoV1-positive patients (45.2%, 112/248). A significant difference in the prevalence of HBoV1 was found in patients in different age groups (p < 0.001), and the peak prevalence was found in patients aged 7–12 months (4.7%, 56/1203). Two HBoV1 prevalence peaks were found in summer (between June and September) and winter (between November and December). The prevalence of HBoV1 was significantly positively correlated with mean temperature and negatively correlated with mean relative humidity, and the mean temperature in the preceding month had better explanatory power than the current monthly temperature. CONCLUSIONS: This study provides a better understanding of the characteristics of HBoV1 infection in children in subtropical regions. Data from this study provide useful information for the future control and prevention of HBoV1 infections. url: https://www.ncbi.nlm.nih.gov/pubmed/30012099/ doi: 10.1186/s12879-018-3225-3 id: cord-257656-z7zx46gd author: Ljubin-Sternak, Sunčanica title: The Emerging Role of Rhinoviruses in Lower Respiratory Tract Infections in Children – Clinical and Molecular Epidemiological Study From Croatia, 2017–2019 date: 2019-12-03 words: 4806.0 sentences: 221.0 pages: flesch: 49.0 cache: ./cache/cord-257656-z7zx46gd.txt txt: ./txt/cord-257656-z7zx46gd.txt summary: title: The Emerging Role of Rhinoviruses in Lower Respiratory Tract Infections in Children – Clinical and Molecular Epidemiological Study From Croatia, 2017–2019 Therefore, we investigated the rhinovirus (RV) infection prevalence over a 2-year period, compared it with prevalence patterns of other common respiratory viruses, and explored clinical and molecular epidemiology of RV infections among 590 children hospitalized with acute respiratory infection in north-western and central parts of Croatia. Therefore, we investigated the rhinovirus (RV) infection prevalence over a 2-year period, compared it with prevalence patterns of other common respiratory viruses, and explored clinical and molecular epidemiology of RV infections among 590 children hospitalized with acute respiratory infection in north-western and central parts of Croatia. This study aims to determine the RV prevalence, compare it with prevalence patterns of other common respiratory viruses, as well as to explore clinical and molecular epidemiological features of RV infections among hospitalized children with acute respiratory infection. abstract: Rhinoviruses (RVs) are increasingly implicated not only in mild upper respiratory tract infections, but also in more severe lower respiratory tract infections; however, little is known about species diversity and viral epidemiology of RVs among the infected children. Therefore, we investigated the rhinovirus (RV) infection prevalence over a 2-year period, compared it with prevalence patterns of other common respiratory viruses, and explored clinical and molecular epidemiology of RV infections among 590 children hospitalized with acute respiratory infection in north-western and central parts of Croatia. For respiratory virus detection, nasopharyngeal and pharyngeal flocked swabs were taken from each patient and subsequently analyzed with multiplex RT-PCR. To determine the RV species in a subset of positive children, 5′UTR in RV-positive samples has been sequenced. Nucleotide sequences of referent RV strains were retrieved by searching the database with Basic Local Alignment Tool, and used to construct alignments and phylogenetic trees using MAFFT multiple sequence alignment tool and the maximum likelihood method, respectively. In our study population RV was the most frequently detected virus, diagnosed in 197 patients (33.4%), of which 60.4% was detected as a monoinfection. Median age of RV-infected children was 2.25 years, and more than half of children infected with RV (55.8%) presented with lower respiratory tract infections. Most RV cases were detected from September to December, and all three species co-circulated during the analyzed period (2017–2019). Sequence analysis based on 5′UTR region yielded 69 distinct strains; the most prevalent was RV-C (47.4%) followed by RV-A (44.7%) and RV-B (7.9%). Most of RV-A sequences formed a distinct phylogenetic group; only strains RI/HR409-18 (along with a reference strain MF978777) clustered with RV-C strains. Strains belonging to the group C were the most diverse (41.6% identity among strains), while group B was the most conserved (71.5% identity among strains). Despite such differences in strain groups (hitherto undescribed in Croatia), clinical presentation of infected children was rather similar. Our results are consistent with newer studies that investigated the etiology of acute respiratory infections, especially those focused on children with lower respiratory tract infections, where RVs should always be considered as potentially serious pathogens. url: https://www.ncbi.nlm.nih.gov/pubmed/31849887/ doi: 10.3389/fmicb.2019.02737 id: cord-337137-0ey40gzw author: Lo, Anthony WI title: How the SARS coronavirus causes disease: host or organism? date: 2005-12-17 words: 5201.0 sentences: 289.0 pages: flesch: 45.0 cache: ./cache/cord-337137-0ey40gzw.txt txt: ./txt/cord-337137-0ey40gzw.txt summary: Published by John Wiley & Sons, Ltd. Severe acute respiratory syndrome (SARS) is a new viral disease caused by a novel coronavirus, SARS-CoV ( Figure 1 ) [1, 2] . Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for pathogenesis and virus transmission pathways Tissue and cellular tropism of the coronavirus associated with severe acute respiratory syndrome: an in-situ hybridization study of fatal cases Detection of severe acute respiratory syndrome-associated coronavirus in pneumocytes of the lung Immunohistochemical, in situ hybridization, and ultrastructural localization of SARS-associated coronavirus in lung of a fatal case of severe acute respiratory syndrome in Taiwan Retroviruses pseudotyped with the severe acute respiratory syndrome coronavirus spike protein efficiently infect cells expressing angiotensin-converting enzyme 2 The severe acute respiratory syndrome coronavirus 3a protein up-regulates expression of fibrinogen in lung epithelial cells Autoantibodies against human epithelial cells and endothelial cells after severe acute respiratory syndrome (SARS)-associated coronavirus infection abstract: The previous epidemic of severe acute respiratory syndrome (SARS) has ended. However, many questions concerning how the aetiological agent, the novel SARS coronavirus (CoV), causes illness in humans remain unanswered. The pathology of fatal cases of SARS is dominated by diffuse alveolar damage. Specific histological changes are not detected in other organs. These contrast remarkably with the clinical picture, in which there are apparent manifestations in multiple organs. Both pathogen and host factors are important in the pathogenesis of SARS. The choice of specific receptors and the unique genome of the SARS‐CoV are important elements in understanding the biology of the pathogen. For the host cells, the outcome of SARS‐CoV infection, whether there are cytopathic effects or not, depends on the cell types that are infected. At the whole‐body level, immune‐mediated damage, due to activation of cytokines and/or chemokines and, perhaps, autoimmunity, may play key roles in the clinical and pathological features of SARS. Continued research is still required to determine the pathogenetic mechanisms involved and to combat this new emerging human infectious disease. Copyright © 2006 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. url: https://www.ncbi.nlm.nih.gov/pubmed/16362992/ doi: 10.1002/path.1897 id: cord-275512-7yik78yc author: Lojkić, Ivana title: Detection and molecular characterisation of bovine corona and toroviruses from Croatian cattle date: 2015-08-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Bovine coronavirus (BCoV) together with bovine torovirus (BToV), both members of the Coronaviridae family, order Nidovirales are the most common viral enteric pathogens. Although studied separately, their joint occurrence and the molecular diversity in cattle in Croatia have not been investigated. METHODS: A survey is carried out on 101 fecal samples from diarrheic young and adult cattle during the 3-year period from i) one large dairy herd, ii) four small herds and iii) three nasal and paired fecal samples from calves with symptoms of respiratory disease. Samples were submitted to RT-PCR and sequencing for BCoV Nucleocapsid gene, BCoV Spike gene and BToV Spike gene. RESULTS: BCoV was detected in 78.8 % of fecal samples from symptomatic cattle and three nasal and paired fecal samples from calves with respiratory symptoms. BToV was detected in 43.2 % of fecal samples from symptomatic cattle and a fecal sample from calves with respiratory symptoms. Molecular characterisation of those viruses revealed some nucleotide and aminoacid differences in relation to reference strains. CONCLUSIONS: BToV should be regarded as a relevant pathogen for cattle that plays a synergistic role in mixed enteric infections. url: https://www.ncbi.nlm.nih.gov/pubmed/26268320/ doi: 10.1186/s12917-015-0511-9 id: cord-282420-0fcyjw7l author: Lu, Cheng-wei title: 2019-nCoV transmission through the ocular surface must not be ignored date: 2020-02-06 words: 309.0 sentences: 27.0 pages: flesch: 59.0 cache: ./cache/cord-282420-0fcyjw7l.txt txt: ./txt/cord-282420-0fcyjw7l.txt summary: key: cord-282420-0fcyjw7l authors: Lu, Cheng-wei; Liu, Xiu-fen; Jia, Zhi-fang cord_uid: 0fcyjw7l On Jan 22, Guangfa Wang, a member of the national expert panel on pneumonia, reported that he was infected by 2019nCoV during the inspection in Wuhan. Unprotected exposure of the eyes to 2019nCoV in the Wuhan Fever Clinic might have allowed the virus to infect the body. 4 Severe acute respiratory syndrome coronavirus (SARSCoV) is predominantly transmitted through direct or indirect contact with mucous membranes in the eyes, mouth, or nose. 5 The fact that exposed mucous membranes and unprotected eyes increased the risk of SARSCoV transmission 4 suggests that exposure of unprotected eyes to 2019nCoV could cause acute respiratory infection. The respiratory tract is probably not the only transmission route for 2019nCoV, and all ophthalmologists examining suspected cases should wear protective eyewear. *Cheng-wei Lu, Xiu-fen Liu, Zhi-fang Jia The severe acute respiratory syndrome abstract: nan url: https://doi.org/10.1016/s0140-6736(20)30313-5 doi: 10.1016/s0140-6736(20)30313-5 id: cord-312613-1nl7q6cy author: Luz Garcia-Garcia, M. title: Pediatric Asthma and Viral Infection() date: 2016-03-26 words: 4089.0 sentences: 231.0 pages: flesch: 48.0 cache: ./cache/cord-312613-1nl7q6cy.txt txt: ./txt/cord-312613-1nl7q6cy.txt summary: Respiratory viral infections, particularly respiratory syncytial virus (RSV) and rhinovirus, are the most importance risk factors for the onset of wheezing in infants and small children. The association between bronchiolitis caused by RSV and the development of recurrent wheezing and/or asthma was first described more than 40 years ago, but it is still unclear whether bronchiolitis causes chronic respiratory symptoms, or if it is a marker for children with a genetic predisposition for developing asthma in the medium or long term. In the Childhood Origins of Asthma (COAST) study, which followed a cohort of 289 newborns with high risk of developing asthma, lower respiratory tract infection associated with rhinovirus was the main risk factor for presenting recurrent wheezing at 3 and 6 years of life, with an odds ratio of 10 for rhinovirus bronchiolitis compared to 2.6 for RSV bronchiolitis. 3 found that 80% of asthma exacerbations in asthmatic children aged 9-11 years were associated with viral respiratory infection, of which two thirds were caused by rhinovirus. abstract: Respiratory viral infections, particularly respiratory syncytial virus (RSV) and rhinovirus, are the most importance risk factors for the onset of wheezing in infants and small children. Bronchiolitis is the most common acute respiratory infection in children under 1 year of age, and the most common cause of hospitalization in this age group. RSV accounts for approximately 70% of all these cases, followed by rhinovirus, adenovirus, metapneumovirus and bocavirus. The association between bronchiolitis caused by RSV and the development of recurrent wheezing and/or asthma was first described more than 40 years ago, but it is still unclear whether bronchiolitis causes chronic respiratory symptoms, or if it is a marker for children with a genetic predisposition for developing asthma in the medium or long term. In any case, sufficient evidence is available to corroborate the existence of this association, which is particularly strong when the causative agent of bronchiolitis is rhinovirus. The pathogenic role of respiratory viruses as triggers for exacerbations in asthmatic patients has not been fully characterized. However, it is clear that respiratory viruses, and in particular rhinovirus, are the most common causes of exacerbation in children, and some type of respiratory virus has been identified in over 90% of children hospitalized for an episode of wheezing. Changes in the immune response to viral infections in genetically predisposed individuals are very likely to be the main factors involved in the association between viral infection and asthma. url: https://api.elsevier.com/content/article/pii/S1579212916300106 doi: 10.1016/j.arbr.2016.03.010 id: cord-026005-f2khcjdy author: López, Alfonso title: Respiratory System, Mediastinum, and Pleurae date: 2017-02-17 words: 57323.0 sentences: 2749.0 pages: flesch: 34.0 cache: ./cache/cord-026005-f2khcjdy.txt txt: ./txt/cord-026005-f2khcjdy.txt summary: Microscopic examination of properly collected, stored, and processed samples may reveal many erythrocytes and siderophages in pulmonary hemorrhage or left-sided heart failure; inclusion bodies or syncytial cells in viral pneumonias; increased number of leukocytes in pulmonary inflammation; abundant mucus in asthma or equine recurrent airway obstruction (RAO); the presence of pulmonary pathogens, such as parasites, fungi, and bacteria; or tumor cells in cases of pulmonary neoplasia. The portal of entry for the respiratory form is typically aerogenous, and the disease is generally transient; thus the primary viral-induced lesions in the nasal mucosa and lungs are rarely seen at necropsy unless complicated by secondary bacterial rhinitis, pharyngitis, or bronchopneumonia. Laryngeal edema occurs in pigs with edema disease; in horses with purpura hemorrhagica; in cattle with acute interstitial pneumonia; in cats with systemic anaphylaxis; and in all species as a result of trauma, improper endotracheal tubing, inhalation of irritant gases (e.g., smoke), local inflammation, and animal species is classified as fibrinous, catarrhal, purulent, or granulomatous (Figs. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7271179/ doi: 10.1016/b978-0-323-35775-3.00009-6 id: cord-258386-aiwzgkq3 author: MCLAREN, Rodney A. title: Delivery For Respiratory Compromise Among Pregnant Women With COVID-19 date: 2020-05-23 words: 896.0 sentences: 59.0 pages: flesch: 49.0 cache: ./cache/cord-258386-aiwzgkq3.txt txt: ./txt/cord-258386-aiwzgkq3.txt summary: Of the remaining nine who continued to need respiratory support, seven 39 (77.8%) had iatrogenic preterm deliveries (six by cesarean delivery) for maternal respiratory 40 distress (needing increasing levels of respiratory support without improved oxygen saturation), 41 one had an early term delivery due to PROM, and one, now 30 weeks, has required intensive 42 care with high-flow nasal cannula for three weeks. Of the eight patients delivering with maternal respiratory distress, seven did not require 45 intubation, and one was intubated for emergent cesarean delivery, and remained on a ventilator 46 for 19 days. Of the eight patients delivering with maternal respiratory distress, seven did not require 45 intubation, and one was intubated for emergent cesarean delivery, and remained on a ventilator 46 for 19 days. abstract: Objective While rapid recourse to delivery after failed CPR has been shown to improve outcomes of pregnant patients with cardiac arrest,1,2 it is not known whether delivery improves or compromises the outcome of COVID patients with respiratory failure.3,4 Our objective was to evaluate the safety and utility of delivery of COVID-19 infected pregnant women needing respiratory support. Study Design This is a retrospective observational study of COVID-19 infected pregnant women (PCR diagnosed), with severe disease (defined per prior publications.3). A subset of these cases was previously presented, but without detail on the effect of delivery on disease (London, et al. “The Relationship Between Status at Presentation and Outcomes Among Pregnant Women with COVID-19” Am J Perinatol., in press). The study was exempted by IRB. Results Of 125 confirmed cases of COVID-19, twelve (9.6%) had severe disease (Table 1). Among the 12, three resolved spontaneously after transient respiratory support in hospital and were discharged home (one subsequently returned in preterm labor and delivered by cesarean two weeks later). Of the remaining nine who continued to need respiratory support, seven (77.8%) had iatrogenic preterm deliveries (six by cesarean delivery) for maternal respiratory distress (needing increasing levels of respiratory support without improved oxygen saturation), one had an early term delivery due to PROM, and one, now 30 weeks, has required intensive care with high-flow nasal cannula for three weeks. Of the eight patients delivering with maternal respiratory distress, seven did not require intubation, and one was intubated for emergent cesarean delivery, and remained on a ventilator for 19 days. Among the non-intubated, four had an improvement in oxygenation within two hours postpartum; two required less respiratory support, and two were taken completely off respiratory support. None of the other three required an increased level of respiratory support, and were off of all support between four and seven days postpartum. Conclusion Delivery did not worsen the respiratory status of women with persistent oxygen desaturation and the need for increasing respiratory support. Among women not needing a ventilator, return of normal respiratory status after delivery occurred within hours to days. The one patient intubated intraoperatively took longer to recover. It is possible delivery may be less salutary when damage to the lungs are sufficient to warrant intubation. This series suggests that maternal respiratory distress should not be a contraindication to delivery. url: https://api.elsevier.com/content/article/pii/S0002937820305676 doi: 10.1016/j.ajog.2020.05.035 id: cord-023711-xz5ftnat author: MORENO-LÓPEZ, J. title: Acute Respiratory Disease in Cattle date: 2013-11-17 words: 1525.0 sentences: 85.0 pages: flesch: 49.0 cache: ./cache/cord-023711-xz5ftnat.txt txt: ./txt/cord-023711-xz5ftnat.txt summary: Acute respiratory disease in cattle is not attributable to a single etiological agent. However, if PI3 virus or BVDV has been isolated, you have diagnosed the infection but not an "acute respiratory/enteric disease", because other viruses and also bacteria might be etiologically involved. At the end of the 1950s, "shipping fever" was described as a disease following massive transports to or from the enormous feedlots of the USA, and PI3 virus was isolated as the first virus of a condition with a multiple viral etiology. The types 4, 5 and 7 have been described each as a single causative agent of acute respiratory-enteric disease in Hungary and Japan, respectively. The isolation of these viruses from apparently healthy cattle as well as from those with acute respiratory-enteric disease indicates that they are widespread. A serosurvey of viruses during outbreaks of acute respiratory and/or enteric disease in Swedish cattle abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173503/ doi: 10.1016/b978-0-444-87312-5.50075-8 id: cord-007222-31o180fz author: MUFSON, MAURICE A. title: EPIDEMIOLOGY OF RESPIRATORY SYNCYTIAL VIRUS INFECTION AMONG INFANTS AND CHILDREN IN CHICAGO date: 1973-08-17 words: 2723.0 sentences: 146.0 pages: flesch: 49.0 cache: ./cache/cord-007222-31o180fz.txt txt: ./txt/cord-007222-31o180fz.txt summary: From January 1, 1967 to December 1971, the temporal pattern of respiratory syncytial virus infection was investigated in infants and children younger than 18 months hospitalized for acute lower respiratory tract disease. Of 4696 infants and children with acute lower respiratory tract disease admitted to the Cook County Hospital, 2530 were tested for virus infection by virus isolation or serologic procedures or both. This report describes the periodic pattern of RSV infection in infants and children with lower respiratory tract disease admitted to the Cook County Hospital in Chicago, between January 1, 1967 and December 31, 1971. The study group comprised infants and children younger than 18 months of age admitted to the Cook County Hospital because of acute lower respiratory tract disease. DISCUSSION This continuing surveillance study of virus infections in infants and young children with acute lower respiratory tract disease describes the cyclical pattern of occurrence of RSV infections. abstract: From January 1, 1967 to December 1971, the temporal pattern of respiratory syncytial virus infection was investigated in infants and children younger than 18 months hospitalized for acute lower respiratory tract disease. Of 4696 infants and children with acute lower respiratory tract disease admitted to the Cook County Hospital, 2530 were tested for virus infection by virus isolation or serologic procedures or both. Overall, respiratory syncytial virus infections were detected in 12% and parainfluenza 3 virus in 10.8% of individuals tested. Other respiratory viruses were less commonly identified. Respiratory syncytial virus epidemics occurred annually and were temporally synchronous with the peak periods of respiratory disease admissions. Only during epidemics of respiratory syncytial virus did admission for respiratory tract disease usually reach 40 patients or more weekly. The peak months of respiratory syncytial virus epidemics were December 1966, January 1968, February-March 1969, April 1970 and January 1971. Epidemics lasted about 17 weeks. No similar annual epidemic pattern was seen with the other myxoviruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7109929/ doi: 10.1093/oxfordjournals.aje.a121542 id: cord-284905-h8xovybl author: MUSK, A.W. (Bill) title: Respiratory infections and lung function in an Australian Aboriginal community date: 2008-02-05 words: 3449.0 sentences: 178.0 pages: flesch: 43.0 cache: ./cache/cord-284905-h8xovybl.txt txt: ./txt/cord-284905-h8xovybl.txt summary: Background and objective: To investigate the association between serological evidence of past infections with common respiratory pathogens and lung function in members of an isolated community of Aborigines from tropical coastal north‐western Australia. 3 Studies of members of an isolated coastal Australian Aboriginal community in the tropical Kimberley region of Western Australia have shown that levels of lung function measured by FEV1 and FVC were lower than those of Australians of European descent. In this tropical Aboriginal community, serological evidence of the burden of previous infections with known viral and other respiratory pathogens was associated with significant decreases in the levels of airway function, consistent with airflow obstruction. The relationship of FEV1 and FEV1/FVC ratio with the total number of positive titres in this study suggests that repeated infections with common respiratory pathogens may have a cumulative detrimental effect on airway function or increase susceptibility to other agents such as tobacco smoke. abstract: Background and objective: To investigate the association between serological evidence of past infections with common respiratory pathogens and lung function in members of an isolated community of Aborigines from tropical coastal north‐western Australia. Methods: FEV(1) and FVC were assessed by dry bellows spirometer. Serum IgG titres to 11 common respiratory pathogens were assayed. Smoking history was assessed by questionnaire. Reciprocal positive IgG titres were taken as ≥10 for all pathogens with the exception of Legionella spp. (≥40) and Burkholderia pseudomallei (≥20). Linear regression analysis examined associations between titres and lung function after adjustment for age, height, gender and smoking, separately for adults (age > 17 years) and children. Results: An increased total number of positive IgG titres was significantly associated with reduced FEV(1) (P = 0.01) and FEV(1)/FVC ratio (P = 0.01) suggesting the presence of airflow obstruction. This association was independent of age, gender, height, weight and smoking status. Conclusions: The burden of past respiratory infections may be an important determinant of airway function in this Aboriginal community. url: https://doi.org/10.1111/j.1440-1843.2007.01221.x doi: 10.1111/j.1440-1843.2007.01221.x id: cord-004397-ypli7wtu author: Ma, Zhan-Ying title: Suspension microarray-based comparison of oropharyngeal swab and bronchoalveolar lavage fluid for pathogen identification in young children hospitalized with respiratory tract infection date: 2020-02-22 words: 3229.0 sentences: 183.0 pages: flesch: 44.0 cache: ./cache/cord-004397-ypli7wtu.txt txt: ./txt/cord-004397-ypli7wtu.txt summary: title: Suspension microarray-based comparison of oropharyngeal swab and bronchoalveolar lavage fluid for pathogen identification in young children hospitalized with respiratory tract infection The primary purpose of this study was to compare the detection rates of OPS and paired BALF in detecting key respiratory pathogens using suspension microarray. In the present study, we used the suspension microarray, a multipathogen detection platform, to simultaneously detect viral and bacterial respiratory pathogens in matched OPS and BALF specimens from pediatric patients for comparison of the sensitivities between the two sample types. To compare the OPS and paired BALF for pathogens detection in young children with RTI, we tested the two sample types using suspension microarray. In the present study, we used suspension array to simultaneously detect multiple viral and bacterial pathogens in paired BALF and OPS specimens from symptomatic patients hospitalized with respiratory illness. We used suspension-array to compare BALF and paired OPS specimens for detecting multiple pathogens in children hospitalized with respiratory illness. abstract: BACKGROUND: Respiratory tract infection (RTI) in young children is a leading cause of morbidity and hospitalization worldwide. There are few studies assessing the performance for bronchoalveolar lavage fluid (BALF) versus oropharyngeal swab (OPS) specimens in microbiological findings for children with RTI. The primary purpose of this study was to compare the detection rates of OPS and paired BALF in detecting key respiratory pathogens using suspension microarray. METHODS: We collected paired OPS and BALF specimens from 76 hospitalized children with respiratory illness. The samples were tested simultaneously for 8 respiratory viruses and 5 bacteria by suspension microarray. RESULTS: Of 76 paired specimens, 62 patients (81.6%) had at least one pathogen. BALF and OPS identified respiratory pathogen infections in 57 (75%) and 49 (64.5%) patients, respectively (P > 0.05). The etiology analysis revealed that viruses were responsible for 53.7% of the patients, whereas bacteria accounted for 32.9% and Mycoplasma pneumoniae for 13.4%. The leading 5 pathogens identified were respiratory syncytial virus, Streptococcus pneumoniaee, Haemophilus influenzae, Mycoplasma pneumoniae and adenovirus, and they accounted for 74.2% of etiological fraction. For detection of any pathogen, the overall detection rate of BALF (81%) was marginally higher than that (69%) of OPS (p = 0.046). The differences in the frequency distribution and sensitivity for most pathogens detected by two sampling methods were not statistically significant. CONCLUSIONS: In this study, BALF and OPS had similar microbiological yields. Our results indicated the clinical value of OPS testing in pediatric patients with respiratory illness. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7036252/ doi: 10.1186/s12879-020-4900-8 id: cord-289697-g24xib4l author: MacDowell, Ana L. title: Infectious triggers of asthma date: 2005-03-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: There is abundant evidence that asthma is frequently exacerbated by infectious agents. Several viruses have been implicated in the inception and exacerbation of asthma. Recent attention has been directed at the role of infections with the atypical bacteria Mycoplasma pneumoniae and Chlamydia pneumoniae as agents capable of triggering asthma exacerbations and potentially as inciting agents for asthma. This article examines the evidence for interaction between specific infectious agents and exacerbations of asthma, including the immunopathology of infection-triggered asthma, and the current therapeutic options for management. url: https://www.sciencedirect.com/science/article/pii/S0889856104000992 doi: 10.1016/j.iac.2004.09.011 id: cord-016499-5iqpl23p author: Mackay, Ian M. title: Rhinoviruses date: 2014-02-27 words: 23394.0 sentences: 1156.0 pages: flesch: 45.0 cache: ./cache/cord-016499-5iqpl23p.txt txt: ./txt/cord-016499-5iqpl23p.txt summary: A convenience population of 15 healthy children (1-9 years old) without asthma were followed during at least three seasons, and picornaviruses were detected in 5 % of 740 specimens (21 % of infections) not associated with symptoms, The impact of HRV typing and of sampling based only on symptoms. Clinical features and complete genome characterization of a distinct human rhinovirus genetic cluster, probably representing a previously undetected HRV species, HRV-C, associated with acute respiratory illness in children Comparison of results of detection of rhinovirus by PCR and viral culture in human nasal wash specimens from subjects with and without clinical symptoms of respiratory illness Detection of human rhinovirus C viral genome in blood among children with severe respiratory infections in the Philippines abstract: Picornaviruses, which include the human rhinoviruses (HRVs) and enteroviruses (EVs), are the most frequent cause of acute human illness worldwide. HRVs are the most prevalent cause of acute respiratory tract illnesses (ARIs) which usually commence in the upper respiratory tract (URT). ARIs are the leading cause of morbidity in children under 5 years and occur in all seasons. ARIs linked to HRV infections are associated with excessive and perhaps inappropriate antibiotic prescribing and with significant direct and indirect healthcare expenditure. ARI incidence is highest in the first 2 years of life, with up to thirteen episodes per year including up to six positive for an HRV, and it is not uncommon to average one infection per child-month. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120790/ doi: 10.1007/978-1-4899-7448-8_29 id: cord-349287-mwj2qby4 author: Mackay, Ian M. title: MERS coronavirus: diagnostics, epidemiology and transmission date: 2015-12-22 words: 14290.0 sentences: 671.0 pages: flesch: 51.0 cache: ./cache/cord-349287-mwj2qby4.txt txt: ./txt/cord-349287-mwj2qby4.txt summary: The first known cases of Middle East respiratory syndrome (MERS), associated with infection by a novel coronavirus (CoV), occurred in 2012 in Jordan but were reported retrospectively. Most human cases of MERS have been linked to lapses in infection prevention and control (IPC) in healthcare settings, with approximately 20 % of all virus detections reported among healthcare workers (HCWs) and higher exposures in those with occupations that bring them into close contact with camels. Since asymptomatic zoonoses have been posited [72] , an absence of antibodies to MERS-CoV among some humans who have regular and close contact with camels may reflect the rarity of actively infected animals at butcheries, a limited transmission risk associated with slaughtering DCs [70] , a pre-existing cross-protective immune status or some other factor(s) resulting in a low risk of disease and concurrent seroconversion developing after exposure in this group. First cases of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infections in France, investigations and implications for the prevention of human-tohuman transmission abstract: The first known cases of Middle East respiratory syndrome (MERS), associated with infection by a novel coronavirus (CoV), occurred in 2012 in Jordan but were reported retrospectively. The case first to be publicly reported was from Jeddah, in the Kingdom of Saudi Arabia (KSA). Since then, MERS-CoV sequences have been found in a bat and in many dromedary camels (DC). MERS-CoV is enzootic in DC across the Arabian Peninsula and in parts of Africa, causing mild upper respiratory tract illness in its camel reservoir and sporadic, but relatively rare human infections. Precisely how virus transmits to humans remains unknown but close and lengthy exposure appears to be a requirement. The KSA is the focal point of MERS, with the majority of human cases. In humans, MERS is mostly known as a lower respiratory tract (LRT) disease involving fever, cough, breathing difficulties and pneumonia that may progress to acute respiratory distress syndrome, multiorgan failure and death in 20 % to 40 % of those infected. However, MERS-CoV has also been detected in mild and influenza-like illnesses and in those with no signs or symptoms. Older males most obviously suffer severe disease and MERS patients often have comorbidities. Compared to severe acute respiratory syndrome (SARS), another sometimes- fatal zoonotic coronavirus disease that has since disappeared, MERS progresses more rapidly to respiratory failure and acute kidney injury (it also has an affinity for growth in kidney cells under laboratory conditions), is more frequently reported in patients with underlying disease and is more often fatal. Most human cases of MERS have been linked to lapses in infection prevention and control (IPC) in healthcare settings, with approximately 20 % of all virus detections reported among healthcare workers (HCWs) and higher exposures in those with occupations that bring them into close contact with camels. Sero-surveys have found widespread evidence of past infection in adult camels and limited past exposure among humans. Sensitive, validated reverse transcriptase real-time polymerase chain reaction (RT-rtPCR)-based diagnostics have been available almost from the start of the emergence of MERS. While the basic virology of MERS-CoV has advanced over the past three years, understanding of the interplay between camel, environment, and human remains limited. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12985-015-0439-5) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12985-015-0439-5 doi: 10.1186/s12985-015-0439-5 id: cord-348490-dqabq6d8 author: Maeder, Muriel N. title: Sickle-cell disease in febrile children living in a rural village of Madagascar and association with malaria and respiratory infections date: 2016-12-01 words: 4287.0 sentences: 210.0 pages: flesch: 49.0 cache: ./cache/cord-348490-dqabq6d8.txt txt: ./txt/cord-348490-dqabq6d8.txt summary: title: Sickle-cell disease in febrile children living in a rural village of Madagascar and association with malaria and respiratory infections From May 2011 to November 2013, a cross-sectional study was conducted in the rural village of Ampasimanjeva in the south east cost of Madagascar aiming to identify blood-borne protein biomarkers that can differentiate the causes of unexplained acute febrile illness in children. Our study shows that prevalence of SCD was 2.4% and that of SCT 23.8% among children aged 2-59 months presenting with fever and living in high endemic area for malaria. However, among the 23 viral and atypical bacteria pathogens studied, there was no statistical difference in prevalence between the three groups for 20 of them and include HRV the most common respiratory virus detected or influenza virus A (H1N1)/ pdm09 known to increase disease severity in children with SCD [29] . abstract: BACKGROUND: In Madagascar, the last study on sickle cell disease (SCD) was done in the early 1980s. The country is known as endemic for malaria and respiratory infections. The main objective of this study was to estimate the prevalence of SCD; the secondary objective was to evaluate its association with malaria and respiratory infections. METHODS: This is a cross-sectional study which was carried out in a rural village in the south east coast of Madagascar between May 2011 and November 2013. Participants were children aged between 2–59 months presenting with fever measured by axillary temperature ≥37.5 °C at inclusion. Genotyping of haemoglobin S was done by PCR and malaria was diagnosed by Rapid Diagnostic Test. Research for viral and atypical bacterial respiratory pathogens was performed on nasopharyngeal swabs. Uni-and multivariate polytomous logistic regression was done to assess associations between microbiological results and SCD status, with HbAA phenotype as reference. RESULTS: A total of 807 children were analysed. Prevalence of SCD among febrile children was 2.4% (95% CI, 1.5–3.7%) and that of SCT was 23.8% (95% CI, 20.9–26.9%). There was no difference in the prevalence of malaria infection according to haemoglobin status (p = 0.3). Rhinovirus (22.5%), adenovirus (14.1%), and bocavirus (11.6%) were the most common respiratory pathogens detected. After univariate analysis, patients with SCD were more frequently infected by parechovirus (p = 0.01), while patients with SCT were more prone to RSV A or B infection (p = 0.01). After multivariate analysis, HbAS phenotype was associated with higher risk of RSV A and B infection compared to HbAA (adjusted OR = 1.9; 95% CI: 1.2–3.1, p = 0.009), while HbSS phenotype was associated with higher risk of parechovirus infection (adjusted OR = 6.0; 95% CI: 1.1–31.3, p = 0.03) compared to HbAA, independently of age, gender, period per quarter, and the other viruses. CONCLUSION: The prevalence of SCD among under-five children presenting with fever was high in the study population. No association was found between SCT and malaria but few viruses, especially parechovirus, seem to play an important role in the occurrence of pneumoniae among SCD patients. url: https://www.ncbi.nlm.nih.gov/pubmed/27980789/ doi: 10.1186/s12878-016-0069-1 id: cord-342993-deuytbml author: Maffey, Alberto F. title: Viruses and atypical bacteria associated with asthma exacerbations in hospitalized children date: 2010-05-06 words: 3285.0 sentences: 167.0 pages: flesch: 47.0 cache: ./cache/cord-342993-deuytbml.txt txt: ./txt/cord-342993-deuytbml.txt summary: 3 Various viral agents, including the respiratory syncytial virus (HRSV), influenza A and B (FLUAV and FLUBV), parainfluenza (HPIV), adenovirus (HAdV), rhinovirus (HRV), enterovirus (HEV), coronavirus (HCoV), and the recently described metapneumovirus (HMPV) 4 and bocavirus (HBoV) 5 have been detected in patients presenting with asthma exacerbation. [10] [11] We performed a cross-sectional study to determine by means of immunofluorescence assay (IFA) and molecular techniques the prevalence of traditional and newly described respiratory viruses and atypical bacteria in children hospitalized due to an acute asthma exacerbation in Buenos Aires, a temperate southern hemisphere city. [30] [31] In conclusion, the present study confirms the high prevalence of respiratory viruses in hospitalized children with an acute asthma exacerbation, highlights the importance both of HRSV and HRV in all age groups, and describes their seasonal pattern in a temperate Southern Hemisphere location. abstract: OBJECTIVES AND WORKING HYPOTHESIS: To evaluate the prevalence of respiratory viruses Mycoplasma pneumoniae and Chlamydophila pneumoniae and gain insight into their seasonal circulation pattern in children with acute asthma exacerbations in a temperate southern hemisphere region. STUDY DESIGN: Patients hospitalized between 3 months and 16 years of age were included in a 1‐year prospective, observational, cross‐sectional study. Respiratory secretions were collected and the presence of different viruses and atypical bacteria analyzed by immunofluorescence and polymerase chain reaction. RESULTS: Two hundred nine patients (118 females) aged (mean ± SD) 4.4 ± 4 years were included. A potential causative agent was detected in 78% of the patients. The most frequently detected viruses were respiratory syncytial virus (HRSV) (n = 85; 40%) and rhinovirus (HRV) (n = 52; 24.5%); M. pneumoniae and C. pneumoniae were detected in 4.5% and 2% of the cases, respectively. Patients with HRSV (vs. HRV) were hospitalized for a longer time (6.7 vs. 5.2 days, P = 0.012), required more days of oxygen supply (5.1 vs. 3.4, P = 0.005), had a longer duration of the exacerbation before hospitalization (3.6 vs. 1.9 days, P = 0.001) and were younger (3.7 vs. 5.1 years, P = 0.012). Three peaks of admissions were observed. A first peak (early autumn) caused by HRV, a second peak (winter) caused mainly by HRSV and a third one (spring), caused by HRSV, an increase in HMPV together with a second outbreak of HRV. CONCLUSIONS: Children with an acute asthma exacerbation presented a high prevalence of respiratory viruses. Most hospitalizations corresponded to seasonal increases in prevalence of HRV and HRSV. Pediatr Pulmonol. 2010; 45:619–625. © 2010 Wiley‐Liss, Inc. url: https://doi.org/10.1002/ppul.21236 doi: 10.1002/ppul.21236 id: cord-027550-yyqsatqw author: Mammas, Ioannis N. title: Update on current views and advances on RSV infection (Review) date: 2020-06-15 words: 7970.0 sentences: 390.0 pages: flesch: 35.0 cache: ./cache/cord-027550-yyqsatqw.txt txt: ./txt/cord-027550-yyqsatqw.txt summary: abstract: Respiratory syncytial virus (RSV) infection represents an excellent paradigm of precision medicine in modern paediatrics and several clinical trials are currently performed in the prevention and management of RSV infection. A new taxonomic terminology for RSV was recently adopted, while the diagnostic and omics techniques have revealed new modalities in the early identification of RSV infections and for better understanding of the disease pathogenesis. Coordinated clinical and research efforts constitute an important step in limiting RSV global predominance, improving epidemiological surveillance, and advancing neonatal and paediatric care. This review article presents the key messages of the plenary lectures, oral presentations and posters of the '5th workshop on paediatric virology' (Sparta, Greece, 12th October 2019) organized by the Paediatric Virology Study Group, focusing on recent advances in the epidemiology, pathogenesis, diagnosis, prognosis, clinical management and prevention of RSV infection in childhood. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7307844/ doi: 10.3892/ijmm.2020.4641 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-257299-z9u12yqb author: Mansi, N. title: Ear, nose and throat manifestation of viral systemic infections in pediatric patients date: 2009-12-31 words: 5779.0 sentences: 291.0 pages: flesch: 42.0 cache: ./cache/cord-257299-z9u12yqb.txt txt: ./txt/cord-257299-z9u12yqb.txt summary: Common childhood viral infections, such as measles and mumps are probably an unrecognized cause of acute or progressive damage to hearing [5] . Measles infection can be avoided by administering a reduced, live-virus vaccine to children between the ages of 12 and 15 months (MMR). The etiology of the acute forms in the respiratory airways is, initially, of a viral nature in most patients, with later, secondary bacterial infections on the mucous lesions caused by the viral agents [31] . Herpangina is an extremely contagious illness caused by a coxackievirus characterized by a presence of a vesicular exanthema at the velopharyngeal mucous level and acute or croup laryngotracheitis [38] [39] [40] [41] when viral infections are associated. The most common manifestation of the primary infection of this organism is infective mononucleosis (IM), a sometimes acute, but often asymptomatic clinical syndrome which more often strikes children, adolescents, and young adults [82] . Viral etiology and epidemiology of acute lower respiratory tract infections in children abstract: Abstract Objective/Methods An exhaustive review of literature was performed to investigate available data and evidences regarding pediatric otolaryngologic manifestations of viral systemic infections. Results/Conclusions Modern otolaryngologists should be familiar with viral systemic infections since many have head and neck manifestations. Cooperation between otolaryngologist, paediatrician and virologist can be considered and excellent tool in diagnosis and treatment of these diseases in particular when complications occur. url: https://www.ncbi.nlm.nih.gov/pubmed/20114152/ doi: 10.1016/s0165-5876(09)70006-0 id: cord-268251-mcg1v24t author: Martins, Ronaldo Bragança title: Detection of respiratory viruses by real-time polymerase chain reaction in outpatients with acute respiratory infection date: 2014-09-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Viruses are the major contributors to the morbidity and mortality of upper and lower acute respiratory infections (ARIs) for all age groups. The aim of this study was to determine the frequencies for a large range of respiratory viruses using a sensitive molecular detection technique in specimens from outpatients of all ages with ARIs. Nasopharyngeal aspirates were obtained from 162 individuals between August 2007-August 2009. Twenty-three pathogenic respiratory agents, 18 respiratory viruses and five bacteria were investigated using multiplex real-time reverse transcriptase polymerase chain reaction (RT-PCR) and indirect immunofluorescence assay (IIF). Through IIF, 33 (20.4%) specimens with respiratory virus were recognised, with influenza virus representing over half of the positive samples. Through a multiplex real-time RT-PCR assay, 88 (54.3%) positive samples were detected; the most prevalent respiratory viral pathogens were influenza, human rhinovirus and respiratory syncytial virus (RSV). Six cases of viral co-detection were observed, mainly involving RSV. The use of multiplex real-time RT-PCR increased the viral detection by 33.9% and revealed a larger number of respiratory viruses implicated in ARI cases, including the most recently described respiratory viruses [human bocavirus, human metapneumovirus, influenza A (H1N1) pdm09 virus, human coronavirus (HCoV) NL63 and HCoV HKU1]. url: https://www.ncbi.nlm.nih.gov/pubmed/25317699/ doi: 10.1590/0074-0276140046 id: cord-265257-p9f0pl3y author: Masoud, Khaldoun title: Viral Etiology of Acute Respiratory Infections in Pediatric Patients in Lebanon date: 2019-11-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Acute respiratory infections (ARI) are the leading cause of death worldwide, especially among children. The majority of these infections in children are of viral etiology. In this study, we evaluated the incidence of viral ARI among children in Lebanon. PATIENTS AND METHODS: Children presenting with symptoms of ARI were prospectively recruited between September 2009 to February 2012. Nasopharyngeal aspirates were obtained from patients and screened for 11 respiratory viruses using a multiplex Luminex-based PCR assay. RESULTS: Two hundred twenty-one patients were recruited with a median age of 1 year (IQR: 0 – 5). Out of 221 patients, 116 (52.5%) were positive for at least one virus, the majority (103/116; 88.8%) of which were in children under 6-year of age. Overall, 188 viruses were detected. Rhinovirus (RhV) was the most common virus detected in 81 (69.8%) patients followed by coxsackie virus and echovirus (CVEV) which were detected as one target in the panel in 45 (38.8%), and parainfluenza viruses (PIV types: 1, 2, 3, 4) in 24 (20.7%) patients. Coinfection with more than one virus was detected in 49 (42.9%) patients. RhV and CVEV were the most common viruses associated with co-infections and higher risk of rhinorrhea. CONCLUSIONS: Viral pathogens account for at least half of the ARIs in Lebanon, with a high frequency of co-infections being detected. url: https://doi.org/10.4084/mjhid.2019.059 doi: 10.4084/mjhid.2019.059 id: cord-347255-fl9lur4h author: May, Larissa title: Rapid Multiplex Testing for Upper Respiratory Pathogens in the Emergency Department: A Randomized Controlled Trial date: 2019-11-05 words: 4057.0 sentences: 181.0 pages: flesch: 40.0 cache: ./cache/cord-347255-fl9lur4h.txt txt: ./txt/cord-347255-fl9lur4h.txt summary: Secondary outcomes included the proportion of patients with a respiratory pathogen identified by the FilmArray Respiratory Panel test or any other upper respiratory pathogen diagnostic test ordered by the physician; the proportion of patients with a laboratory-confirmed influenza diagnosis; the proportion of patients receiving appropriate anti-influenza treatment or prescription in the ED by an emergency medicine clinician (composite rate of anti-influenza treatment in positive patients and nonuse of anti-influenza treatment in negative patients); the proportion of patients discharged home from the ED vs hospital admission; the proportion of patients with all-cause or respiratory illness-related repeat ED visit, hospital or ICU admission, or death within 30 days; clinician adherence to guidelines for the treatment of patients with influenza (recommendations for use of antivirals only); length of ED stay; length of hospital stay; time to influenza test results; and time to other respiratory pathogen test results. Thus, we conducted a randomized clinical trial of the FilmArray RP vs usual care in ED patients with signs or symptoms of upper respiratory infection or influenza-like illness. abstract: BACKGROUND: Acute upper respiratory tract infections are a common cause of emergency department (ED) visits and often result in unnecessary antibiotic treatment. METHODS: We conducted a randomized clinical trial to evaluate the impact of a rapid, multipathogen respiratory panel (RP) test vs usual care (control). Patients were eligible if they were ≥12 months old, had symptoms of upper respiratory infection or influenza-like illness, and were not on antibiotics. The primary outcome was antibiotic prescription; secondary outcomes included antiviral prescription, disposition, and length of stay (ClinicalTrials.gov# NCT02957136). RESULTS: Of 191 patients enrolled, 93 (49%) received RP testing; 98 (51%) received usual care. Fifty-three (57%) RP and 7 (7%) control patients had a virus detected and reported during the ED visit (P = .0001). Twenty (22%) RP patients and 33 (34%) usual care patients received antibiotics during the ED visit (–12%; 95% confidence interval, –25% to 0.4%; P = .06/0.08); 9 RP patients received antibiotics despite having a virus detected. The magnitude of antibiotic reduction was greater in children (–19%) vs adults (–9%, post hoc analysis). There was no difference in antiviral use, length of stay, or disposition. CONCLUSIONS: Rapid RP testing was associated with a trend toward decreased antibiotic use, suggesting a potential benefit from more rapid viral tests in the ED. Future studies should determine if specific groups are more likely to benefit from testing and evaluate the relative cost and effectiveness of broad testing, focused testing, and a combined diagnostic and antimicrobial stewardship approach. url: https://www.ncbi.nlm.nih.gov/pubmed/32128326/ doi: 10.1093/ofid/ofz481 id: cord-324432-k0g3r1lw author: Maykowski, Philip title: Seasonality and clinical impact of human parainfluenza viruses date: 2018-08-29 words: 2340.0 sentences: 123.0 pages: flesch: 41.0 cache: ./cache/cord-324432-k0g3r1lw.txt txt: ./txt/cord-324432-k0g3r1lw.txt summary: PATIENTS/METHODS: This retrospective study was performed from January 2013 to December 2015 in children and adults with HPIV, detected by multiplex reverse transcription polymerase chain reaction, participating in a community surveillance study of acute respiratory infections (ARIs) in New York City and patients admitted to a tertiary care center in the same neighborhood. The community cohort was derived from the Mobile Surveillance for Acute Respiratory Infections (ARIs) and Influenza-like Illness (ILI) in the Community (MoSAIC) study, a 5-year community-based surveillance ordinal logistic regression demonstrated that increased severity of illness was significantly associated with HPIV-4 and chronic cardiovascular and respiratory conditions in children and with age ≥65 years and chronic respiratory conditions in adults. epidemiology, parainfluenza, respiratory, seasonality, viruses F I G U R E 1 Flowcharts depicting the overall number of respiratory viral panel (RVP) tests ordered which yielded the final number of human parainfluenza virus (HPIV) types in the community cohort (1A) and in hospitalized patients (1B) study in New York City (NYC) that includes 250 households annually. abstract: BACKGROUND: Widespread availability of rapid diagnostic testing for respiratory viruses allows more in‐depth studies of human parainfluenza viruses (HPIV). OBJECTIVES: This study aimed to assess seasonality of HPIV types 1‐4, clinical outcomes by HPIV type, and risk factors for illness severity. PATIENTS/METHODS: This retrospective study was performed from January 2013 to December 2015 in children and adults with HPIV, detected by multiplex reverse transcription polymerase chain reaction, participating in a community surveillance study of acute respiratory infections (ARIs) in New York City and patients admitted to a tertiary care center in the same neighborhood. Seasonality trends by HPIV type were compared between the community and hospital groups. The associations between HPIV type, demographics, clinical characteristics, and illness severity were assessed. RESULTS: HPIV was detected in 69 (4%) of 1753 community surveillance participants (median age 9.2 years) and 680 hospitalized patients (median age 6.8 years). Seasonality for HPIV types 1‐3 agreed with previously described patterns; HPIV‐4 occurred annually in late summer and fall. In the community cohort, 22 (32%) participants sought medical care, 9 (13%) reported antibiotic use, and 20 (29%) reported ≥1 day of missed work or school. Among hospitalized patients, 24% had ≥4 chronic conditions. Multivariable ordinal logistic regression demonstrated that increased severity of illness was significantly associated with HPIV‐4 and chronic cardiovascular and respiratory conditions in children and with age ≥65 years and chronic respiratory conditions in adults. CONCLUSIONS: HPIV‐4 presented late summer and early fall annually and was associated with increased severity of illness in hospitalized children. url: https://doi.org/10.1111/irv.12597 doi: 10.1111/irv.12597 id: cord-252012-hdjbxah8 author: McErlean, Peter title: Viral diversity in asthma: Immunology and Allergy Clinics of North America: Asthma and Infectious Disease date: 2010-11-01 words: 5497.0 sentences: 299.0 pages: flesch: 44.0 cache: ./cache/cord-252012-hdjbxah8.txt txt: ./txt/cord-252012-hdjbxah8.txt summary: Traditionally associated with acute respiratory illness (ARI) or symptoms of the "common cold," the respiratory viruses implicated in asthma exacerbations predominantly possess RNA genomes with a distinct genome organization (positive [1] or negative [À] sense), virus particle (virion) morphology (enveloped or nonenveloped), host cell receptor interaction, and well-defined annual or seasonal prevalence. These "newly identified viruses" (NIVs) including human metapneumovirus (HMPV; described pre-SARS), the human rhinovirus (HRV) species C (HRV-Cs), human coronaviruses (HCoVs)-NL63 and -HKU1, human bocavirus (HBoV), and the KI and WU polyomaviruses (KIPyV and WUPyV) are now the focus of intense research, and their involvement in asthma exacerbations is slowly beginning to be determined. 34 In a retrospective study of clinical samples taken over a 20-year period from young children (median age 14.5 months), the percentage of lower respiratory tract illness (LRTI; including asthma exacerbations and bronchiolitis) associated with any HCoV, HCoV-NL63, or HCoV-OC43 was estimated to be 4.6%, 2.6%, and 1.9%, respectively. abstract: Asthma exacerbations are precipitated primarily by respiratory virus infection and frequently require immediate medical intervention. Studies of childhood and adult asthma have implicated a wide variety of respiratory viruses in exacerbations. By focusing on both RNA and DNA respiratory viruses and some newly identified viruses, this review illustrates the diversity and highlights some of the uncertainties that exist in our understanding of virus-related asthma exacerbations. url: https://api.elsevier.com/content/article/pii/S0889856110000652 doi: 10.1016/j.iac.2010.08.001 id: cord-286472-pqtem19t author: McFee, R.B. title: MIDDLE EAST RESPIRATORY SYNDROME (MERS) CORONAVIRUS date: 2020-07-28 words: 5364.0 sentences: 291.0 pages: flesch: 47.0 cache: ./cache/cord-286472-pqtem19t.txt txt: ./txt/cord-286472-pqtem19t.txt summary: This newly identified respiratory viral illness was caused by a novel coronavirus, which was initially designated as human betacoronavirus (2) (3) (4) (5) , but was eventually named Middle East Respiratory Syndrome Coronavirus (MERS CoV). It is important to consider multisystem function as well as pulmonary status in patients with severe respiratory illness, including suspected MERS CoV, especially those returning from regions where aggressive pathogens are noted. Patients recently returning from the Middle East, presenting with significant respiratory illness, with CT findings of peribronchial region abnormalities, organizing pneumonia, should be considered for MERS CoV infection, and if possible, queried about international travel and occupational exposures. Middle East Respiratory Syndrome Coronavirus (MERS CoV) Infection Feasibility, safety, clinical and laboratory effects of convalescent plasma therapy for patients with Middle East respiratory syndrome coronavirus infection: a study protocol abstract: nan url: https://api.elsevier.com/content/article/pii/S0011502920301152 doi: 10.1016/j.disamonth.2020.101053 id: cord-339386-sxyeuiw1 author: McIntosh, Kenneth title: 157 Coronaviruses, Including Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) date: 2015-12-31 words: 8499.0 sentences: 482.0 pages: flesch: 49.0 cache: ./cache/cord-339386-sxyeuiw1.txt txt: ./txt/cord-339386-sxyeuiw1.txt summary: The virus was quickly identified as a new CoV most closely related to several bat CoVs. 6 This report was followed by a number of other reports identifying a total of 537 infected individuals, all of whom had acute respiratory symptoms, severe in most, and fatal in 145 (as of May 11, 2014) . 6 Between then and May 2014, a total of 537 cases occurred, all infected by this virus, now termed the Middle East respiratory syndrome coronavirus (MERS-CoV). In response to the global spread and associated severe disease, the World Health Organization coordinated a rapid and effective control program that included isolation of cases, careful attention to contact, droplet and airborne infection control procedures, quarantine of exposed persons in some settings, and efforts to control spread between countries through travel advisories and travel alerts. abstract: nan url: https://api.elsevier.com/content/article/pii/B9781455748013001570 doi: 10.1016/b978-1-4557-4801-3.00157-0 id: cord-286449-ekvzaae2 author: McManus, Terence E. title: Respiratory viral infection in exacerbations of COPD date: 2008-07-30 words: 3105.0 sentences: 205.0 pages: flesch: 49.0 cache: ./cache/cord-286449-ekvzaae2.txt txt: ./txt/cord-286449-ekvzaae2.txt summary: A respiratory virus was detected in 37% of exacerbations, 12% of stable COPD patients and 12% of non-obstructed smokers, p < 0.0005. Studies using serology and viral culture identified respiratory viruses in 30% of patients during acute exacerbations of COPD. 8 The hypothesis tested in the present study was that acute respiratory viral infection is implicated in the pathogenesis of COPD exacerbations. The detection rate of respiratory viruses during exacerbations of COPD in this study (37%) is comparable to results obtained by Seemungal 9 Lower detection rates may be related to time of sampling as patients presenting to hospital had developed symptoms for a median of 5 days prior to admission. 21 However, several of the patients were seen at different time points during this study and the same virus was not detected by repeat sampling suggesting that those testing positive using the PCR screen were experiencing an acute viral infection. abstract: BACKGROUND: Patients with COPD have frequent exacerbations. The role of respiratory viral infection is just emerging. We wished to determine prospectively the incidence of viral infection in exacerbated and stable COPD patients as well as smokers who do not have airways obstruction. METHODS: Stable and exacerbated COPD patients were recruited along with a group of patients who had smoked but who did not have any airways obstruction. Spirometry was performed and sputum specimens were tested for a range of 12 different respiratory viruses using PCR. RESULTS: One hundred and thirty-six patients with exacerbations of COPD, 68 stable COPD patients and 16 non-obstructed smokers were recruited. A respiratory virus was detected in 37% of exacerbations, 12% of stable COPD patients and 12% of non-obstructed smokers, p < 0.0005. Rhinovirus was most frequently detected. The symptom of fever was associated with virus detection, p < 0.05. Infection with more than one virus was only found in the exacerbated COPD patients. CONCLUSION: Respiratory viral infection is associated with exacerbations of COPD. Rhinovirus was the most common infecting agent identified and in two cases human metapneumovirus was also detected. Dual infections were only seen amongst those patients admitted to hospital with acute exacerbations of COPD. Viruses were more commonly detected in those with more severe airways disease. url: https://doi.org/10.1016/j.rmed.2008.06.006 doi: 10.1016/j.rmed.2008.06.006 id: cord-257805-pcp3qgn0 author: Mehta, Harsh title: Novel coronavirus-related acute respiratory distress syndrome in a patient with twin pregnancy: A case report date: 2020-05-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: We present the case of a 39-year-old woman, G1P0, who had conceived twins via in-vitro fertilization, who presented at 27 weeks of gestation with nasal congestion and dry cough for 7 days. On presentation, her physical examination was benign, except for sinus tachycardia, and she was oxygenating adequately on room air. Laboratory studies were unremarkable, except a PCR test positive for SARS-COV2, and a CT scan of her chest showed bilateral multi-focal ground-glass opacities. A fetal non-stress test was reassuring. She was treated with intravenous fluids, ceftriaxone, azithromycin, and hydroxychloroquine. During her hospital stay, she developed progressively worsening respiratory failure, initially requiring non-invasive ventilation, and subsequently progressed to acute respiratory distress syndrome requiring mechanical ventilation. She then suffered from sudden hypoxemia and hemodynamic collapse, on maximal ventilatory support, prompting an emergency cesarean section at bedside. This led to rapid stabilization of hemodynamic parameters, and of her overall respiratory status. Both the twins were born prematurely, and one of them tested positive for SARS-COV2. url: https://www.sciencedirect.com/science/article/pii/S2214911220300503?v=s5 doi: 10.1016/j.crwh.2020.e00220 id: cord-023721-e0zp2gux author: Meissner, H. Cody title: Bronchiolitis date: 2013-02-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173523/ doi: 10.1016/b978-1-4377-2702-9.00033-7 id: cord-332926-8hdkpkgz author: Meissner, H. Cody title: Bronchiolitis date: 2017-07-18 words: 3934.0 sentences: 246.0 pages: flesch: 35.0 cache: ./cache/cord-332926-8hdkpkgz.txt txt: ./txt/cord-332926-8hdkpkgz.txt summary: During seasonal outbreaks of bronchiolitis from November through March in North America, respiratory syncytial virus (RSV) is identified as the etiologic agent in up to 80% of hospitalized children 7 (Table 33 .1). Unlike other respiratory viral infections, exposure to passive household tobacco smoke has not been associated with an increased risk of RSV hospitalization on a consistent basis. Most infants with bronchiolitis can be managed at home with supportive care, but concerns regarding increasing respiratory effort, apnea, or inability to feed adequately may precipitate hospitalization of a young child. Approximately 30% to 40% of RSV-infected infants experience progression of disease to the lower respiratory tract. Technical report: updated guidance for palivizumab prophylaxis among infants and young children at increased risk of hospitalization for respiratory syncytial virus infection Technical report: updated guidance for palivizumab prophylaxis among infants and young children at increased risk of hospitalization for respiratory syncytial virus infection abstract: nan url: https://api.elsevier.com/content/article/pii/B9780323401814000335 doi: 10.1016/b978-0-323-40181-4.00033-5 id: cord-285587-rggfg60a author: Meligy, Bassant title: Detection of viral acute lower respiratory tract infection in hospitalized infants using real-time PCR date: 2015-12-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: INTRODUCTION: Acute lower respiratory tract infection in children causes significant morbidity in the developing countries. Documentation of virus infection using PCR and clinical characteristics of patients affected with viral pneumonia are reviewed in this study. METHODS: 51 children less than three years admitted to the Pediatric Hospital, Cairo University with viral pneumonia were included. All patients had undergone nasopharyngeal aspirate for PCR viral detection. RESULTS: A total of 51 cases were enrolled in the study, of which 7 cases were negative while 44 children were positive for viruses. The most common respiratory virus was Rhinovirus in 32 patients (72.2%), then parainfluenza virus (PIV) in 12 (27.3%), of which subtypes PIV1 were 2 (4.5%), PIV3 were 5 (11.4%) and PIV4 were 5 (11.4%) cases. The third common viruses were respiratory syncytial virus (RSV) in 9 (20.5%) cases of which 3 (6.8%) were RSVA and 6 (13.6%) were RSVB and adenovirus in 9 cases (20.5%). Boca virus was found in 8 (18.2%) patients, corona virus 2 (4.5%) patients, H1N1 2 (4.5%) patients, enterovirus 2 patients (4.5%) and human metapneumovirus in one case (2.3%). Influenza B and PIV2 were not detected. Coinfection was found in 28 (63.7%). Mortality occurred in 12 (23.5%). There was no significant relation between virus type or coinfection with disease severity. CONCLUSIONS: RV was the most commonly detected virus in children under 3 years admitted with acute lower respiratory tract infections. Coinfection was present in the majority of our patients; however it was not related significantly to parameters of disease severity. url: https://api.elsevier.com/content/article/pii/S1110663815000622 doi: 10.1016/j.epag.2015.11.005 id: cord-315598-qwh72inx author: Mendoza, Jose Luis Accini title: ACTUALIZACION DE LA DECLARACIÓN DE CONSENSO EN MEDICINA CRITICA PARA LA ATENCIÓN MULTIDISCIPLINARIA DEL PACIENTE CON SOSPECHA O CONFIRMACIÓN DIAGNÓSTICA DE COVID-19 date: 2020-10-06 words: 69640.0 sentences: 6489.0 pages: flesch: 54.0 cache: ./cache/cord-315598-qwh72inx.txt txt: ./txt/cord-315598-qwh72inx.txt summary: De otorgarse un Consentimiento Informado amplio, éste debería ser única y exclusivamente para los procesos asociados con COVID-19".(71) AMCI ® Se recomienda considerar la transición del cuidado intensivo al cuidado paliativo en todo paciente con sospecha o diagnóstico de COVID-19 sin mejoría a pesar de las intervenciones óptimas, con empeoramiento progresivo de su pronóstico vital y ante un evidente deterioro; aplicando medidas generales en control de síntomas ( Manejo de secreciones -Tratamiento del dolor -Tratamiento de la disnea -Sedación paliativa), así como apoyo espiritual, siempre acompañando al paciente y nunca abandonarlo en el final de la vida. En cuanto hace referencia a la situación actual de pandemia por SARS-CoV-2 y compromiso pulmonar; Wu y cols, en Marzo de 2.020 realizaron un estudio retrospectivo de 201 pacientes con COVID-19 en China; para aquellos pacientes que desarrollaron SDRA, el tratamiento con metilprednisolona estuvo asociado con una disminución del riesgo de muerte (23/50 [46%] con esteroides vs 21/34 [62%] sin esteroides; HR, 0.38 [IC 95%, 0.20-0.72]), con las limitaciones de los estudios retrospectivo, de un solo centro, con un limitado número de pacientes (400). abstract: Antecedentes y objetivos: La enfermedad por coronavirus de 2019 (COVID-19) es una enfermedad ocasionada por el nuevo coronavirus del síndrome respiratorio agudo grave (SARS-CoV-2). Se identificó por primera vez en diciembre de 2019 en la ciudad de Wuhan, en los meses siguientes se expandió rápidamente a todos los continentes y la Organización Mundial de la Salud (OMS), la reconoció como una pandemia global el 11 de marzo de 2020. La mayoría de los individuos son asintomáticos pero una baja proporción ingresan a cuidados intensivos con una alta morbilidad y mortalidad. Este consenso tiene como objetivo actualizar la declaratoria inicial emitida por la Asociación Colombiana de Medicina Crítica (AMCI) para el manejo del paciente críticamente enfermo con COVID-19 dentro de las áreas críticas de las instituciones de salud. Métodos: Este estudio utilizó dos técnicas de consenso formal para construir las recomendaciones finales: Delphi modificada y grupos nominales. Se construyeron preguntas por la estrategia PICO. 10 grupos nominales desarrollaron recomendaciones para cada unidad temática. El producto del consenso fue evaluado y calificado en una ronda Delphi y se discutió de forma virtual por los relatores de cada núcleo y los representantes de sociedades médicas científicas afines al manejo del paciente con COID-19. Resultados: 80 expertos nacionales participaron en la actualización del consenso AMCI, especialistas en Medicina Critica y Cuidados Intensivos, Nefrología, Neurología, Neumología, bioeticistas, Medicina interna, Anestesia, Cirugía General, Cirugía de cabeza y cuello, Cuidados Paliativos, Enfermeras Especialistas en Medicina crítica, Terapeutas respiratorias especialistas en medicina crítica y Fisioterapia, con experiencia clínica en la atención del paciente críticamente enfermo. La declaratoria emite recomendaciones en los ámbitos más relevantes para la atención en salud de los casos de COVID-19 al interior de las unidades de cuidados intensivos en el contexto nacional de Colombia. Conclusiones: un grupo significativo multidisciplinario de profesionales expertos en medicina crítica emiten mediante técnicas de consenso formal recomendaciones sobre la mejor práctica para la atención del paciente críticamente enfermo con COVID-19. Las recomendaciones deben ser adaptadas a las condiciones específicas, administrativas y estructurales de las distintas unidades de cuidados intensivos del país. Background and objectives: The 2019 coronavirus disease (COVID-19) is caused by the new severe acute respiratory syndrome coronavirus (SARS-CoV-2). It was first identified in December 2019 in Wuhan, China. In the following months it spread quickly to all continents and was recognised as a global pandemic by the World Health Organization (WHO) on March 11th, 2020. Most cases of infection remain asymptomatic, while a low proportion require intensive care, experiencing high morbidity and mortality. This consensus aims to update the initial statement issued by the Colombian Association of Critical Medicine (AMCI) for the management of the critically ill patient with COVID-19 within the critical areas of health institutions. Methods: This study used two formal consensus techniques to construct the final recommendations: modified Delphi and nominal groups. Questions were constructed using the PICO strategy. Recommendations for each thematic unit were developed by 10 nominal groups. The consensus product was evaluated and qualified in a Delphi round, and was discussed virtually by the speaker of each nucleus, as well as the representatives of scientific medical societies related to the management of the patient with COVID-19. Results: A total of 80 national experts participated in the update of the AMCI consensus, all specialists in Critical and Intensive Care Medicine, Nephrologists, Neurologists, Chest physician, bioethicists, Internal medicine specialists, Anaesthetists, General Surgeons, head and neck surgery, palliative care, Nurses Specialised in Critical Medicine, Respiratory therapists specialised in critical medicine and Physiotherapy, with clinical experience in the care of critically ill patients. This update issues recommendations in the most relevant areas for health care of COVID-19 patients within the intensive care units, contextualised for Colombia. Conclusions: A significant multidisciplinary group of professionals, who are experts in critical medicine, reviewed and issued recommendations on best practice for the care of critically ill patients with COVID-19 through formal consensus techniques. Recommendations must be adapted to the specific, administrative, and structural conditions of the different intensive care units in the country. url: https://www.sciencedirect.com/science/article/pii/S0122726220300859?v=s5 doi: 10.1016/j.acci.2020.09.004 id: cord-289139-5ljqnc39 author: Mengelle, C. title: The use of a multiplex real-time PCR assay for diagnosing acute respiratory viral infections in children attending an emergency unit date: 2014-09-03 words: 2574.0 sentences: 146.0 pages: flesch: 51.0 cache: ./cache/cord-289139-5ljqnc39.txt txt: ./txt/cord-289139-5ljqnc39.txt summary: title: The use of a multiplex real-time PCR assay for diagnosing acute respiratory viral infections in children attending an emergency unit BACKGROUND: The use of a multiplex molecular technique to identify the etiological pathogen of respiratory viral infections might be a support as clinical signs are not characteristic. OBJECTIVES: The aim of the study was to evaluate a multiplex molecular real-time assay for the routine diagnosis of respiratory viruses, to analyze the symptoms associated with the pathogens detected and to determine the spread of virus during the period. This assay can detect 15 viruses: influenza viruses (IV) types A and B, parainfluenza viruses 1 to 4 (PiV), respiratory syncytial viruses A and B (RSV), rhinovirus (RV), coronaviruses 229E, OC43 and NL63 (CoV), human metapneumovirus (MPV) and adenovirus (ADV). RSV and RV were the most prevalent pathogens, particularly in the youngest children, and co-infections were associated with more severe respiratory symptoms. abstract: BACKGROUND: The use of a multiplex molecular technique to identify the etiological pathogen of respiratory viral infections might be a support as clinical signs are not characteristic. OBJECTIVES: The aim of the study was to evaluate a multiplex molecular real-time assay for the routine diagnosis of respiratory viruses, to analyze the symptoms associated with the pathogens detected and to determine the spread of virus during the period. STUDY DESIGN: Respiratory samples were collected from children presenting with respiratory symptoms and attending the emergency unit during the 2010–2011 winter seasons. Samples were tested with the multiplex RespiFinder(®) 15 assay (PathoFinder™) which potentially detects 15 viruses. RESULTS: 857 (88.7%) of the 966 samples collected from 914 children were positive for one (683 samples) or multiple viruses (174 samples). The most prevalent were the respiratory syncytial virus (39.5%) and the rhinovirus (24.4%). Influenza viruses were detected in 139 (14.4%) samples. Adenovirus was detected in 93 (9.6%) samples, coronaviruses in 88 (9.1%), metapneumovirus in 51 (5.3%) and parainfluenzae in 47 (4.9%). Rhinovirus (40%) was the most prevalent pathogen in upper respiratory tract infections while respiratory syncytial virus (49.9%) was the most prevalent in lower respiratory tract infections. Co-infections were associated with severe respiratory symptoms. CONCLUSION: The multiplex assay detected clinically important viruses in a single genomic test and thus will be useful for detecting several viruses causing respiratory tract disorders. url: https://doi.org/10.1016/j.jcv.2014.08.023 doi: 10.1016/j.jcv.2014.08.023 id: cord-011095-79ce5900 author: Meskill, Sarah D. title: Respiratory Virus Co-infection in Acute Respiratory Infections in Children date: 2020-01-24 words: 4976.0 sentences: 276.0 pages: flesch: 33.0 cache: ./cache/cord-011095-79ce5900.txt txt: ./txt/cord-011095-79ce5900.txt summary: One study in children under age 5 years old found that respiratory syncytial virus (RSV), human metapneumovirus (HMPV), and parainfluenza viruses (PIV) were more likely to be causative of disease [8] . In an evaluation of children under 18 years old admitted to the hospital with a diagnosis of pneumonia, the most common cause of infection, whether bacterial or viral, was RSV quickly followed by rhinovirus [12] . While some studies do have RSV and rhinovirus as the leading cause of pneumonia in children, another important common viral contributor is influenza [15] . [55] did a systemic review of patients of all ages with respiratory illnesses and found that studies that recruited young children were more likely to report high rates of co-infection and that there were inconclusive results on risk of hospitalization or ICU admission. Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children. abstract: PURPOSE OF REVIEW: This investigation aims to understand the role and burden of viral co-infections for acute respiratory illnesses in children. Co-infection can be either viral-viral or viral-bacterial and with new technology there is more information on the role they play on the health of children. RECENT FINDINGS: With the proliferation of multiplex PCR for rapid diagnosis of multiple viruses as well as innovations on identification of bacterial infections, research has been attempting to discover how these co-infections affect each other and the host. Studies are aiming to discern if the epidemiology of viruses seen at a population level is related to the interaction between different viruses on a host level. Studies are also attempting to discover the burden of morbidity and mortality of these viral-viral co-infections on the pediatric population. It is also becoming important to understand the interplay of certain viruses with specific bacteria and understanding the impact of viral-bacterial co-infections. SUMMARY: RSV continues to contribute to a large burden of disease for pediatric patients with acute respiratory illnesses. However, recent literature suggests that viral-viral co-infections do not add to this burden and might, in some cases, be protective of severe disease. Viral-bacterial co-infections, on the other hand, are most likely adding to the burden of morbidity in pediatric patients because of the synergistic way they can infect the nasopharyngeal space. Future research needs to focus on confirming these conclusions as it could affect hospital cohorting, role of molecular testing, and therapeutic interventions. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223550/ doi: 10.1007/s11908-020-0711-8 id: cord-324601-s3rgxtg6 author: Mhimbira, F. title: Prevalence and clinical significance of respiratory viruses and bacteria detected in tuberculosis patients compared to household contact controls in Tanzania: a cohort study date: 2019-01-31 words: 3260.0 sentences: 156.0 pages: flesch: 43.0 cache: ./cache/cord-324601-s3rgxtg6.txt txt: ./txt/cord-324601-s3rgxtg6.txt summary: title: Prevalence and clinical significance of respiratory viruses and bacteria detected in tuberculosis patients compared to household contact controls in Tanzania: a cohort study We therefore studied the prevalence of respiratory pathogens in TB patients and household contact controls, and assessed the associations between both respiratory viruses and bacterial pathogens and the clinical presentation of TB patients who were prospectively recruited in an area of Dar es Salaam (Tanzania) with a high TB burden. Logistic regression models adjusting for age, sex, and HIV infection were used to assess the associations between respiratory pathogens and clinical presentations of TB at the time of recruitment among TB patients, with the following outcome variables: severe TB score (score of 6) versus mild (score of 1e5), high sputum bacterial load (sputum AFB smear microscopy of 2þ) versus low bacterial load, and presence versus absence of lung infiltrations and cavitations (chest x-ray findings). abstract: Abstract Objectives To describe the prevalence of respiratory pathogens in tuberculosis (TB) patients and in their household contact controls, and to determine the clinical significance of respiratory pathogens in TB patients. Methods We studied 489 smear-positive adult TB patients and 305 household contact controls without TB with nasopharyngeal swab samples within an ongoing prospective cohort study in Dar es Salaam, Tanzania, between 2013 and 2015. We used multiplex real-time PCR to detect 16 respiratory viruses and seven bacterial pathogens from nasopharyngeal swabs. Results The median age of the study participants was 33 years; 61% (484/794) were men, and 21% (168/794) were HIV-positive. TB patients had a higher prevalence of HIV (28.6%; 140/489) than controls (9.2%; 28/305). Overall prevalence of respiratory viral pathogens was 20.4% (160/794; 95%CI 17.7–23.3%) and of bacterial pathogens 38.2% (303/794; 95%CI 34.9–41.6%). TB patients and controls did not differ in the prevalence of respiratory viruses (Odds Ratio [OR] 1.00, 95%CI 0.71–1.44), but respiratory bacteria were less frequently detected in TB patients (OR 0.70, 95%CI 0.53–0.94). TB patients with both respiratory viruses and respiratory bacteria were likely to have more severe disease (adjusted OR [aOR] 1.6, 95%CI 1.1–2.4; p 0.011). TB patients with respiratory viruses tended to have more frequent lung cavitations (aOR 1.6, 95%CI 0.93–2.7; p 0.089). Conclusions Respiratory viruses are common for both TB patients and household controls. TB patients may present with more severe TB disease, particularly when they are co-infected with both bacteria and viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/29581053/ doi: 10.1016/j.cmi.2018.03.019 id: cord-275828-c6d6nk7x author: Mikasa, Keiichi title: JAID/JSC Guidelines for the Treatment of Respiratory Infectious Diseases: The Japanese Association for Infectious Diseases/Japanese Society of Chemotherapy – The JAID/JSC Guide to Clinical Management of Infectious Disease/Guideline-preparing Committee Respiratory Infectious Disease WG date: 2016-07-31 words: 39672.0 sentences: 2522.0 pages: flesch: 42.0 cache: ./cache/cord-275828-c6d6nk7x.txt txt: ./txt/cord-275828-c6d6nk7x.txt summary: -SBT/ABPC, intravenous drip, 3 g/3e4 times a day -CTRX, intravenous drip, 1 g/twice a day or 2 g/once a day -CTX, intravenous drip, 1e2 g/2e3 times a day -LVFX, intravenous drip, 500 mg/once a day (2) Cases of late-onset hospital-acquired pneumonia or ventilator-associated pneumonia in which the risk of resistant bacteria is high An antimicrobial drug with anti-pseudomonal activity that targets non-glucose-fermentative gram-negative rod should be administered [50, 51, 68] -To treat polymicrobial infection, the administration of an antimicrobial drug with an activity against obligate anaerobe is not always necessary [67, 70] . -SBT/ABPC, intravenous drip, 3 g/3e4 times a day -CTRX, intravenous drip, 2 g/once a day or 1 g/twice a day -CTX, intravenous drip, 1e2 g/2e3 times a day -LVFX, intravenous drip, 500 mg/once a day (2) Late-onset hospital-acquired pneumonia or cases in which there is a risk of multi-drug-resistant bacteria In addition to the above pathogens, the involvement of non-glucose-fermentative gram negative bacteria or ESBLproducing enteric bacteria must be considered. For the treatment of immunodeficiency-/blood disease-related pneumonia in children, antimicrobial drug therapy should also be basically selected, considering causative microorganisms. abstract: nan url: https://api.elsevier.com/content/article/pii/S1341321X16000283 doi: 10.1016/j.jiac.2015.12.019 id: cord-291618-166wvdbt author: Mikulska, Małgorzata title: Epidemiology of viral respiratory tract infections in an outpatient haematology facility date: 2013-10-06 words: 4043.0 sentences: 189.0 pages: flesch: 37.0 cache: ./cache/cord-291618-166wvdbt.txt txt: ./txt/cord-291618-166wvdbt.txt summary: Viral respiratory tract infections (VRTI) are an important cause of morbidity and mortality in patients with hematologic malignancies, particularly in allogeneic haematopoietic stem cell transplantation (HSCT) recipients [1] [2] [3] . The symptoms of VRTI were divided into three main categories, and the rate of positive virological results was as follows: ILI 38 % (25 out of 65), fever only 30 % (9 out of 30) and upper VRTI symptoms 22 % (15 out of 67) (Fig. 1) Six patients had pneumonia; thus, BAL was performed and four viruses were detected (co-pathogens are reported in Table 2 ): one influenza A, two RSV and one coronavirus. Prospective study of the incidence, clinical features, and outcome of symptomatic upper and lower respiratory tract infections by respiratory viruses in adult recipients of hematopoietic stem cell transplants for hematologic malignancies abstract: Viral respiratory tract infections (VRTI) are an important cause of morbidity and mortality in haematology patients, particularly after haematopoietic stem cell transplantation (HSCT). The incidence, clinical presentation and outcome of symptomatic and asymptomatic VRTI in HSCT outpatient unit were prospectively evaluated during a single influenza season (January–March 2011). Pharyngeal swabs were performed at the first visit and if new symptoms were present. Molecular multiplex assay for 12 respiratory viruses was performed by the regional reference laboratory. Among 264 swabs from 193 outpatients, 58 (22 %) resulted positive for 61 viruses (influenza, n = 20; respiratory syncytial virus [RSV], n = 21; rhinovirus, n = 12; coronavirus, n = 4; adenovirus, n = 3; parainfluenza, n = 1). VRTI were detected more frequently in the presence of symptoms than in asymptomatic patients: 49 out of 162 (30 %) vs. 9 out of 102 (9 %), p < 0.001. Influenza-like illness syndrome (ILI) was significantly associated with a VRTI if compared to other presentations (42 %), while the European Centre for Disease Prevention and Control definition was not (30 %). Positive predictive value (PPV) of ILI for influenza was 17 %. Influenza and RSV peak periods were contemporary. Influenza prophylaxis was given to 25 patients following exposure. Low rate of progression from upper to lower respiratory tract infection (approximately 5 % for influenza and RSV), no nosocomial epidemics and no VRTI-related deaths were observed. VRTI are very frequent in high-risk haematology outpatients, but symptoms are aspecific and PPV of ILI is low. Symptoms of influenza and RSV overlap. Thus, microbiological diagnosis and contact preventive measures are crucial. Rather than universal influenza prophylaxis, prompt diagnosis and treatment of only documented infections could be pursued. url: https://www.ncbi.nlm.nih.gov/pubmed/24097084/ doi: 10.1007/s00277-013-1912-0 id: cord-285096-g9y3au1a author: Mitchell, Judy A. title: Tropism and pathological findings associated with canine respiratory coronavirus (CRCoV) date: 2013-03-23 words: 7120.0 sentences: 340.0 pages: flesch: 50.0 cache: ./cache/cord-285096-g9y3au1a.txt txt: ./txt/cord-285096-g9y3au1a.txt summary: Following experimental infection in dogs, all five CRCoV isolates gave rise to clinical signs of respiratory disease consistent with that observed during natural infection. Following experimental infection in dogs, all five CRCoV isolates gave rise to clinical signs of respiratory disease consistent with that observed during natural infection. In that study we demonstrated that young dogs were susceptible to experimental infection with both CRCoV isolates, which gave rise to clinical signs of respiratory disease consistent with naturally occurring infection. Analyses specifically focused on the histopathological changes in the canine upper and lower respiratory tissues, virulence differences among CRCoV isolates derived from CIRD cases representing wide geographical locations; UK and USA [MO, NE, UT and MI] , and the demonstration of Koch''s postulates. Consistent with observations made during naturally occurring infection, dogs in this study also displayed clinical signs of mild respiratory disease following viral challenge (nasal discharge, sneezing, and coughing); whilst the control group remained healthy. abstract: Canine infectious respiratory disease (CIRD) occurs frequently in densely housed dog populations. One of the common pathogens involved is canine respiratory coronavirus (CRCoV), however little is known regarding its pathogenesis and the role it plays in the development of CIRD. The pathogenesis of five geographically unrelated canine respiratory coronavirus (CRCoV) isolates was investigated. Following experimental infection in dogs, all five CRCoV isolates gave rise to clinical signs of respiratory disease consistent with that observed during natural infection. The presence of CRCoV was associated with marked histopathological changes in the nares and trachea, with loss and damage to tracheal cilia, accompanied by inflammation. Viral shedding was readily detected from the oropharynx up to 10 days post infection, but there was little or no evidence of rectal shedding. The successful re-isolation of CRCoV from a wide range of respiratory and mucosal associated lymphoid tissues, and lung lavage fluids demonstrates a clear tropism of CRCoV for respiratory tissues and fulfils the final requirement for Koch's postulates. By study day 14 dogs had seroconverted to CRCoV and the antibodies raised were neutralising against both homologous and heterologous strains of CRCoV in vitro, thus demonstrating antigenic homogeneity among CRCoV strains from the two continents. Defining the role that CRCoV and other agents play in CIRD is a considerable, but important, challenge if the disease is to be managed, treated and prevented more successfully. Here we have successfully developed a model for studying the pathogenicity and the role of CRCoV in CIRD. url: https://doi.org/10.1016/j.vetmic.2012.11.025 doi: 10.1016/j.vetmic.2012.11.025 id: cord-312691-ynh84b98 author: Mohd, Hamzah A. title: Predictors of MERS-CoV infection: A large case control study of patients presenting with ILI at a MERS-CoV referral hospital in Saudi Arabia date: 2016-09-24 words: 3296.0 sentences: 167.0 pages: flesch: 56.0 cache: ./cache/cord-312691-ynh84b98.txt txt: ./txt/cord-312691-ynh84b98.txt summary: title: Predictors of MERS-CoV infection: A large case control study of patients presenting with ILI at a MERS-CoV referral hospital in Saudi Arabia BACKGROUND: A case control study to better characterize the clinical features, laboratory, and radiological abnormalities associated with MERS-CoV infection in order to help with early identification of this syndrome from other respiratory infections. METHODS: Eighty patients admitted to a hospital in Riyadh, diagnosed with MERS-CoV infection based on RT-PCR were matched on age, sex, and the presence of a co-morbid condition on a basis of 1:2 to other patients admitted with respiratory symptoms and tested negative for MERS-CoV on RT-PCR. First cases of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infections in France, investigations and implications for the prevention of human-to-human transmission Laboratory-confirmed case of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infection in Malaysia: preparedness and response Middle East Respiratory Syndrome Coronavirus: a case-control study of hospitalized patients abstract: BACKGROUND: A case control study to better characterize the clinical features, laboratory, and radiological abnormalities associated with MERS-CoV infection in order to help with early identification of this syndrome from other respiratory infections. METHODS: Eighty patients admitted to a hospital in Riyadh, diagnosed with MERS-CoV infection based on RT-PCR were matched on age, sex, and the presence of a co-morbid condition on a basis of 1:2 to other patients admitted with respiratory symptoms and tested negative for MERS-CoV on RT-PCR. RESULTS: None of the reported MERS-CoV presenting symptoms was significantly associated with being infected with MERS-CoV. On the other hand, WBC count was significantly lower in patients with confirmed MERS-CoV infection (median 5.7 vs 9.3, P: 0.0004). Neutrophil count was as well significantly lower in MERS-CoV patients (median 3.7 vs 6.7, P: 0.0001). Both AST, and ALT values were significantly higher in MERS-CoV infected group (AST median 42 vs 36, P: 0.03, and ALT median 33 vs 28, P: 0.003). Overall our MERS-CoV mortality rate was (10%) below the national figure of (40%). CONCLUSIONS: None of the presenting symptoms are specific for MERS-CoV infection. And out of all the investigations WBC, neutrophil counts, AST and ALT values have some predictive utility. url: https://api.elsevier.com/content/article/pii/S1477893916301260 doi: 10.1016/j.tmaid.2016.09.008 id: cord-300510-fhpkdqr0 author: Mojoli, Francesco title: Our recommendations for acute management of COVID-19 date: 2020-05-08 words: 1083.0 sentences: 73.0 pages: flesch: 41.0 cache: ./cache/cord-300510-fhpkdqr0.txt txt: ./txt/cord-300510-fhpkdqr0.txt summary: 7. Perform early intubation if poor response to continuous positive airway pressure in terms of oxygenation: do not trust patients'' relatively good respiratory mechanics and feeling of improved dyspnoea, since these patients may have relatively normal lung compliance and the only clinical sign of fatigue may be high respiratory rate. As soon as possible according to gas exchanges (PaO 2 /FiO 2 > 150 with FiO2 < 50%) and lung ultrasound score (≤ 12), start assisted ventilation with a sigh while maintaining moderate to high positive end-expiratory pressure to prevent derecruitment. Abbreviations SARS-CoV-2: Severe acute respiratory syndrome coronavirus 2; ICU: Intensive care unit Assessment of lung aeration and recruitment by CT scan and ultrasound in acute respiratory distress syndrome patients Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China The authors read and approved the final manuscript. abstract: nan url: https://doi.org/10.1186/s13054-020-02930-6 doi: 10.1186/s13054-020-02930-6 id: cord-351008-p0n1fdxw author: Monge, Susana title: Ambulance dispatch calls attributable to influenza A and other common respiratory viruses in the Netherlands (2014‐2016) date: 2020-05-14 words: 3080.0 sentences: 166.0 pages: flesch: 45.0 cache: ./cache/cord-351008-p0n1fdxw.txt txt: ./txt/cord-351008-p0n1fdxw.txt summary: We evaluated whether ambulance dispatch calls of highest urgency reflect the circulation of influenza A virus, influenza B virus, respiratory syncytial virus (RSV), rhinovirus, adenovirus, coronavirus, parainfluenzavirus and human metapneumovirus (hMPV). Specifically, we evaluated the association of syndromes compatible with respiratory infections in ambulance dispatches with trends in detections of influenza A, influenza B, RSV, rhinovirus, adenovirus, coronavirus, parainfluenza and human metapneumovirus (hMPV). Calls with triage codes that were potentially compatible with respiratory infections (Table 1) year, and hMPV (4%) and influenza A (1%) mainly during the winter peaks. Because of its ability to capture variations in respiratory virus circulation, ambulance dispatch data might be useful to signal events and to monitor the respiratory season as a whole, specifically reflecting severe infections and thus complementing existing surveillance systems. Use of ambulance dispatch calls for surveillance of severe acute respiratory infections Ambulance dispatch calls attributable to influenza A and other common respiratory viruses in the Netherlands abstract: BACKGROUND: Ambulance dispatches could be useful for syndromic surveillance of severe respiratory infections. We evaluated whether ambulance dispatch calls of highest urgency reflect the circulation of influenza A virus, influenza B virus, respiratory syncytial virus (RSV), rhinovirus, adenovirus, coronavirus, parainfluenzavirus and human metapneumovirus (hMPV). METHODS: We analysed calls from four ambulance call centres serving 25% of the population in the Netherlands (2014‐2016). The chief symptom and urgency level is recorded during triage; we restricted our analysis to calls with the highest urgency and identified those compatible with a respiratory syndrome. We modelled the relation between respiratory syndrome calls (RSC) and respiratory virus trends using binomial regression with identity link function. RESULTS: We included 211 739 calls, of which 15 385 (7.3%) were RSC. Proportion of RSC showed periodicity with winter peaks and smaller interseasonal increases. Overall, 15% of RSC were attributable to respiratory viruses (20% in out‐of‐office hour calls). There was large variation by age group: in <15 years, only RSV was associated and explained 11% of RSC; in 15‐64 years, only influenza A (explained 3% of RSC); and in ≥65 years adenovirus explained 9% of RSC, distributed throughout the year, and hMPV (4%) and influenza A (1%) mainly during the winter peaks. Additionally, rhinovirus was associated with total RSC. CONCLUSION: High urgency ambulance dispatches reflect the burden of different respiratory viruses and might be useful to monitor the respiratory season overall. Influenza plays a smaller role than other viruses: RSV is important in children while adenovirus and hMPV are the biggest contributors to emergency calls in the elderly. url: https://www.ncbi.nlm.nih.gov/pubmed/32410358/ doi: 10.1111/irv.12731 id: cord-003492-rodqdtfj author: Montaner-Tarbes, Sergio title: Key Gaps in the Knowledge of the Porcine Respiratory Reproductive Syndrome Virus (PRRSV) date: 2019-02-20 words: 9579.0 sentences: 381.0 pages: flesch: 31.0 cache: ./cache/cord-003492-rodqdtfj.txt txt: ./txt/cord-003492-rodqdtfj.txt summary: PRRSV is a complex disease and several gaps in the knowledge of its economic impact, biology and evolution, genetic polymorphism, mechanism of viral infections, elicitation of protective immune responses and novel control strategies, have been reviewed here (Box 1). Nonstructural proteins nsp2TF and nsp2N of porcine reproductive and respiratory syndrome virus (PRRSV) play important roles in suppressing host innate immune responses Immune responses in pigs infected with porcine reproductive and respiratory syndrome virus (PRRSV) Immunodominant epitopes in nsp2 of porcine reproductive and respiratory syndrome virus are dispensable for replication, but play an important role in modulation of the host immune response Nonstructural protein 11 (nsp11) of porcine reproductive and respiratory syndrome virus (PRRSV) promotes PRRSV infection in MARC-145 cells Immune response to ORF5a protein immunization is not protective against porcine reproductive and respiratory syndrome virus infection abstract: The porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most important swine diseases in the world. It is causing an enormous economic burden due to reproductive failure in sows and a complex respiratory syndrome in pigs of all ages, with mortality varying from 2 to 100% in the most extreme cases of emergent highly pathogenic strains. PRRSV displays complex interactions with the immune system and a high mutation rate, making the development, and implementation of control strategies a major challenge. In this review, the biology of the virus will be addressed focusing on newly discovered functions of non-structural proteins and novel dissemination mechanisms. Secondly, the role of different cell types and viral proteins will be reviewed in natural and vaccine-induced immune response together with the role of different immune evasion mechanisms focusing on those gaps of knowledge that are critical to generate more efficacious vaccines. Finally, novel strategies for antigen discovery and vaccine development will be discussed, in particular the use of exosomes (extracellular vesicles of endocytic origin). As nanocarriers of lipids, proteins and nucleic acids, exosomes have potential effects on cell activation, modulation of immune responses and antigen presentation. Thus, representing a novel vaccination approach against this devastating disease. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391865/ doi: 10.3389/fvets.2019.00038 id: cord-010233-772e35kx author: Monto, Arnold S. title: Respiratory illness caused by picornavirus infection: a review of clinical outcomes date: 2002-01-03 words: 4597.0 sentences: 241.0 pages: flesch: 37.0 cache: ./cache/cord-010233-772e35kx.txt txt: ./txt/cord-010233-772e35kx.txt summary: The search terms used were picornavirus, rhinovirus, enterovirus, viral respiratory infection, upper respiratory infection, disease burden, economic, cost, complications, asthma, COPD, immunocompromised, elderly, otitis media, and sinusitis. In fact, because rhinovirus-induced illnesses are so common, they produce more restriction of activity and physician consultations annually than respiratory illnesses caused by other viruses or bacteria.s This article reviews the clinical impact and outcomes associated with picomavirusinduced respiratory infection in specific populations at risk for complications secondary to these infections. 15 In addition, these advances in technology have confirmed the results of earlier studies, further demonstrating the significance of rhinoviruses in causing or predisposing patients to otitis media and sinusitis and exacerbating other chronic respiratory diseases such as asthma, cystic fibrosis, and chronic obstructive pulmonary disease (COPD). abstract: Background: Respiratory infections result from invasion of the respiratory tract, mainly by viruses, and are the leading cause of acute morbidity in individuals of all ages worldwide. During peak season, picornaviruses cause 82% of all episodes of acute nasopharyngitis (the common cold), the most frequent manifestation of acute respiratory infection, and produce more restriction of activity and physician consultations annually than any other viral or bacterial source of respiratory illness. Objective: This article reviews the clinical impact and outcomes of picornavirus-induced respiratory infections in specific populations at risk for complications. It also discusses the potential economic impact of the morbidity associated with picornavirus-induced respiratory infection. Methods: Relevant literature was identified through searches of MEDLINE, OVID, International Pharmaceutical Abstracts, and Lexis-Nexis. The search terms used were picornavirus, rhinovirus, enterovirus, viral respiratory infection, upper respiratory infection, disease burden, economic, cost, complications, asthma, COPD, immunocompromised, elderly, otitis media, and sinusitis. Additional publications were identified from the reference lists of the retrieved articles. Conclusions: Based on the clinical literature, picornavirus infections are associated with severe morbidity as well as considerable economic and societal costs. Future research should focus on identifying patterns of illness and the costs associated with management of these infections. New treatments should be assessed not only in terms of their ability to produce the desired clinical outcome, but also in terms of their ability to reduce the burden of disease, decrease health care costs, and improve productivity. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172950/ doi: 10.1016/s0149-2918(01)80133-8 id: cord-017252-88b3preq author: Morgan, Carrie I. title: Pneumonia date: 2014-02-20 words: 6424.0 sentences: 315.0 pages: flesch: 32.0 cache: ./cache/cord-017252-88b3preq.txt txt: ./txt/cord-017252-88b3preq.txt summary: Despite immunizations and public health initiatives, the most common bacterial causes of CAP have remained largely unchanged over the last several decades and include: Streptococcus pneumoniae , Staphylococcus aureus , Haemophilus infl uenzae (including non-typable strains) and Moraxella catarrhalis [ 7 , 8 , 21 , 23 ] . Chest CT is helpful to further evaluate diffi cult cases, particularly immunocompromised children with ill-defi ned infi ltrates on CXR, complex empyema or effusion, or recurrent or chronic pneumonia [ 11 ] . Respiratory failure in an immunocompromised child frequently necessitates a chest CT to better visualize the pattern and extent of disease, aid in diagnosis of the etiology, determine the need for more invasive procedures, and to increase the sensitivity of assessing treatment response [ 11 ] . Etiology of community-acquired pneumonia in hospitalized school-age children: evidence for high prevalence of viral infections abstract: Respiratory diagnoses continue to make up a large number of admissions to the pediatric intensive care unit (PICU), most notably lower respiratory infections including pneumonia. This chapter will focus on pediatric community-acquired pneumonia (CAP), immunocompromised pneumonia, and aspiration pneumonia. The pathogenesis for developing pneumonia varies; it can occur by direct inhalation of infectious particles in the air or aspiration, direct extension from the upper airways, and hematogenous spread. There are multiple levels of defense against pathogen invasion including anatomic barriers, as well as innate and adaptive immunity, which may be compromised in PICU patients. The etiologies of pediatric pneumonia vary depending on age, host condition, and environmental factors like time of year and location. Viruses remain the most common form of lower respiratory tract infection in children, especially in neonates. Community-acquired bacterial pneumonia continues to be most prevalent in younger children as well, most often affecting children less than 5 years of age who are otherwise healthy. Despite immunizations and public health initiatives, the most common bacterial causes of CAP have remained largely unchanged over the last several decades and include: Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae (including non-typable strains) and Moraxella catarrhalis. Pulmonary infection in an immunocompromised host provides a much broader differential and must be aggressively treated without delay. This chapter will also address various imaging modalities and typical findings with pediatric pneumonia. Methods for pathogen identification are broad and range from non-specific markers of illness to invasive techniques for culture. The mainstay of therapy continues to be antibiotics tailored to the patient and presumed etiology; more novel therapies may include corticosteroids or macrolide antibiotics for immune modulation. In those patients with pneumonia with effusion or empyema, drainage therapies with thoracostomy tubes or a VATS procedure may be indicated. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121765/ doi: 10.1007/978-1-4471-6356-5_6 id: cord-268490-e8jub01m author: Moscona, Anne title: CSI Microbiology: Emerging Pathogens and a Staged Strategy for Detection and Discovery date: 2007-12-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/18190250/ doi: 10.1086/524313 id: cord-345211-4ivqlsgt author: Murdoch, David R. title: How recent advances in molecular tests could impact the diagnosis of pneumonia date: 2016-03-07 words: 5994.0 sentences: 295.0 pages: flesch: 35.0 cache: ./cache/cord-345211-4ivqlsgt.txt txt: ./txt/cord-345211-4ivqlsgt.txt summary: Guidelines for the management of community-acquired pneumonia in children are even more restrictive, again recommending that tests should mainly be used on patients with severe disease, with a focus on blood cultures and detection of respiratory viruses [11, 12] . While not exactly new (polymerase chain reaction (PCR) assays for respiratory pathogens have been around for over 20 years), the widespread adoption of nucleic acid detection tests (NATs) by diagnostic laboratories has been relatively slow. The NATs that are most widely used in diagnostic laboratories are those that detect potential pneumonia pathogens that are not part of the normal flora, namely respiratory viruses and selected non-colonizing bacteria. Quantitative multiplex PCR has been used to determine the etiology of community-acquired pneumonia in adults using cutoffs developed for interpretation of culture results from lower respiratory tract specimens [85, 86] . abstract: Molecular diagnostic tests have been the single major development in pneumonia diagnostics over recent years. Nucleic acid detection tests (NATs) have greatly improved the ability to detect respiratory viruses and bacterial pathogens that do not normally colonize the respiratory tract. In contrast, NATs do not yet have an established role for diagnosing pneumonia caused by bacteria that commonly colonize the nasopharynx due to difficulties discriminating between pathogens and coincidental carriage strains. New approaches are needed to distinguish infection from colonization, such as through use of quantitative methods and identification of discriminating cut-off levels. The recent realization that the lung microbiome exists has provided new insights into the pathogenesis of pneumonia involving the interaction between multiple microorganisms. New developments in molecular diagnostics must account for this new paradigm. url: https://www.ncbi.nlm.nih.gov/pubmed/26891612/ doi: 10.1586/14737159.2016.1156536 id: cord-264079-u0nkjexi author: Murphy, Dianne title: The use of gowns and masks to control respiratory illness in pediatric hospital personnel date: 1981-11-30 words: 2674.0 sentences: 152.0 pages: flesch: 56.0 cache: ./cache/cord-264079-u0nkjexi.txt txt: ./txt/cord-264079-u0nkjexi.txt summary: title: The use of gowns and masks to control respiratory illness in pediatric hospital personnel Nosocomial disease often lengthens the hospital stay and, in some instances, may be severe or even fatal> ~ For certain viruses, particularly respiratory syncytial virus, there is a high frequency of infection in nursing, medical, and other stafP ..... Children with respiratory disease are usually placed in isolation and hospital personnel may be cohorted or required to wear gowns when administering patient care. The efficacy of this approach in the control of RSV therefore designed a prospective study to examine the effect of various control methods on the acquisition of symptomatic respiratory infections by medical personnel caring for infants with respiratory disease. We were unable to demonstrate any effect of adding the use of both gown and mask to the usual handwashing routine on the development of illness in personnel caring for infants with respiratory disease. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/7299552/ doi: 10.1016/s0022-3476(81)80401-5 id: cord-346673-kyc1wks5 author: NICKBAKHSH, S. title: Extensive multiplex PCR diagnostics reveal new insights into the epidemiology of viral respiratory infections date: 2016-03-02 words: 5415.0 sentences: 237.0 pages: flesch: 41.0 cache: ./cache/cord-346673-kyc1wks5.txt txt: ./txt/cord-346673-kyc1wks5.txt summary: In particular, our study shows that (i) human coronavirus infections are more common during influenza seasons and in co-infections than previously recognized, (ii) factors associated with co-infection differ from those associated with viral infection overall, (iii) virus prevalence has increased over time especially in infants aged <1 year, and (iv) viral infection risk is greater in the post-2009 pandemic era, likely reflecting a widespread change in the viral population that warrants further investigation. We analysed diagnostic data generated by NHSGGC using multiplex PCR from 2005 to 2013 with the following objectives: (i) to describe testing and virus prevalence trends, (ii) to examine temporal and patient subgroup distributions for each individual virus, and (iii) to compare factors associated with overall viral infection and co-infection using statistical modelling, in order to provide robust and timely estimates of who is most at risk of viral-associated respiratory illness, and when, within a major urban UK population. abstract: Viral respiratory infections continue to pose a major global healthcare burden. At the community level, the co-circulation of respiratory viruses is common and yet studies generally focus on single aetiologies. We conducted the first comprehensive epidemiological analysis to encompass all major respiratory viruses in a single population. Using extensive multiplex PCR diagnostic data generated by the largest NHS board in Scotland, we analysed 44230 patient episodes of respiratory illness that were simultaneously tested for 11 virus groups between 2005 and 2013, spanning the 2009 influenza A pandemic. We measured viral infection prevalence, described co-infections, and identified factors independently associated with viral infection using multivariable logistic regression. Our study provides baseline measures and reveals new insights that will direct future research into the epidemiological consequences of virus co-circulation. In particular, our study shows that (i) human coronavirus infections are more common during influenza seasons and in co-infections than previously recognized, (ii) factors associated with co-infection differ from those associated with viral infection overall, (iii) virus prevalence has increased over time especially in infants aged <1 year, and (iv) viral infection risk is greater in the post-2009 pandemic era, likely reflecting a widespread change in the viral population that warrants further investigation. url: https://doi.org/10.1017/s0950268816000339 doi: 10.1017/s0950268816000339 id: cord-342853-n3e6yawi author: Naghipour, Mohammadreza title: Human bocavirus in Iranian children with acute respiratory infections date: 2007-03-26 words: 2115.0 sentences: 121.0 pages: flesch: 53.0 cache: ./cache/cord-342853-n3e6yawi.txt txt: ./txt/cord-342853-n3e6yawi.txt summary: Human bocavirus (HBoV), a virus discovered in Sweden in 2005, has been associated with acute respiratory infections in young children and subsequent reports suggest that HBoV may have a worldwide distribution. This report describes the frequency and clinical presentation of HBoV in 261 Iranian children<5 years old with acute respiratory infections attending two regional hospitals in Rasht, Iran in the winter of 2003–2004. Human bocavirus (HBoV) was first described in 2005 [Allander et al., 2005] and it was suggested that the virus might be a cause of acute respiratory infections. Children less than 5 years of age with acute respiratory infections of less than 7 days duration attending the outpatient department or being admitted to hospital from Saturday to Thursday were enrolled after informed parental consent. Given the high frequency of HBoV in Iran, this virus might play a significant role as a cause of acute respiratory infections in children. abstract: Human bocavirus (HBoV), a virus discovered in Sweden in 2005, has been associated with acute respiratory infections in young children and subsequent reports suggest that HBoV may have a worldwide distribution. This report describes the frequency and clinical presentation of HBoV in 261 Iranian children<5 years old with acute respiratory infections attending two regional hospitals in Rasht, Iran in the winter of 2003–2004. Polymerase chain reaction (PCR) and reverse transcription PCR (RT‐PCR) were used for the detection of HBoV and other respiratory pathogens from nasopharyngeal specimens. HBoV was detected in 21 (8%) children. Fifteen (12%) of these children were identified among 122 children admitted to hospital and 6 (4%) from 139 outpatients (P < 0.05). Most children with HBoV were less than 2 years (17/21, 81%) and 7 (33%) were less than 1 year old. Although HBoV was identified in all ages it affected slightly older children than the respiratory syncytial virus (RSV). The frequency of the virus varied from 1 (3%) in 40 patients in November to 7 (12%) of 61 in February, suggesting a seasonal pattern during the autumn and early winter. Seven children had co‐infections with RSV, adenovirus or influenza A. The relatively high frequency of HBoV suggests that the virus may contribute substantially to acute respiratory infections in children. J. Med. Virol. 79:539–543, 2007. © 2007 Wiley‐Liss, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/17385723/ doi: 10.1002/jmv.20815 id: cord-323009-frej2qmb author: Nakouné, Emmanuel title: First introduction of pandemic influenza A/H1N1 and detection of respiratory viruses in pediatric patients in Central African Republic date: 2013-02-08 words: 2839.0 sentences: 149.0 pages: flesch: 46.0 cache: ./cache/cord-323009-frej2qmb.txt txt: ./txt/cord-323009-frej2qmb.txt summary: FINDINGS: A prospective study was conducted in the Central African Republic (CAR) between January and December 2010 among infants and children aged 0–15 years attending sentinel sites for influenza-like illness or acute respiratory illness. The aim of the study reported here was to determine the circulation of 2009 pandemic influenza A/H1N1 virus (H1N1pdm09) by molecular methods and to identify the causative viruses, the incidence and the clinical features of acute respiratory illness among infants and young children at sentinel sites in Bangui and three rural areas. All infants and children aged between 0-15 years who attended sentinel sites in Bangui and three rural areas ( Figure 1 ) for influenza-like illness (ILI) or severe acute respiratory illness between January and December 2010 were included in the study (Figure 2A ). Abbreviations CAR: Central African Republic; ILI: Influenza-like illness; HRSV: Human respiratory syncytial virus; PIV: Parainfluenza viruses. abstract: BACKGROUND: Acute viral respiratory illnesses in children in sub-Saharan Africa have received relatively little attention, although they are much more frequent causes of morbidity and mortality than in developed countries. Active surveillance is essential to identify the causative agents and to improve clinical management, especially in the context of possible circulation of pandemic viruses. FINDINGS: A prospective study was conducted in the Central African Republic (CAR) between January and December 2010 among infants and children aged 0–15 years attending sentinel sites for influenza-like illness or acute respiratory illness. Nasopharyngeal swabs were collected, and one-step real-time and multiplex reverse transcription-polymerase chain reaction were used to detect respiratory viruses. Respiratory viruses were detected in 49 of the 329 (14.9%) nasopharyngeal samples: 29 (8.8%) contained influenza viruses (5 (1.5%) had pandemic influenza A/H1N1 virus and 24 (7.3%) had influenza B viruses), 11 (3.3%) contained parainfluenza viruses types 1 and 3 and 9 (2.7%) contained human respiratory syncytial virus. Most cases were detected during the rainy season in the CAR. Analysis of the amplicon sequences confirmed the identity of each detected virus. CONCLUSIONS: The influenza surveillance system in the CAR has provided valuable data on the seasonality of influenza and the circulation of other respiratory viruses. Our network could therefore play a valuable role in the prevention and control of influenza epidemics in the CAR. url: https://www.ncbi.nlm.nih.gov/pubmed/23391188/ doi: 10.1186/1743-422x-10-49 id: cord-325830-mrtpihc7 author: Nelson, Philipp P. title: Current and Future Point-of-Care Tests for Emerging and New Respiratory Viruses and Future Perspectives date: 2020-04-29 words: 4974.0 sentences: 273.0 pages: flesch: 46.0 cache: ./cache/cord-325830-mrtpihc7.txt txt: ./txt/cord-325830-mrtpihc7.txt summary: In this review, we summarize recently published characteristics of POCTs and discuss their implications for the treatment of RTIs. The second key aspect of this work is a description of new and innovative diagnostic techniques, ranging from biosensors to novel portable and current lab-based nucleic acid amplification methods with the potential future use in point-of-care settings. In this review, we summarize recently published characteristics of POCTs and discuss their implications for the treatment of RTIs. The second key aspect of this work is a description of new and innovative diagnostic techniques, ranging from biosensors to novel portable and current lab-based nucleic acid amplification methods with the potential future use in point-of-care settings. abstract: The availability of pathogen-specific treatment options for respiratory tract infections (RTIs) increased the need for rapid diagnostic tests. Besides, retrospective studies, improved lab-based detection methods and the intensified search for new viruses since the beginning of the twenty-first century led to the discovery of several novel respiratory viruses. Among them are human bocavirus (HBoV), human coronaviruses (HCoV-HKU1, -NL63), human metapneumovirus (HMPV), rhinovirus type C (RV-C), and human polyomaviruses (KIPyV, WUPyV). Additionally, new viruses like SARS coronavirus (SARS-CoV), MERS coronavirus (MERS-CoV), novel strains of influenza virus A and B, and (most recently) SARS coronavirus 2 (SARS-CoV-2) have emerged. Although clinical presentation may be similar among different viruses, associated symptoms may range from a mild cold to a severe respiratory illness, and thus require a fast and reliable diagnosis. The increasing number of commercially available rapid point-of-care tests (POCTs) for respiratory viruses illustrates both the need for this kind of tests but also the problem, i.e., that the majority of such assays has significant limitations. In this review, we summarize recently published characteristics of POCTs and discuss their implications for the treatment of RTIs. The second key aspect of this work is a description of new and innovative diagnostic techniques, ranging from biosensors to novel portable and current lab-based nucleic acid amplification methods with the potential future use in point-of-care settings. While prototypes for some methods already exist, other ideas are still experimental, but all of them give an outlook of what can be expected as the next generation of POCTs. url: https://www.ncbi.nlm.nih.gov/pubmed/32411619/ doi: 10.3389/fcimb.2020.00181 id: cord-346290-my8ow5ee author: Nelson, Philipp P. title: Respiratory Viral Pathogens date: 2020-05-28 words: 4160.0 sentences: 238.0 pages: flesch: 42.0 cache: ./cache/cord-346290-my8ow5ee.txt txt: ./txt/cord-346290-my8ow5ee.txt summary: Respiratory viruses are responsible for a variety of clinical syndromes including the common cold, acute otitis media, laryngitis, sinusitis, pneumonia, bronchiolitis, influenza-like illness, and exacerbations of asthma and chronic obstructive pulmonary disease. Treatment modalities include over-the-counter and non-specific remedies along with a small number of specific antiviral medications such as the influenza neuraminidase inhibitors or palivizumab against respiratory syncytial virus. Viruses of the family of Pneumoviridae form enveloped, spherical or filamentous virions with 100-200 nm in diameter, which contain a single, linear, negative-sense RNA genome. Human bocavirus 1 (HBoV1), a member of the species Primate bocaparvovirus 1, in the genus Bocaparvovirus and the subfamily of Parvovirinae, is strongly associated with upper and lower respiratory tract infections in young children. The common cold is a rather benign clinical entity, which may however be complicated by secondary bacterial infections, otitis media, sinusitis, pneumonia, and asthma exacerbations; severe courses of disease and death may occur in young children and immunocompromised patients. abstract: Respiratory viruses are responsible for a variety of clinical syndromes including the common cold, acute otitis media, laryngitis, sinusitis, pneumonia, bronchiolitis, influenza-like illness, and exacerbations of asthma and chronic obstructive pulmonary disease. Diagnosis of respiratory viral infections is primarily clinical and is further supported by laboratory techniques such as antigen detection, serology, and nucleic acid detection. Preventive strategies are based on avoidance of risk factors and, in case of influenza, vaccination. Treatment modalities include over-the-counter and non-specific remedies along with a small number of specific antiviral medications such as the influenza neuraminidase inhibitors or palivizumab against respiratory syncytial virus. url: https://api.elsevier.com/content/article/pii/B9780128012383116356 doi: 10.1016/b978-0-12-801238-3.11635-6 id: cord-282668-bs634hti author: Niang, Mbayame Ndiaye title: Respiratory viruses in patients with influenza-like illness in Senegal: Focus on human respiratory adenoviruses date: 2017-03-22 words: 4623.0 sentences: 243.0 pages: flesch: 47.0 cache: ./cache/cord-282668-bs634hti.txt txt: ./txt/cord-282668-bs634hti.txt summary: In the present study, we investigate the epidemiologic and viral molecular features of HAdVs circulating in Senegal after 4 consecutive years of sentinel surveillance of influenza-like Illness cases. In the present study, we investigate the epidemiologic and viral molecular features of HAdVs circulating in Senegal after 4 consecutive years of sentinel surveillance of influenzalike Illness cases. From January 2012 to December 2015 we collected specimens (nasal-pharyngeal and oral-pharyngeal swabs) and surveillance data for influenza and other viral respiratory pathogens from outpatients presenting with influenza-like-illness (ILI) at different sentinel sites in Senegal. So the circulation of such HAdV genome types in Senegal emphasizes the need to reinforce HAdV surveillance, especially in hospitalized patients, by including HAdV genome detection and genotyping in the documentation of severe respiratory infections. Molecular epidemiology of human adenovirus isolated from children hospitalized with acute respiratory infection in São Paulo, Brazil abstract: BACKGROUND: Human adenoviruses (HAdVs) are highly contagious pathogens that are associated with a wide spectrum of human illnesses involving the respiratory tract. In the present study, we investigate the epidemiologic and viral molecular features of HAdVs circulating in Senegal after 4 consecutive years of sentinel surveillance of influenza-like Illness cases. METHODOLOGY AND RESULTS: From January 2012 to December 2015 swabs were collected from consenting ILI outpatients. Adenoviral detection is performed by rRT-PCR with the Anyplex(™) II RV16 Detection kit (Seegene) and molecular characterization was performed using a partial hexon gene sequence. 6381 samples were collected. More than half of patients (51.7%; 3297/6381) were children of ≤ 5 years. 1967 (30.8%) were positive for HAdV with 1561 (79.4%) found in co-infection with at least one another respiratory virus. The most common co-detections were with influenza viruses (53.1%; 1045/1967), rhinoviruses (30%; 591/1967), enteroviruses (18.5%; 364/1967) and RSV (13.5%; 266/1967). Children under 5 were the most infected group (62.2%; 1224/1967; p <0.05). We noted that HAdV was detected throughout the year at a high level with detection peaks of different amplitudes without any clear seasonality. Phylogenetic analysis revealed species HAdV-C in majority, species HAdV-B and one HAdV- 4 genome type. The 9 HAdV-B species like strains from Senegal grouped with genome types HAdV-7, HAdV-55 and HAdV-11 as shown by a phylogenetic branch with a high bootstrap value of (88%). CONCLUSION: In conclusion, the results of the present study suggest strong year-round HAdV activity in Senegal, especially in children up to 5 years of age. Molecular studies revealed that the dominant species in circulation in patients with ILI appears to be HAdV-C and HAdV-B species. The circulation of though HAdV-7 and HAdV-55 genome types is of note as these serotypes are recognized causes of more severe and even fatal acute respiratory infections. url: https://doi.org/10.1371/journal.pone.0174287 doi: 10.1371/journal.pone.0174287 id: cord-309120-05bg7rfa author: Niazi, Sadegh title: The role of respiratory droplet physicochemistry in limiting and promoting the airborne transmission of human coronaviruses: A critical review() date: 2020-11-06 words: 2717.0 sentences: 180.0 pages: flesch: 38.0 cache: ./cache/cord-309120-05bg7rfa.txt txt: ./txt/cord-309120-05bg7rfa.txt summary: title: The role of respiratory droplet physicochemistry in limiting and promoting the airborne transmission of human coronaviruses: A critical review() Airborne transmission is an accepted potential route for the spread of some viral infections (measles, chickenpox); however, aerosol features and infectious inoculum vary from one respiratory virus to another. This critical review identifies studies reporting instances of infected patients producing airborne human pathogenic coronaviruses, and evidence for the role of physical/chemical characteristics of human-generated droplets in altering embedded viruses'' viability. Based on previous literature, healthy subjects can produce particles between 0.01 The aerosols generated through speech, coughing, sneezing, and breathing have been 178 surveyed in several studies (Table 1) 290 Hygroscopic salts influence the transport of water vapor, and allow for humidity dependent 359 droplet sizes as described by Köhler theory (Köhler, 1936) . Measurements of airborne influenza virus in 839 aerosol particles from human coughs Measurements of airborne influenza virus in 839 aerosol particles from human coughs abstract: Whether virulent human pathogenic coronaviruses (SARS-CoV, MERS-CoV, SARS-CoV-2) are effectively transmitted by aerosols remains contentious. Transmission modes of the novel coronavirus have become a hot topic of research with the importance of airborne transmission controversial due to the many factors that can influence virus transmission. Airborne transmission is an accepted potential route for the spread of some viral infections (measles, chickenpox); however, aerosol features and infectious inoculum vary from one respiratory virus to another. Infectious virus-laden aerosols can be produced by natural human respiratory activities, and their features are vital determinants for virus carriage and transmission. Physicochemical characteristics of infectious respiratory aerosols can influence the efficiency of virus transmission by droplets. This critical review identifies studies reporting instances of infected patients producing airborne human pathogenic coronaviruses, and evidence for the role of physical/chemical characteristics of human-generated droplets in altering embedded viruses’ viability. We also review studies evaluating these viruses in the air, field studies and available evidence about seasonality patterns. Ultimately the literature suggests that a proportion of virulent human coronaviruses can plausibly be transmitted via the air, even though this might vary in different conditions. Evidence exists for respirable-sized airborne droplet nuclei containing viral RNA, although this does not necessarily imply that the virus is transmittable, capable of replicating in a recipient host, or that inoculum is sufficient to initiate infection. However, evidence suggests that coronaviruses can survive in simulated droplet nuclei for a significant time (>24 h). Nevertheless, laboratory nebulized virus-laden aerosols might not accurately model the complexity of human carrier aerosols in studying airborne viral transport. In summary, there is disagreement on whether wild coronaviruses can be transmitted via an airborne path and display seasonal patterns. Further studies are therefore required to provide supporting evidence for the role of airborne transmission and assumed mechanisms underlying seasonality. url: https://api.elsevier.com/content/article/pii/S0269749120364563 doi: 10.1016/j.envpol.2020.115767 id: cord-325783-pqonn0as author: Nicholls, John M title: Lung pathology of fatal severe acute respiratory syndrome date: 2003-05-24 words: 4022.0 sentences: 250.0 pages: flesch: 49.0 cache: ./cache/cord-325783-pqonn0as.txt txt: ./txt/cord-325783-pqonn0as.txt summary: Methods Post-mortem tissue samples from six patients who died from SARS in February and March, 2003 , and an open lung biopsy from one of these patients were studied by histology and virology. Methods Post-mortem tissue samples from six patients who died from SARS in February and March, 2003 , and an open lung biopsy from one of these patients were studied by histology and virology. Since Nov 1, 2002 , an outbreak of severe acute respiratory syndrome (SARS) has affected 33 countries in five continents, with 7053 reported cases and 506 deaths at the time of writing. The case definition was fever (temperature 38°C or higher), cough or shortness of breath, new pulmonary infiltrates on chest radiograph, and either a history of exposure to a patient with SARS or a lack of response to empirical antimicrobial coverage for typical and atypical pneumonia (beta-lactams and macrolides, fluoroquinolones or tetracyclines). abstract: BACKGROUND: Severe acute respiratory syndrome (SARS) is a novel infectious disease with global impact. A virus from the family Coronaviridae has been identified as the cause, but the pathogenesis is still unclear. METHODS: Post-mortem tissue samples from six patients who died from SARS in February and March, 2003, and an open lung biopsy from one of these patients were studied by histology and virology. Only one full autopsy was done. Evidence of infection with the SARS-associated coronavirus (SARS-CoV) and human metapneumovirus was sought by reverse-transcriptase PCR and serology. Pathological samples were examined by light and electron microscopy and immunohistochemistry. FINDINGS: All six patients had serological evidence of recent infection with SARS-CoV. Diffuse alveolar damage was common but not universal. Morphological changes identified were bronchial epithelial denudation, loss of cilia, and squamous metaplasia. Secondary bacterial pneumonia was present in one case. A giant-cell infiltrate was seen in four patients, with a pronounced increase in macrophages in the alveoli and the interstitium of the lung. Haemophagocytosis was present in two patients. The alveolar pneumocytes also showed cytomegaly with granular amphophilic cytoplasm. The patient for whom full autopsy was done had atrophy of the white pulp of the spleen. Electron microscopy revealed viral particles in the cytoplasm of epithelial cells corresponding to coronavirus. INTERPRETATION: SARS is associated with epithelial-cell proliferation and an increase in macrophages in the lung. The presence of haemophagocytosis supports the contention that cytokine dysregulation may account, at least partly, for the severity of the clinical disease. The case definition of SARS should acknowledge the range of lung pathology associated with this disease. Published online May 16, 2003 http://image.thelancet.com/extras/03art4347web.pdf url: https://www.sciencedirect.com/science/article/pii/S0140673603134137 doi: 10.1016/s0140-6736(03)13413-7 id: cord-280732-u0pncmp0 author: Nicolas, J. C. title: Entérovirus et infections respiratoires date: 1976-09-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Summary The importance of enteroviruses in upper and lower respiratory infections is reviewed. Occasionaly summer epidemics of upper respiratory infections seem due to an enterovirus : on the other hand, the lower respiratory injections rarely seem due to these viruses. The relationship between the enteroviruses and respiratory infections remains to be proved. url: https://www.sciencedirect.com/science/article/pii/S0399077X76800571 doi: 10.1016/s0399-077x(76)80057-1 id: cord-024188-d7tnku8z author: Nissen, Michael D. title: Respiratory Infections date: 2010-03-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Until recently, conventional culture techniques and immunofluorecence assays were considered the gold standard for the detection of respiratory viruses, even though results are mostly available too late or lacked specificity and sensitivity. These methods are now widely replaced with appropriate DNA- and RNA-based amplification techniques, in particular real time PCR amplification, for the detection of an extended number of agents responsible for acute respiratory infections. Real-time PCR offers rapid results, efficiencies in work flow and a reduced risk of false positive results due to contamination. As a result, better patient management or reduction of unnecessary antibiotic administration will be possible leading to enhanced efficiencies in health care. In applying molecular methods to diagnostic use, the laboratory can optimise its diagnostic strategy by applying a combination of real-time amplification tests for respiratory viruses and the non-viral respiratory bacterial pathogens. However this must be done within a context of resource availability, technical expertise available and clinical utility. It seems certain that molecular microbiology will continue to develop, leading to further applications in diagnostic technology, thereby improving our understanding of disease processes and enhancing our knowledge of the pathogens responsible. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7193730/ doi: 10.1007/978-90-481-9039-3_5 id: cord-281085-lqniqui0 author: Nosalova, Gabriela title: Pharmacological modulation of cough reflex date: 2006-12-31 words: 6991.0 sentences: 415.0 pages: flesch: 47.0 cache: ./cache/cord-281085-lqniqui0.txt txt: ./txt/cord-281085-lqniqui0.txt summary: As the pathological cough (especially its chronic form) has significant impact on patient''s quality of life, observed either in physical activity or psychosocial domain, various treatment attitudes are used for different forms of cough (acute, subacute, chronic, productive, nonproductive, psychogenic, asthma-associated, or painful). The most important defensive reflex of the airways is cough, which, together with the mucociliary transport system, forms the main mechanism for cleaning of the respiratory tract (Korpas and Nosalova, 1991; Chung and Chang, 2002; Belvisi and Geppetti, 2004) . Although respiratory-modulated receptors play an important role in the function of the upper airways, they are not generally viewed as a primary factor in the elicitation of cough reflex. The antitussive activity of these agents is associated with their ability to lower the sensitivity of the cough center to nerve impulses coming from airways receptors (Fox, 1996b) . abstract: Abstract The cough reflex is an attack of powerful expiratory efforts produced by active contractions of the expiratory muscles, preceded by deep inspirations. Cough is a normal physiological defensive reflex responsible for keeping the airways free of obstruction and harmful substances. However, cough is also the most frequent symptom of acute respiratory system diseases and is the most common reason why sick patients visit physicians. The largest diagnostic group associated with chronic cough is asthma or asthma-like syndromes and chronic obstructive pulmonary disease. Furthermore, gastroesophageal reflux, rhinitis/postnasal drip syndrome and unpleasant side effects accompanying the therapy with angiotensin-converting enzyme inhibitors (ACEI) represent other causes of chronic cough. The cough reflex may be elicited by the activation of receptors of non-myelinated nociceptive Aδ-fibers and C-fibers and receptors of myelinated Aδ-fibers distributed throughout the respiratory tract. In recent times as proper cough receptors are thought to be rapidly adapting receptors (RARs) of myelinated fibers, C-fibers and transient receptor potential vanilloid 1 (TRPV1) localize on the non-myelinated fibers. As the pathological cough (especially its chronic form) has significant impact on patient's quality of life, observed either in physical activity or psychosocial domain, various treatment attitudes are used for different forms of cough (acute, subacute, chronic, productive, nonproductive, psychogenic, asthma-associated, or painful). Interest of research in this field is accompanied with the fact, that many antitussive drugs (mainly from the opioid group), which have been the antitussives of choice for decades, are limited by their unpleasant and very often adverse reactions. In this chapter the authors divided the drugs used in the pharmacological treatment of cough into several groups. These include the drugs acting at the level of receptors, the drugs affecting the propagation of cough impulses in afferent nerves, the drugs modulating the central coordination of cough reflex, the drugs acting at the level of efferent nerves, and the drugs affecting the effectors. Efficacy of many antitussive agents is connected with their influence on more than one level of cough reflex. Another group used in the therapy of cough are mucoactive substances that change the dry, irritant and nonproductive cough into the so-called productive cough with nonirritating expectoration. The last-mentioned group in this chapter is demulcerative and hydrating drugs, which can create a defense layer protecting the mucous membranes from other irritant stimuli. url: https://api.elsevier.com/content/article/pii/S1572557X05020064 doi: 10.1016/s1572-557x(05)02006-4 id: cord-317619-o7qfugjw author: Nye, Steven title: Viral Infection in the Development and Progression of Pediatric Acute Respiratory Distress Syndrome date: 2016-11-24 words: 6733.0 sentences: 324.0 pages: flesch: 35.0 cache: ./cache/cord-317619-o7qfugjw.txt txt: ./txt/cord-317619-o7qfugjw.txt summary: While the overall incidence of respiratory virus infection, in particular RSV and influenza A (H1N1) virus, leading to lower respiratory tract disease is widely studied (12, 13), the frequency of progression to pediatric ARDS has yet to be clearly determined. While post-pandemic studies suggest a decrease in influenza A (H1N1) virus disease severity and burden (20, 21), it continues to be a significant cause of severe illness and pediatric ARDS (22). In RSV infection, development of lower respiratory track disease in premature infants, with or without chronic neonatal lung disease is associated with a significantly higher risk of hospitalization, intensive care unit admission, need for mechanical ventilation, and death (12, [70] [71] [72] [73] . Disease severity and viral load are correlated in infants with primary respiratory syncytial virus infection in the community Motavizumab treatment of infants hospitalized with respiratory syncytial virus infection does not decrease viral load or severity of illness abstract: Viral infections are an important cause of pediatric acute respiratory distress syndrome (ARDS). Numerous viruses, including respiratory syncytial virus (RSV) and influenza A (H1N1) virus, have been implicated in the progression of pneumonia to ARDS; yet the incidence of progression is unknown. Despite acute and chronic morbidity associated with respiratory viral infections, particularly in “at risk” populations, treatment options are limited. Thus, with few exceptions, care is symptomatic. In addition, mortality rates for viral-related ARDS have yet to be determined. This review outlines what is known about ARDS secondary to viral infections including the epidemiology, the pathophysiology, and diagnosis. In addition, emerging treatment options to prevent infection, and to decrease disease burden will be outlined. We focused on RSV and influenza A (H1N1) viral-induced ARDS, as these are the most common viruses leading to pediatric ARDS, and have specific prophylactic and definitive treatment options. url: https://www.ncbi.nlm.nih.gov/pubmed/27933286/ doi: 10.3389/fped.2016.00128 id: cord-292836-1o2ynvy3 author: Ogimi, Chikara title: What’s New With the Old Coronaviruses? date: 2020-04-21 words: 5194.0 sentences: 267.0 pages: flesch: 44.0 cache: ./cache/cord-292836-1o2ynvy3.txt txt: ./txt/cord-292836-1o2ynvy3.txt summary: In this review, we discuss what is known about the virology, epidemiology, and disease associated with pediatric infection with the common community-acquired human coronaviruses, including species 229E, OC43, NL63, and HKU1, and the coronaviruses responsible for past world-wide epidemics due to severe acute respiratory syndrome and Middle East respiratory syndrome coronavirus. By contrast SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV) are highly pathogenic in humans, with high rates of severe pneumonia and fatal outcomes [21] . A large prospective surveillance study conducted in Norway from 2006 to 2015 that enrolled all hospitalized children aged ≤16 years with respiratory tract infections revealed that HCoVs OC43 and NL63 were detected most frequently and were epidemic every second winter [35] . Large surveillance studies of children and adults to evaluate the prevalence of all major respiratory viruses using multiplex PCR have been conducted in many settings, showing that HCoV infections are the fourth or sixth most common virus detected overall and across all age groups [33, 43] . abstract: Coronaviruses contribute to the burden of respiratory diseases in children, frequently manifesting in upper respiratory symptoms considered to be part of the “common cold.” Recent epidemics of novel coronaviruses recognized in the 21st century have highlighted issues of zoonotic origins of transmissible respiratory viruses and potential transmission, disease, and mortality related to these viruses. In this review, we discuss what is known about the virology, epidemiology, and disease associated with pediatric infection with the common community-acquired human coronaviruses, including species 229E, OC43, NL63, and HKU1, and the coronaviruses responsible for past world-wide epidemics due to severe acute respiratory syndrome and Middle East respiratory syndrome coronavirus. url: https://doi.org/10.1093/jpids/piaa037 doi: 10.1093/jpids/piaa037 id: cord-276348-vr5fit8r author: Ogra, Pearay L. title: Respiratory syncytial virus: The virus, the disease and the immune response date: 2004-01-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract RSV is the primary cause of hospitalisation in the first year of life for children in most parts of the world, and nearly 100% of children in the USA are infected with the virus by 2 to 3 years of age. The agent is an enveloped RNA virus with a non-segmented single-stranded negative-sense genome. The viral genome encodes 8 structural and 2 non-structural proteins. Important structural proteins include the fusion (F) protein and the attachment (G) protein which are essential for viral penetration and attachment to the host cells. Both proteins are important in development of immune responses. The virus is estimated to cause 3000 to 4000 deaths annually. Primary infections are as a rule symptomatic. The spectrum of clinical manifestations ranges from mild upper tract illness, infection in middle ear which progresses to acute otitis media, croup, to apnoea in premature infants, pneumonia and bronchiolitis. Premature babies born at 30–35 weeks of gestation, infants with cyanotic congenital heart disease, HIV-infected subjects, and patients on intensive immunosuppressive therapy especially after bone marrow transplant are considered to be at risk for increased mortality and morbidity during RSV infection. The virus does not normally replicate outside of the bronchopulmonary tree and the infection is exquisitely restricted to the respiratory mucosa. However, development of extrapulmonary disease has been observed in certain T and B cell immunodeficiency states. The association of RSV with asthma and reversible reactive airway disease in early childhood has attracted significant attention. Recurrent wheezing for up to 5 to 7 years of age and established airway disease has been observed in a significant number of children with a strong family history of allergy, after primary infection or reinfection with RSV. Immune response to primary infection is relatively small but on reinfection, a significant booster effect with sustained immunologic reactivity is observed in serum and respiratory mucosa. Both CD4- and CD8-specific as well as Th1- and Th2-cell specific immune responses have been observed during human infection. In addition, proinflammatory as well as immunoregulatory cytokines and chemokines are induced in the respiratory tract after natural and induced (in vitro) infection. Significant progress has been made in understanding the role of Th1 vs. Th2, IgE, viral induced cytokines and chemokines in the mechanisms of pathogenesis of the disease, development of wheezing and in the prevention and treatment of the infection and its sequelae. Respiratory syncytial virus (RSV) is one of the commonest human viral infections, and virtually every child is infected by the third birthday. Because of its restricted mucosal immunopathology, and frequent association with bronchial hyperreactivity and development of wheezing, RSV has served as an important model to investigate mechanisms of mucosal immune responses and development of mucosal disease following infection. The importance of RSV in bronchopulmonary disease and development of bronchial hyperreactivity has been the focus of several recent symposia [Kimpen JL, Simoes EAF. Am J Respir Crit Care Med 2001; 163:S1–S6]. This brief report will only summarise, based on selected references, the historical landmarks of its discovery and current understanding of the mechanisms of immunity, and their possible role in the pathogenesis of bronchopulmonary disease. url: https://www.ncbi.nlm.nih.gov/pubmed/14980256/ doi: 10.1016/s1526-0542(04)90023-1 id: cord-296777-6xz2aslj author: Oosterhof, L title: Fatal lower respiratory tract disease with human corona virus NL63 in an adult haematopoietic cell transplant recipient date: 2009-10-12 words: 1195.0 sentences: 87.0 pages: flesch: 53.0 cache: ./cache/cord-296777-6xz2aslj.txt txt: ./txt/cord-296777-6xz2aslj.txt summary: title: Fatal lower respiratory tract disease with human corona virus NL63 in an adult haematopoietic cell transplant recipient Community-acquired respiratory viruses are known to account for many cases of interstitial pneumonia as a common complication following allo-haematopoietic cell transplantation (HCT). 7 We present a case of fatal HCoV NL63 pulmonary infection during the late-engraftment phase, 5 months after an allo-HCT with a matched unrelated donor in a patient without active GVHD and receiving only modest immune suppressive treatment. The BAL fluid at day 11 of admission and the final PCR analysis post mortem were negative for HCoV NL63, suggesting that the patient had cleared the virus. Although evaluation for corona virus in symptomatic HCT patients is not routinely performed, we believe it should be considered in the differential diagnoses of respiratory failure or as a possible causative agent before the development of IPS after allo-HCT for haematological disease. abstract: nan url: https://doi.org/10.1038/bmt.2009.292 doi: 10.1038/bmt.2009.292 id: cord-283399-iz4l9i0d author: O’Gorman, C. title: Human metapneumovirus in adults: a short case series date: 2006-03-14 words: 1484.0 sentences: 83.0 pages: flesch: 41.0 cache: ./cache/cord-283399-iz4l9i0d.txt txt: ./txt/cord-283399-iz4l9i0d.txt summary: This study was carried out to further the available information on adult cases of human metapneumovirus (hMPV), a recently described cause of respiratory infection. For adults presenting with respiratory symptoms and a background of pre-existing respiratory disease or who are immunocompromised, nucleic acid-based techniques are a cost-effective means of making the viral diagnosis in a clinically relevant time frame. In young children and elderly patients hMPV is most commonly associated with a clinical diagnosis of bronchiolitis or bronchitis, respectively, whereas in middle-aged adults, it may produce an influenza-like illness, which can be complicated by pneumonitis in the presence of immunocompromising factors [5] . This retrospective observational study reviewed all cases of hMPV detected in patients over 18 years of age, from the time the RT-PCR method was adopted in July 2003 through to January 2005. abstract: This study was carried out to further the available information on adult cases of human metapneumovirus (hMPV), a recently described cause of respiratory infection. Among a cohort of 741 symptomatic patients tested since 2003, the virus was diagnosed in six adults using reverse transcriptase polymerase chain reaction. Of the six, two were from the community, two were hospital inpatients with chronic obstructive pulmonary disease and two were immunocompromised patients, both of whom required ventilation and later died. This report discusses the clinical features, epidemiology and diagnosis of hMPV, highlighting that this infection may be associated with death in high-risk adults. For adults presenting with respiratory symptoms and a background of pre-existing respiratory disease or who are immunocompromised, nucleic acid-based techniques are a cost-effective means of making the viral diagnosis in a clinically relevant time frame. url: https://www.ncbi.nlm.nih.gov/pubmed/16534565/ doi: 10.1007/s10096-006-0116-0 id: cord-255711-8lojw5cz author: Palmu, Arto A. title: Nasal swab bacteriology by PCR during the first 24‐months of life: A prospective birth cohort study date: 2019-01-04 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Most respiratory bacterial carriage studies in children are based on cross‐sectional samples or longitudinal studies with infrequent sampling points. The prospective Observational Research in Childhood Infectious Diseases birth cohort study intensively evaluated the community‐based epidemiology of respiratory viruses and bacteria during the first 2‐years of life. Here we report the bacteriologic findings. METHODS: Pregnant women in Brisbane, Australia were recruited between September 2010 and October 2012, and their healthy newborn children were followed for the first 2‐years of life. Parents kept a daily symptom diary for the study child, collected a weekly anterior nose swab and completed an illness burden diary when their child met pre‐defined illness criteria. Specimens were tested for respiratory bacteria by real‐time polymerase chain reaction (PCR) assays and those containing human genomic DNA, deemed as high‐quality, were analyzed. RESULTS: Altogether 8100 high‐quality nasal swab specimens from 158 enrolled children were analyzed. Streptococcus pneumoniae, Moraxella catarrhalis, and Haemophilus influenzae were detected in 42.4%, 38.9%, and 14.8% of these samples, respectively. Concomitant detection of bacteria was common. In contrast, Bordetella pertussis, B. parapertussis, Mycoplasma pneumoniae, Chlamydia pneumoniae, and Simkania negevensis were rarely identified. The prevalence of the three major bacteria was higher with increasing age and in the winter and spring months. Siblings and childcare attendance were the other risk factors identified. CONCLUSIONS: We confirmed the feasibility of frequent nasal swabbing by parents for studying bacterial colonization. PCR detected the major respiratory tract bacteria with expected high frequencies, but atypical bacteria were found rarely in this cohort. url: https://www.ncbi.nlm.nih.gov/pubmed/30609299/ doi: 10.1002/ppul.24231 id: cord-328501-mbwgi56x author: Pang, Junxiong title: Risk factors for febrile respiratory illness and mono-viral infections in a semi-closed military environment: a case-control study date: 2015-07-25 words: 5767.0 sentences: 275.0 pages: flesch: 46.0 cache: ./cache/cord-328501-mbwgi56x.txt txt: ./txt/cord-328501-mbwgi56x.txt summary: title: Risk factors for febrile respiratory illness and mono-viral infections in a semi-closed military environment: a case-control study CONCLUSION: Increasing age, smoker, recruit-camp, stay-out personnel with ill household members and stay-in personnel with ill bunkmates were independent risk factors of FRI in a semi-closed military environment. Previous documented risk factors of FRI in other countries included body mass index equal or greater than 25 kg/m 2 , previous respiratory tract infections [30] , overcrowding and closed units [29, [31] [32] [33] , presence of sand and dust storms, extreme temperature changes [34, 35] , smoking [36] , female, Navy service, poor latrine facilities, increasing age and higher rank [37] . Increasing age, smokers, recruit camp, stay-out personnel with ill household members and stay-in personnel with ill bunkmates were independent risk factors of FRI in a semi-closed military setting. Outbreak of febrile respiratory illness associated with adenovirus 11a infection in a Singapore military training cAMP abstract: BACKGROUND: Febrile respiratory illness (FRI) results in substantial burden in semi-closed environments. Tackling risk factors may reduce transmission and infection. However, risk factors involved in one setting may not be generalizable in all settings due to differences in climate, residential environment, population genetic and cultural backgrounds. This study aims to identify risk factors of FRI and mono-viral infections in a tropical military environment. METHODS: From year 2009 to 2012, military personnel with temperature ≥37.5 °C, cough and/or sore throat, and personnel with no fever or no respiratory symptoms were recruited as cases and controls, respectively. Subjects provided nasal wash specimens and answered a standardized questionnaire. Resplex assays were used to determine the viral etiologies. Descriptive, univariate and multivariate analyses of the variables were performed using appropriate descriptive tests and logistic regression modelling, respectively, with R program. RESULTS: A total of 7,743 FRI cases and 1,247 non-FRI study controls were recruited. Increasing age [adjusted odds ratio (AOR) = 1.03; 95 % confidence interval (CI) = 1.01-1.05], recruit camp (AOR = 4.67; 95 % CI = 3.99-5.46) and smoker (AOR = 1.31; 95 % CI = 1.13-1.52) were independent risk factors of FRI. Malay ethnicity was positively associated with influenza A(H1N1)pdm09 (AOR = 1.50; 95 % CI = 1.04-2.15) and coxsackie/echovirus (AOR = 1.67; 95 % CI = 1.19-2.36) mono-infection. Significant contact risk factors were stay-out personnel with ill household member (AOR = 4.96; 95 % CI = 3.39-7.24), and stay-in personnel with ill bunkmate and household member (AOR = 3.55; 95 % CI = 2.57-4.91). Staying in camp with none ill in bunk and at home was a protective factor against FRI (AOR = 0.80; 95 % CI = 0.64-0.99). These contact risk factors were similarly observed for the five most common viruses detected, namely adenovirus, rhinoviruses, influenza A and B, and coxsackie/echovirus. CONCLUSION: Increasing age, smoker, recruit-camp, stay-out personnel with ill household members and stay-in personnel with ill bunkmates were independent risk factors of FRI in a semi-closed military environment. Early identification and isolation of ill personnel from their bunk may be effective to prevent and reduce transmission and disease burden. url: https://www.ncbi.nlm.nih.gov/pubmed/26208494/ doi: 10.1186/s12879-015-1024-7 id: cord-259927-xh9cw9ao author: Papadopoulos, Nikolaos G. title: Promising approaches for the treatment and prevention of viral respiratory illnesses date: 2017-07-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Viral respiratory tract infections are the most common human ailments, leading to enormous health and economic burden. Hundreds of viral species and subtypes have been associated with these conditions, with influenza viruses, respiratory syncytial virus, and rhinoviruses being the most frequent and with the highest burden. When considering prevention or treatment of viral respiratory tract infections, potential targets include the causative pathogens themselves but also the immune response, disease transmission, or even just the symptoms. Strategies targeting all these aspects are developing concurrently, and several novel and promising approaches are emerging. In this perspective we overview the entire range of options and highlight some of the most promising approaches, including new antiviral agents, symptomatic or immunomodulatory drugs, the re-emergence of natural remedies, and vaccines and public health policies toward prevention. Wide-scale prevention through immunization appears to be within reach for respiratory syncytial virus and promising for influenza virus, whereas additional effort is needed in regard to rhinovirus, as well as other respiratory tract viruses. url: https://api.elsevier.com/content/article/pii/S0091674917311132 doi: 10.1016/j.jaci.2017.07.001 id: cord-260472-xvvfguht author: Papadopoulos, Nikolaos G. title: Antimicrobial strategies: An option to treat allergy? date: 2007-01-31 words: 5105.0 sentences: 255.0 pages: flesch: 30.0 cache: ./cache/cord-260472-xvvfguht.txt txt: ./txt/cord-260472-xvvfguht.txt summary: The association between upper respiratory viral infections and asthma exacerbations in children was demonstrated almost three decades ago using virus cultures and serological techniques [5] . Abbreviations: RTePCR, reverse transcriptionepolymerase chain reaction; RV, rhinovirus; PIV, parainfluenza virus; RSV, respiratory syncytial virus; MPV, human metapneumovirus; ICAM-1, intracellular adhesion molecule-1; IFN-b, interferon-beta; NGF, nerve growth factor; SP, substance P; NK1, neurokinin 1 receptor; MBL, mannose-binding lectin; LABA, long-acting b 2 agonists. In the human respiratory tract, all the above agents are able to produce a spectrum of clinical acute infection phenotypes, ranging from the common cold, croup and acute bronchiolitis, to pneumonia, although each virus has increased propensity for a particular clinical disease (e.g. parainfluenza for croup, RSV for severe bronchiolitis, influenza for pneumonia) [21, 22] . Rhinovirus is the key virus accounting for the majority of exacerbations both in children and adults and thus the effective treatment or prevention of that infection would be a major asset in asthma therapy. abstract: Abstract Respiratory infections by bacteria and viruses often trigger symptoms of asthma in both adults and children. This observation and subsequent mechanistic studies have demonstrated important interactions among allergens, microbes and the atopic host. The mechanisms responsible for microbe-induced asthma exacerbations are only incompletely understood. A focal point of current research is the inflammatory response of the host following an encounter with a pathogenic microbe, including variations in chemokine and cytokine production and resulting in changes in bronchial hyper-responsiveness and lung function. Direct bronchial infection, exposure of nerves with resulting neurogenic inflammation and a deviated host immune response are among the mechanisms underlying these functional disorders. Lately, suboptimal innate immune responses, expressed as defective interferon production, have gained attention as they might be amenable to intervention. This review describes the suggested mechanisms involved in the complex interactions between ‘asthmagenic’ microbes, the immune system and atopy, based on in-vitro and in-vivo experimental models and epidemiological evidence. In addition, it provides a synopsis of potential therapeutic strategies either directly against the microorganisms or in respect to the associated inflammation. url: https://www.sciencedirect.com/science/article/pii/S0753332206003350 doi: 10.1016/j.biopha.2006.10.004 id: cord-353308-e4s8el0s author: Parashar, Umesh D title: Severe acute respiratory syndrome: review and lessons of the 2003 outbreak date: 2004-05-20 words: 4499.0 sentences: 224.0 pages: flesch: 45.0 cache: ./cache/cord-353308-e4s8el0s.txt txt: ./txt/cord-353308-e4s8el0s.txt summary: This dramatic chain of transmission brought to the world''s attention this new respiratory disease, called severe acute respiratory syndrome (SARS), and clearly illustrated the potential for SARS to spread extensively from a single infected person and to rapidly disseminate globally through air travel. Diarrhoea has been reported at presentation in approximately 25% of patients, although this symptom was observed in as many as 73% of all patients affected by an outbreak at an apartment complex in Hong Kong that is believed to have resulted from fecal-oral/respiratory transmission of SARS-CoV. [53] [54] [55] [56] Given that profuse watery diarrhoea is seen in a significant proportion of patients and SARS-CoV can be shed in large quantities in stool, faeces remain a possible source of virus and fecal-oral or fecal-respiratory spread are the leading hypotheses for a large outbreak affecting more than 300 people at an apartment complex in Hong Kong. Fatal severe acute respiratory syndrome is associated with multiorgan involvement by coronavirus (SARS-CoV) abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/15155694/ doi: 10.1093/ije/dyh198 id: cord-307874-0obomty2 author: Pardon, Bart title: Bovine Respiratory Disease Diagnosis: What Progress Has Been Made in Infectious Diagnosis? date: 2020-05-23 words: 7061.0 sentences: 388.0 pages: flesch: 43.0 cache: ./cache/cord-307874-0obomty2.txt txt: ./txt/cord-307874-0obomty2.txt summary: Evidence-based guidelines for precise interpretation of microbiologic tests results are lacking; however, approaches that have been practically useful for the management of bovine respiratory disease outbreaks are presented. However, naturally resistant to fluoroquinolones 71 Escherichia coli, Gallibacterium anatis, Enterobacter hormaechei, staphylococci, streptococci, fungi Secondary Single reports on cattle-specific strains isolated in pure culture in an outbreak of pneumonia in calves 52, [72] [73] [74] Multiple other bacterial species can be detected in the bovine respiratory tract. 10, 35, 54 However, with current knowledge on the interpretation of DNS results at the individual or group level, samples of the lower respiratory tract are likely a better option to evaluate potential involvement of opportunistic pathogens. In the example where the pathogen is causing the disease in 100% of affected calves, the risk of not finding an infected animal after sampling n cases is (1-Se)n , where Se is the test sensitivity. abstract: When it is desired to identify infectious agents involved in an outbreak of bovine respiratory disease, a variety of possible sampling methods may be used. For field use, the deep nasopharyngeal swab, transtracheal wash, and nonendoscopic bronchoalveolar lavage are most feasible. At present, bacterial culture and polymerase chain reaction testing are most commonly used to identify infectious agents. Interpretation of test results can be challenging, particularly for opportunistic pathogens. Evidence-based guidelines for precise interpretation of microbiologic tests results are lacking; however, approaches that have been practically useful for the management of bovine respiratory disease outbreaks are presented. url: https://api.elsevier.com/content/article/pii/S0749072020300220 doi: 10.1016/j.cvfa.2020.03.005 id: cord-286930-c1zkjdgf author: Park, Won-Ju title: Seroprevalence of Respiratory Syncytial Virus IgG among Healthy Young Adults in Basic Training for the Republic of Korea Air Force date: 2014-09-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: This investigation enrolled 570 healthy young males gathered from all over the country for military service at the Republic of Korea Air Force boot camp. It confirmed RSV IgG seroprevalence by utilizing the enzyme immunoassay method just prior to undergoing basic training. The mean age of this study was 20.25±1.34 yr old. The results of their immunoassay seroprofiles showed that 561 men (98.4%) were positive, 2 (0.4%) were negative and 7 (1.2%) were equivocal belonging to the grey zone. It was confirmed that RSV is a common respiratory virus and RSV infection was encountered by almost all people before reaching adulthood in Korea. Nine basic trainees belonging to the RSV IgG negative and equivocal grey zone categories were prospectively observed for any particular vulnerability to respiratory infection during the training period of two months. However, these nine men completed their basic training without developing any specific respiratory illness. GRAPHICAL ABSTRACT: [Image: see text] url: https://doi.org/10.3346/jkms.2014.29.9.1325 doi: 10.3346/jkms.2014.29.9.1325 id: cord-303040-ha8gufh8 author: Park, Won-Ju title: Respiratory Syncytial Virus Outbreak in the Basic Military Training Camp of the Republic of Korea Air Force date: 2015-01-14 words: 3618.0 sentences: 181.0 pages: flesch: 48.0 cache: ./cache/cord-303040-ha8gufh8.txt txt: ./txt/cord-303040-ha8gufh8.txt summary: In the event of an outbreak of an acute febrile illness of a highly infective nature in facilities used by a young adult group, RSV should be considered among the possible causative agents. Recent studies indicate that RSV is an important cause of respiratory infection in elderly patients, either those with compromised immunity or inflicted with chronic illness, as well as in adult populations in a special environment, such as military personnel [7] [8] [9] [10] [11] . A case patient was a person, among military recruits in this boot camp, who was admitted to the medical care center in the boot camp with chief complaints of fever and symptoms of upper respiratory tract illness after May 26, 2011. In the event of an epidemic of acute febrile respiratory illness of a highly infective nature, it is recommended to conduct a test for RSV in the young adult population in the military facilities. abstract: OBJECTIVES: An outbreak of acute febrile illness occurred in the Republic of Korea Air Force boot camp from May to July 2011. An epidemiological investigation of the causative agent, which was of a highly infective nature, was conducted. METHODS: Throat swabs were carried out and a multiplex reverse transcriptase-polymerase chain reaction (RT-PCR) assay was performed to identify possible causative factors. RESULTS: The mean age of patients who had febrile illness during the study period was 20.24 years. The multiplex RT-PCR assay identified respiratory syncytial virus (RSV) as the causative agent. The main symptoms were sore throat (76.0%), sputum (72.8%), cough (72.1%), tonsillar hypertrophy (67.9%), and rhinorrhea (55.9%). The mean temperature was 38.75°C and the attack rate among the recruits was 15.7% (588 out of 3750 recruits), while the mean duration of fever was 2.3 days. The prognosis was generally favorable with supportive care but recurrent fever occurred in 10.1% of the patients within a month. CONCLUSIONS: This is the first epidemiological study of an RSV outbreak that developed in a healthy young adult group. In the event of an outbreak of an acute febrile illness of a highly infective nature in facilities used by a young adult group, RSV should be considered among the possible causative agents. url: https://doi.org/10.3961/jpmph.14.037 doi: 10.3961/jpmph.14.037 id: cord-324217-secnz2ta author: Pasdaran, A. title: Volatile oils: Potential agents for the treatment of respiratory infections date: 2016-08-05 words: 7698.0 sentences: 407.0 pages: flesch: 35.0 cache: ./cache/cord-324217-secnz2ta.txt txt: ./txt/cord-324217-secnz2ta.txt summary: The present chapter reviews natural traditional remedies used in the treatment of respiratory infections with the emphasis on antibacterial, antiviral, and antiinflammation activities of the volatile natural compounds (essential oils, etc.), and provides a brief view in some of structural activity relationships between antibacterial potencies and chemical structures of the essential oil''s constituents. 10 Besides the antimicrobial activity of the essential oils in natural products, other characteristics such as high vapor pressure, low toxicity, and antiinflammatory potential create a worthwhile theme for using of these natural compounds for new drug development in respiratory infections. As a member of the phytochemicals, terpenoids have been observed as a model of lipid soluble agents, which have an impact on the activities of membrane catalyzed enzymes; for 3 SCREENING OF THE ANTIbACTERIAL EFFECTS OF ESSENTIAL OILS example, enzymes involved in respiratory pathways. 98 Among the natural chemical compounds, significant antiinflammatory activities of plant-based essential oil have been reported by many researchers, which showed the basis for folk and traditional uses of these herbs for treatment of inflammatory diseases. abstract: Due to presence of secondary bioactive metabolites, natural compounds are considered a major source of new active molecules that can be developed as new drugs. Infectious diseases, and mainly the common respiratory infections, are major challenges to the current chemotherapy systems and, therefore, there is a requirement to find new compounds with therapeutic potential. The volatile natural compounds and essential oils are the main treasure agents in the natural compounds with antibiotic potential. The present chapter reviews natural traditional remedies used in the treatment of respiratory infections with the emphasis on antibacterial, antiviral, and antiinflammation activities of the volatile natural compounds (essential oils, etc.), and provides a brief view in some of structural activity relationships between antibacterial potencies and chemical structures of the essential oil’s constituents. url: https://www.sciencedirect.com/science/article/pii/B9780128045435000166 doi: 10.1016/b978-0-12-804543-5.00016-6 id: cord-318591-ssnlfjap author: Pecego, AC title: Etiology, clinical, and epidemiological characteristics of severe respiratory infection in people living with HIV date: 2020-01-22 words: 4441.0 sentences: 234.0 pages: flesch: 49.0 cache: ./cache/cord-318591-ssnlfjap.txt txt: ./txt/cord-318591-ssnlfjap.txt summary: We used the severe acute respiratory infection (SARI) definition to describe the etiology, clinical, and epidemiological characteristics in this population. [4] [5] [6] After the recent influenza A (H1N1, H5N1, and H7N9) and the Middle East Respiratory Virus (MERS-CoV) outbreaks, the WHO is encouraging and supporting countries to strengthen surveillance on severe acute respiratory infections (SARI) 7 but with limited information on PLWH regarding etiology and prognosis, despite their increased risk for respiratory infections and adverse outcomes. [8] [9] [10] So, in this study, we described how SARI is represented, according to clinical presentation, epidemiology and etiology in a population of PLWH with respiratory infection residing in a high-prevalence TB area. We observed two cases of influenza in the non-SARI group, respectively 20 and 30 days after symptom onset, and both patients developed respiratory failure that led to death (data not shown). abstract: People living with HIV (PLWH) are more prone to severe respiratory infections. We used the severe acute respiratory infection (SARI) definition to describe the etiology, clinical, and epidemiological characteristics in this population. This was a prospective observational study including PLWH hospitalized with fever and cough. Those with symptom onset up to 10 days were classified as severe acute respiratory infection and 11–30 days as non-severe acute respiratory infection. Blood, urine samples and nasopharyngeal swabs were collected. Data were extracted from patient charts during their hospital stay. Forty-nine patients were included, median CD4 cell count: 80 cells/mm(3), median time since HIV diagnosis and hospital admission: 84 months and 80% were antiretroviral therapy exposed. Twenty-seven patients were classified as SARI. Etiology was identified in 69%, 47% were polymicrobial. Respiratory virus (9 SARI vs. 13 non-SARI), bacteria (5 SARI vs. 4 non-SARI), Mycobacterium tuberculosis (6 SARI group vs. 7 non-SARI group), Pneumocystis jirovecii (4 SARI vs. 1 non-SARI), Cryptococcus neoformans (1 SARI vs. 3 non-SARI), and influenza A (1 SARI vs. 2 non-SARI). Dyspnea was statistically more prevalent in SARI (78% vs. 36%, p = 0.011) but the risk of death was higher in the non-SARI (4% vs. 36%, p = 0.0067). In the severely immunocompromised PLWH, severe acute respiratory infection can be caused by multiple pathogens and codetection is a common feature. url: https://www.ncbi.nlm.nih.gov/pubmed/31969059/ doi: 10.1177/0956462419882587 id: cord-263927-hnsyas9q author: Peci, Adriana title: Community‐acquired respiratory viruses and co‐infection among patients of Ontario sentinel practices, April 2009 to February 2010 date: 2012-08-09 words: 3210.0 sentences: 210.0 pages: flesch: 48.0 cache: ./cache/cord-263927-hnsyas9q.txt txt: ./txt/cord-263927-hnsyas9q.txt summary: Objectives To describe respiratory viruses, including co‐infection and associated attributes such as age, sex or comorbidity, in patients presenting with influenza‐like illness to a community sentinel network, during the pandemic A(H1N1)pdm09 in Ontario, Canada. In multinomial logistic regression analyses adjusted for age, sex, comorbidity, and timeliness of sample collection, single infection was less often detected in the elderly and co‐infection more often in patients <30 years of age. Co‐infection, but not single infection, was more likely detected in patients who had a sample collected within 2 days of symptom onset as compared to 3–7 days. [8] [9] [10] [11] [12] [13] Higher proportions of influenza A, respiratory syncytial virus (RSV), parainfluenza viruses, and rhinovirus, compared with other circulating viruses have been detected in patients with co-infections. 9, 15, 16, 20, 21 This study enrolled community patients presenting with (ILI) to a community sentinel network, during the influenza pandemic A(H1N1)pdm09 in Ontario, Canada and documented the profile of respiratory viruses causing ILI symptoms. abstract: Please cite this paper as: Peci et al. (2012) Community‐acquired respiratory viruses and co‐infection among patients of Ontario Sentinel practices, April 2009 to February 2010. Influenza and Other Respiratory Viruses 7(4), 559–566. Background Respiratory viruses are known to cocirculate but this has not been described in detail during an influenza pandemic. Objectives To describe respiratory viruses, including co‐infection and associated attributes such as age, sex or comorbidity, in patients presenting with influenza‐like illness to a community sentinel network, during the pandemic A(H1N1)pdm09 in Ontario, Canada. Methods Respiratory samples and epidemiologic details were collected from 1018 patients with influenza‐like illness as part of respiratory virus surveillance and a multiprovincial case–control study of influenza vaccine effectiveness. Results At least one virus was detected in 668 (65·6%) of 1018 samples; 512 (50·3%) had single infections and 156 (15·3%) co‐infections. Of single infections, the most common viruses were influenza A in 304 (59·4%) samples of which 275 (90·5%) were influenza A(H1N1)pdm09, and enterovirus/rhinovirus in 149 (29·1%) samples. The most common co‐infections were influenza A and respiratory syncytial virus B, and influenza A and enterovirus/rhinovirus. In multinomial logistic regression analyses adjusted for age, sex, comorbidity, and timeliness of sample collection, single infection was less often detected in the elderly and co‐infection more often in patients <30 years of age. Co‐infection, but not single infection, was more likely detected in patients who had a sample collected within 2 days of symptom onset as compared to 3–7 days. Conclusions Respiratory viral co‐infections are commonly detected when using molecular techniques. Early sample collection increases likelihood of detection of co‐infection. Further studies are needed to better understand the clinical significance of viral co‐infection. url: https://doi.org/10.1111/j.1750-2659.2012.00418.x doi: 10.1111/j.1750-2659.2012.00418.x id: cord-260238-2p209g2p author: Peiris, J S M title: Severe acute respiratory syndrome date: 2004-11-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Severe acute respiratory syndrome (SARS) was caused by a previously unrecognized animal coronavirus that exploited opportunities provided by 'wet markets' in southern China to adapt to become a virus readily transmissible between humans. Hospitals and international travel proved to be 'amplifiers' that permitted a local outbreak to achieve global dimensions. In this review we will discuss the substantial scientific progress that has been made towards understanding the virus—SARS coronavirus (SARS-CoV)—and the disease. We will also highlight the progress that has been made towards developing vaccines and therapies The concerted and coordinated response that contained SARS is a triumph for global public health and provides a new paradigm for the detection and control of future emerging infectious disease threats. url: https://www.ncbi.nlm.nih.gov/pubmed/15577937/ doi: 10.1038/nm1143 id: cord-016070-e9ix35x3 author: Perret Pérez, Cecilia title: Pneumonia Caused by Emerging Viral Agents date: 2020-02-01 words: 3645.0 sentences: 174.0 pages: flesch: 44.0 cache: ./cache/cord-016070-e9ix35x3.txt txt: ./txt/cord-016070-e9ix35x3.txt summary: The SARS coronavirus and MERS-CoV are two pathogens from the coronavirus family that predominantly cause serious lower tract respiratory infections with a high mortality rate, but they are genetically different viruses. This observation suggests that camels are the reservoirs of the virus, which can be transmitted to humans through direct contact with these animals or through consumption of their milk: 1599 cases had been diagnosed by July 2015, with 574 deaths [World Health Organization (WHO)]. HCoV-NL63 and HCoV-HKU1 are viruses that tend to manifest as a common cold, just as the usual coronaviruses HCoV-229E and HCoV-OC43; nevertheless, in small children, elderly patients, and immunosuppressed patients, they can cause serious respiratory disease with a high mortality rate. Isolated cases of avian origin in humans caused by the influenza H10N8 virus and H6N1 have been observed in China. abstract: Emerging viruses that cause pneumonia in humans are agents which normally circulate in the animal population but can move to human hosts under certain circumstances, which determines the occurrence of a new type of disease. The Middle East respiratory syndrome (MERS) is caused by a coronavirus. The disease has a wide symptomatic spectrum that can range from asymptomatic infections to fulminant respiratory failure. Diagnostic confirmation is achieved through viral isolation. Severe acute respiratory syndrome (SARS), also produced by a coronavirus, is capable of producing a serious pulmonary disease outbreak with no reappearance. The clinical presentation includes fever, malaise, cough, and headache followed by diarrhea. Other coronaviruses (HCoV-NL63 and HCoV-HKU1) can cause serious lower respiratory infections in small children, the elderly, and immunosuppressed patients. Influenza virus is widespread in nature, and avian virus may spread to humans, as has been reported with H7N9, H5N1, H10N8, and H6N1. Cardiopulmonary hantavirus syndrome, a feverish disease characterized by respiratory insufficiency and shock, is produced by Andes virus. Other emerging viruses are enterovirus D68 and polyomavirus. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120232/ doi: 10.1007/978-3-030-26961-6_34 id: cord-005583-hmv8jjfl author: Peters, M. J. title: Acute hypoxemic respiratory failure in children: case mix and the utility of respiratory severity indices date: 2013-12-27 words: 3992.0 sentences: 207.0 pages: flesch: 45.0 cache: ./cache/cord-005583-hmv8jjfl.txt txt: ./txt/cord-005583-hmv8jjfl.txt summary: In an individual patient, such a response to intervention should be indicated by their best, rather than worst, measure of gas exchange, Therefore, the purpose of the present prospective, single institution study of AHRF in children was to assess whether the best, early respiratory indices in non-survivors were significantly different from those who survived. Table 2 Comparison of previously published [2] [3] [4] [5] respiratory severity parameters with the present series (PPV positive predictive value for mortality, VI ventilation index, OI oxygenation index, PIP peak inspiratory pressure (cmH20), A-aDO 2 alveolar arterial oxygen gradient (mmHg), MAP mean airway pressure (cmH20), LR + the likelihood ratio for a positive test result, i.e. the ratio of finding the predictor in non-survivors to finding it in survivors) * indicates intermediate to high diagnostic impact, ns not significant Proposed PPV LR + PPV p predictors (95 % confidence interval) in present study abstract: Objective: Acute hypoxemic respiratory failure (AHRF) is a common reason for emergency pediatric intensive care. An objective assessment of disease severity from acute physiological parameters would be of value in clinical practice and in the design of clinical trials. We hypothesised that there was a difference in the best early respiratory indices in those who died compared with those who survived. Design: A prospective observational study of 118 consecutive AHRF admissions with data analysis incorporating all blood gases. Setting: A pediatric intensive care unit in a national children’s hospital. Interventions: None. Results: Mortality was 26/118,22% (95% confidence interval 18–26%). There were no significant differences in the best alveolar-arterial oxygen tension gradient (A-aDO(2), torr), oxygenation index (OI), ventilation index (VI), or PaO(2)/FIO(2) during the first 2 days of intensive care between the survivors and non-survivors. Only the mean airway pressure (MAP, cm H(2)O) used for supportive care was significantly different on days 0 and 1 (p≤0.05) with higher pressure being used in non-survivors. Multiple logistic regression analysis did not identify any gas exchange or ventilator parameter independently associated with mortality. Rather, all deaths were associated with coincident pathology or multi-organ system failure, or perceived treatment futility due to pre-existing diagnoses instead of unsupportable respiratory failure. When using previously published predictors of outcome (VI>40 and OI>40; A-aDO(2)>450 for 24 h; A-aDO(2)>470 or MAP>23; or A-aDO(2)>420) the risk of mortality was overestimated significantly in the current population. Conclusion: The original hypothesis was refuted. It appears that the outcome of AHRF in present day pediatric critical care is principally related to the severity of associated pathology and now no longer solely to the severity of respiratory failure. Further studies in larger series are needed to confirm these findings. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7094931/ doi: 10.1007/s001340050647 id: cord-286602-cdueeg47 author: Petsonk, Edward L. title: Respiratory protection for health care workers: A 2020 COVID‐19 perspective date: 2020-06-04 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: As the US health care system began to respond to the coronavirus disease‐2019 pandemic, demand for respiratory personal protective equipment (PPE) increased precipitously, as did the number of users. This commentary discusses ensuing deviations from accepted respiratory PPE program practices, which potentially increased risk to health care workers. Such lapses included omitting user training and fit testing, provision of unapproved devices, and application of devices in settings and ways for which they were not intended. The temporary compromise of professionally accepted standards due to exigencies must not become the new normal. Rather, the current attention to PPE should be leveraged to enhance practice, motivate vital research, and strengthen professional, governmental, and institutional capabilities to control health care worker exposures to infectious hazards. url: https://doi.org/10.1002/ajim.23144 doi: 10.1002/ajim.23144 id: cord-255623-qdpdsye9 author: Pham, Hien T. title: Clinical and Pathogenic Characteristics of Lower Respiratory Tract Infection Treated at the Vietnam National Children's Hospital date: 2020-03-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Lower respiratory tract infections are commonly caused by viruses and cause significant morbidity and mortality among children. Early identification of the pathological agent causing these infections is essential to avoid unnecessary antibiotic use and improve patient management. Multiplex PCR techniques were recently developed to detect multiple viral pathogens using a single PCR reaction. In this study, we identify viral pathogens in children with respiratory infections. We collected 194 nasopharyngeal aspirates from infants (2–24 months old) with lower respiratory tract infections treated at the Vietnam National Children's Hospital between November 2014 and June 2015 and assessed the presence of 16 virus types and subtypes by multiplex PCR using the xTAG Respiratory Viral Panel (RVP) assay. Overall, 73.7% of the samples were positive for at least one virus, and 24.2% corresponded to infections with multiple viruses. The most common viruses were respiratory syncytial virus and enterovirus/rhinovirus. These viruses were more frequent among younger patients (2–5 months old) and caused symptoms similar to those of bronchiolitis and pneumonia. The most common clinical manifestation caused by respiratory tract infection was bronchiolitis. Elevated neutrophils levels were associated with adenovirus infection. Our results showed that the xTAG Respiratory Viral Panel (RVP) can effectively detect multiple viruses causing respiratory infections in children and that the nasopharyngeal aspirates are a good sample choice to detect respiratory viruses in children. Applying this approach in the clinical setting would improve patient management and allow early diagnosis, thus avoiding the unnecessary use of antibiotics. url: https://doi.org/10.1155/2020/7931950 doi: 10.1155/2020/7931950 id: cord-290505-omszep7u author: Pochon, Cécile title: Respiratory Virus Infections in Hematopoietic Cell Transplant Recipients date: 2019-01-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Highly immunocompromised pediatric and adult hematopoietic cell transplant (HCT) recipients frequently experience respiratory infections caused by viruses that are less virulent in immunocompetent individuals. Most of these infections, with the exception of rhinovirus as well as adenovirus and parainfluenza virus in tropical areas, are seasonal variable and occur before and after HCT. Infectious disease management includes sampling of respiratory specimens from nasopharyngeal washes or swabs as well as sputum and tracheal or tracheobronchial lavages. These are subjected to improved diagnostic tools including multiplex PCR assays that are routinely used allowing for expedient detection of all respiratory viruses. Disease progression along with high mortality is frequently associated with respiratory syncytial virus, parainfluenza virus, influenza virus, and metapneumovirus infections. In this review, we discuss clinical findings and the appropriate use of diagnostic measures. Additionally, we also discuss treatment options and suggest new drug formulations that might prove useful in treating respiratory viral infections. Finally, we shed light on the role of the state of immune reconstitution and on the use of immunosuppressive drugs on the outcome of infection. url: https://www.ncbi.nlm.nih.gov/pubmed/30687278/ doi: 10.3389/fmicb.2018.03294 id: cord-271172-y48dovux author: Potter, Christopher William title: Chapter 25 Respiratory tract viruses date: 1998-12-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Summary Respiratory tract infections are among the commonest of illnesses, and most individuals will experience two to five infections during each year of their lives. The illnesses vary from relatively mild common colds caused by rhinoviruses and coronaviruses, to severe bronchiolitis and pneumonia caused by adenoviruses and influenza viruses and respiratory syncytial virus (RSV) in infants: the former is associated with little morbidity and no mortality, while influenza is responsible annually for between 1 and 25 thousand deaths per 50 million population. Over 140 viruses cause respiratory tract infections, with the added complications of influenza viruses where new antigenic variants are recognized almost annually; and immunity to infection by one virus strain offers little or no protection to infection by others. Knowledge of the mechanisms of spread of respiratory viruses is largely understood and has helped in infection control; however, the clinical signs and symptoms of infection tend not to be diagnostic of the causative agent; and although vaccines have been developed for the more serious infections such as influenza and some adenovirus infection, none are available for other important infections. Treatment is largely symptomatic, but the compounds ribovirin for RSV infection and amantadine for influenza virus infection have been shown to be effective. Much remains to be discovered before more effective measures can be implemented to limit the enormous costs incurred by these infections. The number of viruses involved is large, and the spectrum of illness complex: in the present chapter, the viruses are described, together with the features of the epidemiology, pathogenesis, clinical disease, and treatment. url: https://www.sciencedirect.com/science/article/pii/S1569258297800098 doi: 10.1016/s1569-2582(97)80009-8 id: cord-023942-vrs3je1x author: Powers, Karen S. title: Acute Pulmonary Infections date: 2011-12-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Acute lower respiratory infection is a common cause of morbidity in infants and children, and at times, requires intensive care and mechanical ventilation. Viral bronchiolitis and bacterial pneumonia account for the majority of lower respiratory tract infections that lead to respiratory insufficiency and pediatric intensive care admission. Twenty-seven percent of children who require mechanical ventilation for at least 24 h in pediatric intensive care units are diagnosed with bronchiolitis and 16% have the diagnosis of pneumonia. The median length of time intubated for an acute pulmonary infection leading to respiratory failure is approximately 7 days. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7178869/ doi: 10.1007/978-0-85729-923-9_25 id: cord-323066-tvguutak author: Praznik, Ajda title: Risk factors for bronchiolitis severity: A retrospective review of patients admitted to the university hospital from central region of Slovenia date: 2018-08-09 words: 3074.0 sentences: 178.0 pages: flesch: 41.0 cache: ./cache/cord-323066-tvguutak.txt txt: ./txt/cord-323066-tvguutak.txt summary: METHODS: A retrospective chart review of all children <2 years old diagnosed with bronchiolitis at the University Medical Centre Ljubljana between May 2014 and April 2015, who were treated as outpatients (paediatric emergency department, PED group) or as inpatients in the standard hospital setting (WARD group) or in the paediatric intensive care unit (PICU group). 10 The objective of our study was to ascertain demographic characteristics, clinical findings and presumptive aetiologic agents (respiratory viruses demonstrated in nasopharyngeal swab) associated with bronchiolitis severity defined as length of hospitalization for >24 hours. Electronic medical records of patients included in the study were reviewed, and statistical analysis was performed for the following clinical and laboratory data: gender, chronological age at admission, prematurity (defined as birth before 37 weeks of gestation), birthweight, history of allergies, number of previous bronchiolitis episodes, clinical manifestations of bronchiolitis using the Wang Respiratory Score, 9 comorbidities (chronic lung disease, congenital heart disease, immune deficiency or neuromuscular diseases), body temperature at admission, treatment with bronchodilators, antibiotics or supplemental oxygen and respiratory virus detected in the nasopharyngeal swab. abstract: AIM: Study's objective was to identify risk factors associated with bronchiolitis severity. METHODS: A retrospective chart review of all children <2 years old diagnosed with bronchiolitis at the University Medical Centre Ljubljana between May 2014 and April 2015, who were treated as outpatients (paediatric emergency department, PED group) or as inpatients in the standard hospital setting (WARD group) or in the paediatric intensive care unit (PICU group). Detection of respiratory viruses in nasopharyngeal swab was accomplished by RT‐PCR. Severity was assessed by Wang Respiratory Score and hospitalization longer than 24 hours. RESULTS: The study included 761 children. The three most frequently detected viruses were respiratory syncytial virus (RSV), human rhinovirus (hRV) and human bocavirus (hBoV) (57.5%, 272/473; 25.6%, 121/473; 18.4%, 87/473). Patient groups differed in Wang Respiratory Score for the severity of bronchiolitis (P < 0.001). No differences regarding the causative viruses were found. There was a lower proportion of children with the presence of more than one virus in PICU group compared to other two groups (P = 0.017). The three groups significantly differed in age, birthweight, comorbidities, bronchodilator treatment and antibiotic usage. However, multiple regression analysis revealed that younger age and the use of antibiotics were associated with bronchiolitis severity defined as hospitalization for >24 hours. CONCLUSIONS: Respiratory syncytial virus, hRV and hBoV were the most frequently detected viruses. The majority of patients admitted to the PICU had only one virus detected. Younger age and the use of antibiotics were associated with bronchiolitis severity. url: https://www.ncbi.nlm.nih.gov/pubmed/29944781/ doi: 10.1111/irv.12587 id: cord-342133-khrljehj author: Principi, Nicola title: Bocavirus Infection in Otherwise Healthy Children with Respiratory Disease date: 2015-08-12 words: 5116.0 sentences: 243.0 pages: flesch: 49.0 cache: ./cache/cord-342133-khrljehj.txt txt: ./txt/cord-342133-khrljehj.txt summary: To evaluate the role of human bocavirus (hBoV) as a causative agent of respiratory disease, the importance of the viral load in respiratory disease type and severity and the pathogenicity of the different hBoV species, we studied all hBoV-positive nasopharyngeal samples collected from children who attended an emergency room for a respiratory tract infection during three winters (2009–2010, 2011–2012, and 2013–2014). To evaluate the circulation of the different hBoV types and the possible relationships between viral load, virus genetic characteristics, and the severity of infection, nasopharyngeal swabs were collected from otherwise healthy children attending the emergency room of the Fondazione IRCCS Ca'' Granda Ospedale Maggiore Policlinico, University of Milan, Italy, due to a respiratory tract infection arising between November 1 and March 31 during 3 winters (2009-2010, 2011-2012, and 2013-2014) . Single detection of human bocavirus 1 with a high viral load in severe respiratory tract infections in previously healthy children abstract: To evaluate the role of human bocavirus (hBoV) as a causative agent of respiratory disease, the importance of the viral load in respiratory disease type and severity and the pathogenicity of the different hBoV species, we studied all hBoV-positive nasopharyngeal samples collected from children who attended an emergency room for a respiratory tract infection during three winters (2009–2010, 2011–2012, and 2013–2014). Human bocavirus was detected using the respiratory virus panel fast assay and real-time PCR. Of the 1,823 nasopharyngeal samples, 104 (5.7%) were positive for hBoV; a similar prevalence was observed in all three periods studied. Among hBoV-infected children, 53.8% were between 1–2 years old, and hBoV was detected alone in 57/104 (54.8%) cases. All of the detected hBoV strains belonged to genotype 1. The median hBoV load was significantly higher in samples containing strains with both the N546H and T590S mutations compared to other samples (p<0.05). Children with a single hBoV-1 infection more frequently had upper respiratory tract infections (URTIs) than those who were co-infected (37.0% vs 17.8%, respectively, p = 0.04). The duration of hospitalization was longer among children with high viral loads than that observed among children with low viral loads (8.0 ±2.2 days vs 5.0 ±1.5 days, respectively, p = 0.03), and the use of aerosol therapy was more frequent among children with high viral loads than among those with low viral loads (77.1% vs 55.7%, respectively, p = 0.04). This study shows that hBoV is a relatively uncommon but stable infectious agent in children and that hBoV1 seems to be the only strain detected in Italy in respiratory samples. From a clinical point of view, hBoV1 seems to have in the majority of healthy children relatively low clinical relevance. Moreover, the viral load influences only the duration of hospitalization and the use of aerosol therapy without any association with the site of the respiratory disease. url: https://doi.org/10.1371/journal.pone.0135640 doi: 10.1371/journal.pone.0135640 id: cord-335116-c83xyev5 author: Proença-Módena, José Luiz title: Respiratory viruses are continuously detected in children with chronic tonsillitis throughout the year date: 2014-07-21 words: 3637.0 sentences: 175.0 pages: flesch: 38.0 cache: ./cache/cord-335116-c83xyev5.txt txt: ./txt/cord-335116-c83xyev5.txt summary: Methods: The fluctuations of respiratory virus detection were compared to the major climatic variables during a two-year period using adenoids and palatine tonsils from 172 children with adenotonsillar hypertrophy and clinical evidence of obstructive sleep apnoea syndrome or recurrent adenotonsillitis, without symptoms of acute respiratory infection (ARI), by TaqMan real-time PCR. Methods: The fluctuations of respiratory virus detection were compared to the major climatic variables during a two-year period using adenoids and palatine tonsils from 172 children with adenotonsillar hypertrophy and clinical evidence of obstructive sleep apnoea syndrome or recurrent adenotonsillitis, without symptoms of acute respiratory infection (ARI), by TaqMan real-time PCR. We have previously reported high rates of detection of respiratory virus genomes in tonsils and adenoids from patients with chronic adenotonsillar diseases, suggesting a significant association of viruses, particularly picornaviruses, with severe tonsillar hypertrophy [3] . abstract: OBJECTIVE: To evaluate the oscillations on the viral detection in adenotonsillar tissues from patients with chronic adenotonsillar diseases as an indicia of the presence of persistent viral infections or acute subclinical infections. STUDY DESIGN: Cross-sectional prospective study. SETTING: Tertiary hospital. METHODS: The fluctuations of respiratory virus detection were compared to the major climatic variables during a two-year period using adenoids and palatine tonsils from 172 children with adenotonsillar hypertrophy and clinical evidence of obstructive sleep apnoea syndrome or recurrent adenotonsillitis, without symptoms of acute respiratory infection (ARI), by TaqMan real-time PCR. RESULTS: The rate of detection of at least one respiratory virus in adenotonsillar tissue was 87%. The most frequently detected viruses were human adenovirus in 52.8%, human enterovirus in 47.2%, human rhinovirus in 33.8%, human bocavirus in 31.1%, human metapneumovirus in 18.3% and human respiratory syncytial virus in 17.2%. Although increased detection of human enterovirus occurred in summer/autumn months, and there were summer nadirs of human respiratory syncytial virus in both years of the study, there was no obvious viral seasonality in contrast to reports with ARI patients in many regions of the world. CONCLUSION: Respiratory viruses are continuously highly detected during whole year, and without any clinical symptomatology, indicating that viral genome of some virus can persist in lymphoepithelial tissues of the upper respiratory tract. url: https://www.ncbi.nlm.nih.gov/pubmed/25128448/ doi: 10.1016/j.ijporl.2014.07.015 id: cord-279257-a7d9a2w1 author: Puig, Carme title: Incidence and risk factors of lower respiratory tract illnesses during infancy in a Mediterranean birth cohort date: 2008-07-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Aim: To investigate the incidence rate, viral respiratory agents and determinants of lower respiratory tract illnesses (LRTIs) in infants younger than 1 year. Methods: A total of 487 infants were recruited at birth for the Asthma Multicenter Infant Cohort Study in Barcelona (Spain). Cases of LRTIs were ascertained through an active register including a home visit and viral test in nasal lavage specimens during the first year of life. Cotinine in cord blood, household aeroallergens, indoor NO(2) and maternal and neonatal IgE were measured. Other maternal and infants' characteristics were obtained from structured questionnaires. Results: The incidence rate of at least one LRTI was 38.7 infants per 100 persons‐years. The most frequently isolated viral agent was respiratory syncytial virus (44.7%). The risk of LRTIs was higher in infants with a maternal history of asthma and in those with siblings (OR = 2.4; 95% CI: 0.98–6.08 and OR = 1.8; 95% CI: 1.04–3.21, respectively). The risk of LRTIs was lower in infants who were breast fed for more than 12 weeks (OR = 0.26; 95% CI: 0.26–0.86) and in those from a low socioeconomic class (OR = 0.16; 95% CI: 0.06–0.42). Conclusion: Viral LRTIs are frequent in infants younger than 1 year of age and there is an inter‐relationship between maternal asthma, siblings, breast feeding and socioeconomic status. url: https://www.ncbi.nlm.nih.gov/pubmed/18631341/ doi: 10.1111/j.1651-2227.2008.00939.x id: cord-325611-tu1bn4hu author: Pérez-Sautu, Unai title: Target-independent high-throughput sequencing methods provide evidence that already known human viral pathogens play a main role in respiratory infections with unexplained etiology date: 2019-07-23 words: 5285.0 sentences: 259.0 pages: flesch: 41.0 cache: ./cache/cord-325611-tu1bn4hu.txt txt: ./txt/cord-325611-tu1bn4hu.txt summary: We systematically collected samples from a prospective cohort of pediatric patients with respiratory infections, that returned negative results by validated molecular RT–PCR assays, and studied them with a target-independent, high-throughput sequencing-based approach. In this report, we performed a systematic study of respiratory specimens collected from a carefully characterized and highly representative, prospective cohort of pediatric cases suffering unexplained ARI, and we compared the rate of detection of pathogens by utilizing validated molecular assays, and a comprehensive sequence-independent, high-throughput sequencing-based analysis. In order to assess for the clinical relevance of the viral identifications made by HTS in the specimens collected from the unexplained cases of respiratory infections, a second cohort of age-matched healthy individuals from the same epidemiologic environment was also studied with the same methodology. Respiratory viral pathogens identified by target-agnostic HTS analysis and confirmed by contig-specific molecular assays in the respiratory specimens from the cases of respiratory infection and from the control group. abstract: Despite the advanced PCR-based assays available, a fraction of the pediatric respiratory infections remain unexplained every epidemic season, and there is a perception that novel viruses might be present in these specimens. We systematically collected samples from a prospective cohort of pediatric patients with respiratory infections, that returned negative results by validated molecular RT–PCR assays, and studied them with a target-independent, high-throughput sequencing-based approach. We also included a matched cohort of children with no symptoms of respiratory infection, as a contrast study population. More than fifty percent of the specimens from the group of patients with unexplained respiratory infections were resolved. However, the higher rate of detection was not due to the presence of novel viruses, but to the identification of well-known viral respiratory pathogens. Our results show that already known viral pathogens are responsible for the majority of cases that remain unexplained after the epidemic season. High-throughput sequencing approaches that use pathogen-specific probes are easier to standardize because they ensure reproducible library enrichment and sequencing. In consequence, these techniques might be desirable from a regulatory standpoint for diagnostic laboratories seeking to benefit from the many advantages of these sequencing technologies. url: https://www.ncbi.nlm.nih.gov/pubmed/31335277/ doi: 10.1080/22221751.2019.1640587 id: cord-351990-aham72b9 author: Radin, Jennifer M. title: Epidemiology of Pathogen-Specific Respiratory Infections among Three US Populations date: 2014-12-30 words: 4511.0 sentences: 220.0 pages: flesch: 43.0 cache: ./cache/cord-351990-aham72b9.txt txt: ./txt/cord-351990-aham72b9.txt summary: METHODS: Febrile respiratory illness (FRI) and severe acute respiratory infection (SARI) surveillance was conducted from October 2011 through March 2013 among three US populations: civilians near the US–Mexico border, Department of Defense (DoD) beneficiaries, and military recruits. Recruits with rhinovirus had higher percentages of pneumonia, cough, shortness of breath, congestion, cough, less fever and longer time to seeking care and were more likely to be male compared to those in the no/unknown pathogen group. This study aimed to describe characteristics associated with specific respiratory pathogens, as well as the etiology, seasonality, and coinfection rates among three US populations: military recruits, Department of Defense (DoD) beneficiaries, and civilians living near the US-Mexico border. Additionally, the following demographic and clinical signs and symptoms were collected from each FRI and SARI case: sex, age, study population, month of illness, pneumonia, sore throat, cough, nausea, shortness of breath, congestion, pink eye, body ache, headache, temperature, number of days of symptoms before seeking care, and date of seeking care. abstract: BACKGROUND: Diagnostic tests for respiratory infections can be costly and time-consuming. Improved characterization of specific respiratory pathogens by identifying frequent signs, symptoms and demographic characteristics, along with improving our understanding of coinfection rates and seasonality, may improve treatment and prevention measures. METHODS: Febrile respiratory illness (FRI) and severe acute respiratory infection (SARI) surveillance was conducted from October 2011 through March 2013 among three US populations: civilians near the US–Mexico border, Department of Defense (DoD) beneficiaries, and military recruits. Clinical and demographic questionnaire data and respiratory swabs were collected from participants, tested by PCR for nine different respiratory pathogens and summarized. Age stratified characteristics of civilians positive for influenza and recruits positive for rhinovirus were compared to other and no/unknown pathogen. Seasonality and coinfection rates were also described. RESULTS: A total of 1444 patients met the FRI or SARI case definition and were enrolled in this study. Influenza signs and symptoms varied across age groups of civilians. Recruits with rhinovirus had higher percentages of pneumonia, cough, shortness of breath, congestion, cough, less fever and longer time to seeking care and were more likely to be male compared to those in the no/unknown pathogen group. Coinfections were found in 6% of all FRI/SARI cases tested and were most frequently seen among children and with rhinovirus infections. Clear seasonal trends were identified for influenza, rhinovirus, and respiratory syncytial virus. CONCLUSIONS: The age-stratified clinical characteristics associated with influenza suggest that age-specific case definitions may improve influenza surveillance and identification. Improving identification of rhinoviruses, the most frequent respiratory infection among recruits, may be useful for separating out contagious individuals, especially when larger outbreaks occur. Overall, describing the epidemiology of pathogen specific respiratory diseases can help improve clinical diagnoses, establish baselines of infection, identify outbreaks, and help prioritize the development of new vaccines and treatments. url: https://www.ncbi.nlm.nih.gov/pubmed/25549089/ doi: 10.1371/journal.pone.0114871 id: cord-302833-6kntd89t author: Radonovich, Lewis J. title: The Respiratory Protection Effectiveness Clinical Trial (ResPECT): a cluster-randomized comparison of respirator and medical mask effectiveness against respiratory infections in healthcare personnel date: 2016-06-02 words: 5090.0 sentences: 248.0 pages: flesch: 39.0 cache: ./cache/cord-302833-6kntd89t.txt txt: ./txt/cord-302833-6kntd89t.txt summary: BACKGROUND: Although N95 filtering facepiece respirators and medical masks are commonly used for protection against respiratory infections in healthcare settings, more clinical evidence is needed to understand the optimal settings and exposure circumstances for healthcare personnel to use these devices. Healthcare personnel who work in outpatient settings will be cluster-randomized to wear N95 respirators or medical masks for protection against infections during respiratory virus season. Abbreviations ARI, acute respiratory illness; CDC, centers for disease control and prevention; DSMB, data safety monitoring board; HAI, hemagglutination inhibition antibody; HCP, healthcare personnel; ILI, influenza like illness; LCRI, Laboratory confirmed respiratory illness; MM, medical mask; N95, N95 respirator; NIOSH, National Institute for Occupational Safety and Health; OSHA, Occupational Safety and Health Administration; PPE, occupational protective equipment; ResPECT, respiratory protection effectiveness clinical trial; RPD, respiratory protective devices; RT-PCR, reverse-transcriptase polymerase chain reaction; US, United States. abstract: BACKGROUND: Although N95 filtering facepiece respirators and medical masks are commonly used for protection against respiratory infections in healthcare settings, more clinical evidence is needed to understand the optimal settings and exposure circumstances for healthcare personnel to use these devices. A lack of clinically germane research has led to equivocal, and occasionally conflicting, healthcare respiratory protection recommendations from public health organizations, professional societies, and experts. METHODS: The Respiratory Protection Effectiveness Clinical Trial (ResPECT) is a prospective comparison of respiratory protective equipment to be conducted at multiple U.S. study sites. Healthcare personnel who work in outpatient settings will be cluster-randomized to wear N95 respirators or medical masks for protection against infections during respiratory virus season. Outcome measures will include laboratory-confirmed viral respiratory infections, acute respiratory illness, and influenza-like illness. Participant exposures to patients, coworkers, and others with symptoms and signs of respiratory infection, both within and beyond the workplace, will be recorded in daily diaries. Adherence to study protocols will be monitored by the study team. DISCUSSION: ResPECT is designed to better understand the extent to which N95s and MMs reduce clinical illness among healthcare personnel. A fully successful study would produce clinically relevant results that help clinician-leaders make reasoned decisions about protection of healthcare personnel against occupationally acquired respiratory infections and prevention of spread within healthcare systems. TRIAL REGISTRATION: The trial is registered at clinicaltrials.gov, number NCT01249625 (11/29/2010). url: https://www.ncbi.nlm.nih.gov/pubmed/27255755/ doi: 10.1186/s12879-016-1494-2 id: cord-002590-24o2viv3 author: Rahe, Michael C. title: Mechanisms of Adaptive Immunity to Porcine Reproductive and Respiratory Syndrome Virus date: 2017-06-13 words: 8016.0 sentences: 375.0 pages: flesch: 34.0 cache: ./cache/cord-002590-24o2viv3.txt txt: ./txt/cord-002590-24o2viv3.txt summary: Pig immune response to general stimulus and to porcine reproductive and respiratory syndrome virus infection: A meta-analysis approach Antigen-specific B-cell responses to porcine reproductive and respiratory syndrome virus infection The Chinese highly pathogenic porcine reproductive and respiratory syndrome virus infection suppresses Th17 cells response in vivo Pathogenic and humoral immune responses to porcine reproductive and respiratory syndrome virus (PRRSV) are related to viral load in acute infection Porcine reproductive and respiratory syndrome virus-infected alveolar macrophages contain no detectable levels of viral proteins in their plasma membrane and are protected against antibody-dependent, complement-mediated cell lysis Polyclonal activation of B cells occurs in lymphoid organs from porcine reproductive and respiratory syndrome virus (PRRSV)-infected pigs The role of porcine reproductive and respiratory syndrome virus infection in immune phenotype and Th1/Th2 balance of dendritic cells Porcine reproductive and respiratory syndrome virus induces pronounced immune modulatory responses at mucosal tissues in the parental vaccine strain VR2332 infected pigs abstract: The adaptive immune response is necessary for the development of protective immunity against infectious diseases. Porcine reproductive and respiratory syndrome virus (PRRSV), a genetically heterogeneous and rapidly evolving RNA virus, is the most burdensome pathogen of swine health and wellbeing worldwide. Viral infection induces antigen-specific immunity that ultimately clears the infection. However, the resulting immune memory, induced by virulent or attenuated vaccine viruses, is inconsistently protective against diverse viral strains. The immunological mechanisms by which primary and memory protection are generated and used are not well understood. Here, we summarize current knowledge regarding cellular and humoral components of the adaptive immune response to PRRSV infection that mediate primary and memory immune protection against viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5490824/ doi: 10.3390/v9060148 id: cord-352222-zq9o66i4 author: Rajatonirina, Soatiana title: Outcome Risk Factors during Respiratory Infections in a Paediatric Ward in Antananarivo, Madagascar 2010–2012 date: 2013-09-12 words: 4137.0 sentences: 245.0 pages: flesch: 46.0 cache: ./cache/cord-352222-zq9o66i4.txt txt: ./txt/cord-352222-zq9o66i4.txt summary: BACKGROUND: Acute respiratory infections are a leading cause of infectious disease-related morbidity, hospitalisation and mortality among children worldwide, and particularly in developing countries. MATERIALS AND METHODS: We conducted a prospective study in a paediatric ward in Antananarivo from November 2010 to July 2012 including patients under 5 years old suffering from respiratory infections. CONCLUSION: Co-mordidity, low-income and age under 6 months increase the risk of severe outcome for children infected by numerous respiratory pathogens. Our study aimed to evaluate the risk factors associated with the evolution and outcome of respiratory illnesses in patients aged under 5 years old hospitalised in one of the four main public hospitals in Antananarivo. In our study, Streptococcus pneumoniae was the most common bacterial pathogen as in other studies of hospitalised patients with acute respiratory illness, and Haemophilus influenzae type B was the next most frequent [16] [17] [18] [19] . abstract: BACKGROUND: Acute respiratory infections are a leading cause of infectious disease-related morbidity, hospitalisation and mortality among children worldwide, and particularly in developing countries. In these low-income countries, most patients with acute respiratory infection (ARI), whether it is mild or severe, are still treated empirically. The aim of the study was to evaluate the risk factors associated with the evolution and outcome of respiratory illnesses in patients aged under 5 years old. MATERIALS AND METHODS: We conducted a prospective study in a paediatric ward in Antananarivo from November 2010 to July 2012 including patients under 5 years old suffering from respiratory infections. We collected demographic, socio-economic, clinical and epidemiological data, and samples for laboratory analysis. Deaths, rapid progression to respiratory distress during hospitalisation, and hospitalisation for more than 10 days were considered as severe outcomes. We used multivariate analysis to study the effects of co-infections. RESULTS: From November 2010 to July 2012, a total of 290 patients were enrolled. Co-infection was found in 192 patients (70%). Co-infections were more frequent in children under 36 months, with a significant difference for the 19–24 month-old group (OR: 8.0). Sixty-nine percent (230/290) of the patients recovered fully and without any severe outcome during hospitalisation; the outcome was scored as severe for 60 children and nine patients (3%) died. Risk factors significantly associated with worsening evolution during hospitalisation (severe outcome) were admission at age under 6 months (OR = 5.3), comorbidity (OR = 4.6) and low household income (OR = 4.1). CONCLUSION: Co-mordidity, low-income and age under 6 months increase the risk of severe outcome for children infected by numerous respiratory pathogens. These results highlight the need for implementation of targeted public health policy to reduce the contribution of respiratory diseases to childhood morbidity and mortality in low income countries. url: https://www.ncbi.nlm.nih.gov/pubmed/24069161/ doi: 10.1371/journal.pone.0072839 id: cord-266260-t02jngq0 author: Ramshaw, Rebecca E. title: A database of geopositioned Middle East Respiratory Syndrome Coronavirus occurrences date: 2019-12-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: As a World Health Organization Research and Development Blueprint priority pathogen, there is a need to better understand the geographic distribution of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) and its potential to infect mammals and humans. This database documents cases of MERS-CoV globally, with specific attention paid to zoonotic transmission. An initial literature search was conducted in PubMed, Web of Science, and Scopus; after screening articles according to the inclusion/exclusion criteria, a total of 208 sources were selected for extraction and geo-positioning. Each MERS-CoV occurrence was assigned one of the following classifications based upon published contextual information: index, unspecified, secondary, mammal, environmental, or imported. In total, this database is comprised of 861 unique geo-positioned MERS-CoV occurrences. The purpose of this article is to share a collated MERS-CoV database and extraction protocol that can be utilized in future mapping efforts for both MERS-CoV and other infectious diseases. More broadly, it may also provide useful data for the development of targeted MERS-CoV surveillance, which would prove invaluable in preventing future zoonotic spillover. url: https://doi.org/10.1038/s41597-019-0330-0 doi: 10.1038/s41597-019-0330-0 id: cord-274007-zndtddty author: Rasmussen, Sonja A. title: Coronavirus Disease 2019 (COVID-19) and pregnancy: what obstetricians need to know date: 2020-02-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Coronavirus disease 2019 is an emerging disease with a rapid increase in cases and deaths since its first identification in Wuhan, China, in December 2019. Limited data are available about coronavirus disease 2019 during pregnancy; however, information on illnesses associated with other highly pathogenic coronaviruses (ie, severe acute respiratory syndrome and the Middle East respiratory syndrome) might provide insights into coronavirus disease 2019’s effects during pregnancy. Coronaviruses cause illness ranging in severity from the common cold to severe respiratory illness and death. Currently the primary epidemiologic risk factors for coronavirus disease 2019 include travel from mainland China (especially Hubei Province) or close contact with infected individuals within 14 days of symptom onset. Data suggest an incubation period of ∼5 days (range, 2–14 days). Average age of hospitalized patients has been 49–56 years, with a third to half with an underlying illness. Children have been rarely reported. Men were more frequent among hospitalized cases (54–73%). Frequent manifestations include fever, cough, myalgia, headache, and diarrhea. Abnormal testing includes abnormalities on chest radiographic imaging, lymphopenia, leukopenia, and thrombocytopenia. Initial reports suggest that acute respiratory distress syndrome develops in 17–29% of hospitalized patients. Overall case fatality rate appears to be ∼1%; however, early data may overestimate this rate. In 2 reports describing 18 pregnancies with coronavirus disease 2019, all were infected in the third trimester, and clinical findings were similar to those in nonpregnant adults. Fetal distress and preterm delivery were seen in some cases. All but 2 pregnancies were cesarean deliveries and no evidence of in utero transmission was seen. Data on severe acute respiratory syndrome and Middle East respiratory syndrome in pregnancy are sparse. For severe acute respiratory syndrome, the largest series of 12 pregnancies had a case-fatality rate of 25%. Complications included acute respiratory distress syndrome in 4, disseminated intravascular coagulopathy in 3, renal failure in 3, secondary bacterial pneumonia in 2, and sepsis in 2 patients. Mechanical ventilation was 3 times more likely among pregnant compared with nonpregnant women. Among 7 first-trimester infections, 4 ended in spontaneous abortion. Four of 5 women with severe acute respiratory syndrome after 24 weeks’ gestation delivered preterm. For Middle East respiratory syndrome, there were 13 case reports in pregnant women, of which 2 were asymptomatic, identified as part of a contact investigation; 3 patients (23%) died. Two pregnancies ended in fetal demise and 2 were born preterm. No evidence of in utero transmission was seen in severe acute respiratory syndrome or Middle East respiratory syndrome. Currently no coronavirus-specific treatments have been approved by the US Food and Drug Administration. Because coronavirus disease 2019 might increase the risk for pregnancy complications, management should optimally be in a health care facility with close maternal and fetal monitoring. Principles of management of coronavirus disease 2019 in pregnancy include early isolation, aggressive infection control procedures, oxygen therapy, avoidance of fluid overload, consideration of empiric antibiotics (secondary to bacterial infection risk), laboratory testing for the virus and coinfection, fetal and uterine contraction monitoring, early mechanical ventilation for progressive respiratory failure, individualized delivery planning, and a team-based approach with multispecialty consultations. Information on coronavirus disease 2019 is increasing rapidly. Clinicians should continue to follow the Centers for Disease Control and Prevention website to stay up to date with the latest information (https://www.cdc.gov/coronavirus/2019-nCoV/hcp/index.html). url: https://www.sciencedirect.com/science/article/pii/S0002937820301976 doi: 10.1016/j.ajog.2020.02.017 id: cord-266822-ecq50ye2 author: Rath, Barbara title: Influenza and other respiratory viruses: standardizing disease severity in surveillance and clinical trials date: 2017-05-12 words: 10809.0 sentences: 556.0 pages: flesch: 38.0 cache: ./cache/cord-266822-ecq50ye2.txt txt: ./txt/cord-266822-ecq50ye2.txt summary: Disease burden due to influenza and other respiratory viral infections is reported on a population level, but clinical scores measuring individual changes in disease severity are urgently needed. Standardized measures of disease severity are urgently needed for clinical trials of vaccines and antivirals currently in development for ARI caused by influenza (FLU), respiratory syncytial virus (RSV), human metapneumovirus (HMPV), adenovirus (ADV), or human rhinovirus (HRV) [9] [10] [11] [12] [13] [14] [15] [16] [17] . Considering the variability in disease presentations and courses of illness with influenza and other respiratory viral infections in children, the ViVI Disease Severity Score is not intended to be validated against future clinical events or outcomes. Our contributions are the following: (A) The design of a hospital-based surveillance program and a unique QM cohort of more than 6000 children, where an independent QM team monitored patients daily using standardized clinical assessments and virology at the National Reference Centre for Influenza and Other Respiratory Viruses. abstract: Introduction: Influenza-Like Illness is a leading cause of hospitalization in children. Disease burden due to influenza and other respiratory viral infections is reported on a population level, but clinical scores measuring individual changes in disease severity are urgently needed. Areas covered: We present a composite clinical score allowing individual patient data analyses of disease severity based on systematic literature review and WHO-criteria for uncomplicated and complicated disease. The 22-item ViVI Disease Severity Score showed a normal distribution in a pediatric cohort of 6073 children aged 0–18 years (mean age 3.13; S.D. 3.89; range: 0 to 18.79). Expert commentary: The ViVI Score was correlated with risk of antibiotic use as well as need for hospitalization and intensive care. The ViVI Score was used to track children with influenza, respiratory syncytial virus, human metapneumovirus, human rhinovirus, and adenovirus infections and is fully compliant with regulatory data standards. The ViVI Disease Severity Score mobile application allows physicians to measure disease severity at the point-of care thereby taking clinical trials to the next level. url: https://doi.org/10.1080/14787210.2017.1295847 doi: 10.1080/14787210.2017.1295847 id: cord-316727-ktrlohm9 author: Razavi, Seyed Mansour title: Treatment and prevention of acute respiratory infections among Iranian hajj pilgrims: a 5-year follow up study and review of the literature date: 2014-05-10 words: 4673.0 sentences: 357.0 pages: flesch: 50.0 cache: ./cache/cord-316727-ktrlohm9.txt txt: ./txt/cord-316727-ktrlohm9.txt summary: title: Treatment and prevention of acute respiratory infections among Iranian hajj pilgrims: a 5-year follow up study and review of the literature Background Respiratory diseases/syndromes are the most common causes of referring to physicians among pilgrims in Hajj. The main aim of our study was to determine types, frequencies, etiologies, and epidemiologic factors of respiratory diseases among Iranian Hajj pilgrims and to suggest some preventive and treatment strategies. The aim of our study was to determine types, frequencies, etiologies, and some of other epidemiologic factors of respiratory diseases among Iranian Hajj pilgrims and to suggest some preventive and treatment strategies based on our 10 years of experience and literature review. We used the results of above mentioned studies and reviewed the literature, and offered a guideline for the treatment and prevention of acute respiratory infections (ARIs) in Hajj.  Significant difference values of NBT test before and after travel showed that respiratory diseases of pilgrims might have infectious origins. abstract: Background Respiratory diseases/syndromes are the most common causes of referring to physicians among pilgrims in Hajj. They lead to high morbidity, impose high costs on the health system and are among the major obstacles for pilgrims to perform Hajj duties. The main aim of our study was to determine types, frequencies, etiologies, and epidemiologic factors of respiratory diseases among Iranian Hajj pilgrims and to suggest some preventive and treatment strategies. Methods: To determine the types and frequencies of respiratory syndromes, we implemented a syndromic surveillance method in Iranian health care system for Hajj during 5 consecutive years. To achieve the etiology of these diseases, we performed 4 concurrent before and after studies. We also evaluated efficacy of the flu and pneumovax vaccines among Iranian Hajj pilgrims in 2 studies. To determine some other epidemiological factors, we conducted 4 additional studies. Results: The most common problem was common cold like syndrome. Origins of the most upper respiratory problems were infections, and allergies were less involved. Among infectious agents, viruses were the most common agents and their frequencies were as follows respectively: Adenoviruses 38 (36.2 %), Rhinoviruses 31 (30%), Influenza type B virus 21 (20%). Bacteria were often the secondary causes and their frequencies were as follows respectively: Intestine bacillus 69 (19.4%), Chlamydia pneumonia 20(15.8%), Haemophiluses 32 (9.1%) and Streptococcus (A,C and G) 30 ( 8.5%). We introduced some epidemiological factors as effective in creating respiratory diseases. Conclusion: In this paper, we suggested some applied points for prevention, treatment, and correction of common malpractices in the treatment of respiratory diseases of the pilgrims. url: https://www.ncbi.nlm.nih.gov/pubmed/25250272/ doi: nan id: cord-018302-lmly43rd author: Renaud, Christian title: Respiratory Syncytial Virus and Human Metapneumovirus Infection in Transplant Recipients date: 2016-02-15 words: 10500.0 sentences: 459.0 pages: flesch: 30.0 cache: ./cache/cord-018302-lmly43rd.txt txt: ./txt/cord-018302-lmly43rd.txt summary: Respiratory viral infections due to respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) cause infections in immunocompromised transplant patients ranging from mild upper respiratory infections to severe lower respiratory tract disease with respiratory failure. Surveillance studies of respiratory viruses from transplant centers have established the high frequency and the signifi cant clinical impact of respiratory viral infections in HSCT recipients overall [ 8 -15 , 46 , 47 ] as well as the relative importance of RSV in terms of morbidity and mortality (Table 31 -2 ). A retrospective MDACC study of confi rmed RSV infections in 280 allogeneic HSCT recipients from 1996 to 2009 utilized multivariable logistic regression to demonstrate that lack of ribavirin aerosol therapy at the upper respiratory tract disease stage was an important risk factor associated with RSV LRTI and all-cause mortality [ 99 ] . abstract: Respiratory viral infections due to respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) cause infections in immunocompromised transplant patients ranging from mild upper respiratory infections to severe lower respiratory tract disease with respiratory failure. These viruses are more readily diagnosed due to improvements in sensitive molecular diagnostic methods. The epidemiology of RSV and hMPV is similarly becoming more readily appreciated in hematopoietic stem cell transplant (HSCT) patients of all ages as well as solid organ transplant (SOT) patients, with lung transplant recipients having evidence of more frequent and severe complications related to these viruses. RSV and hMPV infection typically but not always present with upper respiratory signs and symptoms that progress to lower respiratory tract disease. Treatment options for RSV are limited, with aerosolized, intravenous, and oral ribavirin all studied in HSCT and lung transplant patients. No antiviral therapy for the treatment of hMPV is available, although ribavirin has shown some effectiveness in vitro. New antiviral agents including RSV fusion inhibitors and nucleoside analogs are being developed, with some under clinical evaluation. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123147/ doi: 10.1007/978-3-319-28797-3_31 id: cord-007234-hcpa8ej5 author: Renwick, Neil title: A Recently Identified Rhinovirus Genotype Is Associated with Severe Respiratory-Tract Infection in Children in Germany date: 2007-12-15 words: 2510.0 sentences: 135.0 pages: flesch: 40.0 cache: ./cache/cord-007234-hcpa8ej5.txt txt: ./txt/cord-007234-hcpa8ej5.txt summary: title: A Recently Identified Rhinovirus Genotype Is Associated with Severe Respiratory-Tract Infection in Children in Germany Here we report the investigation, by MassTag PCR, of pediatric respiratory-tract infections in Germany, studying 97 cases for which no pathogen was identified through routine laboratory evaluation. In an attempt to gather additional information on the potential pathogenicity, as well as temporal and geographic distribution, of rhinoviruses, including the recently identified genotype, we evaluated specimens collected, during the 2003-2006 seasons in Bad Kreuznach, Germany, from children hospitalized because of severe LRTI. In this study of samples collected, during a 3-year interval, from hospitalized children with severe undiagnosed respiratory infection, MassTag PCR allowed us to detect viral pathogens in 49 (51%) of 97 cases. Although we did not have samples to test for the presence of HRV in the lower respiratory tract, the high frequency at which HRV was identified as being the sole virus detected suggests a correlation between the agent and the observed LRTI symptoms. abstract: Acute respiratory infection is a significant cause of morbidity and mortality in children worldwide. Accurate identification of causative agents is critical to case management and to prioritization in vaccine development. Sensitive multiplex diagnostics provide us with an opportunity to investigate the relative contributions of individual agents andmayalso facilitate the discovery of new pathogens. Recently, application of MassTag polymerase chain reaction (PCR) to undiagnosed infuenza-like illness in New York State led to the discovery of a novel rhinovirus genotype. Here we report the investigation, by MassTag PCR, of pediatric respiratory-tract infections in Germany, studying 97 cases for which no pathogen was identified through routine laboratory evaluation. Respiratory viruses were identified in 49 cases (51%); of the 55 identified viruses, 41 (75%) were rhinoviruses. The novel genotype represented 73% of rhinoviruses and 55% of all identified viruses. Infections with the novel genotype were associated with upper-respiratory-tract symptoms but, more frequently, with bronchitis, bronchiolitis, and pneumonia. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7109967/ doi: 10.1086/524312 id: cord-325353-tx6s4ggu author: Restori, Katherine H. title: Neonatal Immunity, Respiratory Virus Infections, and the Development of Asthma date: 2018-06-04 words: 13653.0 sentences: 618.0 pages: flesch: 42.0 cache: ./cache/cord-325353-tx6s4ggu.txt txt: ./txt/cord-325353-tx6s4ggu.txt summary: The goals of this review are (1) to outline the differences between the neonatal and adult immune systems and (2) to present murine and human data that support the hypothesis that early-life interactions between the immune system and respiratory viruses can create a lung environment conducive to the development of asthma. Because RSV, influenza, and RVs cause a large proportion of respiratorytract infections in neonates, we will focus primarily on these three pathogens as models to better understand how early-life infection and antiviral immune responses might contribute to the subsequent development of asthma. The addition of RSV infection of airway epithelial cells with production of the type-2 innate cytokines, IL-33 (138) , TSLP (123) , and IL-25 (128) , would, therefore, be predicted to create an even more exaggerated type-2-biased microenvironment in the lung with activation of other immune cells (e.g., M2 macrophages, DCs, and/or ILC2 cells) and the development of AHR. abstract: Infants are exposed to a wide range of potential pathogens in the first months of life. Although maternal antibodies acquired transplacentally protect full-term neonates from many systemic pathogens, infections at mucosal surfaces still occur with great frequency, causing significant morbidity and mortality. At least part of this elevated risk is attributable to the neonatal immune system that tends to favor T regulatory and Th2 type responses when microbes are first encountered. Early-life infection with respiratory viruses is of particular interest because such exposures can disrupt normal lung development and increase the risk of chronic respiratory conditions, such as asthma. The immunologic mechanisms that underlie neonatal host–virus interactions that contribute to the subsequent development of asthma have not yet been fully defined. The goals of this review are (1) to outline the differences between the neonatal and adult immune systems and (2) to present murine and human data that support the hypothesis that early-life interactions between the immune system and respiratory viruses can create a lung environment conducive to the development of asthma. url: https://doi.org/10.3389/fimmu.2018.01249 doi: 10.3389/fimmu.2018.01249 id: cord-016882-c9ts2g7w author: Ribeiro, Edna title: Viruses Present Indoors and Analyses Approaches date: 2017-06-12 words: 10251.0 sentences: 466.0 pages: flesch: 37.0 cache: ./cache/cord-016882-c9ts2g7w.txt txt: ./txt/cord-016882-c9ts2g7w.txt summary: It''s well known that approximately 60% of total human respiratory and gastrointestinal infections are acquired indoor, since viruses have a rapid spread in the community and can be transmitted easily, especially in crowded and poorly ventilated environments, causing high morbidity and decline in quality of life and productivity. Viruses'' inductors of Severe Acute Respiratory Syndrome (SARS), influenza and norovirus are transmitted from patients primarily by contact and/or droplet routes, while airborne transmission occurs over a limited distance (Srikanth et al., 2008) . It is well-known that viruses are shed in large numbers, with transmission routes extraordinary diverse, including direct contact with infected persons, faecal-oral transmission (through contaminated food and water), droplet and airborne transmission, and can survive for long periods on surfaces or fomites, emphasizing the possible role of surfaces in the transmission of viruses (Barker et al., 2001; La Rosa et al., 2013) . abstract: Through human history viruses have shown enormous epidemiological and pandemic potential as the occurrence and spread of viruses in pandemic dimensions poses a threat to the health and lives of seven billion people worldwide. Scientific evidence has associated harmful health effects to indoor air hazards recognizing the existence of a vital concern in public health sector. Thus the assessment of human exposure to biological aerosols and droplets indoor became an imperative requirement of investigation. Environmental bioburden assessment of viruses relies in both culture-dependent approaches that comprise classical methodologies, still prominent and vital in the field of modern biotechnology, and culture-independent approaches based on nucleic acid amplification techniques, which are considered the gold standard in clinical virology. The main factor influencing indoor microbiology is the human being and their activities. Indoor environments to be considered are those regularly occupied by humans: residences, offices, schools, industrial buildings, health care facilities, farming activities and other settings occupied all the time, or in which occupant density is high. It’s well known that approximately 60% of total human respiratory and gastrointestinal infections are acquired indoor, since viruses have a rapid spread in the community and can be transmitted easily, especially in crowded and poorly ventilated environments, causing high morbidity and decline in quality of life and productivity. Studies have shown that respiratory syncytial virus, rhinovirus, metapneumovirus, influenza and parainfluenza virus, and human enterovirus infections may be associated with virus-induced asthma, leading to diseases such as pneumonia. Gastroenteritis infectious (about 30±40% of cases) is attributable to viruses. Rotavirus, Astrovirus, Norwalk-like viruses and other caliciviruses are responsible for 48% of all reported outbreaks of infectious intestinal disease. Safe working conditions are essential for healthy living, that’s why the programmes conceived as a result of strategic and preventive policy maintenance, in refrigeration and ventilation systems, are the determining factor for the control of biological pollutants. Moreover, the development of highly sensitive and specific detection and identification methodologies with capacity to be used in diverse applications, such as diagnosis, public health risk assessment, research and for the implementation of preventive measures and protocols are imperative. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121309/ doi: 10.1007/978-3-319-61688-9_7 id: cord-346539-kxnrf5g5 author: Riggioni, Carmen title: A compendium answering 150 questions on COVID‐19 and SARS‐CoV‐2 date: 2020-06-14 words: 15760.0 sentences: 1112.0 pages: flesch: 48.0 cache: ./cache/cord-346539-kxnrf5g5.txt txt: ./txt/cord-346539-kxnrf5g5.txt summary: This paper answers pressing questions, formulated by young clinicians and scientists, on SARS‐CoV‐2, COVID‐19 and allergy, focusing on the following topics: virology, immunology, diagnosis, management of patients with allergic disease and asthma, treatment, clinical trials, drug discovery, vaccine development and epidemiology. The first cases of the coronavirus disease 2019 (COVID19) , caused by the novel severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2), were reported in China in December 2019 1 and rapidly led to pandemic. 40, 41 A seroconversion study in COVID-19 patients has found and association between disease severity and SARS-CoV-2-specific IgA levels. Mesenchymal stem cell therapy may potentiate the low IFN-I and -III levels and moderate IFN-stimulated gene response reported in SARS-CoV-2-infected ferrets and COVID-19 patients. Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial abstract: In December 2019, China reported the first cases of the coronavirus disease 2019 (COVID‐19). This disease, caused by the severe acute respiratory syndrome‐related coronavirus 2 (SARS‐CoV‐2), has developed into a pandemic. To date it has resulted in ~6.5 million confirmed cases and caused almost 400,000 related deaths worldwide. Unequivocally, the COVID‐19 pandemic is the gravest health and socio‐economic crisis of our time. In this context, numerous questions have emerged in demand of basic scientific information and evidence‐based medical advice on SARS‐CoV‐2 and COVID‐19. Although the majority of the patients show a very mild, self‐limiting viral respiratory disease, many clinical manifestations in severe patients are unique to COVID‐19, such as severe lymphopenia and eosinopenia, extensive pneumonia, a “cytokine storm” leading to acute respiratory distress syndrome, endothelitis, thrombo‐embolic complications and multiorgan failure. The epidemiologic features of COVID‐19 are distinctive and have changed throughout the pandemic. Vaccine and drug development studies and clinical trials are rapidly growing at an unprecedented speed. However, basic and clinical research on COVID‐19‐related topics should be based on more coordinated high‐quality studies. This paper answers pressing questions, formulated by young clinicians and scientists, on SARS‐CoV‐2, COVID‐19 and allergy, focusing on the following topics: virology, immunology, diagnosis, management of patients with allergic disease and asthma, treatment, clinical trials, drug discovery, vaccine development and epidemiology. Over 140 questions were answered by experts in the field providing a comprehensive and practical overview of COVID‐19 and allergic disease. url: https://www.ncbi.nlm.nih.gov/pubmed/32535955/ doi: 10.1111/all.14449 id: cord-270647-vn4kirrx author: Romero-Espinoza, Jose A. title: Virome and bacteriome characterization of children with pneumonia and asthma in Mexico City during winter seasons 2014 and 2015 date: 2018-02-15 words: 3513.0 sentences: 201.0 pages: flesch: 48.0 cache: ./cache/cord-270647-vn4kirrx.txt txt: ./txt/cord-270647-vn4kirrx.txt summary: OBJECTIVES: To describe the virome and bacteriome present in the upper respiratory tract of hospitalized children with a clinical diagnosis of asthma and pneumonia during an acute exacerbation and an acute respiratory illness ARI episode respectively. Both groups differ with respect to the associated virus and bacteria: while asthma exacerbations have been associated to a specific rhinovirus infection, pneumonia can be related to a wide range of bacterial, fungal and viral agents, with a high prevalence of Respiratory Syncytial Virus (RSV) [2, 7] . Here we describe the virome and bacteriome present in the Upper Respiratory Tract of hospitalized children clinically diagnosed with asthma and pneumonia, during an acute exacerbation and an ARI episode respectively, at the National Institute of Respiratory Diseases (INER, Mexico City) during 2014 and 2015 winter seasons. Prevalence of respiratory viral infection in children hospitalized for acute lower respiratory tract diseases, and association of rhinovirus and influenza virus with asthma exacerbations abstract: BACKGROUND: Acute asthma exacerbations and pneumonia are important causes of morbidity and mortality in children and may coexist in the same children, although symptom overlap may lead to difficulties in diagnosis. Microbial and viral diversity and differential abundance of either may play an important role in infection susceptibility and the development of acute and chronic respiratory diseases. OBJECTIVES: To describe the virome and bacteriome present in the upper respiratory tract of hospitalized children with a clinical diagnosis of asthma and pneumonia during an acute exacerbation and an acute respiratory illness ARI episode respectively. METHODS: During the winter seasons of 2013–2014 and 2014–2015, 134 nasopharyngeal swabs samples of children <15 years of age with ARI hospitalized at a referral hospital for respiratory diseases were selected based on clinical diagnosis of asthma or pneumonia. The virome and bacteriome were characterized using Whole Genome Sequencing (WGS) and in-house bioinformatics analysis pipeline. RESULTS: The Asthma group was represented mainly by RV-C, BoV-1 and RSV-B and the pneumonia group by Bacteriophage EJ-1 and TTMV. TTV was found in both groups with a similar amount of reads. About bacterial composition Moraxella catarrhalis, Propionibacterium acnes and Acinetobacter were present in asthma and Veillonella parvula and Mycoplasma pneumoniae in pneumonia. Streptococcus pneumoniae and Haemophilus influenzae were mostly found with both asthma and pneumonia. CONCLUSIONS: Our results show a complex viral and bacterial composition in asthma and pneumonia groups with a strong association of RV-C presence in asthmatic children. We observed Streptococcus pneumoniae and Haemophilus influenzae concurrently in both groups. url: https://doi.org/10.1371/journal.pone.0192878 doi: 10.1371/journal.pone.0192878 id: cord-333868-qrnsmhws author: Rothman, Richard E. title: Respiratory Hygiene in the Emergency Department date: 2006-08-23 words: 7437.0 sentences: 362.0 pages: flesch: 35.0 cache: ./cache/cord-333868-qrnsmhws.txt txt: ./txt/cord-333868-qrnsmhws.txt summary: These agents are relatively uncommon, however, in most US EDs, and as recently as 2003, the Centers for Disease Control and Prevention (CDC) reported that health care facility environments are rarely implicated in respiratory pathogen transmission (except in cases of immunocompromised patients). All health care facilities should have policies and procedures in place for respiratory infection control practice with specific operational plans for handling a large influx of potentially infectious patients in the event of a significant outbreak. 3, 5, 16, 17, 39 Underscoring this is the findings from one epidemiologic outbreak of SARS in Toronto that found that 36% of new infections in the hospital occurred in health care workers, with the highest rates in those working in EDs and ICUs. 5 Both the World Health Organization and the CDC provide general recommendations for handling of patients with suspected respiratory infections that include having triage staff adhere to proper hand hygiene procedures and donning face masks and eye protection. abstract: The emergency department (ED) is an essential component of the public health response plan for control of acute respiratory infectious threats. Effective respiratory hygiene in the ED is imperative to limit the spread of dangerous respiratory pathogens, including influenza, severe acute respiratory syndrome, avian influenza, and bioterrorism agents, particularly given that these agents may not be immediately identifiable. Sustaining effective respiratory control measures is especially challenging in the ED because of patient crowding, inadequate staffing and resources, and ever-increasing numbers of immunocompromised patients. Threat of contagion exists not only for ED patients but also for visitors, health care workers, and inpatient populations. Potential physical sites for respiratory disease transmission extend from out-of-hospital care, to triage, waiting room, ED treatment area, and the hospital at large. This article presents a summary of the most current information available in the literature about respiratory hygiene in the ED, including administrative, patient, and legal issues. Wherever possible, specific recommendations and references to practical information from the Centers for Disease Control and Prevention are provided. The “Administrative Issues” section describes coordination with public health departments, procedures for effective facility planning, and measures for health care worker protection (education, staffing optimization, and vaccination). The patient care section addresses the potentially infected ED patient, including emergency medical services concerns, triage planning, and patient transport. “Legal Issues” discusses the interplay between public safety and patient privacy. Emergency physicians play a critical role in early identification, treatment, and containment of potentially lethal respiratory pathogens. This brief synopsis should help clinicians and administrators understand, develop, and implement appropriate policies and procedures to address respiratory hygiene in the ED. url: https://www.sciencedirect.com/science/article/pii/S0196064406007037 doi: 10.1016/j.annemergmed.2006.05.018 id: cord-351323-cbejbm5v author: Roy Mukherjee, Tapasi title: Spectrum of respiratory viruses circulating in eastern India: Prospective surveillance among patients with influenza‐like illness during 2010–2011 date: 2013-06-13 words: 3277.0 sentences: 168.0 pages: flesch: 41.0 cache: ./cache/cord-351323-cbejbm5v.txt txt: ./txt/cord-351323-cbejbm5v.txt summary: The samples were tested further for influenza C virus, parainfluenza viruses 1–4, human rhinovirus, metapneumovirus and respiratory syncytial virus by conventional RT‐ PCR. Hence the information on epidemiology and clinical features of respiratory virus infection in India is based entirely on research studies and the disease burden or seasonal prevalence of respiratory viruses remains largely undefined. This study initiated to complete the information on circulating respiratory viruses among patients attending the outpatients departments of different hospitals with acute respiratory infections in the eastern region of India during 2010 through 2011. Comparative evaluation of real-time PCR and conventional RT-PCR during 2 year surveillance for influenza and respiratory syncytial virus among children with acute respiratory infections in Kolkata, India, reveals a distinct seasonality of infection Prevalence of respiratory syncytial virus group B genotype BA-IV strains among children with acute respiratory tract infection in Kolkata, Eastern India abstract: In developing countries, viruses causing respiratory disease are a major concern of public health. During January 2010–December 2011, 2,737 patients with acute respiratory infection from the outpatient departments as well as patients admitted to hospitals were screened for different respiratory viruses. Nasal and or throat swabs were collected and transported to the laboratory where initial screening of influenza A and influenza B viruses was performed. The samples were tested further for influenza C virus, parainfluenza viruses 1–4, human rhinovirus, metapneumovirus and respiratory syncytial virus by conventional RT‐ PCR. The study revealed that the majority of the patients were under 5 years of age; both due to their higher susceptibility to respiratory infections and presentation to hospitals. Out of 2,737 patients enrolled in this study, 59% were found positive for one or more respiratory viruses. Influenza B infection was detected in 12% of patients followed by influenza A (11.7%), respiratory syncytial virus (7.1%), parainfluenza virus‐2 (6%), metapneumovirus (3%), parainfluenza virus‐3 (1%), parainfluenza virus‐4 (0.6%), parainfluenza virus‐1 (0.3%), influenza C (0.2%) and human rhinovirus (0.2%). Distinct seasonal infection was observed only for influenza A and influenza B viruses. J. Med. Virol. 85:1459–1465, 2013. © 2013 Wiley Periodicals, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/23765782/ doi: 10.1002/jmv.23607 id: cord-292587-hp4zd8lr author: Rubino, Ilaria title: Respiratory Protection against Pandemic and Epidemic Diseases date: 2017-10-31 words: 2608.0 sentences: 153.0 pages: flesch: 34.0 cache: ./cache/cord-292587-hp4zd8lr.txt txt: ./txt/cord-292587-hp4zd8lr.txt summary: We expect that the development of technologies that overcome the existing challenges in current respiratory protective devices will lead to a timely and effective response to the next outbreak. We expect that the development of technologies that overcome the existing challenges in current respiratory protective devices will lead to a timely and effective response to the next outbreak. While effective management and availability of control measures are crucial to an outbreak response, the pathogens [ 1 1 4 _ T D $ D I F F ] (virus/bacteria/ fungi) captured on filters are an intrinsic concern because of fear of cross-infection, new aerosol release, and contaminated waste. Hence, production of a filter that inactivates the collected pathogens would bring key improvements to current surgical masks and respirators, resulting in increased protection, reduced risk of cross[ 1 0 9 _ T D $ D I F F ] -infection, and recyclability without decontamination ( Figure 1 ). abstract: Respiratory protection against airborne pathogens is crucial for pandemic/epidemic preparedness in the context of personal protection, healthcare systems, and governance. We expect that the development of technologies that overcome the existing challenges in current respiratory protective devices will lead to a timely and effective response to the next outbreak. url: https://doi.org/10.1016/j.tibtech.2017.06.005 doi: 10.1016/j.tibtech.2017.06.005 id: cord-015893-e0fofgxq author: Ryhal, Bruce title: Viral Disease, Air Pollutants, Nanoparticles, and Asthma date: 2011-05-03 words: 6327.0 sentences: 316.0 pages: flesch: 49.0 cache: ./cache/cord-015893-e0fofgxq.txt txt: ./txt/cord-015893-e0fofgxq.txt summary: Sulfur dioxide, nitrogen dioxide, ozone, and particulate matter in air pollution may • exacerbate asthma, and patients should be cautioned to stay indoors when levels of these irritants are high. A study of children aged 6-8 years with asthma concluded that an asthma exacerbation was of a greater severity if a viral infection was present as opposed to a nonviral illness (7) . Inhaled corticosteroids and leukotriene receptor antagonists (LTRAs) are well known to control the number of wheezing exacerbations in school-age children with chronic persistent asthma, an effect that appears to encompass those episodes caused by viral illness. Viral respiratory infections, and to a lesser extent air pollution, are common triggers of exacerbations and may interact with individuals to affect the development of some forms of asthma. By understanding and anticipating respiratory viral infections and air pollution as important causes of asthma, the health care provider can provide superior care for those who suffer from this chronic disease. abstract: Health care providers who treat patients with respiratory disease are often asked by their patients, “What caused my asthma? And what causes my asthma suddenly to become worse?” These questions have always been difficult to answer, and moving directly to a discussion of the management of asthma is a much easier road to take. In recent years, though, enough information has accumulated about the causes of asthma that one can weave a story containing useful advice that may help patients participate in the management of their disease. And there are also recent studies that can provide answers to the questions posed by physicians who have watched in puzzlement as their previously well-controlled asthma patients have spiraled rapidly out of control. This story has been growing increasingly complex, with an ever-expanding cast of players that sometimes creates a tangled web of interactions. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119993/ doi: 10.1007/978-1-4419-6836-4_11 id: cord-324950-ux7shvji author: Saade, Georges title: Coinfections and their molecular consequences in the porcine respiratory tract date: 2020-06-16 words: 11744.0 sentences: 522.0 pages: flesch: 36.0 cache: ./cache/cord-324950-ux7shvji.txt txt: ./txt/cord-324950-ux7shvji.txt summary: In pigs, the term "Porcine Respiratory Disease Complex" (PRDC) is often used to describe coinfections involving viruses such as swine Influenza A Virus (swIAV), Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), and Porcine CircoVirus type 2 (PCV2) as well as bacteria like Actinobacillus pleuropneumoniae, Mycoplasma hyopneumoniae and Bordetella bronchiseptica. The outcome of any coinfection or superinfection can be affected by the interactions taking place between the infectious agents, the nature of the cell/host, adverse environmental and management conditions, intestinal and respiratory microbiomes, and the triggered immune response-innate and adaptive-developed afterwards [2, 3] . It is well-known that viral infections can induce an ideal environment for a bacterial superinfection through different mechanisms such as the destruction of the epithelial barrier, the over-expression of the receptors involved in the bacterial adhesion to the cells, and the alteration of the host immune response [1, 2, 94, 95] . abstract: Understudied, coinfections are more frequent in pig farms than single infections. In pigs, the term “Porcine Respiratory Disease Complex” (PRDC) is often used to describe coinfections involving viruses such as swine Influenza A Virus (swIAV), Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), and Porcine CircoVirus type 2 (PCV2) as well as bacteria like Actinobacillus pleuropneumoniae, Mycoplasma hyopneumoniae and Bordetella bronchiseptica. The clinical outcome of the various coinfection or superinfection situations is usually assessed in the studies while in most of cases there is no clear elucidation of the fine mechanisms shaping the complex interactions occurring between microorganisms. In this comprehensive review, we aimed at identifying the studies dealing with coinfections or superinfections in the pig respiratory tract and at presenting the interactions between pathogens and, when possible, the mechanisms controlling them. Coinfections and superinfections involving viruses and bacteria were considered while research articles including protozoan and fungi were excluded. We discuss the main limitations complicating the interpretation of coinfection/superinfection studies, and the high potential perspectives in this fascinating research field, which is expecting to gain more and more interest in the next years for the obvious benefit of animal health. url: https://doi.org/10.1186/s13567-020-00807-8 doi: 10.1186/s13567-020-00807-8 id: cord-261025-y49su5uc author: Sampathkumar, Priya title: SARS: Epidemiology, Clinical Presentation, Management, and Infection Control Measures date: 2003-07-31 words: 3952.0 sentences: 200.0 pages: flesch: 49.0 cache: ./cache/cord-261025-y49su5uc.txt txt: ./txt/cord-261025-y49su5uc.txt summary: Severe acute respiratory syndrome (SARS) is a recently recognized febrile respiratory illness that first appeared in southern China in November 2002, has since spread to several countries, and has resulted in more than 8000 cases and more than 750 deaths. This article summarizes currently available information regarding the epidemiology, clinical features, etiologic agent, and modes of transmission of the disease, as well as infection control measures appropriate to contain SARS. An RT-PCR test specific for RNA from the SARS-CoV has been positive within the first 10 days after fever onset in respiratory specimens from most patients considered probable cases of SARS who have been tested and in stool samples in the second week of illness. Case definitions of SARS are currently based on the presence of epidemiological risk factors (close contact with patients with SARS or travel to SARS-affected areas) and a combination of fever and respiratory symptoms, with or without chest radiographic changes. Severe Acute Respiratory Syndrome (SARS) in Singapore: clinical features of index patient and initial contacts abstract: Severe acute respiratory syndrome (SARS) is a recently recognized febrile respiratory illness that first appeared in southern China in November 2002, has since spread to several countries, and has resulted in more than 8000 cases and more than 750 deaths. The disease has been etiologically linked to a novel coronavirus that has been named the SARS-associated coronavirus. It appears to be spread primarily by large droplet transmission. There is no specific therapy, and management consists of supportive care. This article summarizes currently available information regarding the epidemiology, clinical features, etiologic agent, and modes of transmission of the disease, as well as infection control measures appropriate to contain SARS. url: https://www.sciencedirect.com/science/article/pii/S002561961162689X doi: 10.4065/78.7.882 id: cord-027693-a4up394g author: Sampol, Júlia title: Predictors of respiratory complications in patients with C5–T5 spinal cord injuries date: 2020-06-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: STUDY DESIGN: Retrospective chart audit. OBJECTIVES: Describing the respiratory complications and their predictive factors in patients with acute traumatic spinal cord injuries at C5–T5 level during the initial hospitalization. SETTING: Hospital Vall d’Hebron, Barcelona. METHODS: Data from patients admitted in a reference unit with acute traumatic injuries involving levels C5–T5. Respiratory complications were defined as: acute respiratory failure, respiratory infection, atelectasis, non-hemothorax pleural effusion, pulmonary embolism or haemoptysis. Candidate predictors of these complications were demographic data, comorbidity, smoking, history of respiratory disease, the spinal cord injury characteristics (level and ASIA Impairment Scale) and thoracic trauma. A logistic regression model was created to determine associations between potential predictors and respiratory complications. RESULTS: We studied 174 patients with an age of 47.9 (19.7) years, mostly men (87%), with low comorbidity. Coexistent thoracic trauma was found in 24 (19%) patients with cervical and 35 (75%) with thoracic injuries (p < 0.001). Respiratory complications were frequent (53%) and were associated to longer hospital stay: 83.1 (61.3) and 45.3 (28.1) days in patients with and without respiratory complications (p < 0.001). The strongest predictors of respiratory complications were: previous respiratory disease (OR 5.4, 95% CI: 1.5–19.2), complete motor function impairment (AIS A–B) (OR 4.7, 95% CI: 2.4–9.5) and concurrent chest trauma (OR 3.73, 95% CI: 1.8–7.9). CONCLUSIONS: Respiratory complications are common in traumatic spinal cord injuries between C5–T5. We identified previous respiratory disease, complete motor function impairment and the coexistence of thoracic trauma as predictors of respiratory complications. Identification of patients at risk might help clinicians to implement preventive strategies. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7312109/ doi: 10.1038/s41393-020-0506-7 id: cord-342649-ysossker author: Scagnolari, Carolina title: Evaluation of viral load in infants hospitalized with bronchiolitis caused by respiratory syncytial virus date: 2012-03-10 words: 3759.0 sentences: 161.0 pages: flesch: 42.0 cache: ./cache/cord-342649-ysossker.txt txt: ./txt/cord-342649-ysossker.txt summary: The relationship between viral load, disease severity and antiviral immune activation in infants suffering from respiratory syncytial virus (RSV)-associated bronchiolitis has not been well identified. The main objective of this study was to determine the existence of a correlation between RSV load and disease severity and also between different clinical markers and mRNA levels of the interferon stimulated gene (ISG)56 in infants hospitalized for bronchiolitis. Results indicated that viral load was positively related to the clinical severity of bronchiolitis, the length of hospital stay, the levels of glycemia and the relative gene expression of ISG56, whereas an inverse correlation was observed with the levels of hemoglobin. In the framework of a study aimed at understanding the pathogenesis of RSV infection and at further characterizing viral and host factors involved in determining the severity of bronchiolitis, we addressed whether any diVerences in RSV-RNA levels in the airway tracts of infants with bronchiolitis might explain the broad clinical spectrum of RSVassociated bronchiolitis. abstract: The relationship between viral load, disease severity and antiviral immune activation in infants suffering from respiratory syncytial virus (RSV)-associated bronchiolitis has not been well identified. The main objective of this study was to determine the existence of a correlation between RSV load and disease severity and also between different clinical markers and mRNA levels of the interferon stimulated gene (ISG)56 in infants hospitalized for bronchiolitis. We also evaluated whether viral load tended to be persistent over the course of the RSV infection. The levels of RSV-RNA were quantified in nasopharyngeal washings, collected from 132 infants infected with RSV as a single (90.15%) or as a dual infection with other respiratory viruses (9.85%). Results indicated that viral load was positively related to the clinical severity of bronchiolitis, the length of hospital stay, the levels of glycemia and the relative gene expression of ISG56, whereas an inverse correlation was observed with the levels of hemoglobin. We also found that the RSV load significantly decreased between the first and second nasopharingeal washings sample in most subjects. These results suggest that infants with high RSV load on hospital admission are more likely to have both more severe bronchiolitis and a higher airway activation of antiviral immune response. url: https://www.ncbi.nlm.nih.gov/pubmed/22406873/ doi: 10.1007/s00430-012-0233-6 id: cord-265054-52eqdlef author: Schaller, Matthew title: Respiratory viral infections drive chemokine expression and exacerbate the asthmatic response date: 2006-08-03 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A number of investigations have linked respiratory vial infections and the intensity and subsequent exacerbation of asthma through host response mechanisms. For example, it is likely that the immune-inflammatory response to respiratory syncytial virus can cause a predisposition toward an intense inflammatory reaction associated with asthma, and adenovirus might cause exacerbation of the immune response associated with chronic obstructive pulmonary disease. In each of these situations, the host's immune response plays a critical mechanistic role through the production of certain cytokines and chemokines. Specific aspects of these augmented immune responses are determined by the biology of the virus, the genetic variability of the host, and the cytokine-chemokine phenotype of the involved tissue. For instance, the type 1/type 2 cytokine ratio in the airways during infection with rhinovirus determines how long the viral infection endures. By this same theory, it has been demonstrated that chemokine levels produced during respiratory syncytial virus infection determine host responses to later immune stimuli in the lung, with the potential to augment the asthmatic response. Further research in this area will clarify cytokines, chemokines, or cell targets, which will provide the basis for next-generation therapies. url: https://www.ncbi.nlm.nih.gov/pubmed/16890750/ doi: 10.1016/j.jaci.2006.05.025 id: cord-284266-tbndldhr author: Schippa, Serena title: Nasal Microbiota in RSV Bronchiolitis date: 2020-05-13 words: 5521.0 sentences: 237.0 pages: flesch: 34.0 cache: ./cache/cord-284266-tbndldhr.txt txt: ./txt/cord-284266-tbndldhr.txt summary: Our results indicated that infants with more severe bronchiolitis disease, caused by RSV-A infection, present significant perturbations of both the nasal microbiota structure and the microbial relationships. Evaluation of α diversity by the Shannon and Simpson indexes, as well as the number of observed OTUs, showed a significant lower biodiversity in the RSV-positive group with respect to the virus-negative one, suggesting the presence of a microbial shifts in the nasal microbiota of RSV-positive subjects (Figure 1a) . Evaluation of α diversity by the Shannon and Simpson indexes, as well as the number of observed OTUs, showed a significant lower biodiversity in the RSV-positive group with respect to the virus-negative one, suggesting the presence of a microbial shifts in the nasal microbiota of RSVpositive subjects (Figure 1a) . The main aim of the present study was to characterize the nasal microbiota in pediatric patients hospitalized for bronchiolitis from RSV and in infants affected by bronchiolitis but negative for a respiratory virus. abstract: Respiratory Syncytial Virus (RSV) is the leading cause of bronchiolitis, and the severity may be influenced by the bacterial ecosystem. Our aim was to analyze the nasal microbiota from 48 infants affected by bronchiolitis from RSV virus and 28 infants with bronchiolitis but negative for the virus. Results showed a significantly lower biodiversity in the RSV-positive group with respect to the RSV-negative group, a specific microbial profile associated with the RSV-positive group different from that observed in the negative group, and significant modifications in the relative abundance of taxa in the RSV-positive group, as well as in the RSV-A group, with respect to the negative group. Furthermore, microbial network analyses evidenced, in all studied groups, the presence of two predominant sub-networks characterized by peculiar inter- and intra-group correlation patterns as well as a general loss of connectivity among microbes in the RSV-positive group, particularly in the RSV-A group. Our results indicated that infants with more severe bronchiolitis disease, caused by RSV-A infection, present significant perturbations of both the nasal microbiota structure and the microbial relationships. Patients with a milder bronchiolitis course (RSV-B-infected and patients who have cleared the virus) presented less severe alterations. url: https://doi.org/10.3390/microorganisms8050731 doi: 10.3390/microorganisms8050731 id: cord-008716-38sqkh9m author: Schmidt, Alexander C title: Current research on respiratory viral infections: Third International Symposium date: 2001-06-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133842/ doi: 10.1016/s0166-3542(01)00136-x id: cord-272878-6f0q661e author: Schnepf, Nathalie title: High Burden of Non-Influenza Viruses in Influenza-Like Illness in the Early Weeks of H1N1v Epidemic in France date: 2011-08-17 words: 4177.0 sentences: 217.0 pages: flesch: 45.0 cache: ./cache/cord-272878-6f0q661e.txt txt: ./txt/cord-272878-6f0q661e.txt summary: In the two academic hospitals, Saint-Louis hospital (SLS) in Paris and Tours hospital (TRS), influenza-like illness (ILI) was defined as a patient suffering from at least one general symptom (fever above 38uC, asthenia, myalgia, shivers or headache) and one respiratory symptom (cough, dyspnoea, rhinitis or pharyngitis), in agreement with the guidelines from the French Institut de Veille Sanitaire (InVS), a governmental institution responsible for surveillance and alert in all domains of public health [12] . Two hundred and twelve were positive for non influenza pathogens (189 single infections and 23 mixed infections with two, three or four viruses) and three additional single infections by influenza A were identified in SLS, including two by pandemic H1N1v and one by seasonal H3N2, as determined after molecular typing (data not shown). As RHV was the most frequent aetiology in ILI, we also compared clinical symptoms observed in patients with a single infection by RHV or by H1N1v (data not shown). abstract: BACKGROUND: Influenza-like illness (ILI) may be caused by a variety of pathogens. Clinical observations are of little help to recognise myxovirus infection and implement appropriate prevention measures. The limited use of molecular tools underestimates the role of other common pathogens. OBJECTIVES: During the early weeks of the 2009–2010 flu pandemic, a clinical and virological survey was conducted in adult and paediatric patients with ILI referred to two French University hospitals in Paris and Tours. Aims were to investigate the different pathogens involved in ILI and describe the associated symptoms. METHODS: H1N1v pandemic influenza diagnosis was performed with real time RT-PCR assay. Other viral aetiologies were investigated by the molecular multiplex assay RespiFinder19®. Clinical data were collected prospectively by physicians using a standard questionnaire. RESULTS: From week 35 to 44, endonasal swabs were collected in 413 patients. Overall, 68 samples (16.5%) were positive for H1N1v. In 13 of them, other respiratory pathogens were also detected. Among H1N1v negative samples, 213 (61.9%) were positive for various respiratory agents, 190 in single infections and 23 in mixed infections. The most prevalent viruses in H1N1v negative single infections were rhinovirus (62.6%), followed by parainfluenza viruses (24.2%) and adenovirus (5.3%). 70.6% of H1N1v cases were identified in patients under 40 years and none after 65 years. There was no difference between clinical symptoms observed in patients infected with H1N1v or with other pathogens. CONCLUSION: Our results highlight the high frequency of non-influenza viruses involved in ILI during the pre-epidemic period of a flu alert and the lack of specific clinical signs associated with influenza infections. Rapid diagnostic screening of a large panel of respiratory pathogens may be critical to define and survey the epidemic situation and to provide critical information for patient management. url: https://www.ncbi.nlm.nih.gov/pubmed/21858150/ doi: 10.1371/journal.pone.0023514 id: cord-351046-yq7287k9 author: Schubert, Gena title: How Much Drool Is Too Much?() date: 2019-12-13 words: 3232.0 sentences: 199.0 pages: flesch: 46.0 cache: ./cache/cord-351046-yq7287k9.txt txt: ./txt/cord-351046-yq7287k9.txt summary: There is a broad differential for a patient with respiratory failure, and careful physical examination and history are imperative to reduce morbidity and prevent mortality. There is a broad differential for a patient with respiratory failure, and careful physical examination and history are imperative to reduce morbidity and prevent mortality. The initial vital signs on his third ED presentation were as follows: temperature 36.7°C, heart rate 130 beats per minute, respiratory rate 30 breaths per minute, pulse oximetry 99%, and blood pressure of 113/81 mm Hg. On examination, the patient was awake and calm in his mother''s arms with no acute distress. The differential for a patient presenting to the ED with acute respiratory distress is broad and includes infection, ingestion, trauma, envenomation, muscular disorders, and autoimmune etiologies. Scorpion envenomation often presents with respiratory distress along with increased drooling, abnormal eye movements, muscle twitching, and agitation. 13, 14 The treatment for myasthenia gravis begins with respiratory support including intubation or noninvasive ventilation. abstract: A 3-year-old boy presented to the emergency department with a chief complaint of “lethargy” and was found to have ptosis with eventual respiratory failure and need for emergent intubation. There is a broad differential for a patient with respiratory failure, and careful physical examination and history are imperative to reduce morbidity and prevent mortality. After further evaluation and workup, the diagnosis is ultimately revealed. url: https://api.elsevier.com/content/article/pii/S1522840119300989 doi: 10.1016/j.cpem.2019.100742 id: cord-347262-q88g1561 author: Schutzer‐Weissmann, J. title: Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection risk during elective peri‐operative care: a narrative review date: 2020-07-11 words: 4753.0 sentences: 279.0 pages: flesch: 39.0 cache: ./cache/cord-347262-q88g1561.txt txt: ./txt/cord-347262-q88g1561.txt summary: Whilst none of these were anaesthetists or intensivists, 53/1718 (3.1%) healthcare workers performing or involved in tracheal intubation of patients with confirmed or suspected COVID-19 subsequently reported laboratory-confirmed SARS-CoV-2 infection [4] . Here, we review the evidence from SARS and contemporaneous data from COVID-19 to inform assessment and management of the risk of SARS-CoV-2 transmission to healthcare workers involved in elective peri-operative care. The WHO list of aerosol-generating procedures is based on epidemiological evidence of transmission to healthcare workers caring for SARS patients [30, [36] [37] [38] [39] [40] [41] [42] [43] [44] . The studies upon which the WHO list of aerosol-generating procedures is based do not provide any direct evidence that tracheal intubation itself increases the risk of SARS transmission. Aerosol Generating Procedures and Risk of Transmission of Acute Respiratory Infections to Healthcare Workers: A Systematic Review abstract: The protection of healthcare workers from the risk of nosocomial severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection is a paramount concern. SARS‐CoV‐2 is likely to remain endemic and measures to protect healthcare workers against nosocomial infection will need to be maintained. This review aims to inform the assessment and management of the risk of SARS‐CoV‐2 transmission to healthcare workers involved in elective peri‐operative care. In the absence of data specifically related to the risk of SARS‐CoV‐2 transmission in the peri‐operative setting, we explore the evidence‐base that exists regarding modes of viral transmission, historical evidence for the risk associated with aerosol‐generating procedures and contemporaneous data from the COVID‐19 pandemic. We identify a significant lack of data regarding the risk of transmission in the management of elective surgical patients, highlighting the urgent need for further research. url: https://doi.org/10.1111/anae.15221 doi: 10.1111/anae.15221 id: cord-306266-8qdrshz3 author: Scully, Crispian title: Respiratory medicine date: 2014-06-25 words: 13246.0 sentences: 698.0 pages: flesch: 42.0 cache: ./cache/cord-306266-8qdrshz3.txt txt: ./txt/cord-306266-8qdrshz3.txt summary: Other factors that have been studied include: ■ air pollution -There is an association between air pollution and aggravation of existing asthma ■ allergen avoidance -There is no consistent evidence of benefit ■ breast-feeding -There is evidence of a protective effect in relation to early asthma ■ electrolytes -There is no consistent evidence of benefit ■ fish oils and fatty acid -There is no consistent evidence of benefit ■ house dust mites -Measures to reduce the numbers of house dust mites do not affect asthma severity ■ immunotherapy -Allergenspecific immunotherapy is beneficial in allergic asthma ■ microbial exposure -There is insufficient evidence to indicate that the use of probiotics in pregnancy reduces the incidence of childhood asthma ■ modified milk formulae -There is no consistent evidence of benefit pets -There are no controlled trials on the benefits of removing pets from the home ■ tobacco -Exposure to cigarette smoke adversely affects quality of life, lung function, need for rescue medications and longterm control with inhaled steroids. abstract: ●. Upper respiratory infections are commonplace, especially in young people, and are often contagious; ●. Lower respiratory infections are often contagious and some are potentially fatal; ●. Asthma is common and may be life-threatening; ●. Chronic obstructive pulmonary disease is common and disabling; ●. Tuberculosis worldwide is an important infection, affecting people with HIV/AIDS or malnutrition particularly; ●. Lung cancer is common and usually has a poor prognosis. url: https://api.elsevier.com/content/article/pii/B9780702054013000151 doi: 10.1016/b978-0-7020-5401-3.00015-1 id: cord-345472-qrddwebe author: Sebina, Ismail title: The Contribution of Neutrophils to the Pathogenesis of RSV Bronchiolitis date: 2020-07-27 words: 8184.0 sentences: 411.0 pages: flesch: 28.0 cache: ./cache/cord-345472-qrddwebe.txt txt: ./txt/cord-345472-qrddwebe.txt summary: A vaccine against respiratory syncytial virus (RSV), the leading cause of viral bronchiolitis in infancy, remains elusive, and hence new therapeutic modalities are needed to limit disease severity. (1), degranulation (2), respiratory oxygen species (ROS) production (3), and the release of neutrophil extracellular traps (NETosis) (4) are associated with increased lung inflammation, systemic fever, mucus hypersecretion, airway obstruction, and epithelial cell death. Excessive neutrophil-derived inflammatory cytokine production (1), degranulation (2), respiratory oxygen species (ROS) production (3), and the release of neutrophil extracellular traps (NETosis) (4) are associated with increased lung inflammation, systemic fever, mucus hypersecretion, airway obstruction, and epithelial cell death. Unlike wild-type (WT) control mice, plasmacytoid dendritic cell (pDC)-depleted, Toll-like receptor (TLR)7-deficient, or interferon regulatory factor (IRF)7-deficient neonatal mice develop severe pathology, characterised by increased neutrophilia and lung inflammation in response to acute PVM infection [80] [81] [82] . abstract: Acute viral bronchiolitis causes significant mortality in the developing world, is the number one cause of infant hospitalisation in the developed world, and is associated with the later development of chronic lung diseases such as asthma. A vaccine against respiratory syncytial virus (RSV), the leading cause of viral bronchiolitis in infancy, remains elusive, and hence new therapeutic modalities are needed to limit disease severity. However, much remains unknown about the underlying pathogenic mechanisms. Neutrophilic inflammation is the predominant phenotype observed in infants with both mild and severe disease, however, a clear understanding of the beneficial and deleterious effects of neutrophils is lacking. In this review, we describe the multifaceted roles of neutrophils in host defence and antiviral immunity, consider their contribution to bronchiolitis pathogenesis, and discuss whether new approaches that target neutrophil effector functions will be suitable for treating severe RSV bronchiolitis. url: https://doi.org/10.3390/v12080808 doi: 10.3390/v12080808 id: cord-315949-7id5mitl author: Sentilhes, Anne‐Charlotte title: Respiratory virus infections in hospitalized children and adults in Lao PDR date: 2013-06-25 words: 4098.0 sentences: 246.0 pages: flesch: 49.0 cache: ./cache/cord-315949-7id5mitl.txt txt: ./txt/cord-315949-7id5mitl.txt summary: 8, 9 The purpose of this study was to describe during a limited period of time the viral etiology of acute lower respiratory infections (ALRI) in patients hospitalized in two Lao hospitals by using a set of five multiplex RT-PCR/PCR targeting 18 common respiratory viruses. In this study, we report for the first time in Lao PDR the viral etiologies in patients hospitalized for ALRIs. We identified 186 respiratory viruses in 162 (55%) patients of all ages using 5 multiplex PCR/RT-PCR. Human respiratory syncytial virus is frequently defined as the predominant virus associated with hospitalizations for ALRI in children aged ≤5 years. Respiratory virus coinfections being frequent, 5, 19, 44 it demonstrates the usefulness of the multiplex RT-PCR approach, which allows the detection of the most important viruses in only few reactions while multiple infections are often undetected in viral culture or by direct immunofluorescence. abstract: BACKGROUND: Acute respiratory infections are an important cause of morbidity and mortality worldwide, with a major burden of disease in developing countries. The relative contribution of viruses in acute lower respiratory infections (ALRI) is, however, poorly documented in Lao PDR. OBJECTIVE: The objective of this study is to investigate the etiology of ALRI in patients of all ages in two hospitals of Laos. METHODS: Multiplex PCR/RT‐PCR methods were used to target 18 major common respiratory viruses. Between August 2009 and October 2010, samples from 292 patients presenting with ALRI were collected. RESULTS AND CONCLUSION: Viruses were detected in 162 (55%) samples. In 48% (140/292) of the total ALRI cases, a single virus was detected while coinfections were observed in 8% (22/292) of the samples. The most frequent viruses were rhinovirus/enterovirus (35%), human respiratory syncytial virus (26%), and influenza viruses (13%). Parainfluenza viruses were detected in 9%, adenovirus in 6%, human metapneumovirus in 4%, coronaviruses (229E, NL63, OC43, HKU1) in 4%, and bocavirus in 3% of ALRI specimens. Most viral infections occurred in patients below 5 years of age. The distribution of viruses varied according to age‐groups. No significant correlation was observed between the severity of the disease and the age of patients or the virus species. This study provides the description of viral etiology among patients presenting with ALRI in Lao PDR. Additional investigations are required to better understand the clinical role of the different viruses and their seasonality in Laos. url: https://doi.org/10.1111/irv.12135 doi: 10.1111/irv.12135 id: cord-282867-kbyxdegu author: Shah, Sayed Zulfiqar Ali title: Scaling the Need, Benefits, and Risks Associated with COVID-19 Acute and Postacute Care Rehabilitation: A Review date: 2020-08-26 words: 4542.0 sentences: 247.0 pages: flesch: 39.0 cache: ./cache/cord-282867-kbyxdegu.txt txt: ./txt/cord-282867-kbyxdegu.txt summary: The main aim of this study is to review and summarize the evidence regarding the supportive role of physical rehabilitation techniques in managing COVID-19-associated pneumonia. In this review, we also emphasize the use of rehabilitation techniques in the management of pneumonia in COVID-19-infected patients. The purpose of this study was to review the evidence regarding the supportive role of treatment options available in physical rehabilitation to manage COVID-19 pneumonia effectively. Evidence strongly supports that many rehabilitation techniques including chest physiotherapy and physical therapy modalities can be of great support to manage COVID-19-associated pneumonia [9, 10] . Common problems identified in COVID-19 patients that could be managed by rehabilitation specialists in the postacute phase include musculoskeletal pain, joint pain, reduced range of motion, muscular weakness, neuropathy and myopathy, pulmonary dysfunction, dysphagia, dyspnea, confusion, and impaired activities of daily living. abstract: Coronavirus is an RNA virus, which attacks the respiratory system causing complications including severe respiratory distress and pneumonia and many other symptoms. Recently, a novel coronavirus (COVID-19) outbreak emerged in Wuhan, which caused a significant number of infections in China and resulted in a global pandemic. The main aim of this study is to review and summarize the evidence regarding the supportive role of physical rehabilitation techniques in managing COVID-19-associated pneumonia. In this review, we also emphasize the use of rehabilitation techniques in the management of pneumonia in COVID-19-infected patients. Based on the evidence presented, we conclude that certain physical rehabilitation techniques and modalities could be of great support in the management of COVID-19-associated pneumonia. The safety of staff and patients when applying rehabilitation intervention requires attention. The combination of physical rehabilitation and medical treatment would result in improved treatment outcomes, faster recovery, and shorter hospital stay. Many rehabilitation techniques are safe and feasible and can be easily incorporated into the management protocol of COVID-19 victims. Decisions of early rehabilitation induction should be based on the patient's medical condition and tolerability. url: https://doi.org/10.1155/2020/3642143 doi: 10.1155/2020/3642143 id: cord-265751-q1ecpfyg author: Shahani, Lokesh title: Antiviral therapy for respiratory viral infections in immunocompromised patients date: 2017-01-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Introduction: Respiratory viruses (influenza, parainfluenza, respiratory syncytial virus, coronavirus, human metapneumovirus, and rhinovirus) represent the most common causes of respiratory viral infections in immunocompromised patients. Also, these infections may be more severe in immunocompromised patients than in the general population. Early diagnosis and treatment of viral infections continue to be of paramount importance in immunocompromised patients; because once viral replication and invasive infections are evident, prognosis can be grave. Areas covered: The purpose of this review is to provide an overview of the main antiviral agents used for the treatment of respiratory viral infections in immunocompromised patients and review of the new agents in the pipeline. Expert commentary: Over the past decade, important diagnostic advances, specifically, the use of rapid molecular testing has helped close the gap between clinical scenarios and pathogen identification and enhanced early diagnosis of viral infections and understanding of the role of prolonged shedding and viral loads. Advancements in novel antiviral therapeutics with high resistance thresholds and effective immunization for preventable infections in immunocompromised patients are needed. url: https://www.ncbi.nlm.nih.gov/pubmed/28067078/ doi: 10.1080/14787210.2017.1279970 id: cord-268388-kkhuzf3p author: Sharif-Yakan, Ahmad title: Emergence of MERS-CoV in the Middle East: Origins, Transmission, Treatment, and Perspectives date: 2014-12-04 words: 2507.0 sentences: 141.0 pages: flesch: 50.0 cache: ./cache/cord-268388-kkhuzf3p.txt txt: ./txt/cord-268388-kkhuzf3p.txt summary: Two years have passed since the initial description of the Middle East respiratory syndrome coronavirus (MERS-CoV), yet the epidemic is far from being controlled. First reported in 2012 [1] , Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel coronavirus and the first lineage 2C Betacoronavirus known to infect humans [2] . Middle east respiratory syndrome coronavirus (MERS-CoV) RNA and neutralising antibodies in milk collected according to local customs from dromedary camels, qatar Middle east respiratory syndrome coronavirus (MERS-CoV) in dromedary camels Epidemiological, demographic, and clinical characteristics of 47 cases of middle east respiratory syndrome coronavirus disease from saudi arabia: A descriptive study Clinical features and viral diagnosis of two cases of infection with middle east respiratory syndrome coronavirus: A report of nosocomial transmission Clinical features and virological analysis of a case of middle east respiratory syndrome coronavirus infection Ribavirin and interferon therapy in patients infected with the middle east respiratory syndrome coronavirus: An observational study abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/25474536/ doi: 10.1371/journal.ppat.1004457 id: cord-300711-yibdumij author: Shatizadeh, Somayeh title: Epidemiological and clinical evaluation of children with respiratory virus infections date: 2014-09-22 words: 2024.0 sentences: 119.0 pages: flesch: 48.0 cache: ./cache/cord-300711-yibdumij.txt txt: ./txt/cord-300711-yibdumij.txt summary: This study was performed to detect viruses in children with respiratory infections and describe their epidemiology and clinical characteristics. Methods: In this descriptive cross sectional study, throat swabs and wash specimens from 202 children younger than six years of age with diagnosis of a respiratory tract infection from a total of 897 specimens were evaluated using multiplex PCR method. Results: Respiratory viruses were detected in 92 children: respiratory synsytial virus, 16.8%; influenza virus, 5.4%; parainfluenza virus, 8.4%; adenovirus, 14.4% and human metapneumo virus 0.49% with male predominance and higher distribution in children younger than 1 year of age with preference in the cold months of year. In this study, AdVs followed by RSV were the most frequently detected viral agents in our patients (14.4%) which occurred mostly in the summer and winter months (August, September and February) in male children in all age groups. abstract: Background: Respiratory viruses are the leading cause of respiratory tract infections among children and are responsible for causing morbidity and mortality worldwide. This study was performed to detect viruses in children with respiratory infections and describe their epidemiology and clinical characteristics. Methods: In this descriptive cross sectional study, throat swabs and wash specimens from 202 children younger than six years of age with diagnosis of a respiratory tract infection from a total of 897 specimens were evaluated using multiplex PCR method. Results: Respiratory viruses were detected in 92 children: respiratory synsytial virus, 16.8%; influenza virus, 5.4%; parainfluenza virus, 8.4%; adenovirus, 14.4% and human metapneumo virus 0.49% with male predominance and higher distribution in children younger than 1 year of age with preference in the cold months of year. The clinical presentations of all detected viruses were almost similar. Conclusion: In the present study, nine different respiratory viruses were detected. RSV causes the great majority of respiratory virus infections in children. There was no significant difference in epidemiologic patterns of these viruses in comparison to other studies. url: https://www.ncbi.nlm.nih.gov/pubmed/25664303/ doi: nan id: cord-331228-wbd0s4fo author: Shehata, Mahmoud M. title: Middle East respiratory syndrome coronavirus: a comprehensive review date: 2016-01-20 words: 7512.0 sentences: 372.0 pages: flesch: 46.0 cache: ./cache/cord-331228-wbd0s4fo.txt txt: ./txt/cord-331228-wbd0s4fo.txt summary: authors: Shehata, Mahmoud M.; Gomaa, Mokhtar R.; Ali, Mohamed A.; Kayali, Ghazi Role of the spike glycoprotein of human Middle East respiratory syndrome coronavirus (MERS-CoV) in virus entry and syncytia formation Middle East respiratory syndrome coronavirus (MERS-CoV)-Saudi Arabia Epidemiological, demographic, and clinical characteristics of 47 cases of Middle East respiratory syndrome coronavirus disease from Saudi Arabia: a descriptive study First cases of Middle East respiratory syndrome coronavirus (MERS-CoV) infections in France, investigations and implications for the prevention of human-to-human transmission Clinical features and viral diagnosis of two cases of infection with Middle East respiratory syndrome coronavirus: a report of nosocomial transmission Middle East respiratory syndrome coronavirus infection in dromedary camels in Saudi Arabia abstract: The Middle East respiratory syndrome coronavirus was first identified in 2012 and has since then remained uncontrolled. Cases have been mostly reported in the Middle East, however travel-associated cases and outbreaks have also occurred. Nosocomial and zoonotic transmission of the virus appear to be the most important routes. The infection is severe and highly fatal thus necessitating rapid and efficacious interventions. Here, we performed a comprehensive review of published literature and summarized the epidemiology of the virus. In addition, we summarized the virological aspects of the infection and reviewed the animal models used as well as vaccination and antiviral tested against it. url: https://www.ncbi.nlm.nih.gov/pubmed/26791756/ doi: 10.1007/s11684-016-0430-6 id: cord-300019-8vxqr3mc author: Shi, Ting title: The Etiological Role of Common Respiratory Viruses in Acute Respiratory Infections in Older Adults: A Systematic Review and Meta-analysis date: 2019-03-08 words: 3968.0 sentences: 187.0 pages: flesch: 43.0 cache: ./cache/cord-300019-8vxqr3mc.txt txt: ./txt/cord-300019-8vxqr3mc.txt summary: We aimed to identify all case-control studies investigating the potential role of respiratory viruses in the etiology of ARI in older adults aged ≥65 years. This review supports RSV, Flu, PIV, HMPV, AdV, RV, and CoV as important causes of ARI in older adults and provides quantitative estimates of the absolute proportion of virus-associated ARI cases to which a viral cause can be attributed. Although influenza virus (Flu) is the most widely recognized viral infection associated with respiratory illness, >25 viruses have been linked to pneumonia, causing a substantial disease burden in adults and elderly individuals. Therefore, we aimed to conduct a similar systematic review to identify all case-control studies since 1996 investigating the potential role of respiratory viruses in the etiology of ARIs in older adults aged ≥65 years. abstract: Acute respiratory tract infections (ARI) constitute a substantial disease burden in adults and elderly individuals. We aimed to identify all case-control studies investigating the potential role of respiratory viruses in the etiology of ARI in older adults aged ≥65 years. We conducted a systematic literature review (across 7 databases) of case-control studies published from 1996 to 2017 that investigated the viral profile of older adults with and those without ARI. We then computed a pooled odds ratio (OR) with a 95% confidence interval and virus-specific attributable fraction among the exposed (AFE) for 8 common viruses: respiratory syncytial virus (RSV), influenza virus (Flu), parainfluenza virus (PIV), human metapneumovirus (HMPV), adenovirus (AdV), rhinovirus (RV), bocavirus (BoV), and coronavirus (CoV). From the 16 studies included, there was strong evidence of possible causal attribution for RSV (OR, 8.5 [95% CI, 3.9–18.5]; AFE, 88%), Flu (OR, 8.3 [95% CI, 4.4–15.9]; AFE, 88%), PIV (OR, not available; AFE, approximately 100%), HMPV (OR, 9.8 [95% CI, 2.3–41.0]; AFE, 90%), AdV (OR, not available; AFE, approximately 100%), RV (OR, 7.1 [95% CI, 3.7–13.6]; AFE, 86%) and CoV (OR, 2.8 [95% CI, 2.0–4.1]; AFE, 65%) in older adults presenting with ARI, compared with those without respiratory symptoms (ie, asymptomatic individuals) or healthy older adults. However, there was no significant difference in the detection of BoV in cases and controls. This review supports RSV, Flu, PIV, HMPV, AdV, RV, and CoV as important causes of ARI in older adults and provides quantitative estimates of the absolute proportion of virus-associated ARI cases to which a viral cause can be attributed. Disease burden estimates should take into account the appropriate AFE estimates (for older adults) that we report. url: https://www.ncbi.nlm.nih.gov/pubmed/30849176/ doi: 10.1093/infdis/jiy662 id: cord-336335-spap39b7 author: Silva, Denise R title: Respiratory viral infections and effects of meteorological parameters and air pollution in adults with respiratory symptoms admitted to the emergency room date: 2013-08-26 words: 4176.0 sentences: 244.0 pages: flesch: 47.0 cache: ./cache/cord-336335-spap39b7.txt txt: ./txt/cord-336335-spap39b7.txt summary: OBJECTIVES: The objectives of this study were to determine the number of emergency visits for influenza-like illness (ILI) and severe acute respiratory infection (SARI) and to evaluate the association between ILI/SARI, RVI prevalence, and meteorological factors/air pollution, in the city of Porto Alegre, Brazil, from November 2008 to October 2010. The correlations among meteorological variables, air pollution, ILI/SARI cases, and respiratory viruses demonstrated the relevance of climate factors as significant underlying contributors to the prevalence of RVI. The aims of this study were to determine the number of emergency room visits for influenza-like illness (ILI) and severe acute respiratory infection (SARI) and to evaluate the association between ILI/SARI frequency, respiratory virus prevalence, and meteorological factors/air pollution, especially in adult population, in a humid subtropical climate. The data were analyzed using time-series analysis, through a generalized linear model (GLM) to examine the association between ILI or SARI and air pollution/meteorological variables, using logistic regression. abstract: BACKGROUND: Respiratory viral infections (RVIs) are the most common causes of respiratory infections. The prevalence of respiratory viruses in adults is underestimated. Meteorological variations and air pollution are likely to play a role in these infections. OBJECTIVES: The objectives of this study were to determine the number of emergency visits for influenza-like illness (ILI) and severe acute respiratory infection (SARI) and to evaluate the association between ILI/SARI, RVI prevalence, and meteorological factors/air pollution, in the city of Porto Alegre, Brazil, from November 2008 to October 2010. METHODS: Eleven thousand nine hundred and fifty-three hospitalizations (adults and children) for respiratory symptoms were correlated with meteorological parameters and air pollutants. In a subset of adults, nasopharyngeal aspirates were collected and analyzed through IFI test. The data were analyzed using time-series analysis. RESULTS: Influenza-like illness and SARI were diagnosed in 3698 (30·9%) and 2063 (17·7%) patients, respectively. Thirty-seven (9·0%) samples were positive by IFI and 93 of 410 (22·7%) were IFI and/or PCR positive. In a multivariate logistic regression model, IFI positivity was statistically associated with absolute humidity, use of air conditioning, and presence of mold in home. Sunshine duration was significantly associated with the frequency of ILI cases. For SARI cases, the variables mean temperature, sunshine duration, relative humidity, and mean concentration of pollutants were singnificant. CONCLUSIONS: At least 22% of infections in adult patients admitted to ER with respiratory complaints were caused by RVI. The correlations among meteorological variables, air pollution, ILI/SARI cases, and respiratory viruses demonstrated the relevance of climate factors as significant underlying contributors to the prevalence of RVI. url: https://www.ncbi.nlm.nih.gov/pubmed/24034701/ doi: 10.1111/irv.12158 id: cord-260871-dtn5t8ka author: Silva, Marcus Tulius T. title: SARS-CoV-2: Should We Be Concerned about the Nervous System? date: 2020-07-17 words: 4110.0 sentences: 263.0 pages: flesch: 43.0 cache: ./cache/cord-260871-dtn5t8ka.txt txt: ./txt/cord-260871-dtn5t8ka.txt summary: Besides, several neurological manifestations had been described as complications of two other previous outbreaks of CoV diseases (SARS ad Middle East respiratory syndrome). Several neurological manifestations were described as complications of two other previous outbreaks of CoV diseases, namely, SARS and the Middle East respiratory syndrome (MERS). Stroke is one of the most frequent neurological diseases associated with SARS-CoV-2 infection, 8 and large-vessel stroke in younger patients was recently reported in five patients. Detection of SARS coronavirus RNA in the cerebrospinal fluid of a patient with severe acute respiratory syndrome Mechanisms of host defense following severe acute respiratory syndrome-coronavirus (SARS-CoV) pulmonary infection of mice Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 Central nervous system involvement by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the central nervous system abstract: The COVID-19 pandemic has proved to be an enormous challenge to the health of the world population with tremendous consequences for the world economy. New knowledge about COVID-19 is being acquired continuously. Although the main manifestation of COVID-19 is SARS, dysfunction in other organs has been described in the last months. Neurological aspects of COVID-19 are still an underreported subject. However, a plethora of previous studies has shown that human CoVs might be neurotropic, neuroinvasive, and neurovirulent, highlighting the importance of this knowledge by physicians. Besides, several neurological manifestations had been described as complications of two other previous outbreaks of CoV diseases (SARS ad Middle East respiratory syndrome). Therefore, we should be watchful, searching for early evidence of neurological insults and promoting clinical protocols to investigate them. Our objectives are to review the potential neuropathogenesis of this new CoV and the neurological profile of COVID-19 patients described so far. url: https://doi.org/10.4269/ajtmh.20-0447 doi: 10.4269/ajtmh.20-0447 id: cord-260225-bc1hr0fr author: Sirpilla, Olivia title: SARS-CoV-2-Encoded Proteome and Human Genetics: From Interaction-Based to Ribosomal Biology Impact on Disease and Risk Processes date: 2020-07-20 words: 8918.0 sentences: 582.0 pages: flesch: 44.0 cache: ./cache/cord-260225-bc1hr0fr.txt txt: ./txt/cord-260225-bc1hr0fr.txt summary: Integrating evolutionary, structural, and interaction data with human proteins, we present how the SARS-CoV-2 proteome interacts with human disorders and risk factors ranging from cytokine storm, hyperferritinemic septic, coagulopathic, cardiac, immune, and rare disease-based genetics. The most noteworthy human genetic potential of SARS-CoV-2 is that of the nucleocapsid protein, where it is known to contribute to the inhibition of the biological process known as nonsense-mediated decay. As we understand more of the dynamic and complex biological pathways that the proteome of SARS-CoV-2 utilizes for entry into cells, for replication, and for release from human cells, we can understand more risk factors for severe/lethal outcomes in patients and novel pharmaceutical interventions that may mitigate future pandemics. Additional SARS-CoV-2 proteins with mentions include nsp12 (RNA-directed RNA polymerase, 20/71), nucleocapsid (N, 17/71), membrane (M, 5/48), envelope (E, 4/31), nsp5 (3CLPro/Mpro, 7/26), nsp8 (3/19), nsp16 (2′-O-methyltransferase, 3/14), ORF8 (1/10), nsp10 (3/9), nsp14 (guanine-N7 methyltransferase, 1/8), nsp3 (papain-like protease, 16/6), and nsp15 (uridylate-specific endoribonuclease, 16/4). abstract: [Image: see text] SARS-CoV-2 (COVID-19) has infected millions of people worldwide, with lethality in hundreds of thousands. The rapid publication of information, both regarding the clinical course and the viral biology, has yielded incredible knowledge of the virus. In this review, we address the insights gained for the SARS-CoV-2 proteome, which we have integrated into the Viral Integrated Structural Evolution Dynamic Database, a publicly available resource. Integrating evolutionary, structural, and interaction data with human proteins, we present how the SARS-CoV-2 proteome interacts with human disorders and risk factors ranging from cytokine storm, hyperferritinemic septic, coagulopathic, cardiac, immune, and rare disease-based genetics. The most noteworthy human genetic potential of SARS-CoV-2 is that of the nucleocapsid protein, where it is known to contribute to the inhibition of the biological process known as nonsense-mediated decay. This inhibition has the potential to not only regulate about 10% of all biological transcripts through altered ribosomal biology but also associate with viral-induced genetics, where suppressed human variants are activated to drive dominant, negative outcomes within cells. As we understand more of the dynamic and complex biological pathways that the proteome of SARS-CoV-2 utilizes for entry into cells, for replication, and for release from human cells, we can understand more risk factors for severe/lethal outcomes in patients and novel pharmaceutical interventions that may mitigate future pandemics. url: https://doi.org/10.1021/acs.jproteome.0c00421 doi: 10.1021/acs.jproteome.0c00421 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: 3558.0 sentences: 174.0 pages: flesch: 40.0 cache: ./cache/cord-281418-mvgp6qfv.txt txt: ./txt/cord-281418-mvgp6qfv.txt summary: 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. 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. The present investigation was specifically designed to assess the epidemiology of respiratory viruses in bronchoalveolar lavage (BAL) fluid from lung transplant recipients and to analyze the relationship between these viruses and the presence of acute graft rejection. Because BAL fluid specimens were collected for a variety of clinical conditions, we were able to analyze the association among symptoms, the diagnosis suspected by the physician in charge, and the subsequent presence of a proven upper and/ or lower respiratory tract viral infection. 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-005818-3mzwliiy author: Speer, C. P. title: Surfactantsubstitutionstherapie: Ein entscheidender Durchbruch in der Behandlung des Atemnotsyndroms Frühgeborener date: 2014-04-24 words: 3927.0 sentences: 400.0 pages: flesch: 27.0 cache: ./cache/cord-005818-3mzwliiy.txt txt: ./txt/cord-005818-3mzwliiy.txt summary: Die Surfactantsubstitution stellt einen entscheidenden Durchbruch in der Behandlung des Atemnotsyndroms dar.Durch eine prophylaktische Surfactantgabe oder die Therapie des manifesten Atemnotsyndroms konnten die akuten pulmonalen Komplikationen beatmeter Frühgeborener um 2/3 reduziert und die Sterblichkeit nahezu halbiert werden.Eine frühe Surfactantapplikation innerhalb der ersten 15 Lebensminuten ist besonders bei sehr unreifen Frühgeborenen einer späteren Behandlung bei manifestem Atemnotsyndrom überlegen.Als initiale Dosis werden 100 mg Phospholipide/kg empfohlen; einige Frühgeborene profitieren von einer Mehrfachbehandlung.Natürliche Surfactantpräparate haben eine bessere klinische Wirksamkeit als die zurzeit verfügbaren synthetischen Präparate.Es gibt einige Hinweise, dass eine Surfactanttherapie auch bei pulmonalen Erkrankungen Neugeborener einen therapeutischen Effekt haben kann; diese Erkrankungen wie Mekoniumaspirationssyndrom und neonatale Pneumonie führen u.a.über eine Inaktivierung von Surfactant zu einer sekundären Defizienz dieses oberflächenaktiven Systems. Fujiwara und Mitarbeiter (Morioka) berichteten 1980 erstmals von Frühgeborenen mit manifestem Atemnotsyndrom (engl: respiratory distress syndrom: RDS), die nach einer intratrachealen Applikation eines Rindersurfactants mit einer deutlichen Verbesserung des pulmonalen Gasaustausches reagierten [18] . abstract: Surfactant replacement therapy is a major breakthrough in neonatal medicine. Prophylaxis or treatment of neonatal respiratory distress syndrome (RDS) with various surfactant preparations is now a clinical reality. With either strategy the incidence of air leaks and mortality is reduced; more babies with RDS survive without signs of chronic lung disease. The earlier the treatment, the better the outcome. An initial dose of 100 mg/kg can be recommended for all natural preparations, and some babies may benefit from multiple dose treatment. Meta-analyses show a consistent advantage of natural surfactant preparations over the currently available synthetic ones. There is growing evidence that surfactant may also be beneficial in pulmonary diseases of the newborn which are characterized by inactivation of the surfactant system such as meconium aspiration syndrome or neonatal pneumonia. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095786/ doi: 10.1007/s00112-002-0434-y id: cord-261941-xf1k5uj1 author: Stackhouse, Robin A. title: Severe acute respiratory syndrome and tuberculosis date: 2005-03-01 words: 5420.0 sentences: 306.0 pages: flesch: 55.0 cache: ./cache/cord-261941-xf1k5uj1.txt txt: ./txt/cord-261941-xf1k5uj1.txt summary: Recommendations for limiting secondary transmission are given based on the Centers for Disease Control and Prevention guidelines on infection control in health care facilities. It is confirmed through laboratory testing showing an acute rise in SARS-CoV antibody titers within 4 weeks of developing the disease. Patients who meet the criteria for suspect SARS should immediately be placed in a private respiratory isolation room that has been specially engineered to contain negative pressure in relation to the outside hallway and have a minimum of 12 air exchanges per hour. Prevention of transmission in medical facilities requires a combination of early identification, isolation, and treatment of infectious individuals with active disease, engineering controls, basic infection control measures, and the use of personal protective equipment. Hospital infection control guidance for severe acute respiratory syndrome (SARS) California Department of Health Services: severe acute respiratory syndrome (SARS)-infection control recommendations Infection control measures for operative procedures in severe acute respiratory syndrome-related patients abstract: Respiratory infectious diseases such as severe acute respiratory syndrome and tuberculosis create unique risks for anyone who may be exposed. A brief history of each disease is discussed in this article. The pathogenesis, manifestations, and therapy (where applicable) are also addressed. Recommendations for limiting secondary transmission are given based on the Centers for Disease Control and Prevention guidelines on infection control in health care facilities. url: https://www.ncbi.nlm.nih.gov/pubmed/15325712/ doi: 10.1016/j.atc.2004.06.002 id: cord-016009-qa7bcsbu author: Starkel, Julie L. title: Respiratory date: 2019-10-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Lung disease rivals the position for the top cause of death worldwide. Causes and pathology of the myriad lung diseases are varied, yet nutrition can either affect the outcome or support treatment in the majority of cases. This chapter explores the modifiable risk factors, from lifestyle changes to dietary intake to specific nutrients, anti-nutrients, and toxins helpful for the nutritionist or dietitian working with lung disease patients. General lung health is discussed, and three major disease states are explored in detail, including alpha-1 antitrypsin deficiency, asthma, and idiopathic pulmonary fibrosis. Although all lung diseases have diverse causes, many integrative and functional medical nutrition therapies are available and are not being utilized in practice today. This chapter begins the path toward better nutrition education for the integrative and functional medicine professional. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120155/ doi: 10.1007/978-3-030-30730-1_51 id: cord-255166-sar50ej0 author: Stone, Sophia title: Respiratory disease in pregnancy date: 2007-05-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Breathlessness in the absence of an underlying pathology is common in pregnancy. Asthma affects about 7% of women of childbearing age. Treatment is the same as for the non-pregnant population and most drugs are safe in pregnancy. Educating women to continue preventer inhaled corticosteroid therapy will reduce the risk of attacks. Respiratory infections are associated with a higher morbidity in pregnancy and should be treated aggressively. Most chronic pulmonary diseases do not alter fertility. Large reserves in respiratory function allow the fetus and mother to survive without compromise in most cases. The use of chest X-rays should not be avoided in pregnancy. Women with a chronic respiratory disease should receive pre-pregnancy counselling and education. Women should be managed in a multidisciplinary setting with the respiratory team. The presence of pulmonary hypertension and cor pulmonale is associated with a high risk of death in pregnancy. url: https://www.sciencedirect.com/science/article/pii/S1751721407000553 doi: 10.1016/j.ogrm.2007.03.006 id: cord-306480-wgl4zrnb author: Subissi, Lorenzo title: Capturing respiratory syncytial virus season in Belgium using the influenza severe acute respiratory infection surveillance network, season 2018/19 date: 2020-10-01 words: 4135.0 sentences: 187.0 pages: flesch: 48.0 cache: ./cache/cord-306480-wgl4zrnb.txt txt: ./txt/cord-306480-wgl4zrnb.txt summary: BACKGROUND: Respiratory syncytial virus (RSV) is a common cause of severe respiratory illness in young children (< 5 years old) and older adults (≥ 65 years old) leading the World Health Organization (WHO) to recommend the implementation of a dedicated surveillance in countries. AIM: We tested the capacity of the severe acute respiratory infection (SARI) hospital network to contribute to RSV surveillance in Belgium. CONCLUSION: With only marginal modifications in the case definition and the period of surveillance, the Belgian SARI network would be able to substantially contribute to RSV surveillance and burden evaluation in children and older adults, the two groups of particular interest for WHO. Nevertheless, the SARI case definition we used, even with a less strict fever criterion, allowed to follow RSV circulation in the children population aged < 5 years and to identify comorbidities/indicators potentially associated with disease severity. abstract: BACKGROUND: Respiratory syncytial virus (RSV) is a common cause of severe respiratory illness in young children (< 5 years old) and older adults (≥ 65 years old) leading the World Health Organization (WHO) to recommend the implementation of a dedicated surveillance in countries. AIM: We tested the capacity of the severe acute respiratory infection (SARI) hospital network to contribute to RSV surveillance in Belgium. METHODS: During the 2018/19 influenza season, we started the SARI surveillance for influenza in Belgium in week 40, earlier than in the past, to follow RSV activity, which usually precedes influenza virus circulation. While the WHO SARI case definition for influenza normally used by the SARI hospital network was employed, flexibility over the fever criterion was allowed, so patients without fever but meeting the other case definition criteria could be included in the surveillance. RESULTS: Between weeks 40 2018 and 2 2019, we received 508 samples from SARI patients. We found an overall RSV detection rate of 62.4% (317/508), with rates varying depending on the age group: 77.6% in children aged < 5 years (253/326) and 34.4% in adults aged ≥ 65 years (44/128). Over 90% of the RSV-positive samples also positive for another tested respiratory virus (80/85) were from children aged < 5 years. Differences were also noted between age groups for symptoms, comorbidities and complications. CONCLUSION: With only marginal modifications in the case definition and the period of surveillance, the Belgian SARI network would be able to substantially contribute to RSV surveillance and burden evaluation in children and older adults, the two groups of particular interest for WHO. url: https://www.ncbi.nlm.nih.gov/pubmed/33006303/ doi: 10.2807/1560-7917.es.2020.25.39.1900627 id: cord-256788-h4iv8crq author: Sumino, Kaharu title: Antiviral IFN-γ responses of monocytes at birth predict respiratory tract illness in the first year of life date: 2012-03-27 words: 5026.0 sentences: 238.0 pages: flesch: 47.0 cache: ./cache/cord-256788-h4iv8crq.txt txt: ./txt/cord-256788-h4iv8crq.txt summary: 9 In that regard a decrease in IFN-g production from cord blood mononuclear cells (CBMCs) stimulated by PHA or allergens has been associated with increased risk for acute respiratory tract illness during infancy. We assessed whether each of these immune end points could predict the development of respiratory tract illness during the first year of life in a prospective birth cohort of children at high risk for asthma and allergic disease. Together, these findings reinforce the association of a decreased IFN-g response to RSV with the development of increased viral respiratory tract infections in the first year of life. In this study we provide evidence that a decreased antiviral interferon response at the time of birth is selectively associated with an increase in acute respiratory tract infections in the first year of life among infants at high risk for asthma and allergic disease. abstract: BACKGROUND: Viral respiratory tract infections are the leading cause of acute illness during infancy and are closely linked to chronic inflammatory airway diseases later in life. However, the determinants of susceptibility to acute respiratory tract infections still need to be defined. OBJECTIVE: We investigated whether the individual variation in antiviral response at birth determines the risk for acute respiratory tract illness in the first year of life. METHODS: We studied 82 children who were enrolled in a birth cohort study of inner-city children with at least 1 parent with allergy or asthma. We cultured cord blood monocytes and assessed IFNG and CCL5 mRNA production at 24 hours after inoculation with respiratory syncytial virus. We also monitored the frequency of acute respiratory tract illness at 3-month intervals and analyzed nasal lavage samples for respiratory tract viruses at the time of illness during the first year. RESULTS: Respiratory tract infection was reported for 88% of subjects, and respiratory tract viruses were recovered in 74% of symptomatic children. We observed a wide range of antiviral responses in cord blood monocytes across the population. Furthermore, a decrease in production of IFNG (but not CCL5) mRNA in response to respiratory syncytial virus infection of monocytes was associated with a significant increase in the frequency of upper respiratory tract infections (r = −0.42, P < .001) and the prevalence of ear and sinus infections, pneumonias, and respiratory-related hospitalizations. CONCLUSION: Individual variations in the innate immune response to respiratory tract viruses are detectable even at birth, and these differences predict the susceptibility to acute respiratory tract illness during the first year of life. url: https://www.ncbi.nlm.nih.gov/pubmed/22460071/ doi: 10.1016/j.jaci.2012.02.033 id: cord-308979-qhlvd2mt author: Sumino, Kaharu C. title: Detection of Severe Human Metapneumovirus Infection by Real-Time Polymerase Chain Reaction and Histopathological Assessment date: 2005-09-15 words: 4296.0 sentences: 191.0 pages: flesch: 40.0 cache: ./cache/cord-308979-qhlvd2mt.txt txt: ./txt/cord-308979-qhlvd2mt.txt summary: BackgroundInfections with common respiratory tract viruses can cause high mortality, especially in immunocompromised hosts, but the impact of human metapneumovirus (hMPV) in this setting was previously unknown MethodsWe evaluated consecutive bronchoalveolar lavage and bronchial wash fluid samples from 688 patients—72% were immunocompromised and were predominantly lung transplant recipients—for hMPV by use of quantitative real-time polymerase chain reaction (PCR), and positive results were correlated with clinical outcome and results of viral cultures, in situ hybridization, and lung histopathological assessment ResultsSix cases of hMPV infection were identified, and they had a similar frequency and occurred in a similar age range as other paramyxoviral infections. Each patient with high titers of hMPV exhibited a complicated clinical course requiring prolonged hospitalization ConclusionsOur results provide in situ evidence of hMPV infection in humans and suggest that hMPV is a cause of clinically severe lower respiratory tract infection that can be detected during bronchoscopy by use of real-time PCR and routine histopathological assessment abstract: BackgroundInfections with common respiratory tract viruses can cause high mortality, especially in immunocompromised hosts, but the impact of human metapneumovirus (hMPV) in this setting was previously unknown MethodsWe evaluated consecutive bronchoalveolar lavage and bronchial wash fluid samples from 688 patients—72% were immunocompromised and were predominantly lung transplant recipients—for hMPV by use of quantitative real-time polymerase chain reaction (PCR), and positive results were correlated with clinical outcome and results of viral cultures, in situ hybridization, and lung histopathological assessment ResultsSix cases of hMPV infection were identified, and they had a similar frequency and occurred in a similar age range as other paramyxoviral infections. Four of 6 infections occurred in immunocompromised patients. Infection was confirmed by in situ hybridization for the viral nucleocapsid gene. Histopathological assessment of lung tissue samples showed acute and organizing injury, and smudge cell formation was distinct from findings in infections with other paramyxoviruses. Each patient with high titers of hMPV exhibited a complicated clinical course requiring prolonged hospitalization ConclusionsOur results provide in situ evidence of hMPV infection in humans and suggest that hMPV is a cause of clinically severe lower respiratory tract infection that can be detected during bronchoscopy by use of real-time PCR and routine histopathological assessment url: https://www.ncbi.nlm.nih.gov/pubmed/16107959/ doi: 10.1086/432728 id: cord-017107-sg8n12hs author: Suri, H. S. title: Epidemiology of Acute Respiratory Failure and Mechanical Ventilation date: 2008 words: 4109.0 sentences: 210.0 pages: flesch: 39.0 cache: ./cache/cord-017107-sg8n12hs.txt txt: ./txt/cord-017107-sg8n12hs.txt summary: A recently completed, retrospective, community cohort study in Olmsted County, Minnesota included patients treated with NIV and found an even higher incidence of ALI, 156 per 100,000 person-years (personal communication, Rodrigo Cartin -Ceba), Mortality from ALI varies greatly depending upon the age of the patient, underlying chronic illnesses, ALI risk factors, and non-pulmonary organ dysfunctions [15] . In an international cohort study [4] , acute exacerbation of COPD was a principal indication for initiating mechanical ventilation in 13 % of patients with acute respiratory failure. The majority of patients with interstitial lung disease and acute respiratory failure admitted to the ICU require invasive mechanical ventilation . In a retrospective review [39] of 75 patients with interstitial lung disease who were mechanically ventilated at Mayo Clinic from 2003 to 2005, acute respiratory failure was the most common cause of ICU admiss ion (77 %), followed by sepsis (11 %) and cardiopulmonary arrest (4 %). abstract: Acute respiratory failure, and the need for mechanical ventilation, remains one of the most common reasons for admission to the intensive care unit (ICU). The burden of acute respiratory failure is high in terms of mortality and morbidity as well as the cost of its principal treatment, mechanical ventilation. Very few epidemiologic studies have evaluated the prevalence and outcome of acute respiratory failure and mechanical ventilation in general. Most of the published literature has focused on specific forms of acute respiratory failure, particularly acute lung injury (ALI) and acute respiratory distress syndrome (ARDS). In this chapter, we provide a brief review of the pathophysiology of acute respiratory failure, its definition and classification, and then present the incidence and outcomes of specific forms of acute respiratory failure from epidemiologic studies. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121586/ doi: 10.1007/978-0-387-77383-4_18 id: cord-273620-gn8g6suq author: Szczawinska‐Poplonyk, Aleksandra title: Fatal respiratory distress syndrome due to coronavirus infection in a child with severe combined immunodeficiency date: 2012-11-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Please cite this paper as: Szczawinska‐Poplonyk et al. (2012) Fatal respiratory distress syndrome due to coronavirus infection in a child with severe combined immunodeficiency. Influenza and Other Respiratory Viruses DOI: 10.1111/irv.12059. Coronaviruses have been demonstrated to contribute substantially to respiratory tract infections among the child population. Though infected children commonly present mild upper airway symptoms, in high‐risk patients with underlying conditions, particularly in immunocompromised children these pathogens may lead to severe lung infection and extrapulmonary disorders. In this paper, we provide the first report of the case of a 15‐month‐old child with severe combined immunodeficiency and coronavirus HKU1‐related pneumonia with fatal respiratory distress syndrome. url: https://www.ncbi.nlm.nih.gov/pubmed/23199056/ doi: 10.1111/irv.12059 id: cord-336420-1a2u9p4t author: Söderman, Martina title: Frequent Respiratory Viral Infections in Children with Febrile Neutropenia - A Prospective Follow-Up Study date: 2016-06-16 words: 4200.0 sentences: 208.0 pages: flesch: 46.0 cache: ./cache/cord-336420-1a2u9p4t.txt txt: ./txt/cord-336420-1a2u9p4t.txt summary: title: Frequent Respiratory Viral Infections in Children with Febrile Neutropenia A Prospective Follow-Up Study Advances in molecular methods have increased the sensitivity of viral diagnostics tests, with recent studies reporting the detection of respiratory viruses in the nasopharynx in 44-57% of childhood febrile neutropenia episodes using real-time polymerase chain reaction (PCR) [3] [4] [5] 12] . Viral nucleic acids were extracted from the NPA with a MagAttract Virus Mini M48 kit (Qiagen, Sollentuna, Sweden) and analyzed with in-house real-time PCRs for the following 16 viruses: adenovirus (HAdV); bocavirus (HBoV); coronaviruses NL63/OC43/229E/HKU1 (HCoV); enterovirus (EV); influenza virus A, including A(H1N1)pdm09 and B (Flu); metapneumovirus (HMPV); parainfluenza viruses 1-3 (PIV); respiratory syncytial virus (RSV) and rhinovirus (RV) [19] . These results support the theory holding that there is a causal relationship between respiratory viral infections and episodes of febrile neutropenia, but proving this theory will require more longitudinal studies with asymptomatic neutropenic control cohorts. abstract: OBJECTIVE: Febrile neutropenia is common in children undergoing chemotherapy for the treatment of malignancies. In the majority of cases, the cause of the fever is unknown. Although respiratory viruses are commonly associated with this condition, the etiologic significance of this finding remains unclear and is therefore the subject of this study. STUDY DESIGN: Nasopharyngeal aspirates were collected during 87 episodes of febrile neutropenia in children age 0–18 years, being treated at a children’s oncology unit between January 2013 and June 2014. Real-time polymerase chain reaction was used to determine the presence of 16 respiratory viruses. Follow-up samples were collected from children who tested positive for one or more respiratory viruses. Rhinoviruses were genotyped by VP4/VP2 sequencing. Fisher’s exact test and Mann-Whitney U test were used for group comparisons. RESULTS: At least one respiratory virus was detected in samples from 39 of 87 episodes of febrile neutropenia (45%), with rhinoviruses the most frequently detected. Follow-up samples were collected after a median of 28 days (range, 9–74 days) in 32 of the 39 virus-positive episodes. The respiratory viral infection had resolved in 25 episodes (78%). The same virus was detected at follow-up in one coronavirus and six rhinovirus episodes. Genotyping revealed a different rhinovirus species in two of the six rhinovirus infections. CONCLUSION: The frequency of respiratory viral infections in this group of patients suggests an etiologic role in febrile neutropenia. However, these findings must be confirmed in larger patient cohorts. url: https://doi.org/10.1371/journal.pone.0157398 doi: 10.1371/journal.pone.0157398 id: cord-312024-qdgqif5j author: Talbot, H. Keipp title: The Diagnosis of Viral Respiratory Disease in Older Adults date: 2010-02-01 words: 3423.0 sentences: 175.0 pages: flesch: 39.0 cache: ./cache/cord-312024-qdgqif5j.txt txt: ./txt/cord-312024-qdgqif5j.txt summary: The increasing availability of new rapid and sensitive molecular diagnostics such as polymerase chain reaction testing, should provide more accurate and timely diagnoses of viral respiratory infections in older adults in the near future. This article summarizes what is known about the diagnosis of viral respiratory diseases in elderly adults, with the hope of increasing understanding of the utility and limitations of the currently available diagnostic tests for viral respiratory pathogens, such as culture, rapid antigen testing, polymerase chain reaction (PCR) testing, and serologic analysis. Compared with previous studies that have used viral culture for diagnosis, studies using PCR have more accurately detected the presence of viruses (including influenza virus, RSV, hMPV, parainfluenza virus, rhinoviruses, and coronaviruses) in the lower respiratory tract illness in older adults [5, 13, 31, 36, 40, 42] . abstract: Viral respiratory disease in older adults has been increasingly recognized as a significant cause of hospitalizations and death. Unfortunately, the recognition and diagnosis of infection due to many viral respiratory pathogens in older adults can be elusive due to atypical clinical presentations and the insensitivity of current laboratory diagnostic tests in this population. For influenza diagnosis, rapid antigen tests followed by viral culture if negative, can be useful in older adults as long as clinicians are mindful of test limitations. Although specific, rapid antigen tests are insensitive in this population. Erroneous negative results may lead to delays in timely administration of antiviral treatment and institution of appropriate isolation precautions. The increasing availability of new rapid and sensitive molecular diagnostics such as polymerase chain reaction testing, should provide more accurate and timely diagnoses of viral respiratory infections in older adults in the near future. url: https://www.ncbi.nlm.nih.gov/pubmed/20121411/ doi: 10.1086/650486 id: cord-294062-3esrg1jw author: Tam, Clarence C. title: Association between semi-quantitative microbial load and respiratory symptoms among Thai military recruits: a prospective cohort study date: 2018-09-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Multiplex real-time polymerase chain reaction assays have improved diagnostic sensitivity for a wide range of pathogens. However, co-detection of multiple agents and bacterial colonization make it difficult to distinguish between asymptomatic infection or illness aetiology. We assessed whether semi-quantitative microbial load data can differentiate between symptomatic and asymptomatic states for common respiratory pathogens. METHODS: We obtained throat and nasal swab samples from military trainees at two Thai Army barracks. Specimens were collected at the start and end of 10-week training periods (non-acute samples), and from individuals who developed upper respiratory tract infection during training (acute samples). We analysed the samples using a commercial multiplex respiratory panel comprising 33 bacterial, viral and fungal targets. We used random effects tobit models to compare cycle threshold (Ct) value distributions from non-acute and acute samples. RESULTS: We analysed 341 non-acute and 145 acute swab samples from 274 participants. Haemophilus influenzae type B was the most commonly detected microbe (77.4% of non-acute and 64.8% of acute samples). In acute samples, nine specific microbe pairs were detected more frequently than expected by chance. Regression models indicated significantly lower microbial load in non-acute relative to acute samples for H. influenzae non-type B, Streptococcus pneumoniae and rhinovirus, although it was not possible to identify a Ct-value threshold indicating causal etiology for any of these organisms. CONCLUSIONS: Semi-quantitative measures of microbial concentration did not reliably differentiate between illness and asymptomatic colonization, suggesting that clinical symptoms may not always be directly related to microbial load for common respiratory infections. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-018-3358-4) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12879-018-3358-4 doi: 10.1186/s12879-018-3358-4 id: cord-352684-4o623x3n author: Tan, M. Y. title: Bocavirus infection following paediatric liver transplantation date: 2016-10-23 words: 1628.0 sentences: 109.0 pages: flesch: 50.0 cache: ./cache/cord-352684-4o623x3n.txt txt: ./txt/cord-352684-4o623x3n.txt summary: We report HBoV infection in a child post‐liver transplantation, who presented with persistent fever and mild tachypnea, 3 weeks after a successful transplant. She had episodes of prolonged fever even after her collections were drained, and a respiratory multiplex (PCR-based test) to look for viruses, from nasopharyngeal aspirates, was negative (3 weeks prior to transplant). 4 However, in recent years, it has been emerged that HBoV alone is pathogenic and can cause disease in immunocompetent children, most commonly presenting with respiratory symptoms, such as wheeze and bronchiolitis. 8 There are a few reports of HBoV infections in immunocompromised hosts wherein they have caused respiratory or diarrhoeal illness, and rarely even life-threatening conditions in the stem cell transplant population. 9 HBoV has also been shown to cause disseminated illness in a child, post-stem cell transplant. 11 There are no reports of HBoV-associated respiratory infections in children after liver transplantation. abstract: HBoV is an emergent virus, which is frequently detected as a co‐infective agent. However, it can cause disease on its own. It is associated with respiratory and diarrhoeal illness in children and adults, whether immunocompetent or immunocompromised. We report HBoV infection in a child post‐liver transplantation, who presented with persistent fever and mild tachypnea, 3 weeks after a successful transplant. She recovered spontaneously with no graft dysfunction. url: https://www.ncbi.nlm.nih.gov/pubmed/27774707/ doi: 10.1111/petr.12840 id: cord-274900-s7ft1491 author: Tatarelli, P. title: Prevalence and clinical impact of VIral Respiratory tract infections in patients hospitalized for Community-Acquired Pneumonia: the VIRCAP study date: 2019-11-30 words: 3812.0 sentences: 199.0 pages: flesch: 39.0 cache: ./cache/cord-274900-s7ft1491.txt txt: ./txt/cord-274900-s7ft1491.txt summary: title: Prevalence and clinical impact of VIral Respiratory tract infections in patients hospitalized for Community-Acquired Pneumonia: the VIRCAP study Whilst epidemiology and clinical features of viral respiratory tract infections (VRTIs) were mainly explored in children and outpatients [7, 8] , a few data show increasing prevalence rates also in hospitalized patients, particularly in elderly and in presence of comorbidities such as asthma, chronic obstructive pulmonary disease or immunosuppression [9] [10] [11] . CAP was defined as acute lower respiratory tract infection characterized by the presence of two or more signs and symptoms (among fever, cough, dyspnoea, pleuritic pain, crackles or bronchial breath at pulmonary auscultation), associated with at least one among (a) radiological findings (opacity or infiltrate at radiography or computed tomography interpreted as pneumonia by the attending physician), (b) serum levels of inflammatory markers above normal values and (c) neutrophilic leucocytosis, in patients hospitalized no longer than 48 h [1] . abstract: Prevalence and clinical impact of viral respiratory tract infections (VRTIs) on community-acquired pneumonia (CAP) has not been well defined so far. The aims of this study were to investigate the prevalence and the clinical impact of VRTIs in patients with CAP. Prospective study involving adult patients consecutively admitted at medical wards for CAP and tested for VRTIs by real-time PCR on pharyngeal swab. Patients’ features were evaluated with regard to the presence of VRTI and aetiology of CAP. Clinical failure was a composite endpoint defined by worsening of signs and symptoms requiring escalation of antibiotic treatment or ICU admission or death within 30 days. 91 patients were enrolled, mean age 65.7 ± 10.6 years, 50.5% female. 62 patients (68.2%) had no viral co-infection while in 29 patients (31.8%) a VRTI was detected; influenza virus was the most frequently identified (41.9%). The two groups were similar in terms of baseline features. In presence of a VRTI, pneumonia severity index (PSI) was more frequently higher than 91 and patients had received less frequently pre-admission antibiotic therapy (adjusted OR 2.689, 95% CI 1.017–7.111, p = 0.046; adjusted OR 0.143, 95% CI 0.030–0.670, p = 0.014). Clinical failure and antibiotic therapy duration were similar with regards to the presence of VRTI and the aetiology of CAP. VRTIs can be detected in almost a third of adults with CAP; influenza virus is the most relevant one. VRTI was associated with higher PSI at admission, but it does not affect patients’ outcome. url: https://doi.org/10.1007/s11739-019-02243-9 doi: 10.1007/s11739-019-02243-9 id: cord-254766-585iu5ey author: Tauro, Sharyn title: Molecular and cellular mechanisms in the viral exacerbation of asthma date: 2008-08-13 words: 5251.0 sentences: 246.0 pages: flesch: 39.0 cache: ./cache/cord-254766-585iu5ey.txt txt: ./txt/cord-254766-585iu5ey.txt summary: This review summarizes the evidence associated with factors that may contribute to the development or exacerbation of asthma including age, host factors, genetic polymorphisms, altered immune responses, and aspects of viral antigen expression. These observations suggest that respiratory viral infections lead to a prolonged period of increased antigen presentation in the airways resulting in de novo and memory T-cell responses not only to the virus but also to unrelated antigens including allergens. In addition to studies of primary infections, models studying the interactions between respiratory viral infections and allergen sensitization are essential in understanding the mechanisms of virus induced asthma exacerbations. These studies show that the immune responses to allergen sensitization and respiratory viral infections interact to cause persistent inflammation and AHR, symptomatic of the asthmatic response (Fig. 2) [53] . Recurrent respiratory syncytial virus infections in allergen sensitized mice lead to persistent airway inflammation and hyperresponsiveness abstract: The aetiology of asthma associated with viral infection is complex. The dynamics that contribute to disease pathogenesis are multifactorial and involve overlapping molecular and cellular mechanisms, particularly the immune response to respiratory virus infection or allergen sensitization. This review summarizes the evidence associated with factors that may contribute to the development or exacerbation of asthma including age, host factors, genetic polymorphisms, altered immune responses, and aspects of viral antigen expression. This review also provides an important perspective of key events linked to the development of asthmatic disease and related pulmonary inflammation from human and animal studies, and discusses their relationship as targets for disease intervention strategies. url: https://www.sciencedirect.com/science/article/pii/S128645790800186X doi: 10.1016/j.micinf.2008.07.037 id: cord-255734-038xu4hq author: Taylor, Deborah R. title: Obstacles and advances in SARS vaccine development date: 2006-02-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The emergence of the severe acute respiratory syndrome (SARS) that resulted in a pandemic in 2003 spurred a flurry of interest in the development of vaccines to prevent and treat the potentially deadly viral infection. Researchers around the world pooled their scientific resources and shared early data in an unprecedented manner in light of the impending public health crisis. There are still large gaps in knowledge about the pathogenesis of this virus. While significant advances have been made in the development of animal models, the practicality of their use may be hampered by a lack of pathological similarity with human disease. Described here are issues related to progress in vaccine development and the obstacles that lie ahead for both researchers and regulatory agencies. url: https://www.ncbi.nlm.nih.gov/pubmed/16191455/ doi: 10.1016/j.vaccine.2005.08.102 id: cord-294155-94skyx5f author: Terrosi, Chiara title: Human bocavirus detection in an atopic child affected by pneumonia associated with wheezing date: 2007-08-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Human bocavirus (HBoV) is a newly discovered human parvovirus. HBoV was detected in respiratory samples by PCR, but its aetiologic role in the pathogenesis of acute respiratory infectious diseases is still unclear. RESULTS: In this report, we describe an atopic child affected by pneumonia, with a past history of wheezing. A panel of bacteria and respiratory viruses were searched in the nasopharyngeal swab, only human bocavirus was detected by PCR. CONCLUSIONS: Detection of HboV, as the only microbial agent, in samples from children with wheezing and acute respiratory diseases supports the assumption that this emerging virus could have an aetiologic role in the pathogenesis of respiratory diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/17686654/ doi: 10.1016/j.jcv.2007.06.011 id: cord-339852-9rq7zzqs author: Theamboonlers, Apiradee title: Human Coronavirus Infection among Children with Acute Lower Respiratory Tract Infection in Thailand date: 2006-11-30 words: 2949.0 sentences: 169.0 pages: flesch: 50.0 cache: ./cache/cord-339852-9rq7zzqs.txt txt: ./txt/cord-339852-9rq7zzqs.txt summary: In addition, we performed this study in order to delineate the prevalence, the potential clinical impacts and evaluation of the genetic characterization of this pathogen in young children who presented with acute lower respiratory tract infections (ALRI). In this study we applied molecular biology techniques to identify hCoV in nasopharyngeal secretions (NPs) for the study on the prevalence of molecular characterization and clinical correlation of coronavirus infections in hospitalized infants and young children with acute lower respiratory tract infection (ALRI). In this study, we have identifi ed human coronavirus hCoV-OC43 and hCoV-229E infection in infants and young children presenting with ALRI. hCoV-229E and hCoV-OC43 have previously been proven responsible for infecting people of all age groups and causing severe lower respiratory tract infection primarily in frail patients such as young children and elderly individuals [17] [18] [19] . The clinical features associated with coronavirus infection appear to be similar to those observed with other respiratory viruses, such as RSV, parainfl uenza virus and human metapneumovirus. abstract: OBJECTIVE: This study was performed to further identify the previously uncharacterized human coronavirus 229E (hCoV-229E) and human coronavirus OC43 (hCoV-OC43) in Thailand by using the RT-PCR technique. In addition, we performed this study in order to delineate the prevalence, the potential clinical impacts and evaluation of the genetic characterization of this pathogen in young children who presented with acute lower respiratory tract infections (ALRI). METHODS: We obtained nasopharyngeal secretions (NPs) from 226 children <5 years of age who were either attending the outpatient department or hospitalized with ALRI from March 2002 to July 2003. All clinical, laboratory, RT-PCR, direct sequencing and phylogenetic analysis data were collected and analyzed. RESULTS: Of the 226 NPs samples from infants and young children presented with ALRI, 8 (3.54%) were positive for hCoV-229E, 2 (0.88%) were positive for hCoV-OC43, and 1 (0.44%) had co-infection. The following clinical presentations were noted: fever (100%), rhinitis (44%), acute bronchiolitis (44%), viral pneumonia (33%), viral pneumonia triggering asthma exacerbation (11%) as well as viral pneumonia causing BPD exacerbation (11%). All positive samples were subjected to direct sequencing. The amino acid sequences had 82-99% similarity to previous sequences stored in the GenBank database. CONCLUSION: The molecular technique we applied to detect human coronavirus appears justified as a valuable diagnostic approach to elucidate the prevalence, cause and clinical implications of ALRI among infants and young children. url: https://www.ncbi.nlm.nih.gov/pubmed/17139182/ doi: 10.1159/000097392 id: cord-284889-hth8nf5b author: Tsukagoshi, Hiroyuki title: Molecular epidemiology of respiratory viruses in virus-induced asthma date: 2013-09-12 words: 6955.0 sentences: 353.0 pages: flesch: 43.0 cache: ./cache/cord-284889-hth8nf5b.txt txt: ./txt/cord-284889-hth8nf5b.txt summary: Previous studies have shown that respiratory syncytial virus (RSV), human rhinovirus (HRV), human metapneumovirus (HMPV), human parainfluenza virus (HPIV), and human enterovirus infections may be associated with virus-induced asthma. Therefore, in this article, we review molecular epidemiological studies of RSV, HRV, HPIV, and HMPV infection associated with virus-induced asthma. More than 200 different types of viruses are known to cause ARI, with respiratory syncytial virus (RSV), human rhinovirus (HRV), human metapneumovirus (HMPV), and human parainfluenza virus (HPIV) most commonly identified in ARI patients. In this review, we focus on molecular epidemiological studies of respiratory viruses, including RSV, HRV, HMPV, and HPIV infections, associated with virus-induced asthma. Thus, both the antigenicity of the viruses and host immune conditions may play important roles in the pathophysiology of severe respiratory infections such as bronchiolitis, pneumonia, and virus-induced asthma (Awomoyi et al., 2007) . abstract: Acute respiratory illness (ARI) due to various viruses is not only the most common cause of upper respiratory infection in humans but is also a major cause of morbidity and mortality, leading to diseases such as bronchiolitis and pneumonia. Previous studies have shown that respiratory syncytial virus (RSV), human rhinovirus (HRV), human metapneumovirus (HMPV), human parainfluenza virus (HPIV), and human enterovirus infections may be associated with virus-induced asthma. For example, it has been suggested that HRV infection is detected in the acute exacerbation of asthma and infection is prolonged. Thus it is believed that the main etiological cause of asthma is ARI viruses. Furthermore, the number of asthma patients in most industrial countries has greatly increased, resulting in a morbidity rate of around 10-15% of the population. However, the relationships between viral infections, host immune response, and host factors in the pathophysiology of asthma remain unclear. To gain a better understanding of the epidemiology of virus-induced asthma, it is important to assess both the characteristics of the viruses and the host defense mechanisms. Molecular epidemiology enables us to understand the pathogenesis of microorganisms by identifying specific pathways, molecules, and genes that influence the risk of developing a disease. However, the epidemiology of various respiratory viruses associated with virus-induced asthma is not fully understood. Therefore, in this article, we review molecular epidemiological studies of RSV, HRV, HPIV, and HMPV infection associated with virus-induced asthma. url: https://doi.org/10.3389/fmicb.2013.00278 doi: 10.3389/fmicb.2013.00278 id: cord-007445-2folsh35 author: Tuffaha, Amjad title: THE ROLE OF RESPIRATORY VIRUSES IN ACUTE AND CHRONIC ASTHMA date: 2000-06-01 words: 4973.0 sentences: 217.0 pages: flesch: 34.0 cache: ./cache/cord-007445-2folsh35.txt txt: ./txt/cord-007445-2folsh35.txt summary: To more comprehensively evaluate the relationships among virus infection, atopy (cytokine dysregulation of Thl / Th2 imbalance), and immune system or lung developmental components, a rat model of virus-induced airway dysfunction has been studied extensively.''l'' In this model, infection with PIV type 1 during a critical developmental time period (when the animals are weaning [ 3 4 weeks of age] as opposed to when they are neonates [4-5 days] or adults) produces chronic (8-12 weeks fol-lowing infection), episodic, reversible airway inflammation and remodeling with associated alterations in airway physiology (increased resistance and rnethacholine responsiveness) that resemble human asthma in high (brown Norway strain) but not low (F344 strain) IgEantibody producing rats.62 The temporal progression of this asthma-like syndrome is associated with a Thl / Th2 imbalance within the lung, and its development can be significantly attenuated by the exogenous administration of IFN-8 just prior to and during the viral infection in the brown Norway responder strain.lo2 This model further supports the concept of both genetic (atopy; cytokine dysregulation or imbalance) and environmental factors (virus infection) being important in the inception of the asthmatic phenotype, as well as a developmental component contributing. abstract: Respiratory tract infections caused by viruses, 24, 70 chlamydia, 18, 19, 43, 55, 116 and mycoplasma(61) have been implicated in the pathogenesis of asthma. Viruses have been demonstrated to be associated with asthma epidemiologically in at least two ways (Fig. 1). First, during infancy, certain viruses have been implicated as potentially being responsible for the inception of the asthmatic phenotype. Second, in patients, particularly children, with established asthma, viral upper respiratory tract infections play a significant role in producing acute exacerbations of airway obstruction that may result in frequent outpatient visits or hospitalizations. 24, 55, 56, 57 This article reviews these two areas by focusing first on mechanisms by which virus infections may lead to the development of asthma in infants and children and, second, on mechanisms by which virus infections may produce acute asthmatic symptoms in patients who already have established disease. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7115729/ doi: 10.1016/s0272-5231(05)70267-7 id: cord-325635-don9qjpz author: Turner, Paul title: Respiratory virus surveillance in hospitalised pneumonia patients on the Thailand-Myanmar border date: 2013-09-16 words: 4302.0 sentences: 236.0 pages: flesch: 47.0 cache: ./cache/cord-325635-don9qjpz.txt txt: ./txt/cord-325635-don9qjpz.txt summary: Using global population data for 2005, for children under the age of five years, it was estimated that RSV was responsible for over 30 million episodes of lower respiratory tract infections (LRTI), with~3 million of these requiring hospital admission, and 66,000-199,000 deaths [7] . In 2007, the US Centers for Disease Control and Prevention (CDC) and the Shoklo Malaria Research Unit (SMRU) established a respiratory virus surveillance programme in the Burmese refugee population living in Maela camp, Northwest Thailand. Laboratory-enhanced surveillance has documented the contribution of respiratory viruses to 708 hospitalised clinical pneumonia episodes occurring in a crowded refugee camp on the Thailand-Myanmar border during April 2009 to September 2011. The results are broadly consistent with a similar surveillance programme conducted in two Kenyan refugee camps [22] , where 51.3% patients with severe acute respiratory infection (SARI) had at least one of adenovirus, hMPV, influenza A/B, parainfluenza virus 1-3, or RSV detected. abstract: BACKGROUND: Pneumonia is a significant cause of morbidity and mortality in the developing world. Viruses contribute significantly to pneumonia burden, although data for low-income and tropical countries are scarce. The aim of this laboratory-enhanced, hospital-based surveillance was to characterise the epidemiology of respiratory virus infections among refugees living on the Thailand-Myanmar border. METHODS: Maela camp provides shelter for ~45,000 refugees. Inside the camp, a humanitarian organisation provides free hospital care in a 158-bed inpatient department (IPD). Between 1st April 2009 and 30th September 2011, all patients admitted to the IPD with a clinical diagnosis of pneumonia were invited to participate. Clinical symptoms and signs were recorded and a nasopharyngeal aspirate (NPA) collected. NPAs were tested for adenoviruses, human metapneumovirus (hMPV), influenza A & B, and RSV by PCR. RESULTS: Seven hundred eight patient episodes (698 patients) diagnosed as pneumonia during the enhanced surveillance period were included in this analysis. The median patient age was 1 year (range: < 1-70), and 90.4% were aged < 5 years. At least one virus was detected in 53.7% (380/708) of episodes. Virus detection was more common in children aged < 5 years old (<1 year: OR 2.0, 95% CI 1.2-3.4, p = 0.01; 1-4 years: OR 1.4, 95% CI 0.8-2.3, p = 0.2). RSV was detected in 176/708 (24.9%); an adenovirus in 133/708 (18.8%); an influenza virus in 68/708 (9.6%); and hMPV in 33/708 (4.7%). Twenty-eight episodes of multiple viral infections were identified, most commonly adenovirus plus another virus. RSV was more likely to be detected in children <5 years (OR 12.3, 95% CI 3.0-50.8, p = 0.001) and influenza viruses in patients ≥5 years (OR 2.8, 95% CI 1.5-5.4, p = 0.002). IPD treatment was documented in 702/708 cases; all but one patient received antimicrobials, most commonly a beta-lactam (amoxicillin/ampicillin +/−gentamicin in 664/701, 94.7%). CONCLUSIONS: Viral nucleic acid was identified in the nasopharynx in half the patients admitted with clinically diagnosed pneumonia. Development of immunisations targeting common respiratory viruses is likely to reduce the incidence of pneumonia in children living refugee camps and similar settings. url: https://doi.org/10.1186/1471-2334-13-434 doi: 10.1186/1471-2334-13-434 id: cord-254770-ot9ys10r author: Uçkay, Ilker title: Low incidence of severe respiratory syncytial virus infections in lung transplant recipients despite the absence of specific therapy date: 2009-10-17 words: 2666.0 sentences: 165.0 pages: flesch: 40.0 cache: ./cache/cord-254770-ot9ys10r.txt txt: ./txt/cord-254770-ot9ys10r.txt summary: 20 In Switzerland, pre-emptive therapy in cases of low-grade immunosuppression, prophylaxis in severe immunosuppression, and combined treatment with immunoglobulin (Ig), ribavirin, and palivizumab in cases of proven infection have been suggested for both BMT recipients and LTRs. 20 To get a better overview on the clinical evolution of RSV infections in LTRs we retrospectively searched our virology reports and identified 10 adult LTRs with proven lower respiratory tract RSV infection. Two patients were treated with ribavirin for 7 days (orally with 1,600 mg/day or intravenously with 10 mg/kg 3 times daily) concomitant with intravenous palivizumab (a single dose of 15 mg/kg) ( Table 1) , including Patient 3, who required anti-thymocyte globulins for non-responding conThe detection of RSV by PCR in respiratory secretions is highly sensitive and specific, 24 and is currently considered the best available test for the diagnosis of respiratory tract infections in adult lung transplant recipients. abstract: BACKGROUND: Respiratory syncytial virus (RSV) infections in lung transplant recipients (LTRs) have been associated with significant morbidity and mortality. Immunoglobulins, ribavirin, and palivizumab are suggested treatments for both pre-emptive and therapeutic purposes. However, in the absence of randomized, placebo-controlled trials, efficacy is controversial and there is toxicity as well as cost concerns. METHODS: We retrospectively reviewed cases of lower respiratory tract RSV infections in adult LTRs. Diagnosis was based on clinical history, combined with a positive polymerase chain reaction (PCR) and/or viral cultures of bronchoalveolar lavage (BAL) specimens. RESULTS: Ten symptomatic patients were identified (7 men and 3 women, age range 28 to 64 years). All were hospitalized for community-acquired respiratory tract infections. Two patients had a concomitant acute Grade A3 graft rejection, and 1 patient had a concomitant bacterial pneumonia. Eight patients did not receive a specific anti-RSV treatment because of clinical stability and/or improvement at the time of RSV diagnosis. Only 2 patients (1 with Grade A3 allograft rejection and 1 requiring mechanical ventilation) received ribavirin and palivizumab. All patients recovered without complications and with no persistent RSV infection. However, bronchiolitis obliterans (BOS) staging worsened in 6 patients during the mean follow-up of 45 months. CONCLUSIONS: Our data suggest that mild RSV infections in LTRs might evolve favorably in the absence of specific anti-viral therapy. However, this observation needs confirmation in a large clinical trial specifically investigating the development of BOS in untreated vs treated patients. url: https://doi.org/10.1016/j.healun.2009.08.012 doi: 10.1016/j.healun.2009.08.012 id: cord-271822-ohkki0ke author: Verma, Siddhartha title: Visualizing the effectiveness of face masks in obstructing respiratory jets date: 2020-06-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The use of face masks in public settings has been widely recommended by public health officials during the current COVID-19 pandemic. The masks help mitigate the risk of cross-infection via respiratory droplets; however, there are no specific guidelines on mask materials and designs that are most effective in minimizing droplet dispersal. While there have been prior studies on the performance of medical-grade masks, there are insufficient data on cloth-based coverings, which are being used by a vast majority of the general public. We use qualitative visualizations of emulated coughs and sneezes to examine how material- and design-choices impact the extent to which droplet-laden respiratory jets are blocked. Loosely folded face masks and bandana-style coverings provide minimal stopping-capability for the smallest aerosolized respiratory droplets. Well-fitted homemade masks with multiple layers of quilting fabric, and off-the-shelf cone style masks, proved to be the most effective in reducing droplet dispersal. These masks were able to curtail the speed and range of the respiratory jets significantly, albeit with some leakage through the mask material and from small gaps along the edges. Importantly, uncovered emulated coughs were able to travel notably farther than the currently recommended 6-ft distancing guideline. We outline the procedure for setting up simple visualization experiments using easily available materials, which may help healthcare professionals, medical researchers, and manufacturers in assessing the effectiveness of face masks and other personal protective equipment qualitatively. url: https://doi.org/10.1063/5.0016018 doi: 10.1063/5.0016018 id: cord-322573-1fw1ehzd author: Vicente, Diego title: Human Bocavirus, a Respiratory and Enteric Virus date: 2007-04-17 words: 1296.0 sentences: 78.0 pages: flesch: 48.0 cache: ./cache/cord-322573-1fw1ehzd.txt txt: ./txt/cord-322573-1fw1ehzd.txt summary: To determine the prevalence and clinical characteristics of HBoV, we investigated the presence of this virus in children with respiratory tract infection in our region (Gipúzkoa, Basque Country, Spain). To rule out the possibility that this result could have been due to fecal contamination resulting from swallowing respiratory secretions, and to determine whether the gastrointestinal tract is affected by this new respiratory virus, we studied its presence in patient feces in 527 episodes of acute gastroenteritis, unrelated to respiratory infection, in children <3 years of age, mainly from nonhospital centers (ambulatory clinics). From a second group of 520 children <3 years of age who came to the pediatric emergency unit of our hospital with an episode of acute respiratory infection during the same period, a similar frequency of HBoV detection was obtained (40/520, 7.7%) when nasopharyngeal aspirates were tested. Detection of human bocavirus in Japanese children with lower respiratory tract infections abstract: In Spain, human bocavirus (HBoV) was detected in 48 (9.1%) of 527 children with gastroenteritis at similar frequency as for children with respiratory illness (40/520, 7.7%). Fecal excretion adds new concern about the transmission of HBoV. To our knowledge, this report is the first to document HBoV in human feces. url: https://www.ncbi.nlm.nih.gov/pubmed/17553287/ doi: 10.3201/eid1304.061501 id: cord-003798-nki2sasr author: Vidaur, Loreto title: Human metapneumovirus as cause of severe community-acquired pneumonia in adults: insights from a ten-year molecular and epidemiological analysis date: 2019-07-24 words: 3501.0 sentences: 195.0 pages: flesch: 41.0 cache: ./cache/cord-003798-nki2sasr.txt txt: ./txt/cord-003798-nki2sasr.txt summary: BACKGROUND: Information on the clinical, epidemiological and molecular characterization of human metapneumovirus in critically ill adult patients with severe community-acquired pneumonia (CAP) and the role of biomarkers identifying bacterial coinfection is scarce. METHODS: This is a retrospective epidemiological study of adult patients with hMPV severe CAP admitted to ICU during a ten-year period with admission PSI score ≥ 3. The main objective of this study was to describe the clinical and epidemiological characteristics of adults with severe pneumonia caused by hMPV who required intensive care unit (ICU) admission, over a long period of time. Interestingly, three patients (10.7%) were young adult patients without comorbidities and without bacterial coinfection that developed ARDS pointing out a main role of hMPV in the etiology of severe respiratory infections requiring mechanical ventilation. Main characteristics of immunosuppressed adult patients admitted to the Intensive Care Unit due to a severe community-acquired pneumonia associated with human metapneumovirus infection (Guipuzcoa, Basque Country, Spain, 2007-2017). abstract: BACKGROUND: Information on the clinical, epidemiological and molecular characterization of human metapneumovirus in critically ill adult patients with severe community-acquired pneumonia (CAP) and the role of biomarkers identifying bacterial coinfection is scarce. METHODS: This is a retrospective epidemiological study of adult patients with hMPV severe CAP admitted to ICU during a ten-year period with admission PSI score ≥ 3. RESULTS: The 92.8% of the 28 patients with severe CAP due to human metapneumovirus were detected during the first half of the year. Median age was 62 years and 60.7% were male. The genotyping of isolated human metapneumovirus showed group B predominance (60.7%). All patients had acute respiratory failure. Median APACHE II and SOFA score were 13 and 6.55, respectively. The 25% were coinfected with Streptococcus pneumoniae. 60.7% of the patients had shock at admission and 50% underwent mechanical ventilation. Seven patients developed ARDS, three of them younger than 60 years and without comorbidities. Mortality in ICU was 14.3%. Among survivors, ICU and hospital stay were 6.5 and 14 days, respectively. Plasma levels of procalcitonin were higher in patients with bacterial coinfection (18.2 vs 0.54; p < 0.05). The levels of C-reactive protein, however, were similar. CONCLUSION: Human metapneumovirus was associated with severe CAP requiring ICU admission among elderly patients or patients with comorbidities, but also in healthy young subjects. These patients often underwent mechanical ventilation with elevated health resource consumption. While one out of four patients showed pneumococcal coinfection, plasma procalcitonin helped to implement antimicrobial stewardship. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13613-019-0559-y) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6656825/ doi: 10.1186/s13613-019-0559-y id: cord-265354-ajfjrnr9 author: Vu, D.‐L. title: Respiratory Viruses in Lung Transplant Recipients: A Critical Review and Pooled Analysis of Clinical Studies date: 2011-04-26 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Lung transplant recipients present an increased risk for severe complications associated with respiratory infections. We conducted a review of the literature examining the clinical relationship between viral respiratory infection and graft complications. Thirty‐four studies describing the clinical impact of influenza, respiratory syncytial virus, parainfluenza, human metapneumovirus, rhinovirus, enterovirus, coronavirus, bocavirus or adenovirus were identified. The detection rate of respiratory viral infection ranged from 1.4% to 60%. Viruses were detected five times more frequently when respiratory symptoms were present [odds ratio (OR) = 4.97; 95% CI = 2.11–11.68]. Based on available observations, we could not observe an association between respiratory viral infection and acute rejection (OR = 1.35; 95% CI = 0.41–4.43). We found a pooled incidence of 18% (9/50) of bronchiolitis obliterans syndrome (BOS) in virus‐positive cases compared to 11.6% (37/319) in virus‐negative cases; however, limited number of BOS events did not allow to confirm the association. Our review confirms a causal relationship between respiratory viruses and respiratory symptoms, but cannot confirm a link between respiratory viruses and acute lung rejection. This is related in part to the heterogeneity and limitations of available studies. The link with BOS needs also to be reassessed in appropriate prospective studies. url: https://doi.org/10.1111/j.1600-6143.2011.03490.x doi: 10.1111/j.1600-6143.2011.03490.x id: cord-312952-9gbb4own author: WARDZYŃSKA, ALEKSANDRA title: The profile of respiratory pathogens in induced sputum of elderly and non-elderly asthmatics date: 2020-01-20 words: 2990.0 sentences: 167.0 pages: flesch: 47.0 cache: ./cache/cord-312952-9gbb4own.txt txt: ./txt/cord-312952-9gbb4own.txt summary: While the majority of studies indicate that the detection rate of respiratory viruses in patients with asthma and healthy subjects is similar [10] , they have been found to differ with regard to the bacterial composition of the airways [11] . This technique was chosen for the present study, to test the hypothesis that elderly patients with asthma display a different profile of respiratory pathogens in the airways as compared to non-elderly asthmatics, and that this profile may be related to local airway and/or systemic inflammation. This study is the first to use the IS technique to compare detection rates of respiratory pathogens in the airways of elderly and non-elderly patients with asthma. Although the detection rate and profile of respiratory viruses in IS was similar in elderly and non-elderly patients with asthma, the presence of pathogens was associated with some clinical characteristics only in older subjects. abstract: INTRODUCTION: Respiratory pathogens are thought to be involved in the pathogenesis and exacerbations of asthma at all ages; however, little is known about the airway microbiome in the elderly. AIM OF THE STUDY: To identify respiratory pathogens in the induced sputum (IS) of elderly asthmatics, and to determine the association between pathogens and the markers of asthma activity. MATERIAL AND METHODS: Twenty-nine subjects with stable asthma, 15 above 65 years of age and 14 aged 30-49 years, underwent clinical evaluation, fractional exhaled nitric oxide measurement, and sputum induction. Pathogens were detected by multiplex reverse transcription polymerase chain reaction. The periostin concentration of IS supernatants was measured by enzyme-linked immunosorbent assay. Serum eosinophil cationic protein and total IgE levels were measured by ImmunoCAP. RESULTS: Elderly patients, as compared to non-elderly, had significantly higher eosinophilia in IS, although other markers of eosinophilic inflammation were comparable. Half of the subjects were positive for Haemophilus influenzae. Chlamydophila pneumoniae was found in two subjects. Respiratory viruses were detected in more than 70% of patients. The detection rates and profiles of atypical bacteria and respiratory viruses were similar in both groups. Only in the elderly asthmatics was influenza A positivity associated with lower predicted FVC%, RSV A positivity connected with decreased tIgE concentration, and RSV B positivity related to a lower percentage of lymphocytes in IS. CONCLUSIONS: Despite the existence of differences in some clinical and inflammatory characteristics of asthma between elderly and non-elderly asthmatics, the pathogen detection rates in the IS from the two groups are similar. url: https://www.ncbi.nlm.nih.gov/pubmed/32140050/ doi: 10.5114/ceji.2019.92790 id: cord-323112-e78zpa9c author: WATERER, Grant title: Respiratory infections: A current and future threat date: 2009-07-16 words: 2670.0 sentences: 156.0 pages: flesch: 39.0 cache: ./cache/cord-323112-e78zpa9c.txt txt: ./txt/cord-323112-e78zpa9c.txt summary: This review will focus on the human, pathogen and environmental factors that contribute to the continued global burden or respiratory diseases with a particular focus on areas where we might hope to see some progress in the coming decades. 14 While it is clear that strict infection control can reduce nosocomial infection rates, 15 the practical necessity of pooling vulnerable hosts together combined with the inevitable ageing of health-care facilities will ensure that nosocomial outbreaks continue to be a problem. In recent years the marked increase in tumour necrosis factor antagonists and monoclonal antibodies targeting specific lymphoid populations in patients with inflammatory arthritis (and especially rheumatoid disease) has significantly over taken patients on immunosuppressant therapy after solid organ transplantation as the major cause of iatrogenic immunosuppression. New therapeutic and diagnostic approaches coupled with clinical vigilance, strict infection control and solid public health measures are the hopes for reducing the burden of pulmonary infectious disease over the coming decades. abstract: Despite all the medical progress in the last 50 years pulmonary infections continue to exact and extremely high human and economic cost. This review will focus on the human, pathogen and environmental factors that contribute to the continued global burden or respiratory diseases with a particular focus on areas where we might hope to see some progress in the coming decades. url: https://www.ncbi.nlm.nih.gov/pubmed/19659646/ doi: 10.1111/j.1440-1843.2009.01554.x id: cord-022431-f6caajxy author: WELLEMANS, G. title: Bovine Respiratory Syncytial Virus date: 2013-11-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155685/ doi: 10.1016/b978-0-444-87312-5.50051-5 id: cord-272596-yxvg8357 author: WU, Jian Jun title: Detection of Human Bocavirus in Children with Acute Respiratory Tract Infections in Lanzhou and Nanjing, China date: 2014-11-30 words: 2953.0 sentences: 167.0 pages: flesch: 48.0 cache: ./cache/cord-272596-yxvg8357.txt txt: ./txt/cord-272596-yxvg8357.txt summary: title: Detection of Human Bocavirus in Children with Acute Respiratory Tract Infections in Lanzhou and Nanjing, China In our study, 72.34% of HBoV1-positive patients had co-infection with 10 different respiratory viruses, which is similar to previous reports [12] [13] [14] [46] [47] [48] . Detection of human bocavirus in children with upper respiratory tract infection by polymerase chain reaction Detection of bocavirus in children suffering from acute respiratory tract infections in Saudi Arabia Detection of human bocavirus from children and adults with acute respiratory tract illness in Guangzhou, southern China Clinical relevance of human bocavirus with acute respiratory tract infection and diarrhea in children: a prospective case-control study Frequent detection of bocavirus DNA in German children with respiratory tract infections Human bocavirus infection in children with acute respiratory tract infection in India Human bocavirus in children with acute respiratory infections in Vietnam Human bocavirus infection in young children with acute respiratory tract infection in Lanzhou abstract: Abstract Objective The aim of this study was to explore the prevalent characteristics of HBoV1 and its co-infection. Methods PCR was used to detect HBoV1-DNA (HBoV1) and other viruses. A multivariate logistic regression model was used to explore possibility of co-detected for related viruses. Results The positivity rates in Nanjing and Lanzhou were 9.38% (74/789) and 11.62% (161/1386), respectively (P<0.05). The HBoV1 positive group was younger than negative group (P<0.05). Seasonal differences were noted, with a higher frequency of infection in December and July. HBoV1-positive children [72.34% (169/235)] were co-infected with other respiratory viruses. Multifactorial analysis showed no correlations between HBoV1 and the clinical classification, region, gender, age, or treatment as an outpatient or in a hospital. Correlations were identified between HBoV1 infections with ADV (OR=1.53, 95% CI 1.03-2.28), RSV (OR=0.71, 95% CI 0.52-0.98), and IFVA (OR=1.77, 95% CI 1.00-3.13). Conclusions Presence of HBoV1 in nasopharyngeal aspirates did not correlate with region or gender, although the prevalence of HBoV1 was higher in younger children. There were no correlations between HBoV1 and other variables, except for the season and ADV, RSV, or IFVA infections. url: https://api.elsevier.com/content/article/pii/S0895398814601100 doi: 10.3967/bes2014.110 id: cord-018421-wy3mtafh author: Waghmare, Alpana title: Rhinovirus, Coronavirus, Enterovirus, and Bocavirus After Hematopoietic Cell Transplantation or Solid Organ Transplantation date: 2016-02-15 words: 5430.0 sentences: 264.0 pages: flesch: 36.0 cache: ./cache/cord-018421-wy3mtafh.txt txt: ./txt/cord-018421-wy3mtafh.txt summary: Human rhinoviruses are the most common respiratory viruses detected in the upper respiratory tract of hematopoietic cell transplant and lung transplant recipients, and evidence on the impact on clinical outcomes is mounting. Due to the development of polymerase chain reaction (PCR) assays for viral detection, HRVs are now known to be the most common viruses detected from respiratory specimens in HCT recipients and can account for 25-40% of cases of viral respiratory infections in these patients [ 2 -4 ] (Figure 32-1 ). In that study, approximately one third of the adult HCT recipients who developed symptomatic HRV infections prior to engraftment had progression of upper respiratory tract symptoms to LRTI, and all cases with pneumonias were fatal. Rhinovirus as a cause of fatal lower respiratory tract infection in adult stem cell transplantation patients: a report of two cases Human Rhinovirus RNA Detection in the Lower Respiratory Tract of Hematopoietic Cell Transplant recipients: Association with Mortality. abstract: Respiratory viral infections represent a significant cause of morbidity and mortality in immunocompromised hosts. Newer molecular detection assays have allowed for the characterization of several respiratory viruses not previously recognized as having significant clinical impact in the immunocompromised population. Human rhinoviruses are the most common respiratory viruses detected in the upper respiratory tract of hematopoietic cell transplant and lung transplant recipients, and evidence on the impact on clinical outcomes is mounting. Other respiratory viruses including enteroviruses (EVs), coronaviruses (CoVs), and bocavirus may also contribute to pulmonary disease; however, data is limited in the immunocompromised population. Further studies are needed to define the epidemiology, risk factors, and clinical outcomes of these infections; this data will help inform decisions regarding development of antiviral therapy and infection prevention strategies. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123292/ doi: 10.1007/978-3-319-28797-3_32 id: cord-293897-p30wz7b7 author: Waghmare, Alpana title: Respiratory viruses date: 2020-04-24 words: 5885.0 sentences: 307.0 pages: flesch: 28.0 cache: ./cache/cord-293897-p30wz7b7.txt txt: ./txt/cord-293897-p30wz7b7.txt summary: 14,15 Many immunocompromised adults with PIV infection first present with symptoms of mild upper respiratory tract disease, but in contrast to RSV, influenza, and HMPV, detection of PIV-1 and PIV-3 in asymptomatic HCT recipients is relatively common, reported in 6 of 17 (35%) infection episodes in a prospective study. In immunocompromised hosts, including hematopoietic cell transplant recipients, solid organ transplant recipients, and oncology patients, respiratory viruses can be associated with significant clinical manifestations, including prolonged viral shedding, lower respiratory tract disease, the need for supplemental oxygen, late airflow obstruction, and even death. In immunocompromised hosts, including hematopoietic cell transplant recipients, solid organ transplant recipients, and oncology patients, respiratory viruses can be associated with significant clinical manifestations, including prolonged viral shedding, lower respiratory tract disease, the need for supplemental oxygen, late airflow obstruction, and even death. abstract: Respiratory viruses are commonly detected in both healthy and immunocompromised children. In most healthy children, respiratory viruses are associated with self-limited upper respiratory tract infections and are not accompanied by significant morbidity. In immunocompromised hosts, including hematopoietic cell transplant recipients, solid organ transplant recipients, and oncology patients, respiratory viruses can be associated with significant clinical manifestations, including prolonged viral shedding, lower respiratory tract disease, the need for supplemental oxygen, late airflow obstruction, and even death. This chapter reviews the major respiratory viruses, including respiratory syncytial virus, human metapneumovirus, influenza, parainfluenza viruses, human rhinoviruses, and human coronaviruses. Other viruses can manifest as pulmonary infection; however, these viruses are discussed elsewhere (see Chapter 17 for discussion of cytomegalovirus and Chapter 22 for discussion of adenoviruses). url: https://www.sciencedirect.com/science/article/pii/B9780323641982000300 doi: 10.1016/b978-0-323-64198-2.00030-0 id: cord-349279-wbb7h2zu author: Walker, Gregory J. title: Viruses associated with acute respiratory infection in a community‐based cohort of healthy New Zealand children date: 2019-05-07 words: 2767.0 sentences: 155.0 pages: flesch: 46.0 cache: ./cache/cord-349279-wbb7h2zu.txt txt: ./txt/cord-349279-wbb7h2zu.txt summary: The rates of infection and community epidemiology of respiratory viruses in healthy children needs further definition to assist interpretation of molecular diagnostic assays in this population. The most commonly detected viruses in samples collected during ARI were HRV (52.8%), HCoV (11.0%), parainfluenza virus (PIF) (6.0%), IFV (4.5%), RSV (3.8%), and HMPV (3.5%). Detection of any virus and codetection of viruses were both significantly associated with swabs collected during ARI episodes. While their corresponding risk ratios are not considered significant, the number of detections of these viruses is relatively small, and a larger analysis would be required to rule out the clinical significance of detecting HRV-B, AdV and HBoV in ARIs. The effect of viral coinfection on respiratory disease severity in children has not been well established. New molecular virus detection methods and their clinical value in lower respiratory tract infections in children Viruses associated with acute respiratory infection in a community-based cohort of healthy New Zealand children abstract: Acute respiratory infections (ARIs) are a major cause of morbidity among children. Respiratory viruses are commonly detected in both symptomatic and asymptomatic periods. The rates of infection and community epidemiology of respiratory viruses in healthy children needs further definition to assist interpretation of molecular diagnostic assays in this population. Children otherwise healthy aged 1 to 8 years were prospectively enrolled in the study during two consecutive winters, when ARIs peak in New Zealand. Parents completed a daily symptom diary for 8 weeks, during which time they collected a nasal swab from the child for each clinical ARI episode. A further nasal swab was collected by research staff during a clinic visit at the conclusion of the study. All samples were tested for 15 respiratory viruses commonly causing ARI using molecular multiplex polymerase chain reaction assays. There were 575 ARIs identified from 301 children completing the study, at a rate of 1.04 per child‐month. Swabs collected during an ARI were positive for a respiratory virus in 76.8% (307 of 400), compared with 37.3% (79 of 212) of swabs collected during asymptomatic periods. The most common viruses detected were human rhinovirus, coronavirus, parainfluenza viruses, influenzavirus, respiratory syncytial virus, and human metapneumovirus. All of these were significantly more likely to be detected during ARIs than asymptomatic periods. Parent‐administered surveillance is a useful mechanism for understanding infectious disease in healthy children in the community. Interpretation of molecular diagnostic assays for viruses must be informed by understanding of local rates of asymptomatic infection by such viruses. url: https://doi.org/10.1002/jmv.25493 doi: 10.1002/jmv.25493 id: cord-266716-pghnl980 author: Wang, Hai-Ming title: Isobavachalcone inhibits post-entry stages of the porcine reproductive and respiratory syndrome virus life cycle date: 2018-02-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Porcine reproductive and respiratory syndrome virus (PRRSV) is a pathogen of great economic significance that impacts the swine industry globally. Since the first report of a porcine reproductive and respiratory syndrome (PRRS) outbreak, tremendous efforts to control this disease, including various national policies and plans incorporating the use of multiple modified live-virus vaccines, have been made. However, PRRSV is still a significant threat to the swine industry, and new variants continually emerge as a result of PRRSV evolution. Several studies have shown that pandemic PRRSV strains have enormous genetic diversity and that commercial vaccines can only provide partial protection against these strains. Therefore, effective anti-PRRSV drugs may be more suitable and reliable for PRRSV control. In this study, we observed that isobavachalcone (IBC), which was first isolated from Psoralea corylifolia, had potent anti-PRRSV activity in vitro. Although many biological activities of IBC have been reported, this is the first report describing the antiviral activity of IBC. Furthermore, after a systematic investigation, we demonstrated that IBC inhibits PRRSV replication at the post-entry stage of PRRSV infection. Thus, IBC may be a candidate for further evaluation as a therapeutic agent against PRRSV infection of swine in vivo. url: https://www.ncbi.nlm.nih.gov/pubmed/29411137/ doi: 10.1007/s00705-018-3755-4 id: cord-003357-4qrg6lqu author: Wang, Yingchen title: Prevalence of Common Respiratory Viral Infections and Identification of Adenovirus in Hospitalized Adults in Harbin, China 2014 to 2017 date: 2018-11-27 words: 5191.0 sentences: 260.0 pages: flesch: 47.0 cache: ./cache/cord-003357-4qrg6lqu.txt txt: ./txt/cord-003357-4qrg6lqu.txt summary: Conclusion: This study demonstrated that common respiratory viruses were partially responsible for hospitalized lower respiratory tract infections in adult patients from Harbin, China, with parainfluenza virus as the dominant viral pathogen. Viral infections played an important role in pediatric lower respiratory tract infections, and the corresponding common viral pathogens were influenza A and B virus (IAV and IBV), parainfluenza virus (PIV, type 1 to 3), respiratory syncytial virus (RSV) and human adenovirus (ADV) (Pavia, 2011) . In this report, the prevalence of common viruses in the lower respiratory tract infection of hospitalized adult patients from Harbin, China was explored in hopes of revealing the clinical and pathogenic features of respiratory viruses. The overall detection rate of viral infection among hospitalized adult patients in this report is 14.5%, which was consistent with the result of 16.8% in the age group above 14 years old by a national survey from 2009 to 2013 in China (Feng et al., 2014) . abstract: Background: Respiratory infections pose a great challenge in global health, and the prevalence of viral infection in adult patients has been poorly understood in northeast China. Harbin is one of the major cities in northeast China, and more than half of any given year in Harbin is occupied by winter. To reveal the viral etiology and seasonality in adult patients from Harbin, a 4-year consecutive survey was conducted in Harbin, China. Methods: From January 2014 to December 2017, specimens were obtained from adult patients admitted to the Second Affiliated Hospital of Harbin Medical University with lower respiratory tract infections. Sputum samples were examined by direct immunofluorescence assays to detect seven common respiratory viruses, including influenza virus (type A and B), parainfluenza virus (type 1 to 3), respiratory syncytial virus and adenovirus. Adenovirus positive samples were seeded onto A549 cells to isolate viral strains. Phylogenetic analysis was conducted on the highly variable region of adenoviral hexon gene. Results: A total of 1,300 hospitalized adult patients with lower respiratory tract infections were enrolled, in which 189 patients (14.5%) were detected as having at least one viral infection. The co-infection rate in this study was 25.9% (49/189). The dominant viral pathogen from 2014 to 2017 was parainfluenza virus, with a detection rate of 7.2%, followed by influenza virus, respiratory syncytial virus and adenovirus. Based on the climate seasons determined by daily average temperature, the highest overall viral detection rate was detected in spring (22.0%, 52/236), followed by winter (13.4%, 109/813), autumn (11.4%, 13/114) and summer (10.9%, 15/137). Adenovirus type 3 strains with slight variations were isolated from positive cases, which were closely related to the GB strain from the United States, as well as the Harbin04B strain isolated locally. Conclusion: This study demonstrated that common respiratory viruses were partially responsible for hospitalized lower respiratory tract infections in adult patients from Harbin, China, with parainfluenza virus as the dominant viral pathogen. Climate seasons could be rational indicators for the seasonality analysis of airborne viral infections. Future surveillance on viral mutations would be necessary to reveal the evolutionary history of respiratory viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6277751/ doi: 10.3389/fmicb.2018.02919 id: cord-253279-8j7esl8j author: Wasserman, Richard L. title: RI-002, an intravenous immunoglobulin containing high titer neutralizing antibody to RSV and other respiratory viruses for use in primary immunodeficiency disease and other immune compromised populations date: 2017-10-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Introduction: Novel immune globulin (IG) products (RI-002, RI-001) have been designed to provide protection against respiratory syncytial virus (RSV) mediated respiratory illness while at the same time meeting the manufacturing requirements established by FDA for antibody supplementation in immunocompromised subjects. Areas covered: This review covers the manufacture and development of both RI-001 and RI-002, including the selection of plasma donors for IG preparation with high-titers of anti-RSV antibody, in vitro, and preclinical data in the cotton rat model S. hispidus, and clinical trials including Phase II and compassionate use studies of RI-001 and a multi-center, pivotal Phase III study of RI-002 in PIDD patients. Expert commentary: The data demonstrate that RI-002 is efficacious in the prevention and treatment of RSV in preclinical normal and immune suppressed animal models and is safe and efficacious in the treatment of patients with various forms of primary immunodeficiency disease (PIDD). This product offers potential advantages over other available IG’s for prophylaxis in immunocompromised patients requiring polyclonal immunoglobulin supplementation because of its unique antibody composition. In addition to its enhanced neutralizing anti-RSV activity and its polyclonal IG composition, there is preclinical data to support the use of RI-002 for humoral protection against other respiratory pathogens. url: https://doi.org/10.1080/1744666x.2017.1389647 doi: 10.1080/1744666x.2017.1389647 id: cord-327264-j0efi5vc author: Waterer, Grant title: Respiratory infections in the Asia‐Pacific region date: 2017-05-24 words: 557.0 sentences: 33.0 pages: flesch: 52.0 cache: ./cache/cord-327264-j0efi5vc.txt txt: ./txt/cord-327264-j0efi5vc.txt summary: Lower respiratory tract infections remain the number one cause of death in the developing world. 1 In the developed world, lower respiratory tract infections are still the fifth leading cause of death. As well as host factors, it is the speed of adaptation of the pathogens that makes it most likely that we will not conquer death from respiratory infection any time soon. While some progress has been made in reducing pneumococcal disease with the newer conjugate vaccines, 2 there is evidence that the speed of adaptation (as measured by the proportion of strains not covered by the vaccines) is increasing. In this series on respiratory infections in Respirology, many of the above-mentioned challenges will be covered including the burden of disease due to respiratory pathogens (both acute and long-term), drug-resistant pathogens and newly emerging pathogens. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/28544469/ doi: 10.1111/resp.13077 id: cord-019051-gtruu1op author: Weber, Olaf title: The role of viruses in the etiology and pathogenesis of common cold date: 2009-11-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Numerous viruses are able to cause respiratory tract infections. With the availability of new molecular techniques, the number of pathogens detected in specimens from the human respiratory tract has increased. Some of these viral infections have the potential to lead to severe systemic disease. Other viruses are limited to playing a role in the pathogenesis of the common cold syndrome. This chapter focuses on the viral pathogens that are linked to common cold. It is not the intention to comprehensively review all the viruses that are able to cause respiratory tract infections—this would go beyond the scope of this book. The list of viruses that are briefly reviewed here includes rhinoviruses, respiratory syncytial virus, parainfluenza virus, adenovirus, metapneumovirus and coronavirus. Bocavirus is discussed as one example of a newly identified pathogen with a less established role in the etiology and pathogenesis of common cold. Influenza virus does not cause what is defined as common cold. However, influenza viruses are associated with respiratory disease and the clinical picture of mild influenza and common cold frequently overlaps. Therefore, influenza virus has been included in this chapter. It is important to note that a number of viruses are frequently co-detected with other viruses in humans with respiratory diseases. Therefore, the viral etiology and the role of viruses in the pathogenesis of common cold is complex, and numberous questions remain to be answered. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7124101/ doi: 10.1007/978-3-7643-9912-2_5 id: cord-330919-dep3v1pt author: Whyte, Claire S title: Fibrinolytic abnormalities in acute respiratory distress syndrome (ARDS) and versatility of thrombolytic drugs to treat COVID‐19 date: 2020-04-23 words: 4254.0 sentences: 251.0 pages: flesch: 36.0 cache: ./cache/cord-330919-dep3v1pt.txt txt: ./txt/cord-330919-dep3v1pt.txt summary: The global pandemic of coronavirus disease 2019 (COVID‐19) is associated with the development of acute respiratory distress syndrome (ARDS), which requires ventilation in critically ill patients. Tissue factor (TF) is exposed on damaged alveolar endothelial cells and on the surface of leukocytes promoting fibrin deposition, while significantly elevated levels of plasminogen activator inhibitor 1 (PAI‐1) from lung epithelium and endothelial cells create a hypofibrinolytic state. In severe cases, patients with COVID-19 develop a type of acute respiratory distress syndrome (ARDS), sepsis and multiorgan failure. However, the principal fibrinolytic inhibitor described in the pathogenesis of ARDS is plasminogen activator inhibitor 1 (PAI-1), which is known to be elevated in severe acute respiratory syndrome coronavirus (SARS-CoV) and ALI [11, 61] . Tissue Plasminogen Activator (tPA) as a Novel Treatment for Refractory COVID-19 Associated Acute Respiratory Distress Syndrome (ARDS)? Activator (tPA) Treatment for COVID-19 Associated Acute Respiratory Distress Syndrome (ARDS): A Case Series abstract: The global pandemic of coronavirus disease 2019 (COVID‐19) is associated with the development of acute respiratory distress syndrome (ARDS), which requires ventilation in critically ill patients. The pathophysiology of ARDS results from acute inflammation within the alveolar space and prevention of normal gas exchange. The increase in proinflammatory cytokines within the lung leads to recruitment of leukocytes, further propagating the local inflammatory response. A consistent finding in ARDS is the deposition of fibrin in the air spaces and lung parenchyma. COVID‐19 patients show elevated D‐Dimers and fibrinogen. Fibrin deposits are found in the lungs of patients due to the dysregulation of the coagulation and fibrinolytic systems. Tissue factor (TF) is exposed on damaged alveolar endothelial cells and on the surface of leukocytes promoting fibrin deposition, while significantly elevated levels of plasminogen activator inhibitor 1 (PAI‐1) from lung epithelium and endothelial cells create a hypofibrinolytic state. Prophylaxis treatment of COVID‐19 patients with low molecular weight heparin (LMWH) is important to limit coagulopathy. However, to degrade pre‐existing fibrin in the lung it is essential to promote local fibrinolysis. In this review, we discuss the repurposing of fibrinolytic drugs, namely tissue‐type plasminogen activator (tPA), to treat COVID‐19 associated ARDS. tPA is an approved intravenous thrombolytic treatment, and the nebulizer form has been shown to be effective in plastic bronchitis and is currently in Phase II clinical trial. Nebulizer plasminogen activators may provide a targeted approach in COVID‐19 patients to degrade fibrin and improving oxygenation in critically ill patients. url: https://doi.org/10.1111/jth.14872 doi: 10.1111/jth.14872 id: cord-341765-ml6eo8r3 author: Widhidewi, Ni Wayan title: Identification of viral etiology of acute respiratory tract infections in children and adults in Tabanan, Bali, Indonesia date: 2020-03-25 words: 2740.0 sentences: 153.0 pages: flesch: 45.0 cache: ./cache/cord-341765-ml6eo8r3.txt txt: ./txt/cord-341765-ml6eo8r3.txt summary: title: Identification of viral etiology of acute respiratory tract infections in children and adults in Tabanan, Bali, Indonesia This study was based on utilizing molecular techniques targeting a panel of 11 endemic and emerging respiratory viral pathogens including zoonotic viruses in a cohort of children and adults presenting at Tabanan General Hospital, Bali, with acute respiratory illness, from January to November 2017. In this study, throat swab specimens were collected from patients with respiratory symptoms to identify viral etiological agents of ARTI. Singleplex PCR assays were used for detection of a panel of respiratory viruses using family-level primers for Paramyxoviridae, Herpesviridae, Coronaviridae, Hantaviridae, Adenoviridae, Arenaviridae; genus-level primers for Enterovirus, Henipavirus, Influenza A virus, Bocavirus; and Pneumovirinae sub-family primer including respiratory syncytial virus (RSV) and human metapneumovirus (HMPV). In addition to the influenza virus routinely screened in ARTI studies, other viral agents associated with severity like Herpesviridae, Enterovirus and RSV should be screened in respiratory illnesses. abstract: Acute respiratory tract infection (ARTI) is the most common infectious disease in humans worldwide. The morbidity and mortality rates are high, especially in developing countries from Southeast Asia and Africa. While ARTI is commonly associated with viruses, there is limited data on the spectrum of viruses causing ARTI in developing countries, including Indonesia. This study was based on utilizing molecular techniques targeting a panel of 11 endemic and emerging respiratory viral pathogens including zoonotic viruses in a cohort of children and adults presenting at Tabanan General Hospital, Bali, with acute respiratory illness, from January to November 2017. In total, 98 out of 200 samples (49.0 %) tested positive for viruses. Our study confirmed 64.3 % viral etiology in children and 12.2 % in adults. Viruses that were detected were Herpesviridae (15.0 %) followed by enteroviruses (12.0 %), influenza A virus (11.5 %), respiratory syncytial virus (8.0 %), Adenoviridae (6.5 %), human metapneumovirus (3.5 %), Paramyxoviridae (2.0 %), bocavirus (1.0 %) and Coronaviridae (0.5 %). The study sheds light on the viral spectrum of ARTI in children and adults in Tabanan, Bali, Indonesia url: https://www.ncbi.nlm.nih.gov/pubmed/32974585/ doi: 10.1099/acmi.0.000120 id: cord-023528-z9rc0ubj author: Wilkins, Pamela A. title: Disorders of Foals date: 2009-05-18 words: 42569.0 sentences: 2235.0 pages: flesch: 44.0 cache: ./cache/cord-023528-z9rc0ubj.txt txt: ./txt/cord-023528-z9rc0ubj.txt summary: First, restriction of the thorax or the abdomen can result in impaired ventilation, which can occur easily when one restrains a foal and may result in spuriously abnormal arterial blood gas values (see the discussion on arterial blood gas evaluation, Respiratory Diseases Associated with Hypoxemia in the Neonate). Hypoxic ischemic encephalopathy (HIE), currently referred to as neonatal encephalopathy in the human literature, is one systemic manifestation of a broader syndrome of perinatal asphyxia syndrome (PAS), and management of foals with signs consistent with a diagnosis of HIE requires the clinician to examine other body systems fully and to provide therapy directed at treating other involved systems. Therapy for the various manifestations of hypoxiaischemia involves control of seizures, general cerebral support, correction of metabolic abnormalities, maintenance of normal arterial blood gas values, maintenance of tissue perfusion, maintenance of renal function, treatment of gastrointestinal dysfunction, prevention and recognition and early treatment of secondary infections, and general supportive care. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7171908/ doi: 10.1016/b0-72-169777-1/50021-4 id: cord-326004-wg47sd06 author: Wilson, Patrick T title: Respiratory Pathogens in Children 1 Month to 5 Years of Age Presenting With Undifferentiated Acute Respiratory Distress in 2 District-Level Hospitals in Ghana date: 2018-09-03 words: 2193.0 sentences: 103.0 pages: flesch: 48.0 cache: ./cache/cord-326004-wg47sd06.txt txt: ./txt/cord-326004-wg47sd06.txt summary: A recently conducted prospective randomized controlled trial at 2 district-level hospitals in Ghana revealed that the use of continuous positive airway pressure (CPAP) reduces the allcause mortality rate in children <1 year old who presented with undifferentiated acute respiratory distress [3] . In that study, nasopharyngeal swabs were collected from the children at the time of presentation and tested for common pediatric respiratory pathogens; the goal was to decrease the knowledge gap regarding the incidence of respiratory pathogens that affect children <5 years of age in low-and middle-income countries. In this report, we describe the respiratory pathogens detected in children aged 1 month to 5 years who presented to 1 of 2 district-level hospitals in Ghana with undifferentiated acute respiratory distress. Despite the limitations of this study, our results show that viral respiratory pathogens were frequent among children aged 1 month to 5 years who presented with acute respiratory distress to 1 of 2 district-level hospitals in Ghana. abstract: Ghanaian children (2176) aged <5 years who presented with undifferentiated acute respiratory distress were tested for respiratory pathogens using a BioFire FilmArray polymerase chain reaction assay. Rhinovirus and/or enterovirus was detected in 36% of the assays, respiratory syncytial virus in 11%, and parainfluenza in 7%. Respiratory syncytial virus and metapneumovirus were detected more frequently in the rainy season than in the dry season. url: https://www.ncbi.nlm.nih.gov/pubmed/30189029/ doi: 10.1093/jpids/piy090 id: cord-326122-5m1727m1 author: Wishaupt, Jérôme O. title: PCR testing for Paediatric Acute Respiratory Tract Infections date: 2014-08-04 words: 4910.0 sentences: 259.0 pages: flesch: 41.0 cache: ./cache/cord-326122-5m1727m1.txt txt: ./txt/cord-326122-5m1727m1.txt summary: The Pediatric Infectious Disease Society (PIDS) and the Infectious Diseases Society of America (IDSA) recommend in their guideline ''Community-Acquired Pneumonia (CAP) in Infants and Children'' the use of sensitive and specific tests for the rapid diagnosis of influenza virus and other respiratory viruses in the evaluation of children older than three months of age with CAP [19] . In another recent retrospective study of 177 children with ARI in a general hospital, antibiotic management was not influenced after detecting a viral respiratory pathogen, although the authors state that routine testing of common respiratory pathogens could lead to a better understanding of their role in disease in children with respiratory symptoms [38] . Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children abstract: Acute respiratory tract infection (ARI) is a frequently occurring disease in children. It is a clinical diagnosis for which no internationally accepted diagnostic test is available. The majority of ARI is viral in origin, though diagnostic tests for viruses were rarely performed in the past. In the past 2 decades, new molecular techniques have been introduced in many hospitals. They are capable of generating a high yield of viral and bacterial diagnoses, but their impact upon clinical practices is still questionable. In this paper, we discuss the difficulties of diagnosing ARI in children, the indications for conventional and new diagnostics and their implications. url: https://api.elsevier.com/content/article/pii/S1526054214000803 doi: 10.1016/j.prrv.2014.07.002 id: cord-268729-n7slf5tx author: Wissinger, E L title: Manipulation of acute inflammatory lung disease date: 2008-05-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Inflammatory lung disease to innocuous antigens or infectious pathogens is a common occurrence and in some cases, life threatening. Often, the inflammatory infiltrate that accompanies these events contributes to pathology by deleterious effects on otherwise healthy tissue and by compromising lung function by consolidating (blocking) the airspaces. A fine balance, therefore, exists between a lung immune response and immune-mediated damage, and in some the “threshold of ignorance” may be set too low. In most cases, the contributing, potentially offending, cell population or immune pathway is known, as are factors that regulate them. Why then are targeted therapeutic strategies to manipulate them not more commonplace in clinical medicine? This review highlights immune homeostasis in the lung, how and why this is lost during acute lung infection, and strategies showing promise as future immune therapeutics. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/mi.2008.16) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1038/mi.2008.16 doi: 10.1038/mi.2008.16 id: cord-287178-hu6vlc9u author: Wong-Chew, Rosa M title: Prevalence of respiratory virus in symptomatic children in private physician office settings in five communities of the state of Veracruz, Mexico date: 2015-06-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Acute respiratory tract infections are the leading cause of morbidity and mortality in children worldwide. Many studies have described the frequency of viruses in hospitalized patients, but studies describing the prevalence of viruses in the community setting are limited, particularly in developing countries, where most of the deaths from serious respiratory diseases occur. The aim of this study was to evaluate the diversity of respiratory viruses in the community setting using molecular diagnostic tools, as well as the clinical characteristics of respiratory viral infections in the general pediatric practice in Mexico. METHODS: Children with respiratory tract infections attending private pediatric practices during a 10-month period in five cities of the state of Veracruz were included. Nasal swabs were taken and processed by a multiplex detection kit for 15 respiratory viruses. RESULTS: 525 children were included from July 2011 to May 2012; 44% were female, mean age was 45 months. The 3 most frequent clinical diagnosis were: rhinopharyngitis 68%, pharyngitis 18%, and 3.3% influenza-like illness. 71.5% of the samples were positive for virus. The five most frequent pathogens were respiratory syncycitial virus in 18.3% of the children, rhinovirus in 17.5%, influenza A 9.1%, adenovirus 7.2%, and enterovirus 3.4%, although all 15 viruses were detected; there were viral coinfections in 14.1%, and 28.5% of the samples were negative. CONCLUSIONS: A large proportion of respiratory infections in the community setting in Mexico was associated to viruses. Although testing for common respiratory pathogens in children with acute respiratory tract infections may lead to a better understanding of the role of viral pathogens in, and eventually to improvement in the management of, individual patients, additional prospective studies are required to study the need of routinely using such tests in general pediatric practices in resource-limited countries. url: https://www.ncbi.nlm.nih.gov/pubmed/26108920/ doi: 10.1186/s13104-015-1239-0 id: cord-256930-bz80uxnx author: Xiao, Ni‐guang title: Prevalence of human metapneumovirus in children with acute lower respiratory infection in Changsha, China date: 2013-01-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Human metapneumovirus (hMPV) causes acute respiratory infections in children. The prevalence and clinical characteristics of hMPV were determined in nasopharyngeal aspirates of children in Changsha, China. Reverse transcription‐polymerase chain reaction (RT‐PCR) or PCR was employed to screen for both hMPV and other common respiratory viruses in 1,165 nasopharyngeal aspirate specimens collected from children with lower respiratory tract infections from September 2007 to August 2008. All PCR products were sequenced, and demographic and clinical data were collected from all patients. Seventy‐six of 1,165 (6.5%) specimens were positive for hMPV, of which 85.5% (65/76) occurred in the winter and spring seasons. The hMPV coinfection rate was 57.9% (44/76), and human bocavirus was the most common virus detected in conjunction with hMPV. Phylogenetic analysis revealed that 94.7% of the hMPV detected were of subgroup A2, 5.3% were subgroup B2, and none belonged to either the A1 or B1 subgroups. No significant differences were found in terms of the frequency of diagnosis and clinical signs between either the co‐ and mono‐infection groups, or between patients with and without underlying diseases. It was concluded that hMPV is an important viral pathogen in pediatric patients with lower respiratory tract infections in Changsha. Only hMPV genotypes A2 and B2 were co‐circulating in this locality; human bocavirus was the most common coinfecting virus, and coinfection did not affect disease severity. J. Med. Virol. 85:546–553, 2013. © 2013 Wiley Periodicals, Inc. url: https://doi.org/10.1002/jmv.23501 doi: 10.1002/jmv.23501 id: cord-330079-pdaowkop author: Xu, Lin title: Surveillance and Genome Analysis of Human Bocavirus in Patients with Respiratory Infection in Guangzhou, China date: 2012-09-11 words: 4469.0 sentences: 205.0 pages: flesch: 50.0 cache: ./cache/cord-330079-pdaowkop.txt txt: ./txt/cord-330079-pdaowkop.txt summary: To investigate the epidemiological and genetic variation of HBoV in Guangzhou, South China, we screened 3460 throat swab samples from 1686 children and 1774 adults with acute respiratory infection symptoms for HBoV between March 2010 and February 2011, and analyzed the complete genome sequence of 2 HBoV strains. In our current study, we screened throat swab specimens from patients with acute respiratory tract infection symptoms for HBoV and other common respiratory viruses over a 12-month period using polymerase chain reaction (PCR) methods, and in addition, the molecular phylogeny and complete genome sequences of 2 HBoV strains were also analyzed. Of the 3460 samples collected from patients with respiratory tract infection symptoms and signs enrolled in the study during the period between March 2010 and February 2011, detection for 7 viruses, namely, Influenza, PIV, RSV, HMPV, HCoV, AdV and HBoV, showed that 1275 (36.8%) were found positive for one single virus and 112 (3.2%) were infected by more than one virus. abstract: Human bocavirus (HBoV) is a novel parvovirus associated with respiratory tract diseases and gastrointestinal illness in adult and pediatric patients throughout the world. To investigate the epidemiological and genetic variation of HBoV in Guangzhou, South China, we screened 3460 throat swab samples from 1686 children and 1774 adults with acute respiratory infection symptoms for HBoV between March 2010 and February 2011, and analyzed the complete genome sequence of 2 HBoV strains. Specimens were screened for HBoV by real-time PCR and other 6 common respiratory viruses by RT-PCR or PCR. HBoV was detected in 58 (1.68%) out of 3460 samples, mostly from pediatric patients (52/58) and inpatient children (47/58). Six adult patients were detected as HBoV positive and 5 were emergency cases. Of these HBoV positive cases, 19 (32.76%) had co-pathogens including influenza virus (n = 5), RSV (n = 5), parainfluenza (n = 4), adenovirus (n = 1), coronavirus (n = 7). The complete genome sequences of 2 HBoVs strains (Genbank no. JN794565 and JN794566) were analyzed. Phylogenetic analysis showed that the 2 HBoV strains were HBoV1, and were most genetically close to ST2 (GenBank accession number DQ0000496). Recombination analysis confirmed that HBoV strain GZ9081 was an intra–genotype recombinant strain among HBoV1 variants. url: https://doi.org/10.1371/journal.pone.0044876 doi: 10.1371/journal.pone.0044876 id: cord-269508-d82qjyyr author: Xu, Min title: Implementation of FilmArray Respiratory Viral Panel in a Core Laboratory Improves Testing Turnaround Time and Patient Care date: 2013-01-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The FilmArray respiratory virus panel detects 15 viral agents in respiratory specimens using polymerase chain reaction. We performed FilmArray respiratory viral testing in a core laboratory at a regional children’s hospital that provides service 24 hours a day 7 days a week. The average and median turnaround time were 1.6 and 1.4 hours, respectively, in contrast to 7 and 6.5 hours documented 1 year previously at an on-site reference laboratory using a direct fluorescence assay (DFA) that detected 8 viral agents. During the study period, rhinovirus was detected in 20% and coronavirus in 6% of samples using FilmArray; these viruses would not have been detected with DFA. We followed 97 patients with influenza A or influenza B who received care at the emergency department (ED). Overall, 79 patients (81%) were given oseltamivir in a timely manner defined as receiving the drug in the ED, a prescription in the ED, or a prescription within 3 hours of ED discharge. Our results demonstrate that molecular technology can be successfully deployed in a nonspecialty, high-volume, multidisciplinary core laboratory. url: https://www.ncbi.nlm.nih.gov/pubmed/23270907/ doi: 10.1309/ajcph7x3nlyzphbw id: cord-300116-r93w4jm3 author: Yi, Hana title: Profiling bacterial community in upper respiratory tracts date: 2014-11-13 words: 5063.0 sentences: 271.0 pages: flesch: 39.0 cache: ./cache/cord-300116-r93w4jm3.txt txt: ./txt/cord-300116-r93w4jm3.txt summary: METHODS: We analyzed the upper respiratory tract bacterial content of 57 healthy asymptomatic people (17 health-care workers and 40 community people) and 59 patients acutely infected with influenza, parainfluenza, rhino, respiratory syncytial, corona, adeno, or metapneumo viruses using culture-independent pyrosequencing. In this study, our aim was to determine whether a viral infection-related bacterial profile exists in the respiratory tract and evaluate any disparities in the microbiota structure that develops depending on the infectious virus species. The microbiota profiles of healthy-adult and patient groups also differed in the relative composition of the microbiome, which was highlighted in the graph showing the abundant bacterial genera observed in the tested samples ( Figure 2 and Additional file 3: Figure S2 ). abstract: BACKGROUND: Infection by pathogenic viruses results in rapid epithelial damage and significantly impacts on the condition of the upper respiratory tract, thus the effects of viral infection may induce changes in microbiota. Thus, we aimed to define the healthy microbiota and the viral pathogen-affected microbiota in the upper respiratory tract. In addition, any association between the type of viral agent and the resultant microbiota profile was assessed. METHODS: We analyzed the upper respiratory tract bacterial content of 57 healthy asymptomatic people (17 health-care workers and 40 community people) and 59 patients acutely infected with influenza, parainfluenza, rhino, respiratory syncytial, corona, adeno, or metapneumo viruses using culture-independent pyrosequencing. RESULTS: The healthy subjects harbored primarily Streptococcus, whereas the patients showed an enrichment of Haemophilus or Moraxella. Quantifying the similarities between bacterial populations by using Fast UniFrac analysis indicated that bacterial profiles were apparently divisible into 6 oropharyngeal types in the tested subjects. The oropharyngeal types were not associated with the type of viruses, but were rather linked to the age of the subjects. Moraxella nonliquefaciens exhibited unprecedentedly high abundance in young subjects aged <6 years. The genome of M. nonliquefaciens was found to encode various proteins that may play roles in pathogenesis. CONCLUSIONS: This study identified 6 oropharyngeal microbiome types. No virus-specific bacterial profile was discovered, but comparative analysis of healthy adults and patients identified a bacterium specific to young patients, M. nonliquefaciens. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12879-014-0583-3) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12879-014-0583-3 doi: 10.1186/s12879-014-0583-3 id: cord-002801-6myqgme3 author: Yoon, Byung Woo title: Possible therapeutic effect of orally administered ribavirin for respiratory syncytial virus-induced acute respiratory distress syndrome in an immunocompetent patient: a case report date: 2017-12-20 words: 2560.0 sentences: 144.0 pages: flesch: 38.0 cache: ./cache/cord-002801-6myqgme3.txt txt: ./txt/cord-002801-6myqgme3.txt summary: title: Possible therapeutic effect of orally administered ribavirin for respiratory syncytial virus-induced acute respiratory distress syndrome in an immunocompetent patient: a case report Respiratory syncytial virus-induced severe pneumonia or acute respiratory distress syndrome in immunocompetent adults has been rarely described. We report a case of respiratory syncytial virus-induced acute respiratory distress syndrome occurring in a previously healthy man successfully treated with orally administered ribavirin. CONCLUSION: This case demonstrates the potential usefulness of orally administered ribavirin as a therapeutic option for severe respiratory syncytial virus infection, at least in an immunocompetent host. RSV-induced severe pneumonia or acute respiratory distress syndrome (ARDS) in immunocompromised patients is not uncommon. Here we report a case of ARDS due to RSV occurring in a previously healthy adult successfully treated with orally administered ribavirin. In addition, this case suggests that orally administered ribavirin could be a therapeutic option even for severe pneumonia or ARDS due to RSV, at least in immunocompetent hosts, especially if other antiviral agents are unavailable. abstract: BACKGROUND: Human respiratory syncytial virus usually causes self-limiting upper respiratory infection and occasionally causes pneumonia in immunocompromised hosts. Respiratory syncytial virus-induced severe pneumonia or acute respiratory distress syndrome in immunocompetent adults has been rarely described. Unfortunately, optimal treatment has not been established for this potentially fatal condition. We report a case of respiratory syncytial virus-induced acute respiratory distress syndrome occurring in a previously healthy man successfully treated with orally administered ribavirin. CASE PRESENTATION: An 81-year-old previously healthy Korean man presented with cough, dyspnea, and febrile sensation. He had hypoxemia with diffuse ground glass opacity evident on chest radiography, which progressed and required mechanical ventilation. All microbiological tests were negative except multiplex real-time reverse transcriptase polymerase chain reaction using respiratory specimen, which was positive for human adenovirus. Under the diagnosis of respiratory syncytial virus-induced acute respiratory distress syndrome, orally administered ribavirin was administered and he recuperated completely without complications. CONCLUSION: This case demonstrates the potential usefulness of orally administered ribavirin as a therapeutic option for severe respiratory syncytial virus infection, at least in an immunocompetent host. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5738173/ doi: 10.1186/s13256-017-1514-x id: cord-315934-h70j2jmt author: Yu, Jianxing title: Respiratory Syncytial Virus Seasonality, Beijing, China, 2007–2015 date: 2019-06-17 words: 3994.0 sentences: 216.0 pages: flesch: 52.0 cache: ./cache/cord-315934-h70j2jmt.txt txt: ./txt/cord-315934-h70j2jmt.txt summary: During July 2007–June 2015, we enrolled 4,225 hospitalized children with pneumonia in a study to determine the seasonality of respiratory syncytial virus (RSV) infection in Beijing, China. R espiratory syncytial virus (RSV) is a major cause of lower respiratory tract infection in young children worldwide (1-3); 2.7-3.8 million hospitalizations and 94,600-149,400 deaths occur each year among children <5 years of age as a result of RSV infection (4) . Several previous studies reported an RSV prevalence of 17%-33% among children with severe acute respiratory illness (15, 16) , but few have assessed the seasonality or trends of RSV infections in China. A sharp decrease in sample number and samples positive for RSV were observed each year during this event, resulting in a bimodal distribution curve ( Figure 1, During the study, 335 (8%) hospitalized children with pneumonia were admitted into the PICU, and 8 died (median age 1.4 years, range 4 months-13 years). abstract: During July 2007–June 2015, we enrolled 4,225 hospitalized children with pneumonia in a study to determine the seasonality of respiratory syncytial virus (RSV) infection in Beijing, China. We defined season as the period during which >10% of total PCRs performed each week were RSV positive. We identified 8 distinctive RSV seasons. On average, the season onset occurred at week 41 (mid-October) and lasted 33 weeks, through week 20 of the next year (mid-May); 97% of all RSV-positive cases occurred during the season. RSV seasons occurred 3–5 weeks earlier and lasted ≈6 weeks longer in RSV subgroup A–dominant years than in RSV subgroup B–dominant years. Our analysis indicates that monitoring such RSV subgroup shifts might provide better estimates for the onset of RSV transmission. PCR-based tests could be a flexible or complementary way of determining RSV seasonality in locations where RSV surveillance is less well-established, such as local hospitals throughout China. url: https://www.ncbi.nlm.nih.gov/pubmed/31107230/ doi: 10.3201/eid2506.180532 id: cord-001162-z8cbbit3 author: Yun, Heather C. title: Pandemic Influenza Virus 2009 H1N1 and Adenovirus in a High Risk Population of Young Adults: Epidemiology, Comparison of Clinical Presentations, and Coinfection date: 2014-01-08 words: 3365.0 sentences: 160.0 pages: flesch: 41.0 cache: ./cache/cord-001162-z8cbbit3.txt txt: ./txt/cord-001162-z8cbbit3.txt summary: title: Pandemic Influenza Virus 2009 H1N1 and Adenovirus in a High Risk Population of Young Adults: Epidemiology, Comparison of Clinical Presentations, and Coinfection While coinfections with viral pathogens including 2009 H1N1 have been described in patients with respiratory infections, few prospective studies have related these to clinical presentation and outcomes in adults since molecular diagnostics became available, and none in the setting of high background rates of adenovirus. [12] [13] [14] [15] [16] [17] We sought to describe the epidemiology of 2009 H1N1 and adenovirus in a basic training population, and to correlate differences in clinical presentations and outcomes with each respective pathogen and in coinfections. Subject enrollment was variable throughout the study period, depending on rates of clinical illness within the training population, as well as availability of study personnel to enroll trainees, and given that 2009 H1N1 influenza virus PCR was done as part of clinical care, there could have been some differences in those who enrolled vs. abstract: BACKGROUND: In 2009, pandemic H1N1 influenza virus (2009 H1N1) emerged worldwide, causing morbidity and mortality that disproportionately affected young adults. Upper respiratory infection (URI), largely due to adenovirus, is an endemic cause of morbidity in military training. Whether clinical presentations differ or excess morbidity results from coinfection is unclear. METHODS: The Center for Advanced Molecular Detection evaluates epidemiology and rapid diagnostics of respiratory pathogens in trainees with URI. From May 1, 2009, to November 30, 2009, demographic, clinical, and PCR data from throat and nasal specimens for adenovirus and 2009 H1N1 were prospectively collected. RESULTS: 375 trainees with URI enrolled and were tested for both adenovirus and 2009 H1N1 by PCR (median age 20; 89% male). Adenovirus PCR was positive in 72% (96% serotype E-4) and 2009 H1N1 in 20%. Males were more likely to have adenovirus and females more likely to have 2009 H1N1 (p = 0.047). Subjects with 2009 H1N1 presented an average of 1 week earlier in training, had shorter illness duration before enrollment, less sore throat, diarrhea, and fewer abnormal findings on throat exam. Coryza and cough were more common with 2009 H1N1 compared to adenovirus. Subjects with 2009 H1N1 were less likely to have adenovirus than those without, despite persistently high frequencies of adenovirus detections during peak 2009 H1N1 weeks (15% vs. 83%, p < 0.01). Coinfection with adenovirus and 2009 H1N1 was rare (4%). Rates of hospitalization and pneumonia did not differ between the adenovirus, 2009 H1N1, or coinfected groups. CONCLUSION: Military trainees with 2009 H1N1 vs. adenovirus have differing clinical presentations, and males are more likely to have adenovirus. Despite high frequencies of adenovirus infection, coinfection with adenovirus and 2009 H1N1 is rare and apparently does not result in increased morbidity. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3885690/ doi: 10.1371/journal.pone.0085094 id: cord-303935-qdehf6rb author: Yun, Heather C. title: Changes in Clinical Presentation and Epidemiology of Respiratory Pathogens Associated With Acute Respiratory Illness in Military Trainees After Reintroduction of Adenovirus Vaccine date: 2015-09-01 words: 4250.0 sentences: 199.0 pages: flesch: 43.0 cache: ./cache/cord-303935-qdehf6rb.txt txt: ./txt/cord-303935-qdehf6rb.txt summary: title: Changes in Clinical Presentation and Epidemiology of Respiratory Pathogens Associated With Acute Respiratory Illness in Military Trainees After Reintroduction of Adenovirus Vaccine The Center for Advanced Molecular Detection at Joint Base San Antonio-Lackland prospectively collects demographic, clinical, and polymerase chain reaction data from respiratory specimens (throat swab and nasal wash) among Air Force trainees presenting for care of ARI. Acute respiratory illness in military trainees post-VI is associated with decreased severity of systemic symptoms and reduced fever and heart rate. The purpose of this study was to evaluate (1) changes in clinical presentations of ARI pre-and post-VI, and (2) reductions in proportions of disease due to Ad. We also sought to further evaluate for evidence of nonvaccine type serotype shift and to determine whether the frequencies of common non-Ad respiratory pathogens have changed after VI, in trainees presenting for care of ARI, which have not previously been described in the published literature. abstract: Background. Adenovirus (Ad) has long been the predominant cause of acute respiratory illness (ARI) in military trainees. In 2011, live oral Ad vaccines for serotypes 4 and 7 were reintroduced into US basic military training populations. This study evaluated the impact on clinical presentations and other respiratory pathogens. Methods. The Center for Advanced Molecular Detection at Joint Base San Antonio-Lackland prospectively collects demographic, clinical, and polymerase chain reaction data from respiratory specimens (throat swab and nasal wash) among Air Force trainees presenting for care of ARI. Results. From June 2008 to August 2013, 2660 trainees enrolled and were tested for selected respiratory pathogens. Post-vaccine introduction (VI), reported systemic symptoms were less frequent, including fever (38% vs 94%) and myalgia (37% vs 67%; P < .01). Median temperature and heart rate decreased (98.4 vs 101.3°F, 81 vs 96 beats per minute; P < .01). Ad detection decreased for all Ad (3% vs 68%), Ad4 (1% vs 70%), 7 (0% vs 8%), 14 (0% vs 5%), and 3 (0.1% vs 2%); P < .01). Rhinovirus and cases with no pathogen identified increased in frequency (35% vs 18%, 51% vs 14%; P < .01). Conclusions. Acute respiratory illness in military trainees post-VI is associated with decreased severity of systemic symptoms and reduced fever and heart rate. Marked reductions in frequency of Ad serotypes are seen, including those in the vaccine, with no serotype shift. However, detection of several other respiratory pathogens, most notably rhinovirus, is observed in increasing proportions, and a majority are now undiagnosed clinical syndromes. url: https://doi.org/10.1093/ofid/ofv120 doi: 10.1093/ofid/ofv120 id: cord-016990-ot1wi3xi author: Zaki, Sherif R. title: Viral Infections of the Lung date: 2008 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The lungs are among the most vulnerable to microbial assault of all organs in the body. From a contemporary vantage, lower respiratory tract infections are the greatest cause of infection-related mortality in the United States, and rank seventh among all causes of deaths in the United States.2,3 From a global and historic perspective, the scope and scale of lower respiratory tract infection is greater than any other infectious syndrome, and viral pneumonias have proven to be some of the most lethal and dramatic of human diseases. The 1918–1919 influenza pandemic, perhaps the most devastating infectious disease pandemic in recorded history, resulted in an estimated 40 million deaths worldwide, including 700,000 deaths in the U.S.4 The global outbreak of severe acute respiratory syndrome (SARS) during 2003, although considerably smaller in scale, resulted in 8098 cases and 774 deaths5 and is a dramatic contemporary example of the ability of viral pneumonias to rapidly disseminate and cause severe disease in human populations. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121437/ doi: 10.1007/978-0-387-68792-6_11 id: cord-263141-n200x6z1 author: Zelaya, Hortensia title: Respiratory Antiviral Immunity and Immunobiotics: Beneficial Effects on Inflammation-Coagulation Interaction during Influenza Virus Infection date: 2016-12-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Influenza virus (IFV) is a major respiratory pathogen of global importance, and the cause of a high degree of morbidity and mortality, especially in high-risk populations such as infants, elderly, and immunocompromised hosts. Given its high capacity to change antigenically, acquired immunity is often not effective to limit IFV infection and therefore vaccination must be constantly redesigned to achieve effective protection. Improvement of respiratory and systemic innate immune mechanisms has been proposed to reduce the incidence and severity of IFV disease. In the last decade, several research works have demonstrated that microbes with the capacity to modulate the mucosal immune system (immunobiotics) are a potential alternative to beneficially modulate the outcome of IFV infection. This review provides an update of the current status on the modulation of respiratory immunity by orally and nasally administered immunobiotics, and their beneficial impact on IFV clearance and inflammatory-mediated lung tissue damage. In particular, we describe the research of our group that investigated the influence of immunobiotics on inflammation–coagulation interactions during IFV infection. Studies have clearly demonstrated that hostile inflammation is accompanied by dysfunctional coagulation in respiratory IFV disease, and our investigations have proved that some immunobiotic strains are able to reduce viral disease severity through their capacity to modulate the immune-coagulative responses in the respiratory tract. url: https://www.ncbi.nlm.nih.gov/pubmed/28066442/ doi: 10.3389/fimmu.2016.00633 id: cord-335505-s013j5ex author: Zhang, Chen title: Viral Etiology and Clinical Profiles of Children with Severe Acute Respiratory Infections in China date: 2013-08-22 words: 3186.0 sentences: 173.0 pages: flesch: 44.0 cache: ./cache/cord-335505-s013j5ex.txt txt: ./txt/cord-335505-s013j5ex.txt summary: BACKGROUND: No comprehensive analysis is available on the viral etiology and clinical characterization among children with severe acute respiratory infection (SARI) in China during 2009 H1N1 pandemic and post-pandemic period. The RVP Fast assay simultaneously detects the following viruses: respiratory syncytial virus (RSV); influenza(IFV) A (H1, H3, and H5) and B viruses; parainfluenza viruse (PIV) 1, 2, 3, and 4; human metapneumovirus (hMPV); adenovirus(ADV); piconavirus(PIC) which includes enterovirus (EV) and rhinovirus (RV); human coronaviruse(HCoV) NL63, HKU1, 229E, and OC43; and human bocavirus(BoCA). To find the reason that causes severe infection, we performed complete comparison between VSARI patients and the SARI, including clinical signs, number of viral target, gender, and age(Table 3, Figure 2B ). To find the association between virus infection and clinical signs in SARI, binary logistic regression was performed between 4 commonly diagnosed respiratory abnormality, including anhelation, respiratory failure, heart failure and pleural effusion, and the viral target detected by xTAG® RVP FAST. abstract: BACKGROUND: No comprehensive analysis is available on the viral etiology and clinical characterization among children with severe acute respiratory infection (SARI) in China during 2009 H1N1 pandemic and post-pandemic period. METHODS: Cohort of 370 hospitalized children (1 to 72 months) with SARI from May 2008 to March 2010 was enrolled in this study. Nasopharyngeal aspirate (NPA) specimens were tested by a commercial assay for 18 respiratory viral targets. The viral distribution and its association with clinical character were statistically analyzed. RESULTS: Viral pathogen was detected in 350 (94.29%) of children with SARI. Overall, the most popular viruses were: enterovirus/rhinovirus (EV/RV) (54.05%), respiratory syncytial virus (RSV) (51.08%), human bocavirus (BoCA) (33.78%), human parainfluenzaviruse type 3 (PIV3) (15.41%), and adenovirus (ADV) (12.97%). Pandemic H1N1 was the dominant influenza virus (IFV) but was only detected in 20 (5.41%) of children. Moreover, detection rate of RSV and human metapneumovirus (hMPV) among suburb participants were significantly higher than that of urban area (P<0.05). Incidence of VSARI among suburb participants was also significant higher, especially among those of 24 to 59 months group (P<0.05). CONCLUSION: Piconaviruses (EV/RV) and paramyxoviruses are the most popular viral pathogens among children with SARI in this study. RSV and hMPV significantly increase the risk of SARI, especially in children younger than 24 months. Higher incidence of VSARI and more susceptibilities to RSV and hMPV infections were found in suburban patients. url: https://doi.org/10.1371/journal.pone.0072606 doi: 10.1371/journal.pone.0072606 id: cord-279421-rxocrgfu author: Zhang, Dan title: Clinical Evaluation of a Single-Tube Multiple RT-PCR Assay for the Detection of 13 Common Virus Types/Subtypes Associated with Acute Respiratory Infection date: 2016-04-04 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Respiratory viruses are among the most important causes of human morbidity and mortality worldwide, especially for infants and young children. In the past years, a few commercial multiplex RT-PCR assays have been used to detect respiratory viruses in spite of the high cost. In the present study, an improved single-tube multiplex reverse transcription PCR assay for simultaneous detection of 13 respiratory viruses was evaluated and compared with a previously reported two-tube assay as the reference method using clinical nasopharyngeal aspirates samples. Of 310 prospectively tested respiratory specimens selected from children hospitalized with acute respiratory illness, 226 (72.90%, 226/310) and 214 (69.03%, 214/310) positive for one or more viruses were identified by the single-tube and the two-tube assays, respectively, with combined test results showing good concordance (Kappa value = 0.874). Individually, the single-tube assay for adenovirus (Adv), human metapneumovirus (HMPV), human rhinovirus (HRV), parainfluenza virus type 1 (PIV1), parainfluenza virus type 3 (PIV3) and parainfluenza virus type 4 (PIV4) showed the significantly superior sensitivities to those of the two-tube assay. No false positives were found. In conclusion, our results demonstrates the one-tube assay revealed significant improvements over the two-tube assay in terms of the better sensitivity, more accurate quality control, less nonspecific amplification, more cost-effective and shorter turn-around time and will be a valuable tool for routine surveillance of respiratory virus infection in China. url: https://www.ncbi.nlm.nih.gov/pubmed/27043208/ doi: 10.1371/journal.pone.0152702 id: cord-319814-tyqb473m author: Zhang, Dingmei title: Epidemiology characteristics of respiratory viruses found in children and adults with respiratory tract infections in southern China date: 2014-06-11 words: 3480.0 sentences: 208.0 pages: flesch: 51.0 cache: ./cache/cord-319814-tyqb473m.txt txt: ./txt/cord-319814-tyqb473m.txt summary: METHODS: In this work, a total of 14 237 nasopharyngeal swabs (14 237 patients from 25 hospitals) were analyzed, and seven respiratory viruses (influenza virus, respiratory syncytial virus, parainfluenza virus, adenovirus, human metapneumovirus, human coronavirus, human bocavirus) were detected using PCR/RT-PCR from nasopharyngeal swabs. Flu viruses were detected in 2632 specimens (18.50%), RSV in 1120 (7.86%), PIV in 494 (3.47%), ADV in 493 (3.47%), hMPV in 319 (2.24%), HCoV in 351 (2.47%), and HBoV in 180 (1.26%). A decline in the incidence of viral infections with age was observed for respiratory viruses, except for Flu. The detection rates of RSV, PIV, ADV, hMPV, HCoV, and HBoV among children ( 14 years) were higher than among adults (>14 years old). The total detection rates for the seven respiratory viruses in spring, summer, autumn, and winter were 44.31%, 41.15%, 41.66%, and 30.52%, respectively. abstract: BACKGROUND: The World Health Organization (WHO) ranks respiratory tract infection (RTI) as the second leading cause of death worldwide for children under 5 years of age. The aim of this work was to evaluate the epidemiology characteristics of respiratory viruses found in children and adults with RTI from July 2009 to June 2012 in southern China. METHODS: In this work, a total of 14 237 nasopharyngeal swabs (14 237 patients from 25 hospitals) were analyzed, and seven respiratory viruses (influenza virus, respiratory syncytial virus, parainfluenza virus, adenovirus, human metapneumovirus, human coronavirus, human bocavirus) were detected using PCR/RT-PCR from nasopharyngeal swabs. RESULTS: The demographic characteristics, viral prevalence, age distribution, seasonal distribution, and pathogen spectrum of the patients with RTIs were analyzed. Co-infection was observed in 483 specimens, but it was more common in male patients, inpatients, children, and young adults. It varied by season, being more prevalent in the spring and summer and less so in the winter. Human coronavirus and human bocavirus were the most common pathogens, tending to occur in co-infection with other respiratory viruses. CONCLUSIONS: This work adds to our knowledge of the epidemiology characteristics of these seven common respiratory viruses among patients with RTI in southern China. The detection of the specific viral causes of infection provides a useful starting point for an understanding of illness attributable to respiratory infection, and might also provide data relevant to the development of prevention strategies. url: https://api.elsevier.com/content/article/pii/S1201971214014581 doi: 10.1016/j.ijid.2014.02.019 id: cord-291961-usl8z6ep author: Zheng, Wen-zhi title: Human polyomavirus type six in respiratory samples from hospitalized children with respiratory tract infections in Beijing, China date: 2015-10-13 words: 2915.0 sentences: 162.0 pages: flesch: 54.0 cache: ./cache/cord-291961-usl8z6ep.txt txt: ./txt/cord-291961-usl8z6ep.txt summary: METHODS: The VP1 gene of HPyV6 was detected with an established TaqMan real-time PCR from nasopharyngeal aspirate specimens collected from hospitalized children with respiratory tract infections. All 15 HPyV6-positive patients were diagnosed with lower respiratory tract infections, and their viral loads ranged from 1.38 to 182.42 copies/μl nasopharyngeal aspirate specimen. CONCLUSIONS: The prevalence of HPyV6 was 1.7 % in nasopharyngeal aspirate specimens from hospitalized children with respiratory tract infections, as analyzed by real-time PCR. Previous studies have indicated that a number of HPyVs are associated with human diseases, such as progressive multifocal leukoencephalopathy (JCPyV), hemorrhagic cystitis (BKPyV), Merkel cell carcinoma (MCPyV), and trichodysplasia spinulosa (TSPyV) [3, 7, 9, [17] [18] [19] . Because initial infections with most HPyVs occur in infancy, the prevalence of HPyV6 in NPAs from children was detected with real-time PCR. The detection rate for HPyV6 by real-time PCR assay was 1.7 % in 887 NPA samples collected from hospitalized children with RTI. abstract: BACKGROUND: HPyV6 is a novel human polyomavirus (HPyV), and neither its natural history nor its prevalence in human disease is well known. Therefore, the epidemiology and phylogenetic status of HPyV6 must be systematically characterized. METHODS: The VP1 gene of HPyV6 was detected with an established TaqMan real-time PCR from nasopharyngeal aspirate specimens collected from hospitalized children with respiratory tract infections. The HPyV6-positive specimens were screened for other common respiratory viruses with real-time PCR assays. RESULTS: The prevalence of HPyV6 was 1.7 % (15/887), and children ≤ 5 years of age accounted for 80 % (12/15) of cases. All 15 HPyV6-positive patients were coinfected with other respiratory viruses, of which influenza virus A (IFVA) (8/15, 53.3 %) and respiratory syncytial virus (7/15, 46.7 %) were most common. All 15 HPyV6-positive patients were diagnosed with lower respiratory tract infections, and their viral loads ranged from 1.38 to 182.42 copies/μl nasopharyngeal aspirate specimen. The most common symptoms were cough (100 %) and fever (86.7 %). The complete 4926-bp genome (BJ376 strain, GenBank accession number KM387421) was amplified and showed 100 % identity to HPyV6 strain 607a. CONCLUSIONS: The prevalence of HPyV6 was 1.7 % in nasopharyngeal aspirate specimens from hospitalized children with respiratory tract infections, as analyzed by real-time PCR. Because the coinfection rate was high and the viral load low, it was not possible to establish a correlation between HPyV6 and respiratory diseases. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12985-015-0390-5) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12985-015-0390-5 doi: 10.1186/s12985-015-0390-5 id: cord-017715-99ri6x0y author: Zhou, Bo-Ping title: SARS date: 2015-07-25 words: 8853.0 sentences: 460.0 pages: flesch: 46.0 cache: ./cache/cord-017715-99ri6x0y.txt txt: ./txt/cord-017715-99ri6x0y.txt summary: 2. The patient has been to or lived in areas reported with infectious SARS patients and patients suffering from secondary infections 2 weeks before the disease onset, who also have abovementioned clinical symptoms, not high peripheral blood white cell count and pulmonary shadows on chest X-ray fi lms. 3. The patient has been to or lived in areas reported with infectious SARS patients and patients suffering from secondary infections 2 weeks before the disease onset, who also have abovementioned clinical symptoms, pulmonary shadows on chest X-ray fi lms, and no obvious response to anti-infectious treatment. If the foci could not be absorbed for a long term in SARS recovery phase or patients still have symptoms but normal chest presentations, CT scan need to be carried out for further observation as it can better visualize the subtle pulmonary interstitial changes, such as lung interlobular septum thickening, intralobular septum thickening, subpleural linear shadow, and small ground-glassdensity lesion and regional and segmental bronchiectasis, and therefore is helpful for clinical diagnosis of pulmonary interstitial fi brosis. abstract: Severe acute respiratory syndrome (SARS) is an acute respiratory tract infectious disease induced by SARS-CoV and mainly transmitted through the short-distance air droplets and close contact. Its main clinical characteristics is abrupt onset of the disease and the initial symptom is fever accompanied with systematic symptoms of headache, soreness and fatigue, and respiratory tract symptoms such as cough, chest dullness, and dyspnea. A few cases may progress to acute respiratory distress syndrome (ARDS). Due to its self-limiting feature, the prognosis is predominantly good but may be poor in severe cases, with mortality about 9.3 %. Some patients may develop such complications such as lung fibrosis and necrosis of the head of femur. On April 8, 2003, SARS was defined as a legal infectious disease by the Ministry of Heath of China. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122356/ doi: 10.1007/978-94-017-7363-8_2 id: cord-328086-ji2emajn author: Zhou, Jie‐ying title: Human bocavirus and human metapneumovirus in hospitalized children with lower respiratory tract illness in Changsha, China date: 2018-01-11 words: 2099.0 sentences: 142.0 pages: flesch: 48.0 cache: ./cache/cord-328086-ji2emajn.txt txt: ./txt/cord-328086-ji2emajn.txt summary: BACKGROUND: Lower respiratory tract illness is a major cause of morbidity and mortality in children worldwide, however, information about the epidemiological and clinical characteristics of LRTIs caused by HMPV and HBoV in China is limited. OBJECTIVES: Human bocavirus (HBoV) and human metapneumovirus (HMPV) are two important viruses for children with lower respiratory tract infections (LRTI). Clinical disease and viral load in children infected with respiratory syncytial virus or human metapneumovirus Clinical characteristics and viral load of respiratory syncytial virus and human metapneumovirus in children hospitaled for acute lower respiratory tract infection High viral load of human bocavirus correlates with duration of wheezing in children with severe lower respiratory tract infection High prevalence of human bocavirus detected in young children with severe acute lower respiratory tract disease by use of a standard PCR protocol and a novel real-time PCR protocol Clinical significance of different virus load of human bocavirus in patients with lower respiratory tract infection abstract: BACKGROUND: Lower respiratory tract illness is a major cause of morbidity and mortality in children worldwide, however, information about the epidemiological and clinical characteristics of LRTIs caused by HMPV and HBoV in China is limited. OBJECTIVES: Human bocavirus (HBoV) and human metapneumovirus (HMPV) are two important viruses for children with lower respiratory tract infections (LRTI). We aimed to assay the correlation between viral load and clinical characteristics of HBoV and HMPV with LRTI in Changsha, China. METHODS: Nasopharyngeal aspirates (NPAs) from children with LRTI were collected. Real‐time PCR was used to screen HBoV and HMPV. Analyses were performed using SPSS 16.0 software. RESULTS: Pneumonia was the most frequent diagnosis. There was no significant difference between HBoV‐ and HMPV‐positive patients in age (P = .506) or hospitalization duration (P = .280); 24.1% and 18.2% were positive for HBoV and HMPV. HBoV infections peaked in summer (32.2%), and HMPV infections peaked in winter (28.9%). The HBoV‐positive patients had a shorter hospitalization duration than the HBoV‐negative patients (P = .021), and the HMPV‐positive patients had a higher prevalence of fever than the HMPV‐negative patients (P = .002). The HBoV viral load was significantly higher among patients aged <1 year (P = .006). The mean HBoV and HMPV viral loads were not significantly different between patients with single infections and coinfections. Patients infected with HBoV only were older than those coinfected with HBoV and other respiratory viruses (P = .005). No significant difference was found in the clinical characteristics of patients infected with HMPV only and those coinfected with HMPV and other respiratory viruses. CONCLUSION: Pneumonia was the most frequent diagnosis caused by HBoV and HMPV. Neither HBoV nor HMPV viral load was correlated with disease severity. url: https://doi.org/10.1111/irv.12535 doi: 10.1111/irv.12535 id: cord-278031-vpq4yghn author: Zumla, Alimuddin title: Rapid diagnostics urgently needed for killer infections date: 2013-06-30 words: 1138.0 sentences: 71.0 pages: flesch: 50.0 cache: ./cache/cord-278031-vpq4yghn.txt txt: ./txt/cord-278031-vpq4yghn.txt summary: 3 Clinicians are often unaware of the presence of more than one pathogen, although co-infections of bacteria 4 or other respiratory viruses 5 and infl uenza are well described, as are bacterial, viral, or parasitic infections with pulmonary tuberculosis. Global scientifi c and political attention is currently focused on two new viruses associated with severe RTIs and high mortality: the avian infl uenza A H7N9 virus from China and novel coronavirus from the Arabian Peninsula. 11 Although several new rapid molecular diagnostic plat forms capable of simultaneously identifying both pathogens and the genetic determinants of anti microbial resistance are emerging, 12 they do not seem to be well suited to clinical presentations or downstream manage ment strategies for patients with RTIs. Furthermore, none can identify new emerging organisms for which genetic sequences are unavailable. abstract: nan url: https://api.elsevier.com/content/article/pii/S2213260013700997 doi: 10.1016/s2213-2600(13)70099-7 id: cord-276005-ifn88mjd author: da Silva Filho, Luiz Vicente Ribeiro Ferreira title: The Differential Clinical Impact of Human Coronavirus Species in Children With Cystic Fibrosis date: 2012-08-01 words: 2485.0 sentences: 113.0 pages: flesch: 42.0 cache: ./cache/cord-276005-ifn88mjd.txt txt: ./txt/cord-276005-ifn88mjd.txt summary: We investigated the clinical impact of human coronaviruses (HCoV) OC43, 229E, HKU1 and NL63 in pediatric patients with cystic fibrosis (CF) during routine and exacerbation visits. The proportion of cases with acute respiratory exacerbation among patients infected with different HCoV species was compared by χ 2 or Fisher exact tests. The identification of new species of HCoV [7, 8] and the emergence of SARS HCoV [6] highlighted the potential role of these viruses as causative agents of severe lower respiratory tract infections. However, most of the studies on the clinical impact of different HCoV species were only performed among children who were hospitalized for acute respiratory tract infections, with small sample sizes and short periods of sample collection [10] . New human coronavirus, HCoV-NL63, associated with severe lower respiratory tract disease in Australia abstract: We investigated the clinical impact of human coronaviruses (HCoV) OC43, 229E, HKU1 and NL63 in pediatric patients with cystic fibrosis (CF) during routine and exacerbation visits. A total of 408 nasopharyngeal aspirate samples were obtained from 103 patients over a 1-year period. Samples positive for HCoV were submitted for nucleotide sequencing to determine the species. Nineteen samples (4.65%) were positive for HCoV, of which 8 were positive for NL63, 6 for OC43, 4 for HKU1, and 1 for 229E. Identification of HCoV was not associated with an increased rate of respiratory exacerbations, but NL63-positive patients had higher exacerbation rates than patients who were positive for other HCoV species. url: https://www.ncbi.nlm.nih.gov/pubmed/22459737/ doi: 10.1093/infdis/jis274 id: cord-344271-5aynmdsk author: de Souza Luna, Luciano Kleber title: Spectrum of Viruses and Atypical Bacteria in Intercontinental Air Travelers with Symptoms of Acute Respiratory Infection date: 2007-03-01 words: 2304.0 sentences: 147.0 pages: flesch: 54.0 cache: ./cache/cord-344271-5aynmdsk.txt txt: ./txt/cord-344271-5aynmdsk.txt summary: title: Spectrum of Viruses and Atypical Bacteria in Intercontinental Air Travelers with Symptoms of Acute Respiratory Infection Using sensitive polymerase chain reactions, we studied the spectrum of atypical bacteria and respiratory viruses in travelers fulfilling the case definition of severe acute respiratory syndrome. These assays were used to determine a point prevalence of the full spectrum of respiratory viruses and atypical bacteria in SARS-compatible patients. Inf and PIV were clearly the most prevalent agents in flight patients, at 14.2% and 15.5%, respectively, without significant differences between age groups (1-way analysis of variance [ANOVA], 95% significance level). Baseline data on the prevalence of respiratory viruses and atypical bacteria after air travel are not currently available. It cannot be told whether the high prevalence and diversity of respiratory viruses seen in our study is specific to patients with recent intercontinental air travel. abstract: Respiratory infections after air travel are frequent, but epidemiological data are incomplete. Using sensitive polymerase chain reactions, we studied the spectrum of atypical bacteria and respiratory viruses in travelers fulfilling the case definition of severe acute respiratory syndrome. A pathogen was identified in 67 travelers (43.2%). Influenza and parainfluenza viruses were most prevalent, at 14.2% and 15.5%, respectively. Prevalences of adenoviruses, human metapneumovirus, coronaviruses, and rhinoviruses ranged between 2.6% and 4.8%. Human bocavirus, respiratory syncytial virus, and Legionella, Mycoplasma, and Chlamydophila species were absent or appeared at frequencies of <1%. To our knowledge, these are the first specific baseline data for the mentioned agents in the context of air travel. url: https://www.ncbi.nlm.nih.gov/pubmed/17262708/ doi: 10.1086/511432 id: cord-319877-izn315hb author: de Wit, Emmie title: SARS and MERS: recent insights into emerging coronaviruses date: 2016-06-27 words: 9387.0 sentences: 424.0 pages: flesch: 43.0 cache: ./cache/cord-319877-izn315hb.txt txt: ./txt/cord-319877-izn315hb.txt summary: Scientific advancements since the 2002–2003 severe acute respiratory syndrome coronavirus (SARS-CoV) pandemic allowed for rapid progress in our understanding of the epidemiology and pathogenesis of MERS-CoV and the development of therapeutics. The downregulation of ACE2 results in the excessive production of angiotensin II by the related enzyme ACE, and it has been suggested that the stimulation of type 1a angiotensin II receptor and Middle East respiratory syndrome coronavirus (MERS-CoV) encode two large polyproteins, pp1a and pp1ab, which are proteolytically cleaved into 16 non-structural proteins (nsps), including papain-like protease (PLpro), 3C-like protease (3CLpro), RNA-dependent RNA polymerase (RdRp), helicase (Hel) and exonuclease (ExoN). Both severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) have developed mechanisms to interfere with these signalling pathways, as shown; these subversion strategies involve both structural proteins (membrane (M) and nucleocapsid (N)) and non-structural proteins (nsp1, nsp3b, nsp4a, nsp4b, nsp5, nsp6 and papain-like protease (PLpro); indicated in the figure by just their nsp numbers and letters). abstract: The emergence of Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 marked the second introduction of a highly pathogenic coronavirus into the human population in the twenty-first century. The continuing introductions of MERS-CoV from dromedary camels, the subsequent travel-related viral spread, the unprecedented nosocomial outbreaks and the high case-fatality rates highlight the need for prophylactic and therapeutic measures. Scientific advancements since the 2002–2003 severe acute respiratory syndrome coronavirus (SARS-CoV) pandemic allowed for rapid progress in our understanding of the epidemiology and pathogenesis of MERS-CoV and the development of therapeutics. In this Review, we detail our present understanding of the transmission and pathogenesis of SARS-CoV and MERS-CoV, and discuss the current state of development of measures to combat emerging coronaviruses. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nrmicro.2016.81) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1038/nrmicro.2016.81 doi: 10.1038/nrmicro.2016.81 id: cord-005646-xhx9pzhj author: nan title: 2nd World Congress on Pediatric Intensive Care 1996 Rotterdam, The Netherlands, 23–26 June 1996 Abstracts of Oral Presentations, Posters and Nursing Programme date: 1996 words: 72031.0 sentences: 4734.0 pages: flesch: 56.0 cache: ./cache/cord-005646-xhx9pzhj.txt txt: ./txt/cord-005646-xhx9pzhj.txt summary: Aims and methods The aim of both a prospective and retrospective survey conducted in German pediatric intensive care units in 1993 was to accumulate data on the epidemiology, risk factors, natural history and treatment strategies in a large group of pediatric ARDS patients who were treated in the tt~ee year period from 1991 to 1993.All patients had acute bilateral alveolar infiltration of noncardiogenic origin and a pO2~iO2 ratio < 150mmHg. The influence of sex, underlying disease and single organ failure was analyzed using the Fischer''s exact test, the influence of additional organ failure on mortality was tested with the Cochran-Mantel-Haenszet statistics. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095092/ doi: 10.1007/bf02316512 id: cord-005814-ak5pq312 author: nan title: 8th European Congress of Intensive Care Medicine Athens - Greece, October 18–22, 1995 Abstracts date: 1995 words: 179164.0 sentences: 12028.0 pages: flesch: 56.0 cache: ./cache/cord-005814-ak5pq312.txt txt: ./txt/cord-005814-ak5pq312.txt summary: Results: In 5 patients with treated SS, 16 tests were performed (VL n=8; Dobu n=4; NA n=4 Method: Septic shock was defined as severe sepsis with either persistent hypotension (mean arterial pressure; MAP<70 mmHg) or the requirement for a noradrenaline (NA) infusion ~> 0.1 ~g/kg/min with a MAP _< 90mmHg. Cardiovascular support was limited to NA + dobutamine (DB), 546C88 was administered for up to 8 h at a fixed dose-rate of either i, 2.5, 5, 10 or 20 mg/kg/h iv. Methods: Fourteen cases were s~udied,their gestational age ranged from(27-32)ws.Continnous positive air way pressure was applied to six cases at Peep level from (3-6)cm H2o through nasal pronge,(group I),the other 8 cases were managed as routine,(group II).Blood gases, TcPO2,TcCo2,resp.rate,depth and pattern were monitored for assessment of tissue Oxygenation and ventilation, Results: Our rasults showed that early application of CPAP improve ventilation among (83.3%)of cases,while (16.7%)of cases need IMV.The cases of group II need IMV among (75%)of the studied cases during the second or the third day of life. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095534/ doi: 10.1007/bf02426401 id: cord-017126-7ebo3cy3 author: nan title: Lungenversagen date: 2007 words: 4324.0 sentences: 512.0 pages: flesch: 42.0 cache: ./cache/cord-017126-7ebo3cy3.txt txt: ./txt/cord-017126-7ebo3cy3.txt summary: Nach der „American-European Consensus Conference" (Bernard et al., 1994) wird zwischen einem ARDS — acute respiratory distress syndrom und einem ALI — acute lung injury unterschieden. Bei Patienten mit ALI/ARDS kann das Auftreten apoptotischer Vorgänge an pulmonalen epithelialen Zellen (Song Y et al., 1999 , Li et al., 2004 , Martin et al., 2005 (Abraham, 2003) derselben, sodass es zur Aufrechterhaltung eines von Leukozyten geführten inflammatorischen Prozesses kommt, der typisch für eine akute Lungenschädigung ist (Wang et al., 1999 , Yum et al., 2001 Die verminderte Apoptose der Neutrophilen ist bedingt durch: 1. Beneficial effects of the "Open lung Approach" with low distending pressures in acute respiratory distress syndrom; A prospective randomized study on mechanical ventilation Combining high-frequency oscillatory ventilation and recruitment maneuvers in adults with early acute respiratory distress syndrome: the treatment with oscillation and an Open Lung Strategy (TOOLS) trial pilot study Effect of alveolar recruitment maneuver in early acute respiratory distress syndrome according to antiderecruitment strategy, etiological category of diffuse lung injury, and body position of the patient abstract: Das akute Lungenversagen ist eine schwere diffuse entzündliche Erkrankung der Lunge. Nach der „American-European Consensus Conference“ (Bernard et al., 1994) wird zwischen einem ARDS — acute respiratory distress syndrom und einem ALI — acute lung injury unterschieden. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121608/ doi: 10.1007/978-3-211-29682-0_10 id: cord-020267-0axms5fp author: nan title: RIBAVIRIN AND RESPIRATORY SYNCYTIAL VIRUS date: 1986-02-15 words: 1845.0 sentences: 84.0 pages: flesch: 39.0 cache: ./cache/cord-020267-0axms5fp.txt txt: ./txt/cord-020267-0axms5fp.txt summary: In Britain RSV accounts for yearly hospitaladmission rates of 12 -5 to 24'' 5 per 1000 among infants aged 1-3 months;3 and in North Carolina it is responsible for 24-50% of all admissions for pneumonia in children under 5 years of age.4 In hospital roughly 14% of RSV-infected infants require intensive care and 5% need assisted ventilation.s Although the mortality from RSV infection is generally low, it is especially high in infants with underlying congenital heart disease (37%, rising to 73% with concomitant pulmonary hypertension),5 and in the immunocompromised (23%),6 and is almost certainly raised in infants with bronchopulmonary dysplasia and cystic fibrosis. Striking improvements were noted in 2 infants treated with ribavirin aerosol for parainfluenza virus type 3 infection complicating severe combined immunodeficiency disease13,14-a combination often causing respiratory failure and death. Rather it should be considered for infants with bronchiolitis or pneumonia, and for high-risk patients with underlying cardiopulmonary disorders or immunodeficiency with probable RSV or influenza, and possibly parainfluenza infection. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7134697/ doi: 10.1016/s0140-6736(86)92323-8 id: cord-021277-smw6owql author: nan title: Respiratory distress syndrome: recent research date: 2013-02-17 words: 116.0 sentences: 16.0 pages: flesch: 49.0 cache: ./cache/cord-021277-smw6owql.txt txt: ./txt/cord-021277-smw6owql.txt summary: key: cord-021277-smw6owql authors: nan title: Respiratory distress syndrome: recent research date: 2013-02-17 journal: nan DOI: 10.2165/00128413-199107860-00060 sha: doc_id: 21277 cord_uid: smw6owql nan In infants Effects In adults Use of corticosteroids in the adult respiratory distress syndrome -a clinical review Adult respiratory distress syndrome associated with parainfluenza virus type I in children Effects of prostaglandin EI on oxygen delivery and consumption in patients with the adult respiratory distress syndrome Prophylactic treatment with an aerosolized corticosteroid liposome in a porcine model of early ARDS induced by endotoxaemia Physiologic effects and side effects of prostaglandin E I in the adult respiratory distress syndrome respiratory distress and acute renal failure due to synergic bleomycin-cisplatin toxicity abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149233/ doi: 10.2165/00128413-199107860-00060 id: cord-281754-auqh3vtr author: nan title: EMERGING RESPIRATORY DISEASE - CORONAVIRUSES date: 2017-09-12 words: 3626.0 sentences: 229.0 pages: flesch: 49.0 cache: ./cache/cord-281754-auqh3vtr.txt txt: ./txt/cord-281754-auqh3vtr.txt summary: As a human virus the range of disease is broad, from cold like to severe multisystem involvement (These CoV infections are associated with short incubation periods (2-7 days), such as those found in SARS [2, 5, 6, 17, 18, 24, 25] . The etiology causing his illness was identified as severe acute respiratory syndrome coronavirus (SARS CoV); it was likely transmitted to at least 10 additional persons. Other pathogens, including members of the Paramyxoviridae family, and human metapneumovirus (hMPV) were considered as causative of this new clinical illness which became known as Severe Acute Respiratory Syndrome or SARS. Genomic sequence analysis seems to support the hypothesis that of SARS-CoV is an animal virus for which the normal host is still unknown and that developed the ability to productively infect humans or has the ability to cross species barriers [25] . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/29737283/ doi: 10.1016/j.disamonth.2017.03.019 id: cord-326163-u8nh8cr3 author: van Benten, Inesz J. title: RSV‐induced bronchiolitis but not upper respiratory tract infection is accompanied by an increased nasal IL‐18 response date: 2003-08-18 words: 4379.0 sentences: 231.0 pages: flesch: 46.0 cache: ./cache/cord-326163-u8nh8cr3.txt txt: ./txt/cord-326163-u8nh8cr3.txt summary: The aim of this study was to investigate potential differences in the local nasal immune response between bronchiolitis and upper respiratory tract infection induced by respiratory syncytial virus (RSV). This study investigated whether differences could be observed on the cellular level between the nasal immune responses of infants with RSV-induced bronchiolitis and RSV-induced upper respiratory tract infection. During the acute phase of bronchiolitis as well as during upper respiratory tract infection, there was a marked increase in the numbers of macrophages (CD68positive cells) in nasal brush samples compared with convalescent samples (Fig. 1A) . Most importantly, this study showed a striking difference in cytokine responses between both types of infection, i.e., an increase in the number of IL-18 positive cells in nasal brush samples during bronchiolitis. abstract: The aim of this study was to investigate potential differences in the local nasal immune response between bronchiolitis and upper respiratory tract infection induced by respiratory syncytial virus (RSV). Nasal brush samples were obtained from 14 infants with RSV bronchiolitis and from 8 infants with RSV upper respiratory tract infection. The samples were taken during infection (acute phase) and 2–4 weeks later (convalescent phase). Cytospin preparations were stained immunohistochemically for T cells, macrophages, and eosinophils. Staining also took place for intercellular adhesion molecule‐1 (ICAM‐1), T‐helper 1 (Th1)‐like (interleukin‐12 [IL‐12], interferon‐γ [IFN‐γ]), Th2‐like (IL‐4, IL‐10), and proinflammatory cytokines (IL‐6, IL‐8, IL‐18). During both RSV‐induced bronchiolitis and upper respiratory tract infection, cellular inflammation was observed. This was characterised by an increase in the numbers of nasal macrophages, which tended to be higher in bronchiolitis than in upper respiratory tract infection. Numbers of T lymphocytes and ICAM‐1 positive cells increased during both bronchiolitis and upper respiratory tract infection. There were no differences between numbers in the groups. Interestingly, a distinct nasal proinflammatory cytokine response was observed in RSV‐induced bronchiolitis. This is characterised by an increase in the number of IL‐18 positive cells. This increase is specific for bronchiolitis, as a similar increase could not be detected in RSV‐induced upper respiratory tract infection. Numbers of IL‐6 and IL‐12 positive cells were higher in both bronchiolitis and upper respiratory tract infection, and there were no differences between the groups. By contrast, the number of IL‐8, IFN‐γ, IL‐4, and IL‐10‐positive cells remained constant. In conclusion, clear differences were found in nasal immune responses of children with RSV‐induced upper respiratory tract infection or bronchiolitis. The induction of a strong IL‐18 response was typical for bronchiolitis, as this could not be observed in RSV‐induced upper respiratory tract infection, and could explain the eosinophilia that is observed frequently during bronchiolitis. J. Med. Virol. 71:290–297, 2003. © 2003 Wiley‐Liss, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/12938205/ doi: 10.1002/jmv.10482 id: cord-342476-0rupk21u author: van Rijn, Anneloes L. title: The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease date: 2019-10-24 words: 4036.0 sentences: 220.0 pages: flesch: 44.0 cache: ./cache/cord-342476-0rupk21u.txt txt: ./txt/cord-342476-0rupk21u.txt summary: The sensitivity, specificity and predictive values of mNGS were calculated based on 24 PCR positive and 1120 PCR negative target results of 88 samples and the normalized read counts (Table 5 ). The following markers were tested for potential associations with clinical severity of exacerbation (exacerbation severity, self-reported exacerbation severity), length of exacerbation and a decrease/increase in FEV 1 (control visit compared to baseline): mNGS pathogen positive versus negative exacerbation (qPCR targets), the number of normalized reads (log, cutoff of �5normalized reads) for the different target viruses (species level). The Shannon diversity scores for bacteriophages (normalized reads, cut-off of �5normalized reads) were comparable for COPD exacerbations of viral aetiology in PCR positive versus negative patients (Fig 5) . In this study, the respiratory virome in patients with COPD exacerbations was analysed with both mNGS and qPCR, and combined with clinical data. abstract: INTRODUCTION: Exacerbations are major contributors to morbidity and mortality in patients with chronic obstructive pulmonary disease (COPD), and respiratory bacterial and viral infections are an important trigger. However, using conventional diagnostic techniques, a causative agent is not always found. Metagenomic next-generation sequencing (mNGS) allows analysis of the complete virome, but has not yet been applied in COPD exacerbations. OBJECTIVES: To study the respiratory virome in nasopharyngeal samples during COPD exacerbations using mNGS. STUDY DESIGN: 88 nasopharyngeal swabs from 63 patients from the Bergen COPD Exacerbation Study (2006–2010) were analysed by mNGS and in-house qPCR for respiratory viruses. Both DNA and RNA were sequenced simultaneously using an Illumina library preparation protocol with in-house adaptations. RESULTS: By mNGS, 24/88 samples tested positive. Sensitivity and specificity, as compared with PCR, were 96% and 98% for diagnostic targets (23/24 and 1093/1120, respectively). Additional viral pathogens detected by mNGS were herpes simplex virus type 1 and coronavirus OC43. A positive correlation was found between Cq value and mNGS viral normalized species reads (log value) (p = 0.002). Patients with viral pathogens had lower percentages of bacteriophages (p<0.001). No correlation was found between viral reads and clinical markers. CONCLUSIONS: The mNGS protocol used was highly sensitive and specific for semi-quantitative detection of respiratory viruses. Excellent negative predictive value implicates the power of mNGS to exclude any pathogenic respiratory viral infectious cause in one test, with consequences for clinical decision making. Reduced abundance of bacteriophages in COPD patients with viral pathogens implicates skewing of the virome during infection, with potential consequences for the bacterial populations, during infection. url: https://www.ncbi.nlm.nih.gov/pubmed/31647831/ doi: 10.1371/journal.pone.0223952 id: cord-355165-xc6ythgp author: van den Wijngaard, Cees title: Validation of Syndromic Surveillance for Respiratory Pathogen Activity date: 2008-06-17 words: 4561.0 sentences: 224.0 pages: flesch: 42.0 cache: ./cache/cord-355165-xc6ythgp.txt txt: ./txt/cord-355165-xc6ythgp.txt summary: We defi ned syndrome data as data in health-related registries that refl ect infectious disease activity without identifying causative pathogen(s) or focusing on pathogenspecifi c symptoms (such as routine surveillance data for infl uenza-like illness [11] or surveillance of acute fl accid paralysis for polio [12] ). Six registries were selected ( Table 1 ) that collected data on work absenteeism, general practice (GP) consultations, prescription medications dispensed by pharmacies, diagnostic test requests (laboratory submissions) (13), hospital diagnoses, and deaths. As a reference for the syndrome data, we included specifi c pathogen counts for 1999-2004 from the following sources: 1) Weekly Sentinel Surveillance System of the Dutch Working Group on Clinical Virology (which covers 38%-73% of the population of the Netherlands [14] respiratory disease-related counts of Streptococcus pneumoniae (data in 2003-2004 were interpolated for 2 laboratories during short periods of missing data; total coverage 24%); and 3) national mandatory notifi cations of pertussis. abstract: Syndromic surveillance is increasingly used to signal unusual illness events. To validate data-source selection, we retrospectively investigated the extent to which 6 respiratory syndromes (based on different medical registries) reflected respiratory pathogen activity. These syndromes showed higher levels in winter, which corresponded with higher laboratory counts of Streptococcus pneumoniae, respiratory syncytial virus, and influenza virus. Multiple linear regression models indicated that most syndrome variations (up to 86%) can be explained by counts of respiratory pathogens. Absenteeism and pharmacy syndromes might reflect nonrespiratory conditions as well. We also observed systematic syndrome elevations in the fall, which were unexplained by pathogen counts but likely reflected rhinovirus activity. Earliest syndrome elevations were observed in absenteeism data, followed by hospital data (+1 week), pharmacy/general practitioner consultations (+2 weeks), and deaths/laboratory submissions (test requests) (+3 weeks). We conclude that these syndromes can be used for respiratory syndromic surveillance, since they reflect patterns in respiratory pathogen activity. url: https://doi.org/10.3201/eid1406.071467 doi: 10.3201/eid1406.071467 ==== 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